The Basic Principles of Molecular Mechanics

This chapter explains the basic principles of molecular mechanics (MM), which rests on a view of molecules as balls held together by springs. MM began in the 1940s with attempts to analyze the rates of racemization of biphenyls and of SN2 reactions. 

An excellent treatment of molecular quantum mechanics, on a level comparable to that of Szabo and Ostiund. The scope of this book is quite different, however, as it focuses mainly on the basic principles of quantum mechanics and the theoretical treatment of spectroscopy. 

Stereochemistry is not discussed in great detail, except in the context of the Woodward-Hoffmann rules. Molecular orbital theory is also given generally short shrift, again except in the context of the Woodward-Hoffmann rules. I have found that students must master the basic principles of drawing mechanisms before additional considerations such as stereochemistry and MO theory are loaded onto the edifice. Individual instructors might wish to put more emphasis on stere-oelectronic effects and the like as their tastes and their students abilities dictate. 

The chemistry of molecules consists of three major modules molecular architecture (structure) molecular dynamics (conformational analysis) and molecular transformation (chemical reactions). The molecular architecture consists of the basic principles of molecular structure and it deals with the atomic structure, orbitals, hybridization and bonding. Molecular dynamics deals with the molecular motion involving rotation around chemical bonds, steric interactions, torsional strain and properties associated with the conformational changes. Molecular transformation accounts for bond formation and bond breaking within the molecule or between molecules, which is generally called the chemical reaction, and consists of two major aspects, reaction mechanism and kinetics. The third module is one of the major areas of chemistry. This aims to understand the reaction mechanism and its manipulation to reduce the reaction barrier, improve stereoselectivity, increase product yield, or suppress undesirable side reactions. 

At the beginning of the twentieth century a general understanding of the origins of molecular spectra was achieved with the advent of the quantum theory. According to the basic principle of quantum mechanics, the energy associated... 

TTie CNDO/2 method [46] of Pople et al. was chosen for these types of studies because its computational simplicity allows the feasible consideration of large, complex, and conformationally mobile systems such as cyclodextrin host-guest systems. In contrast to ab initio methods, which seek to directly derive molecular properties from the basic principles of quantum mechanics, CNDO/2 is a semiempirical method, which means that not only are the expressions for wavefunctions simplified algebraically, but also that certain coefficients associated with the resulting approximate functions are arbitrarily assigned in order to duplicate experimental data. 

The purpose of this chapter is to provide an introduction to tlie basic framework of quantum mechanics, with an emphasis on aspects that are most relevant for the study of atoms and molecules. After siumnarizing the basic principles of the subject that represent required knowledge for all students of physical chemistry, the independent-particle approximation so important in molecular quantum mechanics is introduced. A significant effort is made to describe this approach in detail and to coimnunicate how it is used as a foundation for qualitative understanding and as a basis for more accurate treatments. Following this, the basic teclmiques used in accurate calculations that go beyond the independent-particle picture (variational method and perturbation theory) are described, with some attention given to how they are actually used in practical calculations. 

This book deals with the basic principles of asymmetric catalysis and places particular emphasis on its synthetic significance. The mechanisms of most of the chemical reactions that I will discuss are obscure and are therefore treated only briefly. My talks at Cornell relied heavily on chemistry developed in our laboratories at Nagoya University, and the materials in Chapters 2, 3, 5, and 6 are highly subjective. Because asymmetric synthesis with molecular catalysts is a very attractive and rich subject, many academic and industrial laboratories all over the world have contributed to its development. In an attempt to balance my coverage of the entire field, I have tried to include most of the major achievements recorded by the fall of 1992 within Chapter 4. 

The basic principles behind classical mechanics are quite familiar to most of these students. Almost all of them have used F = ma, or can understand that a charge going around in a circle is a current. It is easy to use only these concepts to prove that something is wrong with any classical interpretation of atomic and molecular structure. Quantum mechanics allows us to predict the structure of atoms and molecules in a manner which agrees extremely well with experimental evidence, but the intrinsic logic cannot be understood without equations. 

