Molecular structure concept

The concept of the similarity of molecules has important ramifications for physical, chemical, and biological systems. Grunwald (7) has recently pointed out the constraints of molecular similarity on linear free energy relations and observed that Their accuracy depends upon the quality of the molecular similarity. The use of quantitative structure-activity relationships (2-6) is based on the assumption that similar molecules have similar properties. Herein we present a general and rigorous definition of molecular structural similarity. Previous research in this field has usually been concerned with sequence comparisons of macromolecules, primarily proteins and nucleic acids (7-9). In addition, there have appeared a number of ad hoc definitions of molecular similarity (10-15), many of which are subsumed in the present work. Difficulties associated with attempting to obtain precise numerical indices for qualitative molecular structural concepts have already been extensively discussed in the literature and will not be reviewed here. 

Twenty years have passed since the publication of the original paper by Woolley [3] in which the incompatibility of the molecular structure concept with the rigorous quantum-mechanical description of isolated molecules has been eloquently brought to the attention of chemists. The ensuing flurry of research publications clarified several misconceptions but did little to familiarize the broader scientific audience with this important issue. Regretfully, few quantum or computational chemists are aware of these papers, which are nowadays seldom discussed or quoted. 

III. STRUCTURE AND STRUCTURAL STABILITY A. The Molecular Structure Concept... 

Because of the existence of numerous isomers, hydrocarbon mixtures having a large number of carbon atoms can not be easily analyzed in detail. It is common practice either to group the constituents around key components that have large concentrations and whose properties are representative, or to use the concept of petroleum fractions. It is obvious that the grouping around a component or in a fraction can only be done if their chemical natures are similar. It should be kept in mind that the accuracy will be diminished when estimating certain properties particularly sensitive to molecular structure such as octane number or crystallization point. 

Conservation laws at a microscopic level of molecular interactions play an important role. In particular, energy as a conserved variable plays a central role in statistical mechanics. Another important concept for equilibrium systems is the law of detailed balance. Molecular motion can be viewed as a sequence of collisions, each of which is akin to a reaction. Most often it is the momentum, energy and angrilar momentum of each of the constituents that is changed during a collision if the molecular structure is altered, one has a chemical reaction. The law of detailed balance implies that, in equilibrium, the number of each reaction in the forward direction is the same as that in the reverse direction i.e. each microscopic reaction is in equilibrium. This is a consequence of the time reversal syimnetry of mechanics. 

The concept of connection tablc.s, a.s shown. so far, cannot represent adequately quite a number of molecular structures. Basically, a connection table represents only a single valence bond structure. Thus, any chemical species that cannot he described adequately by a single valence bond (VB) structure with single or multiple bonds between two atom.s is not handled accurately. 

Representation of Molecular Structures by Electron Systems 2.6.2.1 General Concepts... 

We describe here a new structure representation which extends the valence bond concept by new bond types that account for multi-haptic and electron-deficient bonds. This representation is called Representation Architecture for Molecular Structures by Electron Systems (RAMSES) it tries to incorporate ideas from Molecular Orbital (MO) Theory [8T]. 

Obviously, to model these effects simultaneously becomes a very complex task. Hence, most calculation methods treat the effects which are not directly related to the molecular structure as constant. As an important consequence, prediction models are valid only for the system under investigation. A model for the prediction of the acidity constant pfQ in aqueous solutions cannot be applied to the prediction of pKj values in DMSO solutions. Nevertheless, relationships between different systems might also be quantified. Here, Kamlet s concept of solvatochro-mism, which allows the prediction of solvent-dependent properties with respect to both solute and solvent [1], comes to mind. 

The simplest molecular orbital method to use, and the one involving the most drastic approximations and assumptions, is the Huckel method. One str ength of the Huckel method is that it provides a semiquantitative theoretical treatment of ground-state energies, bond orders, electron densities, and free valences that appeals to the pictorial sense of molecular structure and reactive affinity that most chemists use in their everyday work. Although one rarely sees Huckel calculations in the resear ch literature anymore, they introduce the reader to many of the concepts and much of the nomenclature used in more rigorous molecular orbital calculations. 

It IS good chemical practice to represent molecules by their most stable Lewis structure The ability to write alternative resonance forms and to compare their relative stabilities however can provide insight into both molecular structure and chemical behavior This will become particularly apparent m the last two thirds of this text where the resonance concept will be used regularly... 

