Article
Chemistry, Physical
Alessandra G. Ritacca, Anna Rovaletti, Giorgio Moro, Ugo Cosentino, Ulf Ryde, Emilia Sicilia, Claudio Greco
Summary: This study proposes a novel mechanism for the oxidation of CO into CO2 by Mo/Cu CO dehydrogenase, and explores the role of a stable thiocarbonate intermediate. The findings suggest that the thiocarbonate does not interfere with the CO oxidation catalytic cycle, highlighting the importance of environmental effects in computational modeling.
Article
Chemistry, Physical
Dong Zhai, Hong-Lei Wang, Li Yang, Lei Sun, Weiqiao Deng
Summary: The morphology of nanocrystals is crucial for their physical and chemical properties. Developing a time-saving scheme for nanocrystal optimization is important. This study introduces an iterative global optimization method that combines quantum mechanics (QM) and molecular mechanics (MM) methods. The method uses a subtractive approach to describe QM/MM energy and incorporates a genetic algorithm technique. Benchmark simulations on gold nanocrystals demonstrate the efficiency of the proposed scheme in finding the global minimum.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Chemistry, Physical
Hugo Salazar-Lozas, Jose Manuel Guevara-Vela, Angel Martin Pendas, Evelio Francisco, Tomas Rocha-Rinza
Summary: Partitions of electronic energy, such as the Interacting Quantum Atoms (IQA) approach, have provided valuable insights for chemical systems and processes. However, the computational effort required for this analysis is often large and prohibitive. This study aims to carry out partitions of the semiempirical method PM7 in compliance with the IQA approach. The partitioned electronic energies computed via the PM7 method are shown to give further insights into the interactions occurring within complex systems in physical and biological chemistry.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Hunday Govindasamy, Sivanandam Magudeeswaran, Saravanan Kandasamy, Kumaradhas Poomani
Summary: The study demonstrates that naringenin acts as a potential inhibitor of MAO-B enzyme, preventing the development of Parkinson's disease. Molecular docking simulations confirm strong binding between naringenin and MAO-B, with the complex remaining stable throughout molecular dynamics simulations. QM/MM analysis reveals the charge density distribution and strength of intermolecular interactions in the naringenin-MAO-B complex.
Article
Engineering, Electrical & Electronic
Shuang Wang, Shikai Li, Junfeng Jiang, Tianhua Xu, Ke Tan, Xiaoshuang Dai, Zhiyuan Li, Xinyun Sun, Hongyu Liu, Tiegen Liu
Summary: A method is proposed to correct the fringe order jumps in polarization low-coherence interferometry by exploiting the dispersion compensation equation. The relationship between the deviation phase and the envelope peak of the interference fringes is established to eliminate the fringe order jump error caused by dispersion.
IEEE SENSORS JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Cui Liu, Yang Ren, Xiao-qin Gao, Xue Du, Zhong-zhi Yang
Summary: This study developed a new simulation method to accurately simulate the mechanism of DNA glycosylase removing damaged bases. The results confirm that the monofunctional mechanism of Asp-activated nucleophile water is a better deglycosylation mechanism and the base is protonated before the reaction occurs. This research provides a theoretical basis for the study of DNA glycosylase excising damaged bases.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Lukasz Charzewski, Krystiana A. Krzysko, Bogdan Lesyng
Summary: In recent years, molecular covalent docking has been extensively developed for designing inhibitors that form chemical bonds with their biological targets, particularly boron-based inhibitors for antibiotic-resistant bacteria. This study accurately describes the covalent docking process between two model inhibitors representing different classes of inhibitors and three beta-lactamases. The study utilizes quantum mechanical approaches and multi-scale modeling methods to explain the structural changes and geometric preferences leading to covalent docking processes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Energy & Fuels
Jun Zhang, Ting Chen, Yi Jiao, Mei Cheng, Lin-Lin Wang, Jian-Li Wang, Xiang-Yuan Li, Yao-Qiang Chen
Summary: In this study, NieMo/SiO2 bimetallic catalysts were synthesized using different preparation methods and additives, with the sol-gel method showing the best catalytic performance. The introduction of additives by sol-gel method helped modulate acidity and enhance catalytic activity, resulting in improved conversion and heat sink. Overall, the catalyst synthesized via sol-gel method with citric acid addition exhibited the highest conversion and heat sink for the cracking reaction of methylcyclohexane.
