Ab intio methods / H-F Methods

In describing the electron distribution in detail quantum mechanics is the best method (since electrons are very light particles). The time-independent Schrdinger equation is given by H = E and if the solutions are generated without reference to experimental data, the methods are usually called ab initio. An essential part of solving the Schrdinger equation is the BornOppenheimer approximation, where the coupling (interaction) between the nuclei and electrons is neglected. The dynamics (kinetics) of a many-electron system is very complex, and consequently requires elaborate computational methods. A significant simplification can be obtained by introducing independent-particle models, where the motion of one electron is considered to be independent of the dynamics of all other electrons. i.e., the interaction between the particles is approximated, either by considering the most important one and neglecting all others or by taking an average of all interactions. Within electronic structure theory, only the latter has an acceptable accuracy, and is called HartreeFock (HF) theory. HF calculation is the most common type of an initio calculation, in which the many electron Schrodinger equation is broke down into many single electron equation. Each electron is described by a single electron wave function called Orbital and an energy called Orbital energy. The orbital describes the behavior of an electron in the net field of all of the other electrons. The wave functions are as Gaussian functions. Thye total wave function is formed by the linear combination of all the AOs or the basis functions. Since the eclectrons are indistinguishable fermions (spin with ), the overall wave function must be anti symmetrical. (i.e., changes in sign upon inter changing 2 electrons). The best set of orbitals is determined by the variation principle and hence the energy calculated by the H-F approximation is equal to or greater than the exact energy. The energy calculated in units are called Hartrees (1 Hartree = 27.2116eV). The Gaussian functions that put into the determinants are called Gaussian Primitives and the resulting orbitals uses the functions of Mos. This is done to make the calculation to run much faster. The HF procedure can be varied in such a way that the orbitals are constructed to reflect paired or unpaired electrons. If the molecule has a singlet spin, then the same orbital spatial function can be used for both and spin electrons in each pair. This is called the Restricted Hartree Fock method (RHF). There are two techniques for constructing HF wave functions of molecules with unpaired electrons. One technique is to use two completely separate sets of orbitals for the and electrons. This is called an Unrestricted Hartree-Fock (UHF) wave function. i.e., paired electrons will not have the same spatial distribution. This introduces an error into the calculation, called spin contamination. Spin contamination might introduce an insignificant error depending on the chemical system involved. Another way of constructing wave functions for open-shell molecules is the restricted open shell Hartree-Fock method (ROHF). In this method, the paired electrons share the same spatial orbital; thus, there is no spin contamination. The ROHF technique is more difficult to implement than UHF and may require slightly 1

more CPU time to execute. ROHF is primarily used for cases where spin contamination is large using UHF. For singlet spin molecules at the equilibrium geometry, RHF and UHF wave functions are almost always identical. RHF wave functions are used for singlets because the calculation takes less CPU time. In a few rare cases, a singlet molecule has biradical resonance structures and UHF will give a better description of the molecule (i.e., ozone) The shape of a given molecular orbital describes the probability of finding an electron, where the attraction to all the nuclei and the average repulsion to all the other electrons are included. Since the other electrons are described by their respective orbitals, the H-F equations must be solved repeatedly until the energy and orbital co efficient remain constant. This repeat procedure is called Self-Consistent Field Procedure (SCF). CORRELATION One of the limitation if HF calculation is that they do not include electron correlation. i.e., according to H-F theory, the probability of finding an electron around an atom is determined by the distance from the nucleus and not by the distance from other electrons. Since the H-F method has limiting accuracy, the electron correlation must be inluded. Some of the methods that begin with a HF calculation and then correct for correlation are Moller- Plesset perturbation theory (MPn, where n is the order of correction), the generalized valence bond (GVB) method, multi-configurational self-consistent field (MCSCF), configuration interaction (CI), and coupled cluster theory (CC). Including correlation generally improves the accuracy of the computed energy and molecular geometry.

ADVANTAGE & DISADVATAGE

In general ab inito (or Hatree- Fcok) calculations give very good qualitative result and can yield increasingly accurate results as the molecule become smaller. The advantage of ab ignition method is that they really bring together the exact solution once all approximations are made sufficiently small in magnitude. The disadvantage of ab initio method is that they are very expensive and take enormous amount of CPU time, memory and disk space. The H-F methods scale N4, where N id the basis functions. In practice, extremely accurate solutions are only obtainable when the molecule contains a dozen electrons or less.

