Intro Manual 60

Introduction to Materials Studio
Training Manual
Version 6
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Product Roadmap Disclaimer This presentation and/or any related documents contains statements regarding our plans or expectations for future features, enhancements or functionalities of current or future products (collectively "Enhancements"). Our plans or expectations are subject to change at any time at our discretion. Accordingly, Accelrys is making no representation, undertaking no commitment or legal obligation to create, develop or license any product or Enhancements. The presentation, documents or any related statements are not intended to, nor shall, create any legal obligation upon Accelrys, and shall not be relied upon in purchasing any product. Any such obligation shall only result from a written agreement executed by both parties. In addition, information disclosed in this presentation and related documents, whether oral or written, is confidential or proprietary information of Accelrys. It shall be used only for the purpose of furthering our business relationship, and shall not be disclosed to third parties.
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Introduction to Materials Studio

Alexander Goldberg, Accelrys agoldberg@accelrys.com July 2012
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Who are we?

We develop and deliver scientific software solutions and related services We enable the design, discovery, and development of products and processes We serve research organizations in the life sciences, chemicals, and materials industries
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Company Key Facts

Founded: 2001 Worlds largest scientific software provider for chemistry, biology, and materials science Public Company: ACCL (NASDAQ) Revenue: $170M Cash Reserves: $150M Market Leadership: Scientific Informatics Customers: 1350 Employees: 700 Headquarters: San Diego, CA Operations: North America, EMEA, and Asia Pacific
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Our Services
H
Custom Services
Support-us@accelrys.com Support-eu@accelrys.com
Technical
Implementation Services Training
Contract Research
Technical Support
Scientific Support
Scientific
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General Outline
Day 1:
Intro 9 AM 6 PM 1 2 PM lunch
Day 2:
DMol3 9 AM 1 PM 1 2 PM lunch CASTEP 2 6 PM
Day 3:
VAMP 9 AM 1 PM 1 2 PM lunch AC, Forcite 2 6 PM
Day 4:
Mesocite 9 AM 1 PM 1 2 PM lunch DPD, MesoDyn 2 6 PM
Day 5:
Scripting
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Assumptions
Scientists with a familiarity of basic chemistry, physics and mathematics Youre curious about the subject and you will ask questions You dont want to become experts Emphasize applications not theory
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Part I: Introduction to Materials Modeling
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Calculations vs. Experiment

ADVANTAGES Easy relative to output Any molecule Less & less costly Safe DISADVANTAGES Cost increases rapidly with molecular size Different results depending on specific model Cost is independent of molecular size (usually) One result More difficult More difficult with less stability; no transition states More & more costly Dangerous
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Today Outline
What is Materials Studio? (Demo) Break (10 min) Introduction to Modules in Materials Studio (Lecture 1) Hands-on exercises on building structures Break (10min) Case Studies (Lecture 2) Using the client-server architecture (Lecture 3) Problem Solving Approaches (Lecture 4) More Hands-on exercises (home work)
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Part I: What is Materials Studio? (Demo)
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Materials Studio
Tools
Files & Folders
Figures & Tables Properties Jobs running

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Lets draw a molecule!
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We draw 4 carbon atoms
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We draw a double-bond
Option 1 Option 2
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We draw a ring
saturated aromatic Alt +
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We draw a carbon atom and change it to oxygen
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Lets add some hydrogen atoms!

Click the Adjust hydrogen button!
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A more reasonable geometry
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Type of Files
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Menu I
File Menu Edit Menu
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Menu II
View Menu
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Toolbar I
Standard Toolbar
New Document Save Document undo redo
Import Document
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Toolbar II
Sketching Toolbar
Clean Sketch Atom Sketch Ring Sketch Fragment Measure/ Change Adjust Hydrogen Modify Element Modify Bonds
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Toolbar III
3D-viewer Toolbar
Selection Rotation Zoom
Translation
Recenter Reset
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Modules Menu/Modules Toolbar

Adsorption Loc. Amorphous Cell Blends CASTEP ConQuest Conformers Tight Binding (Consortium only) ONETEP DMol3 Polymorph DPD Discover Equilibria Forcite Gaussian Interface QMERA Reflex Sorption Synthia VAMP
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GULP Kinetix (Consortium only) MesoDyn Mesocite Mesotek Morphology
Different Builders
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Building tools developments

Atomistic Polymers, dendrimers Crystals, surfaces Nanostructures Tubes, ropes, clusters
dendrimer generations
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Build Polymers
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Build a Homopolymer
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Build Block Copolymer
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Build Random Copolymer
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Dendrimer
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Define a repeat unit
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Branch Points
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Build Crystals
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Build crystals
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Build Crystals
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Tools for building nanostructures with the Materials Visualizer
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Building single or multi-wall nanotubes
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Building multi-wall nanotubes
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Building tools developments

Nanostructures Tubes, ropes, clusters
Developed by Nanotech Consortium
nanocluster nanorope
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Nanocluster Builders
Wide range of shapes Element substitution function (linear, quadratic or exponential) along symmetry directions. Vacancy function. Optional capping of broken bonds
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Convert atoms to beads

Coarse graining tools enable generation of complex bead models from atomic structures Polymers beads by repeat units PDB files beads by substructures Use templates to coarse grain structures without subunits Convert cells, surfaces, and molecules Exposed through MaterialsScript Coarse grainer Bead data model
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Coarse grain!
TOOLS
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Individual Settings
Some tools in the Materials Visualizer and all Materials Studio modules have default settings for certain parameters. These settings are created when you change the parameters in question from their default values and then save the project. The Settings Organizer dialog allows you to create a template project containing your preferred settings for new projects and also to share your tool and module settings between different projects.
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Individual Settings
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Brillouin Zone Path
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Vectors
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Vectors Dialog
Create vectors on: Atoms Beads Molecules Substructures Properties: Force Velocity Relative Velocity Momentum Dipole Moment
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Display Style
Various styles Scale factor
display length () = scale * vector magnitude
Use with Vectors dialog to select specific vectors
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Scale Bar
Display length scale in Visualizer in Angstroms or nanometers
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Vibrational Analysis
Now with vectors!
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Part II: Introduction to Materials Modeling
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Why modeling?
structures, processes and properties are numerically simulated based fully or in part on fundamental laws of physics besides modeling stable molecules, some methods may be used to model also short-lived species (unstable intermediates and transition states) important in supporting or replacing experimental studies
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What is materials simulation?
e.g., morphology, drug delivery e.g., permeation, crystallisation

e.g., electronics, catalysis
Scale
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Issues that simulation can address

Reactivity, Electronic-Optic-Magnetic Miscibility/Compatibility, Solubility Diffusion, permeation, membrane transport Adhesion (i.e., interactions with surfaces) Crystallization and polymorphism Micelle or vesicle formation and properties Emulsions, kinetics and properties Polymeric microspheres, release profiles
Quantum Mechanics Atomistic Simulation
Accuracy
Mesoscale Simulation
Correlative methods (e.g. QSAR)
Increasing Scale of Study
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Modeling and simulation methods in MS

Quantum Mechanics Atomistic Modeling Mesoscale Modeling Crystal Modeling Correlation Methods - QSAR
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Quantum Mechanics
The Schrdinger equation
H = E
Methods differ in how H and are described H kinetic energy + potential energy + Exc described with electronic wave functions (numerical, STO, GTO) or plane waves
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Quantum Mechanics: DFT

Density Functional Theory (DFT)- All ground-state properties of a system are function of the charge density
Hohenberg Kohn equation
Etotal = T [ ] + U [ ] + E xc [ ]
2 + V ({ri }) ({ri }) = E({ri }) 2m
Kohn Sham equation
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Quantum Mechanics
Strong points Chemical reactions and transition state Electronic, optical and magnetic properties Limitations Simulation time growths as N3 where N is the number of electrons. There is a computational limit of ~ 250 atoms or a few picoseconds
DMol3, CASTEP
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What can be calculated?

DMOL3 (numerical functions)
Molecules in the gas phase/periodic systems Reaction Modeling, (gas phase, solution, on surfaces) Thermodynamics Optical Spectra (IR spectra) TD-DFT (UV-vis and optical properties) Molecular Dynamics (Diffusion) LST/QST Solvent effects workfunctions Dispersion correction
CASTEP (plane waves)

Periodic systems Structural Properties Electronic and Magnetic Properties Diffusion Bulk and Elastic Properties LST/QST STM (scanning tunneling microscopy) analysis Workfunctions EELS/ELNES spectra Raman/Intensities Dispersion Correction
Extra Tool: CASTEP solid state NMR

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Gaussian Interface
HF, Hybrid Functionals and MP2 Interface only customer needs valid Gaussian License
GAUSSIAN Interface
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Semiempirical methods
They solve an approximate form of the Schrdinger equation
F C = SC E
FC =CE
Only valence electrons are considered These methods use parameters derived from experimental data to simplify the computation
VAMP
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Semiempirical methods
Strong points They are relatively inexpensive and provide reasonable qualitative descriptions of molecular systems, can be used on a PC Limitations Can only be used for elements and interactions for which it has been parameterised PM6 covers 70 elements
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Fast structure Optimization Fast transition state localization Structural properties Optical spectra (UV-vis) 13C Chemical shift Electrostatics Solvent effects
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Liner Scaling DFT
ONETEP
quantum mechanics-based program designed specifically for calculations on large systems (>500 atoms the time required for a calculation increases linearly with the number of atoms as opposed to N3 Applications include studies of surface chemistry, the configurations of large molecular systems, and the structure and energetics of nanotubes
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ONETEP
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QM/MM
For Example: Reactive centre on a zeolite Usual approach: selecting a cluster comprising enough framework to mimic the active site plus a bit of the bulk Problem: there is vacuum all around and the electrostatic interactions are severely neglected With QMERA, we can do the following: QM region: electronic structure changes MM region: embedding of QM region environment effects
MM
QM
QMERA
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Molecular Mechanics (MM)

A molecule is described as a series of charged points (atoms) linked by springs (bonds).
A mathematical description of this system is known as a forcefield The forcefield is used to calculate the relative potential energy of the molecule (relative to other conformations of the same molecule).
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MM - Representation of a forcefield
Potential Energy
Etotal=Evalence + Ecrossterm + Enon-bond

Valence Interactions
Evalence=Ebond + Eangle + Etorsion + Eoop + EUB

Non-bond Interactions
Enon-bond=EvdW + ECoulomb + Ehbond

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MM - Representation of a forcefield
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MM - Molecular Dynamics (MD)

Molecular Dynamics (MD) solves the Newtons equations of motion for each atom
fi = mi ai
2ri fi = mi 2 t
Classical equations of motion are deterministic!!! This allows us to study the evolution of systems as a function of time, temperature and pressure which are related by statistical mechanics
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Molecular Mechanics
Strong points We can deal with bigger systems We can simulate dynamic processes (e.g. diffusion, phase transition) Limitations Forcefields are valid for a limited type of material There is no bond breaking or forming involved (i.e. no chemisorption) Size of system ~ 104 atoms or a few nanoseconds (1 s possible)
Discover, GULP, Forcite plus

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Property calculations Pair correlation function - probing specific interactions Length, angle, dihedral distributions - effects on molecular geometry Concentration profiles - interfacial properties Orientational correlation - liquid crystalline phases Dynamic calculations MSD, velocity autocorrelation, space-time correlation transport Dipole autocorrelation - vibrational behaviour spectroscopy Shear-stress time correlation - fluid viscosity Elastic constants - mechanical properties Multicomponent systems Interaction energy compatibility
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Mesoscale modeling
Smallest unit is a group of atoms called bead
Longer time and length scales!!!!

Laws of classical physics
DPD (Dissipative Particle dynamics): Newtons equations of motion MesoDYN: Stochastic Diffusion equations
fi =
(F
j i
Cons ij
Disip Random + Fij + Fij
d A (r ) = M A B [ A B ] + dt
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Mesoscale modeling
Strong points In Meso methods atoms are not specifically treated : reach much larger length and time scales Limitations Specific interactions are harder to model, defining the average forces that best represent a specific system can be difficult Minimum of two components
MesoDYN, DPD
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Segregation Interfacial tension Stress tensor Bulk viscosity Shear viscosity Temperature dependence of miscibility Critical Micelle Concentration (CMC) Pressure Bead correlations Diffusivities
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Mesocite
combines two bead based methods Coarse-grained molecular dynamics (CGMD) Hard body interactions, charged beads Includes steric effects, detailed description of interactions required Dissipative particle dynamics (DPD) Soft potentials, fewer parameters, longer time and length scales, long chain polymers Study properties at longer time and length scales than atomistic simulations (mesophase formation, diffusion in bilayers, nanotube orientation etc.)
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Crystal structure determination from powder diffraction data

Crystal structure important for patenting Crystal structure important as prerequisite for the understanding of most solid state properties Single crystals large enough for diffraction experiments are frequently difficult or impossible to obtain
Reflex, Reflex Plus, Reflex QPA, X-Cell

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Routes to determine crystal structures
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Direct space methods

60000 50000 40000 30000 20000 10000 0 10 20 30 40 50
Indexing
Pawley Refinement
Global Optimization
Rietveld Refinement
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Other crystallography tools

Morpholgy: prediction of the morphology of the crystal starting from the atomic structure of a crystal (crystal shape, surface stability, aids the development of tailor-made additives) Polymorph predictor: prediction of potential polymorphs directly from the molecular structure. Failry rigid, (non-)ionic molecules (C,N,O,H) Possible packing arrangements are generated in all reasonable space groups, searching for minimum lattice energy
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Powder diffraction pattern of a crystal (Reflex Powder Diffraction) Crystal structure From powder data (Powder Solve) From a list of theoretical trial structures (Polymorph) Morphology prediction (Morphology) Consider possible effects (qualitatively) of tailor-made additives and solvents by identifying important interactions at key growth faces. Predict the morphological effects of modifying the growth rates of particular faces Relate predicted morphology to experiment, enabling indexing of experimental data
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ConQuest Search
Cambridge Crystallographic Data Centre Selected fragment in the currently active 3D structure document (or the entire structure if no selection is made) is exported to the CCDC ConQuest desktop tool to be used as the basis for a Cambridge Structural Database (CSD) search. Refcode search Chemical name search Substructure search
Attention: requires you to have a licence for the CSD!!!
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MS Motif
Motif expands Accelrys' toolset for crystal engineering efforts. It is a tool designed to analyze connectivity information in molecular crystals, providing a qualitative and quantitative analysis method of hydrogen bond topologies
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Correlative methods
Addresses two questions: What features of a molecule affect its activity? What can be modified to enhance its properties? Quantitative in that a mathematical model is used to account for the observed activity. Happiness = f(money + love + car + holiday..) QSAR property = f( no. of carbon atoms + surface area +.)
QSAR, Synthia (Polymers)

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Correlative methods
Strong points - Allows to cover time and size range over the standard molecular modeling (ageing, odour, brilliance) Limitations
The correlations are limited to a very specific range of components Success of the correlations depend on the quality of the data
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QSAR-Quantitative Structure Activity Relationship
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Other Modules in MS
Adsorption Locator Amorphous Cell Blends Conformers Scripting Sorption
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Adsorption Locator
Determines energetically favourable positions of a adsorbate in periodic and aperiodic structures
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Amorphous Cell
Construction of complex amorphous systems
Construction Packing Confined Layer
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Blends
A tool to estimate the miscibility behaviour of binary mixtures (solvent-solvent, polymer-solvent, and polymer-polymer mixtures) the thermodynamics of mixing is directly predicted from the chemical structures of the two components (molecular structures and a forcefield as input)
Phase diagrams (critical points, binodal and spinodal curves) Interaction parameter, Mixing energy Free energy of mixing isotherms Energy distribution functions Binding configurations sorted by energy
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Conformers
The module provides methods for searching the conformational space of non-periodic molecular systems in order to derive a reasonable sampling of the low energy conformations The set of rotatable torsion angles of the molecular system is explored systematic and stochastic (random) searches A a set of conformers is obtained and a range of descriptors enabling to perform a detailed analysis of the structures
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Simple!
Not so simple
CIS
TRANS
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Scripting in MS
What is it? Server side scripting Will be an evolving project, will be looking for feedback for improvements for the next release Chemistry model and Forcite, DMol, CCDC, DFTB, Crystallography, CASTEP, Amorphous Cell, Mesocite, VAMP Will be extended to include other modules in future releases Access is to a lot of Materials Visualizer functionality chemistry model and associated objects Perl is the scripting language Write and test script on client before submitting to server Fully documented API and example scripts and tutorial
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Work Flow
Write script on client Debug script on client Run script on server
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Scripting Editor
Syntax highlighting Bookmarks
Line numbers
Syntax Check and Output tabs
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Script Library
Run a script from a customized menu on the active document Set active document type Run on client or server Pass custom arguments
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Add Script to Library
Add to library from current project
Default location is in user folder on client Add a network path to locations for sharing between users
Store important structures and other documents in library Import library documents into current project
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Add and Configure Command
Create a new command
Associate command with a script in the library
Configure behavior and arguments

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Sorption
Put molecules (sorbates) into a three-dimensional periodic structure with pores (sorbent) Typical examples of sorbents include zeolites, aluminophosphates, clays, nanotubes, polymer membranes, silica gels, activated carbons, and metalorganic frameworks. The information that can be obtained: adsorption isotherms, binding sites, binding energies, global minimum sorbate locations, density and energy fields, energy distributions, sorption selectivities, solubilities, isosteric heats, and Henry constants.
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Part III: Case Studies
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Stable Nanostructures
C60
Pentagon (12)
B80
Comparing Distances in
C60 1.46 1.42 1.39 1.25 6.83 10.07 B80 1.73 1.71 1.68 1.70 8.17 11.48 Al92 2.58 2.19 2.48 2.53 11.54 14.67
92 B. I. Yakobson et.al., PRL, 98, 166804, 2007 A. Goldberg et.al., J. Phys. B. 42, 125103, 2009
Al
Side (long) CenterVertex Hexagon Side (short) (20) CenterVertex Diameter VdW diameter
Y. Kawakami et. al.,Thermec 2003

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Visualising Reactivity - II.

