A theoretical study of the structure and electron density of the peptide bond

Saada, Iskandar; Pearson, Jason K.

doi:10.1016/j.comptc.2011.05.023

Cited by 12 publications

(3 citation statements)

References 57 publications

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“…In this database, all structures were obtained via basin-hopping global optimization , performed with a nonreactive force field, followed by a local optimization with the PBE functional including a TS dispersion correction for a numerical atom-centered orbital basis set . For the comparison of reaction energies and the subsequent investigation of pathways for condensation reactions, the dipeptide structures from Saada and Pearson were geometry-optimized using Gaussian09 at the B3LYP/6-311+G(d,p) level of theory with a D2 dispersion correction and a tight root-mean-square gradient (RMSG) convergence criterion of 10 –5 Hartree Å –1 . We will refer to these DFT calculations as the QM results below.…”

Section: Methodsmentioning

confidence: 99%

Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications

Moerman

Furman

Wales

2020

J. Chem. Theory Comput.

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Four established ReaxFF force fields, trained on biochemical systems, have been systematically benchmarked on 20 proteinogenic amino acids and 11 dipeptides. The force fields were compared with respect to geometries, energetics, and atomic charges of conformers for the amino acids. To assess the performance with respect to reactivity, the condensation reactions for the formation of dipeptides were investigated by calculating the reaction energetics and pathways. We found systematic errors in the torsion angles for the amino acids, with deviations over 100°, and a generally incorrect account of relative energies for amino acid conformers. In describing the reactivity, only one of the force fields could reproduce the reaction energies of amino acid condensations quantitatively. All four force fields predict unphysical mechanisms for these reactions, involving highly unstable intermediate structures, proton transfers involving aliphatic protons, and even five-coordinate carbon atoms. The corresponding energy landscapes exhibit fluctuations on small length scales and artificial minima.

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Section: Methodsmentioning

confidence: 99%

Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications

Moerman

Furman

Wales

2020

J. Chem. Theory Comput.

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“…The geometry of the simulated complexes was optimized at the B3LYP/6-311++G(d,p) computational level using Gaussian 09 suite of programs [33]. The B3LYP/6-31++G(d,p) methodology was used to locate the stationary points along the potential energy surface because it is a cost-effective method and has widely been applied to H-bonded complexes as model systems [34][35][36][37][38][39]. The basis set superposition error (BSSE) was calculated by the counterpoise method of Boys and Bernardi [40].…”

Section: Computational Details and Methodologymentioning

confidence: 99%

Theoretical insight to intermolecular hydrogen bond interactions between methyl N-(2-pyridyl) carbamate and acetic acid: substituent effects, cooperativity and energy decomposition analysis

Chalanchi

Ebrahimi

Nowroozi

2019

BCC

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In the present work, the hydrogen bond (HB) interactions between substituted syn and anti rotamers of methyl N-(2-pyridyl) carbamate and acetic acid were investigated using quantum mechanical (QM) calculations. The rotamers have two typical active sites to form hydrogen bonds with acetic acid, such that four stable complexes are found on the potential energy surface. The complexes in which the oxygen atom of carbamate acts as proton acceptor are stabilized by EWSs and are destabilized by EDSs. The trend in the effects of substituents is reversed in the other two complexes, in which the nitrogen atom of ring is involved in the interaction. According to energy data, the substituent effects on the interaction energy can be expressed by Hammett constants. The natural resonance theory (NRT) model was used to investigate the charge distribution on the carbamate group and to discuss the interaction energies. The individual HB energies were estimated to evaluate their cooperative contributions on the interaction energies of the complexes. In addition, the localized molecular orbital energy decomposition analyses (LMO-EDA) demonstrate that the electrostatic interactions are the most important stabilizing components of interactions.

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“…In applications of FMO to polypeptides, CαÀ C bonds [26] are almost always used as fragment boundaries, instead of peptide CÀ N bonds, [31,32] leading to fragments being shifted from conventional residues by a CO group, which can obfuscate analyses detailing the role of residues in molecular recognition studies. Two solutions have been proposed to the shifted residue problem, (1) a compensation [33] for the poor accuracy of the CÀ N detachment by the third-order expansion FMO3 and (2) a repartitioning of properties 34 developed for density-functional tight-binding (DFTB).…”

Section: Introductionmentioning

confidence: 99%

The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation

Fedorov

2024

ChemPhysChem

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The enhancement of the peptide bond order by a resonance in the lone pair of N and the π‐bond of CO is analyzed. A decomposition of the bond order in terms of localized molecular orbitals is developed and applied to the peptide bond. A combination of two rotations of hybrid orbitals is proposed to improve the boundary treatment in the fragment molecular orbital method. The developed approach is applied to peptide bonds, and it is found crucial to retain the π orbital in the variational space of both fragments across the boundary. The interaction energies between conventional amino acid residues in Trp‐cage (1L2Y) are discussed.

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A theoretical study of the structure and electron density of the peptide bond

Cited by 12 publications

References 57 publications

Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications

Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications

Theoretical insight to intermolecular hydrogen bond interactions between methyl N-(2-pyridyl) carbamate and acetic acid: substituent effects, cooperativity and energy decomposition analysis

The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation

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