Molecular description

There is a wide variety of descriptors available to describe molecules the molecular representation they encode is key to the measurement of diversity. Descriptors directly influence the metrics and algorithms used in the design or analysis, the nature of the chemical space in question, and the location of molecules within the chemical space. Therefore, it is important to select descriptors most appropriate to the problem at hand. Such a selection of the appropriate descriptors is nontrivial, the requirement of compound representation is that it contains enough information to incorporate structure and, in some investigations, function. 

These descriptors can vary in complexity from simple atom counts to electronic properties derived from high-level ab initio calculations. Available molecular descriptors fall into three broad categories (1) Two-dimensional, encoding the topology of a molecule. (2) Three-dimensional, based on the 3D structure of a molecule. (3) Physicochemical (and electronic) representing whole molecule properties. 

The following subsection highlights common examples of molecular descriptors, and descriptor selection. A more thorough discussion of chemical descriptors can be found in the following reference.  

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Statistical mechanics is the mathematical means to calculate the thermodynamic properties of bulk materials from a molecular description of the materials. Much of statistical mechanics is still at the paper-and-pencil stage of theory. Since quantum mechanicians cannot exactly solve the Schrodinger equation yet, statistical mechanicians do not really have even a starting point for a truly rigorous treatment. In spite of this limitation, some very useful results for bulk materials can be obtained. 

Analytical Approaches. Different analytical techniques have been appHed to each fraction to determine its molecular composition. As the molecular weight increases, complexity increasingly shifts the level of analytical detail from quantification of most individual species in the naphtha to average molecular descriptions in the vacuum residuum. For the naphtha, classical techniques allow the isolation and identification of individual compounds by physical properties. Gas chromatographic (gc) resolution allows almost every compound having less than eight carbon atoms to be measured separately. The combination of gc with mass spectrometry (gc/ms) can be used for quantitation purposes when compounds are not well-resolved by gc. 

The next level seeks a molecular description, and kinetics again makes a contribution. As will be seen in Chapter 5, the experimental kinetics provides information on both the energetics of the reaction (i.e., the height of the energy barrier on the reaction path) and the atomic composition of the transition state. Any proposed mechanism must therefore be consistent with the kinetic evidence. 

Following the general trend of looldng for a molecular description of the properties of matter, self-diffusion in liquids has become a key quantity for interpretation and modeling of transport in liquids [5]. Self-diffusion coefficients can be combined with other data, such as viscosities, electrical conductivities, densities, etc., in order to evaluate and improve solvodynamic models such as the Stokes-Einstein type [6-9]. From temperature-dependent measurements, activation energies can be calculated by the Arrhenius or the Vogel-Tamman-Fulcher equation (VTF), in order to evaluate models that treat the diffusion process similarly to diffusion in the solid state with jump or hole models [1, 2, 7]. 

Brooks EM et aJ Molecular description of three macro-deletions and an Alu-Alu recombination-mediated duplication in the HPRT gene in four patients with Lesch-Nyhan disease. Mutat Res 2001 476 43. 

We begin this chapter with a discussion of the variabies that characterize gases. Then we develop a molecular description that expiains gas behavior. Next, we expiore additional gas properties and show how to do stoichiometric caicuiations for reactions invoiving gas-phase species. Finally, we return to the Earth s atmosphere and describe some aspects of its composition and chemicai reactions. 

Calakos, N and Scheller, RH (1996) Synaptic vesicle biogenesis, docking and fusion a molecular description. Physiol. Rev. 76 1-29. 

Molecular description of the mechanistic steps of DeNOr process... 

Thus far we have explored the field of classical thermodynamics. As mentioned previously, this field describes large systems consisting of billions of molecules. The understanding that we gain from thermodynamics allows us to predict whether or not a reaction will occur, the amount of heat that will be generated, the equilibrium position of the reaction, and ways to drive a reaction to produce higher yields. This otherwise powerful tool does not allow us to accurately describe events at a molecular scale. It is at the molecular scale that we can explore mechanisms and reaction rates. Events at the molecular scale are defined by what occurs at the atomic and subatomic scale. What we need is a way to connect these different scales into a cohesive picture so that we can describe everything about a system. The field that connects the atomic and molecular descriptions of matter with thermodynamics is known as statistical thermodynamics. 