HOMO LUMO
System: C6H5Cl
Movie
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Towards Improved Zinc Corrosion Inhibitors - Understanding the Role of Silanes on ZnO I
Outline: The aim is to produce coatings which prevent corrosion of zinc as zinc oxide forms as a thin film under atmospheric conditions.
The behaviour of three silane molecules [1] on ZnO oxide surfaces has been studied. Amorphous Cell was used to create solvent-silane cells which are placed on the oxide substrate.
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Towards Improved Zinc Corrosion Inhibitors - Understanding the Role of Silanes on ZnO II
Two configurations: A - only the silane head group binds to the surface B - both the head and tail are in contact with the surface Both effects are only seen in the presence of solvent, without the solvent, the B is the most dominant for all of the silanes. Eads correspond to the degree of polarity; amino > thiol > octyl
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Methanol in Zeolite
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Reaction pathway. Transition State (TS)

Transition State Stationary point on PES Energy gradient vanishes Hessian matrix has one imaginary frequency
Transition State
Energy
Ea
Reactants
Hf
Products
Reaction Coordinates
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Ring-opening polymerization reaction

Two possible sites for the ringopening of caprolactone - the acylic carbon - an alkylic site
Calculation of the potential

surface for a full set of intermediates
Calculation of Transition State

(LST/QST)
Analysis showed that the ring-opening at the acylic site has a much lower energy more favorable. Agreement with NMR results
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Dynamics of Surface-Confined Droplets - DPD The DPD method has been applied at Unilever to study the dynamics of droplets adsorbed onto surfaces under shearing A droplet at a liquid/solid interface, being driven by external forces, is a situation which occurs when oily soil is being removed from fabric cream or lotion is being spread on the skin emulsion droplets are being broken by mixer blades
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Dynamics of Surface-Confined Droplets - DPD

The figure shows the breakup and partial removal of a 90 degree contact angle drop The droplet contact angle at equilibrium for a variety of oil/surface and water/surface interaction energies was measured The effects of shear on contact angle were examined: above a certain shear rate, the droplet continues to deform over time, moves along the surface with an increasing velocity, and eventually detaches
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Note: it enters here due to periodic boundary conditions
QSAR modeling of Sandalwood Odour

Quiral enantiomers of a molecule can exhibit different odor properties (e.g. campholenic derivates) QSAR to correlate the molecular structure and the sandalwood odour Two scales were developed to asses odor strength Six (6) descriptors common to all models
Odour intensity Odourless Very weak Weak Average Strong Very strong Intensity levels Scale 1 1 2 3 4 5 6 Scale 2 0.00 0.05 0.20 0.50 0.80 0.95
Analysis of models showed the importance of the number and position of substituents in the odor properties
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Part IV: Using the client-server architecture
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Client-server architecture
The client machine is the PC where you are running the Materials Visualizer. The server machine is the one running the calculation (i.e., the server program)
Client PC
Windows server
Linux server
NOTE: The client machine can also be configured to be a server machine

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Gateway
Communication between client and server is handled by a software application called a gateway that is installed on the server You need to install the gateway in each machine you want to run MS calculations Materials Visualizer on the client machine communicates with a server gateway to:
Request information about the installed servers Launch and/or queue a job Terminate a job Check on a job's status
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Gateway access via Server console 1

Access through the Server Console
Choose the Start | Programs | Accelrys MS Modeling [version] | Server Console Choose Tools | Server Console from the MS menu bar
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It has two main sections 1.- Server Gateways 2.- Jobs
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Server Gateways
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Jobs
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Gateway access via web browser

Access the gateway using a web browser
Uses a standard web browser (e.g., Netscape Navigator) Uses a URL of the form "http://<gateway>:<port>"
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Submitting a job 1
You can submit a MS to a server using the user interface of the application (MS Visualizer PC Client)
Set gateway location Set number of processors (if available)
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Submitting a job 2 The following models have parallel codes DMol3 CASTEP Gulp MesoDyn Mesocite QMERA Discover Forcite
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Submitting a job 3
Allows job reconnection to the client PC to the server You may wish to exit MS Modeling before the job completes Next time you start MS Modeling Any jobs that were initiated in the selected project are automatically reconnected If a reconnected job has completed successfully, the files associated with each job are retrieved from the server and displayed in the Project Explorer
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Demo: how to submit a Job
Geometry optimisation with VAMP
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Job Explorer - slide 1

The Job Explorer is displayed automatically when you launch a server job via the gateway. It provides basic information about each job, as it progresses
Job Explorer
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To obtain more detailed information about a server job, double-click on a row in the Job Explorer to open a job log window for the corresponding job
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You can also stop a job using the Job Explorer
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You may like to see the files generated in the server for the selected job
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Transferring input files to the server using FTP

For FTP, choose Tools | File Transfer from the menu bar
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Live Updates
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Part V: Problem Solving Approach in Molecular Modeling or what a modeler does

How to Choose? Which Method?
Results what do they mean?
???????
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Which method?
All methods for everything? REMEMBER If larger time and space domains are accessed , specificity and accuracy are lost QM Atomistic Mesoscale Time Size Accuracy Specificity
It is essential to choose the right method for getting the best results. Results have to be analyzed. This is the work of a modeler, too.
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How to choose?
DFT - Electronic properties or chemical phenomena
Break/form bonds Electronic properties Accuracy is my main concern, time is secondary The system is small (about 100 atoms)
Semiempiric - Electronic properties or chemical phenomena
Still interested in breaking/forming bonds and electronic properties but - Interested only in a first guess - Time is more important than accuracy - Need to deal with a big quantity of atoms
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How to choose?
Atomistic - Physical phenomena Not interested in electrons Huge quantity of molecules/atoms Targeting systems of 100 maximum Processes involving < 1 x 10-9 s Mesoscale - Soft materials Not interested in electrons Not interested in conformations My systems are not crystalline/semi-crystalline I have at least 2 different components Im targeting systems size < micrometer and time < microsecond
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Rule of thumb part 1

How much time do you have? How accurately do you need your results to be? (or what approximations are acceptable and what arent) How many atoms do you have in your system? What computational resources do you have access to? What Materials do you want to study?
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Small organic molecules All techniques applicable
Polymers Usually too big to use QM techniques. Generally use Molecular Mechanics, Mesoscale and QSAR tools to study them. Recently, have been able to use QM methods to study small oligomers Inorganic materials Quantum Mechanics and Molecular Mechanics. Limited applications of QSAR Pure metals Quantum Mechanics. Some limited studies using Molecular Mechanics, GULP
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When using forcefields Forcefield parameters are derived empirically. Typically the parameters are adjusted iteratively to match experimental data Not all materials have been parameterized Polymers Most forcefields do well. COMPASS is the preferred approach (also good for molecular crystals) Small organic molecules - As above Inorganic materials Limited availability, some parameters in COMPASS, some in cvff_aug. Forcefields from the open literature. Pure metals special forcefields
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But
What if you want to study the evolution of a system during hours or a phenomena that has a size of 1 cm? Try to study the problem from another angle
What about studying the initial and the final systems (before and after a reaction)? What about studying the interface?
If reducing the time/size scale does not give you the information
QSAR
If you have a lot of data but little chemical or physical knowledge of the system Useful to generate correlations in systems or to find out which factors control a certain property
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Steps required for molecular modeling

Molecular Modeling (in most cases) involves four main steps Model Building
Sketch molecule, Build Surface, Crystal, Polymer Clean (Data Base, Literature) Refine, Optimize, Minimize with the chosen method Minimize + Dynamics Production stage Calculation, Dynamics
Model Refinement
Simulation Algorithm
Analysis
Calculation of Properties, Spectra, Orbitals
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How to proceed ?
Define the topic
Define the question
Choose the technique/model Modifications Make calculations NO YES Validation Satisfied ?
Answer to the question
Analyse Results
Make more calculations
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Important
Sometimes not only one technique will give all the answers
Different techniques will tackle different angles of the problem

You need scientific background on the domain of study
Right choice of model/simulation tool Correct analysis of the results You want to keep the referees happy
Minimum computer requirements are ok but
Memory - the more RAM your computer has, the better CPU speed - the faster, the better
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On-line Survey
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Hands-On Exercise: Project management

Purpose: Introduces the concept of a Project in MS Modeling and illustrates how they are used to manage your workflow. Modules: Materials Visualizer, Reflex Time: Prerequisites: None
Background When you are running advanced operations such as Discover and Amorphous Cell jobs, many different documents with a number of different document types, can be generated. To make the management of these documents simpler, MS Modeling has a feature called the Project Explorer.
Left hand-side of the visualizer
This is similar to the document management systems seen in advanced programming language packages such as Visual C++. As well as the folders and documents that are created by the program, you can create your own folders to customize the document organization and create your own documents to help you track what you are doing.
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Introduction This tutorial is split into two parts. The first section describes a sample project, in which you see how performing calculations such as energy minimizations affects the structure of your project. The second and subsequent sections guide you through creating your own project. Since working with projects is an essential part of using MS Modeling, references are also made to the Project Explorer in other tutorials. This tutorial covers: Illustrated breakdown of a sample project Creating a new project Using Autosave Importing a structure Generating a chart document Creating a new folder and moving documents Adding and renaming an HTML document Importing into a pre-built folder Saving a project Changing focus Removing documents Note. Sections of this tutorial require use of the Reflex module.
Lesson 1: Illustrated breakdown of a sample project

This section of the tutorial consists of a breakdown of a sample project. It is used for illustrative purposes only and does not include any work for you to complete. In this sample project, a molecule of m-xylene has been loaded and minimized, then a dynamics run has been performed and the dynamics run has been analyzed. It has been broken down to reflect the changes in the Project Manager after each step.
1. The initial project entitled sample with an m-xylene structure imported.
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2. After a minimization run, a new folder called m-xylene Disco Min is opened and the minimized structure is placed in that folder. Here, it is highlighted in blue. The .out document contains the information from the Discover calculation.
3. A dynamics calculation has been performed and the data are placed in the mxylene Disco Dynamics folder. The document m-xylene.xtd is the trajectory document that contains the dynamics simulation.
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4. Analysis has been performed to assess the Length distribution throughout the dynamics run. This information is stored in the highlighted m-xylene.tbl document. This is the layout of a standard calculation. As each new calculation is performed on the results from a previous calculation, a new sub-folder is added to the tree. This allows you to follow the path of an experiment from the directory tree. If you were to construct and minimize a second molecule within the same project, you would see a second tree appearing from the root project. Note. The folder containing the active document is displayed in bold. Now you can proceed and create a small project of your own.
LESSON 2: Creating a new project

If MS Modeling is not already open: Double-click the MS Modeling icon on your desktop to start the program or, alternatively, select Programs|Accelrys MS Modeling [version]|MS Modeling from the Windows Start menu. When MS Modeling starts, a dialog box is displayed asking if you want to open an existing project or create a new one.
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Click the Create a new project radio button and press the OK button. A dialog box appears requesting a name for the new project. You will create a project called Management. Delete the text Untitled and type in Management. Press the OK button. If MS Modeling is already open: Choose File | New Project... from the menu bar. The New Project dialog is displayed. In the File name text box, type Management and click OK. You have now created a MS Modeling project. MS Modeling will open with menu and toolbars along the top, the Project Explorer on the left side and a large gray area in the centre, known as the workspace. The Project Explorer window, called Project, contains the title of the project, Management, in bold next to the MS Modeling icon.
LESSON 3: Using Autosave

MS Modeling includes an Autosave feature which automatically writes changes to documents in the current project to disk at specified intervals during a session. If you want Autosave to operate during a session, you should ensure that it is switched on and, if necessary, adjust the interval between updates. Select Tools | Options... from the MS Modeling menu bar. The Options dialog is displayed. On the General tab, ensure that the Enable Autosave checkbox is checked and that the update interval is set to 10 minutes. If an MS Modeling session ends unexpectedly, because of a loss of power or a computer failure, for example, before you have an opportunity to save your work, when you restart, you will be given the opportunity to restore the latest auto-saved versions of the documents in the current project. Note. The option to recover files is only offered once. If you decline to restore autosaved files, then the versions on disk will be deleted. Alternatively, you can recover the autosaved documents manually from the location specified on the Folder Locations tab of the Options dialog. Choose the Folder Locations tab on the Options dialog. Inspect the default location of the Autosave folder. Click OK to close the Options dialog.
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Tip. Autosave is not a replacement for regularly saving the documents in your project.
LESSON 4: Importing a structure

The next step is to import a structure to see where it fits into the Project Explorer hierarchy. Press the Import button on the Standard toolbar.
The Import dialog is displayed. You should import the MnO structure that is located in the 3D Model folder. Navigate to the Examples\Documents\3D Model folder in the Import Document dialog. Select the MnO.xsd document and press the Import button. The MnO.xsd document is displayed in the Project Explorer in the first level under the MS Modeling icon. If you do not see the extension .xsd in the Project Explorer, you should change your Windows file settings as described below. If you do see the file extension, you can move directly to Lesson 5. The Windows file settings are changed in My Computer not in Materials Studio! Double-click the My Computer icon on your Desktop. The My Computer explorer window is opened. Select Tools | Folder Options... from the menu bar. On the Folder Options dialog, select the View tab. In the Hidden files and folders section, click the Show hidden files and folders radio button and uncheck the Hide extensions for known file types checkbox. Press the OK button. Note: You have now changed the default view settings. However, you will have to save the project and restart MS Modeling for the changes to take effect. Select File | Save Project, then File | Exit from the MS Modeling menu bar. Restart MS Modeling. By default, the last project that you worked on is selected. Press OK. You can now continue.
LESSON 5: Generating a chart document

In order to see the practical applications of the Project Explorer, you need to generate some documents to work with. This can be achieved quickly by calculating a powder pattern. You will not be analyzing this data, since you are generating it solely for the purposes of document manipulation.
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Powder diffraction patterns are generated using the Reflex module. This can be accessed via the Modules menu or toolbar. Press the Reflex button on the toolbar or choose Modules | Reflex from the menu bar, then select Powder Diffraction. As you are not using these results for any scientific analysis, you do not need to change any of the options. Press the Calculate button on the Reflex Powder Diffraction dialog. A chart is displayed, showing a simulated powder diffraction pattern. Click the button to close the Reflex Powder Diffraction dialog.
In the Project Explorer window, there are now two documents, one called MnO.xsd, a 3D Atomistic document, and the other called MnO.xcd, a chart document. Later, you are going to generate a chart for a different structure, therefore, you should place the current structure and chart in a new folder to keep the Project Explorer tidy.
LESSON 6: Creating a new folder and moving documents

Click the root icon in the Project Explorer.
The buttons highlighted on the Project Explorer toolbar should change so that the new folder button is now highlighted. Press the New Folder button on the Project Explorer toolbar.
A new folder is displayed with the default name, New Folder, highlighted. Change this name to something more appropriate. Type MnO and press ENTER. You now have a new folder in the management project called MnO and you can move the chart and structure documents into it. Move the cursor over MnO.xcd in the Project Explorer, then click and hold the left mouse button and drag the document onto the MnO folder. Release the mouse button. Repeat this procedure for the MnO.xsd document.
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LESSON 7: Adding and renaming an HTML document

MS Modeling also features the ability to add HTML documents to projects. These can be very useful for adding experimental notes or calculation settings for reference as you work. HTML documents have advantages over plain text documents, as they allow text formatting that can be loaded into any word processor that supports HTML and they are easy to share. If you create a new document, it is added to the folder that is currently selected. For example, if the MnO folder is selected and you create a new document, it is automatically placed in the MnO folder. As you want this HTML document to be in the root folder, you need to select the Management project icon. Click the root icon in the Project Explorer.
Now create a new document. Select File | New... from the menu bar. The New Document dialog will appear, containing the different document types that can be added to the current project. You should add an HTML document from the document options available. Select HTML and press OK. A new window appears, entitled HTML. This is a basic HTML text editor that can be used in conjunction with the HTML Formatting toolbar to create standard HTML text with features such as bold and italic text, and justification. It is used in much the same way as a word processing package. Type the following in the HTML text editor window: This is the first project I have created and it contains: MnO Folder - holds the MnO structure document and results from a powder diffraction calculation with default values. Now give the document a more informative name. Select HTML.htm in the Project Explorer. Right-click and select Rename from the context menu.Type Project Information and press ENTER.
LESSON 8: Importing into a pre-defined folder

As well as importing documents into the Project Explorer, you can direct them into a specific folder when you start. You do this by selecting the folder before you add the structure. To demonstrate this, you are going to import another metal oxide structure
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called CeO2.msi. First, you need to create a new folder called CeO2. Select the root icon and right-click. Select New | Folder from the context menu. Change the name of the folder to CeO2 and press ENTER. You have now created the folder into which you are going to import your documents. The new folder should already be selected but if not, you should select it. Click the CeO2 folder to select it. Now you can import the document. Select File | Import... from the menu bar. Navigate to the Examples\Documents\3D Model directory in the Import Document dialog. Select CeO2 from the list of documents and press Import. Note. The text box at the bottom of the Import Document dialog indicates where the document will be imported to. The structure is imported into the CeO2 folder. Now, you will use Reflex again to calculate a powder diffraction pattern. Press the Reflex button on the toolbar or choose Modules | Reflex from the menu bar, then select Powder Diffraction. Before you calculate the diffraction pattern, you must change an option on the Display tab of the Powder Diffraction dialog. Select the Display tab. Under View management, change the Chart view option from Replace to New. Now when you calculate a new diffraction pattern, it will be written to a new chart document rather than replacing the original chart, which is the default behaviour. Press Calculate on the Powder Diffraction dialog. Close the dialog. A chart document, CeO2.xcd, is displayed in the CeO2 folder in the Project Explorer. Now, you can also update the Project Information HTML document. Double-click Project Information.htm. On a new line, type the following:
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CeO2 Folder - contains CeO2 structure and results from a powder diffraction calculation with default values.
LESSON 9: Saving a project

Now that you have some results, you can save the project. Select File | Save Project from the menu bar. All the documents have been saved into the project and they have all been saved in their current state. Note: If you were working on a large project with many documents and wanted to save selected documents occasionally as you proceeded, you could do this by selecting File | Save from the menu bar. The Project Explorer now looks like this.
Project Explorer with expanded nodes You can compress the nodes to hide the folder contents. This may make it easier to navigate large projects. Click the symbols next to the folder icons to compress the nodes. Only the items at the top level of the project are displayed.
Project Explorer with compressed nodes
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LESSON 10: Changing focus

Using focus is a very important part of the MS Modeling experience. If you have many documents open in the workspace area, it can sometimes be unclear which document belongs to what folder. However, using the Project Explorer, you can easily navigate around. The active document in the workspace area is highlighted in gray in the Project Explorer and the folder containing the document is displayed in bold. If you double-click a document name in the Project Explorer, it becomes the active document in the workspace area. Double-click MnO.xsd in the Project Explorer. The 3D Atomistic document is brought to the front of the workspace area and the document name is highlighted in gray. Double-click MnO.xcd in the Project Explorer. The MnO chart document becomes active and is highlighted in gray in the Project Explorer. It is also possible to change the focus in the workspace area. Click the title bar or frame of any of the windows that are visible in the workspace area. The document you selected becomes active and the document name in the Project Explorer is highlighted in gray. This is just a simple example of the use of changing focus. When you perform experimental calculations using the other modules, a good knowledge of the way focus works will be invaluable.
LESSON 11: Removing documents

You can remove individual documents from the project. This is done by selecting the document you wish to remove in the Project Explorer and clicking the Delete button. Now remove the HTML Document from the current project. In the Project Explorer, select the Project Information.htm document and press the Delete button on the Project Explorer toolbar.
A dialog box is displayed asking if you want to remove the document. Click Yes.
The HTML document window will disappear from the workspace area and the
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document will disappear from the Project Explorer. This means that you have completely erased the HTML document from the project. Note: if you want to remove a document from the workspace area, but not remove the document from the project, you can do this by pressing the Close button on the window you wish to close. If the project is saved and no further alterations have been made, this will remove the document from the workspace area, but not from the project. Close the MnO.xcd chart document by clicking the button corner of the chart window. in the top right-hand
The chart will disappear from the workspace area, but not from the Project Explorer window. It is very easy to redisplay the chart. Double-click MnO.xcd in the Project Explorer. The chart document is re-displayed in the workspace area. As well as removing single documents from the Project Explorer, you may also need to remove entire folders. This task is performed in a similar way. Select the CeO2 folder in the Project Explorer and press the DELETE key. A dialog box is displayed asking if you want to remove the folder. Click Yes. Now you can shut down MS Modeling. Select File | Exit from the menu bar. At the prompt, click Yes to save the project. This is the end of the tutorial.
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Hands-on Exercise: Setting project defaults

Purpose: Introduces the concept of settings in MS Modeling. Modules: Materials Visualizer Time: Prerequisites: None Materials Studio allows you to alter the default settings of many parameters for some Materials Visualizer tools and all the Materials Studio modules by creating a template project that governs the initial state of all these configurable parameters in new projects. This means that you only need to set all your preferences once for your template project. Thereafter, whenever you create a new project, your preferred settings will automatically be imported and applied, overwriting the default values set by Accelrys. You can also transfer settings between projects, including the template project, allowing you rapidly to configure your projects. Tip. Use these instructions after you have done one of the hands-on examples where we ask you to change settings. So you actually have different settings to our default ones you want to save. This Tutorial covers: Setting up a template project Exchange settings with an external project More about the Settings Organizer dialog
LESSON 1: Setting up a template project

1. Open the project containing the settings that you wish to transfer to the template project. 2. Open the Settings Organizer: Tools|Settings Organizer
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3. Open the template project using the Saved settings in external project entry box.
The template project (Normal.stp) is automatically created in the location defined on the Locations tab of the Options dialog. If you have previously customized any settings in the template project, they will be shown in the Saved settings in external project tree view. If you are altering the template project for the first time, this field will be blank. 4. Select the settings that you wish to transfer from the All settings in current project tree view and press the Save >> button. Any existing settings defined for the template project will be overwritten by the transferred settings. Tip. The All settings in current project and Saved settings in external project fields support multiple selections. Select multiple items by holding down the CTRL key and clicking on them individually or by holding down SHIFT and selecting the first and last items in a range. Alternatively, click and drag to the right of the tree view items to describe a rectangular selection region or click on a parent item to select all its children. 5. Repeat steps 1-3 to export further settings to the template project from other projects. If you make any errors, you can return settings in the template project to their Accelrys default values by selecting the appropriate settings in the Saved settings in external project tree view and pressing the Delete button. Tip. It is also possible to manually configure parameter settings in the template project by opening it in the normal way, displaying the dialog containing the parameters you wish to set, and then closing the dialog. Your references will be saved in the template project and will be applied to any new projects you create subsequently.
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LESSON 2: Exchange settings with an external project

1. Open a project that you wish to transfer settings into or out from. 2. Select an external project that you wish to transfer settings into and out of from the Saved settings in external project dropdown list. Alternatively, press the button to display the Choose Project dialog and browse to an external project, then press Open. 3. If you wish to export settings from the current project to the external project, select the settings that you wish to transfer from the All settings in current project tree view and press the Save >> button. Any existing settings defined for the external project will be overwritten by the transferred settings. Tip. The All settings in current project and Saved settings in external project fields support multiple selections. Select multiple items by holding down the CTRL key and clicking on them individually or by holding down SHIFT and selecting the first and last items in a range. Alternatively, click and drag to the right of the tree view items to describe a rectangular selection region or click on a parent item to select all its children. 4. If you want to import settings from the external project into the current project, select the settings that you wish to transfer from the Saved settings in external project tree view and press the <<Load button. Any existing settings defined for the current project will be overwritten by the transferred settings. 5. If you wish to return settings in the external project to their Accelrys default values, select the appropriate settings in the Saved settings in external project tree view and press the Delete button. Note. Unlike the << Load and Reset buttons, the action of the Delete button cannot be undone; however, the deleted files can be restored from the Windows Recycle Bin if necessary. The action of the Save >> button cannot be undone. 6. If you want to return any settings in the current project to the default values set by Accelrys, select the appropriate settings in the All settings in current project tree view and press the Reset button.
LESSON 3: More about the Settings Organizer dialog

