Journal of Chemical Physics最新文献_第4页

Interplay of tail length and confinement in the formation of interior loops in flexible chains. 尾长和约束在柔性链内环形成中的相互作用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0287554

Vrinda Garg, Rejoy Mathew, Kunal Rai, Jaeoh Shin, Surya K Ghosh

{"title":"Interplay of tail length and confinement in the formation of interior loops in flexible chains.","authors":"Vrinda Garg, Rejoy Mathew, Kunal Rai, Jaeoh Shin, Surya K Ghosh","doi":"10.1063/5.0287554","DOIUrl":"https://doi.org/10.1063/5.0287554","url":null,"abstract":"Loop formation between distant interior segments of a polymer is a fundamental process for biological functions such as gene regulation and protein folding. While prior studies predominantly focus on end-to-end looping, interior loop formation is more relevant in vivo. Using Langevin dynamics simulations, we investigate the kinetics of interior loop formation in confined flexible polymers with specific internal segments having attractive interactions, focusing on the effect of tail length (lt) and spatial confinement. The probability distribution function of the distance between attractive beads forming the interior loop, P(ra), and the corresponding free energy profile, F(ra), exhibit a bimodal structure due to the coexistence of two distinct conformational states: a compact folded state and an unlooped relaxed configuration. We observe a non-monotonic dependence of the looping probability (Pl) and looping time (Tl) on lt under strong confinement. We identify the optimal combination of the cavity size and the tail length that leads to maximizing the looping time Tl and minimizing the looping probability Pl. In addition, the interior loop dynamics for distinct loop lengths (ll) of a fixed polymer chain (L) showcase that Tl changes rapidly with the addition of the first few monomers and then plateaus as the tail grows, which is exactly verified with analytical results. The observed coexistence of looped and extended states is a hallmark of intermediate ɛ, disappearing for weak or strong attractions, highlighting the tunability of looping dynamics via interaction strength.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238701","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

Levy-Perdew-Sahni equation and its application to perform atomic calculations. levy - perdu - sahni方程及其在原子计算中的应用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0293565

Rabeet Singh, Ashish Kumar, Manoj K Harbola

引用次数: 0

Computation of the heat capacity of water from first principles. 从第一性原理计算水的热容。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0285698

Motoyuki Shiga, Jan Elsner, Jörg Behler, Bo Thomsen

{"title":"Computation of the heat capacity of water from first principles.","authors":"Motoyuki Shiga, Jan Elsner, Jörg Behler, Bo Thomsen","doi":"10.1063/5.0285698","DOIUrl":"https://doi.org/10.1063/5.0285698","url":null,"abstract":"Water is a unique solvent with many remarkable properties. An example is its exceptionally high heat capacity, which plays an important role in storing and transporting thermal energy, with implications for many processes from regulating the body temperature of living organisms to moderating our climate at the global scale. To elucidate the microscopic origin of the heat capacity of water from first principles, highly accurate computer simulations are required. Apart from a reliable description of the atomic interactions, the presence of light hydrogen atoms necessitates the explicit consideration of nuclear quantum effects through path integral molecular dynamics (PIMD) simulations. The high computational costs of PIMD simulations, which are even further increased by the need for an extensive statistical sampling of energy fluctuations to determine the heat capacity, can be strongly reduced by replacing first principles calculations with machine learning potentials to represent the atomic interactions. In this study, we use high-dimensional neural network potentials constructed from density functional theory calculations employing the RPBE-D3 and revPBE0-D3 functionals. To further enhance the computational performance, we introduce a highly efficient PIMD algorithm that computes in parallel not only the energies and forces but also the coordinate and thermostat time evolutions. Using this approach, we are able to determine converged data for the heat capacity from a 4 ns simulation employing 128 beads. In particular, for the revPBE0-D3 functional, we find excellent agreement with experiment, providing evidence that our approach represents a promising framework for the quantitative understanding of the thermodynamic properties of water and aqueous solutions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232764","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

How special are the dynamics of deep eutectic solvents? A look at the prototypical case of ethaline. 深共晶溶剂的动力学有多特殊？看一下典型的乙胺案例。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0289812

Mohammad Nadim Kamar, Armin Mozhdehei, Basma Dupont, Ronan Lefort, Alain Moréac, Jacques Ollivier, Markus Appel, Denis Morineau

