Journal of Chemical Physics最新文献_第2页

Systematic analysis of biomolecular conformational ensembles with PENSA. 生物分子构象系的PENSA系统分析。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0235544

Martin Vögele, Neil J Thomson, Sang T Truong, Jasper McAvity, Ulrich Zachariae, Ron O Dror

{"title":"Systematic analysis of biomolecular conformational ensembles with PENSA.","authors":"Martin Vögele, Neil J Thomson, Sang T Truong, Jasper McAvity, Ulrich Zachariae, Ron O Dror","doi":"10.1063/5.0235544","DOIUrl":"10.1063/5.0235544","url":null,"abstract":"Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions-for example, with various mutations or bound ligands-in order to identify differences between the molecular conformations adopted under these conditions. However, the large amount of data produced by simulations of ever larger and more complex systems often renders it difficult to identify the structural features that are relevant to a particular biochemical phenomenon. We present a flexible software package named Python ENSemble Analysis (PENSA) that enables a comprehensive and thorough investigation into biomolecular conformational ensembles. It provides featurization and feature transformations that allow for a complete representation of biomolecules such as proteins and nucleic acids, including water and ion binding sites, thus avoiding the bias that would come with manual feature selection. PENSA implements methods to systematically compare the distributions of molecular features across ensembles to find the significant differences between them and identify regions of interest. It also includes a novel approach to quantify the state-specific information between two regions of a biomolecule, which allows, for example, tracing information flow to identify allosteric pathways. PENSA also comes with convenient tools for loading data and visualizing results, making them quick to process and easy to interpret. PENSA is an open-source Python library maintained at https://github.com/drorlab/pensa along with an example workflow and a tutorial. We demonstrate its usefulness in real-world examples by showing how it helps us determine molecular mechanisms efficiently.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698571/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914951","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

A composite hydrogel of porous gold nanorods and gelatin: Nanoscale structure and rheomechanical properties. 多孔金纳米棒和明胶的复合水凝胶：纳米级结构和流变力学性能。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0238568

Irfan Khan, Snigdharani Panda, Sugam Kumar, Sunita Srivastava

{"title":"A composite hydrogel of porous gold nanorods and gelatin: Nanoscale structure and rheomechanical properties.","authors":"Irfan Khan, Snigdharani Panda, Sugam Kumar, Sunita Srivastava","doi":"10.1063/5.0238568","DOIUrl":"https://doi.org/10.1063/5.0238568","url":null,"abstract":"Incorporating nanomaterials into hydrogels allows for the creation of versatile materials with properties that can be precisely tailored by manipulating their nanoscale structures, leading to a wide range of bulk properties. Investigating the structural and property characteristics of composite hydrogels is crucial in tailoring their performance for specific applications. This study focuses on investigating the correlation between the structural arrangement and properties of a composite hydrogel of thermoresponsive polymer, gelatin, and light-responsive antimicrobial porous gold nanorods (PAuNRs). The rheomechanical properties of the composite hydrogels are correlated with their nanoscale structural characteristics, investigated using small-angle neutron scattering (SANS). Analysis of SANS data reveals a decrease in the fractal dimension of PAuNRs incorporated hydrogel matrix, as compared to pure gelatin. Incorporating PAuNRs results in the formation of a softer composite hydrogel, as evident from the decrease in viscoelastic moduli, critical yield strain, denaturation temperature, and swelling ratio. Our results demonstrate that the structural modulation at the nanoscale can be precisely controlled through adjusting PAuNRs concentration and temperature, providing a fabrication mechanism for hydrogels with desired elastic properties. The reduced elasticity of the composite hydrogel and light-sensitive/antimicrobial property of the PAuNRs make this system suitable for specific biomedical applications, such as tissue engineering, device fabrication, and stimuli-based controlled drug delivery devices.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931985","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

Influence of nonequilibrium vibrational dynamics on spin selectivity in chiral molecular junctions. 非平衡振动动力学对手性分子结中自旋选择性的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0235411

R Smorka, S L Rudge, M Thoss

{"title":"Influence of nonequilibrium vibrational dynamics on spin selectivity in chiral molecular junctions.","authors":"R Smorka, S L Rudge, M Thoss","doi":"10.1063/5.0235411","DOIUrl":"https://doi.org/10.1063/5.0235411","url":null,"abstract":"We explore the role of molecular vibrations in the chirality-induced spin selectivity (CISS) effect in the context of charge transport through a molecular nanojunction. We employ a mixed quantum-classical approach that combines Ehrenfest dynamics for molecular vibrations with the hierarchical equations of motion method for the electronic degrees of freedom. This approach treats the molecular vibrations in a nonequilibrium manner, which is crucial for the dynamics of molecular nanojunctions. To explore the effect of vibrational dynamics on spin selectivity, we also introduce a new figure of merit, the displacement polarization, which quantifies the difference in vibrational displacements for opposing lead magnetizations. We analyze the dynamics of single trajectories, investigating how the spin selectivity depends on voltage and electronic-vibrational coupling. Furthermore, we investigate the dynamics and temperature dependence of ensemble-averaged observables. We demonstrate that spin selectivity is correlated in time with the vibrational polarization, indicating that the dynamics of molecular vibrations is the driving force of CISS in this model within the Ehrenfest approach.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931987","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

