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Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. 力场 X：利用理论和实验研究基因变异和有机晶体的计算显微镜。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-07-07 DOI: 10.1063/5.0214652
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan Grove, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
{"title":"Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.","authors":"Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan Grove, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders","doi":"10.1063/5.0214652","DOIUrl":"10.1063/5.0214652","url":null,"abstract":"<p><p>Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11223778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
On the thermodynamic stability of polycations. 关于多阳离子的热力学稳定性。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0207526
Denis S Tikhonov, Jason W L Lee, Melanie Schnell
{"title":"On the thermodynamic stability of polycations.","authors":"Denis S Tikhonov, Jason W L Lee, Melanie Schnell","doi":"10.1063/5.0207526","DOIUrl":"https://doi.org/10.1063/5.0207526","url":null,"abstract":"<p><p>We present a simple approximation to estimate the largest charge that a given molecule can hold until fragmentation into smaller charged species becomes more energetically favorable. This approximation solely relies on the ionization potentials, electron affinities of the parent and fragment species, and also on the neutral parent's dissociation energy. By parameterizing these quantities, it is possible to obtain analytical phase diagrams of polycationic stability. We demonstrate the applicability of this approach by discussing the maximal charge dependence on the size of the molecular system. A numerical demonstration for linear polyenes, monocyclic annulenes, and helium clusters is provided.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
3-center and 4-center 2-particle Gaussian AO integrals on modern accelerated processors. 现代加速处理器上的 3 中心和 4 中心 2 粒子高斯 AO 积分。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0217001
Andrey Asadchev, Edward F Valeev
{"title":"3-center and 4-center 2-particle Gaussian AO integrals on modern accelerated processors.","authors":"Andrey Asadchev, Edward F Valeev","doi":"10.1063/5.0217001","DOIUrl":"https://doi.org/10.1063/5.0217001","url":null,"abstract":"<p><p>We report an implementation of the McMurchie-Davidson (MD) algorithm for 3-center and 4-center 2-particle integrals over Gaussian atomic orbitals (AOs) with low and high angular momenta l and varying degrees of contraction for graphical processing units (GPUs). This work builds upon our recent implementation of a matrix form of the MD algorithm that is efficient for GPU evaluation of 4-center 2-particle integrals over Gaussian AOs of high angular momenta (l ≥ 4) [A. Asadchev and E. F. Valeev, J. Phys. Chem. A 127, 10889-10895 (2023)]. The use of unconventional data layouts and three variants of the MD algorithm allow for the evaluation of integrals with double precision and sustained performance between 25% and 70% of the theoretical hardware peak. Performance assessment includes integrals over AOs with l ≤ 6 (a higher l is supported). Preliminary implementation of the Hartree-Fock exchange operator is presented and assessed for computations with up to a quadruple-zeta basis and more than 20 000 AOs. The corresponding C++ code is part of the experimental open-source LibintX library available at https://github.com/ValeevGroup/libintx.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Kinetic isotope effects on hydrogen/deuterium disordering and ordering in ice crystals: A Raman and dielectric study of ice VI, XV, and XIX. 冰晶中氢/氘无序和有序的动力学同位素效应：冰 VI、XV 和 XIX 的拉曼和介电研究。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0211427
Alexander V Thoeny, Tobias M Gasser, Lars Hoffmann, Markus Keppler, Roland Böhmer, Thomas Loerting
{"title":"Kinetic isotope effects on hydrogen/deuterium disordering and ordering in ice crystals: A Raman and dielectric study of ice VI, XV, and XIX.","authors":"Alexander V Thoeny, Tobias M Gasser, Lars Hoffmann, Markus Keppler, Roland Böhmer, Thomas Loerting","doi":"10.1063/5.0211427","DOIUrl":"https://doi.org/10.1063/5.0211427","url":null,"abstract":"<p><p>Ice XIX and ice XV are both partly hydrogen-ordered counterparts to disordered ice VI. The ice XIX → XV transition represents the only order-to-order transition in ice physics. Using Raman and dielectric spectroscopies, we investigate the ambient-pressure kinetics of the two individual steps in this transition in real time (of hours), that is, ice XIX → transient ice VI (the latter called VI‡) and ice VI‡ → ice XV. Hydrogen-disordered ice VI‡ appears intermittent between 101 and 120 K, as inferred from the appearance and subsequent disappearance of the ice VI Raman marker bands. A comparison of the rate constants for the H2O ices reported here with those from D2O samples [Thoeny et al., J. Chem. Phys. 156, 154507 (2022)] reveals a large kinetic isotope effect for the ice XIX decay, but a much smaller one for the ice XV buildup. An enhancement of the classical overbarrier rate through quantum tunneling for the former can provide a possible explanation for this finding. The activation barriers for both transitions are in the 18-24 kJ/mol range, which corresponds to the energy required to break a single hydrogen bond. These barriers do not show an H/D isotope effect and are the same, no matter whether they are derived from Raman scattering or from dielectric spectroscopy. These findings favor the notion that a dipolar reorientation, involving the breakage of a hydrogen bond, is the rate determining step at the order-to-order transition.