Chemical bonds, molecular mechanical treatment

The classical treatment for the quantitative determination of the steric effects operative in molecules was developed by Westheimer. Steric effects were considered as the sum of various independent strain producing mechanisms (bond strain, angle strain, torsional strain, non-bonded interaction strain). Westheimer s assumptions proved to be the fundamental basis for the BIGSTRN program as well as for all subsequent molecular mechanics treatments of neutral hydrocarbons and carbocations. Reactivities ranging over 10 ° could be correlated by the strain differences between cation and the neutral precursor. Gleicher and Schleyer s work was a historical breakthrough in the development of molecular mechanics and provided the basis for the predictions of rate constants of solvolysis reactions. For the first time chemical reactions could reliably be predicted by the means of computational chemistry. 

The harmonic oscillator is an important system in the study of physical phenomena in both classical and quantum mechanics. Classically, the harmonic oscillator describes the mechanical behavior of a spring and, by analogy, other phenomena such as the oscillations of charge flow in an electric circuit, the vibrations of sound-wave and light-wave generators, and oscillatory chemical reactions. The quantum-mechanical treatment of the harmonic oscillator may be applied to the vibrations of molecular bonds and has many other applications in quantum physics and held theory. 

To make QM studies of chemical reactions in the condensed phase computationally more feasible combined quantum me-chanical/molecular mechanical (QM/MM) methods have been developed. The idea of combined QM/MM methods, introduced first by Levitt and Warshell [17] in 1976, is to divide the system into a part which is treated accurately by means of quantum mechanics and a part whose properties are approximated by use of QM methods (Fig. 5.1). Typically, QM methods are used to describe chemical processes in which bonds are broken and formed, or electron-transfer and excitation processes, which cannot be treated with MM methods. Combined QM and MM methods have been extensively used to study chemical reactions in solution and the mechanisms of enzyme-catalyzed reactions. When the system is partitioned into the QM and MM parts it is assumed that the process requiring QM treatment is localized in that region. The MM methods are then used to approximate the effects of the environment on the QM part of the system, which, via steric and electrostatic interactions, can be substantial. The... 

A rigorous mathematical formalism of chemical bonding is possible only through the quantum mechanical treatment of molecules. However, obtaining analytical solutions for the Schrodinger wave equation is not possible even for the simplest systems with more than one electron and as a result attempts have been made to obtain approximate solutions a series of approximations have been introduced. As a first step, the Bom-Oppenheimer approximation has been invoked, which allows us to treat the electronic and nuclear motions separately. In solving the electronic part, mainly two formalisms, VB and molecular orbital (MO), have been in use and they are described below. Both are wave function-based methods. The wave function T is the fundamental descriptor in quantum mechanics but it is not physically measurable. The squared value of the wave function T 2dT represents probability of finding an electron in the volume element dr. 

The contributions of Erich Hiickel to the development of molecular orbital theory have already been mentioned in the subsection on Germany (Section 5.4.1) the development of semi-empirical quantum mechanical treatments in organic chemistry by M. J. S. Dewar has been discussed in Section 5.5. In the early development of the application of quantum mechanics to chemistry, Linus Pauling (1901-1994)359 was pre-eminent. He was associated with CalTech for most of his career. His work before World War II generated two influential books the Introduction to Quantum Mechanics (with E. Bright Wilson, 1935)360 and The Nature of the Chemical Bond (1939).361 He favoured the valence-bond treatment and the theory of resonance. 

We now turn from the use of quantum mechanics and its description of the atom to an elementary description of molecules. Although most of the discussion of bonding in this book uses the molecular orbital approach to chemical bonding, simpler methods that provide approximate pictures of the overall shapes and polarities of molecules are also very useful. This chapter provides an overview of Lewis dot structures, valence shell electron pair repulsion (VSEPR), and related topics. The molecular orbital descriptions of some of the same molecules are presented in Chapter 5 and later chapters, but the ideas of this chapter provide a starting point for that more modem treatment. General chemistry texts include discussions of most of these topics this chapter provides a review for those who have not used them recently. 

One might imagine that, with the advent of quantum mechanics and its application to chemistry, Dalton s atomic theory would have been reinforced. This has not happened. Quantum mechanics has been shown to account for the properties of isolated atoms and for the total properties of a molecular system. The increased understanding that would result from the discovery of a firm theoretical basis for Dalton s theory has not been obtained because of the lack of a quantum definition of an atom in a molecule. This is not to say that the concepts of atoms,and bonds do not appear in the quantum mechanical treatments of chemical systems. They do, but in the reverse manner to that described above. Rather than finding its quantum basis, the... 

The theory of the chemical bond is one of the clearest and most informative examples of an explanatory phenomenon that probably occurs in some form or other in many sciences (psychology comes to mind) the semiautonomous, nonfundamental, fundamentally based, approximate theory (S ANFFBAT for short). Chemical bonding is fundamentally a quantum mechanical phenomenon, yet for all but the simplest chemical systems, a purely quantum mechanical treatment of the molecule is infeasible especially prior to recent computational developments, one could not write down the correct Hamiltonian and solve the Schrodinger equation, even with numerical methods. Immediately after the introduction of the quantum theory, systems of approximation began to appear. The Born Oppenheimer approximation assumed that nuclei are fixed in position the LCAO method assumed that the position wave functions for electrons in molecules are linear combinations of electronic wave functions for the component atoms in isolation. Molecular orbital theory assumed a characteristic set of position wave functions for the several electrons in a molecule, systematically related to corresponding atomic wave functions. 

The EVB method proposed by Warshel [6] is an elegant and computationally very efficient method of describing the entire BO surface, thus allowing treatment of chemical reactions such as proton transfer in hydrogen bonds. It can also be used in vibrational analysis. In conjunction with the environment described at the molecular mechanics level it was the first QM/MM method. Vibrational analyses of hydrogen bonded systems and of enzymatic catalysis have a lot in common. 

The more recent treatment of the covalent bond, based on the application of the principles of wave mechanics, has developed in two distinct forms, usually termed the valence-bond and molecular-orbital theories, respectively. Although ultimately there is no inconsistency between these two theories, they do in fact approach the problem of chemical binding from different points of view, and we shall generally find that for our purposes the valence-bond treatment is the more suitable. This theory starts from concepts already familiar to the chemist and its conclusions can usually be expressed verbally in qualitative terms the molecular-orbital theory, on the other hand, is more mathematical in its approach and lends itself less readily to such an interpretation. We shall, therefore, first discuss the valency-bond theory, and refer only briefly to the molecular-orbital treatment later in the chapter. 

These simple ideas were formulated before the advent of wave mechanics. Quantum theory not only justifies their use but enables us to refine and extend them. In attempting quantitative quantum-mechanical treatment of chemical bonds, approximations must be made. Traditionally, there have been two broad groups of approximations, called the valence bond (VB) and the molecular orbital (MO) treatments. The former is essentially a direct attempt to invest the qualitative ideas just outlined with quantum-mechanical validity, and it is therefore logical to continue the discussion with a summary of the valence-bond formalism, including such concepts as resonance, valence states and hybridization that arise within this framework. The molecular-orbital formalism will be presented in a following Section. 

The hydrogen molecule H2 is the simplest molecule which forms an electron-pair bond. Many calculations have been made for this molecule, which is a prototype for many other chemical bonds. One of the two basic quantum-mechanical treatments of the hydrogen molecule involves constructing a molecular orbital for the bond from a linear combination of atomic orbitals (LCAO method). The other involves constructing the molecular orbital as the product of wave functions for each of the two electrons forming the bond. Both of these methods will be outlined. 

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