ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
We report the first molecular dynamics simulation of an amide in water in which the solute is fully described through quantum mechanics methods (density functional theory in our case). All solute's degrees of freedom are allowed to vary. The solvent is described through a classical potential. We have chosen for our study the simple formamide molecule since it allows hybrid simulations to be carried out at a sophisticated quantum level. More precisely, we have considered two computational schemes: in the first one, we use a small double-ζ basis set and a local approximation of the exchange-correlation functional whereas, in the second, an extended triple-ζ+polarization basis set, as well as a gradient-corrected functional, has been employed. The analysis of the results is focused on both structural and energetic aspects. Particular attention is paid to the time variation of dihedral angles in formamide connected to nitrogen pyramidalization and NH2 subunit rotation. The agreement with available experimental and theoretical data is satisfactory. Nevertheless, the limits of the method are pointed out, in particular the need to improve the description of the nonelectrostatic term of the solute-solvent interaction potential. One of the main advantages of the hybrid approach is that polarization effects are included in a rigorous manner. This renders possible a detailed discussion on the role of hydration effects on amides structure, a point of considerable relevance due to the biochemical importance of the peptidic bond. © 1999 American Institute of Physics.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.479299
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