Molecular probes, such as optical or magnetic tweezers,64-71 micropipets,72 and microfibers,73-74 have been developed to manipulate single molecules and to measure their response to mechanical actions such as stretching, torsion, and compression. A force resolution down to 0.1 pN enabled quantitative measurement of the molecular forces and provided novel information on the basic principles of folding, motion, and interactions of individual molecules. Complementary to the local mechanical probes, actions of external fields were monitored on individual polymer molecules.75 77... 

Molecular mechanics (force field) calculation is the most commonly used type of calculation in computational medicinal chemistry, and a large number of different force fields have been developed over the years. The results of a molecular mechanics (MM) calculation are highly dependent on the functional forms of the potential energy functions of the force field and of the quality of their parameterization. Thus in order to obtain reliable computational results it is crucial that the merits and limitations of the various available force fields are taken into account. In this chapter, the basic principles of force-field calculations are reviewed, and a comparison of calculated and experimental conformational energies for a wide range of commonly used force fields is presented. As quantum mechanical (QM) methods have undergone a rapid development in the last decade, we have also undertaken a comparison of these force fields with some commonly employed QM methods. The chapter also includes a review of force fields with respect to their abilities to calculate intermolecular interactions. 

Each of these aspects of the field of chemistry is connected through the basic principle of chemical structure, which is a profound physical feature of the molecular world where we live. At its most fundamental, stereoelectronic structure is a quantum-mechanical reality of all molecules, with the intrinsic uncertainty that this reality implies. Thus, perfectly accurate structural descriptions of molecules are both elusive and potentially cumbersome. Instead, chemists have devised an exceptional model of molecular structure by inference. This model has been built over decades between evolving theory and experiments that measure various molecular properties that derive from structure itself. Closely aligned with our intuitive definition of structure , of course, are methods that provide direct information about... 

Two different approaches to the fabricating of nanostructures have been developed, so called top-down and bottom-up methods [11.5]. The basic principle of agglomeration, the attachment of small entities to similar ones or to other solid surfaces by binding mechanisms (Chapter 3) to form larger units, is used in bottom-up manufacturing. Nanoparticles, having at least one dimension of between 1 and 100 nm, are produced by processes that allow fundamental control over the physical and chemical attributes of molecular-scale structures and are then combined to form larger units with superior chemical, mechanical, electrical, or optical properties. 

Relativistic quantum chemistry is the relativistic formulation of quantum mechanics applied to many-electron systems, i.e., to atoms, molecules and solids. It combines the principles of Einstein s theory of special relativity, which have to be obeyed by any fundamental physical theory, with the basic rules of quantum mechanics. By construction, it represents the most fundamental theory of all molecular sciences, which describes matter by the action, interaction, and motion of the elementary particles of the theory. In this sense it is important for physicists, chemists, material scientists, and biologists with a molecular view of the world. It is important to note that the energy range relevant to the molecular sciences allows us to operate with a reduced and idealized set of "elementary" particles. "Elementary" to chemistry are atomic nuclei and electrons. In most cases, neither the structure of the nuclei nor the explicit description of photons is required for the theory of molecular processes. Of course, this elementary level is not always the most appropriate one if it comes to the investigation of very large nanometer-sized molecular systems. Nevertheless it has two very convenient features ... 

The above is a very simplified account of the chemiosmotic theory and a number of the details of oxidative phosphorylation remain to be elucidated, in particular the molecular mechanism of proton pumping and the exact mechanism of action of the ATPase. However, the basic principles of the theory are now widely accepted. This theory is also able to account for photosynthetic phosphorylation in chloroplasts and for the synthesis of ATP by bacteria. 

The basic principle of most Doppler-free techniques relies on a proper selection of a subgroup of molecules with velocity components v in the direction of the incident monochromatic wave, which fall into a small interval Av around v = 0. This selection can be achieved either by mechanical apertures which select a collimated molecular beam, or by selective saturation within the velocity distribution of absorbing molecules caused by a... 

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