Journal of Chemical Physics最新文献_第5页

The structure and symmetry of modular state space for complex quantum systems.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0245447

Guohua Tao

{"title":"The structure and symmetry of modular state space for complex quantum systems.","authors":"Guohua Tao","doi":"10.1063/5.0245447","DOIUrl":"https://doi.org/10.1063/5.0245447","url":null,"abstract":"Understanding the state space structure of complex quantum systems can help to effectively characterize the system properties and explore underlying mechanisms. The structure of the state space could be quite complicated for quantum many-body systems, and the systematic decomposition of the state space is normally involved. Recently, a modular tensor diagram approach was proposed to reorganize the state space hierarchically based on a modular basis. Here, we review the construction of spin eigenfunctions for multiple exciton systems and further develop modular tensor diagrams to exemplify the hierarchical symmetry of the state space. The newly constructed spin eigenfunctions for quadruple excitons, along with the results for triple excitons, are used to demonstrate the effective decomposition of the state space into hierarchical tensorial structures. A universal recursive relation is derived to determine the coefficients of spin eigenfunctions exhibiting transformation symmetry between different classes of elementary modules for an arbitrary number of exciton units. Interestingly, different coupling schemes mapped to quantum many-body interactions lead to different spin adapted basis states, which may correspond to different realistic systems upon the breakdown of spin degeneracy. This work highlights the hierarchical symmetry of the tensorial structure of quantum many-body systems, which may facilitate a better understanding of the structure property relationship toward the object-oriented materials design.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657449","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

Efficient exploration of reaction pathways using reaction databases and active learning.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0235715

Domantas Kuryla, Gábor Csányi, Adri C T van Duin, Angelos Michaelides

{"title":"Efficient exploration of reaction pathways using reaction databases and active learning.","authors":"Domantas Kuryla, Gábor Csányi, Adri C T van Duin, Angelos Michaelides","doi":"10.1063/5.0235715","DOIUrl":"https://doi.org/10.1063/5.0235715","url":null,"abstract":"The fast and accurate simulation of chemical reactions is a major goal of computational chemistry. Recently, the pursuit of this goal has been aided by machine learning interatomic potentials (MLIPs), which provide energies and forces at quantum mechanical accuracy but at a fraction of the cost of the reference quantum mechanical calculations. Assembling the training set of relevant configurations is key to building the MLIP. Here, we demonstrate two approaches to training reactive MLIPs based on reaction pathway information. One approach exploits reaction datasets containing reactant, product, and transition state structures. Using an SN2 reaction dataset, we accurately locate reaction pathways and transition state geometries of up to 170 unseen reactions. In another approach, which does not depend on data availability, we present an efficient active learning procedure that yields an accurate MLIP and converged minimum energy path given only the reaction end point structures, avoiding quantum mechanics driven reaction pathway search at any stage of training set construction. We demonstrate this procedure on an SN2 reaction in the gas phase and with a small number of solvating water molecules, predicting reaction barriers within 20 meV of the reference quantum chemistry method. We then apply the active learning procedure on a more complex reaction involving a nucleophilic aromatic substitution and proton transfer, comparing the results against the reactive ReaxFF force field. Our active learning procedure, in addition to rapidly finding reaction paths for individual reactions, provides an approach to building large reaction path databases for training transferable reactive machine learning potentials.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674055","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

Exploring combined spin-labeling approach for structural studies of mRNA in the human ribosome. 探索人类核糖体中 mRNA 结构研究的组合自旋标记法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0245722

Mikhail Kolokolov, Alexey Malygin, Dmitri Graifer, Mariya Meschaninova, Mariya Vorobyeva, Matvey Fedin, Olesya Krumkacheva, Elena Bagryanskaya

