Journal of Chemical Physics最新文献_第3页

Dimerization of model polymer chains under nonequilibrium conditions.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0249314

Sangita Mondal, Ved Mahajan, Biman Bagchi

{"title":"Dimerization of model polymer chains under nonequilibrium conditions.","authors":"Sangita Mondal, Ved Mahajan, Biman Bagchi","doi":"10.1063/5.0249314","DOIUrl":"https://doi.org/10.1063/5.0249314","url":null,"abstract":"Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed, or the final folded native state, the dynamics of dimerization can follow a course sensitive to both the initial conditions and the conformational dynamics. Here, we study the dimerization process by using computer simulations and analytical theory, where the two monomeric polymer chains are in the elongated state and are initially placed at a separation distance, d0. Subsequent dynamics lead to the concurrent processes of collapse, dimerization, and/or escape. We employ Langevin dynamics simulations with a coarse-grained model of the polymer to capture certain aspects of the dimerization process. At separations d0 much shorter than the length of the monomeric polymer, the dimerization could happen fast and irreversibly from the partly extended polymer state itself. At an initial separation larger than a critical distance, dc, the polymer collapse precedes dimerization, and a significant number of single polymers do not dimerize within the time scale of simulations. To quantify these competitions, we introduce several time-dependent order parameters, namely, (i) the time-dependent radius of gyration RG(t) of individual polymers describing the conformational state of the polymer, (ii) a center-to-center of mass distance parameter RMM, and (iii) a time dependent overlap function Q(t) between the two monomeric polymers, mimicking the contact order parameter popular in protein folding. In order to better quantify the findings, we perform a theoretical analysis to capture the stochastic processes of collapse and dimerization by using the dynamical disorder model.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709941","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

Disentangling signal contributions in two-dimensional electronic spectroscopy in the pump-probe geometry.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0256813

Daniel Timmer, Daniel C Lünemann, Antonietta De Sio, Giulio Cerullo, Christoph Lienau

{"title":"Disentangling signal contributions in two-dimensional electronic spectroscopy in the pump-probe geometry.","authors":"Daniel Timmer, Daniel C Lünemann, Antonietta De Sio, Giulio Cerullo, Christoph Lienau","doi":"10.1063/5.0256813","DOIUrl":"https://doi.org/10.1063/5.0256813","url":null,"abstract":"Since its introduction almost three decades ago, two-dimensional electronic spectroscopy (2DES) has evolved into a mature and powerful technique to reveal the inner workings of quantum systems with high temporal and spectral resolution. In general, this technique can isolate different contributions to the nonlinear response and provides access to different dynamical quantum pathways of the system evolution. Such isolation of pathways can be achieved in different experimental geometries. In its original, fully noncollinear implementation, directional phase matching allows for such signal isolation, while in the modern commonly employed pump-probe geometry, experimentally challenging phase-cycling schemes are employed. Here, we show how rephasing, non-rephasing, and zero- and double-quantum 2DES signals can be isolated in the pump-probe geometry without a need for phase-cycling. For this, we utilize established causality restrictions of the nonlinear response, allowing us to separate the different contributions in the spectral domain. We demonstrate this using data recorded for a molecular J-aggregate, acting as an effective three-level system. This approach bridges the gap between the capabilities of shaper-based and fully noncollinear 2DES and experimentally simpler implementations, such as those based on birefringent common-path interferometers.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709944","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

Triplet pair dynamics of singlet fission in orthorhombic polycrystalline powder of rubrene as revealed by magnetoluminescence.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0251084

Yusuke Wakikawa, Tadaaki Ikoma

引用次数: 0

Electron correlation in benzene: A QMC study of neutral and charged states.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0244421

Edson Rodrigues de Oliveira, Renato Pessoa, Ladir Cândido

引用次数: 0

Fine analysis of the effect of NH3 on the microstructure of mixed KCl and NH4Cl aqueous solutions.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0252593

Qingqing Zhang, Fei Li, Xiaofu Guo, Mengdan Qiao, Jie Liu, Yingying Zhao, Shizhao Wang, Junsheng Yuan, Zhiyong Ji

