Computational chemistry semiempirical methods

A highly readable account of early efforts to apply the independent-particle approximation to problems of organic chemistry. Although more accurate computational methods have since been developed for treating all of the problems discussed in the text, its discussion of approximate Hartree-Fock (semiempirical) methods and their accuracy is still useful. Moreover, the view supplied about what was understood and what was not understood in physical organic chemistry three decades ago is... 

Stewart HP. Semiempirical molecular orbital methods. In Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry, Vol. 1. New York VCH, 1990. p. 45-81. 

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. 

Many other approaches for finding a correct structural model are possible. A short description of ab-initio, density functional, and semiempirical methods are included here. This information has been summarized from the paperback book Chemistry with Computation An Introduction to Spartan. The Spartan program is described in the Computer Software section below.65 Another description of computational chemistry including more mathematical treatments of quantum mechanical, molecular mechanical, and statistical mechanical methods is found in the Oxford Chemistry Primers volume Computational Chemistry,52... 

The continued success of the extended Hiickel method in transition metal chemistry, where it was the method of choice until the mid 1980 s is surely related to the problems of other semiempirical methods in this area of chemistry. While methods like MOP AC [21] or AMI [22] have been extremely productive in the field of organic chemistry, they have found little success in transition metal chemistry. These methods are based in equation 2, similar to 1, but with the very significant difference that the Fock matrix F is computed from the molecular orbitals, in an iterative way, though through an approximate formula. 

The semiempirical molecular orbital (MO) methods of quantum chemistry [1-12] are widely used in computational studies of large molecules. A number of such methods are available for calculating thermochemical properties of ground state molecules in the gas phase, including MNDO [13], MNDOC [14], MNDO/d [15-18], AMI [19], PM3 [20], SAMI [21,22], OM1 [23], OM2 [24,25] MINDO/3 [26], SINDOl [27,28], and MSINDO [29-31]. MNDO, AMI, and PM3 are widely distributed in a number of software packages, and they are probably the most popular semiempirical methods for thermochemical calculations. We shall therefore concentrate on these methods, but shall also address other NDDO-based approaches with orthogonalization corrections [23-25],... 

Stewart, J. J. P., Optimization of Parameters for Semiempirical Methods I. Method , J. Comput. Chemistry, 10, 209 (1989a). 

At the present time, it appears that the applicability of semiempirical methods to the study of carbohydrate chemistry has been neglected. Methods are now available for the non—theoretician to investigate molecular systems, reaction mechanisms, and fundamental physical properties, without the need for any extensive knowledge of theoretical methods. Despite this, most computational studies appear to be limited to the use of molecular mechanics techniques. 

Thiel, W. 2000. Semiempirical Methods in Modern Methods and Algorithms of Quantum Chemistry, Proceedings, 2nd Edn., Grotendorst, J., Ed., NIC Series, Vol. 3, John von Neumann Institute for Computing Jiilich, 261. 

Ab initio and semiempirical methods have been applied to the interpretation of many aspects of dithiolene chemistry electronic spectra, ESR, Mossbauer, XPS, charge distributions, redox properties, reaction mechanisms, metal binding in biological systems and ligand-exchange behavior. We shall focus our attention on the theoretical deductions of some representative research groups. For computational details, the reader is referred to the original papers and references therein. 

Abstract You can calculate molecular geometries, rates and equilibria, spectra, and other physical properties. The tools of computational chemistry are molecular mechanics, ab initio, semiempirical and density functional methods, and molecular dynamics. Computational chemistry is widely used in the pharmaceutical industry to explore the interactions of potential drugs with biomolecules, for example by docking a candidate drug into the active site of an enzyme. It is also used to investigate the properties of solids (e.g. plastics) in materials science. It does not replace experiment, which remains the final arbiter of truth about Nature. 

The quantum mechanical methods described in this book are all molecular orbital (MO) methods, or oriented toward the molecular orbital approach ab initio and semiempirical methods use the MO method, and density functional methods are oriented toward the MO approach. There is another approach to applying the Schrodinger equation to chemistry, namely the valence bond method. Basically the MO method allows atomic orbitals to interact to create the molecular orbitals of a molecule, and does not focus on individual bonds as shown in conventional structural formulas. The VB method, on the other hand, takes the molecule, mathematically, as a sum (linear combination) of structures each of which corresponds to a structural formula with a certain pairing of electrons [16]. The MO method explains in a relatively simple way phenomena that can be understood only with difficulty using the VB method, like the triplet nature of dioxygen or the fact that benzene is aromatic but cyclobutadiene is not [17]. With the application of computers to quantum chemistry the MO method almost eclipsed the VB approach, but the latter has in recent years made a limited comeback [18],... 

Nowadays chemists do not worry much about the virtues of semiempirical versus ab initio methods. Ab initio methods, it must be conceded, dominate computational chemistry studies in the leading journals, and indeed the study of... 

---