Journal of Chemical Physics最新文献_第10页

Modeling the bio-nano interactions of polypropylene nanoparticles. 模拟聚丙烯纳米颗粒的生物纳米相互作用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0325442

Brian Maloney, Julia Subbotina, Ian Rouse, Vladimir Lobaskin

{"title":"Modeling the bio-nano interactions of polypropylene nanoparticles.","authors":"Brian Maloney, Julia Subbotina, Ian Rouse, Vladimir Lobaskin","doi":"10.1063/5.0325442","DOIUrl":"https://doi.org/10.1063/5.0325442","url":null,"abstract":"The environmental degradation of industrial and consumer plastics leads to the widespread presence of plastic micro- and nanoparticles in marine and terrestrial environments. Yet, their impacts on environmental safety and human health remain poorly understood. A key step in assessing these impacts is elucidating the bio-nano interactions that govern particle behavior in biological media. Here, we combine all-atom molecular dynamics with coarse-grained simulations to investigate protein adsorption and corona formation on polypropylene nanoparticles. The coarse-grain potentials are systematically derived from atomistic simulations of individual amino acids interacting with polypropylene fragments and surfaces. Using these potentials, we evaluated protein binding affinities on various polypropylene surfaces. Corona formation and composition are investigated using a kinetic Monte Carlo approach that mimics the competitive adsorption and desorption dynamics of proteins from a model solution. We show that the final corona composition reflects the relative binding energies and the number of favorable binding orientations of the competing proteins. Understanding the driving forces of adsorption and corona formation may help design safer polymeric materials and inform environmental risk assessment.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147772741","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 Bayesian desmearing algorithm for Bonse-Hart USANS with anisotropic scattering. 具有各向异性散射的Bonse-Hart USANS的贝叶斯去噪算法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0325436

Chi-Huan Tung, Guan-Rong Huang, Yangyang Wang, Jan-Michael Carrillo, Yuya Shinohara, Changwoo Do, Gernot Rother, Yingrui Shang, Wei-Ren Chen

{"title":"A Bayesian desmearing algorithm for Bonse-Hart USANS with anisotropic scattering.","authors":"Chi-Huan Tung, Guan-Rong Huang, Yangyang Wang, Jan-Michael Carrillo, Yuya Shinohara, Changwoo Do, Gernot Rother, Yingrui Shang, Wei-Ren Chen","doi":"10.1063/5.0325436","DOIUrl":"https://doi.org/10.1063/5.0325436","url":null,"abstract":"Ultra-small-angle neutron scattering (USANS) using Bonse-Hart optics provides micrometer-scale structural insights but suffers from severe slit-geometry smearing. While well-established for isotropic systems, quantitative desmearing of anisotropic data remains a challenge because conventional corrections break down for non-radial scattering. We address this by developing a resolution-aware Bayesian framework that explicitly incorporates anisotropy via an affine deformation to the scattering pattern, guided by the principle of parsimony. This results in orientation-resolved point-spread functions that enable a self-consistent determination of both the resolution and deformation parameters. Using Gaussian process regression with uncertainty quantification and a probabilistic correction for multiple scattering, we demonstrate the framework's effectiveness through numerical benchmarks and experimental studies of a stretched polymer melt. Our approach enables the seamless integration of SANS and USANS data, facilitating quantitative structural analysis of deformed materials at nanometer to micrometer scales.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147772662","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

Erratum: Predicting random close packing of binary hard-disk mixtures via third-virial-based parameters [J. Chem. Phys. 164, 124501 (2026)]. 基于第三病毒的参数预测二进制硬盘混合物的随机紧密排列[J]。化学。物理学报，2004,26(4):559 - 564。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0336864

Andrés Santos, Mariano López de Haro

引用次数: 0

Realistic transition paths for large biomolecular systems: A Langevin bridge approach. 大型生物分子系统的现实过渡路径：朗格万桥方法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0314611