The Settings Organizer dialog allows you to define a template project containing default settings for Materials Studio modules and various tools in the Materials Visualizer. You can also use the Settings Organizer dialog to exchange settings from external projects into the current project or to restore any of the settings in the current project to their Accelrys default values.
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All settings in current project: Displays all the settings that are present in the current project. The settings are organized into two folders: the Modules folder contains module settings and the Visualizer folder contains settings for Materials Visualizer tools. The exact contents of the folders are dependent on the modules and tools that are available in your installation. Double-clicking in this window will transfer settings in exactly the same way as pressing the Save >> button. Saved settings in external project: Select an external project from which to import customized settings from the dropdown list. The dropdown list shows the template project, if you have created one, and the 10 most recently accessed projects. Alternatively, enter the path to a project file (.stp) directly into the field or press the button to display the Choose Project dialog and browse to an external project. Doubleclicking in this window will transfer settings in exactly the same way as pressing the << Load button. Tip. The All settings in current project and Saved settings in external project fields support multiple selections. Select multiple items by holding down the CTRL key and clicking on them individually or by holding down SHIFT and selecting the first and last items in a range. Alternatively, click and drag to the right of the tree view items to describe a rectangular selection region or click on a parent item to select all its children. Save >>: Copies the selected settings in the current project into the specified external or template project, overwriting any existing settings. << Load: Copies the selected settings in the specified external into the current project, overwriting any existing settings. Reset: Returns the selected settings in the current project to the default values set by Accelrys. Projects may also be reset by pressing the Delete key while in the All Settings in Current Project view. Delete: Removes the selected settings from the specified external project, restoring the settings to the default values set by Accelrys. Pressing the Delete key while in the Saved settings in external project has the same action. Note. The Save >>, << Load, and Delete buttons are enabled only if an external project is displayed in the Saved settings in external project field. Unlike the << Load and Reset buttons, the action of the Delete button cannot be undone; however, the deleted files can be restored from the Windows Recycle Bin if necessary. The action of the Save>> button cannot be undone. This is the end of the tutorial.
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Hands-on exercise: Sketching simple molecules

Purpose: Introduces the basic sketching tools allowing you to sketch chains and rings, edit bond type, edit element type, and measure different geometrical properties. Modules: Materials Visualizer Time: Prerequisites: None Introduction In this tutorial, you will learn how to sketch structures within MS Modeling. You will build a variety of simple organic compounds by following the detailed instructions provided. At the end of the tutorial, there are some additional structures for you to build on your own. Note: In many cases, there is more than one way to modify a structure. This tutorial introduces you to the different methods so that you can determine which is best in a given situation. This tutorial covers: Opening MS Modeling Sketching phenol Sketching dicyclopentadiene Sketching pyridine Sketching methyl methacrylate Sketching using the Fragment sketcher
LESSON 1: Opening MS Modeling

Double-click the MS Modeling icon on your desktop to start the program or click Start |Programs | Accelrys MS Modeling [version] and select MS Modeling. After the splash screen has loaded, a dialog box is displayed asking whether you wish to create a new project or open an existing one. You will create a new project. Select the Create a new project radio button and press OK. From the standard New Project dialog box, type Sketching in the File name area and click Save. You have now started a new project called Sketching. The concept of a project is introduced in the Project management tutorial.
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The first task is to open a new 3D Atomistic document in which to sketch a structure. Select File | New... from the menu bar. Select 3D Atomistic from the options listed and click OK. A 3D Atomistic document is displayed in the workspace area.
LESSON 2: Sketching phenol

The structure of phenol is shown below.
Structure of phenol First, you must draw the phenyl ring. Four-, five-, and six-membered rings are provided as templates in MS Modeling and can be sketched easily using the Sketch Ring tool. Click the Sketch Ring button down menu. on the toolbar and select 6 Member on the scroll-
Scroll-down menu The pointer will change to the Sketch Ring tool, with a number 6 in the centre of the ring to denote that a six-membered ring will be drawn. The next step is to place the phenyl ring in the 3D Atomistic document. The Sketch Ring tool generates a ring of carbons connected by single bonds by default. So, typically, it produces a cyclohexane ring after hydrogens have been added. However, you can add a phenyl ring directly. Hold down the ALT key and click in the 3D Atomistic document.
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Note: By default, creates rings where the atoms are connected via single bonds if you want an aromatic ring you have to use the ALT key! A phenyl ring is displayed in the 3D Atomistic document, with dotted lines indicating that it has partial double bonds and is aromatic.
Now, you should sketch an oxygen atom and link it to the ring. You do this with the Sketch Atom tool. The default sketching element is carbon, so you need to specify that you wish to sketch with oxygen. Click the Sketch Atom button . Click the options arrow associated with this tool and select Oxygen from the dropdown menu.
Dropdown menu of Sketch atom
Because the phenyl ring is symmetrical, you can attach the oxygen to any of the carbon atoms. Move the pointer over one of the carbon atoms in the 3D Atomistic document. When the atom changes its colour to light blue, click it. Move the cursor away to sprout a bond. Click again to place the oxygen atom. Press the ESC key to cancel further drawing. Note: The change in colour of the carbon atom as the cursor moves over it indicates that you can select it. You should now have a structure containing a red oxygen atom attached to a grey carbon ring.
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The final step is to add the hydrogen atoms. The Adjust Hydrogen tool automatically fills up the empty valences with hydrogen atoms. Click the Adjust Hydrogen button .
The hydrogen atoms will fill up the empty valences so that you have a structure that looks similar to the one shown below.
Model of phenol Now that you have sketched the structure, you should use the Clean tool to tidy up the geometry. Note: This is not an energy minimization, but, instead, uses a look-up table of standard bond lengths and angles to give a first approximation to the correct geometry. Click the Clean button .
When the mouse button is released, the cleaning operation begins. A progress bar is displayed in the bottom right of the screen and disappears on completion. This may happen so quickly that the box disappears as soon as it is created. The final step is to save the structure.
Select File | Save As... from the menu bar. In the Save As dialog, type the filename phenol and press the Save button. The structure is saved in .xsd format. This is a new file format based on XML (eXtensible Markup Language) and is very flexible, allowing future changes, such as
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hierarchical searching. The structure you have drawn can be rotated and translated in three dimensions using the right mouse button. Hold down the right mouse button and move the cursor in the centre of the 3D Atomistic document. Moving the mouse up, down, left, and right rotates the model in the X and Y planes. Move the cursor to the edge of the 3D Atomistic document. Hold down the right mouse button and move the cursor along the edge. The model rotates in the Z plane. The model can be translated along the X and Y axis using the translate tool. on the toolbar. Click and hold down Press the 3D Viewer Translation Mode button the left mouse button in the 3D Atomistic document and move the cursor around the screen. The model follows the movements of the mouse. If you find that you have rotated or translated the model too far, there are three buttons to help you get back to the original view. Reset View Re-centre Fit to View document. Resets the view to the original position. Translates the structure to its original centre position. - Fits the molecule in its current conformation into the 3D Atomistic
Click the Reset View button
The structure is rescaled to fit the screen and reoriented to the default setting.
LESSON 3: Sketching dicyclopentadiene

The structure of dicyclopentadiene is shown below.
Structure of dicyclopentadiene It is used as an intermediate in the synthesis of insecticides and herbicides. Open a new model window in which to draw the model.
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Select File | New... from the menu bar. Double-click 3D Atomistic. Now draw a six-membered ring. Click the Sketch Ring button place a six-membered ring. . In the empty 3D Atomistic document, click once to
Next, you should add a five-membered ring and fuse it to the six-membered ring. Click the options arrow associated with the Sketch Ring button and select 5 member from the dropdown menu. Hover the pointer over the middle of one of the bonds. When it changes to light blue, click to fuse a five-membered ring. A five-membered ring is fused to the six-membered ring. Now, you should add the bridging carbon atom. You do this using the Sketch Atom tool. Click the Sketch Atom button . Check that C is the sketch atom. If it is not, click the options arrow and choose Carbon from the dropdown list.
Adding the bridging carbon atom Move the pointer over atom 1 in the diagram above. When the atom changes colour to light blue, click it. Move the cursor to the middle of the ring and click again to place the bridging atom. Move the cursor to atom 2 and when its colour changes to orange, click a final time. You have now created a bridging carbon atom between two carbon atoms in the sixmembered ring. If at any point you make a mistake, you can click Undo to go back one step. To undo the last action, click the Undo button on the toolbar.
If you undo too many steps, you can redo them using the Redo button. To redo the last action, click the Redo button on the toolbar.
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To complete the structure, you must add double bonds to the two rings. You do this with the Bond Type tool. The first step is to select the two bonds you wish to modify.
Modifying the bond type Click the Selection button on the toolbar. Select bond 3 in the diagram above.
A yellow square will appear in the middle of the bond, indicating that it has been selected. You can increase the bond order of both bonds simultaneously to save time. Hold down the SHIFT key and move the pointer over bond 4. Click the middle of the bond. A yellow square appears on the second bond, indicating that it too has been selected. Now you change the bond order using the Bond Type tool. Click the options arrow associated with the Bond Type button toolbar. Then select double bond. on the Sketch
The bond type on the diagram will change to show two new double bonds. Now deselect the bonds by clicking anywhere in the 3D Atomistic document so that the next action affects all of the atoms. The final step is to add hydrogens and clean the structure. Click in 3D Atomistic document.xsd to deselect all of the atoms. Click the Adjust Hydrogen button . Press the Clean button .
The final structure will look similar to the one shown below.
Structure of dicyclopentadiene
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Finally, save the structure. Click the Save button on the Standard toolbar. This saves the structure with the default document name. If you are constructing a project with multiple structures, it is simpler to use the Save As... command, as this allows you to specify the model name that appears in the Project Explorer.
LESSON 4: Sketching 2-chloropyridine

The next structure you are going to look at is 2-chloropyridine.
Structure of 2-chloropyridine Click the options arrow associated with the New button on the Standard toolbar. Select 3D Atomistic Document from the dropdown menu. Before sketching, you should rename the empty 3D Atomistic document. In the Project Explorer, right-click 3D Atomistic (2).xsd and select Rename from the context menu. Type pyridine and press ENTER. First, you should place a phenyl ring in the new 3D Atomistic document. Select the Sketch Ring tool from the toolbar. Click the options arrow and select 6 member from the dropdown list. Hold down the ALT key and click once in the 3D Atomistic document. A phenyl ring is displayed in the 3D Atomistic document. Now, you should edit one of the carbon atoms to change it to a nitrogen atom. This time you will make this change using the Properties Explorer. Select View | Explorers | Properties Explorer from the menu bar. The Properties Explorer opens on the left side of the screen under the Project Explorer. It looks similar to the spreadsheets you may have encountered in programs such as Excel and contains two columns labelled Property and Value.
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Click the 3D Viewer Selection Mode button document.
. Click an atom in the 3D Atomistic
The Properties Explorer box will update with information about the selected atom. The first few items in the list are Charge, ElementName, ElementSymbol, and ForcefieldType. This box can be enlarged and reduced by moving the cursor to the top of the Explorer box and, when the icon changes to a standard enlarge icon, clicking and holding and moving the top of the box up.
Properties Explorer Change the selected atom from carbon to nitrogen. Double-click ElementSymbol in the Property column. A dialog containing the periodic table opens. Select N and click OK. The selected atom will change color from gray to blue. Other information, such as the MassNumber, will also change. Scroll down the list of Properties to see what else has changed. Note: The given Name of the atom is not important in this context. Changing the Name does not change the element type. Click in the 3D Atomistic document to deselect all of the atoms. The next step is to connect a chlorine atom to the ring. This is done using the Sketch Atom tool. . Click the options arrow and change the sketch atom Click the Sketch Atom tool from Carbon to Chlorine. Select one of the carbon atoms adjacent to the nitrogen in the ring, click it, move the mouse to sprout a bond, and double-click.
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A green chlorine atom appears connected to the ring at the 2-position. Next add the hydrogens. Click the Adjust Hydrogen button on the Sketch toolbar.
Before you clean the structure, look at some of the measurement tools included in MS Modeling. You should set up bond length and bond angle measurements, and monitor these before and after they are cleaned by writing the values in an HTML document. Select the Measure/Change tool from the toolbar. Click the options arrow
associated with it and, from the dropdown menu, select Distance . Hover the cursor over the middle of the bond connecting the chlorine and carbon atoms and when it changes to light blue, click it. A set of red dashes appears on the bond and a number is displayed in red. This is the C-Cl bond length and its value is dependent on how you drew the structure. Look at the Project Explorer and note which name is highlighted. This is important as this is the name of the active 3D Atomistic document. After you perform the next step, you will need to make the 3D Atomistic document active again. An easy way to do this is by double-clicking on its filename in the Project Explorer. Instead of recording information on paper, MS Modeling has the facility to add HTML documents to projects. This enables you to track any settings or results as you change aspects of the calculations. Select File | New... from the menu bar. From the New Document dialog box, select HTML. A basic HTML editor window opens, in which you can type information. This HTML editor also appears in the Project Explorer window. Click in the HTML document and type C-Cl bond length before cleaning is: then type the result from the distance measurement on the same line. You should also measure the bond angle between the chlorine atom and the ring. Double-click pyridine.xsd in the Project Explorer to make it active. Click the options arrow adjacent to the Measure/Change tool . Select Angle from the dropdown list of options. Click the chlorine, carbon, and Nitrogen atoms to measure the Cl-C-N bond angle. The bond angle is displayed in red with a dotted red line indicating the measured angle. The distance monitor has changed to green. You should record this number in the HTML document.
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Double-click the HTML document in the Project Explorer to make it active. On a new line, type Cl-C-N bond angle is: followed by the value obtained from the bond angle measurement. Return to the 3D Atomistic document by double-clicking on the filename in the Project Explorer. Now clean the structure. Click the Clean button on the Sketch toolbar.
The values of the bond angle and bond length will change after the cleaning process, indicating the improvement in the geometry provided by the Clean tool. The new bond lengths and bond angles can be recorded in the HTML document. Select the HTML document window and type in the new information. Click File | Save Project on the menu bar. You have now saved the project. The final structure will look like the one shown below.
Structure of chloropyridine
LESSON 5. Sketching methyl methacrylate

The structure of methyl methacrylate is shown below.
Structure of methyl methacrylate You will not actually draw this structure initially, as it is a good example of how to add
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atoms to an existing structure. First, you will create the structure shown below.
The intermediate structure Then you will add the linking oxygen atom. The first stage is to construct the carbon chain. Click the options arrow associated with the New button on the Standard toolbar. Select 3D Atomistic Document from the dropdown menu. Rename the new document Methylmethacrylate.xsd. You now have a new document window in which to sketch the structure. Click the Sketch Atom button on the toolbar. Make sure the sketch atom is C. Click in the 3D Atomistic document to draw a carbon atom. Move away and click again. Repeat this until you have drawn four carbon atoms, forming the backbone of the molecule. Press the ESC key to cancel the sketching action. The next step is to add a methyl group to one of the carbon atoms to form the branched carbon chain. Move the cursor over the second carbon atom in the chain. When it changes colour to light blue, click it and move the cursor away to sprout the bond. Click once more to fix the carbon and press the ESC key. Now you should add the oxygen to the chain. Change the sketch atom by clicking on the options arrow associated with the Sketch Atom button and selecting Oxygen. Move the cursor over the third carbon along the chain and, when it changes color, click it. Move away to sprout the bond and click to place the oxygen atom. Press the ESC key to cancel the sketching action. Having added the oxygen, you must change the bond type. This can also be done using the Sketch Atom tool. With the Sketch Atom tool selected, move the cursor so that it is over the middle of the carbon-oxygen bond. When the bond changes colour to light blue, click it. The bond type will increase to double. Now you just need to add hydrogens and clean the structure.
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Click the Adjust Hydrogen button
on the toolbar and then the Clean button
You have now drawn the second structure. However, to obtain the methyl methacrylate structure, it must be modified. An oxygen link atom must be added. You can do this by adding an oxygen atom in between two carbons and then deleting the carbon-carbon bond. Click the Sketch Atom tool on the toolbar. In the 3D Atomistic document, click the terminal carbon atom and move the cursor away to form a bond. Click again to place an oxygen atom. Then move to the carbonyl carbon and click to select it. You will now have a structure that looks similar to the one shown below.
The intermediate model The next step is to delete the bond that joins the two carbons so that the oxygen bridge is the only link between the methyl and the carbonyl groups. Hold down the SHIFT key to access Selection Mode functions whilst still in Sketch Mode and select the bond joining the two carbon atoms. Press the DELETE key. The bond disappears leaving only the oxygen atom joining the carbonyl and methyl groups. The last step is to add hydrogens and clean the structure. Click the Adjust Hydrogen button on the toolbar and then the Clean button .
The final structure of methyl methacrylate should look like the one shown below.
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Structure of methyl methacrylate
LESSON 6. Sketching methyl methacrylate with the Sketch Fragment Tool
Structure of methyl methacrylate Click the options arrow associated with the New button on the Standard toolbar. Select 3D Atomistic Document from the dropdown menu. Rename the new document Methylmethacrylate_frag.xsd. You now have a new document window in which to sketch the structure. Click the options arrow adjacent to the Sketch Fragment Button Fragment browser of the dropdown list of options. The fragment browser will appear on the screen. and select
Fragment Browser
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Click the + icon associated with Functional groups and select Methanal. Click once in the 3D Atomistic document.
Methanal You will change the display style to Ball and Stick. Right click in the 3D Atomistic Document and go to Display Style. Select Ball and Stick. You should see a molecule of formaldehyde on you screen now:
Formaldehyde
Now you will add all the other parts. Click the options arrow adjacent to the Sketch Fragment Button and select Fragment browser of the dropdown list of options. Click the + icon associated with Functional groups and select Methoxy. You see one of the hydrogen atoms of the CH3 groups in a red cage. This marks the connection point.
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However you need the OH hydrogen atom to be the connection point: Double-click the OH hydrogen atom in the Fragment Browser: As a result, the red cage (connection point) is now around the OH hydrogen atom.
is still selected, and move the curser Make sure the Sketch Fragment Button over one of the hydrogen atoms of Formaldehyde in your 3D Atomistic document. When its colour changes to light-blue, click it to add the O-CH3 group. You will obtain:
Now you need to add the iso-propyl group:
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and select Click the options arrow adjacent to the Sketch Fragment Button Fragment browser of the dropdown list of options. Click the + icon associated with Hydrocarbons and select Isopropyl. Make sure the Sketch Fragment Button is still selected, and move the curser over the hydrogen atom of the aldehyde moiety in your 3D Atomistic document. When its colour changes to light-blue, click it to add the CH(CH3)2 group. You will obtain:
the wrong conformation! Here the O-CH3 group is not correctly orientated the two CH3 groups are certainly too close. Clean would not help as it doesnt change the torsion. You can change the geometry by hand. With the Sketch Atom tool selected, click the CH3 carbon atom which is indicated with a black arrow in the figure above. Leave the left mouse button pressed and drag the carbon to the spot marked with the black circle. Then press the Clean button The final structure should look like that:
Now you can save all the structures and documents you have generated into one project. Select File | Save Project or click the Save Project button on the Project toolbar.
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The project is now saved.
LESSON 7: Additional structures

By now you should be able to sketch molecules quite easily using different methods for selecting and changing bond type and atom type. Below are a few structures that you can build by yourself. There are hints with each structure to help you work out how to build them. Trichlorophenol (TCP)
An antiseptic liquid. Import the phenol model (File | Import...) - make sure the file type is .xsd. Edit the hydrogens - try using the different methods for editing the atom types. 4-Pentyl-4-cyanoterphenyl
The first viable room temperature nematic liquid crystal. Start with the rings// Use Sketch Atom to link the rings// Remember the CN bond is a triple bond//Add the hydrogens at the end. This is the end of the tutorial.
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Hands-on Exercise: Sketching organometallic structures

Purpose: Introduces the Fragment Browser as an aid to sketching complex structures and illustrates one use of the Find Symmetry tool for nonperiodic systems. Modules: Materials Visualizer Time: Prerequisites: None Introduction The Materials Visualizer contains tools for determining the symmetry of both periodic and nonperiodic structures. The concept and application of symmetry in periodic systems is well known, but the use of symmetry when building nonperiodic systems is less common. However, symmetry can play an important role when you are looking at organometallic structures. In this tutorial, you will use the symmetry tools in MS Modeling to construct two enantiomers of an organometallic structure. After this, you will use the fragment library to construct and define your own fragments and use these to build a more complex organometallic structure. This tutorial covers: Sketching the initial structure Using the Find Symmetry tool Adding the rings and cleaning the structures Creating user-defined fragments Sketching with the user-defined fragments
LESSON 1: Sketching the initial structure

