Article
Chemistry, Multidisciplinary
Ankita Tripathi, Kshatresh Dutta Dubey
Summary: This study demonstrates a method to enhance promiscuity, called allostery-driven promiscuity, using molecular dynamics simulations and hybrid QM/MM calculations. By studying the AEE enzyme, the authors show that a single site mutation can induce conformational changes in the capping loop, allowing recognition of different substrates for different functions.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Chemistry, Medicinal
Bharath Raghavan, Florian K. Schackert, Andrea Levy, Sophia K. Johnson, Emiliano Ippoliti, Davide Mandelli, Jogvan Magnus Haugaard Olsen, Ursula Rothlisberger, Paolo Carloni
Summary: MiMiC is a flexible and scalable multiscale modeling framework that combines quantum mechanics (QM) and molecular mechanics (MM) codes. The paragraph introduces MiMiCPy, a user-friendly tool written in Python 3 that automates the preparation of MiMiC input files. It also highlights the modular structure of MiMiCPy, allowing for easy extensions to new program formats.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Yuzhuang Fu, Fangfang Fan, Binju Wang, Zexing Cao
Summary: Enzymatic degradation of pesticides paraoxon (PON) and parathion (PIN) by phosphotriesterase (PTE) has been studied using QM/MM calculations and MD simulations. The results reveal that the hydrolysis reactions are driven by nucleophilic attack and the rate-limiting step is the two-step hydrolytic process.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Shunya Suenaga, Yu Takano, Toru Saito
Summary: A quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) study was conducted on three representative competitive inhibitors of urease. The study found that N-(n-butyl)phosphorictriamide (NBPTO) exhibited the highest inhibitory activity and the lowest IC50 value, followed by acetohydroxamic acid (AHA) and hydroxyurea (HU). The structural and thermodynamical properties of the inhibitors were found to be correlated with their inhibition efficiency.
Article
Chemistry, Physical
Jia-Ning Wang, Wei Liu, Pengfei Li, Yan Mo, Wenxin Hu, Jun Zheng, Xiaoliang Pan, Yihan Shao, Ye Mei
Summary: A novel adaptive QM/MM scheme was developed and applied to the study of a nucleophilic addition reaction, demonstrating computational stability and numerical convergence through configuration sampling and extrapolation computations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Chemistry, Multidisciplinary
Himani Sharma, Baddipadige Raju, Gera Narendra, Mohit Motiwale, Bhavna Sharma, Himanshu Verma, Om Silakari
Summary: Computational enzymology is a rapidly developing field that provides deep insights into the process of biological catalysis, aiding in the design of potential inhibitors. The combined quantum mechanics/molecular mechanics approach has gained attention for understanding enzymatic reactions at both structural and energetic levels. It offers a new mechanism for designing potent enzyme inhibitors.
Article
Chemistry, Physical
Junbo Chen, Jason B. Harper, Junming Ho
Summary: This paper introduces an economical approach to improve the accuracy and convergence of quantum mechanics/ molecular mechanics models. By using quantum-level charges on molecular mechanics atoms, the accuracy and convergence of QM/MM models can be significantly improved.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Qiang Cui, Tanmoy Pal, Luke Xie
Summary: This article discusses the challenges and issues in QM/MM simulations, emphasizing the importance of these issues for applications in biomolecular systems. Despite its limited scope, the hope is to stimulate further developments in the field of QM/MM simulation methods.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Fabiola E. Medina, Gonzalo A. Jana
Summary: The hydrolysis of carbapenem antibiotics by metallo-beta-lactamase enzymes is a crucial reaction that promotes antibiotic resistance. Understanding the catalytic mechanism of this reaction, particularly in VIM-1 enzymes, can aid in rational drug design to inhibit enzyme activity or develop new antibiotics. The reaction was found to occur in three stages with the rate-limiting step being the initial stage with a Gibbs energy barrier of 15.7 kcal.mol(-1).
Article
Biochemistry & Molecular Biology
Francisco Andres Peralta, J. Pablo Huidobro-Toro, Raul Mera-Adasme
Summary: QM/MM molecular dynamic simulations were used to study the allosteric modulator role of Zn(II) on P2X4R, revealing insights into the nature of Zn(II) modulation and the effects of mutations, potentially explaining elusive modulation mechanisms in other extracellular or membrane proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Phujinn Honorio, Supawadee Sainimnuan, Supa Hannongbua, Patchreenart Saparpakorn
Summary: The research discovered that protoberberine alkaloids isolated from natural resources are potent inhibitors of acetylcholinesterase (AChE) and have the potential to reduce symptoms of Alzheimer's disease. The key interactions of palmatine and berberine with AChE were identified as 7C-7C interactions with specific amino acids and H-bond interactions. In contrast, cyclanoline showed a different binding mode and preference for a deeper site within AChE.
