Semi-empirical quantum mechanical methods

HyperChem uses two types of methods in calculations molecular mechanics and quantum mechanics. The quantum mechanics methods implemented in HyperChem include semi-empirical quantum mechanics method and ab initio quantum mechanics method. The molecular mechanics and semi-empirical quantum mechanics methods have several advantages over ab initio methods. Most importantly, these methods are fast. While this may not be important for small molecules, it is certainly important for biomolecules. Another advantage is that for specific and well-parameterized molecular systems, these methods can calculate values that are closer to experiment than lower level ab initio techniques. 

The accuracy of a molecular mechanics or semi-empirical quantum mechanics method depends on the database used to parameterize the method. This is true for the type of molecules and the physical and chemical data in the database. Frequently, these methods give the best results for a limited class of molecules or phenomena. A disadvantage of these methods is that you must have parameters available before running a calculation. Developing parameters is time-consuming. 

Semi-empirical quantum mechanics methods have evolved over the last three decades. Using today s microcomputers, they can produce meaningful, often quantitative, results for large molecular systems. The roots of the methods lie in the theory of % electrons, now largely superseded by all-valence electron theories. 

HyperChem can calculate transition structures with either semi-empirical quantum mechanics methods or the ab initio quantum mechanics method. A transition state search finds the maximum energy along a reaction coordinate on a potential energy surface. It locates the first-order saddle point that is, the structure with only one imaginary frequency, having one negative eigenvalue. 

HyperChem quantum mechanical calculations are ab initio and semi-empirical. Ab initio calculations use parameters (contracted basis functions) associated with shells, such as an s shell, sp shell, etc., or atomic numbers (atoms). Semi-empirical calculations use parameters associated with specific atomic numbers. The concept of atom types is not used in the conventional quantum mechanics methods. Semi-empirical quantum mechanics methods use a rigorous quantum mechanical formulation combined with the use of empirical parameters obtained from comparison with experiment. If parameters are available for the atoms of a given molecule, the ab initio and semi-empirical calculations have an a priori aspect when compared with a molecular mechanics calculation, letting... 

For small molecules, the accuracy of solutions to the Schrodinger equation competes with the accuracy of experimental results. However, these accurate ab initio calculations require enormous computation and are only suitable for the molecular systems with small or medium size. Ab initio calculations for very large molecules are beyond the realm of current computers, so HyperChem also supports semi-empirical quantum mechanics methods. Semi-empirical approximate solutions are appropriate and allow extensive chemical exploration. The inaccuracy of the approximations made in semi-empirical methods is offset to a degree by recourse to experimental data in defining the parameters of the method. Indeed, semi-empirical methods can sometimes be more accurate than some poorer ab initio methods, which require much longer computation times. 

Note The capping atoms are only supported in the semi-empirical quantum mechanics methods in HyperChem. If you want to use the mixed model in the ab mi/io method in HyperChem, you must select an entire molecule or molecules without any boundary atom between the selected and unselected regions and then carry out the calculation. 

An Introduction to the Theoretical Basis of Semi-Empirical Quantum-Mechanical Methods for Biological Chemists... 

Semi-empirical quantum-mechanical methods combine fundamental theoretical treatments of electronic behavior with parameters obtained from experiment to obtain approximate wavefunctions for molecules composed of hundreds of atoms20-22. Originally developed in response to the need to evaluate the electronic properties of organic molecules, especially those possessing unusual structures and/or chemical reactivity in organic chemistry,... 

BASIS OF SEMI-EMPIRICAL QUANTUM-MECHANICAL METHODS 13... 

The most difficult problem encountered in the design of semi-empirical quantum mechanical methods is the determination of a satisfactory way of calculating the two-center two-electron integrals. 

Conformational studies of diastereoisomeric alcohols of the 6,14-endo-ethenotetrahydrothebaine series, using a PCILO semi-empirical quantum-mechanical method, have been made in relation to the different agonist/ antagonist properties of the isomers.170 [N-Methyl-11 C]- and [N-methyl-14C]-morphine have been prepared.171,172... 

In this study, we have chosen the supermolecule approach and have used the semi-empirical quantum mechanical method called PCILO (Perturbative Configuration Interaction using Localized Orbitals) (16) to calculate intermolecular interactions. This method has recently been used successfully to calculate the intermolecular energies and geometries of hydrogen-bonded dimers of hydrocarbons and water (17,18). H-bonded complexes are particularly well characterized by this method (19). 

Carles and Van Assche (68,69) have proposed a dipeptide model for the herbicide binding site and have used the CNDO/s semi-empirical quantum mechanical method to study herbicide-dipeptide interactions. Two hydrogen bonds are important for the energetics of herbicide binding to the dipeptides. Coulombic isopotential maps were used as a guide to the way the herbicide molecules might interact with protein. 

The determination of the charge distribution in a molecule, needed here for the latter term, Ges, has been a considerable problem in force-field calculations, especially for transition metal compounds (see Sections 3.2.6 and 3.3.6). Most promising, but not yet fully tested for transition metal complexes, are semi-empirical quantum-mechanical methods [ 148,150]. Future studies might show whether a combination of approximate methods for the computation of charge distributions and solvation will lead to a reliable approximation of solvation parameters of coordination compounds. 

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