Carbohydrates computational methods

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

Molecular mechanics calculations have been carried out on a wide range of chemical compounds including hydrocarbons, heteroatomic molecules, steroids, carbohydrates and proteins. Furthermore, a variety of information has been obtained such as heats of formation, rotational barriers, and rates of reaction (18,2,19). The major advantage of this method over other computational methods is that it is reasonably fast to perform in comparison to formal molecular orbital calculations. 

The computational method selected for use in carbohydrate conformational analysis depends on the data amount available and accuracy and on the project goal to find a single conformation that satisfies the experimental data or to generate a statistically accurate ensemble of conformations. Advances in... 

The aim of this report is to collect the most important results in sugar studies by NMR methods in the last two years. This review covers determination of new and previously known structures of sugars isolated from natural sources, as well as the structures of carbohydrates obtained by chemical or enzymatic synthesis. Moreover, we have included herein the papers describing non-covalent interactions between carbohydrates and other sugars, peptides, proteins and DNA fragments, as well as the application of NMR techniques to identification and quantification of sugars. The development in rare and unusual NMR methods used to study the sugar structures is also included. The last section focuses on the computational methods used to calculate NMR parameters, and on the carbohydrate databases. 

Nowadays, computational methods is an inherent and parallel tool for research of new compoimds. As mentioned previously, the interactions, between carbohydrates and metal ions usually are very weak. There are several aspects, which can be considered by using computational approaches e g. structures of complexes, their sta-... 

This is an area that has received considerable amount of attention and the literature covering this area has been divided into the following sub-sections Reviews and General studies, Orienting Media, New Experimental Methodologies, New Pulse Schemes, Computational Methods, Structure, Conformation, Domain Orientation and Dynamics Studies on Proteins, Peptides, Nucleic Acids and Carbohydrates. 

Computational methods for predictions NMR parameters such as chemical shifts, spin-spin coupling constants or relaxation rates facilitate determination of carbohydrate structure and shorten the evaluation time of the results. For this reason empirical methods of NMR spectra... 

Selected applications of small-scale preparative l.c. of carbohydrates are given in Table IV. Although the amounts of carbohydrate isolated are low (several pig to 20 mg), they are often enough for subsequent qualitative methods such as H-n.m.r. spectroscopy. By computer automa-... 

At the present time, it appears that the applicability of semiempirical methods to the study of carbohydrate chemistry has been neglected. Methods are now available for the non—theoretician to investigate molecular systems, reaction mechanisms, and fundamental physical properties, without the need for any extensive knowledge of theoretical methods. Despite this, most computational studies appear to be limited to the use of molecular mechanics techniques. 

With the advent of molecular dynamics simulations applied to carbohydrates, one can anticipate the direct computation of more conceptually appealmg surfaces of V in 0s) space from a given U( qint,qext)) in the near future. Monte Carlo integration over (qext) and (b,x, 0h) for fix (0s) provides an alternative procedure, but one which is probably less attractive in terms of efficiency than the molecular dynamics approach. A second alternative, known as adiabatic mapping, provides an approximation to V((0s ), and applications of this method to carbohydrates have recently begun to appear. 12,13 in this approach the conformational... 

Structural study of polysaccharides and other carbohydrates in solution or in the amorphous state has been significantly enhanced through the application of Fourier-transform, infrared spectroscopy. Among the advantages of this method may be mentioned the high quality of the spectra, and the in-house ability to interact with the computer, so that the digitized spectra may be stored and manipulated in such a way that additional information is obtained. The application of F.t.-i.r. spectroscopy in the field of carbohydrate chemistry and biochemistry is still in its infancy,182 but... 

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