Journal of Chemical Physics最新文献_第2页

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

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

Are nanocubes more efficient than nanospheres to enhance the nuclear magnetic relaxation of water protons? A Monte Carlo simulation study.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0251512

Florent Fritsche, Gilles Rosolen, Alice De Corte, Bjorn Maes, Yves Gossuin, Quoc Lam Vuong

{"title":"Are nanocubes more efficient than nanospheres to enhance the nuclear magnetic relaxation of water protons? A Monte Carlo simulation study.","authors":"Florent Fritsche, Gilles Rosolen, Alice De Corte, Bjorn Maes, Yves Gossuin, Quoc Lam Vuong","doi":"10.1063/5.0251512","DOIUrl":"https://doi.org/10.1063/5.0251512","url":null,"abstract":"Iron oxide superparamagnetic nanoparticles have been extensively studied as T2 contrast agents in magnetic resonance imaging. The theory of nuclear magnetic relaxation induced by superparamagnetic nanoparticles has been validated by numerous experimental studies in the case of spherical particles. Recently, several studies focused on the synthesis of cubic nanoparticles. Some of them reported significantly higher relaxivities compared to their spherical counterpart and attributed this increase to their specific shapes. This work investigates the impact of cube-shaped nanoparticles on nuclear magnetic relaxation through Monte Carlo methods. Transverse relaxation at high static magnetic field is simulated by modeling the proton diffusion in the magnetic field generated by a cubic or a spherical nanoparticle. The results indicate that, in the case of magnetite nanoparticles, there is no significant difference between both shapes for sizes above 30 nm when particles are compared at equal volumes and magnetization. Below this size, a -40%-15% variation of the relaxation rates is predicted for the cubic case compared to the spherical case. These results are explained using general relaxation models that incorporate the distribution of the magnetic field generated by the nanoparticles. The simulation predictions are compared to some experimental results from the literature, revealing that, in some cases, the magnetic field specific to the nanoparticle shape alone cannot explain the observed increase in the relaxation rate of cubic nanoparticles.","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":"143709930","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

Thermostatting nonequilibrium systems: A thermal energy constraint for systems under directive perturbations.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0257970

J P Martínez Cordeiro, N R Aluru

{"title":"Thermostatting nonequilibrium systems: A thermal energy constraint for systems under directive perturbations.","authors":"J P Martínez Cordeiro, N R Aluru","doi":"10.1063/5.0257970","DOIUrl":"https://doi.org/10.1063/5.0257970","url":null,"abstract":"This paper brings attention back to discussions about the use of equilibrium thermostats for nonequilibrium molecular dynamics simulations. It argues that, due to the fluctuation-dissipation theorem, the justification for using equilibrium thermostats for nonequilibrium simulations is inherited only by cases in which the perturbation is small enough for the perturbed system to behave like the unperturbed equilibrium system. In the process, this paper categorizes models of external perturbations in molecular dynamics as either responsive-i.e., perturbations that impose a force-or directive-i.e., perturbations that impose a trajectory. Since directive perturbations have not been studied enough in the literature but are becoming more relevant, their effects on simple perturbed thermostatted systems are considered. Finally, using a perturbed two-point harmonic oscillator as well as a driven particle immersed in a simple Lennard-Jones fluid, it gives an approximation for the limit of justified equilibrium thermostat use for perturbed systems. This paper hopes to inspire further research in the fields of nonequilibrium statistical mechanics and nonequilibrium molecular dynamics.","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":"143709983","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

Layer-by-layer NH3 plasma treatment for area-selective atomic layer deposition of high-quality SiO2 thin films.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0257779

Sanghun Lee, Seunggi Seo, Tae Hyun Kim, Hwi Yoon, Seonyeong Park, Seunggyu Na, Jeongwoo Seo, Soo-Hyun Kim, Seung-Min Chung, Hyungjun Kim

