Theory and Method

L. A. Gribov, W. J. Orville-Thomas, Theory and Methods of Calculation of Molecular Spectra, Wdey, Chichester, 1988. 

Choose the atoms of interest for the sem i-empirical calculation, then use the Bctend to sp option on the. Select menu to establish the appropriate atomic boundaries for the c uantnm mechanics calculation. TTyperChem substitutes pararmeteri/ed pseudo-fluorine atom s for th e portion s of the molecule n ot included directly in the calculation (see the second part of this book, Theory and Methods). 

I h c Hiickel eon stari t (k) scales Ih e in teraetiou energy between two atomic orbitals (see Kxtended Hiickel Method on page 125). HyperChem uses the defatill value of 1.75 (see the second part of th is book. Theory and Methods). You shoti Id tise th is value for m ost eases, A suggested ran ge for experimcri tal adjiistmen L of th is eon -stant is 1,6 2,0.- ... 

HyperChem Computational Chemistry contains two parts. Part 1, the Practical Guide, contains an overview and introduction to the types of calculations that you can perform with HyperChem . Part 2, Theory and Methods, provides detailed information on the specific implementation of calculations in HyperChem. 

Theory and Methods includes the equations, analytical descriptions, and data you need to understand the calculations. It deals with the science behind HyperChem calculations. Information on parameters and settings lets you modify and customize calculations. 

This discussion focuses on the individual components of a typical molecular mechanics force field. It illustrates the mathematical functions used, why those functions are chosen, and the circumstances under which the functions become poor approximations. Part 2 of this book. Theory and Methods, includes details on the implementation of the MM-t, AMBER, BlO-t, and OPES force fields in HyperChem. 

HyperChem supplements the standard MM2 force field (see References on page 106) by providing additional parameters (force constants) using two alternative schemes (see the second part of this book. Theory and Methods). This extends the range of chemical compounds that MM-t can accommodate. MM-t also provides cutoffs for calculating nonbonded interactions and periodic boundary conditions. 

Choose the region (single or multiple molecules) of interest for an ab initio calculation from the total molecular system. HyperChem performs the ab initio calculation for the selected region using the perturbation of an electrostatic potential arising from the net charges on the atoms of the un selected part. (For further details of this electrostatic potential perturbation implemented in HyperChem, please see the second part of this book. Theory and Methods). 

The theory and methods discussed in this book are HyperChem s two fundamental force-energy-generator modules one for molecular mechanics and one for quantum mechanics. Molecular mechanics and quantum mechanics are described in subsequent chapters as modules capable of delivering an energy, or derivatives of the energy. Other chapters describe the uses for these energies and their derivatives in more generic parts of HyperChem. 

A. Watts, T. J. VanderNoot. The electrical double layer at hquid-hquid interfaces. In A. G. Volkov, D. W. Deamer, eds. Liquid-Liquid Interfaces. Theory and Methods. Boca Raton CRC Press, 1996, pp. 77-102. 

T. C. Farrar, E. D. Becker, Pulse and Fourier Transform NMR. Introduction to Theory and Methods, Academic Press, New York, 1971. 

Limbird, L. E. (1995). Cell surface receptors A short course on theory and methods. Martinns Nihjoff, Boston. 

I. M. Klotz and R. M. Rosenburg, Chemical Thermodynamics Basic Theory and Methods, W. A. Benjamin Inc. Menlo Park, California. 1972, p. 276. 

James R. Holton. An Introduction to Dynamic Meteorology, Third Edition. 1992 Alexander A. Kaufman. Geophysical Field Theory and Method. 

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