The two structures you are going to draw are enantiomers. The structures are shown below in both meso and rac forms.
Meso form with C1 symmetry
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Rac form with C2 symmetry
First you will draw the core of this structure, shown below, define it as having C1 symmetry, find the alternative C2 symmetry, and finally add the rings.
The core structure You begin by sketching the core structure. Click the options arrow associated with the New button and select 3D Atomistic Document. From the Sketch toolbar, click the options arrow associated with the Sketch Fragment button and choose Fragment Browser.
The Fragment Browser dialog is displayed.
Fragment Browser dialog On the left, a list of the fragments available in MS Modeling is displayed, and on the right, a model of the currently selected fragment is shown. This model can be rotated. The red cage around the hydrogen atom indicates that this is the connection point for the fragment. This can be changed to any other atom by simply double-clicking on the desired atom.
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Click to compress the Hydrocarbons node then click + to expand the Metal Templates node.
A list of the different metal center fragments in MS Modeling is displayed. The metallocene you will sketch has a tetrahedral conformation. Click 4 coordinate Td. The default metal center is iron, but you require a zirconium center. Instead of sketching the fragment and then editing the metal atom, you can tell MS Modeling to replace the metal center before sketching. Click the further options button associated with Replace undefined atoms. From the Periodic Table, select Zr then click OK. Click once anywhere in the 3D Model document to add the tetrahedral structure and close the dialog. A tetrahedral structure is displayed in the 3D Model document. Before you add the other substituents to this structure, you should rotate the structure core so that it appears as shown below. Right-click in the 3D Model document and select Display Style to open the Display Style dialog. Select Stick from the list of display styles, then close the dialog. Right-click and drag in the 3D Model document to rotate the fragment until it is aligned in the + shape illustrated below.
Alignment of metal core Now you are ready to add the chlorine substituents. on the toolbar and hold down the SHIFT key. Click the Click the Selection button two hydrogen atoms to the left and right of the Zr center to select them. Click the options arrow associated with the Modify Element button Click in the 3D Model document to deselect everything. and select Chlorine.
The two hydrogen atoms you selected are now chlorine atoms. The next stage is to add
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the cyclopentadiene ligands. Click the options arrow associated with the Sketch Fragment button and select Fragment Browser. Compress the Metal Templates node and expand the Ligands node. Select the Cyclopentadienyl fragment. The cyclopentadienyl ligand uses a dummy atom to denote its connection point. In the 3D Model document, click the top and bottom hydrogen atoms to add two cyclopentadienyl rings. The core structure is displayed.
The core model Press the Clean button on the toolbar. Close the Fragment Browser dialog.
LESSON 2: Using the Find Symmetry tool

The next step is to determine the symmetry of the system. Press the Find Symmetry button on the toolbar.
The Find Symmetry dialog is displayed.
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Find Symmetry dialog Click the Options tab and ensure that Reorient structure after update is unchecked. Click the Find tab and press the Find Symmetry button. The Results window should display the symmetry group for the structure, C1. Press the Snap To Symmetry button. If it displays Cs instead, you must decrease the tolerance for the Find Symmetry operation to increase your chances of finding the correct C1 symmetry. Open the dropdown menu associated with tolerance and change the value from 0.1 to 0.01 (Fine). Repeat as necessary, until you find C1 symmetry. Close the Find Symmetry dialog. Change to Selection mode. Now you should make a copy of the core structure and change the symmetry to C2. To alter the symmetry of the core structure you must change the orientation of the cyclopentadienyl ring. In the Project Explorer, right-click 3D Atomistic.xsd and select Rename. Change the filename to meso and press the ENTER key. Next, click once in meso.xsd, then press CTRL-C, or select Edit | Copy from the menubar, to copy the structure. Open a new 3D Atomistic document and press CTRL-V, or select Edit | Paste from the menubar. Click in the 3D Model document to deselect all the atoms. The core is pasted into a new 3D Model document. In the Project Explorer, right-click the new 3D Atomistic.xsd, select Rename and change the filename to rac. Right-click and drag to rotate the molecule so that it is in the same orientation as the meso structure.
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MS Modeling allows you to organize how you view the open documents in the workspace area. Make sure that meso.xsd is the active document. Select Window | Tile Vertically from the menubar. Right-click in meso.xsd and select Display Style. Select Ball and stick from the list of display styles. Click once in rac.xsd and select Ball and stick again, then close the Display Style dialog. You will now change the symmetry of the core of the rac structure from C1 to C2.
Torsions that need to be defined to convert rac.xsd to C2 symmetry In the meso structure, illustrated on the left above, the torsion angle 1234 is approximately 90. To set the symmetry of rac.xsd to C2, you must set the torsion angle in the rac.xsd structure, illustrated on the right above, to the same value as that of the meso structure. The Find Symmetry tool has different levels of sensitivity and, at this level, your two structures should be mirror images of each other. Therefore, you should measure the torsion angle 1234 in meso.xsd and then set torsion angle 5678 in rac.xsd to the same value. Make sure that meso.xsd is the active document. Click the options arrow associated with the Measure/Change button and select Torsion. Click atoms 1, 2, 3, and 4, indicated in the diagram above, in that order. A torsion angle is displayed in red. Make a note of this value. Now change the torsion angle in rac.xsd to the value you recorded above. Note. To define a geometry monitor that can be changed, you must choose atoms that are all connected. If you do not do this, you will not able to change the value of the geometry monitor. In this case, the dummy atom is bonded by bonds to the carbon atom, but the bonds are not visible in this display style. Make rac.xsd the active document. Click the options arrow associated with the Measure/Change button diagram above, in that order. and select Torsion. Click atoms 5, 6, 7, and 8 in the
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Since you know exactly what value you want to use, you can use the Properties Explorer to make the change. If the Properties Explorer is not visible, select View | Explorers | Properties Explorer from the menubar. Change the Properties Explorer Filter: to Torsion. Angle is the first property in the list. Double-click Angle to open the Edit Angle dialog. Change the value to the one you recorded for the C1 structure. Click OK. The 3D Model document updates with the new geometry. The next stage is to use the Find Symmetry tool to calculate the symmetry of the new structure. Press the Find Symmetry button on the toolbar. On the Find Symmetry dialog, make sure the tolerance is 0.1 and press the Find Symmetry button. This time symmetry group C2 should be found. If it is not, use the Clean functionality again to make small adjustments to the torsion angles and recalculate the symmetry function. Press the Snap to Symmetry button. This may change the coordinates of the atoms in the structure slightly so they are exactly consistent with the symmetry found. Before continuing, remove the torsion monitors. Press the Selection button on the toolbar. Select the torsion angle and when it changes color to yellow, press the DELETE key. Make meso.xsd the active document and repeat the procedure.
LESSON 3: Adding the rings and cleaning the structures

Now that you have built the core structures and defined their symmetries, it is easy to add the rings required to complete the meso and rac structures. The meso structure
The meso structure with C1 symmetry
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Make meso.xsd the active document by double-clicking on meso.xsd in the Project Explorer. Now add the phenyl rings that are fused directly to the cyclopentadienyl rings. Press the Sketch Ring button on the toolbar. Hover the cursor over the bond that you want to fuse the ring to and when it changes colour to blue, hold down the ALT key and click once. Repeat the procedure for the equivalent bond in the other cyclopentadienyl ring. As the Find Symmetry tool is very sensitive to small changes in geometry, you should adjust the hydrogens and clean the structure before checking the symmetry again. Press the Adjust Hydrogen button on the toolbar, followed by the Clean button on the toolbar to open the Find Symmetry
. Press the Find Symmetry button dialog. Press theFind Symmetry button.
The structure should now look like the one shown below and it should still have C1 symmetry.
The intermediate meso model The final step is to add the unfused phenyl rings, add hydrogens, and clean the structure. Press the Sketch Ring button on the toolbar. Hold down the ALT key and click the hydrogen on the cyclopentadienyl ring that is opposite the fused bond. Repeat this for the second ligand. Press the Adjust Hydrogen Finally, you should check the symmetry once more. Press the Find Symmetry button on the toolbar to open the Find Symmetry dialog. Press Find Symmetry then Snap to Symmetry. and Clean buttons .
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The rac structure
The rac structure with C2 symmetry Make rac.xsd the active document by double-clicking on rac.xsd in the Project Explorer. This time you should add phenyl rings to opposing sides of the two cyclopentadienyl ligands to maintain the C2 symmetry. Press the Sketch Ring button on the toolbar. Hover the cursor over the bond that you want to fuse the ring to and, when it changes colour to blue, hold down the ALT key and click once. Repeat the procedure for the opposite bond in the other cyclopentadienyl ring. As before, add hydrogens and clean the structure after each step.
The intermediate rac model Finally, add the two unfused phenyl rings. Add the phenyl rings to the second hydrogen of the cyclopentadienyl ring as described above. Remember to press the ALT button to generate aromatic rings. Press the Adjust Hydrogen and Clean buttons .
Now check the symmetry again. on the toolbar. Press the Find Symmetry button. Press the Find Symmetry button The system should still have C2 symmetry. Before you continue, save the project. Click the Save Project button .
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LESSON 4: Creating user-defined fragments

MS Modeling allows you to define your own fragments and save them to the library. In this section, you will build a ligand similar to those constructed in the previous sections and use it to make a more complex metallocene. The ligand you are going to construct is shown below.
The ligand You should start with the cyclopentadienyl ligand from the fragment sketcher. Open a new 3D Atomistic Document. Click the options arrow associated with the Sketch Fragment button on the toolbar and choose Fragment Browser. Select the Cyclopentadienyl fragment from the Ligands section. Click once in the 3D Model document to place the cyclopentadienyl fragment. Close the Fragment Browser dialog. Now you should sketch the two phenyl rings. Press the Sketch Ring button on the toolbar. Hold down the ALT key and click one of the C-C bonds in the cyclopentadiene ring. A 6-membered ring is fused to the cyclopentadienyl ring. Hold down the ALT key and click the hydrogen opposite to the bond with the fused 6-membered ring. Press the Adjust Hydrogens button. Now add the tertiary butyl substituents in the meta positions on the unfused ring. Instead of sketching the substituents, they can be obtained from the fragment library. Open the Fragment Browser and select the Tertiary Butyl fragment from the Hydrocarbons library. Click the two hydrogens in the meta positions on the unfused phenyl ring to add the tbutyl groups. Close the Fragment Browser. Press the Clean button on the toolbar.
The next step is to define this new fragment. To maintain consistency in the display styles in the Fragment Browser, you should view this in ball and stick format. If the document is not already in ball and stick format, right-click in the 3D Model document and select Display Style. Select Ball and stick. Close the Display Style dialog. Now you can define the fragment.
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Click the options arrow associated with the Sketch Fragment button and select Define Fragment. You have to select a connection point. For this fragment, the connection point is the hydrogen atom that is attached to the dummy atom in the cyclopentadienyl ring. Press the Selection button on the toolbar. Click the hydrogen atom attached to the dummy atom. Press the Define button on the Fragment Definition dialog. A red cage is displayed around the connecting atom. The final step in this procedure is to choose a fragment library and name for the fragment. In this case, you will put the new fragment in the User library and call it t-but-cp. Click the Fragment Name text box and type in t-but-cp. Press the Add button. If you get a dialog about the creation of the User library, select Yes. Close the Fragment Definition dialog. You have successfully added a new fragment to the fragment library.
LESSON 5: Sketching with the user-defined fragments

Now that you have defined a new fragment, you can use it to sketch this molecule.
The target structure The first step is to sketch the metal center. Open a new 3D Atomistic Document. Open the Fragment Browser and select 4 coordinate Td from Metal Templates. Click once in the 3D Model document to place the metal atom. Now you can add on the ligands. In the Fragment Browser, select the t-but-cp ligand from the User library. Click the first hydrogen attached to the Zr atom. Click and hold the mouse button on the second hydrogen. Holding the mouse button down while sketching a fragment displays a torsion monitor. The fragment can be rotated by moving the mouse. Move the mouse to rotate the fragment until it is in a similar configuration to the one shown above.
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Press the Clean button
Note. The Clean operation is not an energy minimization, so for an accurate structure, you should optimize the geometry using an appropriate semiempirical or ab initio program. The final step is to edit the remaining two hydrogens attached to the metal center to make them chlorines. on the toolbar. Select the two hydrogens Press the Selection Mode button attached to Zr by clicking on them while holding down the SHIFT key. Press the Modify Element button and select Chlorine. Double-click in the 3D Model document to .
deselect the atoms. Press the Clean button
You have now finished sketching the structure. If you wish to experiment further with this structure, try changing the dihedral angle as you did for the meso and rac structures so that it looks similar to the one shown below.
The target model Using the Project Explorer, rename this 3D Atomistic document t-butyl. Right-click the name highlighted in the Project Explorer and select Rename. Type in tbutyl and press ENTER. Before finishing the tutorial, change the window view so that you can see all three structures you have drawn. Select File | Save Project from the menubar. Select Window | Close All from the menubar. In the Project Explorer, double-click to open meso.xsd, rac.xsd, and tbutyl.xsd. Select Window |Tile Vertically from the menubar. This is the end of the tutorial.
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Hands-On Exercise: Overlaying and aligning molecules

Purpose: Introduces the collection document and demonstrates how it can be used to overlay and align molecules. Modules: Materials Visualizer Time: Prerequisites: None Introduction Whether you are comparing two crystal structures from a Polymorph prediction or comparing optimized conformations of molecules, the ability to overlay sets of molecules or crystals for visualization is a vital part of molecular modeling. The 3D Atomistic Collection document in the Materials Visualizer allows you to overlay molecules, slabs, and crystals in the same 3D Cartesian space without any physical interaction between the systems. This tutorial illustrates how you can use collection documents to overlay molecules and demonstrates how to align multiple structures. This tutorial covers: Getting started Inserting and selecting structures in a collection document Aligning structures by their principal moments Tip. This tutorial is best carried out with the file extensions for each document displayed. If the file extensions are not displayed in your Project Explorer, refer to the Project Explorer topic for instructions on how to reconfigure.
LESSON 1: Getting started

Begin by starting Materials Studio and creating a new project. If Materials Studio is on your desktop to not already open, double-click on the Materials Studio icon start the program or, alternatively, select Programs | Accelrys Materials Studio [version] | Materials Studio from the Windows Start menu. When Materials Studio starts, a dialog is displayed asking if you want to open an existing project or create a new one. Click on the Create a new project radio button and press OK. A dialog appears requesting a name for the new project. You will create a project called Collection.
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Enter the project name Collection and press OK.
LESSON 2: Inserting and selecting structures in a collection document

The first step is to load in a series of structures. You will use the corrosion inhibitors from the QSAR tutorial and import them into a study table. Click on the options arrow associated with the New button on the Standard toolbar and select Study Table Document from the dropdown list to create a new study table document. Press the Insert From File button on the Standard toolbar to display the Insert Into Active Document dialog and locate the Examples\QSAR\Structures folder. Double-click on the Corrosion.sd file. The corrosion data are displayed in the study table. You can extract the structures from the study table into a 3D Atomistic Collection document (.xod file). Select the set of structures in rows 1 to 7 of column A in the study table. Right-click on any of the selected cells and select Extract To Collection from the context menu. The selected structures are extracted to a collection document entitled Extracted From Study Table.xod.
Note. You can also insert structures into a collection document from a series of separate 3D Atomistic documents within the current project. To do so, create a new 3D Atomistic Collection document, select the documents that you wish to insert in the Project Explorer, then right-click on one of them and select Insert Into from the context menu. If you wish to view the contents of a 3D Atomistic Trajectory document in a collection document, you must first insert the frames into a study table and then extract the structures as described above. Collection documents support many of the features that are available in 3D Atomistic documents; the structure viewing and manipulation tools, for example. In addition, molecules imported into a collection document retain certain types of data that may have been calculated for that structure, such as field, surfaces, or habits. The most
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important difference between .xsd and .xod documents is that in the latter, molecules are chemically isolated, allowing them to be in close proximity (e.g., for the purposes of alignment) without interacting with each other. In contrast, molecules in 3D Atomistic documents are affected by their environment. You can control the selection of molecules in a collection document using the Physical Systems dialog. Right-click in the collection document and select Physical Systems from the context menu.
The Physical Systems dialog is displayed. You can use this dialog to select and change the visibility of the structures in the collection document. In the Physical Systems dialog, click on Corrosion - 1 and then Corrosion - 7. As you click on the structure names in the Physical Systems dialog, the structures are selected in the collection document. Tip. You can select multiple structures by using the SHIFT and CTRL keys to modify selection in the usual way. You can change the visibility of molecules irrespective of whether they are selected in the Physical Systems dialog. With Corrosion - 7 selected, click on the checkbox for Corrosion - 3 in the Physical Systems dialog. The Corrosion - 3 structure disappears from view, although it is still present in the collection document. You can also delete molecules from the collection document.
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Select Corrosion - 1 using the Physical Systems dialog and press the DELETE key. The molecule is deleted from the collection document and is no longer shown in the Physical Systems dialog.
LESSON 3. Aligning structures by their principal moments

There are two tools available for aligning molecules in the Materials Visualizer. One tool allows you to align a set of molecules in a specific direction and the other, Superpose Structures, allows to align the molecules with respect to each other. For this tutorial, you will align the molecules in a specific direction. In the Physical Systems dialog, select Corrosion - 2. Click on the options arrow associated with the Create Centroid button the dropdown list. and select Principal Axes from
The principal axes are calculated and displayed in the collection document for the selected molecule. Tip. You can perform alignment using any of the averaged geometry objects that can be calculated using the Create Centroid tool. Repeat the above steps for molecules Corrosion - 3 through to Corrosion - 7. Close the Physical Systems dialog by pressing the Close button . Now that the principal axes have been calculated and displayed for each molecule in the collection document, you can align the molecules. Click in the Extracted From Study Table.xod document to deselect all the objects. Hold down the ALT key and double-click on one of the principal axes objects. All the principal axes objects are selected. To align molecules in Materials Visualizer, you first align the view and then align the molecules to fit the view. In this tutorial, you will align the principal moments with the x, y, and z axes, so you must set up the view appropriately. Press the 3D Viewer Reset View button Align Onto View button . on the toolbar and then click on the
The molecules are rotated and aligned so that their principal moments are aligned with the x, y, and z axes. If you wish to continue working on these structures, you can return them to the study table or extract them to separate 3D Atomistic documents.
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Right-click in Extracted From Study Table.xod and select Return To Study Table from the context menu. The molecules are returned to the study table, overwriting the original structures. You could now proceed by optimizing these structures or calculating properties using the Models dialog. With the collection document in focus, click in it to deselect the principal axes objects, then right-click and select Extract To Atomistic Documents from the context menu. The structures contained within the collection document are extracted to separate 3D Atomistic documents and are placed within the folder that is currently selected in the Project Explorer. Note. If you have particular molecules selected in the Physical Systems dialog when you choose Extract To Atomistic Documents from the context menu, only the selected molecules will be extracted into .xsd documents. This is the end of the tutorial.
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Hands-On Exercise: Using the polymer builder

Purpose: Introduces the polymer builder which can be used to build homopolymers, block copolymers, random copolymers and dendrimers. Modules: Materials Visualizer Time: Prerequisites: None Introduction The Build Polymers tool available in the Materials Visualizer makes constructing complex polymers easy. The polymer builder includes an extensive library of common monomer units and it can also be used with custom repeat units. You can build homopolymers, block polymers, and random copolymers and control a range of properties such as tacticity and reactivity of the monomers. MS Modeling also allows you to construct dendrimers. This tutorial covers: Building a homopolymer Building a block copolymer Building a random copolymer Building a dendrimer
LESSON 1: Building a homopolymer