Patrice Koehl, Marc Delarue, Henri Orland

{"title":"Realistic transition paths for large biomolecular systems: A Langevin bridge approach.","authors":"Patrice Koehl, Marc Delarue, Henri Orland","doi":"10.1063/5.0314611","DOIUrl":"https://doi.org/10.1063/5.0314611","url":null,"abstract":"We introduce a computational framework for generating realistic transition paths between distinct conformations of large biomolecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin bridge formalism, which constrains molecular trajectories to reach a prescribed final state within a finite time and yields an efficient low-temperature approximation of the exact bridge equation. To obtain physically meaningful protein transitions, we couple this formulation to a new coarse-grained potential, combining a Gō-like term that preserves native backbone geometry with a Rouse-type elastic energy term from polymer physics; we refer to the resulting approach as the Stochastic Integro-Differential Equation (SIDE). We evaluate SIDE on several proteins undergoing large-scale conformational changes and compare its performance with established methods, such as MinActionPath and eBDIMS. SIDE generates smooth, low-energy trajectories that maintain molecular geometry and frequently recover experimentally supported intermediate states. Although challenges remain for highly complex motions-largely due to the simplified coarse-grained potential-our results demonstrate that SIDE offers a powerful and computationally efficient strategy for modeling biomolecular conformational transitions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147772702","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

Expansion of time-convolutionless non-Markovian quantum master equations: A case study using the Fano-Anderson model. 无时间卷积非马尔可夫量子主方程的扩展：使用Fano-Anderson模型的案例研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0323348

Tim Alhäuser, Heinz-Peter Breuer

引用次数: 0

Why dibenzo[b,f][1,4,5]oxadiazepine fails for molecular solar thermal energy storage: Mechanistic insights and a synergistic optimization strategy. 为什么二苯并[b，f][1,4,5]恶二氮卓不能用于分子太阳能热能储存：机理见解和协同优化策略。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0323055

Haozhe Hua, Jialei Huo, Jianzheng Ma, Di Zhao, Le Yu, Chenwei Jiang, Fuli Li

{"title":"Why dibenzo[b,f][1,4,5]oxadiazepine fails for molecular solar thermal energy storage: Mechanistic insights and a synergistic optimization strategy.","authors":"Haozhe Hua, Jialei Huo, Jianzheng Ma, Di Zhao, Le Yu, Chenwei Jiang, Fuli Li","doi":"10.1063/5.0323055","DOIUrl":"https://doi.org/10.1063/5.0323055","url":null,"abstract":"Azobenzene derivatives, especially seven-membered cyclic compounds such as dibenzo[b,f][1,4,5]thiadiazepine (DBTD), are considered promising candidates for molecular solar thermal (MOST) energy storage systems due to their significant energy storage capabilities. In contrast, its structural analogue, dibenzo[b,f][1,4,5]oxadiazepine (DBOD), fails to exhibit substantial Z → E photoisomerization, despite possessing a higher isomerization energy. In this study, we investigated the underlying mechanistic causes of this paradox by comparing the photoisomerization dynamics of DBTD and DBOD through electronic structure calculations and nonadiabatic molecular dynamics (NAMD) simulations. Our results revealed that, while photoexcitation leads to the formation of the E-isomer in DBOD, its metastable E-configuration rapidly relaxes back to the Z-form within 400 fs at room temperature. This rapid back-conversion arises from three synergistic factors: (i) a lower thermal isomerization barrier, (ii) substantial kinetic energy retained upon de-excitation, and (iii) preferential allocation of kinetic energy into azo-group torsional modes, which together accelerate the reverse reaction on the ground state. To mitigate this issue, we proposed a synergistic strategy combining fluorine substitution with low-temperature regulation. Fluorination yields perfluorodibenzo[b,f][1,4,5]oxadiazepine (PDOD), which increases the thermal E → Z isomerization barrier while preserving a high isomerization energy of 164.3 kJ/mol. NAMD simulations at 100 K show that the E-isomer of PDOD remained stable for over 400 fs, with a Z → E quantum yield of 26%, significantly higher than the 19% quantum yield of DBOD at 300 K. This study provides mechanistic insights into the \"high isomerization energy yet poor stability\" paradox observed in DBOD and establishes a practical strategy for developing high-performance MOST photoswitches.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147771855","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

Water at low frequencies: Vibrational decomposition reveals spectral fingerprints of surface charge and dynamic surfaces. 低频率的水：振动分解揭示了表面电荷和动态表面的光谱指纹。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0323450

J P Martínez Cordeiro, N R Aluru

{"title":"Water at low frequencies: Vibrational decomposition reveals spectral fingerprints of surface charge and dynamic surfaces.","authors":"J P Martínez Cordeiro, N R Aluru","doi":"10.1063/5.0323450","DOIUrl":"https://doi.org/10.1063/5.0323450","url":null,"abstract":"The low-frequency vibrational dynamics of water (i.e., 0-1000cm-1) encodes rich details about its local environment, hydrogen bonding, and collective motion that are essential to water's various unique properties that are incredibly important for life in a manner that is easily comparable between experiments and simulations. This study uses molecular dynamics to perform a comprehensive mode-resolved analysis of the low-frequency spectrum of water, decomposing it into individual translational and rotational components, and investigates how ionic concentration, confinement, surface charge, and surface oscillations modulate the spectral intensity of the peaks and their corresponding frequencies. The reported results reveal a distinct spectroscopic signature associated with the sign of surface charge polarity that suggests a potential practical route for experimentally inferring surface charge identity from interfacial experimental spectroscopic measurements. It also demonstrates that surface-driven perturbations-particularly at or near 50cm-1-couple most strongly to the translational modes, while their additional energy dissipates quickly along translational and librational modes. This paper increases the fundamental understanding of the dynamics of water in various local environments.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147771935","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

