DFT study on reaction mechanisms of cyclic dipeptide generation

Li, Yue; Li, Fangfang; Zhu, Yanyan; Xue, Li; Zhou, Ziyuan; Liu, Chunmei; Zhang, Wenjing; Tang, Mingsheng

doi:10.1007/s11224-016-0740-y

Cited by 22 publications

(19 citation statements)

References 53 publications

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“…Its neutral form is generally favored in the gas phase, while its zwitterionic form is favored in solution and the solid-state [ 20 ]. Li and coworkers studied the solvent effects on the cyclization of a dipeptide from neutral monomers [ 21 ]. Numerous computational studies have been conducted to investigate the formation mechanism of glycine through a radical-radical reaction involving t-HOCO and CH 2 NH 2 [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Assisted dipeptide bond formation: glycine as a case study

Achour

Hosni

Darghouthi

et al. 2021

Heliyon

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Peptide bond formation is a crucial chemical process that dominates most biological mechanisms and is claimed to be a governing factor in the origin of life. Dipeptides made from glycine are studied computationally via Density Functional Theory (DFT) using two different basis sets. This reaction was investigated from both a thermodynamic and kinetic point of view. The effect of explicit assistance via the introduction of discrete solvent molecules was investigated. Water, methanol, and cyclohexane were all employed as solvent media in addition to gas to investigate their effects on the mechanism of peptide bond formation. This computational investigation revealed that methanol is slightly better than water to leverage peptide bond formation both kinetically and thermodynamically, while cyclohexane, a non-polar and non-protic solvent, is the least effective after gas as a medium of solvation. Energetic results in the gas environment are very close to those obtained in polar and protic solvents, suggesting that peptide bonds can be formed under interstellar conditions.

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Section: Introductionmentioning

confidence: 99%

Assisted dipeptide bond formation: glycine as a case study

Achour

Hosni

Darghouthi

et al. 2021

Heliyon

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“…[62][63][64] Two possible reaction pathways (Path-1 and Path-2) have been proposed for this process. [65] In the first path (Path-1) the dipeptide is generated through transfer of a hydrogen atom from the amino group of one amino acid to the carboxyl group of the other amino acid. This leads to the elimination of a water molecule together with the formation of a CÀ N bond.…”

Section: Resultsmentioning

confidence: 99%

“…The peptide bond formation has been reported to be preferred via an intermolecular pathway rather than an intramolecular route. [65] The GlyGly dipeptide formation through uncatalyzed intermolecular hydrogen transfer encounters a barrier of 0.96 eV ( Figure 5). The Au 3 cluster catalyst directs this process through a barrier of 0.57 eV ( Figure 6).…”

Section: Resultsmentioning

confidence: 99%

Mechanistic Details and Conformational Behavior of Selective Peptide Linkage Facilitated by Au_n Clusters

et al. 2020

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The interactions of amino acids Glycine and Alanine with gold clusters, Aun (n=3, 8, 16) have been studied in both gas and aqueous phase within the formalism of density functional theory (DFT). The amino acid binds to the cluster with its amine/carboxyl end securely anchored to the cluster. Selective peptide synthesis has been explored for Glycylglycine (GlyGly) and Glycylalanine (GlyAla) dipeptides in aqueous medium via two different reaction pathways. Path‐

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“…2 were performed with the Gaussian 09 program 77 by using the density functional theory, which has been credited as a powerful tool for clarifying detailed reaction mechanisms and predicting stereoselectivity and chemoselectivity in both organic and biological reactions. 78 All geometries of the molecules were fully optimized in water with CPCM solvent model at the B3LYP/ 6-31G(d) level of DFT theory with Gaussian 09 soware package. 79…”

Section: Dft Optimization Of the Structuresmentioning

confidence: 99%