Maymand, Vahid Mahmoudi Bavi, Omid Karami, Abbas
Published in
Chemical Physics
SARS-CoV-2-encoded accessory protein ORF3a was found to be a conserved coronavirus protein that shows crucial roles in apoptosis in cells as well as in virus release and replications. To complete the knowledge and identify the unknown of this protein, further comprehensive research is needed to clarify the leading role of ORF3a in the functioning o...
Nguyen, Trung Hai Tam, Nguyen Minh Tuan, Mai Van Zhan, Peng Vu, Van V Quang, Duong Tuan Ngo, Son Tung
Published in
Chemical physics
Inhibiting the biological activity of SARS-CoV-2 Mpro can prevent viral replication. In this context, a hybrid approach using knowledge- and physics-based methods was proposed to characterize potential inhibitors for SARS-CoV-2 Mpro. Initially, supervised machine learning (ML) models were trained to predict a ligand-binding affinity of ca. 2 millio...
Thakur, Yamini Pande, Rama
Published in
Chemical physics
In the present investigation, molecular docking studies have been performed using AutoDock Vina to investigate the role of ligand-binding affinity at the hydrophobic pocket of COVID-19. The knowledge of the binding of protein receptors with ligand molecules is essential in drug discovery processes. Hydroxamic acids with reported biological activity...
Faisal, H.M. Nasrullah Katti, Kalpana S. Katti, Dinesh R.
Published in
Chemical Physics
The SARS-CoV-2 coronavirus (COVID-19) that is causing the massive global pandemic exhibits similar human cell invasion mechanism as the coronavirus SARS-CoV, which had significantly lower fatalities. The cell membrane protein Angiotensin-converting enzyme 2 (ACE2) is the initiation point for both the coronavirus infections in humans. Here, we model...
Amir Karton
Published in
Chemical Physics
Shape-shifting molecules such as bullvalene undergo rapid structural reorganizations via degenerate Cope rearrangements. Here, we obtain accurate CCSD(T)/CBS barrier heights and reaction energies for a wide range of Cope rearrangements in substituted bullvalenes (C10H9R, R = NH3, OH, CH3, H, F, Cl, SH, and CN). We use this benchmark dataset to eval...
Liu, Jian Zhai, You Liang, Lijun Zhu, Danyan Zhao, Qingwei Qiu, Yunqing
Published in
Chemical Physics
Coronavirus disease 2019 (COVID-19) has caused more than 840,000 deaths as of 31 August 2020 in the whole world. The COVID-19 main protease (Mpro) has been validated as an attractive target for drug design. In this work, the binding mechanisms of five protease inhibitors (e.g., danoprevir, darunavir, ASC09, lopinavir and ritonavir) to COVID-19 Mpro...
Kerboua, Kaouther Oualid Hamdaoui
Published in
Chemical Physics
A particular case of harmonics excitation using ultrasonic waves with the frequencies of 200, 300 and 500 kHz at an acoustic amplitude of 2 atm is numerically investigated in the present paper, as a new method aiming to improve the sonochemical production of hydrogen within active cavitation bubble. The modification of the conventional sine signal,...
Sen, Dwaipayan Roy, Proyasha Nandy, Ashesh Basak, Subhash C Das, Sukhen
Published in
Chemical physics
Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes. © 2018 Elsevier B.V. All rights reserved.
Yu, Li-Juan Sarrami, Farzaneh O’Reilly, Robert J. Amir Karton
Published in
Chemical Physics
We introduce a database of 20 accurate cycloreversion barrier heights of 5-membered heterocyclic rings (to be known as the CRBH20 database). In these reactions, dioxazole and oxathiazole rings are fragmented to form isocyanates, isothiocyanates, and carbonyls. The reference reaction barrier heights are obtained by means of the high-level, ab initio...
Rajaboopathi Mani Rietveld, Ivo B. Nicolaï, Béatrice Varadharajan, Krishnakumar Louhi-Kultanen, Marjatta Narasimhan, Surumbarkuzhali
Published in
Chemical Physics
Organic salt 2-chloro-4-nitrobenzoate (CNBA−) 3-ammonium-phenol (AP+) exhibits fluorescence at 338 nm in solution and frontier molecular orbitals generated from TDDFT calculations indicate that the ground state and the excited state are physically separated on AP+ and CNBA−. The crystal structure and physical–chemical properties of the CNBA− · AP+ ...