You can use any of the polymer building tools to construct polymers consisting of either your own repeat units or you can use the extensive library provided. The first example shows how to build and define your own repeat unit and later examples use pre-built repeat units. Building the repeat unit Open an empty 3D Atomistic document. Click on the options arrow associated with the New button on the toolbar and select 3D Atomistic Document. The structure you are going to sketch is called p-phenylene vinylene and forms a polymer called PPV.
Structure of p-phenylene vinylene
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You will start by sketching a phenyl ring. Press the Sketch Ring button on the toolbar. Hold down the ALT key and click in the 3D Atomistic document. A phenyl ring is displayed in the 3D Atomistic document, with dotted lines indicating it has partial double bond order and is aromatic. The next step is to draw the carbon chain. Press the Sketch Atom button on the toolbar. Ensure that carbon is the current element. Place the cursor over one of the carbon atoms in the ring. When it changes colour to light blue, click and drag to form a bond. Click again to place the first carbon atom in the side chain. Drag the mouse away and then click once more to add the second carbon atom. Press ESC on the keyboard to cancel any further sketching. Now you should add the double bond between the two carbon atoms in the side chain. Place the cursor over the middle of the bond connecting the two carbon atoms in the side chain. When it changes color to light blue, click on it once. The bond order increases to two, i.e., it changes from a single to a double bond. The final step is to add hydrogens to the structure and clean up the geometry. Press the Adjust Hydrogen and Clean buttons on the toolbar. Setting the head and tail atoms Change to selection mode. Press the 3D Viewer Selection Mode button on the toolbar. Now specify the head and tail atoms using the Repeat Unit dialog. Select Build | Build Polymers | Repeat Unit from the menu bar. The Repeat Unit dialog is displayed.
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Repeat Unit dialog
Head and tail atoms In the 3D Atomistic document, select the hydrogen atom labeled Head in the diagram shown above. On the Repeat Unit dialog, press the Head Atom button. A blue circle is displayed on the hydrogen atom, indicating it is the head atom. In the 3D Atomistic document, select the hydrogen atom labeled Tail in the diagram shown above. On the Repeat Unit dialog, press the Tail Atom button. Close the Repeat Unit dialog. A magenta circle is displayed on the hydrogen atom and the backbone of the polymer is highlighted, as shown below.
Polymer backbone, shown in Stick display style
Finally, before building the polymer, rename the monomer so that it is easy to find later when you have several documents open that contain monomers or polymers.
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Click on 3D Atomistic in the Project Explorer. Right-click and select Rename from the context menu. Change the name of the file to p-phenylene vinylene. Building the polymer You have now built and defined your new monomer. To build the homopolymer, you will use the Homopolymer dialog. Select Build | Build Polymers | Homopolymer from the menu bar. The Homopolymer dialog is displayed.
Homopolymer dialog, Polymerize tab The Polymerize tab displays a list of libraries that contain repeat units that you can select. To use the repeat unit you have just drawn, you should change the library to Current project. Open the dropdown menu associated with the Library option. Scroll down and select Current project from the list. Now that you have defined a library, you can select the Repeat unit. If more than one repeat unit is defined in the current project, they will all be listed. Open the dropdown menu associated with the Repeat unit option. Select pphenylene vinylene from the list. You should build a polymer with a chain length of 20 units. Since the default is 10, you must change it. Click on the Chain length text box and change the value from 10 to 20. Now build the polymer. Press the Build button.
The new polymer is displayed in a new 3D Atomistic document called Polyp-
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phenylene vinylene.xsd. Save this polymer and the project. Select File | Save Project from the menu bar. Now close all of the open documents. Select Window | Close All from the menu bar. Close the Homopolymer dialog.
LESSON 2: Building a block copolymer

The first step is to open the Block Copolymer dialog. Select Build | Build Polymers | Block Copolymer from the menu bar. The Block Copolymer dialog is displayed.
Block Copolymer dialog, Polymerize tab The Block Copolymer dialog consists of three tabs: the Polymerize tab contains the initial block definition section, the Advanced tab contains information about initiators and terminators, and the Branches tab has a check box for information about attaching branches to the polymer. Select the Advanced and Branches tabs to view the options available. When you are finished, select the Polymerize tab again. Now that you are familiar with the Block Copolymer dialog, you can start to construct the polymer.
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Specifying the repeat units First add the repeat units and specify the block sizes. You are going to build a block copolymer constructed of 5 units of polyethylene oxide, 10 units of polypropylene oxide and a further 5 units of polyethylene oxide. Click in the empty Repeat unit cell in the Block Definition grid on the Polymerize tab. The Add Block Definition dialog is displayed.
Add Block Definition dialog Move the Add Block Definition dialog on the screen so that you can view both the Block Copolymer and the Add Block Definition dialogs at the same time. The next step is to select the Library from which you want to choose the monomers. Since the polymer you are going to build contains oxypropylene and oxyethylene monomers, you should select the oxides library. Open the dropdown menu associated with the Library option. Scroll down and select oxides from the list. Now select the Repeat unit. Open the dropdown menu associated with the Repeat unit option. Select oxyethylene from the list. As the Block size is set to 5 by default, there is no need to change it. The Flip probability is the probability of head-to-head or tail-to-tail interactions occurring in the polymer. As you only want the head-to-tail interactions, you should leave this set to zero. You can now add this block of monomers to the block definition. Press the Add button. The oxyethylene block you have defined appears in the Block definition grid on the Polymerize tab. You should now add another monomer to the block. The next block consists of 10 units of oxypropylene.
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Open the Repeat unit dropdown menu on the Add Block Definition dialog and select oxypropylene. Set the Block size to 10. Press Add. The second block appears in the Block definition grid on the Polymerize tab. The final step is to define a further block of 5 oxyethylene units. Change the Repeat unit back to oxyethylene. Change the Block size back to 5. Press Add and then Close. Close dismisses the Add Block Definition dialog. You have now defined the block copolymer fully and the Block Copolymer dialog should look similar to this.
Block Copolymer dialog with polymer definition Building and manipulating the polymer The final step is to build the block copolymer. Press the Build button. A new 3D Viewer displaying the block copolymer structure is opened. The structure should look similar to this.
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The block copolymer, shown in Stick display style This is one unit of the block copolymer. If you want to build multiple units, you should use the Numberof superunits option. Type 2 in the Number of superunits text box. Press the Build button. Now there are two copies of the block copolymer linked together. If you want to build two separate chains instead, you should use the Number of chains option on the Block Copolymer dialog. Change the Number of chains from 1 to 3. Press Build. A system containing three sets of two unit block copolymers is displayed. These can be separated using the CTRL and ALT hotkeys. Click on one of the atoms on the screen. Right-click and select Select Repeat Unit from the context menu. One polymer repeat unit is selected. Double-click on the selected repeat unit. The polymer chain is selected. Hold down the SHIFT + ALT keys on the keyboard and press the right mouse button. Move the mouse. As you move the mouse, the chain moves with it. Use this technique to move the polymer chains apart to check you have three separate fragments.
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Try rotating the chains using the SHIFT key and the right mouse button. When you have finished, save the project and close the new windows. Select File | Save Project then Window | Close All from the menu bar. Tip. This is a quick way to clear many documents from the workspace. If you save the project and the documents as you proceed, you can still use Close All to clear the workspace whilst keeping the documents accessible from the Project Explorer.
LESSON 3: Building a random copolymer

The Random Copolymer dialog allows you to construct copolymers of any number of species, controlling connectivity and composition independently. In this example, a random mixture of butadiene and acrylonitrile will be constructed. The acrylonitrile content of the commercial polymer can be anywhere between 18 and 48%. As the nitrile content is increased, the temperature flexibility decreases, but the resistance to petroleum-based compounds increases. The polymer has many applications in the sealant industry. You are going to build two copolymers. The first will use the default values and will be a 50:50 mix of the two monomers, and the second will be 20:80 mix of acrylonitrile and butadiene. The Random Copolymer dialog is accessed from the Build Polymers options on the Build menu. It looks similar to the Block Copolymer dialog. Select Build | Build Polymers | Random Copolymer from the menu bar. The Random Copolymer dialog is displayed.
Random Copolymer dialog, Polymerize tab
The first step is to tell the copolymer builder which units you want to build with and
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what size of polymer you want. Click in the empty Repeat unit cell in the Define Repeat Units grid on the Polymerize tab. The Add Repeat Unit dialog is displayed. Open the dropdown menu associated with the Library option. Scroll down and select dienes from the list. Open the dropdown menu associated with the Repeat unit option. Select c_butadiene from the list. Press the Add button. The cis-butadiene monomer appears in the Define Repeat Units grid on the Random Copolymer dialog. Repeat this procedure for the acrylonitrile monomer which is located in the acrylates library. Close the Add Repeat Unit dialog by pressing the button in the top right corner. Now you should increase the chain length from 10 to 20. Click in the Chain length text box on the Random Copolymer dialog and change the value from 10 to 20. There are two different ways you can propagate the polymer; using either probabilities or reactivity ratios. Probabilities: Give the relative likelihood of each monomer being attached to the chain at the next step of the reaction and can be used to mimic the concentrations. Reactivity Ratios: Determine the copolymer composition in an analogous way to experimental synthesis. Inputs required are concentrations of reactants and rate constants for the various attachment alternatives. In this tutorial, you will build a 50:50 mix of ingredients, initially, and then a 20:80 mix of acrylonitrile and butadiene using probabilities to set the composition. Using probabilities to set composition Probabilities are specified as a matrix on the Probabilities tab. Select the Probabilities tab.
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Random Copolymer dialog, Probabilities tab The tab contains the probability matrix. The numbers in the matrix are read by row. So, in the example shown above, the first row shows that there is a 30% probability of cis-butadiene attaching to a chain that ends in a cis-butadiene unit, and a 70% chance that acrylonitrile will come next if the previous unit is a cis-butadiene. Clearly the row contents must sum to unity. The second row displays similar information for a growing chain ending with acrylonitrile. The default values are 0.5 in each cell, since we require a 50:50-mix of the two repeat units, the default is fine. Since you do not need to set any initiator or terminator settings, you can ignore the Advanced tab. So now you can build the random copolymer. Select the Polymerize tab and press the Build button. A new 3D Atomistic document containing the random copolymer is displayed. Move the Random Copolymer dialog so that you can see the new structure, but do not close it. As there is a 50% chance of either of the monomer units adding to the previous one, the numbers of the different units in each polymer can change. Build three more polymers to see if there is a difference in the number of monomers in each structure. Press the Build button on the Random Copolymer dialog several more times to build new polymers. There may be small differences in the composition for each build. Now, you are going to construct the 20:80-mix of monomers. This entails changing the probabilities in the probability matrix. As you want less of the acrylonitrile than the butadiene, you have to adjust the probabilities so that they favour the first repeat unit.
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Select the Probabilities tab on the Random Copolymer dialog. Click on the 1,1 matrix cell. Change the value from 0.5 to 0.8. Press TAB. You have set the probability of one unit of butadiene adding to a previous unit of butadiene to 0.8. As the row must add up to 1.0 and you want the probability of a unit of acrylonitrile adding to a unit of butadiene to be low, you should set the 1,2 matrix element to 0.2. Click on the 1,2 matrix cell. Change the probability from 0.5 to 0.2. Press TAB. Repeat this procedure for the second row of the matrix. The final matrix should look like the one shown below.
Random Copolymer dialog showing probability settings These settings will produce an approximately 20:80 ratio of acrylonitrile to butadiene. The last step is to build the polymer once more. Press the Build button. The polymer is displayed in a new 3D Atomistic document, as before. Press the Build button a few more times and check the percentage of the repeat units in each case. Forcing the concentrations In the limit of infinitely long chains, these probabilities become exact, but for finite chains, there are often small deviations. To guarantee a 20:80 ratio, you can use the Force concentrations option on the Polymerize tab.
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Select the Polymerize tab. Check the Force concentrations checkbox. Press Build. Note: If you repeat the build several times, you will see that each time the ratio of repeat units is exactly constant because the concentrations are forced. This is useful if you want an exact ratio of monomer repeat units.
LESSON 4: Building a dendrimer

Dendrimers are branched compounds that grow from a central core. You can specify branch points and change the levels of branching using MS Modeling. In this tutorial, you will build up a dendrimer layer-by-layer using the Dendrimer dialog. You can also build many layers in one step using the Dendrimer dialog, but the first approach helps to visualize the construction process. Building the dendrimer You will start by specifying the dendrimer seed and repeat unit. Select Build | Build Polymers | Dendrimer from the menu bar. The Dendrimer dialog is displayed.
Dendrimer dialog, Construct tab
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Now you should set the Seed Structure, as this is the top of the dendrimer tree. Open the dropdown menu associated with Seed Structure and change the seed to ammonia. Now define the Repeat unit. This is the structure that is added to the seed. Open the dropdown menu associated with Repeat unit and select 35dihydroxy_benzyl_alcohol. For the time being, you can leave the Number of generations as 1. Press the Build button. The initial structure is displayed. It consists of an ammonia core with three benzyl alcohol repeat units attached. The connection points for the next layer are displayed as meshed spheres.
The initial dendrimer Before building a second layer, you should clean up the first structure. Press the Clean button on the toolbar. A second layer of benzyl alcohol can be added easily using the Dendrimer dialog, since the build option has changed from Create a new dendrimer to Add generations to constructed dendrimer. Press the Build button on the Dendrimer dialog, followed by the Clean button on the toolbar. A second layer of benzyl alcohol repeat units is added to the dendrimer. You can change the repeat unit you are adding so that you have different repeat units in each dendrimer. On the Dendrimer dialog, change the Repeat unit to propylene oxide and press Build.
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A third layer of repeat units is added to the dendrimer, but this time, they are propylene oxide units instead of benzyl alcohols. Coloring the dendrimer At this stage, the display can get confusing and it helps to colour the dendrimer by repeat unit. You can do this by selecting connected atoms and working down through the layers. The first step is to colour the whole dendrimer. Right-click in the 3D Atomistic document and select Display Style from the context menu. In the Coloring section on the Atom tab, select Custom and click on the color selector. The Color dialog is displayed. Select red from the Basic colors and press OK. Keep the Display Style dialog open. The dendrimer is now coloured in red. The next step is to select the nitrogen atom in the ammonia seed and work through the molecule. Press the Selection Mode button on the toolbar. Click on the nitrogen atom. You can use the Connected option on the Atom Selection dialog to select atoms that are linked to the nitrogen. Select Edit | Atom Selection from the menu bar. Change the Select by Property setting to Connected. Set the Selection mode to Add to the existing selection. Press the Select button. The three atoms closest to the nitrogen are selected. Keep on pressing the Select button until all of the groups except those in the propylene oxide layer are selected. Change the colour on the Display Style dialog to blue. Every time you press the Select button, more connected atoms are selected. This allows you to work down the tree selecting the layers you want. Repeat this procedure, selecting a different colour each time, until all of the different layers in the dendrimer are coloured individually. Select the Stick option on the Display Style dialog. You should end up with a dendrimer that looks similar to the one shown below.
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The dendrimer coloured by generation An alternative method for generating a coloured dendrimer is to save each layer as a different colour in the dendrimer folder in a similar manner to that which you used to generate a custom monomer. However, for dendrimers, head atoms and connection points can be defined through the ConnectionPoint tab of the Dendrimer dialog. Once you have coloured and saved all of the layers, the repeat units that have been defined (and coloured) can be saved in MS Modeling <version>\Data\Resources\PolymerBuilder\dendrimer\structures. Seed structures that havebeen custom defined can be saved in MS Modeling<version>\Data\Resources\PolymerBuilder\dendrimer\seed. Note. This will not work if the file is saved to a similarly named folder, for example, C:\Program Files\Accelrys\MS Modeling <version>\Structures\repeat-units\dendrimers. In the correct folder, you can simply add the files together when you build a dendrimer. This method is most appropriate for the generation of large dendrimers, since it is a much faster. Finally, you should save the project. Select File | Save Project from the menu bar. This is the end of the tutorial.
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Hands-On Exercise: Working with isosurfaces and slices

Purpose: Introduces the isosurfaces and slices tool available in the Materials Visualiser Modules: Materials Visualizer Time: Prerequisites: None Background The Materials Visualizer provides a range of powerful tools for viewing and analyzing volumetric data, such as fields, isosurfaces, and slices. Many MS Modeling applications generate fields, such as particle densities, potentials, etc., and you can generate isosurfaces and slices to view and analyze particular aspects of a field. You can also view and analyze fields and surfaces generated by other modeling packages, for example, surfaces generated in Cerius2 can be imported via the .msi file format. Introduction This tutorial shows how to manipulate isosurfaces and slices for a benzene molecule. The benzene structure has been optimized and the electron density and electrostatic potential for this molecule have been calculated using DMol3. This tutorial covers: Adding an isosurface Changing the display style of an isosurface Working with color maps Adding and coloring slices Manipulating slices
LESSON 1: Adding an isosurface

An example document has been provided containing the data for the electron density and electrostatic potential of benzene. Press the Import button on the toolbar and open Examples/Documents/3D Model/benzene.xsd. The volumetric rendering tools are available from the Volume Visualization toolbar. Select View | Toolbars | Volume Visualization from the menu bar. Select the Create Isosurfaces tool a field to isosurface. .A dialog is displayed asking you to choose
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Select DMol3 total electron density and press OK. A white isosurface, indicating the electron density, is displayed.
LESSON2: Changing the display style of an isosurface

You can change how an isosurface is displayed using the Display Style dialog. Right-click in benzene.xsd and select Display Style from the context menu. Choose the Isosurface tab. The Isosurface tab is displayed.
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Display Style dialog, Isosurface tab
You can change the display style of the isosurface from solid to dots. In the Display style section, select the Dots option. Increase the Dot size to 3. This can be useful if you are looking at a complex system, since it speeds up the redraw time. For the rest of this tutorial, you will use the solid display style. In the Display style section, select the Solid option. You can change the transparency of a surface to make it less opaque. Before you do this, you should set the atom display style to Ball and stick so that you can see the effect of the transparency. Choose the Atom tab and select Ball and stick. Return to the Isosurface tab and drag the Transparency slider to the second mark. The surface becomes transparent.
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Rotate the molecule. Change the transparency back to fully opaque. As you rotate the model, the isosurface automatically changes to a dot representation. This is the volumetric equivalent of the fast render on move functionality that can be seen when rotating atoms and bonds in the higher quality display modes. You may notice a slight "halo" displayed on the edges of the isosurface where it meets a dark background. This is an artifact of the rendering process and can usually be removed using the Properties Explorer. In the Properties Explorer, select the Isosurface filter. Double-click on IsInsideVisible and select No. Press OK. The "halo" should disappear. The isosurface is a surface formed by points whose field values are identical. Therefore, you can increase or decrease the size of the isosurface by changing the isovalue. Use the Iso-value up spin control on the Isosurface tab of the Display Style dialog to increase the isovalue. As you increase the isovalue, the isosurface decreases in size and vice versa. Note: If the specified isovalue falls outside the range for which the field of the isosurface is defined, then no isosurface will be displayed. You can change the color of the isosurface in various ways. The most simple of these is to use the color chooser to change the color of the entire isosurface. Click on the color selector next to the Custom option. Select a new color from the Color dialog and press OK. The whole of the isosurface changes color.
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Note. If more than one isosurface is present, you should select the one that you want to modify before selecting a new color. Otherwise, all the isosurfaces will change color. You can also color by mapped field. This allows you to, for example, map the electrostatic potential onto the electron density. Select DMol3 electrostatic potential from the Mapped field dropdown list. Close the Display Style dialog. The color of the isosurface changes to reflect the mapped electrostatic potential.
In the Display style section, the Banded checkbox becomes active. This subdivides the isosurface into uniformly colored regions, each of which corresponds to a range of values for the mapped field.
LESSON 3: Working with color maps

You can also change the coloring of the isosurface using the Color Maps dialog. Right-click in benzene.xsd and select Color Maps from the context menu. The Color Maps dialog is displayed
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Color Maps dialog
The From and To boxes indicate the range of values covered by the spectrum of colors. There are numerous spectrum color ranges defined. Change the Spectrum to Blue-White-Red. The color of the isosurface changes so that any section of the isosurface with a value equal or lower than that of the From box is colored blue.
These colors change with the increasing values until any part of the isosurface that has a value equal to or higher than that in the To box is colored red. You can see which color refers to which value of isosurface by hovering over that color in the color chooser. Hover the mouse pointer over any of the colors in the color chooser bar on the Color Maps dialog.
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A number is displayed as a tooltip. This indicates the value of the isosurface assigned to that color with an error. You can make certain colors transparent by selecting them in the color chooser. In the color chooser bar, click and drag your mouse to select any three sections.
Color Maps dialog with 3 sections transparent
The sections of the isosurface with the colors that you selected are now transparent in the model document.
Tip. You can make individual sections transparent by clicking on the section or you can drag the mouse to make many contiguous sections transparent. Click on the first of the three sections you made transparent and drag your mouse to the third one. You can also change the number of bands into which the sections are cut.
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Change the number of Bands to 128. The isosurface appears to be smoother as the bands are now much smaller. As stated earlier, the values in the From and To boxes define the color ranges and these can be changed. You can either simply enter a new value or use pre-calculated values. The pre-calculated values are available by clicking on the right arrow button associated with the From and To boxes. Click on the right arrow button associated with the From box. You should see field minimum, mean, and maximum values and mapped minimum, mean, and maximum values. The field values correspond to the values in the whole field of data, i.e., the electron density. The mapped values correspond only to the values contained in the mapped field, i.e., the specific electron density at the specified isovalue. To see this in action, you can change the isovalue. Right-click on benzene.xsd and select Display Style from the context menu. Select the Isosurface tab and change the Iso-value. Close the Display Style dialog. The coloring on the isosurface changes. On the Color Maps dialog, click on the right arrow associated with the From box. The mapped field ranges will have changed to indicate the new range of mapped field data within the isosurface. Select Mapped Minimum for the From box. Click on the right arrow associated with the To box and select Mapped Maximum. The isosurface should now have the same coloring as it did previously. The mean value is provided for occasions when the maximum value is very high due to presence of large outlying values. In these cases, coloring to those large values is not relevant and using the mean value gives a much better spread of colors. You will use these values again in the section on coloring slices.
LESSON 4: Adding and coloring slices

