Journal of Chemical Physics最新文献

Applying the active learning strategy to the construction of full-dimensional neural network potential energy surfaces: Critical tests in H2O-He spectroscopic calculation.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0263653

You Li, Xiao-Long Zhang, Hui Li

{"title":"Applying the active learning strategy to the construction of full-dimensional neural network potential energy surfaces: Critical tests in H2O-He spectroscopic calculation.","authors":"You Li, Xiao-Long Zhang, Hui Li","doi":"10.1063/5.0263653","DOIUrl":"https://doi.org/10.1063/5.0263653","url":null,"abstract":"An uncertainty-driven active learning strategy was employed to achieve efficient point sampling for full-dimension potential energy surface constructions. Model uncertainty is defined as the weighted square energy difference between two neural network models, and the local maximums of uncertainty would be added to the training set by two criteria. A two-step sampling procedure was introduced to reduce the computational costs of expansive double-precision neural network training. A reference potential energy surface (PES) of the 6-D H2O-He system was constructed first by the MLRNet model with a weighted Root-Mean-Square-Error (RMSE) of 0.028 cm-1. The full-dimension long-range function was fitted by a pruned basis expansion method. The current sampling method is reliable for the long-range switched fundamental invariant neural network (LS-FI-NN) to construct spectroscopically accurate PES, where the single precision model achieves a test set RMSE of 0.3253 cm-1 with 472 fitting points and the double precision model is 0.0710 cm-1 with only 613 points. In comparison, the MLRNet requires 652 points to reach a similar accuracy. However, the MLRNet, with fewer parameters, shows lower training errors across all sampling cycles and lower test errors in the first few cycles, indicating its potential with an appropriate sampling procedure. The spectroscopic calculations were performed to validate the accuracy of PESs. The energy levels of the double precision LS-FI-NN showed great agreement with the reference PES's results, with only 0.0161 and 0.0044 cm-1 average errors for vibrational levels and the band origin shifts.","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":"143709915","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

Theoretical approach to the crystal structure of poly(butylene 2,5-furandicarboxylate) as revealed by density functional theory.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0253473

Óscar Toledano, Óscar Gálvez, Esther Rebollar, Aurora Nogales, Tiberio A Ezquerra

{"title":"Theoretical approach to the crystal structure of poly(butylene 2,5-furandicarboxylate) as revealed by density functional theory.","authors":"Óscar Toledano, Óscar Gálvez, Esther Rebollar, Aurora Nogales, Tiberio A Ezquerra","doi":"10.1063/5.0253473","DOIUrl":"https://doi.org/10.1063/5.0253473","url":null,"abstract":"In this work, we present a new model of the crystalline structure of the poly(butylene 2,5-furandicarboxylate) (PBF). This new structure has been derived using an ab initio density functional theory methodology and focusing on the agreement between the experimental and theoretical x-ray diffraction patterns. An extensive study has been performed to analyze the possible conformations that the polymeric strand can adopt in its crystalline form, leading to 60 initial crystalline structures. Due to thermal motion, which cannot be easily tackled with the ab initio methodology, and small inaccuracies, which are intrinsic to this calculation method, the theoretical unit cell dimensions can slightly differ from those obtained in the crystallization experiments. Thus, a structural refinement method has been employed to overcome these discrepancies and procure a crystalline structure whose x-ray diffraction pattern is consistent with the experimental one. For the proposed crystalline structure of PBF, both the powder diffraction pattern and the fiber diffraction diagram show a remarkable agreement with those available in the literature.","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":"143709982","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

Transient absorption and anisotropy studies of a push-pull azo derivative with an isomerization path-selective local minimum in the ground state.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0251286

