Geometrical and vibrational properties of nucleic acid constituents interacting with explicit water molecules as analyzed by density functional theory calculations. 1. Uracil + n(sub w)H2O (n(sub w) = 1,...,7)

Article Abstract:

The study was done to analyze the preferential sites of interaction of water molecules with uracil (RNA base) through the first hydration shell by using density functional theory (DFT) calculations. The results obtained from the experiment allowed us to estimate the energy difference separating optomized configurations by taking into account both electronic and vibrational energies.

Usage, Binding sites (Biochemistry), Active sites (Biochemistry), Chemical reactions, Density functionals, Density-functional theory

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Vibrational analysis of amino acids and short peptides in hydrated media. II. Role of KLLL repeats to induce helical conformations in minimalist LK-peptides

Article Abstract:

Circular dichroism (CD) and Raman scattering techniques are used for analyzing the aqueous solution secondary structures of minimalist LK-peptides, with the generic sequence defined as KLL[(KLLL).sub.n]KLLK. The results have shown that the conformational flexibility of the shortest peptides is high enough to adopt random, [beta]-type and helical chains in aqueous solution.

Peptides, Spectra, Peptide synthesis, Amino acids, Raman effect, Structure, Circular dichroism

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How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study

Article Abstract:

A comprehensive ab initio conformational analysis of thymidine, DNA canonical nucleoside was performed. It was confirmed that dozens of energetically representative conformers are necessary to reproduce satisfactorily the T low temperature matrix isolation IR spectrum.

Biological Product (except Diagnostic) Manufacturing, Nucleic Acid Derivatives, Conformational analysis, Nucleosides, Quantum chemistry

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