The Importance of Molecular Structure

The values of K, thus derived can in many cases be interpreted in terms of molecular structure. The increase in acidity ( 4 pK units) produced by introducing a halogen atom into acetone can be classified as an inductive effect, depending upon the stabilization of the anion by interaction between its charge and the carbon-halogen dipole, e.g., 

This effect is of course paralleled in the effect of halogen substitution on the strength of aliphatic carboxylic acids, though here it is of smaller 

149 Wheland and Farr, 150), but their rates of reaction with hydroxyl ion are in the reverse order, so that the dependence of velocity upon acid strength is the exact opposite of that usually found. Moreover, the effect of alkyl substitution in increasing the acidity is the opposite of the usual inductive effect (e.g., in the carboxylic acids). It seems likely that the sequence of acid strengths results from the stabilization of the undissociated molecule by a hyperconjugative effect which depends on the number of hydrogen atoms on the carbon adjacent to the nitro group, e.g., in nitromethane we can write three structures of the type 

This type of structure is not possible for the anion (or for carboxylic acids). The sequence of velocities is then explained on the basis of the ordinary inductive effect (Cardwell, 151). 

This problem is in principle the same as that of the structure of the substrate, but there are some differences in practice. In the first place, the acid-base strength of the catalyst is usually measurable by direct means, and a large part of the variations in reaction velocity merely parallel these variations in acid-base strength. In the second place, it is rarely practicable to vary the strength of the catalyst over a very wide range (because of the catalytic effect of the molecules or ions of the solvent). Moreover, most measurements on catalyzed reactions have been confined to a series of very similar catalysts, and little evidence is available as to how far catalysts of widely differing structure conform to a single Bronsted relation. 

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Most theoretical studies of outer-sphere (nonbond-breaking) electron transfer reactions at the metal-solution interface involve major simplifying assumptions regarding the molecular and electronic structure of the solvents and the metal. Although the importance of molecular structure and the dynamics of the solvent has been recognized, most of the theoretical work in this area has been based on a highly simplified continuum model. ... 

Chemical similarities can quite easily explain the observation of cross-allergies. Small conformational differences are enough indeed to create common epitopes (etymologically, superficial place ). An epitope is a part of molecule with a specific three-dimensional structure. One more time, we can see the importance of molecular structures in biology. Epitope is also called antigenic determinant. It can be incorporated in a macromolecular antigen by a group of specific amino acids, often exposed on the surface of the molecule (Fig. 3.27). ... 

Intensive use of cross-terms is important in force fields designed to predict vibrational spectra, whereas for the calculation of molecular structure only a limited set of cross-terms was found to be necessary. For the above-mentioned example, the coupling of bond-stretching (f and / and angle-bending (B) within a water molecule (see Figure 7-1.3, top left) can be calculated according to Eq. (30). 

In the chapter on vibrational spectroscopy (Chapter 6) 1 have expanded the discussions of inversion, ring-puckering and torsional vibrations, including some model potential functions. These types of vibration are very important in the determination of molecular structure. 

Another broad approach to the description of molecular structure that is of importance in organic chemistry is molecular orbital theory. Molecular orbital (MO) theory pictures electrons as being distributed among a set of molecular orbitals of discrete... 

The need for an overall and combined chemical structure and data search system became clear to us some time ago, and resulted in the decision to build CHIRBASE, a molecular-oriented factual database. The concept utilized in this database approach is related to the importance of molecular interactions in chiral recognition mechanisms. Solely a chemical information system permits the recognition of the molecular key fingerprints given by the new compound among thousands of fingerprints of known compounds available in a database. 

Single crystal x-ray diffraction is, without doubt, one of the most important techniques for the determination of molecular structures in the solid state. The technique is also pivotal to the determination of accurate bond lengths in molecules. However, the analysis of x-ray... 

These electron densities provide detailed information that gives important insight into the fundamentals of molecular structure and a better understanding of chemical reactions. The results of electron density analysis are used in a variety of applied fields, such as pharmaceutical drug discovery and biotechnology. 

Perturbative reasoning can be used to justify conceptual models of chemistry that are far from evident in Eq. (1.1) itself. An important example is the concept of molecular structure - the notion that nuclei assume a definite equilibrium configuration R0, which determines the spatial shape and symmetry of the molecule. At first glance, this concept appears to have no intrinsic meaning in Eq. (El),... 

In comparison with other measurement methods, NMR has important strengths. Its great virtue is its noninvasive nature, allowing one to obtain spatially resolved metabolic profiles and to investigate metabolomics in vivo. 10 There is little or no sample preparation. It is nondestructive. It is information-rich with regard to the determination of molecular structures because it can detect different chemical groups of metabolites simultaneously. 

The basic theories of physics - classical mechanics and electromagnetism, relativity theory, quantum mechanics, statistical mechanics, quantum electrodynamics - support the theoretical apparatus which is used in molecular sciences. Quantum mechanics plays a particular role in theoretical chemistry, providing the basis for the valence theories which allow to interpret the structure of molecules and for the spectroscopic models employed in the determination of structural information from spectral patterns. Indeed, Quantum Chemistry often appears synonymous with Theoretical Chemistry it will, therefore, constitute a major part of this book series. However, the scope of the series will also include other areas of theoretical chemistry, such as mathematical chemistry (which involves the use of algebra and topology in the analysis of molecular structures and reactions) molecular mechanics, molecular dynamics and chemical thermodynamics, which play an important role in rationalizing the geometric and electronic structures of molecular assemblies and polymers, clusters and crystals surface, interface, solvent and solid-state effects excited-state dynamics, reactive collisions, and chemical reactions. 

Symmetry has for many years played a vital role in the elucidation of molecular structure although apart from some special situations it was not thought to have a dominant influence on the structure or chemical properties of molecules. In recent years however it has played a large part in the interpretation of many organic reactions through the work of Woodward and Hoffman, and the concept of symmetry allowed or forbidden reaction is now an important part of mechanistic organic chemistry. 

Concerning the properites of tannins, we have stressed the importance of their structure, even more than their state of condensation or molecular weight. As it is impossible to separate and identify the flavolans in a given plant sample, one must be content with finding the aggregate indexes expressing the median state of polymerization. 

AS is well known, the quantity known as the overlap integral is of considerable importance in the theory of molecular structure. Although the existing literature1 contains a number of formulas and some numerical values for overlap integrals, it was thought worth while to carry through the much more systematic and comprehensive study whose results are presented below. 

This volume covers the structural relations between thermotropic and lyotropic liquid crystals (Chapters 1 and 2) and compares them with the micellar systems (Chapter 3). The interfacial aspects and the accompanying stability problems are covered in Chapters 5 and 6. The molecular dynamics in liquid crystals, the importance of water structure and of counter-ion binding for their stability are three essential factors for long range order systems, which are treated in Chapters 7, 8, and 9. The final chapter by E. J. Ambrose illustrates the change of order in a biological system under malignant conditions. 

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