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Tutorial on Umbrella Sampling Simulation with a Combined QM/MM Potential: The Potential of Mean Force for an S2 Reaction in Water.
J Phys Chem B
October 2024
Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
We present a tutorial to carry out umbrella-sampling free-energy simulations with a combined quantum mechanical and molecular mechanical (QM/MM) potential, which may also be used in a computational or biophysical chemistry curriculum for first-year graduate and undergraduate students. In this article, we choose the Type II S2 Menshutkin reaction between ammonia and chloromethane to construct the potential of mean force (PMF) for the reaction in aqueous solution. In this exercise, we wish to accomplish three tasks: (1) an understanding of the concept of PMF and the umbrella-sampling free-energy simulation method, (2) the use of a combined QM/MM potential in molecular dynamics simulation of chemical reactions, and (3) an understanding of solvent effects and intermolecular interactions on chemical reactions through comparison with gas-phase results.
View Article and Find Full Text PDFSurface-Like Diffusion of Fast Ions in Framework Energy Materials for Li- and Na-Ion Batteries.
Angew Chem Int Ed Engl
August 2024
State Key Lab of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, 100084, Beijing, China.
The rate performance, power density, and energy efficiency of electrochemical devices are often limited by ionic conductivities in electrolyte and electrode materials. Framework Prussian blue analogs and dense niobium oxides have been identified as high-rate electrodes for sodium- and lithium-ion batteries, respectively, yet the origin of the extremely high solid-state Na/Li transport is not fully understood. Of critical importance is the fact that their ultra-low activation energy and anomalous pre-exponent factor cannot be satisfactorily rationalized from conventional theory of solid-state diffusion in the crystal lattice.
View Article and Find Full Text PDFThe discovery of three-dimensional Van Hove singularity.
Nat Commun
March 2024
State Key Laboratory of Precision Spectroscopy, East China Normal University, 200241, Shanghai, China.
Arising from the extreme/saddle point in electronic bands, Van Hove singularity (VHS) manifests divergent density of states (DOS) and induces various new states of matter such as unconventional superconductivity. VHS is believed to exist in one and two dimensions, but rarely found in three dimension (3D). Here, we report the discovery of 3D VHS in a topological magnet EuCdAs by magneto-infrared spectroscopy.
View Article and Find Full Text PDFVan Hove singularity driven enhancement of superconductivity in two-dimensional tungsten monofluoride (WF).
J Phys Condens Matter
March 2024
Department of Physics, Indian Institute of Technology Ropar, Rupnagar 140001, Punjab, India.
Superconductivity in two-dimensional materials has gained significant attention in the last few years. In this work, we report phonon-mediated superconductivity investigations in monolayer Tungsten monofluoride (WF) by solving anisotropic Migdal Eliashberg equations as implemented in EPW. By employing first-principles calculations, our examination of phonon dispersion spectra suggests that WF is dynamically stable.
View Article and Find Full Text PDFClassification of the HCN isomerization reaction dynamics in Ar buffer gas via machine learning.
J Chem Phys
September 2023
Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
The effect of the presence of Ar on the isomerization reaction HCN ⇄ CNH is investigated via machine learning. After the potential energy surface function is developed based on the CCSD(T)/aug-cc-pVQZ level ab initio calculations, classical trajectory simulations are performed. Subsequently, with the aim of extracting insights into the reaction dynamics, the obtained reactivity, that is, whether the reaction occurs or not under a given initial condition, is learned as a function of the initial positions and momenta of all the atoms in the system.
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