Semiempirical molecular orbital

Quantum-chemical calculations were carried out using the LabVision Software Package on a Silicon Graphics Iris Indigo workstation. The molecular orbital semiempirical method was performed using the AMI Hamiltonian. 

Stewart J J P 1991 Semiempirical molecular orbital methods Reviews in Computationai Chemistry vo 1, ed K B Lipkowitz and D B Boyd (New York VCH) pp 45-81... 

Thiel W 1996 Perspectives on semiempirical molecular orbital theory New Methods in Computationai Quantum Meohanios (Adv. Chem. Phys. XCiti) ed I Prigogine I and S A Rice (New York Wiley) pp 703-57 Earlier texts dealing with semi-empirical methods include ... 

The logical order in which to present molecular orbital calculations is ab initio, with no approximations, through semiempirical calculations with a restricted number of approximations, to Huckel molecular orbital calculations in which the approximations are numerous and severe. Mathematically, however, the best order of presentation is just the reverse, with the progression from simple to difficult methods being from Huckel methods to ab initio calculations. We shall take this order in the following pages so that the mathematical steps can be presented in a graded way. 

Semiempirical molecular orbital calculations have gone through many stages of refinement and elaboration since Pople s 1965 papers on CNDO. Programs like PM3, which is widely used in contemporary research, are the cumulative achievement of numerous authors including Michael Dewar (1977), Walter Thiel (1998), James Stewart (1990), and their coworkers. 

The cornerstone of semiempirical and ab initio molecular orbital methods is the Harhee equation and its extensions and variants, the Harhee-Fock and Roothaan-Hall equations. We have seen that the Hamiltonian for the hydrogen atom. 

Having the Slater atomic orbitals, the linear combination approximation to molecular orbitals, and the SCF method as applied to the Fock matrix, we are in a position to calculate properties of atoms and molecules ab initio, at the Hartree-Fock level of accuracy. Before doing that, however, we shall continue in the spirit of semiempirical calculations by postponing the ab initio method to Chapter 10 and invoking a rather sophisticated set of approximations and empirical substitutions... 

A basis set is a set of 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. Most semiempirical methods use a predehned basis set. When ah initio or density functional theory calculations are done, a basis set must be specihed. Although it is possible to create a basis set from scratch, most calculations are done using existing basis sets. The type of calculation performed and basis set chosen are the two biggest factors in determining the accuracy of results. This chapter discusses these standard basis sets and how to choose an appropriate one. 

Stewart, J.J.P. MOPAC A Semiempirical Molecular Orbital Program. J. Computer-Aided Molecular Design 4 1-105, 1990. 

Thermodynamic properties such as heats of reaction and heats of formation can be computed mote rehably by ab initio theory than by semiempirical MO methods (55). However, the Hterature of the method appropriate to the study should be carefully checked before a technique is selected. Finally, the role of computer graphics in evaluating quantum mechanical properties should not be overlooked. As seen in Figures 2—6, significant information can be conveyed with stick models or various surfaces with charge properties mapped onto them. Additionally, information about orbitals, such as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), which ate important sites of reactivity in electrophilic and nucleophilic reactions, can be plotted readily. Figure 7 shows representations of the HOMO and LUMO, respectively, for the antiulcer dmg Zantac. 

A particularly useful property of the PX monomer is its enthalpy of formation. Conventional means of obtaining this value, such as through its heat of combustion, are, of course, excluded by its reactivity. An experimental attempt was made to obtain this measure of chemical reactivity with the help of ion cyclotron resonance a value of 209 17 kJ/mol (50 4 kcal/mol) was obtained (10). Unfortunately, the technique suffers from lack of resolution in addition to experimental imprecision. It is perhaps better to rely on molecular orbital calculations for the formation enthalpy. Using a semiempirical molecular orbital technique, which is tuned to give good values for heat of formation on experimentally accessible compounds, the heat of formation of /5-xylylene has been computed to be 234.8 kj/mol (56.1 kcal/mol) (11). 

Theoretical Studies. Theoretical models for the Si(OR)4 hydrolysis, polycondensation, and dehydration reactions involved in sol—gel processes have been developed using semiempirical molecular orbital models. These have been reviewed (3,5). 

The type of conjugation is also reflected in the frontier orbital profile, the charge distribution, and the permanent dipole moments. The results of semiempirical calculations on l-methylpyridinium-3-olate (16), Malloapeltine (17), Trigollenine (18), and Homarine (19) are presented in Scheme 7. Characteristically for the class of conjugated mesomeric betaines, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are distributed over the entire molecule as examplifled for l-methylpyridinium-3-olate. It was shown that 90% of the... 

Semiempirical molecular orbital PM 3 calculations of the parent thiepin (Table 4) differ from the data of 2,7-di-fe/7-butylthiepin concerning the bow angle, probably reflecting the strong influence of the /erf-butyl groups.29... 

Data obtained by semiempirical molecular orbital PM 3 calculations. b Data obtained by X-ray structural analysis. 

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). 

Molecular orbital calculations, whether by ab initio or semiempirical methods, can be used to obtain structures (bond distances and angles), energies (such as heats of formation), dipole moments, ionization energies, and other properties of molecules, ions, and radicals—not only of stable ones, but also of those so unstable that these properties cannot be obtained from experimental measurements." Many of these calculations have been performed on transition states (p. 279) this is the only way to get this information, since transition states are not, in general, directly observable. Of course, it is not possible to check data obtained for unstable molecules and transition states against any experimental values, so that the reliability of the various MO methods for these cases is always a question. However, our confidence in them does increase when (1) different MO methods give similar results, and (2) a particular MO method works well for cases that can be checked against experimental methods. ... 

Even though molecular mechanics has given satisfactory results (i.e., results that agree with experimental measurements) for many molecules, it is still not totally reliable, since it does fail in certain cases. A further limitation is that it can be used only in cases for which transferable parameters can be obtained from simple molecules. Molecular orbital calculations do not have this limitation, but to some extent semiempirical MO methods do. 

Molecular orbital calculations for the parent vinyl cation, Cj H3, were first reported by Hoffmann (161), who used the extended Hiickel method, and more recently by Yonezawa and co-workers (162), who used a semiempirical SCF procedure. Both treated the problem of classical, 172 (R = H), versus bridged structures, 173, but the methods suffered from their inability to account satisfactorily for bond-length changes, and neither discussed the question of linear, 172a, versus bent, 172b, structures. 

It is not intended that the equations of this study be used to supplant the much more elegant molecular orbital calculations, both semiempirical and ab initio, and the mechanical modeling studies of radical forming reactions. However, it may be possible to make some hypotheses about differences in mechanisms between reaction families, based on the values of the slopes in Table IV. The slopes could be considered "sensitivity factors" (like rho values) for measuring the relative magnitude of transition state effects (U) and reactant state effects (N) on the rates of the four reactions of this study. 

Stewart HP. MOPAC A semiempirical molecular orbital program. J Computer-Aided Mol Des 1990 4 1-105. 

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. 

Molecular Orbital Electronegativity as Electron Chemical Potential in Semiempirical SCF Schemes... 

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. 

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