Molecular structure approach chemistry physics

Poly(p-pheny lene)s, PPPs, constitute the prototype of rigid-rod polymers and are currently being intensively investigated [1]. The key role of PPPs follows from their conceptually simple and appealing molecular structure, from their chemical stability, and from their superior physical properties [2], In turn, this is the result of important advances made in aromatic chemistry over the last few years. The following section gives an overview of the most common methods to generate poly(p-phenylene)s via different synthetic approaches. 

A good deal of this work had no impact in the development of models of molecular structure and the elucidation of reaction mechanisms one reason was Perrin s own coolness to quantum wave mechanics. 108 Another, according to Oxford s Harold Thompson, who studied with Nernst and Fritz Haber, was that researchers like Lecomte "did not know enough chemistry he was a physicist." 109 Perrin, too, approached physical chemistry as a physicist, not as a chemist. He had little real interest or knowledge of organic chemistry. But what made his radiation hypothesis attractive to many chemists was his concern with transition states and the search for a scheme of pathways defining chemical kinetics. 

Theoretical approaches to structural biophysics, like the theories of transport and reaction kinetics explored in other chapters of this book, are grounded in physical chemistry concepts. Here we explore a few problems in molecular structural dynamics using those concepts. The first two systems presented, helix-coil transitions and actin polymerization, introduce classic theories. The material in the remainder of the chapter arises from the study of macromolecular interactions and is motivated by current research aimed at uncovering and understanding how large numbers of proteins (hundreds to thousands) interact in cells [7],... 

Theoretical chemistry has two problems that remain unsolved in terms of fundamental quantum theory the physics of chemical interaction and the theoretical basis of molecular structure. The two problems are related but commonly approached from different points of view. The molecular-structure problem has been analyzed particularly well and eloquent arguments have been advanced to show that the classical idea of molecular shape cannot be accommodated within the Hilbert-space formulation of quantum theory [161, 2, 162, 163]. As a corollary it follows that the idea of a chemical bond, with its intimate link to molecular structure, is likewise unidentified within the quantum context [164]. In essence, the problem concerns the classical features of a rigid three-dimensional arrangement of atomic nuclei in a molecule. There is no obvious way to reconcile such a classical shape with the probability densities expected to emerge from the solution of a molecular Hamiltonian problem. The complete molecular eigenstate is spherically symmetrical [165] and resists reduction to lower symmetry, even in the presence of a radiation field. 

This synthetic approach offers many opportunities, both with molecular weight control and side-chain chemistry, for tailoring molecular structure to prepare different mesophases and optimize physical properties for nonlinear optical applications. 

The success of the application of quantum mechanical methods to the description of physical and chemical properties of molecules is evident in every facet of modern chemical research and is well documented. It may be of special interest to point out some of the very recent uses of quantum chemical approaches applied as a tool in the study of molecular structure and interactions. The examples below were not selected for their relative importance in the field of quantum chemistry nor for the use of the most advanced methodology. Each represents one of many illustrations of a specific application. 

The idea that the behavior and properties of a molecule are concealed in the fundamental structural formulae has been aroimd for a long time. Modern physical chemistry has become increasingly orientated toward understanding how these properties can be decoded from the structure. Ideally, all properties of a chemical compound would be calculated from first principles. This is, however, unlikely in the foreseeable future because of a number of reasons, including the lack of sufficient theory and limits of available computational power. An alternative approach to finding qualitative mathematical relationships between the intrinsic molecular structure and observable properties of a chemical compound will be extremely valuable to both industrial and academic chemists. 

The comeretone of this framework has been, as always, the premise on which the science of organic chemistry rests that chemical behavior is determined by molecular structure. Chemical behavior—what happens, where in a molecule it happens, even whether it happens—comes down to a matter of relative rates of competing reactions. By and large, molecules tend to do what is easiest for them rate depends chiefly on the energy difference between the reactants and the transition state. We approach the matter of reactivity, then, by examining—mentally and, by means of models, physically—the structures involved. But what is meant by molecular structure is constantly expanding, and our interpretation of chemical behavior must reflect this. 

---