{"title":"Layer-by-layer NH3 plasma treatment for area-selective atomic layer deposition of high-quality SiO2 thin films.","authors":"Sanghun Lee, Seunggi Seo, Tae Hyun Kim, Hwi Yoon, Seonyeong Park, Seunggyu Na, Jeongwoo Seo, Soo-Hyun Kim, Seung-Min Chung, Hyungjun Kim","doi":"10.1063/5.0257779","DOIUrl":"https://doi.org/10.1063/5.0257779","url":null,"abstract":"Area-selective atomic layer deposition (area-selective ALD) has been extensively studied because of its versatility in nanotechnological applications. The priority focus in area-selective ALD is to achieve the desired selectivity; thus, most studies to date have been concentrated on the reaction mechanism of ALD on growth/nongrowth substrates or the development of novel methodologies to resolve the challenges associated with its implementation in high-volume manufacturing. In this study, we performed area-selective ALD of SiO2 on SiO2, where SiO2 was not grown on SiNx, and suggested area-selective ALD approaches that could simultaneously enhance selectivity and film quality. An NH3 plasma treatment was applied to functionalize the SiNx surface with more Si-NH bonds, which exhibited low reactivity toward Si precursors. Although the SiO2 surface was also functionalized with Si-NH bonds, it was not fully converted into Si-NH because of its thermodynamic nature at low temperatures. Consequently, the results showed that NH3 plasma pretreatment was effective in increasing selectivity. Therefore, we performed a layer-by-layer NH3 plasma treatment during the ALD of SiO2 to deposit high-quality films without losing selectivity. The SiO2 film was densified, as confirmed by x-ray reflection spectra without nitrogen impurity incorporation. Electrical property measurements of metal-oxide-semiconductor capacitors confirmed that this approach enabled simultaneous selectivity and SiO2 film-quality enhancement.","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":"143730040","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

Comment on "Third density and acoustic virial coefficients of helium isotopologues from ab initio calculations" [J. Chem. Phys. 160, 244305 (2024)]. 关于 "从 ab initio 计算得出的氦同素异形体的第三密度和声 virial 系数 "的评论 [J. Chem. Phys. 160, 244305 (2024)].

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0253448

Kohei Tada

引用次数: 0

Construction of high-performance sodium ion hybrid capacitors based on MXene surface modulation and electrolyte matching.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0256598

Jiangtao Chen, Ting Wang, Yirun Zhu, Xu Zhang, Juan Yang, Pengjun Ma, Bingjun Yang

{"title":"Construction of high-performance sodium ion hybrid capacitors based on MXene surface modulation and electrolyte matching.","authors":"Jiangtao Chen, Ting Wang, Yirun Zhu, Xu Zhang, Juan Yang, Pengjun Ma, Bingjun Yang","doi":"10.1063/5.0256598","DOIUrl":"https://doi.org/10.1063/5.0256598","url":null,"abstract":"Sodium-ion hybrid capacitors have garnered significant attention due to their high power and energy densities, as well as the abundance of sodium reserves. However, the mismatch between anode and cathode dynamics is the biggest barrier to improving their performance. To address this issue, we propose a strategy for the preparation of porous MXene by hydrogen peroxide (H2O2)-controlled etching to solve the capacity degradation and ion diffusion limitation, which are caused by van der Waals forces between MXene nanosheets. This approach facilitates the realization of three-dimensional ion channels with both vertical and horizontal pathways, significantly enhancing the availability of active sites and improving the ion diffusion rate. By adjusting the amount of oxidant, porous MXene (P-MXene-2) with an optimal pore size range was obtained. The assembled half-cell has a capacity of 180 mAh g-1 at a rate of 0.05 A g-1. Furthermore, by combining a porous carbon cathode with porous MXene and electrolyte screening, a SIHC with a high energy density of 110.6 Wh kg-1 at 1000 W kg-1 and 71.1 Wh kg-1 at 20 kW kg-1 was successfully constructed. This study provides useful insights into the design and preparation of porous MXene electrodes and their energy storage applications.","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":"143729538","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

Low-temperature nucleation rate calculations using the N-Fold way.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-28 DOI: 10.1063/5.0255066

Federico Ettori, Dipanjan Mandal, David Quigley

引用次数: 0