Photochemical pathways in astronomical ices: A computational study of singlet oxygen reactions with hydrocarbons. 天文冰中的光化学途径：单线态氧与碳氢化合物反应的计算研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0214165

Amit Daniely, Alon Zamir, Helen R Eisenberg, Ester Livshits, Elettra Piacentino, Jennifer B Bergner, Karin I Öberg, Tamar Stein

{"title":"Photochemical pathways in astronomical ices: A computational study of singlet oxygen reactions with hydrocarbons.","authors":"Amit Daniely, Alon Zamir, Helen R Eisenberg, Ester Livshits, Elettra Piacentino, Jennifer B Bergner, Karin I Öberg, Tamar Stein","doi":"10.1063/5.0214165","DOIUrl":"https://doi.org/10.1063/5.0214165","url":null,"abstract":"Complex organic molecules are widespread in different areas of the interstellar medium, including cold areas, such as molecular clouds, where chemical reactions occur in ice. Among the observed molecules are oxygen-bearing organic molecules, which are of high interest given their significant role in astrobiology. Despite the observed rich chemistry, the underlying molecular mechanisms responsible for molecular formation in such cold dilute areas are still not fully understood. In this paper, we study the unique chemistry taking place in astronomically relevant ices, where UV radiation is a central driving force for chemical reactions. Photofragmentation of ice components gives rise to highly reactive species, such as the O(1D) atom. These species provide a pathway for chemical complexity even in cold areas. Using quantum chemistry calculations, we demonstrate that O(1D) reacts barrierlessly with hydrocarbons. Moreover, photoprocessing of the reaction products (and other components of the ice), followed by radical recombination, is found to be an essential part of the overall mechanism. In ice containing O(1D) and hydrocarbons, the formation of formaldehyde in methane ice, acetaldehyde in ethane ice, and carbon monoxide in acetylene ice, and the consumption of alcohol in all systems, was predicted in agreement with experimental results.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931990","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

Solvatochromic charge model of isonitrile probes for investigating hydrogen-bond dynamics with 2DIR spectroscopy. 用2DIR光谱研究氢键动力学的异腈探针溶剂致变色电荷模型。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0242857

Michał Maj

{"title":"Solvatochromic charge model of isonitrile probes for investigating hydrogen-bond dynamics with 2DIR spectroscopy.","authors":"Michał Maj","doi":"10.1063/5.0242857","DOIUrl":"https://doi.org/10.1063/5.0242857","url":null,"abstract":"Isonitrile-derivatized amino acids are emerging as highly effective infrared (IR) probes for investigating the structures and dynamics of hydrogen (H)-bonds. These probes enable the quantification of chemical exchange processes in solute-solvent complexes via two-dimensional IR spectroscopy and hold significant promise for site-specific dynamic studies within proteins. Despite their potential, theoretical models that elucidate the solvatochromism of isonitriles remain underdeveloped. Here, we present the development and validation of a solvatochromic charge model for isonitrile (N≡C) probes. Using density functional theory calculations, we parameterized solvatochromic charges for isonitrile and integrated them into classical molecular dynamics (MD) simulations of β-isocyanoalanine in various solvents, including water and fluorinated alcohols. The model incorporates solvent-induced frequency shifts and accurately reproduces complex experimental line shapes, including asymmetric features from non-Gaussian dynamics. The model successfully reproduced the bimodal distribution of frequency shifts corresponding to free and H-bonded species in alcohols, as well as cross-peaks due to chemical exchange. Achieving reproducibility required long MD trajectories, which were computationally demanding. To manage this, we implemented graphics processing unit acceleration, drastically reducing the computational time and enabling the efficient processing of extensive MD data. While some discrepancies in population ratios suggest the need for refined solvent force field parameters and modeling transition dipole moment variations, the developed solvatochromic model is a reliable tool for studying the solvation dynamics. The model enables more detailed investigations of ultrafast dynamics in solute-solvent complexes and represents important steps toward modeling site-specific dynamics of biomolecules with isonitrile probes.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931992","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

Polariton spectra under the collective coupling regime. I. Efficient simulation of linear spectra and quantum dynamics. 集体耦合下的极化子谱。线性光谱和量子动力学的有效模拟。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0243535

M Elious Mondal, A Nickolas Vamivakas, Steven T Cundiff, Todd D Krauss, Pengfei Huo

