Conformational and electronic study of<i>N</i>‐acetyl‐<scp>L</scp>‐isoleucine‐<i>N</i>‐methylamide using DFT and IPCM calculations

Rodrı́guez, Ana; Koo, Joseph C.P; Rojas, Dante Emanuel; Peruchena, Nélida María; Enriz, Ricardo D.

doi:10.1002/qua.20883

Cited by 6 publications

(10 citation statements)

References 67 publications

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“…Although the conformational space was significantly narrow because of the tert-butyl cap, it is clearly seen that the a-helical conformation [(u, w) 5 (290, 230)] became relatively stable in water and in ether compared with that in vacuo. The tendency was consistent with previous calculation results for the stable conformers of isoleucine (Ile), 49 a proteinogenic amino acid with a bulky side chain. On the other hand, the solvent effects on the side-chain potential energy surfaces were found to be marginal as seen in Figures 7-9, where the potentials are classified according to the dimensions.…”

Section: Saap Force Field Parameters For 20 Amino Acidssupporting

confidence: 90%

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like beta-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units.

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Section: Saap Force Field Parameters For 20 Amino Acidssupporting

confidence: 90%

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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“…Furthermore the N-acetyl and N-methylamide derivatives of homocysteine [15,16] and selenocysteine [17] and of the normal amino acids tryptophane [18,19] histidine [20], methionine [16], isoleucine [21][22][23]23], aspartic acid [24][25][26][27] and glutamine [28] have been theoretically investigated. A further theoretical study combined with FT-IR and Raman measurements on KBr pellets has been performed on N-acetyl-L-alanine [29], N-acetyl-L-aspartic and glutamic acid [30].…”

Section: Introductionmentioning

confidence: 99%

A theoretical and matrix-isolation FT-IR investigation of the conformational landscape of N-acetylcysteine

Boeckx

Ramaekers

Maes

2010

Journal of Molecular Spectroscopy

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“…Concerning isoleucine, we reported an exhaustive conformational and electronic study of N -acetyl- l -isoleucine- N -methylamide in the gas phase and in solution showing the influence of its nonpolar side chain on the conformational preferences …”

Section: Introductionmentioning

confidence: 99%

Conformational Preferences of N-Acetyl-l-leucine-N‘-methylamide. Gas-Phase and Solution Calculations on the Model Dipeptide

et al. 2007

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A DFT study of N-acetyl-l-leucine-N'-methylamide conformers in the gas phase and in solution was carried out. The theoretical computational analysis revealed 43 different conformations at the B3LYP/6-31G(d) level of theory in the gas phase. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) and the Poisson-Boltzmann self-consistent reaction field (PB-SCRF) method. The stability order of the different conformers in solution has been analyzed. The theoretical results were compared with some experimental data (X-ray, IR, and NMR).

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Conformational and electronic study ofN‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

Cited by 6 publications

References 67 publications

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

A theoretical and matrix-isolation FT-IR investigation of the conformational landscape of N-acetylcysteine

Conformational Preferences of N-Acetyl-l-leucine-N‘-methylamide. Gas-Phase and Solution Calculations on the Model Dipeptide

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