Conformations of flexible molecules

There has been considerable recent activity developing appropriate parameters to allow semi-empirical methods to describe a variety of biologically important systems, and their related properties, such as (i) enzyme reactivity, including both over- and through-barrier processes, (ii) conformations of flexible molecules such as carbohydrates, (iii) reactivity of metalloenzymes and (iv) the prediction of non-covalent interactions by addition of an empirical dispersive correction. In this review, we first outline our developing parameterisation strategy and then discuss progress that has been made in the areas outlined above. 

IMS-MS applications published in the literature can be grouped into two categories. The first contains studies of conformations of flexible molecules. Such flexible molecules include synthetic polymers and biopolymers such as peptides, proteins, and oligonucleotides. The studies of the second category deal with the geometry of cluster ions such as carbon clusters, semiconductor clusters, metal clusters, salt clusters, ion-ligand clusters. The major conclusions regarding structure of these systems are reviewed in Sect. 5. 

A number of review articles have appeared. (560 564) One of these (563) discusses the problems of using computerized searches for the most likely conformations of flexible molecules. Generally, a single conformation is not preferred but rather a set or family of conformations. Conformational studies of a variety of Ln(iii) complexes of amino-acids and peptides have been discussed. The lanthanides La(iii) to Dy(iii) are bound to carboxylate ligands in a bidentate manner whereas the other lanthanides, typified by Tm(iii), are bound through a single oxygen. 

Flexible peptides can be conformationally restricted by a variety of methods other than macrocyclization of the peptide. For example, Marshall et al. introduced a-methyl amino acid substituents into peptides as a way to decrease the conformational space available to the resulting peptide (42) these types of approaches led to his "Active Analog" approach for determining bioactive conformations of flexible molecules (43). Some other traditional... 

Use of Computer Graphics in the Display of Low Energy Conformations of Flexible Molecules. ... 

The use of tethers and templates in the chemistry described above can furnish valuable information about the conformations of flexible molecules, and in appropriate cases can lead to selective functionalization reactions, including those at unactivated positions. Thus these reactions are biomimetic, imposing geometric control over the normal substrate reactivity control. It remains for the future to develop such reactions, and catalysts, to the point at which they take their place in the tools of synthesis for research and manufacturing. However, such progress seems likely, judging from the progress that has been made to date. 

Our computational studies were done in concert with an HNMR study of the conformations in deuterium oxide. The problem of how to determine the conformation of flexible molecules in solution has challenged researchers for decades and will continue to do so. The problem is even more difficult for flexible molecules that are either quite polar or charged, especially if these molecules interact with the solvent. The techniques of NMR spectroscopy and computational chemistry, CH2COO- CH2COO-... 

Because knowledge of atomic arrangements facilitates the progress of research in many scientific disciplines, structural research has played a valuable role in scientific progress. Many areas of chemistry include structure determination as a part of the research regime. Applications include the structural analysis of substances such as natural products, reaction intermediates, photorearrangement products, and the final products of synthetic or reaction processes. Such information relates structure to function, clarifies synthetic pathways and reaction mechanisms, establishes the conformation of flexible molecules and provides the geometric parameters for calculations in theoretical chemistry. 

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