CHEMICO-BIOLOGICAL INTERACTIONS
(2021)
Article
Chemistry, Physical
Ramachandren Dushanan, Samantha Weerasinghe, Dhammike P. Dissanayake, Rajendram Senthilinithy
Summary: This study investigated the effect of HDAC inhibitors on the stability of the HDLP enzyme through various analyses, finding that LBH589 and PCI24781 are excellent candidates for further research as HDLP inhibitors.
MOLECULAR SIMULATION
(2022)
Article
Biochemistry & Molecular Biology
Raul Alvarado, Gustavo Cardenas, Juan J. Nogueira, Nicolas Ramos-Berdullas, Marcos Mandado
Summary: This study simulated the permeation of dioxin-like pollutants through lipid membranes using CMD and umbrella sampling. The results showed that TCDD and TCDF reached energy minima at distances of 8 angstrom and 9.5 angstrom from the centre of the membrane, respectively. The interactions between the molecules and the lipid membrane were mainly governed by dispersion forces, independent of the toxicity of the molecules.
Article
Chemistry, Physical
Md Al Mamunur Rashid, Mofizur Rahman, Thamina Acter, Nizam Uddin
Summary: The controversies on the water surface were addressed using large scale quantum mechanical molecular dynamics simulations, revealing that the location and dipole orientation of ions strongly influence the thermodynamic and kinetic properties of the surface.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Zhaoxi Sun, Zhirong Liu
Summary: The study explores indirect free energy simulation methods at quantum mechanics and molecular mechanics levels, as well as attempts to optimize multi-scale treatment by changing the region for electronic structure calculations. The numerical tests show that the estimates from the indirect nonequilibrium perturbation framework are almost identical to the direct results, while the indirect equilibrium estimates deviate from the direct references.
ADVANCED THEORY AND SIMULATIONS
(2021)
Correction
Chemistry, Physical
Chen Luo, Yan Shao, Hua Yu, Hong-zhi Ma, Yu-hao Zhang, Long Gu, Bo Yin, Ming-bo Yang
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Stefano Borocci, Armando Camerlingo, Felice Grandinetti, Maria Rutigliano, Nico Sanna
Summary: The complexes of He, Ne, Ar, Kr, and Xe with B3N3H6 were investigated using MP2, CCSD(T), and SAPT ab initio methods. The complexes can be described as mono-, di-, and tri-coordinated to the N atoms, with stability following the order N-mono < N-di < N-tri. The interactions are dominated by dispersion and the binding energies are within the range of 1 or 2 kcal mol(-1). The results were compared with a recent DFT study on larger BN sheets complexes [Phys. Chem. Chem. Phys. 24 (2022) 2554-2566.].
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
V. Nagarajan, R. Bhuvaneswari, R. Chandiramouli
Summary: In this study, stable phosphoborane was used as a sensor to detect isobutane and n-propane in Liquefied Petroleum Gas (LPG). Phosphoborane demonstrated structural stability and semiconducting nature, and exhibited promising adsorption properties for the LPG molecules.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Xiaoxi Xu, Zijiang Yang, Bayaer Buren, Maodu Chen
Summary: In this study, the time-dependent wave packet method was used to investigate the reaction channels and mechanisms of Ca+ + HD. The results show that the CaH+ + D reaction channel plays a primary role, which is consistent with experimental results. Complex forming and direct-abstraction reaction mechanisms exist in this reaction process.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Keshab Pandey, Hae Kyung Jeong
Summary: A free-standing silicon-carbon nanofiber composite film was synthesized and investigated for supercapacitor applications. It exhibited high specific capacitance, energy density, and power density. After 5000 cycles, the film showed excellent specific capacitance retention and Coulombic efficiency.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Xinyu Zhang, Haosong Li, Xiaoyu Cao, Jing Gao, Yong Wei, Jianzhuo Zhu
Summary: The evaporation behavior of nanosized water aggregations on two-dimensional electroneutral solid surfaces with different surface polar unit densities was investigated. The results showed that the evaporation rate changes non-monotonically with the surface polar unit density, and the minimum evaporation rate is obtained when the surface has a modest surface polar unit ratio of 66.7%.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Yanyan Xu, Rui Dai, Xiaojie Wang, Zhijun Qiao, Haowei Wen, Dianbo Ruan, Yuzuo Wang
Summary: This article presents an innovative solvothermal sodium insertion method for synthesizing Triphylite-NaFePO4, which demonstrates optimal electrochemical performance in sodium-ion batteries.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Meiyi Jiang, Kun Yang, Yancheng Liu, Li Yao