Rafael de Q Garcia, Tiago Buckup, Éléna Ishow, Leonardo De Boni

{"title":"Transient absorption and anisotropy studies of a push-pull azo derivative with an isomerization path-selective local minimum in the ground state.","authors":"Rafael de Q Garcia, Tiago Buckup, Éléna Ishow, Leonardo De Boni","doi":"10.1063/5.0251286","DOIUrl":"https://doi.org/10.1063/5.0251286","url":null,"abstract":"The ultrafast excited-state dynamics of the E and Z isomers of a push-pull nitroazobenzene containing an octupolar bis(4'-tert-butylbiphenyl-4-yl)aminophenyl electron donor group were studied with transient absorption (TA) and TA anisotropy. A comprehensive study with two excitation wavelengths and a broadband white-light continuum probe (400-1400 nm) has determined that a torsional isomerization mechanism is the most probable for both isomers. This has shed light on the excited state behavior of the elusive push-pull Z isomer, which has its properties mostly predicted by simulations and systematically lacks experimental observations. Meanwhile, another unproductive relaxation pathway, associated with a symmetric bending motion, was found only for the E isomer. When relaxing through this pathway, the molecule encounters a potential barrier in the ground state, which requires significant structural reorganization before full relaxation. This local minimum can be more general than expected and may be behind unsolved issues in the literature of azobenzenes.","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":"143719154","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

Heteroatom decorated C2N monolayer for gas-sensing application: Insight from first-principles.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0258025

Xugen Shi, Wei An, Yunyi Li, Yibo Wang, Enduo Dai, Mingming Liu, Ruixian Guo, Jinguo Wang

{"title":"Heteroatom decorated C2N monolayer for gas-sensing application: Insight from first-principles.","authors":"Xugen Shi, Wei An, Yunyi Li, Yibo Wang, Enduo Dai, Mingming Liu, Ruixian Guo, Jinguo Wang","doi":"10.1063/5.0258025","DOIUrl":"https://doi.org/10.1063/5.0258025","url":null,"abstract":"Development of novel gas-sensing materials is essential to high-performance gas sensors for monitoring target gases in industrial production and environmental protection. Herein, we investigate two types of the heteroatom-decorated C2N monolayer, denoted as M@C2N (M = Mn and Ni) and B-C2N, for their gas-sensing functionality toward seven small gaseous molecules (H2, O2, N2, CO, CO2, NH3, and H2O). The key gas-sensing characteristics concerning chemiresistive (CR) and field-effect transistor (FET) gas sensing have been thoroughly explored. The results show that Mn@C2N and Ni@C2N can work as either CR or FET gas-sensing materials for detecting H2, O2, N2, CO, CO2, NH3, and H2O, whereas B-C2N can work as a disposable gas sensor for O2, H2O, and NH3. Mn@C2N and Ni@C2N are the most selective toward O2 and NH3, followed by CO and H2O in an oxygen- and ammonia-free environment, while B-C2N is the most selective toward H2O and NH3. More importantly, the adsorption strength of target molecule plays a critical role in gas-sensing mechanism as well as selectivity, recovery time, and sensitivity. This study offers theoretical perspectives on 2D hybrid carbon-based nanomaterials for efficient gas sensing.","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":"143718857","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-based non-adiabatic simulations of the polariton relaxation dynamics.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0246099

Deping Hu, Benjamin X K Chng, Wenxiang Ying, Pengfei Huo

引用次数: 0

Ehrenfest dynamics with localized atomic-orbital basis sets within the projector augmented-wave method.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0252559

Vladimír Zobač, Mikael Kuisma, Ask Hjorth Larsen, Tuomas Rossi, Toma Susi

引用次数: 0

Response to "Comment on 'Third density and acoustic virial coefficients of helium isotopologues from ab initio calculations'" [J. Chem. Phys. 162, 244305 (2025)].

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0264330

Daniele Binosi, Giovanni Garberoglio, Allan H Harvey

引用次数: 0

Memory, hysteresis, and kinetic cooperativity in stochastic mnemonic networks.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0252386

Subham Pal, Manmath Panigrahy, R Adhikari, Arti Dua

{"title":"Memory, hysteresis, and kinetic cooperativity in stochastic mnemonic networks.","authors":"Subham Pal, Manmath Panigrahy, R Adhikari, Arti Dua","doi":"10.1063/5.0252386","DOIUrl":"https://doi.org/10.1063/5.0252386","url":null,"abstract":"Mnemonic networks are cyclic catalytic networks of monomeric enzymes that exhibit kinetic cooperativity as departures of the mean velocity from the hyperbolic, Michaelis-Menten-like response. In addition, such networks admit a hysteretic response when conformational fluctuations are slow compared to the catalytic rate. Here, we show how these fluctuation-driven effects emerge from the underlying stochasticity in the network. We use the chemical master equation to study the stochastic kinetics of mnemonic networks, which, in their minimal form, include a pair of conformers and triangular reaction pathways. We introduce statistical measures that are conditional on the turnovers to comprehensively analyze molecular fluctuations in the transient and stationary states of these networks. In the transient state, temporal correlations between enzyme turnovers lead to an inequivalence between number and temporal fluctuations, yielding a hysteretic response of the mean velocity to substrates. The transient relaxes to a stationary state with independent and identically distributed turnovers and equality between number and temporal fluctuations. This state is a non-equilibrium stationary state (NESS) when the Kolmogorov loop criterion is not satisfied, leading to the emergence of kinetic cooperativity. The symmetry of the number correlation functions allows us to distinguish between the absence of cooperativity in equilibrium and the accidental vanishing of cooperativity in a NESS. We conclude that memory and hysteresis are transient effects while kinetic cooperativity emerges as the macroscopic manifestation of the microscopic irreversibility of the NESS in a network with cyclic reaction pathways.","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":"143709966","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

Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0254388

Jaehyeok Jin, Gregory A Voth

{"title":"Understanding dynamics in coarse-grained models. V. Extension of coarse-grained dynamics theory to non-hard sphere systems.","authors":"Jaehyeok Jin, Gregory A Voth","doi":"10.1063/5.0254388","DOIUrl":"https://doi.org/10.1063/5.0254388","url":null,"abstract":"Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics, faithfully recapitulate structural correlations at equilibrium, they lead to ambiguously accelerated dynamics. In Paper I [J. Jin, K. S. Schweizer, and G. A. Voth, J. Chem. Phys. 158(3), 034103 (2023)], we proposed the excess entropy scaling relationship to understand the CG dynamics. Then, in Paper II [J. Jin, K. S. Schweizer, and G. A. Voth, J. Chem. Phys. 158(3), 034104 (2023)], we developed a theory to map the CG system into a dynamically consistent hard sphere system to analytically derive an expression for fast CG dynamics. However, many chemical and physical systems do not exhibit hard sphere-like behavior, limiting the extensibility of the developed theory. In this paper, we aim to generalize the theory to the non-hard sphere system based on the Weeks-Chandler-Andersen perturbation theory. Since non-hard sphere-like CG interactions affect the excess entropy term as it deviates from the hard sphere description, we explicitly account for the extra entropy to correct the non-hard sphere nature of the system. This approach is demonstrated for two different types of interactions seen in liquids, and we further provide a generalized description for any CG models using the generalized Gaussian CG models using Gaussian basis sets. Altogether, this work allows for extending the range and applicability of the hard sphere CG dynamics theory to a myriad of CG liquids.","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":"143719246","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

Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0254255

Rafael García-Meseguer, Elise Duboué-Dijon, Sergio Martí, J Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón, James T Hynes

{"title":"Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity.","authors":"Rafael García-Meseguer, Elise Duboué-Dijon, Sergio Martí, J Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón, James T Hynes","doi":"10.1063/5.0254255","DOIUrl":"https://doi.org/10.1063/5.0254255","url":null,"abstract":"It is now well established that the transition state of a chemical reaction is not a single, static structure but rather a distribution of configurations. However, the implications of this distributed nature remain incompletely characterized, particularly for quantum proton and hydride transfer reactions, where variations in donor-acceptor separations at the transition state are key: they can determine whether or not tunneling contributes to the transfer. Consequently, the transition state's characterization critically depends on the chosen reaction coordinate, and several geometry-based and energy-based coordinates have been proposed for empirical valence bond and hybrid QM/MM molecular dynamics simulations of such reactions. Here, we systematically evaluate these coordinates, using a general analytic model for proton- and hydride-transfer reactions alongside important aspects of the enzymatic hydride transfer in formate dehydrogenase as a case study. Our analysis reveals significant limitations of common geometry-based and vertical energy gap coordinates, which often fail to isolate environmental effects and can bias the description of transition states. To address these issues, we propose an equilibrium energy difference coordinate that excludes the rapid fluctuations of the transferring quantum proton or hydride, focusing instead on the environment's polarization. Additionally, we demonstrate that the broad distribution of transition state configurations implies that key reaction properties, such as rate constants and kinetic isotope effects, may not always report on the same subset of transition state configurations. This insight helps resolve some mechanistic ambiguities and highlights the importance of carefully selecting reaction coordinates for simulating reaction dynamics (especially for quantum particle transfers) in enzymatic and condensed-phase chemistry.","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":"143752809","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