Article
Chemistry, Physical
Gustavo Cardenas, Juan J. Nogueira
Summary: An algorithm is proposed to evaluate molecular orbital overlap between different geometries to improve the accuracy of excitation energy calculations. Based on this algorithm, correct active space was recovered for 90% of the cases, enhancing computational efficiency.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Christina Eleftheria Tzeliou, Markella Aliki Mermigki, Demeter Tzeli
Summary: The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach is a powerful tool for investigating chemical reactions' mechanisms, drug delivery, molecular devices properties, etc. This review briefly discusses the main methodologies in multiscaling approaches and provides a review on calculations and reactions on metalloproteins.
Article
Chemistry, Multidisciplinary
Veronica Macaluso, Giacomo Salvadori, Lorenzo Cupellini, Benedetta Mennucci
Summary: Phytochromes, red-light sensing proteins with important light-regulatory roles, undergo large structural relaxation in solution compared to crystal structure, revealing new insights into the activation pathway.
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
Multidisciplinary Sciences
Yongbin Zhang
Summary: When the channel height is reduced to a small value, the physical adsorbed layers on the channel walls will contribute to the flow, and not just the continuum fluid flow. Through multiscale simulation, the importance of incorporating adsorbed layer flow in calculating mass transfer in microchannels is highlighted.
SCIENTIFIC REPORTS
(2021)
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
Biochemistry & Molecular Biology
Mohsen Sargolzaei, Hossein Nikoofard
Summary: In this study, we designed a suitable ester prodrug of omapatrilat for CNS diseases by considering its ability to penetrate the blood-brain barrier. The most potent stereoisomers against brain carboxylesterase were determined through molecular docking and homology modeling. Molecular dynamics simulation and structural analysis were performed to confirm the suitability of the prodrug structure for crossing the blood-brain barrier and binding to brain carboxylesterase. Additionally, the QM/MM calculation revealed the catalytic reaction mechanism of the prodrug against brain carboxylesterase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
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
Engineering, Mechanical
Zhinan Zhang, Shuaihang Pan, Nian Yin, Bin Shen, Jie Song
Summary: The friction behavior at fretting interfaces is crucial in tribology, and the contact intervals can accurately determine the friction characteristics of a material. The differences in hardness, stiffness modulus, and material configuration have considerable influence on the fretting process. Molecular dynamics simulations and new energy theories provide insights for predicting fretting processes, material selection, and optimization.
Article
Biochemistry & Molecular Biology
Changyue Deng, Tiantian Zhang, Xiumei Zhang, Tingting Gu, Li Xu, Zhenyu Yu, Mingming Zheng, Yibin Zhou
Summary: This study precipitated debranched starch (DBS) from pullulanase-hydrolyzed starch using ethanol, n-butanol, and isopentanol, and investigated the chain conformation and precipitation mechanism of DBS in different alcohols using molecular dynamics (MD) simulation. The results showed that DBS precipitated by n-butanol had the largest proportion of short chain, the highest V-type crystallinity, and the largest single-helix content.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Mathematics, Applied
Frederic Legoll, Tony Lelievre, Upanshu Sharma
Summary: The aim of this article is to design parareal algorithms for thermostated molecular dynamics simulations. The traditional parareal algorithm is not suitable for molecular dynamics due to its limitations. This article proposes a modified version of the parareal algorithm that is better suited for molecular dynamics simulations. However, the modified algorithm still has some limitations, including intermediate trajectory blow-up, encounters with undefined values, and no computational advantage in long time horizons. Through numerical experiments, this article demonstrates that the adaptive algorithm overcomes the limitations of the standard algorithm and achieves significant improvements.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2022)
Article
Chemistry, Physical
Jiankang Gu, Yunzhe Jia, Xiaozhe Ren, Shu Li, Tianying Yan
Summary: In salt-in-ionic liquid electrolytes (SILEs), the coordination of lithium ion (Li+) with its anions affects the internal resistance and the formation of Li+-containing agglomerates (AGGs). Molecular dynamics simulations showed that a methyl substitution in the imidazolium cation can release trapped Li+ ions and reduce the formation of AGGs. This structural modification alters the transport properties of SILEs and improves the transference number of Li+.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Multidisciplinary Sciences
