Molecular conformation, functional properties

Molecular conformation is highly related to functional properties. Since the conformation of the crystalline solids can be precisely determined by diffraction methods, molecular modeling is most important for interpreting molecular structures in solution. This is, however, even more difficult for theoreticians. While carbohydrates dissolve in a variety of solvents, the important solvent for biological systems is water and this solvent deserves special emphasis. 

Although the molecular conformation of organic solids profoundly affects their properties, In the case of coals this characteristic has been little studied compared to their chemical composition and functionality Studies of coal at any level of structure are difficult because of the complex heterogeneity of any particular coal and the great variability of coal types that occur ... 

The whey produced during cheese and casein manufacturing contains approximately 20% of all milk proteins. It represents a rich and varied mixture of secreted proteins with wide-ranging chemical, physical and functional properties (Smithers et al., 1996). Due to their beneficial functional properties, whey proteins are used as ingredients in many industrial food products (Cheftel and Lorient, 1982). According to Kinsella and Whitehead (1989), functional properties of foods can be explained by the relation of the intrinsic properties of the proteins (amino acid composition and disposition, flexibility, net charge, molecular size, conformation, hydrophobicity, etc.), and various extrinsic factors (method of preparation and storage, temperature, pH, modification process, etc.). 

For many years, different spectroscopic methods were used to study conformations of polynucleotides in different environments [64, 65], Spectroscopy offers most developed techniques for studying structural and functional properties of varieties of molecules. Absorption spectroscopy is one of the oldest and most common methods used in chemical science to elucidate molecular structures. Since... 

The more general view is that non-local interaction within a molecule determines the charge distribution and conformation holistically. All local features are consequences of the whole. However, molecules of any complexity are rarely the product of a one-step reaction starting from the atomic constituents and are more likely built up from intermediate fragments that retain some of their own molecular properties on incorporation into a bigger whole. This mechanism explains the large number of additive rules that have been discovered empirically for molecular systems [51] and the existence of isomers. A molecule whose conformation and properties are functions of its chemical history, is not holistic, but partially holistic [2], which means that its wave function is a product function, albeit with a limited number of factors (fragments),... 

Our preliminary MD simulations provided similar results as the MC method for the calculation of the static properties of confined PFPE nanofilms, especially the radius of gyration and end-bead density profiles. The anisotropic molecular conformation and experimental layering structures in the film were also verified. MD simulations provide a powerful tool for examining the dynamics of nanofilms through correlation functions by tracking the trajectories of molecules, including the space and velocity coordinates. MD simulations, therefore, are suitable for... 

Pressure affects a reaction system in two ways (1) reduction of the available molecular space, which has to do with conformation, and (2) increase of intrachain reactions (Hoover et al., 1989), which affect the d)mamics and reactions of biomolecules. The effect of HP on microbial inactivation, chemical or enzymatic reactions, and structural and /or functional properties of foods is based on the principle of Le Chatelier-Braun and on the State Transition Theory. 

Hence, in the light of our both accounts of causality, the molecular dynamics model represents causal processes or chains of events. But is the derivation of a molecule s structure by a molecular dynamics simulation a causal explanation Here the answer is no. The molecular dynamics model alone is not used to explain a causal story elucidating the time evolution of the molecule s conformations. It is used to find the equilibrium conformation situation that comes about a theoretically infinite time interval. The calculation of a molecule s trajectory is only the first step in deriving any observable structural property of this molecule. After a molecular dynamics search we have to screen its trajectory for the energetic minima. We apply the Boltzmann distribution principle to infer the most probable conformation of this molecule.17 It is not a causal principle at work here. This principle is derived from thermodynamics, and hence is statistical. For example, to derive the expression for the Boltzmann distribution, one crucial step is to determine the number of possible realizations there are for each specific distribution of items over a number of energy levels. There is no existing explanation for something like the molecular partition function for a system in thermodynamic equilibrium solely by means of causal processes or causal stories based on considerations on closest possible worlds. 

Biological functions (enzymatic activities, specific ligand binding, etc.) are intimately governed by the native conformation and are lost upon denaturation, and so those of the functional properties, in the technological sense of the terms, which derive directly from molecular characteristics of the native structure. This aspect of the question is the best known, but not necessarily the most important, as to protein functionality. ... 

---