{"title":"How special are the dynamics of deep eutectic solvents? A look at the prototypical case of ethaline.","authors":"Mohammad Nadim Kamar, Armin Mozhdehei, Basma Dupont, Ronan Lefort, Alain Moréac, Jacques Ollivier, Markus Appel, Denis Morineau","doi":"10.1063/5.0289812","DOIUrl":"https://doi.org/10.1063/5.0289812","url":null,"abstract":"We investigated the molecular dynamics of the prototypical deep eutectic solvent (DES) ethaline. We disentangled the different motions of its two constituents, namely choline chloride and ethylene glycol, on a spatiotemporal range that extends from sub-nanometer to micrometer distances and from picoseconds to milliseconds. This was achieved by a combination of pulsed-field-gradient NMR, time-of-flight, and backscattering quasielastic neutron scattering experiments with isotopically labeled samples. On the micrometer scale, we observe that the translational motions of the two DES constituents obey classical hydrodynamics, with distinct diffusivities that reflect their different hydrodynamic radii. This is no longer valid at the nanometer scale, where the two DES components present similar short-ranged diffusivities, indicating a significant effect of their supramolecular association. The sub-nanometer scale motions include jumps that precede Fickian diffusion and localized dynamics that precede the breaking of the transient cage formed by neighboring molecules. Therein, the spatial amplitude of the localized motions mirrors their different molecular sizes and chemical structures, while their respective correlation times contrast with observations made for other choline-based DESs such as glyceline. This result underlines the importance of more subtle effects, such as the different H-bond propensities of the polyol donor, and demonstrates the difficulty in anticipating the nanoscale dynamic behavior of DESs from knowledge of their macroscopic properties.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232735","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

Freezing line of polydisperse hard spheres via direct-coexistence simulations. 多分散硬球直接共存模拟的冻结线。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0281621

Antoine Castagnède, Laura Filion, Frank Smallenburg

{"title":"Freezing line of polydisperse hard spheres via direct-coexistence simulations.","authors":"Antoine Castagnède, Laura Filion, Frank Smallenburg","doi":"10.1063/5.0281621","DOIUrl":"https://doi.org/10.1063/5.0281621","url":null,"abstract":"In experimental systems, colloidal particles are virtually always at least somewhat polydisperse, which can have profound effects on their ability to crystallize. Unfortunately, accurately predicting the effects of polydispersity on phase behavior using computer simulations remains a challenging task. As a result, our understanding of the equilibrium phase behavior of even the simplest colloidal model system, hard spheres, remains limited. Here, we present a new approach to map out the freezing line of polydisperse systems that draws on direct-coexistence simulations in the semi-grand canonical ensemble. We use this new method to map out the conditions where a hard-sphere fluid with a Gaussian size distribution becomes metastable with respect to partial crystallization into a face-centered-cubic crystal. Consistent with past predictions, we find that as the polydispersity of the fluid increases, the coexisting crystal becomes increasingly size-selective, exhibiting a lower polydispersity and larger mean particle size than the fluid phase. Finally, we exploit our direct-coexistence simulations to examine the characteristics of the fluid-crystal interface, including surface stress and interfacial absorption.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244778","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

Incorporating the molecular-scale into a hydrodynamic description of confined aqueous systems. 将分子尺度纳入受限水系统的流体动力学描述。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0279626

Haoyuan Shi, Christopher J Mundy, Gregory K Schenter, Jaehun Chun

{"title":"Incorporating the molecular-scale into a hydrodynamic description of confined aqueous systems.","authors":"Haoyuan Shi, Christopher J Mundy, Gregory K Schenter, Jaehun Chun","doi":"10.1063/5.0279626","DOIUrl":"https://doi.org/10.1063/5.0279626","url":null,"abstract":"Hydrodynamics provides a continuum-level description of fluid motion, but its applicability at the nanoscale becomes uncertain due to the emerging importance of molecular-level effects such as spatial heterogeneity. Hydrodynamic boundary conditions that incorporate molecular details allow us to partition the system into a near-wall region and a bulk fluid region. We identify a hydrodynamic wall located inside the fluid that determines where slip begins. By extending the hydrodynamic wall with the slip length, the position of the extrapolated wall is established. This offers a unified description of both slip and stagnant flow behaviors, with wall hydrophobicity characterized by the relative location of the extrapolated wall with respect to the physical wall. Employing this concept in analyses of equilibrium molecular dynamics (MD) and non-equilibrium MD simulations of Couette and Poiseuille flows, our results demonstrate consistency between equilibrium and non-equilibrium approaches across different flow types and confinement levels. This demonstrates the robust nature of linear response theory. We then explore the effects of fluid-wall and bulk fluid interactions on the hydrodynamic properties. These findings enhance the effectiveness of molecular-based simulations for investigating complex confined systems in nanofluidics, biology, and colloidal science, offering a complementary molecular-scale perspective to traditional continuum approaches.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244811","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

Ab initio study of the far infrared spectrum and gas phase formation reactions of methyl ethyl ketone (CH3-CO-CH2-CH3). 甲基乙基酮（CH3-CO-CH2-CH3）的远红外光谱和气相生成反应的从头算研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0282661

