Journal of Chemical Physics最新文献_第9页

Machine learning molecular dynamics for reaction rates of CO oxidation on Pt(111): Impact of site preference and oxygen coverage. Pt（111）上CO氧化反应速率的机器学习分子动力学：位置偏好和氧气覆盖的影响。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0354277

Ruihao Fan, Chen Li, Bin Jiang

{"title":"Machine learning molecular dynamics for reaction rates of CO oxidation on Pt(111): Impact of site preference and oxygen coverage.","authors":"Ruihao Fan, Chen Li, Bin Jiang","doi":"10.1063/5.0354277","DOIUrl":"https://doi.org/10.1063/5.0354277","url":null,"abstract":"The kinetics of elementary surface reactions lay the foundation of our understanding of heterogeneous catalysis. However, accurate determination of surface reaction rates is by no means a trivial task. A prominent example is the oxidation of CO on Pt(111), where accurate rate constants were determined recently by experiments, challenging the harmonic transition state theory based on the revised Perdew-Burke-Ernzerhof (RPBE) density functional. However, RPBE is known to predict the incorrect favorable adsorption site for CO on Pt(111), whereas a van der Waals-corrected functional (vdW-DF2) correctly describes this site preference. In addition, the experimental data were derived at a low oxygen coverage, which was not represented well by previous models using small supercells. In this work, we constructed a machine-learned potential energy surface (PES) using vdW-DF2 for the CO + O/Pt(111) system. Based on this vdW-DF2 PES, we performed reactive flux rate constant calculations through molecular dynamics with enhanced sampling and varying periodic supercell sizes. Our results show improved agreement with the experiment compared to earlier RPBE-based calculations. Furthermore, the oxidation rate constants are found to modestly decrease with the decreasing oxygen coverage due to minor increase in the barrier height.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110342","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

Coexistence of two molecular environments in liquid cis-decalin revealed by spin probe. 自旋探针揭示液体顺十氢化萘中两种分子环境的共存。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0349032

Miroslava Lukešová, Jakov Slade, Dalibor Merunka, Miroslav Peric

{"title":"Coexistence of two molecular environments in liquid cis-decalin revealed by spin probe.","authors":"Miroslava Lukešová, Jakov Slade, Dalibor Merunka, Miroslav Peric","doi":"10.1063/5.0349032","DOIUrl":"https://doi.org/10.1063/5.0349032","url":null,"abstract":"We used a nitroxide radical as a spin probe in electron paramagnetic resonance (EPR) to study the highly fragile glass-forming molecular liquid cis-decalin and the similar liquid cis-perfluorodecalin. The EPR spectra of the radical dissolved in cis-decalin were measured upon cooling from its equilibrium liquid state at 373 K to its supercooled state below 229 K. The analysis of the EPR spectra revealed the anomalous temperature behavior of the EPR parameters and rotational diffusivity of the radical in cis-decalin, which was not found in cis-perfluorodecalin. The anomalous behavior in cis-decalin led us to conclude that a distinct slow environment appears around the radical upon cooling through the equilibrium state and that the exchange rate between fast and slow radical environments decreases upon cooling into the supercooled state. Because of the slowing down of exchange, we were able to simulate the radical's low-temperature EPR spectra by two spectral components corresponding to the two radicals' environments. By using the theory of environment exchange in EPR, we performed the fitting of EPR parameters to determine temperature dependences of environment-exchange quantities and rotational radical diffusivities in each environment. The fraction of the slow environment was found to continuously grow on cooling, implying that cis-decalin does not exhibit liquid-liquid transition and fluid polyamorphism. However, the coexistence of two local liquid environments in cis-decalin deserves further examination as it may be closely related to very high fragility and other properties of this material. We broadly discuss our spin-probe results and their relations with the literature data for cis-decalin.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110329","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

Modeling of structure and phase transitions in CsPb(I1-xBrx)3 using a DFT-parameterized transferable force field. 基于dft参数化可传递力场的CsPb(I1-xBrx)3结构和相变建模