{"title":"Fine analysis of the effect of NH3 on the microstructure of mixed KCl and NH4Cl aqueous solutions.","authors":"Qingqing Zhang, Fei Li, Xiaofu Guo, Mengdan Qiao, Jie Liu, Yingying Zhao, Shizhao Wang, Junsheng Yuan, Zhiyong Ji","doi":"10.1063/5.0252593","DOIUrl":"https://doi.org/10.1063/5.0252593","url":null,"abstract":"In this study, a solution system of KCl-NH4Cl-NH3-H2O with different mass fractions was prepared at room temperature using x-ray scattering, Raman spectroscopy, and molecular dynamics simulations. From x-ray scattering, it was obtained that the peak near Q = 2.50 Å-1 in the F(Q) function changed from a flat-topped blunt peak to a bimodal peak as the concentration of ammonia increased. This change indicated that increased ammonia altered the hydrogen bonding network within the mixed solution. In the G(r) function, the peak near 3.25 Å enhances with the increase in ammonia concentration, suggesting a higher occurrence of N(NH4+)-N(NH3) interactions. Raman spectroscopy findings demonstrated that in the KCl-NH4Cl aqueous mixture, the area of DDAA-type hydrogen bonds increased as KCl concentration decreased and NH4Cl concentration increased. This suggests that KCl disrupts DDAA-type hydrogen bonds more significantly than NH4Cl. The situation was reversed when ammonia was added to the system, implying that KCl damages the DDAA-type hydrogen bonding structure less than NH4Cl when NH3 is present in the solution. Molecular dynamics simulations indicated that the coordination number of K-Cl increases with ammonia concentration, as ammonia's lone pair of electrons can bind to NH4+ to stabilize the [NH4(H2O)m-n(NH3)n]+ complex. This study elucidates the underlying microscopic mechanisms behind the decrease in KCl solubility and the increase in NH4Cl solubility upon increased ammonia.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730033","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

Frontal polymerization in thin layers: Hydrodynamic effects and asymptotic dynamics.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0252137

R Tiani, John A Pojman, L Rongy

{"title":"Frontal polymerization in thin layers: Hydrodynamic effects and asymptotic dynamics.","authors":"R Tiani, John A Pojman, L Rongy","doi":"10.1063/5.0252137","DOIUrl":"https://doi.org/10.1063/5.0252137","url":null,"abstract":"Buoyancy-driven convection currents arise from temperature gradients in thermal frontal polymerization (FP) when the spatially localized polymerization reaction travels perpendicularly to the gravity field. We propose a theoretical study of the system dynamics under adiabatic conditions. The polymer and the reactant mixture are considered to be in the same liquid phase, but the viscosity can increase with the degree of polymerization. We find that the reaction zone propagates as a hot spot-like pattern with a broken symmetry in both the vertical and horizontal directions. Furthermore, the system can reach an asymptotic dynamics characterized by a front with a steady shape that propagates at constant speed with a steady vortex surrounding it. As the strength of the vortex is increased, either by decreasing the reactants' viscosity or by increasing the layer's thickness, we observe a transition between (i) a passive regime predicted by pure reaction-diffusion and hydrodynamic models and (ii) an active chemo-hydrodynamic regime where such models separately break down. In the active regime (ii), the front speed decreases as convection intensifies. By means of a scaling analysis, we explain how hydrodynamic currents might lower the velocity of a polymerization wave. As the viscosity of the polymer is enlarged, the flow is shifted ahead of the reaction zone and becomes more symmetrical with respect to the middle of the system, as recently observed in solid-liquid FP experiments [Y. Gao et al., Phys. Rev. Lett. 130, 028101 (2023) and Y. Gao et al., Int. J. Heat Mass Transf. 240, 126622 (2025)].","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709949","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

On the spectral shape of the structural relaxation in supercooled liquids.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0254534

