How to model solvation of peptides? Insights from a quantum-mechanical and molecular dynamics study of N-methylacetamide. 1. Geometries, infrared, and ultraviolet spectra in water.
This paper represents the first part of a study of solvation in peptides using quantum-mechanical and classical approaches. In this study, the peptide is modeled as its simplest analogue, namely, N-methyl-acetamide, and the effects of the solvent (here water, and in the second part of the study, water and acetone) are introduced at three different levels, e.g., through a continuum description, using solute-solvent clusters, and using the same clusters embedded in an external continuum. In turn, the solute-solvent clusters have been obtained in two alternative ways, either by using QM optimization procedures or extracting a proper set of structures from MD simulations. In this part of the study, geometries, IR, and UV spectra are calculated in terms of the different solvation models, and the results are analyzed and compared to get insights about different aspects of solvation involving dynamic and static effects on one hand and bulk or specific interactions on the other hand.
Mennucci
Benedetta
B
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy. bene@dcci.unipt.it
Martínez
José M
JM
D000081:Acetamides / Q000737:chemistry*; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004735:Energy Transfer; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D007536:Isomerism; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011789:Quantum Theory; D012995:Solubility; D012996:Solutions / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D013056:Spectrophotometry, Ultraviolet; D014867:Water / Q000737:chemistry*
D000081:Acetamides; D010455:Peptides; D012996:Solutions; D014867:Water; D006859:Hydrogen; D010100:Oxygen; C018595:N-methylacetamide