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introduction to the computational methods such as Ab-initio and HF

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In describing the electron distribution in detail quantum mechanics is the best method (since electrons are very light particles). The time-independent Schrödinger 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 Schrödinger equation is the Born–Oppenheimer 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 Hartree–Fock (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 AO’s or the basis functions. Since the eclectrons are indistinguishable fermions (spin with ½), 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 Mo’s. 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 α and β 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 α and β 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

The H-F methods scale N4. the electron correlation must be inluded. In practice.e. Since the other electrons are described by their respective orbitals.e. RHF wave functions are used for singlets because the calculation takes less CPU time.. extremely accurate solutions are only obtainable when the molecule contains a dozen electrons or less. 2 . and coupled cluster theory (CC). ROHF is primarily used for cases where spin contamination is large using UHF. where the attraction to all the nuclei and the average repulsion to all the other electrons are included.Plesset perturbation theory (MPn. ozone) The shape of a given molecular orbital describes the probability of finding an electron. This repeat procedure is called Self-Consistent Field Procedure (SCF). the H-F equations must be solved repeatedly until the energy and orbital co efficient remain constant. Some of the methods that begin with a HF calculation and then correct for correlation are Moller. memory and disk space. a singlet molecule has biradical resonance structures and UHF will give a better description of the molecule (i. i. configuration interaction (CI).Fcok) calculations give very good qualitative result and can yield increasingly accurate results as the molecule become smaller. 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. according to H-F theory.more CPU time to execute. Since the H-F method has limiting accuracy. ADVANTAGE & DISADVATAGE In general ab inito (or Hatree. Including correlation generally improves the accuracy of the computed energy and molecular geometry. The disadvantage of ab initio method is that they are very expensive and take enormous amount of CPU time.. CORRELATION One of the limitation if HF calculation is that they do not include electron correlation. RHF and UHF wave functions are almost always identical. The advantage of ab ignition method is that they really bring together the exact solution once all approximations are made sufficiently small in magnitude. multi-configurational self-consistent field (MCSCF). where N id the basis functions. the generalized valence bond (GVB) method. For singlet spin molecules at the equilibrium geometry. where n is the order of correction). In a few rare cases.

The Semiempirical methods reduce the computational cost by approximating or omitting certain information such as two electron integrals. This repeat procedure is called a selfconsistent field procedure (SCF). There are two techniques for constructing HF wave functions of molecules with unpaired electrons.Semi empirical methods The semi empirical methods are derived from ab initio method. One technique is to use two completely separate sets of orbitals for the α and β electrons. then the same orbital spatial function can be used for both the α and β spin electrons. the H-F equations must be solved repeatedly until the energies and orbital coefficients remain constant. . Semi empirical calculations have been very successful in the description of organic chemistry. exponential functions). The ab initio methods often take enormous amounts of CPU time. py and pz). This is called the Restricted Hartree Fock method (RHF). If the molecule being computed is significantly different from anything in the parameterization set. If the molecule being computed is similar to molecules in the data base used to parameterize the method. However the accuracy of H-F calculation is very poor. This means that paired electrons will not have the same spatial distribution. and the basis functions are taken to be Slater type orbitals (i. Only a minimum basis set is used for the valence electrons. and disk space and the cost of performing these methods is in the order of fourth power of basis functions (N4). This is called an Unrestricted Hartree-Fock wave function (UHF). Self Consistent Field In a Hartre-Fock calculation the many electron Schrodinger equation is broken down to single electron equations. The disadvantage of semiempirical calculations is that the results can be less acurate.and p functions.e. The advantage of semiempirical calculations is that they are much faster than the ab initio calculations. In order to correct for the errors introduced by omitting part of the calculation. This introduces an error 3 . The HF procedure can be varied in such a way that the orbitals are constructed to reflect paired or unpaired electrons. the answers may be very poor. Each electron is described by a single electron wave function called ‘Orbital’. 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. The large majority of semi-empirical methods use only s. Since each electron is described by their respective orbitals. the method is parameterized in order to give the best possible agreement with experimental data. where there are only a few elements used extensively and the molecules are of moderate size. memory. The central assumption of semi-empirical methods is the Zero Differential Overlap (ZDO) approximation. If the molecule has a singlet spin. then the results may be very good. 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. Hydrogen thus has one basis function.

