Semiempirical molecular orbital theory applications

Li, J. Cramer, and Truhlar, D. G. 1999. Application of a Universal Solvation Model to Nucleic Acid Bases. Comparison of Semiempirical Molecular Orbital Theory, Ab Initio, Hartree-Fock Theory, and Density Functional Theory , Biophys. Chem.. 78, 147. 

One way to keep the cost of the calculations low but improve the accuracy is to use semiempirical molecular orbital calculations in which some of the parameters are fit to data for the specific reaction of interest or for a limited range of reactions. We call this approach SRP for specific reaction parameters or specific range parameters. In several applications we have combined the SRP approach with semiempirical molecular orbital theory employing the neglect of diatomic differential overlap (NDDO) approximation. This is called the NDDO-SRP approach [49]. 

M. M. Karelson, T. Tamm, A. R. Katritzky, S. J. Cato, and M. C. Zerner, Tetrahedron Comput. Methodol., 2, 295 (1989). Molecular Orbital Calculations Applicable to Condensed Phases The Combination of Self-Consistent Reaction Field Theory with Semiempirical Quantum Chemical Models. 

The application of molecular orbital theory to predict structures and properties of C species started with the pioneering work of Pitzer and dementi in 1959 [225]. By using semiempirical MO theory, these authors found the cumulenic linear conformation to be the most stable geometry for except possibly for very large values of n. They predicted that the n-odd clusters would have closed-shell structures and lower energies than the singlet n-even species. Cyclic molecules were found to be unimportant under most conditions. 

Transition States in Organic Reacrions. General Theory and an Application to the Cyclobutene-Butadiene Isomerization Using a Semiempirical Molecular Orbital Method. 

Ab initio and semiempirical computational methods have proved extremely useful. But also needed is a simple conceptual scheme that enables one to predict the broad outlines of a calculation in advance, or else to rationalize a coii5)uted result in a fairly simple way. Chemistry requires conceptual schemes, simple enough to carry around in one s head, with which new information can be evaluated and related to other information. Such a theory has developed alongside the mathematical methods described in earlier chapters. We shall refer to it as qualitative molecular orbital theory (QMOT). In this chapter we describe selected aspects of this many-faceted subject and illustrate QMOT applications to questions of molecular shape and conformation, and reaction stereochemistry. 

J. W, Mclver, Jr. and A. Komornicki, Structure of transition states in organic reactions. General theory and its application to the cyclobutene-butadiene isomerization using a semiempirical molecular orbital method, J. Amer. Chem. Soc. 94 2615 (1972). 

Molecular orbital calculations (ah initio or semiempirical methods) are also often used to provide a description of radical species and their reactions. High levels of theory are required to provide reliable data. However, rapid advances in computer power and computational methods are seeing these methods more widely used and with greater success (for leading references on the application of theory to describe radical addition reactions, see Section 1.2.7). 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

A key question about the use of any molecular theory or computer simulation is whether the intermolecular potential model is sufficiently accurate for the particular application of interest. For such simple fluids as argon or methane, we have accurate pair potentials with which we can calculate a wide variety of physical properties with good accuracy. For more complex polyatomic molecules, two approaches exist. The first is a full ab initio molecular orbital calculation based on a solution to the Schrddinger equation, and the second is the semiempirical method, in which a combination of approximate quantum mechanical results and experimental data (second virial coefficients, scattering, transport coefficients, solid properties, etc.) is used to arrive at an approximate and simple expression. 

For some enzymes, for example many metalloenzymes, a semiempirical QM/MM treatment is inadequate due to the limitations of the semiempirical methods. In such situations, a more sophisticated level of QM treatment (such as ab initio molecular orbital or density-functional theory) may well be required. An recent example of the application of ab initio QM/MM techniques to an enzyme mechanism is a study of acetyl-CoA enolization in citrate synthase... 

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