Denis Maag, Thilo Mast, Marcus Elstner, Qiang Cui, Tomas Kubar
Summary: Extensive QM/MM molecular dynamics simulations were used to study the structural features and conversion process of the O state in bR, revealing the crucial roles of PRG and Arg82 in modulating protein hydration level. Proton exchange through a water network was found to be facilitated by the generation and propagation of a proton hole, explaining the mechanism behind chloride ion pumping in the D85S mutant.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Mathematics, Applied
Yangshuai Wang, Huajie Chen, Mingjie Liao, Christoph Ortner, Hao Wang, Lei Zhang
Summary: Hybrid quantum/molecular mechanics models, known as QM/MM methods, are commonly used in material and molecular simulations to strike a balance between accuracy and computational cost. Adaptive QM/MM coupling methods, with on-the-fly classification of atoms, allow for real-time updates of the QM and MM subsystems as needed. This study proposes a new adaptive QM/MM method for material defect simulations based on a residual from a posteriori error estimator, showcasing its effectiveness through numerical simulations.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2021)
Article
Chemistry, Physical
You Lu, Kakali Sen, Chin Yong, David S. D. Gunn, John A. Purton, Jingcheng Guan, Alec Desmoutier, Jamal Abdul Nasir, Xingfan Zhang, Lei Zhu, Qing Hou, Joe Jackson-Masters, Sam Watts, Rowan Hanson, Harry N. Thomas, Omal Jayawardena, Andrew J. Logsdail, Scott M. Woodley, Hans M. Senn, Paul Sherwood, C. Richard A. Catlow, Alexey A. Sokol, Thomas W. Keal
Summary: Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are powerful tools for studying catalysis, providing an accurate description of reactions in complex electrostatic environments. ChemShell, a scriptable computational chemistry environment, is a leading software package for QM/MM calculations, offering a flexible and high-performance framework for biomolecular and materials catalysis. This article gives an overview of recent applications of ChemShell in catalysis, as well as new functionality introduced in the Python-based version to support catalytic modeling.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Norio Takenaka, Taichi Inagaki, Tatau Shimada, Yuki Yamada, Masataka Nagaoka, Atsuo Yamada
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
David Reber, Norio Takenaka, Ruben-Simon Kuhnel, Atsuo Yamada, Corsin Battaglia
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Nanoscience & Nanotechnology
Kasumi Miyazaki, Norio Takenaka, Eriko Watanabe, Yuki Yamada, Yoshitaka Tateyama, Atsuo Yamada
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Chemistry, Physical
Yukichi Kitamura, Masataka Nagaoka
Summary: The CS-CpH method is a new molecular simulation method for obtaining pH-dependent physical properties, which generates configurations with changed protonation states through short equilibrium MD and searching MD, and accepts or rejects them according to the Metropolis MC procedure.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Shaoxiong Yang, Yuping Zhang, Zhongliang Li, Norio Takenaka, Yan Liu, Hanqin Zou, Wenting Chen, Mingcong Du, Xu-Jia Hong, Rui Shang, Eiichi Nakamura, Yue-Peng Cai, Ya-Qian Lan, Qifeng Zheng, Yuki Yamada, Atsuo Yamada
Summary: The research team designed a nonflammable cyclic phosphate-based electrolyte to adjust the component of the electrode/electrolyte interface, which enables the battery to maintain high elasticity and robustness even under high volume changes, achieving extremely high energy density and cycling stability.
ACS ENERGY LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Norio Takenaka, Amine Bouibes, Yuki Yamada, Masataka Nagaoka, Atsuo Yamada
Summary: SEI is an ion conductive yet electron-insulating layer on battery electrodes, impacting the safety, power, and lifetime of batteries. Traditional theoretical calculations and experimental approaches have limitations in revealing intermediate steps of SEI growth, but recent multiscale simulation methods have made a significant breakthrough.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Physical
Tatau Shimada, Norio Takenaka, Yasunobu Ando, Minoru Otani, Masashi Okubo, Atsuo Yamada
Summary: In this study, the atomic-scale double-layer structure of MXene electrodes with different terminated halogen elements was systematically investigated using density functional theory calculations. The results showed a clear relationship between the atomic number of the terminated halogen atoms and the capacitance.