The variational polaron formalism for photoinduced proton-coupled electron transfer. 光诱导质子耦合电子转移的变分极化子形式。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0324969

Charulatha Venkataraman

{"title":"The variational polaron formalism for photoinduced proton-coupled electron transfer.","authors":"Charulatha Venkataraman","doi":"10.1063/5.0324969","DOIUrl":"https://doi.org/10.1063/5.0324969","url":null,"abstract":"The variational polaron formalism is employed to describe photoinduced proton-coupled electron transfer at a donor-acceptor site. The variational minimization criterion and the fluctuation decoupling make this a versatile approach that is applicable at all phonon bath reorganization energies, including at intermediate regimes where many of the perturbative approaches fail. Factors influencing the isotope effect such as energy bias, temperature, and initial wavepacket displacement are studied across reorganization energies. In some regimes, a transition from an inverse to a normal isotope effect is observed with an increase in electron-phonon coupling strength. The population decay rates show a complex dependency on the driving force for small to intermediate reorganization energies, exhibiting Marcus inverted region type behavior; this transitions to a normal region behavior at higher reorganization energies. The variational polaron results reduce to Redfield and to the full polaron in the weak and strong electron-phonon coupling limits, respectively. While the Fermi golden rule rate coincides with that of the variational polaron for large bath reorganization energies, it shows significant deviation at small-to-intermediate reorganization energies.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147771466","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

Trajectory excited-state dynamics study of pyrazine: Assessment of potential energy surfaces and simulation of picosecond timescales. 吡嗪的轨迹激发态动力学研究：势能面评估和皮秒时间尺度的模拟。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0320535

D Buzsáki, S Mandal, M Pápai

{"title":"Trajectory excited-state dynamics study of pyrazine: Assessment of potential energy surfaces and simulation of picosecond timescales.","authors":"D Buzsáki, S Mandal, M Pápai","doi":"10.1063/5.0320535","DOIUrl":"https://doi.org/10.1063/5.0320535","url":null,"abstract":"The femtosecond and picosecond excited-state dynamics of pyrazine are studied using full-dimensional trajectory surface hopping (TSH) dynamics simulations. We assess how different types of potential energy surfaces (PESs) influence the simulated dynamics; these include on-the-fly potentials vs those obtained by the linear vibronic coupling (LVC) model, calculated by multistate multiconfigurational perturbation theory (MS-CASPT2) and time-dependent density functional theory (TD-DFT) as well as machine-learning (ML) PESs. We find that MS-CASPT2 delivers a reliable excited-state description utilizing on-the-fly and LVC PESs for short (fs) and long (ps) timescales, respectively. TD-DFT (B3LYP) provides qualitatively accurate dynamics for short timescales but is unable to account for the coupling with the ground state and is even qualitatively wrong for longer timescales (i.e., failing to account for the internal conversion to the ground state). We observe and rationalize the oscillations (with a period of ∼40 fs) in the populations of 1B3u(nπ*) and 1Au(nπ*) excited states. Both MS-CASPT2- and TD-DFT-based TSH simulations identify significant singlet-triplet intersystem crossing (ISC) on picosecond timescales (∼10 ps). With our simulations, we established the excited-state mechanism for both the internal conversion to the singlet ground state and singlet-triplet ISC that involves the 1B3u(nπ*) and 1Au(nπ*) states with similar weights. Finally, we successfully used pyrazine as a benchmark model for TSH carried out on ML-PESs.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 16","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147771839","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

CW and TR EPR study of photomagnetic properties of heptanuclear Fe(II)-Fe(III) complex. 七核Fe(II)-Fe（III）配合物光磁性能的CW和TR EPR研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-04-28 DOI: 10.1063/5.0319549

Ekaterina Batueva, Andrey Sukhanov, Yuri Kandrashkin, Alsu Sharipova, Liudmila Savostina, Olga Turanova, Alexander Turanov

引用次数: 0