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0343809

Praveen Nagaraju, Sudhir K Sahoo

{"title":"Modeling of structure and phase transitions in CsPb(I1-xBrx)3 using a DFT-parameterized transferable force field.","authors":"Praveen Nagaraju, Sudhir K Sahoo","doi":"10.1063/5.0343809","DOIUrl":"https://doi.org/10.1063/5.0343809","url":null,"abstract":"Inorganic lead halide perovskites, CsPbX3 (X = I and Br), have attracted considerable attention in the scientific community for their improved thermal stability compared to their hybrid counterparts and for their use in highly efficient solar cells. The mixed halide compositions CsPb(I1-xBrx)3 are widely used to tune optoelectronic properties while improving phase stability by suppressing the transformation of the photoactive black γ phase into the non-perovskite, photo-inactive yellow δ phase. Despite these advantages, no transferable classical force fields within a rigid-ion framework reliably describe both pure and mixed-halide systems. We report here a transferable force field comprising Lennard-Jones and Coulomb terms for inorganic lead halides CsPb(I1-xBrx)3. The force field is trained against density functional theory-computed energy-volume equations of state over a wide range of structural deformations. The developed force field is benchmarked by reproducing structural and mechanical properties, pressure dependent structural behavior, and temperature-driven phase transitions for the pure and mixed halide perovskites. These results demonstrate the transferability and robustness of the proposed force field for large-scale simulations of halide perovskites.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110335","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

MPID polarizable force field: GPU implementation and biomolecular simulations. MPID极化力场：GPU实现和生物分子模拟。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0345546

Qiaozhu Tan, Andrew C Simmonett, Bernard R Brooks, Jing Huang

{"title":"MPID polarizable force field: GPU implementation and biomolecular simulations.","authors":"Qiaozhu Tan, Andrew C Simmonett, Bernard R Brooks, Jing Huang","doi":"10.1063/5.0345546","DOIUrl":"https://doi.org/10.1063/5.0345546","url":null,"abstract":"The multipole and induced dipole (MPID) model provides a sophisticated description of electrostatics through permanent atomic multipoles up to the octupole level and point induced dipoles, but its high computational cost has limited its routine application to biomolecular simulations. Here, we present a GPU-accelerated implementation of the MPID model in OpenMM. The implementation produces energies and forces fully consistent with those obtained from CHARMM and enables routine microsecond-scale molecular dynamics simulations of explicitly solvated protein systems. Moreover, force field parameters were transferred directly from the Drude oscillator model to the MPID framework without reparameterization, yielding the MPID-2019 protein force field. Tests on five proteins show that MPID-2019 reproduces a range of NMR observables, including scalar couplings and relaxation order parameters. These results demonstrate that MPID-2019 is a valid polarizable force field that is readily applicable to protein simulations and that the effective equivalence of the induced dipole and Drude oscillator formalisms can be established at the biomolecular level.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110355","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

Thawed Gaussian Ehrenfest dynamics. 解冻高斯Ehrenfest动力学。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0352624

Jiří J L Vaníček

{"title":"Thawed Gaussian Ehrenfest dynamics.","authors":"Jiří J L Vaníček","doi":"10.1063/5.0352624","DOIUrl":"https://doi.org/10.1063/5.0352624","url":null,"abstract":"Ehrenfest dynamics is a widely used mixed quantum-classical approach for nonadiabatic molecular dynamics, whereas thawed Gaussian wavepacket dynamics provides an efficient semiclassical description of adiabatic nuclear quantum dynamics. Here, we describe thawed Gaussian Ehrenfest dynamics (TGED), which unifies and generalizes these two methods to capture both electronic nonadiabaticity and nuclear quantum effects within a single framework. The fully variational formulation of TGED is derived by applying the time-dependent variational principle to a Hartree product of electronic and Gaussian nuclear wavepackets. Replacing the effective locally quadratic molecular potential obtained from this variational treatment by alternative effective locally quadratic potentials yields an infinite family of TGED methods, of which we present several members. We analyze the limiting cases of the general formalism and show, in particular, that it reduces to conventional Ehrenfest dynamics in the classical limit for the nuclei and to thawed Gaussian wavepacket dynamics in the absence of electronic coupling. Finally, we present explicit geometric integrators for the entire family of methods and identify the conditions under which the different approximations become exact.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110308","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

Effect of crystal size on triplet pair dynamics in singlet fission of rubrene. 晶体尺寸对rubrene单线态裂变中三重态对动力学的影响。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0350351

