Modeling the protein-nucleic acid base interactions through hydrogen-bonded complexes of N-heterocyclic analogs of Inden
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ORIGINAL RESEARCH
Modeling the protein-nucleic acid base interactions through hydrogen-bonded complexes of N-heterocyclic analogs of Indene with amino acid side-chain mimics Neha Chopra 1 & Geetanjali Chopra 1 & Damanjit Kaur 1 Received: 15 April 2020 / Accepted: 22 July 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract A series of hydrogen-bonded complexes between N-heterocyclic analogs of Indene and amino acid side-chain mimics have been analyzed employing second-order Møller-Plesset perturbation (MP2) theory and density functional theory with dispersion function (DFT-D) calculations with the aim of gaining greater insight in to the nature of intermolecular interactions in these systems. In this study, the hydrogen bonding ability of N-heterocyclic analogs of Indene towards amino acid side-chain mimics follows the sequence Azaindazole (AIND) > Indazole (IND) > Azaindole (AIN) > Indole (IN) whereas the hydrogen bonding ability of amino acid side-chain mimics towards N-heterocyclic analogs of Indene follows the sequence AcOH > MeNH2 > MeOH > MeSH. Bader’s theory of atoms in molecules (AIM) and natural bond orbitals (NBO) analyses are employed to elucidate the interaction characteristics in the complexes under study. The purpose of conducting these studies is to measure the relative strength of hydrogen bonding interactions such as N-H···O=C, N-H···O, N-H···S, N-H···N, and O-H···N in these complexes and their role in providing stability to the complexes. The AIM theory shows good correlation of the electron density and its Laplacian at the bond critical points (BCP) with the computed stabilization energy for all the complexes under study. Keywords Hydrogen bonding . N-heterocyclic analogs of Indene . Amino acid side-chain mimics . NBO . AIM
Introduction Hydrogen bonding is thought to play a critical role in stabilizing the structures of biological molecules such as proteins or nucleic acid [1, 2]. The participation of the amino acid in hydrogen bonding interaction is a well-recognized factor in many biologically relevant processes such as protein-nucleic acid interaction, protein-protein interaction, α-helices, and βsheets formation. There are a number of amino acid residues that can form hydrogen bonds (HBs) via their side chains. Perhaps most notable of this category are side chains that contain hydroxyl (serine and threonine), acetic acid (aspartic Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11224-020-01600-1) contains supplementary material, which is available to authorized users. * Neha Chopra [email protected] 1
Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
and glutamic acids), amino (lysine and arginine), and thiol (cysteine) that are known to participate in HBs. Among the molecules of biological interest, N-heterocyclic analogs of Indene (Indole, Indazole, Azaindole, Azaindazole) are structural constituents of many bioactive natural products and have gained much research pursuit in the fi
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