{"title":"Exploring combined spin-labeling approach for structural studies of mRNA in the human ribosome.","authors":"Mikhail Kolokolov, Alexey Malygin, Dmitri Graifer, Mariya Meschaninova, Mariya Vorobyeva, Matvey Fedin, Olesya Krumkacheva, Elena Bagryanskaya","doi":"10.1063/5.0245722","DOIUrl":"https://doi.org/10.1063/5.0245722","url":null,"abstract":"In this study, we investigated the structural variability of mRNA in the human ribosome by comparing two spin-labeling strategies: one involving an mRNA analog bearing two spin labels attached to the ribose-phosphate backbone and the other placing labels at the nucleotide bases. The use of two strategies of spin labeling of mRNAs allowed us to study for the first time the effect of the structure and location of spin labels on the measured interspin distances in human ribosome complexes. Experiments using dipolar EPR spectroscopy, supported by molecular dynamics calculations, demonstrated that labels introduced at nucleotide bases provide a higher resolution between mRNA conformations in the ribosome mRNA channel, compared to labels introduced at the ribose-phosphate backbone. Although ribose-phosphate labeling turned out to be less informative on its own for studying mRNA conformations in the ribosome than the previously used base labeling, it can find application in other complex studies of the structure of RNAs and their complexes.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674056","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

Gas-phase reactivity of protonated oxazolone: Chemical dynamics simulations and graph theory-based analysis reveal the importance of ion-molecule complexes. 质子化恶唑酮的气相反应性：化学动力学模拟和基于图论的分析揭示了离子-分子复合物的重要性。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0245766

Ariel F Perez Mellor, Thomas Bürgi, Riccardo Spezia

{"title":"Gas-phase reactivity of protonated oxazolone: Chemical dynamics simulations and graph theory-based analysis reveal the importance of ion-molecule complexes.","authors":"Ariel F Perez Mellor, Thomas Bürgi, Riccardo Spezia","doi":"10.1063/5.0245766","DOIUrl":"https://doi.org/10.1063/5.0245766","url":null,"abstract":"This study delves into the fragmentation mechanisms of the oxazolone form (OXA) of protonated cyclo-di-glycine using chemical dynamics simulations at multiple internal energies. While we focus our in-depth analyses on a representative total energy of 178 kcal/mol, we also performed simulations over the 127-187 kcal/mol range. This broader energy sampling reveals how the population of states evolves with increasing internal energy, enabling us to compute rate constants and then effective energy thresholds using a previously introduced three-state model [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. By transforming molecular geometries into graph representations, we systematically analyze fragmentation processes and identify key intermediates and ion-molecule complexes (IMCs) that play a crucial role in fragmentation dynamics. The study highlights the distinct isomerization landscapes of OXA, driven by IMC formation, which contrasts with the previously reported behavior of cyclic and linear forms [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. The resulting fragmentation channels are characterized by their unique energetic thresholds and branching ratios and can provide a molecular explanation of what was observed experimentally. Thanks to an accurate analysis of the trajectories using our graph-theory-based tools, it was possible to point out the particular behavior of OXA fragmentation, which is different from other isomers. In particular, the important role of IMCs is shown, which has an impact on populating different isomeric structures.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674061","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

Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0253522

J Holland, T J Nott, D G A L Aarts

{"title":"Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces.","authors":"J Holland, T J Nott, D G A L Aarts","doi":"10.1063/5.0253522","DOIUrl":"10.1063/5.0253522","url":null,"abstract":"The localization of biomolecular condensates to intracellular membrane surfaces has emerged as an important feature of sub-cellular organization. In this work, we study the wetting behavior of biomolecular condensates on various substrates. We use confocal microscopy to measure the contact angles of model condensates formed by intrinsically disordered protein Ddx4N. We show the importance of taking optical aberrations into account, as these impact apparent contact angle measurements. Ddx4N condensates are seen to partially dry (contact angles above 90°) a model membrane, with little dependence on the magnitude of charge on, or tyrosine content of, Ddx4N. Further contact angle measurements on surfaces of varying hydrophilicity reveal a preference of Ddx4N condensates for hydrophobic surfaces, suggesting an intrinsic repulsion between protein condensates and hydrophilic membrane surfaces. This observation is in line with previous studies relating protein adsorption to surface hydrophilicity. Our work advances the understanding of the molecular details governing the localization of biomolecular condensates.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648786","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

Mid-infrared strong nonreciprocal thermal radiation with extremely small applied magnetic field.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0262471

Jun Wu, Ye Ming Qing

引用次数: 0

Modeling entanglement dynamics of molecules interacting with entangled photons through Lindblad master equation approach.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0254272

