Journal of Chemical Physics最新文献_第9页

Dynamic heterogeneity of short semi-crystalline polymer chains during recrystallization. 短半结晶聚合物链在重结晶过程中的动态非均质性。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0243325

Maziar Heidari, Matthieu Labousse, Ludwik Leibler

{"title":"Dynamic heterogeneity of short semi-crystalline polymer chains during recrystallization.","authors":"Maziar Heidari, Matthieu Labousse, Ludwik Leibler","doi":"10.1063/5.0243325","DOIUrl":"https://doi.org/10.1063/5.0243325","url":null,"abstract":"The instant crystallization of semi-crystalline polymers has become possible following the recent advances in Fast Scanning Calorimetry (FSC) and enables us to make a bridge between the time scale available experimentally with those accessible with computer simulations. Although the FSC observations have provided new information on the crystallization kinetics and evolution of the crystals, the molecular details on the chain exchange events between the ordered and disordered domains of crystals have remained elusive. Using molecular dynamics simulations, we examined the detailed chain dynamics and thermodynamics of polyamide 6 (PA6) system under two heating treatments: (i) quenching PA6 melt deeply below the melting temperature Tm and (ii) annealing the resulting quenched system to a temperature close to Tm. We categorized the chains into mobile amorphous fraction (MAF) and rigid amorphous fraction (RAF), based on the length of consecutive chain's bond angles in the trans state. In the deep quenched system close to the glass transition temperature Tg, the mobility of the MAF chains is strongly suppressed and they remain in the glassy state. However, upon rising the temperature close to melting temperature, the system undergoes recrystallization, leading to the coexistence of RAF and supercooled liquid MAF chains. The highly mobile unentangled MAF chains explore the interphase domains, and during the late-stage of crystallization, they are thermally translocated into the lamella by reducing the fold number of RAF chains. The chain mobility in the annealed system could potentially lead to improved biodegradation in semi-crystalline chains.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604887","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

Evidence and origin of anomalous diffusion of Ag+ ion in amorphous silica: A molecular dynamics study with neural network interatomic potentials. Ag+离子在无定形二氧化硅中异常扩散的证据和起源：基于神经网络原子间电位的分子动力学研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0251120

Salomé Trillot, Nathalie Tarrat, Nicolas Combe, Patrizio Benzo, Caroline Bonafos, Magali Benoit

{"title":"Evidence and origin of anomalous diffusion of Ag+ ion in amorphous silica: A molecular dynamics study with neural network interatomic potentials.","authors":"Salomé Trillot, Nathalie Tarrat, Nicolas Combe, Patrizio Benzo, Caroline Bonafos, Magali Benoit","doi":"10.1063/5.0251120","DOIUrl":"https://doi.org/10.1063/5.0251120","url":null,"abstract":"The release of Ag+ ions into the environment through silica layers is a promising strategy for the development of anti-microbial surface coating devices. The aim of the present study is to provide some insight into the elementary mechanisms of diffusion of Ag+ ions through silica with the objective of proposing control strategies. Thanks to the development of interaction potentials based on neural networks, the diffusion processes were studied via molecular dynamics simulations. Silver diffusion was found to be anomalous and sub-diffusive, the origin of which could be attributed to deceleration and temporal anti-correlations. This sub-diffusion has been attributed primarily to the disordered nature of the silica matrix. Furthermore, it is magnified by the presence of coordination defects within the silica matrix. These defects, in particular the under-coordinated oxygen atoms, act as traps for Ag+ by forming O-Ag bonds, thereby limiting the jump length and retaining the ion for long duration. By comparison with existing diffusion models, the diffusion mechanism in the absence of defects appears to be of the fractional Brownian motion type, substantially modified by the presence of defects. Two possible approaches have emerged to tune the release of Ag+ ions through the silica layer: the monitoring of the number of defects and the opening/closing of diffusion paths via, e.g., a modification of the silica density.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604978","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

Revisiting the manganese dimer on the base of first-principles theory. 在第一性原理理论的基础上重新审视锰二聚体。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0234648

