Article
Chemistry, Medicinal
Raffaello Potestio, Raffaele Fiorentini, Thomas Tarenzi
Summary: In recent years, multiple-resolution modeling strategies have been developed to describe biomolecules using a combination of atomistic and coarse-grained models. However, the parametrization of the coarse-grained model is often time-consuming and requires reference simulations. In this study, a novel multiresolution modeling scheme called CANVAS is introduced, which allows user-defined resolution modulation, fast parametrization, and easy usage on molecular dynamics platforms. The method is validated using two case studies and the modeling software is made freely available for the community.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Haohao Fu, Haochuan Chen, Wensheng Cai, Xueguang Shao, Christophe Chipot
Summary: BFEE2 aims to automate and streamline accurate absolute binding free-energy estimation, eliminating the need for extensive human intervention. It supports a wide range of force fields, provides standardized workflows, and monitors the convergence of free-energy calculations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Multidisciplinary
Moritz Thurlemann, Sereina Riniker
Summary: Electronic structure methods offer accurate predictions but with high computational costs. Empirical methods are cheaper but have inherent approximations and data dependence. Machine learning force fields exacerbate limitations related to training data. A proposed hybrid model combines machine learning and classical force fields, providing accuracy and flexibility.
Article
Chemistry, Medicinal
Kaycee Low, Michelle L. Coote, Ekaterina I. Izgorodina
Summary: This study proposes a graph neural network model for predicting the solvation Gibbs free energy of molecules. By incorporating chemically intuitive solvation-relevant parameters into the featurization process, the model accurately predicts solvation energy. In testing, the model shows comparable accuracy to traditional methods and provides clear explanations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Andrea Rizzi, Paolo Carloni, Michele Parrinello
Summary: The method presented extends the theory of targeted free energy perturbation to accurately calculate free energy differences and surfaces at a quantum mechanical level from a cheaper reference potential. Accelerated convergence is achieved by increasing the overlap between target and reference distributions. The method is validated through numerical evaluations in different systems, demonstrating its effectiveness in avoiding systematic errors.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Mechanics
Jiayi Zhao, Shuo Chen, Damin Cao
Summary: We have proposed a generalized mean-field equation of state for the many-body dissipative particle dynamics method, which accurately predicts the pressure at any level of coarse-graining. By mitigating the truncation effects caused by finite cutoff radius, we satisfy the assumption of mean-field theory, and replace the local density with the global density in a homogeneous system. Our work represents an advancement towards establishing a robust and reliable one-to-one parameter mapping protocol based on mean-field theory.
Article
Chemistry, Physical
Paolo Suating, Nicholas E. Ernst, Busayo D. Alagbe, Hannah A. Skinner, Joel T. Mague, Henry S. Ashbaugh, Bruce C. Gibb
Summary: This study focuses on the synthesis and conformational properties of TEEtOA2, a cavitand with flexible ethyl groups, and its binding affinity to carboxylates. It also explores the wetting mechanism of the cavity and proposes a novel triggered wetting, guest complexation mechanism.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Thomas J. Oweida, Ho Shin Kim, Johnny M. Donald, Abhishek Singh, Yaroslava G. Yingling
Summary: This study assessed the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, and found that the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experimental data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Carl Oester, Kumar Tekwani Movellan, Benjamin Goold, Kitty Hendriks, Sascha Lange, Stefan Becker, Bert L. de Groot, Wojciech Kopec, Loren B. Andreas, Adam Lange
Summary: This study investigates the structure and interactions of potassium ions in ion channels using solid-state NMR. The findings reveal differences in ion binding and water molecule interactions in different selective ion channels, despite having identical amino acid sequences and crystal structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Sara Gomez, Natalia Rojas-Valencia, Santiago A. Gomez, Chiara Cappelli, Gabriel Merino, Albeiro Restrepo
Summary: This study comprehensively explores the molecular basis for hydrophobicity using theoretical tools and organic solvent S/water binary systems, revealing no evidence of repulsion between water and S molecules, but rather a complex interplay of entropic, enthalpic, and dynamic factors maintaining stable water interfaces.
Article
Chemistry, Physical
Ming Ma, Junjie Song, Yi Dong, Weihai Fang, Lianghui Gao
Summary: In this study, a novel coarse-grained force field was developed to reproduce the structural and thermodynamic properties of triglycerides in bulk phase, as well as at air and water interfaces. The force field accurately reproduced the self-assembled network and diverse molecular conformations of triglycerides in water, and correctly predicted experimental macroscopic thermodynamic properties. This work paves the way for studying complex systems involving triglycerides on a larger scale.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Krishan Kanhaiya, Michael Nathanson, Pieter J. In't Veld, Cheng Zhu, Ilia Nikiforov, Ellad B. Tadmor, Yeol Kyo Choi, Wonpil Im, Ratan K. Mishra, Hendrik Heinz
Summary: The simulation of metals, oxides, and hydroxides can greatly aid in the design of various materials. The introduction of the INTERFACE force field (IFF) and surface models provide improved reliability, compatibility, and interpretability in simulating these materials. The models have been shown to outperform previous methods in terms of accuracy and applicability.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Han Liu, Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
Summary: In this study, a hybrid quantum mechanical/molecular mechanics approach was used to characterize the interaction of cations and anions, and Lennard-Jones parameters were optimized to improve the description of solvent-exposed salt-bridge interactions. The findings indicate that the new parameters enhance the structural and thermodynamic description of solvent-exposed salt-bridge interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Sadra Kashefolgheta, Shuzhe Wang, William E. Acree, Philippe H. Hunenberger
Summary: In this study, nine condensed-phase force fields were compared based on their correlation coefficients, root-mean-square errors (RMSEs), and average errors (AVEEs) in predicting experimental salvation free energies. The results showed that GROMOS-2016H66 and OPLS-AA had the highest accuracy, while other force fields exhibited varying levels of accuracy. The differences in performance were statistically significant but not pronounced, showing heterogeneous distribution across the set of compounds within each force field.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Engineering, Chemical
Xiaoxia Yang, Yufan Mu, Yongjun Peng
Summary: Lead ions can counteract the negative effects of free cyanide on pyrite flotation in alkaline conditions and significantly activate pyrite flotation. The adsorption of lead ions on pyrite surface counteracts the depression of free cyanide by covering lead species on top of iron cyanide and thiocyanate, but the preference for adsorption on thiocyanate limits the ability of lead ions to counteract free cyanide.
MINERALS ENGINEERING
(2022)
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)