called spin contamination. RHF wave functions are used for singlets because the calculation takes less CPU time. at least for 1s. The ROHF technique is more difficult to implement than UHF and may require slightly more CPU time to execute. such as very high activation energies. Molecular orbitals and entire wave functions are created by taking linear combinations of basis functions and angular functions. AO’s are represented by the atom centered Gaussian in most quantum chemistry programs.into the calculation. rather than two H atoms. Hence 2s and 2p orbitals cannot be computed by STO methods. The type of calculations performed and basis set chosen are the te biggest factors in determining the accuracy of the results. a series of RHF calculations for H2 with successively longer bond lengths will show that H2 dissociates into H+ and H-. ozone) The RHF scheme results in forcing electrons to remain paired. a singlet molecule has biradical resonance structures and UHF will give a better description of the molecule (i. Most semiempirical methods use a predefined basis set. An “orbital” is a one-electron function. they lack radial nodes and are not pure spherical harmonics. UHF calculations are popular because they are easy to implement and run fairly efficiently. even though it is made of CGTO {Contracted Gaussian-Type Orbitals (CGTO’s)}] 4 . however. In a few rare cases. the paired electrons share the same spatial orbital.e. RHF and UHF wave functions are almost always identical. bond lengths slightly too short. The advantage of using STO methods is the correct short-range and long-range behavior. This is responsible for certain systematic errors in HF results. STO’s are more accurate. there is no spin contamination. Some older programs use Slater functions. For example. thus. vibrational frequencies too high. In this method. ROHF is primarily used for cases where spin contamination is large using UHF. Another way of constructing wave functions for open-shell molecules is the restricted open shell Hartree-Fock method (ROHF). 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. Basis sets The “basis set” usually refers to the set of non orthogonal. Use of a linear combination of enough GTO’s mimics an STO and are often called an “STO-nG” basis. and dipole moments and atomic charges that are too large. This means that the calculation will fail to reflect cases where the electrons should uncouple. but it takes longer to compute integrals using them. For singlet spin molecules at the equilibrium geometry. one-particle functions used to describe the shape of the orbitals in an atom.. UHF wave functions usually dissociate correctly. [Slater-Type Orbitals (STO’s): These are H-atom-like.

Furthermore. The simplest is called the Xα method. This original theorem applied only to find the ground-state electronic energy of a molecule. called a local density approximation (LDA). Thus DFT. the electron density is expressed as a linear combination of basis functions similar in mathematical form to HF orbitals. Density functionals can be broken down into several classes. This result in faster calculations than HF calculations (which scale as N4) and computations that is a bit more accurate as well. The Xα method is similar in accuracy to HF and sometimes better. scales as N3. but provides significantly better results. A functional is a function of a function. called Kohn-Sham orbitals. this is called the local spin density approximation (LSDA). A determinant is then formed from these functions.DFT(Density Functional Theory) Density Functional Theory (DFT) can be considered as an improvement on HF theory. The simplest approximation to the complete problem is one based only on the electron density. 5 . the electron density. It is the electron density from this determinant of orbitals that is used to compute the energy. they do describe the behavior of electrons in a molecule. which is a three-dimensional function. For high-spin systems. A density functional is used to obtain the energy for the electron density. A practical application of this theory was developed by Kohn and Sham who formulated a method similar in structure to the Hartree-Fock method. It is comparable to HF computationally. The advantage of using electron density is that the integrals for Coulomb repulsion need be done only over the electron density. at least some electron correlation can be included in the calculation. Some of these functionals were developed from fundamental quantum mechanics and some were developed by parameterizing functions to best reproduce experimental results. in this case. Even though Kohn – Sham determinant is not mathematically equivalent to HF. In this formulation. DFT is an independent-particle model just like H-F. The basic assumption behind DFT is that the energy of a molecule can be determined from the electron density instead of a wave function. where the many-body effect of electron correlation is modeled by a function of the electron density. LDA calculations have been widely used for band structure calculations. This procedure is necessary because Fermion systems can only have electron densities that arise from an ant symmetric wave function. LDA is known to give less accurate geometries and predicts binding energies significantly too large. This type of calculation includes electron exchange but not correlation.

