An ab initio study of the side chain of Nafion

The stabilization effect of the Me group with respect to H has been determined for peptides of the type HCO-(NH-CHR-CO)n-NH2 for 1 ≤ n ≤ 3. It was found that for the Me group the stabilization energy was in the vicinity of 5.4 kcal/mol. The site of substitution had no appreciable effect on the stabilization energy. The stabilization energy for monomethyl substitution (R=CH3) ranged from 5.21 to 5.60 kcal/mol. For dimethyl substitution the values were between 10.53 and 10.81 kcal/mol, and for trimethyl substitution it was 15.99 kcal/mol. Keywords: stabilization effects of substituents, oligopeptide conformations, ab initio study on HCO-(NHCHRCO)n-NH2.

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Quantum-Chemical ab initio Study of Side Chain pKa of Linear and Cyclic Lysine Dipeptides

Journal of Computational Biophysics and Chemistry ◽

10.1142/s2737416520420028 ◽

2020 ◽

pp. 1-9

Author(s):

Mohsen Sargolzaei ◽

Hossein Nikoofard ◽

Majid Namayandeh Jorabchi

Keyword(s):

Experimental Data ◽

Hydrogen Bond ◽

Ab Initio ◽

Quantum Chemical ◽

Biological Activities ◽

Side Chain ◽

Ab Initio Study ◽

Cyclic Dipeptides ◽

Pka Values ◽

Pka Value

Cyclic dipeptides show interesting biological activities such as antitumor, antiviral and so on. In biological systems, the bioavailability of drugs is determined by several parameters such as pKa values. In this study, we used DFT and thermodynamics cycle to determine pKa value of side chain of lysine in linear and cyclic dipeptides. All considered dipeptides were optimized using B3LYP and RMSD tool was used to compare the optimized structures. The calculated pKa values were compared with the available experimental data. Our results show that pKa of side chain of lysine increases for cyclic dipeptides compared to the linear ones. To justify the reason of increasing of pKa of cyclic dipeptides, we used NBO and AIM analyses. The analyses showed that a hydrogen bond in cyclic lysine dipeptides is responsible for increasing of pKa.

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An exploratory ab initio study on the conformations of ethylguanidine in its neutral [CH3-CH2-NH-C(=NH)NH2] and protonated [CH3-CH2-NH-C(NH2)2] forms

Canadian Journal of Chemistry ◽

10.1139/v00-065 ◽

2000 ◽

Vol 78 (5) ◽

pp. 626-641 ◽

Cited By ~ 2

Author(s):

Melody L Mak ◽

Salvatore J Salpietro ◽

R Daniel Enriz ◽

Imre G Csizmadia

Keyword(s):

Dft Calculations ◽

Conformational Analysis ◽

Ab Initio ◽

Internal Symmetry ◽

Basis Sets ◽

Side Chain ◽

Torsional Angle ◽

Ab Initio Study ◽

Single Isomer ◽

Arginine Side Chain

To explore the conformation intricacies of the guanidine group in the arginine side chain, ab initio computations have been carried out with ethylguanidine and the ethyl guanidinium ion. HF computations have been performed using 3-21G and 6-31G basis sets and DFT calculations were carried out at the B3LYP/6-31G(d) level of theory. The ethyl guanidinium ion has a single isomer due to its internal symmetry, although this structure has at least three conformations. However, several structures were found and optimized for ethylguanidine, involving the endo- and exo- orientation of the lone NH and torsional angle χ6, as well as the torsional modes associated with χ4 and χ5. Torsional angle χ5 gives rise to s-cis and s-trans structures.Key words: ethylguanidine, ethylguanidinium ion, ab initio MO, arginine side-chain, conformational analysis.

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