Semi empirical methods

The semi empirical methods are derived from ab initio method. The ab initio methods often take enormous amounts of CPU time, memory, and disk space and the cost of performing these methods is in the order of fourth power of basis functions (N4). However the accuracy of H-F calculation is very poor. The Semiempirical methods reduce the computational cost by approximating or omitting certain information such as two electron integrals. In order to correct for the errors introduced by omitting part of the calculation, the method is parameterized in order to give the best possible agreement with experimental data. The central assumption of semi-empirical methods is the Zero Differential Overlap (ZDO) approximation, which neglects all products of basis functions that depend on the same electron coordinates when located on different atoms. The first step is the consideration of precise valence electrons. Only a minimum basis set is used for the valence electrons. Hydrogen thus has one basis function, and all atoms in the second and third rows of the periodic table have four basis functions (one sand one set of p-orbitals (px, py and pz). The large majority of semi-empirical methods use only s- and p functions, and the basis functions are taken to be Slater type orbitals (i.e. exponential functions). . The advantage of semiempirical calculations is that they are much faster than the ab initio calculations. The disadvantage of semiempirical calculations is that the results can be less acurate. If the molecule being computed is similar to molecules in the data base used to parameterize the method, then the results may be very good. If the molecule being computed is significantly different from anything in the parameterization set, the answers may be very poor. Semi empirical calculations have been very successful in the description of organic chemistry, where there are only a few elements used extensively and the molecules are of moderate size.

Self Consistent Field

In a Hartre-Fock calculation the many electron Schrodinger equation is broken down to single electron equations. Each electron is described by a single electron wave function called Orbital. Since each electron is described by their respective orbitals, the H-F equations must be solved repeatedly until the energies and orbital coefficients remain constant. This repeat procedure is called a selfconsistent field procedure (SCF). The HF procedure can be varied in such a way that the orbitals are constructed to reflect paired or unpaired electrons. If the molecule has a singlet spin, then the same orbital spatial function can be used for both the and spin electrons. This is called the Restricted Hartree Fock method (RHF). There are two techniques for constructing HF wave functions of molecules with unpaired electrons. One technique is to use two completely separate sets of orbitals for the and electrons. This is called an Unrestricted Hartree-Fock wave function (UHF). This means that paired electrons will not have the same spatial distribution. This introduces an error 3

into the calculation, called spin contamination. Spin contamination might introduce a significant error or the error could be large enough to make the results unusable depending on the chemical system involved. UHF calculations are popular because they are easy to implement and run fairly efficiently. Another way of constructing wave functions for open-shell molecules is the restricted open shell Hartree-Fock method (ROHF). In this method, the paired electrons share the same spatial orbital; thus, there is no spin contamination. The ROHF technique is more difficult to implement than UHF and may require slightly more CPU time to execute. ROHF is primarily used for cases where spin contamination is large using UHF. For singlet spin molecules at the equilibrium geometry, RHF and UHF wave functions are almost always identical. RHF wave functions are used for singlets because the calculation takes less CPU time. In a few rare cases, a singlet molecule has biradical resonance structures and UHF will give a better description of the molecule (i.e., ozone) The RHF scheme results in forcing electrons to remain paired. This means that the calculation will fail to reflect cases where the electrons should uncouple. For example, a series of RHF calculations for H2 with successively longer bond lengths will show that H2 dissociates into H+ and H-, rather than two H atoms. This is responsible for certain systematic errors in HF results, such as very high activation energies, bond lengths slightly too short, vibrational frequencies too high, and dipole moments and atomic charges that are too large. UHF wave functions usually dissociate correctly.

Basis sets
The basis set usually refers to the set of non orthogonal, one-particle functions used to describe the shape of the orbitals in an atom. Molecular orbitals and entire wave functions are created by taking linear combinations of basis functions and angular functions. An orbital is a one-electron function. Most semiempirical methods use a predefined basis set. The type of calculations performed and basis set chosen are the te biggest factors in determining the accuracy of the results. AOs are represented by the atom centered Gaussian in most quantum chemistry programs. Some older programs use Slater functions. [Slater-Type Orbitals (STOs): These are H-atom-like, at least for 1s; however, they lack radial nodes and are not pure spherical harmonics. Hence 2s and 2p orbitals cannot be computed by STO methods. The advantage of using STO methods is the correct short-range and long-range behavior. STOs are more accurate, but it takes longer to compute integrals using them. Use of a linear combination of enough GTOs mimics an STO and are often called an STO-nG basis, even though it is made of CGTO {Contracted Gaussian-Type Orbitals (CGTOs)}]

