Article
Version 1
Preserved in Portico This version is not peer-reviewed
Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotides Fragments
Version 1
: Received: 4 June 2024 / Approved: 5 June 2024 / Online: 6 June 2024 (11:31:12 CEST)
A peer-reviewed article of this Preprint also exists.
Tarek Ibrahim, M.; Wait, E.; Ren, P. Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments. Molecules 2024, 29, 3258. Tarek Ibrahim, M.; Wait, E.; Ren, P. Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments. Molecules 2024, 29, 3258.
Abstract
Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structures and functions, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides’ structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragment and water were analyzed. Different quantum mechanical methods were compared for their accuracy in captuing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab-initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These caculations provide the benchmark for different QM methods while providing valuable understanding of the roles of various interamolecular forces in hydrogen bonding and aromatic stacking.
Keywords
Nucleotides; ALMO EDA2; SAPT2+(3)/dmp2; Dispersion; Induction
Subject
Chemistry and Materials Science, Physical Chemistry
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Comments (0)
We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.
Leave a public commentSend a private comment to the author(s)
* All users must log in before leaving a comment
