The Basics

 Input a molecular structure

 In some cases, electronic configuration
may need to be known
 Three basic types of calculations
 Single-point energy
 Geometry optimization
 Frequency calculation

 Interpret the data

Single-point Energy
 In the simplest terms, it is the
energy intrinsic to the structure
 Useful for determining the stability
of a compound
 The structure may be in an excited
state
 Defines a potential energy surface
(PES)
Potential Energy Surface
Geometry Optimization
 Determination of the equilibrium
geometry
 Generally, the geometry associated with the
lowest single-point energy
 Can also be used to find transition state
geometry by minimizing the energy in all
coordinates on the PES except for one
 SCF theory finds a stationary point, a
place where the energy gradient is zero
 May correspond to either a minimum or a
saddlepoint
Frequency Calculation
 Predicts the intensities of the vibrations
associated with a molecule
 This is useful for predicting the absorption
spectra of compounds
 It can also be used to verify whether the
structure was fully optimized
 If it was not fully optimized, reaction
coordinates appear as imaginary frequencies.
 NMR spectra can also be predicted
Computational Methods:
Molecular Mechanics
 Treats molecules classically
 Ball-and-spring model
 Assumes “ideal” bond angles and lengths
 Fastest method
 Predicts geometries well
 For normal systems, the bond angles and
lengths will be close to ideal
 Relatively poor prediction of energies
 Total energy only takes into account deviation
from ideal bond length, bond angles,
dihedrals, and van der Waals interactions
Computational Methods:
Semi-empirical
 Based on quantum mechanics, but
uses empirical data to simplify the
calculations
 Fast, but not as fast as molecular
mechanics
 Produces good energies and good
geometries for simple organic
compounds
Computational Methods:
Ab Initio
 Calculations based on quantum
mechanics, without use of empirical data
 Slowest method because it involves
approximating a solution to the
Schrödinger equation strictly from
quantum mechanical principles
 Generally finds approximations using self-
consistent field (SCF) theory
 Produces the best energies and
geometries, overall
Popular Procedures
 Molecular Mechanics
 AMBER, DRIEDING, UFF, MMFF
 Force-fields, not methods

 Semi-Empirical
 AM1, PM3, MNDO, CNDO, INDO
 Ab Initio
 Hartree-Fock, BLYP, DFT methods
Basis Sets
 A basis set is a set of functions that
restrict the electrons considered to
specific regions of space
 Larger basis sets impose fewer
restrictions, and so give better
predictions
 However, larger basis sets are
computationally more expensive
Interpretation
 Computational data are not a replacement for
physical experiments
 Keep the basis set and computational method in
mind when deciding how much credence to give
the result of a calculation
 Cross-checking each calculation with another is
invaluable
 E.g., checking a geometry optimization with a
frequency calculation: if imaginary
frequencies exist, the structure is not fully
optimized and some of the numbers may not
be accurate
Implementations
 Titan
 Easy to use GUI
 Not as flexible as other programs
 Gaussian
 No native GUI, but GaussView is available as a front
end
 Very flexible, but syntax is profuse and often confusing
 GAMESS
 Text-only interface, even more bare than Gaussian
 Free
 Well-known and used by researchers