{"title":"Polariton spectra under the collective coupling regime. I. Efficient simulation of linear spectra and quantum dynamics.","authors":"M Elious Mondal, A Nickolas Vamivakas, Steven T Cundiff, Todd D Krauss, Pengfei Huo","doi":"10.1063/5.0243535","DOIUrl":"https://doi.org/10.1063/5.0243535","url":null,"abstract":"We outline two general theoretical techniques to simulate polariton quantum dynamics and optical spectra under the collective coupling regimes described by a Holstein-Tavis-Cummings (HTC) model Hamiltonian. The first one takes advantage of sparsity of the HTC Hamiltonian, which allows one to reduce the cost of acting polariton Hamiltonian onto a state vector to the linear order of the number of states, instead of the quadratic order. The second one is applying the well-known Chebyshev series expansion approach for quantum dynamics propagation and to simulate the polariton dynamics in the HTC system; this approach allows us to use a much larger time step for propagation and only requires a few recursive operations of the polariton Hamiltonian acting on state vectors. These two theoretical approaches are general and can be applied to any trajectory-based non-adiabatic quantum dynamics methods. We apply these two techniques with our previously developed Lindblad-partially linearized density matrix approach to simulate the linear absorption spectra of the HTC model system, with both inhomogeneous site energy disorders and dipolar orientational disorders. Our numerical results agree well with the previous analytic and numerical work.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949441","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

Full-dimensional accurate potential energy surface and dynamics for the unimolecular isomerization reaction CH3NC ⇌ CH3CN. CH3NC + CH3CN单分子异构化反应的全维精确势能面和动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0245188

Junlong Li, Junhong Li, Jun Li

引用次数: 0

TIP 4 P 2005 Ice : Simulating water with two molecular states. TIP 4p2005冰：模拟具有两种分子状态的水。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-01-07 DOI: 10.1063/5.0247832

Lucía F Sedano, Carlos Vega, Eva G Noya, Eduardo Sanz

{"title":"TIP 4 P 2005 Ice : Simulating water with two molecular states.","authors":"Lucía F Sedano, Carlos Vega, Eva G Noya, Eduardo Sanz","doi":"10.1063/5.0247832","DOIUrl":"https://doi.org/10.1063/5.0247832","url":null,"abstract":"Rigid, non-polarizable water models are very efficient from a computational point of view, and some of them have a great ability in predicting experimental properties. There is, however, little room for improvement in simulating water with this strategy, whose main shortcoming is that water molecules do not change their interaction parameters in response to the local molecular landscape. In this work, we propose a novel modeling strategy that involves using two rigid non-polarizable models as states that water molecules can adopt depending on their molecular environment. During the simulation, molecules dynamically transition from one state to another depending on a local order parameter that quantifies some local structural feature. In particular, molecules belonging to low- and high-tetrahedral order environments are represented with the TIP4P/2005 and TIP4P/Ice rigid models, respectively. In this way, the interaction between water molecules is strengthened when they acquire a tetrahedral coordination, which can be viewed as an effective way of introducing polarization effects. We call the resulting model TIP4P2005Ice and show that it outperforms either of the rigid models that build it. This multi-state strategy only slows down simulations by a factor of 1.5 compared to using a standard non-polarizable model and holds great promise for improving simulations of water and aqueous solutions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949483","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

Reflections on Zwanzig's theories of dielectric friction. 对茨万齐格介电摩擦理论的思考。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0248521

Mischa Bonn, James T Hynes

引用次数: 0

Rovibrationally resolved Rayleigh and Raman scattering cross sections for molecular hydrogen. 分子氢的振动分辨瑞利和拉曼散射截面。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0235703

Adam J C Singor, Liam H Scarlett, Mark C Zammit, Igor Bray, Dmitry V Fursa

{"title":"Rovibrationally resolved Rayleigh and Raman scattering cross sections for molecular hydrogen.","authors":"Adam J C Singor, Liam H Scarlett, Mark C Zammit, Igor Bray, Dmitry V Fursa","doi":"10.1063/5.0235703","DOIUrl":"https://doi.org/10.1063/5.0235703","url":null,"abstract":"Accurate Rayleigh and Raman scattering cross sections, tensor components, depolarization ratios, and reversal coefficients for all rovibrational transitions within the X1Σg+ ground electronic state of H2 have been calculated. Raman spectra have been generated using these data. A method for calculating Raman scattering cross sections is formulated that is valid below the ionization threshold and in the region containing resonances, which explicitly accounts for all bound and dissociative vibrational levels of the bound intermediate electronic states and approximately accounts for the ionization continuum. A representative set of cross sections is presented for incident photon energies below 15 eV and compared with existing results in the literature where possible. Convergence of our results with an increasing number of bound intermediate electronic states is demonstrated. The accuracy of the Placzek-Teller approximation is discussed. The effect of accounting for the intermediate ionization continuum is investigated. Local thermal equilibrium cross sections are calculated for Rayleigh and Raman scattering. This work represents the most accurate and complete treatment of Raman scattering for molecular hydrogen to date. A total of 9582 Rayleigh and Raman scattering cross sections have been generated and are openly available on Zenodo under an open-source Creative Commons Attribution license at https://zenodo.org/doi/10.5281/zenodo.13441471.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894784","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