Yusuke Wakikawa, Kazuma Kachi, Tadaaki Ikoma

{"title":"Effect of crystal size on triplet pair dynamics in singlet fission of rubrene.","authors":"Yusuke Wakikawa, Kazuma Kachi, Tadaaki Ikoma","doi":"10.1063/5.0350351","DOIUrl":"https://doi.org/10.1063/5.0350351","url":null,"abstract":"Singlet fission proceeds via spin-correlated triplet (TT) pairs and offers promising applications in solar cells, magneto-optical sensors, and quantum technologies. Here, we quantitatively investigated how crystalline morphology influences TT pair dynamics during singlet fission in rubrene orthorhombic crystals by combining experimental and theoretical analyses of the magnetic field dependence of the magnetoluminescence (ML) effect, defined as the magnetic-field-induced change in fluorescence intensity, up to 300 mT at room temperature. Rapidly annealed thin films exhibit an anomalous low-field ML effect, whose maximum reaches -25.2%, and the negative effect persists up to 300 mT. By contrast, millimeter-sized single crystals exhibit a decrease of approximately one order of magnitude in the negative ML effect, accompanied by a low-field shift of the zero-crossing field separating negative and positive ML. The observed results were successfully reproduced by density-matrix simulations based on a four-site model and could be explained by an enhancement in an effective TT pair dissociation rate with increasing crystal size, which shortens the lifetime of the spin-correlated TT pairs undergoing repeated cycles of hopping and spin mixing. The optically detected magnetic resonance measurements at zero field further suggest that long-lived triplet excitons are more readily detected in rapidly annealed films with micrometer-sized crystals than in millimeter-sized single crystals, providing complementary evidence for morphology-dependent triplet localization and transport. These results demonstrate that crystalline morphology provides an effective route to tune TT pair lifetime and spin mixing in rubrene singlet fission, which is crucial for optimizing singlet-fission-based applications.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110321","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

Economized path integrals. 节省路径积分。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0351653

Zezhu Zeng, David E Manolopoulos

{"title":"Economized path integrals.","authors":"Zezhu Zeng, David E Manolopoulos","doi":"10.1063/5.0351653","DOIUrl":"https://doi.org/10.1063/5.0351653","url":null,"abstract":"The Hessian of the ring polymer spring potential in the standard Trotter path integral is a P × P symmetric circulant matrix with a centroid eigenvalue of zero. All such matrices commute and are diagonalized by the same bead-to-normal mode transformation matrix, and their eigenvalues contain ⌈P/2⌉ - 1 degenerate pairs by symmetry. However, this still leaves some freedom to improve on the Trotter approximation: one can optimize the remaining ⌊P/2⌋ independent non-zero normal mode frequencies to fit the exact quantum mechanical radii of gyration of harmonic ring polymers with frequencies in the range 0 ≤ ω ≤ ωmax, where ωmax is the maximum physical frequency in the problem of interest. The optimization involves solving a simple least squares problem for the optimum (economized or \"Eco\") internal mode frequencies. The remainder of the calculation then proceeds in the same way as a Trotter path integral calculation. An example application to hexagonal ice shows that the convergence of the Eco path integral is comparable to that of the fourth order Suzuki-Chin path integral, but with purely second order Trotter effort. There is no need to calculate the projected Hessians that arise in the Suzuki-Chin method by finite differences; there is no need to develop any new estimators for observables, and once the Eco frequencies have been calculated, the implementation of the Eco path integral involves changing just a few lines of a Trotter path integral code. To provide a more impressive example, we have implemented the Eco method in GPUMD and used it to converge the (negative) thermal expansion coefficient and the constant pressure heat capacity of MOF-5 with a machine-learned neuroevolution potential.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110323","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

Measurements of temperatures and species in CO2 post-shock thermochemical non-equilibrium. 二氧化碳冲击后热化学不平衡中的温度和物种测量。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0336781

Yufan Chen, Renjie Li, Wentao Wang, Zhuo Liu, Pan Shen, Qiu Wang, Fei Li, Sangdi Gu

{"title":"Measurements of temperatures and species in CO2 post-shock thermochemical non-equilibrium.","authors":"Yufan Chen, Renjie Li, Wentao Wang, Zhuo Liu, Pan Shen, Qiu Wang, Fei Li, Sangdi Gu","doi":"10.1063/5.0336781","DOIUrl":"https://doi.org/10.1063/5.0336781","url":null,"abstract":"Accurate characterization and prediction of shock-induced CO2 thermochemical non-equilibrium are crucial for current and future Mars entry missions. To investigate these phenomena, measurements of CO2 rotational temperature, mode-specific vibrational temperatures, and partial pressure were conducted behind incident shock fronts at intermediate velocities (3.2-5 km/s) at the ϕ800 shock tube at the Institute of Mechanics, Chinese Academy of Sciences, via a newly developed high-frequency mid-infrared beam-splitting fiber-coupled tunable diode laser absorption spectroscopy technique. Possible shock-tube nonidealities, including shock deceleration, water contamination, flow-cutter-induced two-dimensional effects, and boundary-layer mass removal, were examined and found to have limited influence on the present post-shock test flows. Notably, to the best of the authors' knowledge, these measurements may provide the first evidence that distinct CO2 vibrational modes exhibit similar relaxation rates at the centimeter spatial scale under highly dissociating conditions. When compared with one-dimensional post-shock calculations, the modified Stellar CO2 vibrational state-to-state database was found to reasonably predict the post-shock relaxation process but overestimate the mode-specific vibrational temperatures at the early post-shock stage. The measured post-shock temperature profiles are generally bounded by the Johnston and Cruden predictions, with a tendency toward the Cruden mechanism, whereas the measured CO2 partial-pressure profiles show good agreement with the Johnston mechanism. The obtained results provide benchmark data for validating and improving CO2 thermochemical models.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110389","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