DFT(Density Functional Theory)

Density Functional Theory (DFT) can be considered as an improvement on HF theory, where the many-body effect of electron correlation is modeled by a function of the electron density. DFT is an independent-particle model just like H-F. It is comparable to HF computationally, but provides significantly better results. The basic assumption behind DFT is that the energy of a molecule can be determined from the electron density instead of a wave function. This original theorem applied only to find the ground-state electronic energy of a molecule. A practical application of this theory was developed by Kohn and Sham who formulated a method similar in structure to the Hartree-Fock method. In this formulation, the electron density is expressed as a linear combination of basis functions similar in mathematical form to HF orbitals. A determinant is then formed from these functions, called Kohn-Sham orbitals. It is the electron density from this determinant of orbitals that is used to compute the energy. This procedure is necessary because Fermion systems can only have electron densities that arise from an ant symmetric wave function. Even though Kohn Sham determinant is not mathematically equivalent to HF, they do describe the behavior of electrons in a molecule. A density functional is used to obtain the energy for the electron density. A functional is a function of a function, in this case, the electron density. Some of these functionals were developed from fundamental quantum mechanics and some were developed by parameterizing functions to best reproduce experimental results. The advantage of using electron density is that the integrals for Coulomb repulsion need be done only over the electron density, which is a three-dimensional function. Thus DFT, scales as N3. Furthermore, at least some electron correlation can be included in the calculation. This result in faster calculations than HF calculations (which scale as N4) and computations that is a bit more accurate as well. Density functionals can be broken down into several classes. The simplest is called the X method. This type of calculation includes electron exchange but not correlation. The X method is similar in accuracy to HF and sometimes better. The simplest approximation to the complete problem is one based only on the electron density, called a local density approximation (LDA). For high-spin systems, this is called the local spin density approximation (LSDA). LDA calculations have been widely used for band structure calculations. LDA is known to give less accurate geometries and predicts binding energies significantly too large.

Z-Matrix
Z-matrix is a convenient way of specifying a molecular geometry in terms of bond distances, angles, and conformational angles. Every molecule has multiple geometries. Choosing the correct molecular equilibrium geometry is very important when carrying out computational studies. This is because the energy of a molecule depends on its geometry. Even small changes in the structure can lead to drastic changes in total energy. The geometry of a molecule can be described using one of three different methods. The first is by using cartesian coordinates. Using the x-y-z coordinate system, the coordinates for each atom in the molecule. However, this method is only efficient for small molecules.The second method uses a molecular editor or graphical user interface (GUI). These are computer programs which allow you to construct various molecules. The program then automatically calculates the geometry of the molecule. GUIs work well for larger molecules. The third method is called a Z-Matrix. The ZMatrix is a simple, but rough, geometrical approximation. It works by identifying each atom in a molecule by a bond distance, bond angle and dihedral angle in relation to other atoms in the molecule. Z-Matrices work well for large molecules because the Z-Matrix can be easily converted to cartesian coordinates. Geometry optimizations are often performed in Z-matrix variables and since optimizations are good, they are significantly faster than in Cartesian coordinates. Many ab initio and semiempirical programs optimize the geometry of the molecule by changing the parameters in the Z-matrix. In general, this can be a very good way to change the geometry because these parameters correspond to molecular motions similar to those in the vibrational modes. Thus Z-matrices help to find an easy way that the Cartesian coordinates of each atom in a molecule. These coordinates are used to describe characteristics of their molecule. However, if the geometry is specified in such a way that a slight change of one of the parameters could result in a large distortion to some portion of the molecule, then the geometry optimization is less efficient. Thus, a poorly constructed Z-matrix can result in a very inefficient geometry optimization. Many computational chemistry programs will do the geometry optimization in Cartesian coordinates. This is often the only way to optimize geometry in molecular mechanics programs and an optional method in orbital-based programs. A Cartesian coordinate optimization may be more efficient than a poorly constructed Z-matrix. This is often seen in ring systems, where a badly constructed Z-matrix will perform very poorly. Conversely Cartesian coordinates can be less efficient than a well constructed Z-matrix. Cartesian coordinates are often preferable when regenerating (reproducing) more than one molecule since they allow complete freedom of motion between separate molecules. In order to have the advantages of a well-constructed Z-matrix, a system called redundant internal coordinates was created. When redundant internal coordinates are used, the input geometry is first converted to a set of Cartesian coordinates. The algorithm then checks the distances between every pair of atoms to determine the reasonable bonding distance. The program then generates a list of 6