Slices can be added to your model allowing you to see field value distributions through a plane rather than on a surface. You can add slices in several ways depending on how you want them to be oriented. There are several preset orientations such as best fit and parallel to different axes. You will initially add a slice using the Best Fit method.
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Click on the options arrow associated with the Create Slices button Best Fit. A dialog is displayed asking which field you wish to slice. Select DMol3 electrostatic potential and click on the OK button. A red slice is displayed in the plane of the benzene ring.
and select
No color shading is displayed as it is using the full field range. To add colors, you need to use the Color Maps dialog once more. Click on the slice to select it. When a slice is selected, the border changes color to yellow and a yellow cross-hair is displayed at its center of rotation. Right-click in benzene.xsd and select Color Maps. Change the From value to Mapped Minimum and the To value to Mapped Mean. In this case, the mapped maximum value is very high due to the presence of outlying values and you should therefore use the mapped mean, as this gives a more accurate representation of the spread of values. The isosurface is obstructing the view of the slice, therefore, you will remove it from view. Select the Volumetric Selection tool . Expand both the nodes. Under the DMol3 electron density node is your isosurface and under the DMol3 electrostatic potential is your slice. You can either delete your isosurface or make it transparent. Click on the checkbox associated with Isosurface1.
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This removes the isosurface from view but does not delete it. As with the isosurface, you can use the Color Maps dialog to make certain values transparent. On the Color Maps dialog, click on the red left arrow and the first two red bars on the color chooser. When the colors are removed, you can see a box that represents the edge of the slice. This can be removed using the Display Style dialog. Right-click in benzene.xsd and select Display Style. Select the Slice tab. Uncheck Show frame.
You can add multiple slices to the model. Press the Reset View button on the toolbar. Click on the options arrow associated
with the Create Slices tool and select Parallel to 1st & 3rd Axis. Select DMol3 electrostatic potential and press OK. A second slice is displayed along the x-z plane. It uses the same color map settings as the first slice.
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Note. Any slice can have custom color settings, regardless of the number of slices on screen. You can also add slices through bonds or atoms by selecting the objects and adding the slice. Select a C-C bond. Select the Create Slices tool. Choose DMol3 electrostatic potential from the Select Fields to Slice dialog and press OK. A slice is displayed perpendicular to the bond. The cross-hair is displayed on the selected object. Tip. You can also generate slices through selected atoms.
LESSON 5: Manipulation of slices

Slices can be rotated and translated using the normal methods for selected objects. From the menu bar, select View | Display Options. Uncheck Fast render on move. Select the last slice you generated by clicking on the frame. Hold down SHIFT and ALT on the keyboard and drag with the right mouse button pressed. The slice is translated normal to its axis and the slice information is updated as the slice moves through the field. Hold down the SHIFT key and drag with the right mouse button pressed.
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The slice rotates with the center of rotation indicated by the cross-hair. Tip. If you have a three-button mouse or wheel mouse, you can translate and rotate using SHIFT and the middle mouse button/wheel and SHIFT and the right mouse button, respectively. Note. If you wish to align the slice along a precisely known crystallographic direction, you can use the Properties Explorer to specify slice position and slice normal. You can use the Volumetric Selection dialog to remove slices. Select the Volumetric Selection tool on the toolbar. Expand the DMol3 electrostatic potential node. The Volumetric Selection dialog is displayed.
Volumetric Selection dialog Press the DELETE key. The slice is removed from the model. In the Volumetric Selection dialog, double-click on Slice2. Press the DELETE key. The second slice is removed from the model. In the Volumetric Selection dialog, expand the DMol3 total electron density node and check Isosurface1. The isosurface overlays on the slice. This is the end of the tutorial.
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Hands-on Exercise: Precise positioning and movement of atoms

Purpose: Illustrates the use of Move To mode, the precise Movement tools, and the alignment tools in the Materials Visualizer Time: Modules: Materials Visualizer Prerequisites: None Background The ability to move and place fragments or atoms in specific positions can be important when setting up initial structures. For example, the ability to place a molecule in the center of a zeolite channel or a specific distance from a surface gives you the ability to accurately set up a complex system with ease. The Materials Visualizer has a set of tools available from the Movement toolbar designed to help with these tasks. There are tools that translate and rotate selected atoms by specific amounts and tools are also available that enable you to move an entire fragment to a geometrical center and to align objects. A range of geometrical objects are available, such as centroids, best fit lines and planes, and principal axes to enable you to perform many different types of alignment. Introduction In this tutorial, you will use the precise positioning and alignment tools to place a chloromethane molecule in the main channel of a zeolite framework. You will then use the movement tools to move the chloromethane along the zeolite pore. This tutorial covers: Getting started Importing the zeolite and defining a centroid Sketching chloromethane and aligning it along the channel Moving chloromethane to the center of the channel Positioning the chlorine atom at the edge of the cell Moving the chloromethane molecule by specific amounts
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Lesson 1: Getting started

Begin by starting MS Modeling and creating a new project. If MS Modeling is not already open, double-click on the MS Modeling icon on the desktop to start the program or select Programs | Accelrys MS Modeling [version] | MS Modeling from the Windows Start menu. When MS Modeling starts, a dialog is displayed asking if you want to open an existing project or create a new one. Click on the Create a new project radio button and press OK. A dialog box appears requesting a name for the new project. You will create a project called Zeolite. Enter the project name Zeolite and press OK.
LESSON 2: Importing the zeolite and defining a centroid

The first step is to import the zeolite framework. Select File | Import... from the menu bar or click on the Import button toolbar. On the Import Document dialog, navigate to and select Structures\zeolites\MOR.msi, then press Import. on the
The zeolite framework is imported into the project. Initially, it has a high order of symmetry and this should be reduced to P1 before continuing with the tutorial. Select Build | Symmetry | Make P1 from the menu bar. To place the chloromethane molecule in the center of the zeolite channel, you must first define a centroid. A centroid is an object that defines the center of a set of atoms. In this tutorial, you will place the chloromethane in the center of the central channel. To do this, you need to select all the atoms that define the channel, shown in 'Ball and Stick' display style below.
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Selected atoms for centroid definition
The easiest way to do this is to use the lasso selection tool. Position your mouse pointer in the position indicated by the X in the image above. Hold down the SHIFT and Q keys. Left-click and carefully move your mouse in a circle around the outside of the atoms that define the channel so that the lasso selects all the atoms. The next step is to define the centroid. Click on the options arrow associated with the Create Centroid button and select Centroid from the dropdown list. Click in the 3D Atomistic document to deselect the atoms. A green centroid object is defined and displayed at the center of the channel. Tip. You can change the properties of the centroid using the Properties Explorer. For example, you can change whether the centroid is defined by a mass-weighted average of the atom coordinates or a simple geometric average by changing the IsWeighted property. The default value is mass weighted.
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LESSON 3: Sketching chloromethane and aligning it along the channel

Start by sketching chloromethane.
Structure of chloromethane Click on the options arrow associated with the New button on the toolbar and select 3D Atomistic Document from the dropdown menu. In the Project Explorer, right-click on 3D Atomistic.xsd and select Rename from the context menu to change the name of the document to chloromethane.xsd. Use the tools on the Sketch toolbar to construct chloromethane, which has the structure shown above. Add the correct number of hydrogen atoms to the structure by pressing the Adjust Hydrogen button and then give the structure a .
reasonable initial geometry by pressing the Clean button
You need to copy and paste the penetrant molecule into the document containing the zeolite framework. Ensure that chloromethane.xsd is the active document and press CTRL and C. Double-click on MOR.xsd in the Project Explorer and press CTRL and V. The chloromethane molecule should be pasted into the bottom left-hand corner of the cell. Tip. The copy and paste actions can also be accessed via the menu bar by selecting Edit | Copy and Edit | Paste. Before you place the molecule in the center of the channel, you can use the alignment tools to orient the carbon-chlorine bond so that it runs parallel to the channel. Holding the SHIFT key, click on the carbon and chlorine atoms of the chloromethane molecule. Click on the options arrow associated with the Create Centroid button and select Best Fit Line from the dropdown list. A green dashed line is displayed, showing the best fit line between the two atoms. You can now align this line with the plane of the screen.
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Press the HOME key to reset the view. Select the green best fit line object, click on the options arrow associated with the Align Onto View button In/Out from the dropdown list. and select Align
The carbon-chlorine bond should now be pointing down the channel. You can delete the best fit object you created. Rotate the model so that you can see the best fit line. Select the best fit line object and press the DELETE key.
LESSON 4: Moving chloromethane to the center of the channel

The next stage is to use the Move To tool to position the carbon atom of chloromethane on the centroid. Rotate the cell so that you can see the gray carbon atom of the chloromethane molecule. Note. You will see three centroids displayed. The two centroids outside the cell are symmetry replicates of the one in the center of the cell. on the toolbar. Move the cursor over the gray Click on the Move To button carbon atom of the chloromethane and when it changes color to blue, click once. Move the cursor over the centroid and wait for it to change color to blue, then click once. The chloromethane molecule moves to the center of the channel and the carbon atom of the chloromethane is positioned at the centroid. Tip. The default behavior is for the entire fragment to move. You can move selected atoms by holding down the ALT key and using the Move To functionality. . Right-click in MOR.xsd and select Select the 3D Viewer Selection Mode button Display Style from the context menu. Select the Lattice tab and change the Style to In-Cell. Use the arrow keys on the keyboard to rotate the cell to view it from different angles. The molecule is displayed in the center of the zeolite channel. Select the centroid object and press the DELETE key.
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LESSON 5: Positioning the chlorine atom at the edge of the cell

You can use another property of centroids to help position the chloromethane so that the chlorine atom is at the edge of the cell. As moving the centroid moves the parent fragment, you can define a centroid on the chlorine and then edit the properties of the centroid to move the chlorine atom. Select the chlorine atom. Click on the options arrow associated with the Create Centroid button and select Centroid from the dropdown list.
A centroid is defined on the chlorine atom. If the Properties Explorer is not visible, select View | Explorers | Property Explorer from the menu bar to display it. The Properties Explorer shows all the properties of the centroid. Properties that are displayed in gray cannot be edited, but those in black can be altered. Select the centroid object. In the Properties Explorer, double-click on the CentroidXYZ property. Change the Z value to 0.00. Click on the OK button. In the 3D view, rotate the cell by holding down either the X, Y or Z key on the keyboard plus the right mouse button and dragging the mouse pointer across the screen. The chloromethane will now be oriented so that the chlorine is exactly on the edge of the cell at Z=0.
LESSON 6: Moving the chloromethane molecule by specific amounts

The Materials Visualizer has a set of tools for moving fragments and objects by specific amounts. Press the 3D Viewer Reset View button and then press the left arrow key twice.
This rotates the cell so that the channel runs from left to right across the screen. Double-click on the chloromethane fragment and press the Movement button
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The Movement dialog is displayed. This allows you to translate or rotate the selected fragment by an amount that you can specify. Select the Distance option in the Translation section of the dialog. Click on the Move Right button and then the Move Left button .
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The chloromethane fragment is translated by exactly 0.5 with each click. Note. The translation and rotation tools act relative to the x-, y-, and z-axes of the screen, not the axis indicators displayed in the bottom right-hand corner of the 3D Atomistic document. You could explore the potential energy surface of this channel by moving the chloromethane around inside the channel in increments of 0.5 , saving the resulting structures in a study table, and then performing energy calculations on the series. Note. You can use Scripting in MS to write a script doing everything you did in this tutorial by hand! This is the end of the tutorial.
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Hands-On Exercise: Using the crystal builder

Purpose: Introduces the powerful crystal building and visualization tools, including hydrogen bond visualization. Modules: Materials Visualizer Time: Prerequisites: None Introduction Materials Studio features a powerful crystal building tool which allows you to build your own crystals. Using the different visualization techniques available in Materials Studio, you can create high quality graphics that can be easily pasted into other Windows-based software programs or saved as bitmaps. This tutorial covers: Importing a pre-built crystal structure into Materials Studio Changing the display styles Building a crystal of urea Calculating hydrogen bonds Adding lighting effects Note. In order to ensure that you can follow this tutorial exactly as intended, you should use the Settings Organizer dialog to ensure that all your project settings are set to their Accelrys default values. See the Creating a project tutorial for instructions on how to restore default project settings.
LESSON 1. Importing a prebuilt crystal structure into Materials Studio

Included in Materials Studio is a structure library that contains many different types of structures from ceramic materials to organic compounds. The structure that you should import is a molecular crystal called histidine. Press the Import button on the toolbar.
The Import Document dialog is displayed. Locate the file histidine_resolved.xsd in the folder Examples\Documents\3D Model\. Click on the Import button.
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The 3D Atomistic document histidine_resolved.xsd opens and the filename is listed in the Project Explorer. The structure can be rotated using the Rotation tool on the toolbar; this tool should be selected by default. Rotation of the structure is achieved by clicking and moving the mouse within the 3D Atomistic document. If you wish to force rotation in a single direction, i.e., x, y, or z, you can do this by holding down the relevant key on the keyboard, plus the right mouse button, and then moving the mouse. Hold down both the Z key on the keyboard and the right mouse button. Move the mouse to the left and right. The molecule rotates in the z direction. If you wish to set the view back to the original viewpoint, you can use the Reset View button. Press the Reset View button on the toolbar.
LESSON 2: Changing the display styles

Materials Studio has a range of powerful display options and you will be introduced to some of these in the course of this tutorial. You will start off with the basic display settings, such as ball and stick, etc. With your mouse on the 3D Atomistic document, right-click and select Display Style from the context menu. The Display Style dialog is displayed.
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Display Style dialog, Atom tab
This dialog has several tabs that deal with, amongst other things, changing the display of atoms or surfaces, adding thermal ellipsoids, and lattice display options for periodic structures. Select the Stick option on the Atom tab.
Stick The model changes from being a simple line structure to a stick model constructed from cylinders. If the 3D Viewer window is not occupying all of the workspace area, you can resize it by clicking on the Maximize button on the top right corner of the window. Press the Maximize button on the 3D Viewer window.
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The 3D Atomistic document now occupies the full workspace area. You can see that the double bonds in the system are displayed as two cylinders running parallel to each other. If you do not want the display to differentiate between the bond orders, you can remove this using the Display Style controls. Uncheck the Bond order checkbox. The display styles for different bond orders are now the same. Change the display style to Ball and stick. Select the Ball and stick option.
Ball and Stick Next, you will change the display style of groups of atoms. To demonstrate this, you will display the chlorine atoms in CPK style. You must first select all the chlorine atoms. Hold down the ALT key and double-click on one of the green chlorine atoms. All four of the chlorine atoms change color to yellow, indicating that they are selected. This is a shortcut key that allows you to select all examples of a particular element on the screen. Now, you simply change the display style. Select the CPK option.
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Chlorine shown in CPK style The display style of the chlorine atoms changes to large CPK (Corey-Pauling-Koltun) spheres with their radii dependent on the van der Waals radius of the element they represent. However, most structures look better with a slightly smaller CPK size, so that the spheres do not dominate the structure too much. The overall CPK size can be scaled down. Click in the CPK scale text box and change the value from 0.7 to 0.5. Click in another text box or press the TAB key to apply this change to the structure. Reset the CPK scale back up to 0.7 again using the slider. Deselect the chlorine atoms before continuing. Double-click in histidine_resolved.xsd. The cell display can also be changed. Select the Lattice tab on the Display Style dialog.
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Display Style dialog, Lattice tab The Lattice tab contains two distinct areas. The Display style area contains information about the style of the cell representation and the range of cells viewed. The Lattice area allows you to change the style of the cell lattice box representation. You will change the cell display style. Click on the Style dropdown list. The Style dropdown list contains four options: Default Molecules are translated so that their centers of geometry lie within the cell. In-Cell All atoms are translated into the unit cell. Exactly one cells worth of atoms are displayed. Original Atoms are shown where their symmetry defines them. No extra translations are made. None - Neither the atoms nor the lattice are shown. Select In-Cell from the Style dropdown list. Observe the change in the 3D Atomistic document. Repeat this for the Original option. Finally, return the Style setting to Default. Now, change the Range values so that more than one cell is displayed. In the Range section, click in the Max box for the A parameter and change the value from 1.00 to 3.00. Press the TAB key.
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Three cells are displayed in the x direction. Now increase the B and C values similarly. Change the Max value for B from 1.00 to 3.00 and that for C from 1.00 to 5.00. Press the TAB key after each change to apply the new settings. The cells are extended in all three dimensions. Do not rotate the structure yet. When you have this number of cells, you may want to remove the lattice in order to improve visualization of the bulk material. Select the None option in the Lattice section. Close the Display Style dialog. The lattice is removed from the display. Now that you have a good representation of the structure, you can increase the quality for a final output image. It is best to leave this stage until last, as otherwise, the calculation times required for manipulation of the image can become excessive. Select View | Display Options from the menu bar. Note. The Display Options dialog can also be accessed by right-clicking in the 3D Atomistic document and selecting Display Options from the context menu. The Display Options dialog is displayed.
Display Options dialog The projection commands on the Graphics tab allow you to choose either orthographic or perspective projection. For large structures such as the one you are visualizing, perspective projection is useful.
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Select the Perspective radio button. The display changes to a perspective view and the structure is zoomed in. To return to a view where the structure fits to the screen, press the Fit to View button. Click on the Fit to View button on the toolbar.
Now increase the image quality to a higher level suitable for output. Drag the Quality slider towards High. Stop 2 divisions from the right. The quality of the image increases as the slider is moved to the right. Note. If you plan to print the structure, you should change the background color to white. Select the Backgrounds tab. On the color control palette, select the background color you require and press OK. This structure should look similar to the one below.
Extended structure of histidine
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You can now export this structure as a bitmap that can be inserted into any document. Select File | Export... from the menu bar. Click in the Export as type field and select Structure Bitmap (*.bmp) from the dropdown list. Enter a filename and press Export. Tip. If you need a larger version of a structure, e.g., for a poster, you can increase the output resolution using the Options... button on the Export dialog. Before you move to the next section, decrease the quality of image representation using the Display Options dialog in order to increase the display speed. Then, remove histidine_resolved.xsd from the project. On the Options dialog, drag the Quality slider to the left until it is about a quarter of the distance from the left. Change the Projection back to Orthographic. Close the Options dialog and then click on the button to close histidine_resolved.xsd. A warning dialog is displayed asking if you want to save the document as part of the project. Press No.
LESSON 3: Building a crystal of urea

Now that you have been introduced to the visualization functions, you are going to build a crystal of urea. You will do this by building a crystal cell and placing the atoms into the cell. Constructing the cell The first step is to open a new 3D Atomistic document to construct your cell in. Click on the New button from the dropdown menu. on the toolbar and select 3D Atomistic Document
Now that you have an empty 3D Atomistic document, you can construct your cell. In this section, you will just construct a cell without adding any atoms into it. Select Build | Crystals | Build Crystal from the menu bar. The Build Crystal dialog is displayed.
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Build Crystal dialog
This consists of three tabs entitled Space Group, LatticeParameters, and Options. You should build a cell which has a space group of P-421m and whose lattice parameters are: a = b = 5.576 , c = 4.686 , = = = 90. You can enter the space group information as either the name or the number of the space group or you can choose one from the dropdown menu. Click in the Enter group text box and type in P-421m. Press the TAB key. This sets the space group at 113 P-421M and the Space group information box changes to display details of the space group. The Operators box also updates with the symmetry operations that are related to that space group. The next step is to set up the lattice parameters. Select the Lattice Parameters tab. This displays the lattice parameters. Due to the symmetry of the selected space group, only certain parameters can be set. Under the Lengths fields, the constraints implied by the symmetry are stated. In this case, you know that parameter a must be equal to b. Click in the Length a text box and change the value to 5.576. The b value changes to reflect the value that you have entered for a. Click in the c text box. Type in the value 4.686.
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You are now ready to build your cell. Press the Build button on the Build Crystal dialog. The dialog disappears and an empty cell is displayed in the 3D Atomistic document. Before you begin to introduce atoms into your cell, it is a good idea to change the display settings from CPK back to Ball and stick. Select Modify | Default Atom Style from the menu bar to display the Default Atom Style dialog. Select the Ball and stick option. Close the Display Style dialog. Now you can start to add atoms into your cell. Select Build | Add Atoms from the menu bar. The Add Atoms dialog is displayed.
Add Atoms dialog
This allows you to specify the atoms you want to add, the name you want to give that atom and the a, b, and c fractional coordinates. The Options tab contains extra bond settings and the choice of either fractional or Cartesian coordinates. You will enter the coordinates in fractional form. As the symmetry of the space group is so high, you have only to enter the coordinates for three of the heavy atoms and two hydrogens. In some cases, where the symmetry requirements are lower, you can use the Adjust Hydrogen tool to add the hydrogens after you have constructed the initial model.
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The coordinates of the atoms that you want to add are: Atom C1 O2 N3 H4 H5 a 0.0000 0.0000 0.1480 0.2620 0.1290 b 0.5000 0.5000 0.6448 0.7620 0.6290 c 0.3284 0.5966 0.1787 0.2910 -0.0420
Before you start to add the atoms, make sure that the Test for bonds as atoms are created option is enabled. Select the Options tab on the Add Atoms dialog. The Test for bonds as atoms are created should be checked. Select the Atoms tab again. Carbon is the default atom type and so you just need to add a name for it. In the Name text box, enter C1. Enter 0.500 in the b field and set the value of c to 0.3284. Press the Add button.
The atom appears in the crystal cell and a further three atoms are also displayed, due to the symmetry of the cell. Repeat this for the other atoms, remembering to set the coordinates each time and to change the name of the atom as well as the element type. When you have added all the atoms into the cell, it will look like this:
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Intermediate crystal model of urea
LESSON 4: Calculating hydrogen bonds