A study of the molecular descriptions provided by geneticists and molecular biologists reveals at least three different levels. The first can be illustrated by the schematic models of signal-transduction pathways. In such models, the precise shape of the different proteins, their atomic composition, is of no importance. Sometimes, only the name of the protein is given. What is important is the place of these proteins in the pathways, how they receive upstream signals and transfer them to downstream molecular components. 

Finally, the third level of molecular description can be illustrated by the complex formed between a transcription factor and the DNA molecule. In such a complex, the atoms involved in the interaction, the hydrogen bonds formed between the amino acids and the bases are shown, because this description, is necessary to explain the specificity of molecular recognition. 

Through these examples, I wanted to illustrate the fact that the expression molecular description can have at least three different meanings. These three levels of representation are not independent. For instance, the atoms and bonds that make up the jaws of RNA polymerase II can be described, as well as RNA polymerase II can be integrated, with transcription factors and DNA, in the general picture of the preinitiation transcription complex. However, in order to answer a specific question, one particular level of description is always more significant, better adapted than others, with a greater explanatory value. 

This impossibility of reducing a complex process to single macromolecules explains the co-existence of different levels of explanation in biologists molecular descriptions. This does not mean that the nature of the molecular components is of no importance, nor that the complex functions originate only from the rules of assembly of the different macromolecular components. The organization of living beings is based both on the precise nature of the molecular components and on the way that these molecular components are assembled. 

Hair cells are specialized mechanoreceptors located in the inner ear these cells transduce mechanical forces transmitted by sound and head movement, and permit an organism to sense features of the external world. Well-characterized biophysically, a molecular description of hair-cell transduction has finally begun to emerge. 

Over the years, a large number of models of water structure have been developed in an attempt to reconcile all the known physical properties of water and to arrive at a molecular description of water that accounts correctly for its behavior over a large range of thermodynamic conditions. Early models of water structure have been categorized by Fennema (1996) and Ball (2001) into three general types mixture, uniformist, and interstitial. Mixture models are based on the concept of intermolecular hydrogen bonds... 

This homogeneity does depend both on the level of the molecular description and on the definition of the ad hoc molecular descriptors. 

Electron transfer reactions of metal ion complexes in homogeneous solution are understood in considerable detail, in part because spectroscopic methods and other techniques can be used to monitor reactant, intermediate, and product concentrations. Unfavorable characteristics of oxide/water interfaces often restrict or complicate the application of these techniques as a result, fewer direct measurements have been made at oxide/water interfaces. Available evidence indicates that metal ion complexes and metal oxide surface sites share many chemical characteristics, but differ in several important respects. These similarities and differences are used in the following discussions to construct a molecular description of reductive dissolution reactions. 

Molecular Description of Redox Polyelectrolyte-Modified Electrodes 89... 

Gel permeation chromatography Is the method of choice for analysis of thermoplastic resin systems. Corrected for imperfect resolution, chromatogram interpretation yields accurate molecular descriptions, including theoretical, kinetic distributions (, ) The current research is designed to extend the utility of this analytical tool to the analysis of thermoset resins. 

The emphasis of the current research is on molecular structure of oligomeric fractions leached from quality cured, industrial resins. However, the potential for applications in quality control should not be overlooked. Chromatography analysis provides positive feedback capable of molecular descriptions of extent of cure actually achieved. Oligomeric distributions coupled to kinetic reaction analysis allows for detailed estimates of crosslink architecture within the resin (7). 

A synergy approach which is the combination of linear/neural net and neighborhood behavior models that are independent ways of identifying correlations between molecular description and experimental activity. 

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