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
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
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
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)
Article
Biochemistry & Molecular Biology
Julien Diharce, Emmanuelle Bignon, Sebastien Fiorucci, Serge Antonczak
Summary: Flavonoids are widely present secondary metabolites in plants, with antioxidant properties, making them interesting natural compounds for pharmacology. Among the enzymes involved in flavonoid biosynthesis, dihydroflavonol-4-reductase (DFR) plays a crucial role in the production of anthocyanins and proanthocyanidins. New insights into the mechanism of action of DFR have been provided through QM/MM-MD simulations on DHQ and DHK substrates, highlighting the enzyme's role in stabilizing the transition state and activating the substrate before the reaction.
Article
Chemistry, Physical
Siwarut Siwaipram, Philippe A. Bopp, Panyapat Ponchai, Jean-Christophe Soetens, Jun-ya Hasegawa, Rochus Schmid, Sareeya Bureekaew
Summary: This study investigates the structural evolution of MOF under the influence of methanol vapor at different loadings using classical MD simulations. The results reveal that at low loadings, methanol molecules aggregate around ions, while at high loadings, the MOF exhibits structural features similar to liquid methanol.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Yuzhuang Fu, Binju Wang, Zexing Cao
Summary: Detailed mechanisms for the chemical steps involved in the biodegradation of 2-oxoadipate (2OA) by HglS enzyme have been explored using MD simulations and QM/MM calculations. The study reveals the presence of two coordination modes of the Fe(IV)-oxo species, with the proximal mode responsible for C-H bond activation. Additionally, residues in the second coordination sphere play a crucial role in substrate binding and facilitate the ferryl-flip, leading to the proximal Fe(IV)-oxo conformation ideal for C-H bond activation.
JOURNAL OF CATALYSIS
(2023)
Article
Chemistry, Physical
Giacomo Saielli
Summary: The thermal stability of Ionic Liquid Crystal (ILC) phases is influenced by factors such as alkyl chain length, counter-anion, and hydration. Hydration increases stability of the monohydrated phase, leading to enhanced nano-segregation and increased order of the alkylic layer.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Bella Grigorenko, Tatiana Domratcheva, Alexander Nemukhin
Summary: The oxygenase activity of the flavin-dependent enzyme RutA is associated with the formation of flavin-oxygen adducts in the enzyme active site. Using quantum mechanics/molecular mechanics (QM/MM) modeling, we investigated potential reaction pathways initiated by triplet state complexes of molecular oxygen with reduced flavin mononucleotide (FMN) in protein cavities. The results show that these complexes can be located at different positions on the isoalloxazine ring of flavin, and the activated dioxygen attacks specific positions in the ring, resulting in covalent adducts or direct oxidation of flavin.
Article
Crystallography
Satayu Suwannasopon, Fabian Meyer, Christian Schlickriede, Papichaya Chaisakul, Jiraroj T-Thienprasert, Jumras Limtrakul, Thomas Zentgraf, Nattaporn Chattham
Article
Chemistry, Applied
Pratya Promchana, Adisak Boonchun, Jiraroj T-Thienprasert, Tawan Sooknoi, Tosapol Maluangnont
Summary: The conversion of acids to long chain olefins via ketonization shows promising results in terms of activity and selectivity, with oxygen vacancy defects playing a crucial role in the process. The presence of V-O was spectroscopically confirmed and its relationship with ketonization activity was deduced through DFT calculations. The Pt-loaded catalyst enabled the direct transformation of acids into olefins with high yields of long chain products.