Summary: The geometric structure and electronic properties of transition metal M (M = Cu, Fe, Mn)-TiO2 (101) surface adsorbed by NO2 and N2O were calculated by density functional theory (DFT) and DFT + U theory. The results showed that the adsorption of NO2 and N2O on Mn and Fe atoms is more stable, and a large number of active electrons are formed around these atoms, facilitating the catalytic reactions.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Sergey A. Vyrko, Yulia G. Polynskaya, Nikita A. Matsokin, Andrey M. Popov, Andrey A. Knizhnik, Nikolai A. Poklonski, Yurii E. Lozovik
Summary: In this study, carbon nanobracelets, which are cyclic molecules composed of alternating polycyclic regions and double carbon chains, were investigated using spin-polarized density functional theory. The results show that carbon nanobracelets with odd number of monomers exhibit distinct electronic energy levels, band gaps, and carbon chain deformation compared to those with even number of monomers.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Chanchan Wang, Quan Yang, Yanzhi Ding, Xiaoyong Lu, Dong Tian
Summary: It has been found that the introduction of buffer layers improves the electrical performance of solid oxide fuel cells (SSOFCs). In this study, varying ratios of Gd-doped CeO2 were used as buffer layers in YSZ-based SSOFCs. The results demonstrate that the performance of SSOFCs is enhanced when a buffer layer is added, with the highest performance achieved using Ce0.8Gd0.2O2-delta (GDC20) as the buffer layer. This suggests that the use of GDC series buffer layers is an attractive strategy to optimize performance loss due to electrolyte-electrode interactions.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Wang Li, Yi-Fan Zhang, Jia-Bin Huang, Chang-Yang Wang, Feng Zhang, Jiu-Zhong Yang, Long Zhao
Summary: The gas-phase reaction of propargyl with vinylacetylene was investigated using synchrotron photoionization and molecular-beam mass spectrometry methodologies. The formation mechanisms of the resulting cyclic structures were examined using quantum computations. Two previously unidentified isomers were detected and identified for the first time.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Avijit Pramanik, Sanchita Kundu, Olorunsola Praise Kolawole, Kaelin Gates, Paresh Chandra Ray
Summary: This study investigates the influence of aspect ratio and quantum confinement on the single-photon and two-photon absorption cross-section of perovskite CsPbI3 nanorods. Experimental data shows that CsPbI3 nanorods have an extremely high two-photon absorption cross-section, significantly surpassing organic chromophores and other CsPbBr3 nanocrystals. Moreover, adjusting the aspect ratio can significantly enhance the absorption ability. Additionally, the study also reveals a moderate quantum confinement effect on the single-photon and two-photon absorption cross-section of the nanorods.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Hyon-Tae Pak, Jin-A Choe, Kyong-Sik Ju, Yong -Son Rim
Summary: Drug-loaded cellulose diacetate (CDA) membranes were prepared using different compositions of mixed solvent. The microstructure and performance of the membranes were investigated, and a method to predict drug release properties was proposed. The results showed that the composition of the mixed solvent significantly affected the overall performance of CDA membranes, and the release rates of drugs were related to Δdelta and the intrinsic viscosity of CDA.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Gabriella E. Ravin, E. Curotto
Summary: We have developed a systematic approach to optimize the training set sizes for neural networks in fitting ab initio potential energy surfaces. Using this approach, we have constructed several spectroscopic quality potential energy surfaces for [Li(H2)n]+, n = 1 - 9. The ground state properties have been computed for all the systems and selected states.
CHEMICAL PHYSICS LETTERS
(2024)
Article
Chemistry, Physical
Guohua Xu, Lei Xu, Feng Zhang, Chunling Yu, Yu Song
Summary: NiS1.03@Ni7S6/carbon composite was successfully prepared using corn stalk as a carbon source via a simple adsorption-sulphurization process. The composite exhibited a specific capacitance of 1554.6 F/g at 1 A/g as a supercapacitor electrode, with a capacitance retention rate of 80.4% after 5000 cycles. Furthermore, the NiS1.03@Ni7S6/carbon//AC asymmetric supercapacitor showed a high energy density of 41.2 Wh kg-1 at a power density of 750 W kg-1, and excellent cycling stability with 86.8% capacitance retention after 10,000 cycles.
CHEMICAL PHYSICS LETTERS
(2024)