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

the algorithm does the job of constructing a sort of Z-matrix that has more coordinates than are necessary to specify the geometry completely. and an angle to the other atom. The first three atoms. N: 1. The third line defines another oxygen with an O-O distance of 1. an angle and a torsional angle to uniquely specify the position. The next line lists an oxygen atom and specifies the internuclear distance between it and the hydrogen as 0. All subsequent atoms need a distance.e. A=S. Any numbering will result in a valid Z-matrix. 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. N: 1. an angle and a torsional angle relative to other atoms.00.4 1 105.30 A≡B: A.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. the other oxygen) and having an O-O-H angle (with atoms 2 and 1) of 105 degrees. B =C. P: 1.0 The first line of the Z-matrix simply specifies hydrogen. The third atom is specified by a distance to either atom 1 or 2.40–1.4 Angstroms (i.20 A—B: A=C.N: 1.0 H 3 0.9 Angstroms. however. are slightly different. The fourth and final line is the only one for which all three internal coordinates need be given. B=S.9 2 105.50 A=B: A. 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. This way.0 1 120.O. Some typical bond lengths (Å) and angles are given below. B=C. B=C. consider hydrogen peroxide. A=O. The Z-matrix specifies the position of each atom in terms of a distance. A—H: where A=C: 1. It defines the other hydrogen as bonded to 7 . N: 1. from atom 2.10.40 A—B: A.20–1. The first atom is always positioned at the origin of the coordinate system. This is usually the most efficient way to optimize geometry. O. 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).atom distances and angles for nearby atoms. The atoms are normally identified either by the chemical symbol or by their atomic number. A Z-matrix for this structure would be: H O 1 0..9 O 2 1. Constructing a Z-Matrix Construction of a Z-matrix begins with a drawing of the molecule and a suitable numbering of the atoms.P: 1.

0 H2 N1 1.0 H1 107 H2 107 Negative distance and one negative angle reverses the chirality ZMATRIX -.9 Angstroms.the second oxygen with an H-O distance of 0.0 H1 -107 H2 107 8 .3000 O 1 1.NH3 (using simple angles only.0 H1 107 H3 N1 -1. ZMATRIX -. an H-O-O angle of 105 degrees and a H-O-O-H dihedral angle of 120 degrees.NH3 (using simple angles only) N1 H1 N1 1.CO2 C O 1 1. reversed chirality) N1 H1 N1 1.0 H2 N1 1.3000 2 2 180 2 ZMATRIX -.0 H1 107 H3 N1 -1.

08 OHO = 107.Z matrix – water H O 1 OH H 2 OH 1 OHO OH = 1.5 Ethylene 9 .

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. 6.4 120. Alchemy : Alchemy 2000 is a G I (Graphic Interface) for running molecular mechanics and semi empirical calculations. N W Chem : Program for molecular dynamics.0 180. 4. 10 . computational and visualization package. Chem Sketch & ACD softwares suit : Chem Sketch is a G I that is used for a 2D structure drawing siftware. ab initio. 2. Hyper Chem : Integrated G I .0 Software used in Chemistry 1. Chem 3D : Molecular modeling package for PC 3.08 1. It works with every PC. Uni Chem : G I made for running calculation on remote mechines. bad – structure molecular mechanics and 5.0 0.

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