Sinhué López-Moreno, Esther Elena Hernández-Vázquez, Ana Paulina Ponce-Tadeo, José Luis Ricardo-Chávez, José Luis Morán-López

{"title":"Revisiting the manganese dimer on the base of first-principles theory.","authors":"Sinhué López-Moreno, Esther Elena Hernández-Vázquez, Ana Paulina Ponce-Tadeo, José Luis Ricardo-Chávez, José Luis Morán-López","doi":"10.1063/5.0234648","DOIUrl":"https://doi.org/10.1063/5.0234648","url":null,"abstract":"Manganese is one of the most intriguing elements showing multiple magnetic phases. In order to shed some light on the complex behavior, the manganese dimer has been the focus of extensive interest in theoretical research. Various quantum techniques have been utilized to comprehend the characteristics of the Mn dimer. Several approaches and functionals have been employed that suggest that the ferromagnetic (FM) state is its lowest energy configuration. Nevertheless, these findings are inconsistent with the experimental results showing that Mn2 has an antiferromagnetic (AFM) Σg+1 configuration at an interatomic Mn-Mn distance of dMn-Mn = 3.40 Å. This work presents a comparative assessment of outcomes obtained through several levels of the exchange-correlation functional: generalized gradient approximation (GGA), meta-GGA, GGA+U, and the hybrid Heyd-Scuseria-Ernzerhof (HSE06), the Perdew-Burke-Ernzerhof 0, and the Becke, 3-parameter, Lee-Yang-Parr. The results of our investigation are discussed based on previous theoretical and experimental reports. We found that the best description is obtained with the hybrid HSE06 functional. The Mn2 has a FM coupling at short distances and the characteristic AFM Σg+1 state at dMn-Mn = 3.27 Å. Furthermore, we obtained a magnetic moment (μ) per Mn atom of μ = 4.527 μB, a stretching frequency of ω = 80 cm-1, and a binding energy of Eb = -195 meV, which is in good agreement with the experimental results.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605094","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

Mechanistic insights into hole spin dynamics in colloidal Ag+-doped CdSe nanosheets: Interplay between two counteracting surface effects. 胶体Ag+掺杂CdSe纳米片中空穴自旋动力学的机理：两种相互抵消的表面效应之间的相互作用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0259383

Qinglong Wu, Shenlong Jiang, Qun Zhang

{"title":"Mechanistic insights into hole spin dynamics in colloidal Ag+-doped CdSe nanosheets: Interplay between two counteracting surface effects.","authors":"Qinglong Wu, Shenlong Jiang, Qun Zhang","doi":"10.1063/5.0259383","DOIUrl":"https://doi.org/10.1063/5.0259383","url":null,"abstract":"We present a mechanistic study of hole spin dynamics in colloidal cadmium selenide (CdSe) nanosheets, aiming to gain insights into the elusive interplay between two counteracting surface effects, i.e., hole-trapping interaction [between the valence-band heavy-hole (HH) state and its nearby localized surface trap (LST) state] vs spin-exchange interaction [between the HH spin state and the surface dangling-bond spin (DBS) state]. Differently from our previous work adopting a strategy of ligand engineering [see Wu et al., Adv. Opt. Mater. 12, 2400583 (2024)], we here implement an alternative strategy of element doping to regulate the LST and DBS states in the Ag+-doped CdSe nanosystem. It is observed that the hole spin-flip lifetime is shortened when the Ag+-doping level is elevated, demonstrating that the hole-DBS exchange interaction can effectively compete against the coexisting hole-LST trapping interaction, mainly due to the doping-induced increase in the density of the DBS state. Markedly, this observation is contrary to that in the ligand-engineering case, where the hole-trapping interaction plays a predominant role due to the strong ligand/CdSe orbital hybridization. This work elucidates the interplay between the two surface effects and enriches the understanding about the subtle DBS-related effect, providing valuable mechanistic information for rational design and optimization of spintronic applications based on colloidal nanostructures.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624796","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

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence. 用人工智能学习细菌视紫红质（BR）片段折叠途径中的过渡路径和膜拓扑特征。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0250082

