Article
Polymer Science
Aleksandr Vasilev, Tommy Lorenz, Cornelia Breitkopf
Summary: This article discusses two main approaches to predicting thermal conductivities through molecular dynamics simulations: non-equilibrium molecular dynamics (NEMD) and the application of the Green-Kubo formula, i.e., EMD. NEMD methods are more affected by size effects compared to EMD methods. The thermal conductivities of silicone rubbers and thermoplastic polyurethane were found to be functions of crosslinking degree and mass fraction of soft segments, respectively. The results obtained from the simulations are in good agreement with experimental data, and it is revealed that heat in polymers is mainly transferred by low-frequency phonons.
Article
Chemistry, Physical
Ryo Kawada, Katsuhiro Endo, Daisuke Yuhara, Kenji Yasuoka
Summary: Molecular dynamics simulation is a method for studying the behavior of molecules, but its high computational cost has always been a problem. MD-GAN is a machine learning-based method that accelerates the generation of molecular dynamics data. This study explores the effectiveness of incorporating information from other particles in the training process and successfully predicts molecular diffusion.
Article
Chemistry, Multidisciplinary
Fangbai Xie, Haochuan Mao, Chenjian Lin, Yuanning Feng, J. Fraser Stoddart, Ryan M. Young, Michael R. Wasielewski
Summary: This study demonstrates that a photogenerated spin-correlated radical ion pair can be used to sense an electric field change through molecular recognition. The experiment shows that the distance between the two charges decreases when a certain molecule encapsulates one of the charges, indicating that the system can function as a quantum sensor to detect electric field changes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
N. B. Asanbaeva, D. S. Novopashina, O. Yu. Rogozhnikova, V. M. Tormyshev, A. Kehl, A. A. Sukhanov, A. V. Shernyukov, A. M. Genaev, A. A. Lomzov, M. Bennati, A. Meyer, E. G. Bagryanskaya
Summary: The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is a powerful technique for obtaining structural information about proteins and nucleic acids. This study explored the capability of Mims F-19 ENDOR experiments to report intermolecular distances in trityl- and F-19-labeled DNA duplexes. The results showed that the hyperfine splittings observed in the ENDOR spectra were consistent with the predicted interspin distances between F-19 and the trityl radical.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Mechanics
Samuel S. Schoenholz, Ekin D. Cubuk
Summary: JAX MD is a software package for differentiable physics simulations, focusing on molecular dynamics. It includes physics simulation environments, interaction potentials, and neural networks. The simulations are differentiable, allowing for meta-optimization.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Chemistry, Physical
Farzad Khorrami, Mohammad H. Kowsari
Summary: This research uses molecular dynamics simulations to study the behavior of ionic liquids confined in nanopores. The results reveal heterogeneous local structures and dynamics, with significant differences depending on the position of the ions relative to the pore walls. The interaction between the ionic liquid and different wall materials, such as rutile and graphite, also affects the behavior of the confined system.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Monica L. Fernandez-Quintero, Eugene F. DeRose, Scott A. Gabel, Geoffrey A. Mueller, Klaus R. Liedl
Summary: In this study, the conformational diversity of an anti-GFP-binding nanobody was characterized using molecular dynamics simulations and experimental data from NMR spectroscopy. The results showed excellent agreement between the distance maps obtained from NMR and MD simulations, as well as similar conformational spaces for simulations with and without time-averaged restraints. The motions observed in the ps-ns timescale, particularly in the CDR3 loop, also showed good agreement between measured and calculated order parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Davide Sala, Andrea Giachetti, Antonio Rosato
Summary: ZnT8, a human zinc transporter, shows significant differences in zinc ion transport kinetics and conformational dynamics between different variants, which may lead to different disease risks.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Marceau Henot, Pierre-Michel Dejardin, Francois Ladieu
Summary: This study investigates the orientational dynamics of supercooled glycerol using molecular dynamics simulations and compares the results with experimental data. The findings suggest that the depolarized dynamic light scattering (DDLS) method has low sensitivity to cross-correlations, supporting the idea of directly comparing data from dielectric spectroscopy (DS) and DDLS to evaluate the impact of cross-correlations in polar liquids.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Jake Williams, Eric Jonas
Summary: This study presents a novel machine learning technique that combines uncertainty-aware deep learning with rapid estimates of conformational geometries to accurately simulate solution NMR spectra. The method improves the accuracy of chemical shift values and can predict all scalar coupling values. The uncertainty quantification results show a strong correlation with accuracy and the method is able to handle stereoisomerism and disagreement regularization.
Article
Chemistry, Physical
Claudia E. Tait, Anna Reckwitz, Malavika Arvind, Dieter Neher, Robert Bittl, Jan Behrends
Summary: The study characterizes the spin properties of P3HT after different molecular dopings using EPR spectroscopy. Results show different spin behaviors under various doping conditions, including free spins and exchange-coupled spins. Additionally, ENDOR measurements reveal reduced spin dispersal in F(4)TCNQ-doped P3HT films.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Alican Gulsevin, Jens Meiler
Summary: The AmphiScan protocol is a tool developed to predict the interaction of amphipathic helices with membranes, with features of fast, accurate, and highly customizable.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Fanny Kozak, Dennis Kurzbach
Summary: This review discusses recent advances in modeling structural ensembles of transcription factors using NMR and EPR spectroscopic data integrated with MD simulations. The focus is on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. Recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors using integrative approaches are highlighted.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Physical
Bin Ma, Chen Chen, Zi-Xian Du, Li Zhang
Summary: In this study, PIM-1 membranes were prepared using a 21-step method via molecular dynamics simulations. The structure and separation performance of these membranes for CO2/N2 mixture were explored. The results revealed that the permeation behavior of CO2/N2 mixture through PIM-1 membrane is dominated by solubility, and the cyano group and terminal hydroxyl groups in the PIM1 chain play important roles in gas adsorption and permeation.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
N. A. Chumakova, Vorobiev A. Kh, D. A. Astvatsaturov, T. S. Yankova, A. T. Rebrikova, M. Matveev
Summary: The orientational alignment of graphene oxide membranes was quantitatively determined using the spin probe technique. The values of the orientational order parameters up to the 6th rank were obtained. It was found that nitroxide probes and Cu(ii) complexes effectively reflected the alignment of the membranes. Moreover, the orientation alignment of the membranes prepared by vacuum filtration and drying the graphite oxide suspension were significantly different, with the latter showing poor alignment.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(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)