An ab initio exploratory study of the full conformational space of MeCO-l-threonine-NH-Me

Sahai, Michelle A.; Motiwala, Sanober S.; Chass, Gregory A.; Pai, E.F.; Penke, Botond; Csizmadia, Imre G.

doi:10.1016/j.theochem.2003.08.031

Cited by 7 publications

(4 citation statements)

References 28 publications

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“…The relative energies (∆E) and associated relative thermodynamic functions (∆H, ∆G, and ∆S) for all conformers of the trans and cis isomers are tabulated in Tables A and B of the Supporting Information, respectively. The trans global minimum was previously 30 reported to be γ L [+-] at the HF/3-21G level of theory. However, the trans global minimum γ L [-+] reported in this work (Table A of the Supporting Information) was used to calculate relative values for the conformers.…”

Section: Resultsmentioning

confidence: 99%

“…A previous ab initio study on the trans peptide bond of MeCO−Thr−NH−Me diamide resulted in 39 out of the possible 81 conformations at the RHF/3-21G level of theory . This undoubtedly describes the conformational diversity of Thr and underscores the importance of a conformational study of this amino acid residue.…”

Section: Introductionmentioning

confidence: 81%

“…2 A previous ab initio study on the trans peptide bond of MeCO-Thr-NH-Me diamide resulted in 39 out of the possible 81 conformations at the RHF/3-21G level of theory. 30 This undoubtedly describes the conformational diversity of Thr and underscores the importance of a conformational study of this amino acid residue. As such, the present study aims to fully understand the conformational space of Thr in the (S) absolute configuration of the backbone and in the (R) absolute configuration of the side chain.…”

Section: Introduction Biological Considerations Of the First-principl...mentioning

confidence: 92%

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First-Principle Computational Study on the Full Conformational Space of l-Threonine Diamide, the Energetic Stability of Cis and Trans Isomers

et al. 2006

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First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi1=chi2=anti). Similarly, two side chain PESs for the cis and trans isomers were generated for the (phi=psi=anti) orientation corresponding to approximately the betaL backbone conformation. Besides correlating the relative Gibbs free energy of the various stable conformations with the number of stabilizing hydrogen bonds, the process of trans-->cis isomerization is discussed in terms of intrinsic stabilities as measured by the computed thermodynamic functions.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 81%

Section: Introduction Biological Considerations Of the First-principl...mentioning

confidence: 92%

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First-Principle Computational Study on the Full Conformational Space of l-Threonine Diamide, the Energetic Stability of Cis and Trans Isomers

et al. 2006

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“…Control parameters of the MNC genetic algorithm. D, b L , g L , g D , d D , and ε D ) among the nine legitimate predefined areas on the Ramachandran map, where the fold a L appears this time as a potential minimum, a fold which usually presents as a minimum on the PESs of diamide models whose side chains comprise the hydroxyl grouping eOH[38,39], whereas no structure corresponding to the polyproline II ε L (4 ¼ À75 ± 30 , j ¼ 160 ± 30 )…”

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An exhaustive conformational analysis of N-formyl-l-tyrosinamide using a genetic algorithm for multimodal search

Guerdaoui¹,

Merbouh²,

Tijar³

et al. 2016

Comptes Rendus. Chimie

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This work reports a detailed conformational study on N-formyl-L-tyrosinamide diamide system through genetic algorithm based on multiniche crowding technique. We tried to evaluate the effect of the OH hydroxyl substitution of the benzene ring on the adopted folds by comparing them with those found previously for the N-formyl-L-phenylalaninamide. Among the 26 and 28 conformations detected for both systems N-formyl-Ltyrosinamide and N-formyl-L-phenylalaninamide successively, 19 conformations have similar geometrical structures (identical backbones and side-chain orientations). The comparison of 19 common conformation geometries of both systems revealed nearly perfect linear adjustments with R 2 values of 0.9997, 0.9996, 0.9998, and 0.9996 for the dihedral angles 4, j, c 1 , and c 2 successively. This work also includes a comparison between theoretical calculations and experimental results of X-ray crystallography and nuclear magnetic resonance spectroscopy extracted from protein data bank.

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Quantum Chemical Calculations on Small Protein Models

et al. 2014

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An ab initio exploratory study of the full conformational space of MeCO-l-threonine-NH-Me

Cited by 7 publications

References 28 publications

First-Principle Computational Study on the Full Conformational Space of l-Threonine Diamide, the Energetic Stability of Cis and Trans Isomers

First-Principle Computational Study on the Full Conformational Space of l-Threonine Diamide, the Energetic Stability of Cis and Trans Isomers

An exhaustive conformational analysis of N-formyl-l-tyrosinamide using a genetic algorithm for multimodal search

Quantum Chemical Calculations on Small Protein Models

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