CHEMISTRY OF MATERIALS
(2022)
Article
Chemistry, Physical
Ikuo Kurisaki, Yume Takahashi, Yukichi Kitamura, Masataka Nagaoka
Summary: This study focuses on the impact of chloride ions on the allosteric mechanisms of human adult hemoglobin (HbA) and specifically examines the different theoretical explanations proposed by Ueno and Perutz. The research found that chloride ions loosely interact with amino acid residues inside the central cavity of HbA, and theoretically demonstrated that the effects of chloride ions compete against solvated oxygen, destabilizing the T-state through non-site-specific interactions, implying a coordinated regulation of HbA under physiological conditions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Tatau Shimada, Norio Takenaka, Eriko Watanabe, Yuki Yamada, Yi-Tao Cui, Yoshihisa Harada, Masashi Okubo, Atsuo Yamada
Summary: This study investigates the electrolyte properties of highly salt-concentrated aqueous solutions, revealing that the structure and electronic states of water molecules in hydrate melts evolve with salt concentration, exhibiting electrical properties more similar to gas phase rather than liquid phase.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Spectroscopy
Yukichi Kitamura, Hajime Torii
Summary: Relating vibrational properties to intermolecular configurations is crucial for accurate analysis and interpretation of spectra in condensed-phase systems. Through theoretical calculations on hydrogen-bonded water clusters, it is found that secondary descriptors related to the other OH bonds in the same water molecule significantly improve the performance of theoretical modeling, in addition to the primary descriptor related to the vibrating OH bond. The electric charge configuration is shown to be an important factor for good performance of the electric field descriptor.
JOURNAL OF RAMAN SPECTROSCOPY
(2022)
Article
Chemistry, Physical
Carlos Bistafa, Yukichi Kitamura, Masataka Nagaoka
Summary: We propose a self-contained theoretical methodology to predict the pH effects on the molecular electronic spectra in aqueous solution. By combining the configuration-selection constant-pH simulation method with quantum mechanics/molecular mechanics method, we can obtain the theoretical description of the pH dependent electronic spectra.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Energy & Fuels
Seongjae Ko, Tomohiro Obukata, Tatau Shimada, Norio Takenaka, Masanobu Nakayama, Atsuo Yamada, Yuki Yamada
Summary: In this study, the authors investigate the factors affecting the reversibility of lithium-metal anodes and propose an electrolyte design to improve the cycling performance. They find that the lithium electrode potential and its association with the Li+ coordination structure play a crucial role in Coulombic efficiency and electrolyte decomposition. By enhancing ion-pairing solution structure, the authors achieve a significantly improved cycling performance.
Article
Chemistry, Multidisciplinary
Kosuke Kawai, Xiang-Mei Shi, Norio Takenaka, Jeonguk Jang, Benoit Mortemard de Boisse, Akihisa Tsuchimoto, Daisuke Asakura, Jun Kikkawa, Masanobu Nakayama, Masashi Okubo, Atsuo Yamada
Summary: Integrating anionic-redox with cationic-redox is a promising strategy, but hysteresis is a challenge in oxygen-redox cathodes. In this study, nonpolarizing and polarizing oxygen-redox reactions are found to coexist and compete in a specific material. Preventing the polarizing reaction is crucial for achieving nonpolarizing and energy-efficient oxygen-redox reactions.
ENERGY & ENVIRONMENTAL SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Miho Tanaka, Yume Takahashi, Kei Takami, Yukichi Kitamura, Masataka Nagaoka
Summary: The investigation found that bridging hydrogen bonds via Cl- do not significantly contribute to the structural regulation of human adult hemoglobin.
JOURNAL OF COMPUTER CHEMISTRY-JAPAN
(2021)
Article
Chemistry, Multidisciplinary
Kei Takami, Yukichi Kitamura, Masataka Nagaoka
Summary: In this article, the time-series clustering method was applied to classify molecular dynamics trajectories of human adult hemoglobin, and the proper clustering conditions were discussed based on the comparison of silhouette indices.
JOURNAL OF COMPUTER CHEMISTRY-JAPAN
(2020)
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)
