Molecular modelling semi-empirical methods

In this section, the conceptual framework of molecular orbital theory is developed. Applications are presented and problems are given and solved within qualitative and semi-empirical models of electronic structure. Ab Initio approaches to these same matters, whose solutions require the use of digital computers, are treated later in Section 6. Semi-empirical methods, most of which also require access to a computer, are treated in this section and in Appendix F. 

The algorithms of the mixed classical-quantum model used in HyperChem are different for semi-empirical and ab mi/io methods. The semi-empirical methods in HyperChem treat boundary atoms (atoms that are used to terminate a subset quantum mechanical region inside a single molecule) as specially parameterized pseudofluorine atoms. However, HyperChem will not carry on mixed model calculations, using ab initio quantum mechanical methods, if there are any boundary atoms in the molecular system. Thus, if you would like to compute a wavefunction for only a portion of a molecular system using ab initio methods, you must select single or multiple isolated molecules as your selected quantum mechanical region, without any boundary atoms. 

Semi-empirical methods, such as those implemented in the MOPAC [9] program, simplify the equations considerably by neglecting many terms, but then compensate for this by parameterising some of them so that the calculations reproduce experimental information on, for example, the heat of formation. Once the various approximations are made, the molecular properties to which the parameters are fitted, and the molecules used in the fitting, define a model Hamiltonian, of which the most commonly used are the AMI and the PM3 Hamiltonians found in MOPAC. A major advantage of semi-empirical methods is... 

The second problem also reflects the exceptional difficulty of exploring complex conformational energy surfaces. Quite simply, only the lowest-cost methods are applicable to anything but molecules with only a few degrees of conformational freedom. In practice and at the present time, this translates to molecular mechanics models. (Semi-empirical quantum chemical models might also represent practical alternatives, except for the fact that they perform poorly in this role.) Whereas molecular mechanics models such as MMFF seem to perform quite well, the fact of the matter is, outside the range of their explicit parameterization, their performance is uncertain at best. 

Various theoretical methods and approaches have been used to model properties and reactivities of metalloporphyrins. They range from the early use of qualitative molecular orbital diagrams (24,25), linear combination of atomic orbitals to yield molecular orbitals (LCAO-MO) calculations (26-30), molecular mechanics (31,32) and semi-empirical methods (33-35), and self-consistent field method (SCF) calculations (36-43) to the methods commonly used nowadays (molecular dynamic simulations (31,44,45), density functional theory (DFT) (35,46-49), Moller-Plesset perturbation theory ( ) (50-53), configuration interaction (Cl) (35,42,54-56), coupled cluster (CC) (57,58), and CASSCF/CASPT2 (59-63)). 

The construction of exchange correlation potentials and energies becomes a task for which not much guidance can be obtained from fundamental theory. The form of dependence on the electron density is generally not known and can only to a limited extent be obtained from theoretical considerations. The best one can do is to assume some functional dependence on the density with parameters to satisfy some consistency criteria and to fit calculated results to some model systems for which applications of proper quantum mechanical theory can be used as comparisons. At best this results in some form of ad-hoc semi-empirical method, which may be used with success for simulations of molecular ground state properties, but is certainly not universal. 

Before any computational study on molecular properties can be carried out, a molecular model needs to be established. It can be based on an appropriate crystal structure or derived using any other technique that can produce a valid model for a given compound, whether or not it has been prepared. Molecular mechanics is one such technique and, primarily for reasons of computational simplicity and efficiency, it is the most widely used. Quantum mechanical modeling of metal complexes with ab-initio or semi-empirical methods often remains prohibitive because these methods are so computationally intensive. The approximations that are introduced in order to reduce central processing unit (CPU) time and allow quantum mechanical calculations to be used routinely are often severe and such calculations are then less reliable. 

The effect of induced dipoles in the medium adds an extra term to the molecular Hamilton operator. = -r R (16.49) where r is the dipole moment operator (i.e. the position vector). R is proportional to the molecular dipole moment, with the proportional constant depending on the radius of the originally implemented for semi-empirical methods, but has recently also been used in connection with ab initio methods." Two other widely available method, the AMl-SMx and PM3-SMX models have atomic parameters for fitting the cavity/dispersion energy (eq. (16.43)), and are specifically parameterized in connection with AMI and PM3 (Section 3.10.2). The generalized Bom model has also been used in connection with force field methods in the Generalized Bom/Surface Area (GB/SA) model. In this case the Coulomb interactions between the partial charges (eq. (2.19)) are combined... 

By considering the respective molecular size of both entities which are present in the inclusion complexes, it is possible to propose a reasonable model for the structure of these inclusion complexes [18,21,22]. This model was obtained by means of simple calculations of the BPHT molecular structure, based on the AMI semi-empirical method. 

As the name implies, semi-empirical calculations simplify the computational problem presented by the Schrodinger equation. Semi-empirical approaches eliminate some of the direct number crunching involved in ab initio calculations and instead replace portions of the calculation with values that may be taken from experimental data or other calculations that are parameterized to agree with empirical data. There is a variety of semi-empirical schemes that differ in the types of parameterizations that are made. Three common semi-empirical methods that are included in Spartan02 are called AMI, PM3, and MNDO. Each has strengths and weaknesses depending on the specific molecular environment one wishes to model. 

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