Hindol Chatterjee, Pallab Dutta, Martin Zacharias, Neelanjana Sengupta

{"title":"Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence.","authors":"Hindol Chatterjee, Pallab Dutta, Martin Zacharias, Neelanjana Sengupta","doi":"10.1063/5.0250082","DOIUrl":"https://doi.org/10.1063/5.0250082","url":null,"abstract":"Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the biological milieu. Studying such structural changes in membrane-embedded proteins and understanding the associated topological signatures in membrane leaflets, therefore, remain relatively unexplored. Herein, we first aim to estimate the free energy barrier and the minimum free energy path (MFEP) connecting the membrane-embedded fully and partially inserted states of the bacteriorhodopsin fragment. To achieve this, we have considered independent sets of simulations from membrane-mimicking and membrane-embedded environments, respectively. An autoencoder model is used to elicit state-distinguishable collective variables for the system utilizing membrane-mimicking simulations. Our in-house Expectation Maximized Molecular Dynamics algorithm is initially used to deduce the barrier height between the two membrane-embedded states. Next, we develop the Geometry Optimized Local Direction search as a post-processing algorithm to identify the MFEP and the corresponding peptide conformations from the autoencoder-projected trajectories. Finally, we apply a graph attention neural network (GAT) model to learn the membrane surface topology as a function of the associated peptide structure, supervised by the membrane-embedded simulations. The resultant GAT model is then utilized to predict the membrane leaflet topology for the peptide structures along MFEP, obtained from membrane-mimicking simulations. The combined framework is expected to be useful in capturing key phenomena accompanying folding transitions in membranes. We discuss opportunities and avenues for further development.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604984","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

Hamiltonian replica-exchange method α-REMD for ring spearing elimination in polymers. 哈密顿复制交换法α-REMD消除聚合物中的环矛形。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0241538

Artem Yu Kunitsyn, Nadezhda A Nekrasova, Nikolai V Krivoshchapov, Eugeny V Alexandrov, Alexander A Pavlov, Michael G Medvedev

{"title":"Hamiltonian replica-exchange method α-REMD for ring spearing elimination in polymers.","authors":"Artem Yu Kunitsyn, Nadezhda A Nekrasova, Nikolai V Krivoshchapov, Eugeny V Alexandrov, Alexander A Pavlov, Michael G Medvedev","doi":"10.1063/5.0241538","DOIUrl":"https://doi.org/10.1063/5.0241538","url":null,"abstract":"Accurate prediction of polymer properties using molecular dynamics (MD) simulations requires a properly relaxed starting structure. Polymer models built from scratch by specialized algorithms (self-avoiding random walk, Monte Carlo, etc.) are far from relaxed and, moreover, often possess a large number of structural defects: close contacts between atoms, wrong bond distances, voids, unfavorable molecular conformations or packing, etc. This is especially problematic for ring-containing polymers whose initial structures also include ring spearing (bonds passing through cycles, including benzene rings). All these defects must be eliminated before running an MD simulation to correctly predict polymer properties. Short MD simulations can be enough to remove close contacts; however, ring spearing elimination and general structure relaxation cannot be achieved this way. In this work, we propose α-Replica Exchange MD (α-REMD)-a Hamiltonian replica-exchange MD protocol that reliably eliminates ring spearing defects and performs a general relaxation of the system. Its efficiency is demonstrated on five polyethersulfones whose initial geometries contained numerous ring intersections that were completely removed by α-REMD.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605005","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

Coherent control of the efficient ladder-type population transfer by four-color harmonic laser pulses. 四色谐波激光脉冲对高效阶梯型种群转移的相干控制。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0253782

