AMBER refinement calculations

In conjunction with a study on the reactivity of dimeric quinone me-thides, Elder et al. (56) examined the physical and electronic structure of guaiacylglycerol-/ -coniferyl ether, which is substituted in a manner representative of the lignin polymer. Calculations were performed using AMBER (Assisted Model Building with Energy Refinement) (24), which is a force-field method, and the energetic minimum was determined to be a folded structure similar to that reported by Gravitis and Erins (55). 

Based on DFT calculations on chlorophylls and, additionally, on ubiquinone and the RC main detergent, lauryl dimethylamine oxide or LDAO, we have then developed a force field for their classical modelization. Our approach to this undertaking was straightforward. We initially use the DFT optimized structures and the vibrational analysis to determine the bonded part of the potential parameters described by the AMBER potential function. Then, atomic ab initio partial charges on the chromophore are used to account for electrostatic effects. At a later stage, experimental data from X-ray crystallography are used to check the structural properties of the molecule in the condensed state and to refine the intermolecular Lennard-Jones parameters. 

Modifications have been made to the AMBER force field to improve the correlations between calculated and observed molecular properties of a-linked saccharides these led to refinements in solvation studies on maltose, a-, p- and Y-cyclodextrin and two larger cyclodextrins (DP 10 and 21). A molecular dynamics simulation investigation of the solvation patterns of the model disaccharide 4 in aqueous DMSO defined regions in which competition exists... 

As suggested above, developments in AMBER tend to be problem-driven. Our conviction of the power and usefulness of free energy calculations, NMR refinement, and the importance of non-additive effects have made these distinctive features of the program. AMBER, like some of the other programs noted above, has always been available in source code form and that has encouraged others to use it as a platform for developments, often for our own and others benefit. 

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