The tool for calculating and displaying hydrogen bonds in Materials Studio is very flexible and is located in the Build menu. Select Build | Hydrogen Bonds from the menu bar. The Hydrogen Bond Calculation dialog is displayed.
Hydrogen Bond Calculation dialog
There are different hydrogen bonding schemes available within the dialog and, hence, you can change the atoms that are allowed to hydrogen bond using the dropdown list at the top of the H-bonding Scheme tab. If you wish to add in extra atoms, you can edit the Donor-acceptor list. There are also two sliders that relate to the hydrogen bond length and angle. These values can range from 1 to 4 and from 0 to 180, respectively. Press the Calculate button.
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The hydrogen bonds are displayed by default as cyan dotted lines. If you increase the maximum distance to 4 , more hydrogen bonds are displayed. Tip. You can change the color of the dotted lines via the Properties Explorer. Hold down the ALT key and double-click on one of the cyan dotted lines. In the Properties explorer click on the Color field and change the color to black
Hydrogen bonds displayed in black Select the H-bond Geometry tab. Drag the Maximum hydrogen-acceptor distance slider to 4. Press the Calculate button. Hold down the ALT key and double-click on one of the cyan dotted lines. In the Properties explorer click on the Color field and change the color to black.
Hydrogen bonds displayed in black
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Hydrogen bonds are now displayed between more of the atoms as the acceptance distance has been increased.
LESSON 5. Adding lighting effects

The ability to control lighting effects is often overlooked, but can be used to produce some impressive images. In this section, you are going to change the position of the first light and add a second light to enhance the image. The Lighting dialog can be accessed from the View menu or via the context menu displayed when you right-click in a 3D Atomistic document. With the cursor in the 3D Atomistic document, right-click and select Lighting from the context menu. The Lighting dialog is displayed.
Lighting dialog This dialog controls the presence of up to three lights, their colors and positions. In the first step, you will move Light 1 so that it is at the top right-hand corner of the ball. Click on the ball and move your mouse up and to the right. The lighting on the molecule changes as the light is moved. When you have the light in the correct position, it will look similar to this:
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Preview ball with one light
Now you can add a second light into the display. Check the Enable Light 2 checkbox to add a second light. A second light is displayed in the Preview box and the position of the first light is fixed. The second light is light gray, but this can be changed to a more suitable color. Click on the gray color indicator associated with Enable Light 2. This displays the color palette. For this tutorial, you will select light blue. Click on the light blue color box in the top row, then press OK. The light changes to light blue and the 3D Atomistic document is updated. Now you can move the light into the position you require. Click and move the light to the bottom of the ball. The preview ball now looks like this:
Preview ball with two lights
Now you can change the display styles and the quality of the image until you get one you are satisfied with. When you have finished, you can save the project. Select File | Save Project from the menu bar. The project is now saved. This is the end of the tutorial.
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Hands-on Exercise: Docking molecules onto surfaces

Purpose: Introduces using the Surface Builder to cleave a crystal structure and place a fragment on a new surface. Modules: Materials Visualizer Time: Prerequisites: None Introduction Surface chemistry, with emphasis on chemisorption and heterogeneous catalysis, plays a vital role in many industrial processes. Valuable insights into the chemistry and physics of these processes can be obtained using molecular modeling and computational methods. This knowledge forms a crucial input into the chemical design process. This tutorial illustrates how Materials Studio can help with computational research in surface chemistry. It details how to build an atomistic surface model and how to dock a small chemical component to that surface. This tutorial covers: Getting started Cleaving and aligning the surface Building a supercell Building a vacuum slab Positioning molecules on a surface
LESSON 1: Getting started

Begin by starting Materials Studio and creating a new project. If Materials Studio is not already open, double-click on the Materials Studio icon your desktop to start the program or, alternatively, select Programs | Accelrys Materials Studio [version] | Materials Studio from the Windows Start menu. When Materials Studio starts, a dialog is displayed asking if you want to open an existing project or create a new one. Click on the Create a new project radio button and press OK. on
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A dialog appears requesting a name for the new project. You will create a project called Platinum. Enter the project name Platinum and press OK.
LESSON2: Cleaving and aligning the surface

In this tutorial, you are going to work with the crystal structure of platinum metal, which you can import from the extensive library of pre-built molecules, crystals, and materials supplied with your Materials Studio installation. on the Select File | Import... from the menu bar or click on the Import button Standard toolbar to display the Import Document dialog. Navigate to and select Examples\Documents\3DModel\Pt.xsd, then press Import. The 3D Atomistic document Pt.xsd, containing the crystal structure of platinum metal, is imported into the current project and displayed in a 3D Viewer.
Crystal structure of Platinum Now open the Cleave Surface dialog. Select Build | Surfaces | Cleave Surface from the menu bar. The Cleave Surface dialog is displayed.
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Cleave Surface dialog, Surface Box tab Blue dashed lines are displayed on the crystal indicating the plane you are cleaving. This information is also given in the Cleave Plane field the top of the Surface Box tab of the Cleave Surface dialog. The default plane is (-1 0 0). The active surface in platinum that you want to cleave is the (1 1 1) surface. In the Cleave plane text box, enter 1 1 1 and press the TAB key. Click on the 3D Viewer Reset View button on the 3D Viewer toolbar.
Blue Box indicating cleaving plane
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The blue box indicating the cleave plane moves to the (1 1 1) crystal plane. You can choose where you want the top of the surface to be and the depth of the surface using the Position controls on the Surface Box tab. Click once on the up spin control to increase the Top value in the Fractional column to 1.0. The cleave plane box moves up to the next set of atoms. (Notice that the equivalent physical distance value increases to 2.265 .) If you use the spin controls to move the position of the box, each click will make the cleave plane box jump to the next set of atoms. This is particularly useful if you have a cell containing various different types of atoms. You can also change the depth of the cell. Click twice on the up spin control to increase the Thickness setting in the Fractional column to 3.0. The depth of the cleave plane box extends and the equivalent physical distance increases to 6.796 . Now that you have set up the surface parameters, you can cleave the cell. Click on the Cleave button and then press the Display Style button on the 3D Viewer toolbar to display the Display Style dialog. On the Atom tab, select the Ball and stick display option.
2D periodic structure, shown in ball and stick style A new 3D Atomistic document, Pt(1 1 1).xsd, is opened and a 2D periodic structure is displayed as a white rhombus alongside the platinum atoms. You can alter the Top and Depth settings for the surface again on the Recleave Surface dialog and both 3D Atomistic documents will be updated automatically.
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Note. The Cleave Surface dialog is renamed as the Recleave Surface dialog when a surface has been generated and is in scope. You can observe this change by switching the focus between Pt.xsd and Pt(1 1 1).xsd. Click twice on the up spin control to increase the Thickness. Press the Reset View button on the Standard toolbar.
Re-cleaved structure, shown in ball and stick style Pt(1 1 1).xsd is updated with the new surface structure. Close the Recleave Surface dialog by clicking on the button .
The cleave plane is at an angle to the Cartesian axes shown by the axis indicator. The molecule can be aligned to the Cartesian axes by selecting either the surface atoms or the 2D lattice. Select the 2D lattice (represented by the white rhombus). Aligning the 2D lattice will align all the atoms associated with the surface. Generally, you should align the view first and then align the molecule or object to the view. As you have already reset the view, you can now align the molecule. The Align Onto View tool provides a range of alignment options. You will use the default option first. Click on the Align Onto View button on the 3D Movement toolbar.
The surface is rotated so that the 2D lattice is aligned along the x-axis and in the xy plane:
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aligned surface, shown in ball and stick style Click on the options arrow associated with the Align Onto View button and select Align With View YZ Plane from the dropdown list. Click on the options arrow associated with the Align Onto View button dropdown list. and select Align Horizontal from the
The platinum surface is now aligned in the xz plane:
aligned surface, shown in ball and stick style
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LESSON 3: Building a supercell

You have now built a 2D cell from a 3D crystal. However, for many applications, it is desirable to view the contents of several cells. You can increase the number of cells that are displayed whilst retaining the periodicity of one cell, or you can make a supercell from a number of cells. To illustrate this, you will first increase the number of cells you are visualizing and then make a supercell. Click in Pt(1 1 1).xsd to deselect the 2D lattice. Press the Display Style button the 3D Viewer toolbar to display the Display Style dialog. Select the Lattice tab. on
You can change the number of cells viewed by increasing the U and V display ranges on the Lattice tab of the Display Style dialog. Click twice on the up spin controls for both Max U and Max V. Close the Display Style dialog. Each time you click on one of the spin controls, the 3D Atomistic document is updated. The final document contains a 3 x 3 surface. However, this surface still retains the original periodicity.
Although useful for visualization purposes, increasing the display ranges for U and V does not increase the size of the surface unit cell. To do this, you must use the supercell building functionality in Materials Studio. Select Build | Symmetry | Supercell from the menu bar. The Supercell dialog is displayed.
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Supercell dialog The supercell range is read from the currently displayed 3D Atomistic document. This can be changed, if necessary, but for this tutorial, you will create a 3 x 3 supercell. Click on the Create Supercell button. A larger surface is built, comprising nine of the original unit cells:
This structure is now a reasonable size such that calculations can be performed without molecules on the surface interacting with periodic images of themselves. Close the Supercell dialog by clicking on the button .
This system has 2D periodicity. In order to use it with a quantum mechanics program, such as CASTEP or DMol3, you need to convert it to a 3D lattice by creating a vacuum slab.
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4. Building a vacuum slab

A vacuum slab is a 3D periodic cell with the surface at the bottom and a layer of vacuum above it. This enables you to put molecules onto the surface, within the vacuum region, so that the molecule does not interact with a periodic image of the surface above it. Select Build | Crystals | Build Vacuum Slab... from the menu bar. The Build Vacuum Slab Crystal dialog is displayed.
Build Vacuum Slab Crystal dialog, Vacuum Slab tab
This dialog allows you to specify the orientation, thickness, and position of the vacuum slab. Increase the Vacuum thickness from 10.00 to 20.00 . Click on the Build button. Pt(1 1 1).xsd is updated to display a cell with the platinum surface at the bottom and a large area of vacuum above.
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Surface plus Vacuum As this system is 3D periodic, there is a layer of atoms at the top of the cell. You can change the display style so that these atoms are not visible. Select View | Display Style from the menu bar to display the Display Style dialog. Choose the Lattice tab and change the Style from Default to Original. Close the Display Style dialog.
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LESSON 5: Positioning molecules on a surface

The final stage in this tutorial is to build a small molecule and then position it on the surface. To do this, you will sketch a molecule of methane in a new 3D Atomistic document, copy and paste it into the vacuum slab, and dock it with the surface. Click on the options arrow associated with the New button on the Standard toolbar and select 3D Atomistic Document from the dropdown list. Press the Sketch Atom button on the Sketch toolbar, click once in the new 3D Atomistic document, and press the ESC key to finish sketching. You have sketched a single carbon atom in the 3D Atomistic document. You will change this into methane by using the Adjust Hydrogen and Clean tools. Click on the Adjust Hydrogen button Clean button . on the Sketch toolbar, followed by the
The next step is to copy and paste the methane molecule into the document containing the vacuum slab. Select Edit | Copy from the menu bar. Double-click on Pt(1 1 1).xsd in the Project Explorer, then press the Paste button on the Standard toolbar.
Tip. You can also use the standard Windows shortcut keys, CTRL + C and CTRL + V, to copy and paste structures. The methane molecule is pasted into the vacuum slab cell. Now you have to select, translate, and rotate the molecule until it is docked with the surface. Hold down the SHIFT and ALT keys, plus the right mouse button. Drag the cursor upward. Tip. If you have a three-button mouse or a mouse with a wheel, you can drag while pressing the wheel or middle button along with the SHIFT key to translate without having to hold down the ALT key as well. The molecule translates up the screen. Position the methane molecule just above the surface. It is useful to visualize the surface and the methane molecule using the spacefilling representation in order to help with the positioning of the methane molecule. Double-click in the 3D Atomistic document to deselect everything. Press the Display Style button on the 3D Viewer toolbar. Select the CPK option on the Atom tab of the Display Style dialog. Close this dialog.
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The vacuum slab should look similar to that shown below:
Pt surface and CH4 molecule in CPK display style
Double-click on the methane molecule to select it. Translate the molecule to the middle of the surface. You may have to change your view of the entire surface to do this. To successfully dock your molecule on a surface, you should rotate it so that a hydrogen atom is orientated downward towards the surface. You can rotate a fragment by holding down the SHIFT key and the right mouse button while dragging the cursor. Materials Studio uses a trackball rotation system. This means that the location of the cursor on the screen affects the axis around which you rotate. When the cursor is in the middle of the screen, dragging up and down rotates about the y-axis, while moving left and right rotates about the x-axis. If you wish to rotate in the z plane, move the cursor to the edge of the screen and then drag it along the edge. Position the cursor in the middle of the 3D Viewer. Hold down the SHIFT key and the right mouse button. Drag the cursor left and right, then up and down. The fragment rotates about the x and y axes, respectively. Move the cursor to the edge of the 3D Viewer. Hold down the SHIFT key and the right mouse button. Drag the cursor along the edge of the document. The fragment rotates in the z plane. Use this rotation and translation functionality to position your methane molecule. When you have finished, deselect the methane molecule by double-clicking in an empty part of the 3D Viewer.
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Your system should look similar to that shown below.
Pt surface with CH4 molecule docked You have successfully docked a methane molecule onto your platinum surface. You can now perform energy or dynamics calculations on this structure using tools such as CASTEP, DMol3, Discover, or Forcite. This is the end of the tutorial.
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Hands-On Exercise: Field segregation and analysis

Purpose: Demonstrates how to perform field segregation on an Atom Volumes Field. Modules: Materials Visualizer Time: Prerequisites: Working with isosurfaces and slices Introduction The volumetric visualization tools in Materials Visualizer provide a powerful way of visualizing field data generated by mesoscale, Sorption and quantum methods and also by the atom volumes and surfaces tool. Isosurfaces are used to aid the visualization of field data by linking field points at a specific isovalue. If an isosurface which contains isolated segments is generated, it is not possible to select these individual segments without selecting all segments for an isosurface. One approach to solve this is to allow the underlying field to be segregated into many subfields. Each subfield, or segregate, represents a unique segment of the original field. A segregate field can be selected, and various useful properties such as the field volume and geometric center can be obtained, allowing improved analysis of field data. Field segregation can be used on any field in Materials Visualizer, providing access to free volume distributions from an amorphous cell, micelle size distributions from mesoscale calculations, and allowing you to perform Sorption calculations on restricted pores in a zeolite. In this tutorial, you will calculate a Connolly surface for a zeolite. Using the underlying Atom Volumes Field, you will segregate the field at a specific isovalue and then analyze the segregates. This tutorial covers: Getting Started To calculate a Connolly surface To segregate an Atom Volumes Field To analyze the segregates
Intro 265
LESSON 1. Getting started

Begin by starting Materials Studio and creating a new project called Segregates. If Materials Studio is not already open, double-click on the Materials Studio icon on your desktop to start the program or, alternatively, select Programs | Accelrys Materials Studio [version] | Materials Studio from the Windows Start menu. Open the New Project dialog, enter Segregates as the name and click the OK button. The new project is created with Segregates listed in the Project Explorer.
LESSON 2: To calculate a Connolly surface

The first step is to generate field data to segregate. You will generate a Connolly surface which is based on an underlying Atom Volumes Field. You can generate an Atom Volumes Field for any structure, but in this example you will use a zeolite. Click on the Import button on the Standard toolbar to open the Import Document dialog, navigate to and open Examples\Documents\3D Model\TON.msi. Now you can calculate a Connolly surface using the Atom Volumes & Surfaces tool. Select Tools | Atom Volumes & Surfaces from the menu bar. This opens the Atoms Volumes & Surfaces dialog. The default task is to calculate a Connolly surface. You can also calculate Solvent surfaces by changing the task, but we will use a Connolly surface for this tutorial. Click the Create button. Isosurfaces are generated in the atomistic document and the dialog changes to the Analysis tab.
Intro 266
Analysis tab on Atom Volumes & Surfaces dialog The tree view on the dialog shows the presence of an Atom Volumes Field even though it is not displayed at the moment. The checkbox shows that the Connolly surface is visible. You can display the field by checking the Atom Volumes Field checkbox. Check the Atom Volumes Field checkbox. The field is displayed with low values in red and high values in blue. You can make the field invisible for now. Uncheck the Atom Volumes Field checkbox. You can change the radius of the Connolly probe to see the effect of probe size on free volume in the structure. Click on the Connolly radius spin down control. As you decrease the size of the Connolly probe, the free volume in the structure increases as the isosurfaces increase in size and form connected structures. For the rest of this tutorial, you need to have some isolated segregates so you should increase the probe radius. Set the Connolly radius to 0.90. Close the Atom Volumes & Surfaces dialog.
Intro 267
LESSON 3: To segregate the Atom Volumes Field

If you try to select one of the sections of the isosurface, you will see that the entire isosurface is selected. This is a limitation if you want to find the volume of an isolated section of isosurface. Click on one of the sections of isosurface. The segregation splits the underlying field into separate field segregates. Each of these can be selected to examine properties like the volume and the center of the segregate. The tools for creating, managing, and manipulating segregates are on the Volume Visualization toolbar. Click anywhere in the 3D Viewer to deselect everything. Select View | Toolbars | Volume Visualization from the menu bar. Click on the Create Segregates button .
Segregated fields are displayed as smaller field boxes within the structure with the fields in different colors. You can select individual field segregates to see the volumes. With the Properties Explorer open, click on one of the small field segregates. The Properties Explorer Filter changes to Segregate. Here you can see the different properties such as the FieldVolume indicating the volume of the field and the SegregateXYZ which displays the center of the segregate. Click in the model document to deselect the segregate. You can select segregates using the Volumetric Selection tool on the Volume Visualization toolbar. Click the Volumetric Selection button toolbar. on the Volume Visualization
This opens the Volumetric Selection dialog which displays a tree view of the volumetric data. You can hide the Connolly surface. Uncheck the Connolly Surface checkbox. The segregates are represented by the Segregator branch indicated by the + Segregator @0 line. The @0 shows that the field was segregated at an isovalue of 0. You can expand the branch to see the segregates by clicking on +. Click on + to expand the Segregator @0 branch.
Intro 268
There are several segregates in the structure. You can increase the size of the Volumetric Selection dialog to see all the segregates. Move your cursor to the bottom-right of the dialog. When the cursor changes to a double-headed arrow, click and drag right and down. You should see there are 14 segregates.
Expanded Volumetric Selection dialog. You can control which areas of field are segregated using either the Properties Explorer or the Display Style dialog. Right-click in the 3D Viewer and select Display Style from the dropdown list to open the Display Style dialog, change to the Segregate tab. You can use the Display style and Coloring sections to control how the segregates appear. The Constraints section allows you to control which type of segregates are displayed. The isovalue controls the threshold in the field for the segregation, similar to the isovalue property of an isosurface. Increase and decrease the Isovalue. Set the value back to 0.0. Changing the isovalue dynamically recalculates the segregates. Tip. When changing the isovalue, the field display updates can be quite time consuming if you have a large, heavily segregated field. In this case, it is better to set the value explicitly rather than use the spin controls.
Intro 269
You can also specify whether you want the segregates to be field values that are higher or lower than the isovalue or you can choose both. Change Values to Low. Choosing Low selects the field points that are the inverse of the default High settings. In this example, the low values are the field values where there are atoms. Changing the Value to All includes both higher and lower values in separate segregates. Change Values back to High. The final constraints are the Connectivities. This controls whether the segregates are accessible or isolated. Isolated segregates are self-contained in the cell, while accessible segregates are infinitely connected. Change Connectivities to Isolated. Only the twelve segregates which are not infinitely connected are displayed. Change Connectivities to Accessible. Only the two segregates which are infinitely connected are displayed. Tip. Using only the accessible, connected segregates would allow you to limit the search space for a Sorption calculation to only the accessible pores in a zeolite. Change Connectivities back to All. Note. The above properties are also available through the Properties Explorer and through the MaterialsScript API. If you wish to perform the same calculation on numerous structures, it may be more efficient to use MaterialsScript. In their initial state, the field segregates are only displayed as fields. You can add isosurfaces to them using the standard isosurface tool. On the Volumetric Selection dialog, hold down the Shift key and select all the segregates. Click on the Create Isosurfaces button .
Isosurfaces are created on all the segregates. They use the isovalue which was used for the segregation and are colored the same as their segregate fields.
Intro 270
LESSON 4: To analyze the segregates