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chemically reactive and aging macromolecular mixtures I: Phase diagrams, spinodals, and gelation. 化学反应和老化大分子混合物 I. 相图、旋光和凝胶：相图、旋光和凝胶化。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0196793
Ruoyao Zhang, Sheng Mao, Mikko P Haataja
{"title":"Chemically reactive and aging macromolecular mixtures I: Phase diagrams, spinodals, and gelation.","authors":"Ruoyao Zhang, Sheng Mao, Mikko P Haataja","doi":"10.1063/5.0196793","DOIUrl":"https://doi.org/10.1063/5.0196793","url":null,"abstract":"<p><p>Multicomponent macromolecular mixtures often form higher-order structures, which may display non-ideal mixing and aging behaviors. In this work, we first propose a minimal model of a quaternary system that takes into account the formation of a complex via a chemical reaction involving two macromolecular species; the complex may then phase separate from the buffer and undergo a further transition into a gel-like state. We subsequently investigate how physical parameters such as molecular size, stoichiometric coefficients, equilibrium constants, and interaction parameters affect the phase behavior of the mixture and its propensity to undergo aging via gelation. In addition, we analyze the thermodynamic stability of the system and identify the spinodal regions and their overlap with gelation boundaries. The approach developed in this work can be readily generalized to study systems with an arbitrary number of components. More broadly, it provides a physically based starting point for the investigation of the kinetics of the coupled complex formation, phase separation, and gelation processes in spatially extended systems.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Continuous Floquet theory in solid-state NMR. 固态 NMR 中的连续 Floquet 理论。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0213078
Matías Chávez, Matthias Ernst
{"title":"Continuous Floquet theory in solid-state NMR.","authors":"Matías Chávez, Matthias Ernst","doi":"10.1063/5.0213078","DOIUrl":"https://doi.org/10.1063/5.0213078","url":null,"abstract":"<p><p>This article presents the application of continuous Floquet theory in solid-state nuclear magnetic resonance (NMR). Continuous Floquet theory extends the traditional Floquet theory to non-continuous Hamiltonians, enabling the description of observable effects not fully captured by the traditional Floquet theory due to its requirement for a periodic Hamiltonian. We present closed-form expressions for computing first- and second-order effective Hamiltonians, streamlining integration with the traditional Floquet theory and facilitating application in NMR experiments featuring multiple modulation frequencies. Subsequently, we show examples of the practical application of continuous Floquet theory by investigating several solid-state NMR experiments. These examples illustrate the importance of the duration of the pulse scheme regarding the width of the resonance conditions and the near-resonance behavior.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Insights into the structure and dynamics of K+ ions at the muscovite-water interface from machine learning potential simulations. 从机器学习电位模拟中洞察麝香石-水界面上 K+ 离子的结构和动力学。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0217720
Abhinav S Raman, Annabella Selloni
{"title":"Insights into the structure and dynamics of K+ ions at the muscovite-water interface from machine learning potential simulations.","authors":"Abhinav S Raman, Annabella Selloni","doi":"10.1063/5.0217720","DOIUrl":"https://doi.org/10.1063/5.0217720","url":null,"abstract":"<p><p>The surfaces of many minerals are covered by naturally occurring cations that become partially hydrated and can be replaced by hydronium or other cations when the surface is exposed to water or an aqueous solution. These ion exchange processes are relevant to various chemical and transport phenomena, yet elucidating their microscopic details is challenging for both experiments and simulations. In this work, we make a first step in this direction by investigating the behavior of the native K+ ions at the interface between neat water and the muscovite mica (001) surface with ab-initio-based machine learning molecular dynamics and enhanced sampling simulations. Our results show that the desorption of the surface K+ ions in pure ion-free water has a significant free energy barrier irrespective of their local surface arrangement. In contrast, facile K+ diffusion between mica's ditrigonal cavities characterized by different Al/Si orderings is observed. This behavior suggests that the K+ ions may favor a dynamic disordered surface arrangement rather than complete desorption when exposed to deionized water.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A size-consistent multi-state mapping approach to surface hopping. 表面跳跃的尺寸一致多态映射法