Article
Geochemistry & Geophysics
Haoyu Lin, Yunkai Deng, Heng Zhang, Jili Wang, Yongwei Zhang
Summary: This letter proposes an extended model to describe the ionospheric dispersion effects of nonlinear frequency modulation (NLFM) signals, and compares the differences in ionospheric dispersion effects between NLFM and linear frequency modulation (LFM) signals. Additionally, a method embedded into the focusing procedure is proposed to eliminate ionospheric dispersion effects for NLFM signals.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Article
Chemistry, Physical
Hai-Yang Sun, Zi-Yue Yu, Ai-Ping Zhou, Shu-Li Wei, Qiang Chang, Tian Zhang, Yu-Ping Sun
Summary: The luminescent mechanism of two novel TADF emitters with aggregation-induced emission (AIE) features, PPZTPI and PPZPPI, are theoretically studied in this article using first-principles calculations. Both PPZTPI and PPZPPI exhibit excellent TADF and AIE properties with similar luminescence mechanisms. In the solid state, the delayed fluorescence of the molecules mainly depends on the reverse intersystem crossing process, and the aggregation enhances the molecular radiation rates by 1-2 orders of magnitude. The solid-state environment has a greater influence on PPZTPI's molecular properties due to the substitution of tert-butyl groups and their steric hindrance effects.
Article
Chemistry, Multidisciplinary
Dhaval Patel, Mohd Athar, Prakash C. Jha
Summary: Recent advancements in metal-organic frameworks have led to the discovery of novel metal-based compounds with anticancer, antibacterial, and antimalarial properties. By mimicking hypervalent carbon atoms with transition metals, it is possible to design bioactive compounds with optimized parameters for molecular docking and dynamics simulations. Computational drug discovery and parameterization of organometallic ligands show promising potential for developing new treatments for diseases like cancer.
Review
Chemistry, Multidisciplinary
Taehwan Jang, Dooam Paik, Seung-Jae Shin, Hyungjun Kim
Summary: Solid-liquid interfaces play a crucial role in various scientific and technological systems. However, the research on interfacial structures is still limited due to the difficulties in experimental techniques. Computational methods provide a possible solution, but current molecular simulation methods have limitations in simulating large interfacial systems. In order to overcome these limitations, a mean-field quantum mechanics/molecular mechanics (QM/MM) method has been developed.
BULLETIN OF THE KOREAN CHEMICAL SOCIETY
(2022)
Article
Oceanography
Peitao Wang, Lining Sun, Lianda Zhao
Summary: This study proposes an effective depth-correction method to reduce the arrival time differences between observed and modeled waveforms in the deep ocean. The method utilizes the derivation of effective ocean depth to mimic secondary physical effects, resulting in a significant improvement in computational efficiency and accuracy for tsunami warning and waveform inversion.
Article
Chemistry, Multidisciplinary
Yuyang He, Caihong Gao, Wei Wei, Yun Liu
Summary: Molybdenum is a redox-sensitive metal element that can be used to reconstruct oceanic oxygenation extent. This study provides a method to accurately predict the isotope fractionation factors of molybdenum in aqueous systems, allowing for better reconstruction of ancient seawater compositions.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yuyang He, Caihong Gao, Wei Wei, Yun Liu
Summary: Molybdenum isotope composition has the potential to reconstruct oceanic oxygenation extent in deep time. Understanding the Mo isotope fractionation mechanism is necessary for accurate reconstruction. The ONIOM method proves to be efficient in predicting beta factors of MoOxS42- species in aqueous phases, providing basic data for reconstructing delta 98Mo values in various sediments.