atom distances and angles for nearby atoms. This way, the algorithm does the job of constructing a sort of Z-matrix that has more coordinates than are necessary to specify the geometry completely. This is usually the most efficient way to optimize geometry. There are many different algorithms for finding the set of coordinates corresponding to the minimum energy. These are called optimization algorithms because they can be used equally well for finding the minimum or maximum of a function.

Constructing a Z-Matrix
Construction of a Z-matrix begins with a drawing of the molecule and a suitable numbering of the atoms. Any numbering will result in a valid Z-matrix, although assignment of numerical values to the parameters is greatly facilitated if the bonding and symmetry of the molecule is considered when the numbering is performed. The Z-matrix specifies the position of each atom in terms of a distance, an angle and a torsional angle relative to other atoms. The first three atoms, however, are slightly different. The first atom is always positioned at the origin of the coordinate system. The second atom is specified as having a distance to the first atom and is placed along one of the Cartesian axis (usually x or z). The third atom is specified by a distance to either atom 1 or 2, and an angle to the other atom. All subsequent atoms need a distance, an angle and a torsional angle to uniquely specify the position. The atoms are normally identified either by the chemical symbol or by their atomic number. Some typical bond lengths () and angles are given below. AH: where A=C: 1.10; A=O, N: 1.00; A=S,P: 1.40 AB: A, B=C, O, N: 1.401.50 A=B: A, B =C,O,N: 1.201.30 AB: A, B=C, N: 1.20 AB: A=C, B=S, P: 1.80 Angles around sp3-hybridized atoms: 110 Angles around sp2-hybridized atoms: 120 Angles around sp-hybridized atoms: 180 Torsional angles around sp3-hybridized atoms: separated by 120 Torsional angles around sp2-hybridized atoms: separated by 180 As an initial example, consider hydrogen peroxide. A Z-matrix for this structure would be: H O 1 0.9 O 2 1.4 1 105.0 H 3 0.9 2 105.0 1 120.0 The first line of the Z-matrix simply specifies hydrogen. The next line lists an oxygen atom and specifies the internuclear distance between it and the hydrogen as 0.9 Angstroms. The third line defines another oxygen with an O-O distance of 1.4 Angstroms (i.e., from atom 2, the other oxygen) and having an O-O-H angle (with atoms 2 and 1) of 105 degrees. The fourth and final line is the only one for which all three internal coordinates need be given. It defines the other hydrogen as bonded to 7

the second oxygen with an H-O distance of 0.9 Angstroms, an H-O-O angle of 105 degrees and a H-O-O-H dihedral angle of 120 degrees.

ZMATRIX -- CO2

C O 1 1.3000 O 1 1.3000

2 2 180 2

ZMATRIX -- NH3 (using simple angles only)

N1 H1 N1 1.0 H2 N1 1.0 H1 107 H3 N1 -1.0 H1 107 H2 107 Negative distance and one negative angle reverses the chirality ZMATRIX -- NH3 (using simple angles only; reversed chirality) N1 H1 N1 1.0 H2 N1 1.0 H1 107 H3 N1 -1.0 H1 -107 H2 107 8

Z matrix water

H O 1 OH H 2 OH 1 OHO OH = 1.08 OHO = 107.5

Ethylene

H C H C H H HC CC A1 D1 D2 1 2 2 4 4 = = = = = HC HC CC HC HC 1 3 2 2 A1 A1 1 D1 A1 1 D1 A1 1 D2

1.08 1.4 120.0 180.0 0.0

Software used in Chemistry

1. Alchemy : Alchemy 2000 is a G I (Graphic Interface) for running molecular mechanics and semi empirical calculations. 2. Chem 3D : Molecular modeling package for PC 3. Hyper Chem : Integrated G I , computational and visualization package. It works with every PC. 4. N W Chem : Program for molecular dynamics. ab initio, bad structure molecular mechanics and

5. Uni Chem : G I made for running calculation on remote mechines. 6. Chem Sketch & ACD softwares suit : Chem Sketch is a G I that is used for a 2D structure drawing siftware.

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