Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2008-11-08
Biology
Quantitative Biology
Quantitative Methods
21 pages, 5 figures, in press in Philosophical Nature
Scientific paper
Small peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to correctly describe the conformational behaviour of small peptides constitutes an unavoidable first step. In this work, we present an study of several potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The PESs are calculated using the B3LYP density-functional theory (DFT) method, with Dunning's basis sets cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, and cc-pVQZ. These calculations, whose cost amounts to approximately 10 years of computer time, allow us to study the basis set convergence of the B3LYP method for this model peptide. Also, we compare the B3LYP PESs to a previous computation at the MP2/6-311++G(2df,2pd) level, in order to assess their accuracy with respect to a higher level reference. All data sets have been analyzed according to a general framework which can be extended to other complex problems and which captures the nearness concept in the space of model chemistries (MCs).
Chass Gregory A.
Echenique Pablo
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