Samira Dalbouha, Victoria Gámez, Muneerah Mogren Al Mogren, María Luisa Senent

{"title":"Ab initio study of the far infrared spectrum and gas phase formation reactions of methyl ethyl ketone (CH3-CO-CH2-CH3).","authors":"Samira Dalbouha, Victoria Gámez, Muneerah Mogren Al Mogren, María Luisa Senent","doi":"10.1063/5.0282661","DOIUrl":"https://doi.org/10.1063/5.0282661","url":null,"abstract":"Highly correlated ab initio calculations are employed for a complete spectroscopic characterization of methyl ethyl ketone (MEK). Thermochemical and kinetic properties of formation processes, suitable for the gas phase atmospheric and astrophysical environments, are determined. Among 13 formation processes, three bi-radical addition reactions were found as the most likely, for which the temperature-dependent rate coefficients are provided. The search of conformers at the CCSD(T)-F12 level of theory leads to two stable structures Ap (Cs) and Sp (C1), which depend strongly on the correlation energy. The stability of Ap-MEK is noticeable, whereas Sp can transform into Ap by vibrational excitations at very low temperatures since conformers are separated by low energy barriers. Three internal rotations, the torsion of ethyl group (α), and the torsions of the two methyl groups (θac and θet) interconvert 27 minima of the potential energy surface. In both conformers, V3ac <<< V3et. To explore the far infrared region and to map the low torsional energy levels and splittings, a variational procedure of reduced dimensionality is employed. The ground vibrational state splits into nine components distributed in two groups at 0.0 cm-1 (A1 and E2) and 0.289 cm-1 (E1, E3, and E4). Accurate rotational parameters are provided.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232813","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

Interaction at pre-bonding distances and bond formation for open p-shell atoms with different orientations of their angular momenta. 不同角动量方向下开p壳原子成键前距离的相互作用和成键过程。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0288344

Aleksandra Foerster, O I Obolensky, Bang C Huynh, T P Doerr, Yi-Kuo Yu

{"title":"Interaction at pre-bonding distances and bond formation for open p-shell atoms with different orientations of their angular momenta.","authors":"Aleksandra Foerster, O I Obolensky, Bang C Huynh, T P Doerr, Yi-Kuo Yu","doi":"10.1063/5.0288344","DOIUrl":"https://doi.org/10.1063/5.0288344","url":null,"abstract":"We employ the ΔSCF framework to build and optimize, via the Maximum Overlap Method (MOM), non-Aufbau Hartree-Fock determinants for molecular systems containing atoms with open p-shells. We use these determinants in the coupled-cluster (CC) Ansatz to calculate interaction energies at pre-bonding distances and to study bond formation pathways for the ground and excited states of the molecules. We propose that the MOM-CC combination presents a straightforward and general way to study interatomic forces between open-shell atoms with arbitrarily populated orbitals. As a practical application of the MOM combined with CC with singles, doubles, and perturbative triples, we demonstrate that fixed multipole Coulomb interactions between open p-shell atoms play an important role at pre-bonding distances and can lead to an overall repulsive interaction between two neutral atoms. Using three diatomic molecules, B2, Al2, and AlB, as examples, we illustrate how the mutual orientation of atomic p-orbitals at large separations determines the type of the established chemical bond. Implementation of the proposed method for atoms with other configurations of unfilled shells is straightforward. We also demonstrate that a previously proposed classical small dielectric spheres model, which has been shown to be highly accurate for interactions between closed-shell atoms, remains more accurate than density-functional theory calculations also for atoms with open shells. This suggests that rigorous classical electrostatics is capable of capturing a significant part of electron correlation and polarization effects and potentially can be used for accurate yet low-cost calculations of pre-bonding interactions between larger molecules, for which high-level quantum chemical methods would be computationally impractical.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238713","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

Coarse graining photo-isomerization reactions: Thermodynamic consistency and implications for molecular ratchets. 粗粒光异构化反应：分子棘轮的热力学一致性和意义。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0290281

Francesco Avanzini, Massimiliano Esposito, Emanuele Penocchio

引用次数: 0

Spatial landscape and flux for exploring protein pattern formation in rod-shaped bacteria. 探索杆状细菌蛋白质模式形成的空间景观和通量。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-10-07 DOI: 10.1063/5.0284776

DingGe Wu, Jie Su, Jin Wang

{"title":"Spatial landscape and flux for exploring protein pattern formation in rod-shaped bacteria.","authors":"DingGe Wu, Jie Su, Jin Wang","doi":"10.1063/5.0284776","DOIUrl":"https://doi.org/10.1063/5.0284776","url":null,"abstract":"Spatial patterns formed by biomacromolecules such as proteins are widely present in biological systems and are closely related to fundamental cellular processes. A classic example is the spatial patterning of Min proteins in bacteria, where pole-to-pole oscillations of these patterns guide symmetric cell division. To uncover the underlying mechanisms behind the formation and transition of spatial patterns in the Min protein system, we applied nonequilibrium landscape-flux theory combined with the mode expansion method. By quantifying and visualizing the potential landscape in mode space, we identified distinct stable spatial patterns as potential wells, providing a global perspective on the system's stability. Moreover, we revealed that nonequilibrium flux acts as the driving force for spatial pattern switching with increasing cell length or molecular detachment rates. Peaks in the average flux and entropy production rate near phase boundaries highlight significant changes in dynamical nature and thermodynamic cost during critical transitions, offering deeper insights into the physical mechanisms underlying spatial pattern transitions. These findings not only underscore how spatial landscape topography and flux dynamics collectively govern the formation, stability, and switching of protein patterns but also establish a powerful framework for linking nonequilibrium physical mechanisms to biological functions. Furthermore, this framework holds potential applications, such as the detection of early warning signals for cell division.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 13","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232774","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