Till Böhmer, Florian Pabst, Jan Philipp Gabriel, Rolf Zeißler, Thomas Blochowicz

引用次数: 0

Deciphering the structural code for the face-centered-cubic ligand protected intermetallic AuAg nanoclusters.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0250770

Endong Wang, Yi Gao

{"title":"Deciphering the structural code for the face-centered-cubic ligand protected intermetallic AuAg nanoclusters.","authors":"Endong Wang, Yi Gao","doi":"10.1063/5.0250770","DOIUrl":"https://doi.org/10.1063/5.0250770","url":null,"abstract":"The incorporation of Ag atoms into ligand-protected gold nanoclusters is an effective way to tune their properties for applications in optics, electronics, and catalysis. However, the precise identification of preferred doping sites is challenging owing to its high structural complexity, which hinders establishing the structure-activity relationship. Here, through density functional theory calculations coupled with energy evaluation, delicate structural analysis, valence electron counting, and localized molecular orbital topology, we characterize the tetrahedral Au3Ag with closed-shell two valence electrons [Au3Ag(2e)] as a fundamental building block in face-centered-cubic (FCC) ligand-protected AuAg (LP-AuAg) alloy nanoclusters. The kernel structures of FCC LP-AuAg alloy clusters are constructed by rational spatial packing of Au3Ag(2e), Au4(2e), and Au3(2e) blocks, aligning with the grand unified model of ligand-protected Au nanoclusters. In addition, we predict 40 FCC LP-AuAg alloy nanoclusters with 141 low-energy isomers. This work underscores the crucial role of subset blocks in stabilizing the entire cluster and provides valuable insights into the structural features of FCC LP-AuAg alloy clusters.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718383","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: "Inference of Onsager coefficient from microscopic simulations by machine learning" [J. Chem. Phys. 162, 034901 (2025)].

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0266496

Kaihua Zhang, Shuanhu Qi, Yongzhi Ren, Jiajia Zhou, Ying Jiang

引用次数: 0

Primitive and non-primitive model electrolytes: Comparing ion-related Helmholtz energies using molecular simulations.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0257401

Anja Reimer, Isabell Reisch, Joachim Gross

{"title":"Primitive and non-primitive model electrolytes: Comparing ion-related Helmholtz energies using molecular simulations.","authors":"Anja Reimer, Isabell Reisch, Joachim Gross","doi":"10.1063/5.0257401","DOIUrl":"https://doi.org/10.1063/5.0257401","url":null,"abstract":"Two main frameworks are commonly used to describe electrolyte solutions: the non-primitive model, which rigorously accounts for all interactions between ions and solvent molecules; and the primitive model, which treats the solvent as a dielectric continuum, only describing ion-ion interactions explicitly. The primitive model offers simple Helmholtz energy expressions, including the Debye-Hückel (DH) equation, the primitive mean spherical approximation (MSA), and the Born theory of solvation. In this work, we evaluate the accuracy of primitive model approaches by comparing their Helmholtz energies with data from molecular simulations obtained for non-primitive model electrolyte solutions. We model electrolyte solutions as mixtures of equally sized, charged, and (non-polarizable) dipolar Lennard-Jones particles. Using thermodynamic integration, we isolate the Helmholtz energy contributions related to solvent-solvent, ion-solvent, and ion-ion interactions. Molecular simulations are performed across two temperatures and two densities, a range of charges, dipole moments, and ion mole fractions (0.005 ≤ xions ≤ 0.05). Our results show that while the primitive model expressions provide a qualitatively reasonable description of electrolyte solutions, they systematically underestimate the Helmholtz energy contributions associated with ion-solvent and ion-ion interactions. Achieving quantitative agreement requires empirical adjustments to the Born radius. Notably, the optimized Born radii are significantly larger than the actual ion sizes used in the molecular simulations, questioning the primitive model's applicability. This work presents rigorous benchmarks for the use of MSA, DH, and Born theories, along with molecular simulation data for non-primitive model electrolytes. These benchmarks provide insights for refining existing models and advancing the development of new equations of state for electrolyte solutions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709975","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