You can analyze properties such as the size and separation distributions of the segregates using the Create Segregates tool. Click on the Create Segregates arrow and select Analyze Segregated Field. This opens the Segregate Analysis dialog. The default option is to analyze the segregate size. Click the Analyze button. A chart is generated showing you the distribution of the segregate sizes. You should see a large peak near zero indicating the smaller isolated segregates and two small peaks above 140 which correspond to the two accessible segregates. Tip. You can get the actual volumes for each segregate automatically by using MaterialsScript to iterate through all the segregates in the collection. Change focus back to TON.xsd. In the Segregate Analysis dialog, select Segregate major axis and click on the Analyze button. This analysis fits an ellipsoid to the segregate and then plots the major axis of the ellipsoid. Change focus back to TON.xsd. In the Segregate Analysis dialog, select Segregate radius (best-fit sphere) and click on the Analyze button. This analysis fits a best fit sphere to the segregate and then plots the radius of the sphere. Change focus back to TON.xsd. In the Segregate Analysis dialog, select Segregate separation and click on the Analyze button. This analysis plots the distribution of the distances between the segregates. Tip. You can perform analysis on a subset of the visible segregates by selecting the segregates first before analyzing them. Select File | Save Project from the menu bar or click on the Save Project button on the Project toolbar.
This is the end of the tutorial.
Intro 271
Hands-On Exercise: Field segregation and analysis

Purpose: Demonstrates how to perform field segregation on an Atom Volumes Field. Modules: Materials Visualizer Time: Prerequisites: Working with isosurfaces and slices Introduction The volumetric visualization tools in Materials Visualizer provide a powerful way of visualizing field data generated by mesoscale, Sorption and quantum methods and also by the atom volumes and surfaces tool. Isosurfaces are used to aid the visualization of field data by linking field points at a specific isovalue. If an isosurface which contains isolated segments is generated, it is not possible to select these individual segments without selecting all segments for an isosurface. One approach to solve this is to allow the underlying field to be segregated into many subfields. Each subfield, or segregate, represents a unique segment of the original field. A segregate field can be selected, and various useful properties such as the field volume and geometric center can be obtained, allowing improved analysis of field data. Field segregation can be used on any field in Materials Visualizer, providing access to free volume distributions from an amorphous cell, micelle size distributions from mesoscale calculations, and allowing you to perform Sorption calculations on restricted pores in a zeolite. In this tutorial, you will calculate a Connolly surface for a zeolite. Using the underlying Atom Volumes Field, you will segregate the field at a specific isovalue and then analyze the segregates. This tutorial covers: Getting Started To calculate a Connolly surface To segregate an Atom Volumes Field To analyze the segregates
Intro 272
LESSON 1. Getting started

Begin by starting Materials Studio and creating a new project called Segregates. If Materials Studio is not already open, double-click on the Materials Studio icon on your desktop to start the program or, alternatively, select Programs | Accelrys Materials Studio [version] | Materials Studio from the Windows Start menu. Open the New Project dialog, enter Segregates as the name and click the OK button. The new project is created with Segregates listed in the Project Explorer.
LESSON 2: To calculate a Connolly surface

The first step is to generate field data to segregate. You will generate a Connolly surface which is based on an underlying Atom Volumes Field. You can generate an Atom Volumes Field for any structure, but in this example you will use a zeolite. Click on the Import button on the Standard toolbar to open the Import Document dialog, navigate to and open Examples\Documents\3D Model\TON.msi. Now you can calculate a Connolly surface using the Atom Volumes & Surfaces tool. Select Tools | Atom Volumes & Surfaces from the menu bar. This opens the Atoms Volumes & Surfaces dialog. The default task is to calculate a Connolly surface. You can also calculate Solvent surfaces by changing the task, but we will use a Connolly surface for this tutorial. Click the Create button. Isosurfaces are generated in the atomistic document and the dialog changes to the Analysis tab.
Intro 273
Analysis tab on Atom Volumes & Surfaces dialog The tree view on the dialog shows the presence of an Atom Volumes Field even though it is not displayed at the moment. The checkbox shows that the Connolly surface is visible. You can display the field by checking the Atom Volumes Field checkbox. Check the Atom Volumes Field checkbox. The field is displayed with low values in red and high values in blue. You can make the field invisible for now. Uncheck the Atom Volumes Field checkbox. You can change the radius of the Connolly probe to see the effect of probe size on free volume in the structure. Click on the Connolly radius spin down control. As you decrease the size of the Connolly probe, the free volume in the structure increases as the isosurfaces increase in size and form connected structures. For the rest of this tutorial, you need to have some isolated segregates so you should increase the probe radius. Set the Connolly radius to 0.90. Close the Atom Volumes & Surfaces dialog.
Intro 274
LESSON 3: To segregate the Atom Volumes Field

If you try to select one of the sections of the isosurface, you will see that the entire isosurface is selected. This is a limitation if you want to find the volume of an isolated section of isosurface. Click on one of the sections of isosurface. The segregation splits the underlying field into separate field segregates. Each of these can be selected to examine properties like the volume and the center of the segregate. The tools for creating, managing, and manipulating segregates are on the Volume Visualization toolbar. Click anywhere in the 3D Viewer to deselect everything. Select View | Toolbars | Volume Visualization from the menu bar. Click on the Create Segregates button .
Segregated fields are displayed as smaller field boxes within the structure with the fields in different colors. You can select individual field segregates to see the volumes. With the Properties Explorer open, click on one of the small field segregates. The Properties Explorer Filter changes to Segregate. Here you can see the different properties such as the FieldVolume indicating the volume of the field and the SegregateXYZ which displays the center of the segregate. Click in the model document to deselect the segregate. You can select segregates using the Volumetric Selection tool on the Volume Visualization toolbar. Click the Volumetric Selection button toolbar. on the Volume Visualization
This opens the Volumetric Selection dialog which displays a tree view of the volumetric data. You can hide the Connolly surface. Uncheck the Connolly Surface checkbox. The segregates are represented by the Segregator branch indicated by the + Segregator @0 line. The @0 shows that the field was segregated at an isovalue of 0. You can expand the branch to see the segregates by clicking on +. Click on + to expand the Segregator @0 branch.
Intro 275
There are several segregates in the structure. You can increase the size of the Volumetric Selection dialog to see all the segregates. Move your cursor to the bottom-right of the dialog. When the cursor changes to a double-headed arrow, click and drag right and down. You should see there are 14 segregates.
Expanded Volumetric Selection dialog. You can control which areas of field are segregated using either the Properties Explorer or the Display Style dialog. Right-click in the 3D Viewer and select Display Style from the dropdown list to open the Display Style dialog, change to the Segregate tab. You can use the Display style and Coloring sections to control how the segregates appear. The Constraints section allows you to control which type of segregates are displayed. The isovalue controls the threshold in the field for the segregation, similar to the isovalue property of an isosurface. Increase and decrease the Isovalue. Set the value back to 0.0. Changing the isovalue dynamically recalculates the segregates. Tip. When changing the isovalue, the field display updates can be quite time consuming if you have a large, heavily segregated field. In this case, it is better to set the value explicitly rather than use the spin controls.
Intro 276
You can also specify whether you want the segregates to be field values that are higher or lower than the isovalue or you can choose both. Change Values to Low. Choosing Low selects the field points that are the inverse of the default High settings. In this example, the low values are the field values where there are atoms. Changing the Value to All includes both higher and lower values in separate segregates. Change Values back to High. The final constraints are the Connectivities. This controls whether the segregates are accessible or isolated. Isolated segregates are self-contained in the cell, while accessible segregates are infinitely connected. Change Connectivities to Isolated. Only the twelve segregates which are not infinitely connected are displayed. Change Connectivities to Accessible. Only the two segregates which are infinitely connected are displayed. Tip. Using only the accessible, connected segregates would allow you to limit the search space for a Sorption calculation to only the accessible pores in a zeolite. Change Connectivities back to All. Note. The above properties are also available through the Properties Explorer and through the MaterialsScript API. If you wish to perform the same calculation on numerous structures, it may be more efficient to use MaterialsScript. In their initial state, the field segregates are only displayed as fields. You can add isosurfaces to them using the standard isosurface tool. On the Volumetric Selection dialog, hold down the Shift key and select all the segregates. Click on the Create Isosurfaces button .
Isosurfaces are created on all the segregates. They use the isovalue which was used for the segregation and are colored the same as their segregate fields.
Intro 277
LESSON 4: To analyze the segregates

You can analyze properties such as the size and separation distributions of the segregates using the Create Segregates tool. Click on the Create Segregates arrow and select Analyze Segregated Field. This opens the Segregate Analysis dialog. The default option is to analyze the segregate size. Click the Analyze button. A chart is generated showing you the distribution of the segregate sizes. You should see a large peak near zero indicating the smaller isolated segregates and two small peaks above 140 which correspond to the two accessible segregates. Tip. You can get the actual volumes for each segregate automatically by using MaterialsScript to iterate through all the segregates in the collection. Change focus back to TON.xsd. In the Segregate Analysis dialog, select Segregate major axis and click on the Analyze button. This analysis fits an ellipsoid to the segregate and then plots the major axis of the ellipsoid. Change focus back to TON.xsd. In the Segregate Analysis dialog, select Segregate radius (best-fit sphere) and click on the Analyze button. This analysis fits a best fit sphere to the segregate and then plots the radius of the sphere. Change focus back to TON.xsd. In the Segregate Analysis dialog, select Segregate separation and click on the Analyze button. This analysis plots the distribution of the distances between the segregates. Tip. You can perform analysis on a subset of the visible segregates by selecting the segregates first before analyzing them. Select File | Save Project from the menu bar or click on the Save Project button on the Project toolbar.
This is the end of the tutorial.
Intro 278
Appendix 1: Chart mouse and keyboard actions

Certain mouse and keyboard actions are available regardless of the Chart Viewer's tool mode. These are labelled as Default actions in the following table, and can be used in any tool mode. Other mouse and keyboard actions are specific to a particular tool mode, and may behave very differently between modes. Default modes The actions described in this section can be performed in any tool mode. To Reset to original view Translate View Translate View Translate View Translate View Translate View Page Translate View Zoom Zoom In Zoom Out Zoom In Zoom Out Zoom X-scale Zoom Y-scale Zoom with Zoom Rectangle Press Home Middle mouse drag Mouse wheel drag Cursor keys Scroll bars Press T + Left mouse drag CTRL + Cursor keys Left-and-right mouse drag + (on keypad) - (on keypad) Mouse wheel up Mouse wheel down Press X in combination with desired zoom operation Press Y in combination with desired zoom operation Press R + Left mouse drag
Selection Note that selection applies to data points and chart markers. To Select All Clear selection Object selection Toggle object selection Add object to current selection Rectangle selection of objects Toggle rectangle selection of objects Add rectangle selection of objects Marker selection Toggle marker selection Add marker to current selection Rectangle marker selection Toggle rectangle marker selection Add rectangle marker selection Data point selection Press CTRL + A CTRL + D E + Left mouse click E + CTRL + Left mouse click E + SHIFT + Left mouse click E + Left mouse click and drag E + CTRL + Left mouse click and drag E + SHIFT + Left mouse click and drag M + Left mouse click M + CTRL + Left mouse click M + SHIFT + Left mouse click M + Left mouse click and drag M + CTRL + Left mouse click and drag M + SHIFT + Left mouse click and drag I + Left mouse click
Intro 279
Toggle data point selection Add data point to current selection Rectangle data point selection Toggle rectangle data point selection Add data point selection Editing To Copy marker selection Delete marker selection Move marker
I + CTRL + Left mouse click I + SHIFT + Left mouse click I + Left mouse click and drag I + CTRL + Left mouse click and drag I + SHIFT + Left mouse click and drag
Press CTRL + C DELETE Middle mouse drag a selected marker
Tool modes The actions described in the following tables can be performed only in the specified tool modes, and may behave very differently in other tool modes. Selection mode The Selection mode actions described here apply to data points and chart markers. Selection mode cursor To Toggle object selection Add object to current selection Rectangle selection Toggle rectangle selection Add rectangle selection Press CTRL + Left mouse click SHIFT + Left mouse click Left mouse click and drag CTRL + Left mouse click and drag SHIFT + Left mouse click and drag
Zoom mode The actions described in this table apply only in Zoom mode. Zoom mode cursor To Zoom Constrained Zoom Zoom X-scale Zoom Y-scale Press Left mouse drag CTRL + Left mouse drag Press X + Left mouse drag Press Y + Left mouse drag
Translation mode The actions described in this table apply only in Translation mode. Translation mode cursor To Translate Press Left mouse drag
Intro 280
Marker mode The actions described in this table apply only in Marker mode. Marker mode cursor To Add marker Highlight marker Move marker Snap marker to nearest data point Press Left mouse click on background Hover mouse cursor over existing marker Left mouse drag the highlighted marker CTRL + Move marker
Cluster cursor mode The actions described in this table apply only in Cluster cursor mode. Cluster cursor mode cursor To Position the cluster cursor Press Left mouse click and drag the cluster cursor
Intro 281
Appendix 2: Recommended Literature

General Overview
1. Leach AR. 1999. Molecular Modelling. Singapore: Longman. 595pp. For a good overview of all aspects. 2.- Frenkel D, Smit B. 2001.Understanding Molecular Simulation. 2nd edition. London.Academic Press. 600 pp. For an understanding of basic modeling methods and approaches 3.- Allen MP, Tildesley DJ. 2004. Computer Simulation of Liquids. Bristol: Clarendon Press. 385pp. More in depth - A must for molecular dynamics methods.
Other computational chemistry texts

1.- Goodman JM. 1998. Chemical applications of Molecular Modelling. Royal Society of Chemistry. 216 pp. 2.- Young D. 2001. Computational Chemistry: A Practical Guide for Applying Techniques toReal World Problems. Wiley-Interscience. 408 pp.
Case Studies
Accelrys maintains a library of case studies demonstrating how our software has been used to solve real scientific problems in industry, government, and academia. The complete listing of case studies is available on the following webpage: http://www.accelrys.com/reference/cases/
Intro 282
Appendix 1: Chart mouse and keyboard actions

Certain mouse and keyboard actions are available regardless of the Chart Viewer's tool mode. These are labelled as Default actions in the following table, and can be used in any tool mode. Other mouse and keyboard actions are specific to a particular tool mode, and may behave very differently between modes. Default modes The actions described in this section can be performed in any tool mode. To Reset to original view Translate View Translate View Translate View Translate View Translate View Page Translate View Zoom Zoom In Zoom Out Zoom In Zoom Out Zoom X-scale Zoom Y-scale Zoom with Zoom Rectangle Press Home Middle mouse drag Mouse wheel drag Cursor keys Scroll bars Press T + Left mouse drag CTRL + Cursor keys Left-and-right mouse drag + (on keypad) - (on keypad) Mouse wheel up Mouse wheel down Press X in combination with desired zoom operation Press Y in combination with desired zoom operation Press R + Left mouse drag
Selection Note that selection applies to data points and chart markers. To Select All Clear selection Object selection Toggle object selection Add object to current selection Rectangle selection of objects Toggle rectangle selection of objects Add rectangle selection of objects Marker selection Toggle marker selection Add marker to current selection Rectangle marker selection Toggle rectangle marker selection Add rectangle marker selection Data point selection Press CTRL + A CTRL + D E + Left mouse click E + CTRL + Left mouse click E + SHIFT + Left mouse click E + Left mouse click and drag E + CTRL + Left mouse click and drag E + SHIFT + Left mouse click and drag M + Left mouse click M + CTRL + Left mouse click M + SHIFT + Left mouse click M + Left mouse click and drag M + CTRL + Left mouse click and drag M + SHIFT + Left mouse click and drag I + Left mouse click
Intro 283
Toggle data point selection Add data point to current selection Rectangle data point selection Toggle rectangle data point selection Add data point selection Editing To Copy marker selection Delete marker selection Move marker
I + CTRL + Left mouse click I + SHIFT + Left mouse click I + Left mouse click and drag I + CTRL + Left mouse click and drag I + SHIFT + Left mouse click and drag
Press CTRL + C DELETE Middle mouse drag a selected marker
Tool modes The actions described in the following tables can be performed only in the specified tool modes, and may behave very differently in other tool modes. Selection mode The Selection mode actions described here apply to data points and chart markers. Selection mode cursor To Toggle object selection Add object to current selection Rectangle selection Toggle rectangle selection Add rectangle selection Press CTRL + Left mouse click SHIFT + Left mouse click Left mouse click and drag CTRL + Left mouse click and drag SHIFT + Left mouse click and drag
Zoom mode The actions described in this table apply only in Zoom mode. Zoom mode cursor To Zoom Constrained Zoom Zoom X-scale Zoom Y-scale Press Left mouse drag CTRL + Left mouse drag Press X + Left mouse drag Press Y + Left mouse drag
Translation mode The actions described in this table apply only in Translation mode. Translation mode cursor To Translate Press Left mouse drag
Intro 284
Marker mode The actions described in this table apply only in Marker mode. Marker mode cursor To Add marker Highlight marker Move marker Snap marker to nearest data point Press Left mouse click on background Hover mouse cursor over existing marker Left mouse drag the highlighted marker CTRL + Move marker
Cluster cursor mode The actions described in this table apply only in Cluster cursor mode. Cluster cursor mode cursor To Position the cluster cursor Press Left mouse click and drag the cluster cursor
Intro 285
Appendix 2: Recommended Literature

General Overview
1. Leach AR. 1999. Molecular Modelling. Singapore: Longman. 595pp. For a good overview of all aspects. 2.- Frenkel D, Smit B. 2001.Understanding Molecular Simulation. 2nd edition. London.Academic Press. 600 pp. For an understanding of basic modeling methods and approaches 3.- Allen MP, Tildesley DJ. 2004. Computer Simulation of Liquids. Bristol: Clarendon Press. 385pp. More in depth - A must for molecular dynamics methods.
Other computational chemistry texts

1.- Goodman JM. 1998. Chemical applications of Molecular Modelling. Royal Society of Chemistry. 216 pp. 2.- Young D. 2001. Computational Chemistry: A Practical Guide for Applying Techniques toReal World Problems. Wiley-Interscience. 408 pp.
Case Studies
Accelrys maintains a library of case studies demonstrating how our software has been used to solve real scientific problems in industry, government, and academia. The complete listing of case studies is available on the following webpage: http://www.accelrys.com/reference/cases/
Intro 286
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Fax: +1 858 799 5100 Fax: +44 1223 228501 Fax: +81 3 3206 3572
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Introduction to Materials Studio

Introduction to Materials Studio

Who are we?

Company Key Facts

Implementation Services Training

Part I: Introduction to Materials Modeling

Calculations vs. Experiment

Part I: What is Materials Studio? (Demo)

Files & Folders

Figures & Tables Properties Jobs running

Lets draw a molecule!

We draw 4 carbon atoms

We draw a carbon atom and change it to oxygen

Lets add some hydrogen atoms!

A more reasonable geometry

New Document Save Document undo redo

Selection Rotation Zoom

Modules Menu/Modules Toolbar

GULP Kinetix (Consortium only) MesoDyn Mesocite Mesotek Morphology

Building tools developments

Build Block Copolymer

Build Random Copolymer

Define a repeat unit

Tools for building nanostructures with the Materials Visualizer

Building single or multi-wall nanotubes

Building multi-wall nanotubes

Building tools developments

Convert atoms to beads

Brillouin Zone Path

Use with Vectors dialog to select specific vectors

Part II: Introduction to Materials Modeling

What is materials simulation?

e.g., morphology, drug delivery e.g., permeation, crystallisation

Issues that simulation can address

Quantum Mechanics Atomistic Simulation

Correlative methods (e.g. QSAR)

Increasing Scale of Study

Modeling and simulation methods in MS

Quantum Mechanics: DFT

Kohn Sham equation

What can be calculated?

CASTEP (plane waves)

Extra Tool: CASTEP solid state NMR

What can be calculated?

Liner Scaling DFT

Molecular Mechanics (MM)

Etotal=Evalence + Ecrossterm + Enon-bond

Evalence=Ebond + Eangle + Etorsion + Eoop + EUB

Enon-bond=EvdW + ECoulomb + Ehbond

MM - Molecular Dynamics (MD)

Discover, GULP, Forcite plus

What can be calculated?

Longer time and length scales!!!!

Disip Random + Fij + Fij

What can be calculated?

Crystal structure determination from powder diffraction data

Reflex, Reflex Plus, Reflex QPA, X-Cell

Routes to determine crystal structures

Direct space methods

Other crystallography tools

What can be calculated?

QSAR, Synthia (Polymers)

QSAR-Quantitative Structure Activity Relationship