Sajal Kumar Giri, George C Schatz

引用次数: 0

Perturbation of water-ethanol solvent structural relaxation by a bis-urea supramolecular gel and paracetamol.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0252501

Riccardo Morbidini, Robert M Edkins, Kirill Nemkovskiy, Gøran Nilsen, Tilo Seydel, Katharina Edkins

引用次数: 0

Revisiting the question of what instantaneous normal modes tell us about liquid dynamics.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0239061

Sha Jin, Xue Fan, Matteo Baggioli

{"title":"Revisiting the question of what instantaneous normal modes tell us about liquid dynamics.","authors":"Sha Jin, Xue Fan, Matteo Baggioli","doi":"10.1063/5.0239061","DOIUrl":"https://doi.org/10.1063/5.0239061","url":null,"abstract":"The lack of a well-defined equilibrium reference configuration has long hindered a comprehensive atomic-level understanding of liquid dynamics and properties. The Instantaneous Normal Mode (INM) approach, which involves diagonalizing the Hessian matrix of potential energy in instantaneous liquid configurations, has emerged as a promising framework in this direction. However, several conceptual challenges remain, particularly related to the approach's inability to capture anharmonic effects. In this study, we present a set of \"experimental facts\" through a comprehensive INM analysis of simulated systems, including Ar, Xe, N2, CS2, Ga, and Pb, across a wide temperature range from the solid to gas phase. First, we examine the INM density of states (DOS) and compare it to the DOS obtained from the velocity auto-correlation function. We then analyze the temperature dependence of the fraction of unstable modes and the low-frequency slope of the INM DOS in search of potential universal behaviors. Furthermore, we explore the relationship between INMs and other properties of liquids, including the liquid-like to gas-like dynamical crossover and the momentum gap of collective shear waves. In addition, we investigate the INM spectrum at low temperatures as the system approaches the solid phase, revealing a significant fraction of unstable modes even in crystalline solids. Finally, we confirm the existence of a recently discussed cusp-like singularity in the INM eigenvalue spectrum and uncover its complex temperature-dependent behavior, challenging current theoretical models.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657399","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

Non-perturbative exciton transfer rate analysis of the Fenna-Matthews-Olson photosynthetic complex under reducing and oxidizing conditions.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0251613

Hallmann Ó Gestsson, Charlie Nation, Jacob S Higgins, Gregory S Engel, Alexandra Olaya-Castro

{"title":"Non-perturbative exciton transfer rate analysis of the Fenna-Matthews-Olson photosynthetic complex under reducing and oxidizing conditions.","authors":"Hallmann Ó Gestsson, Charlie Nation, Jacob S Higgins, Gregory S Engel, Alexandra Olaya-Castro","doi":"10.1063/5.0251613","DOIUrl":"https://doi.org/10.1063/5.0251613","url":null,"abstract":"Two-dimensional optical spectroscopy experiments have examined photoprotective mechanisms in the Fenna-Matthews-Olson (FMO) photosynthetic complex, showing that exciton transfer pathways change significantly depending on the environmental redox conditions. Higgins et al. [Proc. Natl. Acad. Sci. U. S. A. 118(11), e2018240118 (2021)] have theoretically linked these observations to changes in a quantum vibronic coupling, whereby onsite energies are altered under oxidizing conditions such that exciton energy gaps are detuned from a specific vibrational motion of the bacteriochlorophyll a. These arguments rely on an analysis of exciton transfer rates within Redfield theory, which is known to provide an inaccurate description of the influence of the vibrational environment on the exciton dynamics in the FMO complex. Here, we use a memory kernel formulation of the hierarchical equations of motion to obtain non-perturbative estimations of exciton transfer rates, which yield a modified physical picture. Our findings indicate that onsite energy shifts alone do not reproduce the reported rate changes in the oxidative environment. We systematically examine a model that includes combined changes in both site energies and the frequency of a local vibration in the oxidized complex while maintaining consistency with absorption spectra and achieving qualitative, but not quantitative, agreement with the measured changes in transfer rates. Our analysis points to potential limitations of the FMO electronic Hamiltonian, which was originally derived by fitting spectra to perturbative theories. Overall, our work suggests that further experimental and theoretical analyses may be needed to understand the variations of exciton dynamics under different redox conditions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657405","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