Carbohydrate parameter sets

Carbohydrate Parameter Sets in Biomolecular (Quadratic) Force Fields 223... 

Carbohydrate Parameter Sets in General Purpose Force Fields 227... 

Carbohydrate Parameter Sets in Class U Force Fields 229... 

CARBOHYDRATE PARAMETER SETS IN GENERAL PURPOSE FORCE FIELDS... 

In the following sections, several current and historically relevant carbohydrate force fields or parameter sets are described. Owing to the number of methods. It is impossible to present all of therietails for each method in this article. Rather, an introductory overview, along with appropriate citations, is provided. 

The CFF-PEF force field for carbohydrates proposed by Rasmussen has undergone several developmental refinements leading to numerous parameter sets. The emphasis of the PEF development has been to employ as few parameters and as simple energy expressions as possible. As such, torsion terms were kept to a minimum and no explicit term for the exo-anomeric effect was introduced. The consistent force field (CFF) developed by Lifson and Warshel was chosen as the original framework for the PEF development. The CFF-PEF functional form is similar to that of most macromolecular force fields (equation 9). ... 

Each of the traditional biomolecular force fields has been p meterized for carbohydrates, and in several instances more than one parameter set may exist, offering alternative levels of sophistication, internal consistency, and compatibility with parameters for.energy expression is very often augmented by a component intended to jreproduce the conformational energies associated with the exo-anomeric effect. 

A CHARMm-type parameter set for carbohydrates was reported by Ha and co-workers in 1988, and remains the standard for application with CHARMm. The internal force constants, and Ke. and equilibrium parameter values, r q and 0eq were derived by fitting to the experimental vibrational and structural properties of a representative monosaccharide, a-D-Glcp. The fitting was performed with the parameter optimization capability of CHARMm on the isolated monosaccharide with a dielectric value of unity. Partial charges were... 

A united atom CHARMm-based parameter set for carbohydrates has been introduced that offers a unique method for overcoming the multiple minima problem associated with inter-residue hydrogen bonding. In analogy with united atom force fields that treat C-H atomic pairs as extended atoms, the CHEAT approach unites O-H atomic pairs. The default... 

Limited testing of this parameterization led Glennon and co-workers to conclude that it was possible to reproduce experimental data regarding the structure and dynamics of carbohydrates. However, raP simulations indicated that the parameter set was unable to reproduce the experimental solvation free energy differences between a- and -Glcp (see Table 1). The poor performance of these parameters in the FEP simulations was suggested to be related to overestimation of intramolecular interaction energies in AMBER. ... 

There are numerous force fields and parameter sets available for modeling carbohydrates. Some focus specifically on carbohydrates, while others aim at treating biomolecules in general, and yet others profess to be appropriate for virtually any molecular class. Direct comparisons between force fields are rare and validation of any of the force fields requires extensive and critical comparison with experimental data. Consequently, carbohydrate force fields ate frequently selected on the basis of past familiarity. The advent of convenient graphical modeling interfaces provides a tremendous opportunity to extend carbohydrate modeling to both new users and new molecular systems. Ease of access is not, however, a guarantee of force field suitability. 

As had been observed in the synthesis of carbohydrate-substituted polymers of different lengths, the reactivity of the monomers was an important parameter in generating the triblock polymers. If the mannose-substituted 7-oxanor-bornene derivative was first polymerized, followed by the galactose-derivatized norbornene and the mannose-substituted norbornene monomers, two distinct sets of products were observed. These were identified by modification of the resulting polymers by acetylation, and analysis of the products by GPC. With this protocol, it was found that the product was composed of short polymers (DP=... 

The way to start a CFF parametrization is Select a set of PEFs, with associated parameters. Choose a set of molecules, closely related to the problem in hand (for carbohydrates alkanes, cycloalkanes, ethers, alcohols) their structures should be determined and their vibrational spectra assigned to a reasonable precision. Put in their structures by specifying atomic coordinates they need not be accurate. 

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