ACS EARTH AND SPACE CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Buthaina Hussein, Balqis Ikhmais, Manikandan Kadirvel, Rachael N. Magwaza, Gavin Halbert, Richard A. Bryce, Ian J. Stratford, Sally Freeman
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2019)
Article
Microbiology
Priyanka Panwar, Kepa K. Burusco, Muna Abubaker, Holly Matthews, Andrey Gutnov, Elena Fernandez-Alvaro, Richard A. Bryce, James Wilkinson, Niroshini Nirmalan
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2020)
Article
Chemistry, Medicinal
Mohammad A. Ghattas, Sara Al Rawashdeh, Noor Atatreh, Richard A. Bryce
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Multidisciplinary Sciences
Vibha Singh, Siddhant Bhoir, Rupesh V. Chikhale, Javeena Hussain, Donard Dwyer, Richard A. Bryce, Sivapriya Kirubakaran, Arrigo De Benedetti
Article
Chemistry, Multidisciplinary
Ebru Aksanoglu, Yee Hwee Lim, Richard A. Bryce
Summary: The deoxydehydration of carbohydrates can be achieved using a vanadium(V)-based catalyst, with different mechanisms involved for trans-diol and cis-diol substrates. The process involves stepwise cleavage of C-O bonds for cyclic trans-diols, while cyclic cis-diols and linear diols can proceed via a concerted singlet mechanism. This work opens up new possibilities for efficiently converting carbohydrates into alkenes.
Article
Biology
Jack P. Green, Tessa Swanton, Lucy Morris, Lina Y. El-Sharkawy, James Cook, Shi Yu, James Beswick, Antony D. Adamson, Neil E. Humphreys, Richard Bryce, Sally Freeman, Catherine Lawrence, David Brough
Article
Chemistry, Medicinal
Mai A. Elhemely, Asma A. Belgath, Sherihan El-Sayed, Kepa K. Burusco, Manikandan Kadirvel, Annalisa Tirella, Katherine Finegan, Richard A. Bryce, Ian J. Stratford, Sally Freeman
Summary: A set of meta-substituted 3-arylisoquinolinones with substantial cytotoxicity in various cancer cell lines has been discovered. These compounds have the potential to mimic colchicine and interact with microtubules, leading to antiproliferative effects and inhibition of endothelial cell formation.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Lara Alzyoud, Richard A. Bryce, Mohammad Al Sorkhy, Noor Atatreh, Mohammad A. Ghattas
Summary: The druggability of 12 commonly targeted PPIs was assessed using the computational tool SiteMap. The binding sites of PPIs were found to have varying druggability scores due to unique structural and physiochemical features. A classification system based on these features was proposed to assess the druggability of PPI targets. The study also found that protein flexibility and drug-likeness are important factors to consider in the design of PPI inhibitors.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Ismaeel Ramzan, Jas Kalayan, Linghan Kong, Richard A. Bryce, Neil A. Burton
Summary: This work presents a machine learning approach based on pairwise interatomic forces to predict atomic forces in a molecule with quantum chemical accuracy. The method uses a neural network to predict Cartesian forces as a linear combination of force components, which exhibit chemically intuitive profiles and reduce computational costs for molecular dynamics simulations.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Linghan Kong, Richard A. Bryce
Summary: This research evaluates the ability of machine learning potentials and semiempirical quantum chemical methods to model ring pucker conformers of carbohydrates. The results show that the machine learning method ANI-1ccx accurately reproduces the ring pucker energy landscape and provides the most accurate estimate of the energetics. The study also finds that all three models reproduce chair more accurately than non-chair geometries.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Sherihan El-Sayed, Sally Freeman, Richard A. Bryce
Summary: The NLRP3 inflammasome is an important target in drug discovery, and natural products have been explored as potential inhibitors for the design of novel selective NLRP3 inhibitors.
Article
Biochemistry & Molecular Biology
Sherihan El-Sayed, Sally Freeman, Richard A. Bryce
Summary: This study investigates the impact of NEK7 and cofactor interactions on the conformation and dynamics of NLRP3 in aqueous solution through the construction and simulation of computational models. The results demonstrate that molecular dynamics simulation accurately reproduces the characteristics of the ADP-bound NLRP3-NEK7 complex and reveals a more compact closed form of NLRP3 upon the removal of NEK7 during simulations.
Article
Biochemical Research Methods
Richard A. Bryce, James A. Platts
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Biochemical Research Methods
Linghan Kong, Rasha Alqus, Chin W. Yong, Ilian Todorov, Stephen J. Eichhorn, Richard A. Bryce
Summary: The interaction between graphene and cellulose has potential in designing new graphene-carbohydrate biopolymer materials. The hydrophilicity of cellulose and the interactions between cellulose chains and graphene play important roles in the adsorption and structural accommodation process.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Meeting Abstract
Oncology
Siddhant Bhoir, Javeena Hussain, Vibha Singh, Rupesh Chikhale, Richard Bryce, Sivapriya Kirubakaran, Arrigo DeBenedetti