It has been shown that description of bonding based on the bent-bond concept can be just as successful in describing molecular structure as the hybridization concept. We will, however, use the hybridization terminology. 

Several methods of quantitative description of molecular structure based on the concepts of valence bond theory have been developed. These methods employ orbitals similar to localized valence bond orbitals, but permitting modest delocalization. These orbitals allow many fewer structures to be considered and remove the need for incorporating many ionic structures, in agreement with chemical intuition. To date, these methods have not been as widely applied in organic chemistry as MO calculations. They have, however, been successfully applied to fundamental structural issues. For example, successful quantitative treatments of the structure and energy of benzene and its heterocyclic analogs have been developed. It remains to be seen whether computations based on DFT and modem valence bond theory will come to rival the widely used MO programs in analysis and interpretation of stmcture and reactivity. 

The standard free energy can be divided up in two ways to explain the mechanism of retention. First, the portions of free energy can be allotted to specific types of molecular interaction that can occur between the solute molecules and the two phases. This approach will be considered later after the subject of molecular interactions has been discussed. The second requires that the molecule is divided into different parts and each part allotted a portion of the standard free energy. With this approach, the contributions made by different parts of the solvent molecule to retention can often be explained. This concept was suggested by Martin [4] many years ago, and can be used to relate molecular structure to solute retention. Initially, it is necessary to choose a molecular group that would be fairly ubiquitous and that could be used as the first building block to develop the correlation. The methylene group (CH2) is the... 

It is seen that by taking a mean value for the slope, there is very little divergence between the calculated and experimental values. Consequently, the methylene groups can, indeed, be taken as a reference group for assessing the effect of molecular structure on solute retention. The concept will now be applied to a simple n-alkanes series as discussed above, the data for which was obtained on the stationary phase n-heptadecane. 

In standard quantum-mechanical molecular structure calculations, we normally work with a set of nuclear-centred atomic orbitals Xi< Xi CTOs are a good choice for the if only because of the ease of integral evaluation. Procedures such as HF-LCAO then express the molecular electronic wavefunction in terms of these basis functions and at first sight the resulting HF-LCAO orbitals are delocalized over regions of molecules. It is often thought desirable to have a simple ab initio method that can correlate with chemical concepts such as bonds, lone pairs and inner shells. A theorem due to Fock (1930) enables one to transform the HF-LCAOs into localized orbitals that often have the desired spatial properties. 

Although sophisticated electronic structure methods may be able to accurately predict a molecular structure or the outcome of a chemical reaction, the results are often hard to rationalize. It therefore becomes difficult to apply the findings to other similar systems. Qualitative theories, on the other hand, are unable to provide accurate results, but they may be useful for gaining insight, e.g. why a certain reaction is favoured over another. They also provide a link to many concepts used by experimentalists. 

This book is addressed to all those for whon orbitals have ceased to be an abstract concept, but have instead become concrete and useful in the daily practice of chemistry. It is especially directed to the new generation of chemists eager to understand molecular structure at the electronic level. 

A reactive polymer (RP) is simply a device to alloy different materials by changing their molecular structure inside a compounding machine. True reactive alloying induces an interaction between different phases of an incompatible mixture and assures the stability of the mixture s morphology. The concept is not new. This technology is now capable of producing thousands of new compounds to meet specific design requirements. 

After the discovery of quantum mechanics in 1925 it became evident that the quantum mechanical equations constitute a reliable basis for the theory of molecular structure. It also soon became evident that these equations, such as the Schrodinger wave equation, cannot be solved rigorously for any but the simplest molecules. The development of the theory of molecular structure and the nature of the chemical bond during the past twenty-five years has been in considerable part empirical — based upon the facts of chemistry — but with the interpretation of these facts greatly influenced by quantum mechanical principles and concepts. 

Some of the most important applications for conducting polymers which might show at least some commercial viability in the near future are listed in Table 3. The list is by no means complete, and is growing all the time. However, one should not expect fundamental progress in practical applications until basic research on conducting polymers moves beyond the stage of trial and error, and develops concepts to obtain quantitative information about molecular structures and properties, on the one hand, and the resultant material properties on the other hand. 

However, there is much to be harvested by seeking the underlying rules governing molecular properties of a similar family and distinguishing those rules from the sophisticated numerical results for individual molecules. For this purpose, qualitative theories are still desirable to provide useful concepts for elucidating intriguing molecular structures and chemical reactions, and more importantly, to predict the observable properties of new molecules before we carry out resource-consuming computations or experiments. 

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