Abstract

The goal of the present work was to evaluate the chemical reactivity of amino acids with polar uncharged side chains (serine, threonine, asparagine and glutamine) using density functional theory (DFT) and thermodynamics modeling by calculating a series of molecular descriptors and properties of their optimized geometries. The predictive calculations were achieved with Spartan software from Wavefunction, Inc. Irvine, CA, USA, hybrid algorithm B3LYP (Becke’s three-term functional; Lee, Yang, Parr exchange hybrid) and polarization basis set 6-31G(d,p) for equilibrium geometry at ground state in vacuum and in water, after energy minimization and geometry optimization. Thermodynamic properties (zero-point energy, enthalpy, constant volume heat capacity, entropy and Gibbs energy) for these derivatives were calculated and related to electrochemical ligand behavior. Reduction and oxidation potentials were correlated to their calculated energy levels for molecular orbitals.

Highlights

  • The group of amino acids with polar uncharged side chains is composed of serine, threonine, asparagine and glutamine

  • The characteristics were obtained on the optimized geometries of these amino acids by energy minimization in order to obtain the most stable conformer

  • The computed data represent important information for physicochemical behavior of the studied amino acids; the presence of a second, additional hydroxyl group on the amino acid skeleton, at serine, strongly affects the electron charge distribution, and the polar surface area (PSA) and the dipole moment are greatest for serine

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Summary

Introduction

One of the most useful manners by which to classify the standard amino acids is based on the polarity of the side chain. The group of amino acids with polar uncharged side chains is composed of serine, threonine, asparagine and glutamine. The side chains in this group possess a spectrum of functional groups. The main aim of this study was to investigate all possible intermolecular interactions of these amino acids using density functional theory. The ground state geometries of the molecules in gas phase were optimized using density functional theory (DFT) [1]. To improve the description of the van der Waals interactions, we employed the empirical van der Waals correction proposed by Grimme, as implemented in the B3LYP functional in conjunction with 6-31G(d,p) basis set [2]

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