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-28 DOI: 10.1063/5.0208575
Joseph E Lawrence, Jonathan R Mannouch, Jeremy O Richardson
{"title":"A size-consistent multi-state mapping approach to surface hopping.","authors":"Joseph E Lawrence, Jonathan R Mannouch, Jeremy O Richardson","doi":"10.1063/5.0208575","DOIUrl":"https://doi.org/10.1063/5.0208575","url":null,"abstract":"<p><p>We develop a multi-state generalization of the recently proposed mapping approach to surface hopping (MASH) for the simulation of electronically nonadiabatic dynamics. This new approach extends the original MASH method to be able to treat systems with more than two electronic states. It differs from previous approaches in that it is size consistent and rigorously recovers the original two-state MASH in the appropriate limits. We demonstrate the accuracy of the method by applying it to a series of model systems for which exact benchmark results are available, and we find that the method is well suited to the simulation of photochemical relaxation processes.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dynamics of reduced perylene bisimide cyclophane redox species by ultrafast spectroelectrochemistry. 通过超快光谱电化学研究还原过烯双亚胺环烷氧化还原物种的动力学。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-21 DOI: 10.1063/5.0210490
Rebecca Fröhlich, Jessica Rühe, Michael Moos, Laura Kontschak, Patrik Ehrmann, Frank Würthner, Christoph Lambert, Tobias Brixner
{"title":"Dynamics of reduced perylene bisimide cyclophane redox species by ultrafast spectroelectrochemistry.","authors":"Rebecca Fröhlich, Jessica Rühe, Michael Moos, Laura Kontschak, Patrik Ehrmann, Frank Würthner, Christoph Lambert, Tobias Brixner","doi":"10.1063/5.0210490","DOIUrl":"https://doi.org/10.1063/5.0210490","url":null,"abstract":"<p><p>Charged molecules play essential roles in many natural and artificial functional processes, ranging from photosynthesis to photovoltaics to chemical reactions and more. It is often difficult to identify the optical dynamic properties of relevant redox species because they cannot be easily prepared, their spectra overlap, or they evolve on a femtosecond timescale. Here, we address these challenges by combining spectroelectrochemistry, ultrafast transient absorption spectroscopy, and suitable data analysis. We illustrate the method with the various redox species of a cyclophane composed of two perylene bisimide subunits. While singular-value decomposition is a well-established tool in the analysis of time-dependent spectra of a single molecular species, we here use it additionally to separate transient maps of individual redox species. This is relevant because at any specific applied electrochemical potential, several redox species coexist in the ensemble, and our procedure allows disentangling their spectroscopic response. In the second step, global analysis is then employed to retrieve the excited-state lifetimes and decay-associated difference spectra. Our approach is generally suitable for unraveling ultrafast dynamics in materials featuring charge-transfer processes.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Steady-state probabilities for Markov jump processes in terms of powers of the transition rate matrix. 马尔可夫跳跃过程的稳态概率，以转换率矩阵的幂表示。
IF 3.1 2区 化学
Journal of Chemical Physics Pub Date : 2024-06-21 DOI: 10.1063/5.0217202
Diego Frezzato
{"title":"Steady-state probabilities for Markov jump processes in terms of powers of the transition rate matrix.","authors":"Diego Frezzato","doi":"10.1063/5.0217202","DOIUrl":"https://doi.org/10.1063/5.0217202","url":null,"abstract":"<p><p>Several types of dynamics at stationarity can be described in terms of a Markov jump process among a finite number N of representative sites. Before dealing with the dynamical aspects, one basic problem consists in expressing the a priori steady-state occupation probabilities of the sites. In particular, one wishes to go beyond the mere black-box computational tools and find expressions in which the jump rate constants appear explicitly, therefore allowing for a potential design/control of the network. For strongly connected networks admitting a unique stationary state with all sites populated, here we express the occupation probabilities in terms of a formula that involves powers of the transition rate matrix up to order N - 1. We also provide an expression of the derivatives with respect to the jump rate constants, possibly useful in sensitivity analysis frameworks. Although we refer to dynamics in (bio)chemical networks at thermal equilibrium or under nonequilibrium steady-state conditions, the results are valid for any Markov jump process under the same assumptions.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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