Bin-Bin Wang, Yuan Li, Su-Hua Jing, Xiao-Yun Zhou, Yong-Chang Han

{"title":"Coherent control of the efficient ladder-type population transfer by four-color harmonic laser pulses.","authors":"Bin-Bin Wang, Yuan Li, Su-Hua Jing, Xiao-Yun Zhou, Yong-Chang Han","doi":"10.1063/5.0253782","DOIUrl":"https://doi.org/10.1063/5.0253782","url":null,"abstract":"The ladder-type population transfer of the HF molecule steered by four-color harmonic laser pulses (HLPs) is investigated using the time-dependent quantum wave packet method. It is found that although there exist large background excitations and many (resonant) transition pathways during the driving, nearly 100% of the population could be transferred to the target state. In particular, such a process could be coherently controlled by changing the phases of the four HLPs, especially the phases of the fundamental and second HLPs, which can be accounted for in large part by the combined effects of the corresponding transition pathways and the maximal amplitude of the total electric field. However, for manipulating the phases of the third and fourth HLPs, both the changes in the maximal electric field amplitude and the asymmetry size fail to guide the variation of the target-state population because of the correlated effects of all these transition pathways, particularly the ones that do not contain the third and fourth HLP excitations. Importantly, our results also denote that the variation of the maximal electric field amplitude may give a well qualitative prediction about the phase-controlled population when the manipulated phase is directly related to all the transition pathways, which is the general case in the widely used two-color scheme. In addition, the maximal amplitude of the total electric field tends to play a more important role than its asymmetry size in the phase-controlled population transfer process.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624778","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 relativistic third-order algebraic diagrammatic construction theory for electron detachment, attachment, and excitation problems. 电子分离、附着和激发问题的相对论三阶代数图解构造理论。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0246920

Sudipta Chakraborty, Tamoghna Mukhopadhyay, Malaya K Nayak, Achintya Kumar Dutta

引用次数: 0

Langevin integration for isothermal-isobaric condition with a large time step. 大时间步长等温-等压条件下的Langevin积分。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0251642

Jaewoon Jung, Yuji Sugita

引用次数: 0

Stereodynamics of cold HD and D2 collisions with He. 冷HD和D2与He碰撞的立体动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0250522

Bikramaditya Mandal, Konrad Patkowski, Pablo G Jambrina, F Javier Aoiz, Naduvalath Balakrishnan

{"title":"Stereodynamics of cold HD and D2 collisions with He.","authors":"Bikramaditya Mandal, Konrad Patkowski, Pablo G Jambrina, F Javier Aoiz, Naduvalath Balakrishnan","doi":"10.1063/5.0250522","DOIUrl":"https://doi.org/10.1063/5.0250522","url":null,"abstract":"We present a comprehensive quantum mechanical study of stereodynamic control of HD + He and D2 + He collisions that have been probed experimentally by Perreault et al. [J. Phys. Chem. Lett. 13, 10912 (2022)] using Stark-induced adiabatic Raman passage (SARP) techniques. Our calculations utilize a highly accurate full-dimensional H2 + He interaction potential with diagonal Born-Oppenheimer correction appropriate for HD and D2 isotopomers. The results show that rotational quenching of HD from j = 2 → j' = 0 in v = 2, j = 2 → j' = 1 in v = 2 and v = 4, and j = 4 → j' = 3 in v = 4 is dominated by an l = 1 shape resonance located between 0.1 and 1.0 cm-1. For collision energies less than 0.1 cm-1, isotropic scattering prevails. An l = 1 resonance centered around 0.02 cm-1 is also found to dominate the j = 2 → j' = 0 and j = 4 → j' = 2 transitions in v = 4 for He-D2 collisions consistent with our prior studies of Δj = -2 transition in He + D2(v = 2, j = 2) collisions. Our analysis does not support the hypothesis of Perreault et al. [J. Phys. Chem. Lett. 13, 10912 (2022)] that a strong l = 2 resonance controls the angular distribution for Δj = -2 transition for both systems. Despite improvements in the development of the potential energy surface, a good agreement with SARP experiments for v = 2 is achieved only when contributions from collision energies less than 1.0 cm-1 were excluded in the computation of velocity averaged differential rate coefficients for both systems. This could be due to some uncertainties in the velocity spread in the experiment that employs co-propagation of the collision partners and possibly, the neglect of transverse velocities in the simulation of the experiment.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605096","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