Molecular structure and vibrational spectra of N‐acetylglycine oligomers and polyglycine I using DFT approach

Abstract

We have determined the geometric, vibrational, and electronic properties of N-acetylglycine oligomers by performing density functional theory quantum chemical calculations. The normal mode analysis was performed and the potential energy distribution was calculated among the internal coordinates. The optically active vibrational modes of PGI have been determined by selecting the modes from the calculated results of the pentamer and the observed vibrational spectra of PGI have been explained. The molecular electrostatic potential surface of N-acetylglycine pentamer reveals the sites of electrophilic attack and also provides clues for the role of electrostatic interactions involved in the reactivity. Natural bond orbital analysis has been performed to understand the charge transfer and various hyperconjugative interactions in the molecular system. The electronic properties of the oligomers have been discussed by calculating the transitions with the help of time dependent density functional theory method. The global reactivity descriptors such as hardness, chemical potential, and electrophilicity index have also been calculated.

Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects

“…It can be deduced that a conventional β-strand cannot be stabilized in GGG embedded in continuum. This result corroborates the previous DFT calculations on other G repeats placed in vacuum [59]. The peptides Ac-(Gly)n-COOH (where n=3-5) show all a planar backbone whatever their initial conformation (PG-I or PG-II) [60].…”

Molecular basis of the recognition of arachidonic acid by cytochrome P450 2E1 along major access tunnel

“…Remarkably, in both ligands, the most important contributions of binding affinity are coming from the intermolecular electrostatic interactions which are generally presented as hydrogen bonds between the receptor and the ligand. The intermolecular electrostatic contributions for AA are much lower than that for x-imidazolyl dodecanoic acid by 2169.01 kcal mol 21 . The large differences between the intermolecular electrostatic contributions may be attributed to the larger amount of hydrogen bonds formed between AA and His107, Ala108, His109, and Lys243, as compared to x-imidazolyl dodecanoic acid, which can only form hydrogen bonds with His109 during the simulation.…”

“…In the present study, AA is deprotonated. The structural optimization of AA was conducted using B3LYP combined with 6–31+G* basis set using the Gaussian09 software. RESP fitting procedure was used for charge derivation based on the optimal conformation.…”

“…where DG represents the free energy change between the initial and final states, W 0!k is the work performed from state 0 to state k. b 5 (k B T) 21 , where k B and T are the Boltzmann constant and temperature, respectively. The term in broken brackets on the right-hand side is the exponential average, and it is highly possible that insufficient sample data cause large statistical errors.…”

Exploring the structure characteristics and major channels of cytochrome P450 2A6, 2A13, and 2E1 with pilocarpine

“…Hydrogen atoms were subsequently added to the complexes structures using the t‐leap module of AMBER 12 . The structural optimization of pilocarpine was conducted using B3LYP/6–31G* basis set by using the Gaussian09 software . The restrained electrostatic potential (RESP) fitting procedure was used for charge derivation based on the optimal conformation of pilocarpine (Supporting Information Figure S2).…”