Correction
Multidisciplinary Sciences
Klichchupong Dabsamut, Jiraroj T-Thienprasert, Sirichok Jungthawan, Adisak Boonchun
SCIENTIFIC REPORTS
(2020)
Article
Materials Science, Multidisciplinary
Jittiporn Ruangtong, Jiraroj T-Thienprasert, Nattanan Panjaworayan T-Thienprasert
MATERIALS TODAY COMMUNICATIONS
(2020)
Article
Physics, Condensed Matter
Sutassana Na-Phattalung, Sukit Limpijumnong, Jiraroj T-Thienprasert
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS
(2020)
Article
Medicine, Research & Experimental
Damita Jevapatarakul, Jiraroj T-Thienprasert, Sunchai Payungporn, Tanit Chavalit, Ariya Khamwut, Nattanan Panjaworayan T-Thienprasert
BIOMEDICINE & PHARMACOTHERAPY
(2020)
Article
Chemistry, Inorganic & Nuclear
Thanit Tangcharoen, Wantana Klysubun, Jiraroj T-Thienprasert, Chanapa Kongmark
JOURNAL OF SOLID STATE CHEMISTRY
(2020)
Article
Physics, Condensed Matter
Nirawith Palakawong, Siwakorn Sukharom, Sukit Limpijumnong, Sirichok Jungthawan, Surachate Limkumnerd, Adisak Boonchun, Pakpoom Reunchan, Jiraroj T-Thienprasert
Summary: The study reveals that only aluminum vacancy defects in alpha-Al2O3 crystals can provide absorption lines in the visible light region; Ti-Fe impurities cause sapphire to appear blue, with the intervalence charge transfer (IVCT) mechanism believed to be the reason behind the blue color in sapphire.
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS
(2021)
Article
Physics, Applied
Thanasee Thanasarnsurapong, Klichchupong Dabsamut, Tosapol Maluangnont, Jiraroj T-Thienprasert, Sirichok Jungthawan, Adisak Boonchun
Summary: The hydrogenated penta-BCN (H-BCN) structure has been studied and found to be stable within a certain range. Compared to pristine BCN, H-BCN exhibits a wider bandgap, higher polarization, and different mechanical properties.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Physics, Applied
Klichchupong Dabsamut, Thanasee Thanasarnsurapong, Tosapol Maluangnont, Jiraroj T-Thienprasert, Sirichok Jungthawan, Adisak Boonchun
Summary: The study demonstrates that the penta-BCN monolayer has a stable structure with low in-plane Young's moduli under no strain. However, strain within a certain range can lead to irreversible changes in its structure, affecting its electronic structure and thermal conductivity.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Article
Physics, Applied
Klichchupong Dabsamut, Tosapol Maluangnont, Pakpoom Reunchan, Jiraroj T-Thienprasert, Sirichok Jungthawan, Adisak Boonchun
Summary: Recently, the C2N monolayer has gained attention as a new two-dimensional material for optoelectronic devices with a bandgap of 1.96 eV. In this study, we demonstrate the modulation of the bandgap by a simple bilayer structure using an electric field and strain. Our findings highlight the potential of electric field and strain in tuning the electronic properties of C2N.
APPLIED PHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Supparat Charoenphon, Auttasit Tubtimtae, Isao Watanabe, Sirichok Jungthawan, Jiraroj T-Thienprasert, Adisak Boonchun, Pakpoom Reunchan
Summary: In this study, the effects of point defects and impurities on the electrical properties of ZnSb2O4 ceramic material were investigated using hybrid density-functional calculations. It was found that oxygen vacancies had the lowest formation energy, but acted as deep acceptors, unable to provide free electron carriers for conduction. Zinc vacancies and zinc substitution for antimony were dominant acceptors. Doping with Al, Ga, In, and F impurities hindered high n-type conductivity due to self-compensation. This work lays the foundation for point defect engineering in this class of ternary oxides.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Thanasee Thanasarnsurapong, Panyalak Detrattanawichai, Klichchupong Dabsamut, Intuon Chatratin, Jiraroj T-Thienprasert, Sirichok Jungthawan, Adisak Boonchun
Summary: Based on first-principles calculations, we proposed new pentagonal materials penta-BGeN and penta-BSnN, which exhibit good thermodynamic, dynamic, mechanical, and thermal stability. Among them, penta-BSnN showed the highest intrinsic piezoelectricity, especially in terms of the e(22) piezoelectric stress. Therefore, penta-BSnN has tremendous potential as a nanoscale piezoelectric material.
Article
Chemistry, Physical
Aroon Ananchuensook, Klichchupong Dabsamut, Thanasee Thanasarnsurapong, Tosapol Maluangnont, Jiraroj T-Thienprasert, Sirichok Jungthawan, Adisak Boonchun
Summary: Penta-BCN is a promising anode material for Li-ion batteries, with high theoretical capacity and favorable lithium adsorption sites, demonstrating metallic conductivity and facilitating quick charge/discharge.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Supparat Charoenphon, Adisak Boonchun, Daungruthai Jarukanont, Jiraroj T-Thienprasert, Pakpoom Reunchan
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