Solvation structure and dynamics of choline chloride-based deep eutectic solvents with isomeric butanediol hydrogen bond donors. 异分异构体丁二醇氢键给体的氯化胆碱型深共晶溶剂的溶剂化结构和动力学。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0352863

Daniel Kim, Rathiesh R Pandian, Yong Zhang, Clemens Burda, Edward J Maginn

{"title":"Solvation structure and dynamics of choline chloride-based deep eutectic solvents with isomeric butanediol hydrogen bond donors.","authors":"Daniel Kim, Rathiesh R Pandian, Yong Zhang, Clemens Burda, Edward J Maginn","doi":"10.1063/5.0352863","DOIUrl":"https://doi.org/10.1063/5.0352863","url":null,"abstract":"Choline chloride-based deep eutectic solvents (DESs) are being investigated as redox flow battery electrolytes, where solvent viscosity plays a central role in governing ionic mobility, mass transport, and pumping efficiency. In this combined experimental and computational study, a series of DESs formed from choline chloride and butanediol isomer hydrogen bond donors (HBDs) is examined to probe how HBD molecular geometry affects liquid structure and dynamics while holding the molecular formula and hydroxyl group count constant. Density, viscosity, ionic conductivity, and ET(30) polarity are measured experimentally, while molecular dynamics simulations are used to quantify coordination numbers, hydrogen-bond lifetimes, self-diffusivities, dynamic heterogeneity, and local packing. Although the dominant first-shell interaction motifs are preserved across all isomers, systematic differences in hydrogen-bond dynamics, diol-diol connectivity, and spatial heterogeneity give rise to distinct transport behaviors, including substantial variations in viscosity and conductivity, that cannot be attributed to changes in local coordination structure alone. These results establish hydroxyl group arrangement as a key structural parameter governing DES transport properties and provide a controlled molecular framework for the rational design of choline chloride-based electrolytes.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149127541","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

Probing mechanisms of allosteric regulation in AAA+ ATPases for microtubule severing and protein disaggregation. AAA+ atp酶在微管切断和蛋白质分解中的变构调节机制的探索。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0347970

Maryum Irshad, Krishan Walpalage, Zhaocheng Zhang, Maria S Gillen, Ruxandra I Dima, George Stan

{"title":"Probing mechanisms of allosteric regulation in AAA+ ATPases for microtubule severing and protein disaggregation.","authors":"Maryum Irshad, Krishan Walpalage, Zhaocheng Zhang, Maria S Gillen, Ruxandra I Dima, George Stan","doi":"10.1063/5.0347970","DOIUrl":"https://doi.org/10.1063/5.0347970","url":null,"abstract":"Ring-like AAA+ (ATPases associated with diverse cellular activities) biological machines mediate protein remodeling to assist a broad range of essential cellular functions. The nucleotide-dependent remodeling action involves intra- and inter-ring allosteric communication to generate mechanical force applied onto the substrate by a set of loops that protrude into the central channel. In this study, we probe these allosteric mechanisms through a comparative study of the katanin, a microtubule severing protein including a clade 3 AAA domain, and the double-ring ClpB, a protein disaggregase including both a clade 3 and a clade 5 AAA domain. Our molecular dynamics simulations, combined with machine learning and bioinformatic analysis, reveal both similar mechanisms involving the clade 3 domain and ClpB-specific ones involving communication with the clade 5 domain. We find that both nucleotide and substrate polypeptide binding restrict the conformational landscape sampled by katanin and ClpB, with ligand-specific conformations observed in the latter case. Allosteric contributions of secondary structure elements, ranked using SHapley Additive exPlanations analysis in machine learning approaches and binary classification of features in ligand states, highlight the important role of regions adjacent to the nucleotide-binding site and the pore loops. Amino acid-level analysis of the allosteric paths reveals that intra-ring cooperativity modulates long-distance communication within the AAA+ protomers.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110357","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