Journal of Chemical Physics最新文献_第3页

Structuring in thin films during meniscus-guided deposition. 半月板引导沉积过程中的薄膜结构。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0225995

René de Bruijn, Anton A Darhuber, Jasper J Michels, Paul van der Schoot

{"title":"Structuring in thin films during meniscus-guided deposition.","authors":"René de Bruijn, Anton A Darhuber, Jasper J Michels, Paul van der Schoot","doi":"10.1063/5.0225995","DOIUrl":"10.1063/5.0225995","url":null,"abstract":"We theoretically study the evaporation-driven phase separation of a binary fluid mixture in a thin film deposited on a moving substrate, as occurs in meniscus-guided deposition for solution-processed materials. Our focus is on the limit of rapid substrate motion where phase separation takes place far away from the coating device. In this limit, demixing takes place under conditions mimicking those in a stationary film because substrate and film move at the same speed. We account for the hydrodynamic transport of the mixture within the lubrication approximation. In the early stages of demixing, diffusive and evaporative mass transport predominates, consistent with earlier studies on evaporation-driven spinodal decomposition. In the late-stage coarsening of the demixing process, the interplay of solvent evaporation, diffusive, and hydrodynamic mass transport results in several distinct coarsening mechanisms. The effective coarsening rate is dictated by the dominant mass transport mechanism and therefore depends on the material properties, evaporation rate, and time: slow solvent evaporation results in initially diffusive coarsening that for sufficiently strong hydrodynamic transport transitions to hydrodynamic coarsening, whereas rapid solvent evaporation can preempt and suppress hydrodynamic and diffusive coarsening. We identify a novel hydrodynamic coarsening regime for off-critical mixtures, arising from the interaction of the interfaces between solute-rich and solute-poor regions in the film with the solution-gas interface. This interaction induces a directional motion of solute-rich droplets along gradients in the film thickness, from regions where the film is relatively thick to where it is thinner. The solute-rich domains subsequently accumulate and coalesce in the thinner regions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667543","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: "Stress auto-correlation tensor in glass-forming isothermal fluids: From viscous to elastic response" [J. Chem. Phys. 149, 084502 (2018)]. 更正："玻璃态等温流体中的应力自相关张量：从粘性响应到弹性响应" [J. Chem. Phys. 149, 084502 (2018)]。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0245831

M Maier, A Zippelius, M Fuchs

引用次数: 0

Structural and bonding properties of Ta2Cn-/0 (n = 1-7) clusters: Size-selected anion photoelectron spectroscopy and theoretical calculations. Ta2Cn-/0（n = 1-7）团簇的结构和成键特性：尺寸选择阴离子光电子能谱和理论计算。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0233496

Chao-Jiang Zhang, Hong-Guang Xu, Xi-Ling Xu, Wei-Jun Zheng

{"title":"Structural and bonding properties of Ta2Cn-/0 (n = 1-7) clusters: Size-selected anion photoelectron spectroscopy and theoretical calculations.","authors":"Chao-Jiang Zhang, Hong-Guang Xu, Xi-Ling Xu, Wei-Jun Zheng","doi":"10.1063/5.0233496","DOIUrl":"https://doi.org/10.1063/5.0233496","url":null,"abstract":"The structures and chemical bond evolution of ditantalum doped carbon clusters Ta2Cn-/0 (n = 1-7) were studied via size-selected anion photoelectron spectroscopy and theoretical calculations. It is found that Ta2C-/0 has a triangular structure and Ta2C2-/0 has a quasi-rhombus structure with C2v symmetry. Ta2C3- has a quasi-planar structure with a carbon atom and a C2 unit interacting with two tantalum atoms, and the lowest-energy isomer of neutral Ta2C3 has a triangular bipyramid structure with three carbon atoms around the Ta2 unit. Ta2C4-/0 has two C2 units connected with the Ta2 unit in parallel. Two isomers of Ta2C5- are observed, where both isomers have one carbon atom and two C2 units bound to the Ta2 unit in different ways. The most stable structure of neutral Ta2C5 has one carbon atom added on top of the Ta2C4 cluster. The most stable structures of Ta2C6-7-/0 can be viewed as a C2 unit and a C3 unit capping a butterfly like Ta2C4 structure, respectively. Molecular orbital analysis shows that neutral Ta2C3 has a large gap between its highest occupied molecular orbital and lowest unoccupied molecular orbital. Chemical bonding analysis reveals that the Ta-Ta interactions in Ta2Cn-/0 (n = 1-7) clusters are slightly weaker than the Ta-Ta interaction in bare Ta2 due to the participation in forming multicenter bonds.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675947","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

Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir. 混合 neMD/MC 脂质交换算法，使膜模拟与热力学库达到平衡。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0230226

Florence Szczepaniak, François Dehez, Benoît Roux

{"title":"Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir.","authors":"Florence Szczepaniak, François Dehez, Benoît Roux","doi":"10.1063/5.0230226","DOIUrl":"10.1063/5.0230226","url":null,"abstract":"Molecular dynamics (MD) simulations based on detailed all-atom models offer a powerful approach to study the structure and dynamics of biological membranes. However, the complexity of biological membranes in terms of chemical diversity presents an outstanding challenge. Particularly, difficulties are encountered when a given lipid type is present at very low abundance. While considering a very large simulation system with a small number of the low abundance lipid may offer a practical solution in some cases, resorting to increasingly large system rapidly becomes computationally costly and impractical. More fundamentally, an additional issue may be encountered if the low abundance lipid displays a high affinity for some protein in the simulation system. What is needed is to treat the simulation box as an open system in which the number of lipids can naturally fluctuate, as in the Grand Canonical Monte Carlo (MC) algorithm. However, this approach, in which a whole lipid molecule needs to be inserted or annihilated, is essentially impractical in the context of an all-atom simulation. To enforce equilibrium between a simulated system and an infinite surrounding bath, we propose a hybrid non-equilibrium (neMD)-MC algorithm, in which a randomly chosen lipid molecule in the simulated system is swapped with a lipid picked in a separate system standing as a thermodynamic \"reservoir\" with the desired mole fraction for all lipid components. The neMD/MC algorithm consists in driving the system via short non-equilibrium trajectories to generate a new state of the system that are subsequently accepted or rejected via a Metropolis MC step. The probability of exchanges in the context of an infinite reservoir with the desired mole fraction for all lipid components is derived and tested with a few illustrative systems for phosphatidylcholine and phosphatidylglycerol lipid mixtures.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647285","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 non-Hermicity: Accurate dynamics with the multiple Davydov D2Ansätze. 哈密顿非恒定性：多重达维多夫 D2Ansätze 的精确动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0243861

Lixing Zhang, Kaijun Shen, Yiying Yan, Kewei Sun, Maxim F Gelin, Yang Zhao

引用次数: 0

Enzyme kinetics simulation at the scale of individual particles. 单个粒子尺度的酶动力学模拟。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0216285

Taylor Kearney, Mark B Flegg

{"title":"Enzyme kinetics simulation at the scale of individual particles.","authors":"Taylor Kearney, Mark B Flegg","doi":"10.1063/5.0216285","DOIUrl":"https://doi.org/10.1063/5.0216285","url":null,"abstract":"Enzyme-catalyzed reactions involve two distinct timescales: a short timescale on which enzymes bind to substrate molecules to produce bound complexes and a comparatively long timescale on which the molecules of the complex are transformed into products. The uptake of the substrate in these reactions is the rate at which the product is made on the long timescale. Models often only consider the uptake to reduce the number of chemical species that need to be modeled and to avoid explicitly treating multiple timescales. Typically, the uptake rates cannot be described by mass action kinetics and are traditionally derived by applying singular perturbation theory to the system's governing differential equations. This analysis ignores short timescales by assuming that a pseudo-equilibrium between the enzyme and the enzyme-bound complex is maintained at all times. This assumption cannot be incorporated into current particle-based simulations of reaction-diffusion systems because they utilize proximity-based conditions to govern the instances of reactions that cannot maintain this pseudo-equilibrium for infinitely fast reactions. Instead, these methods must directly simulate the dynamics on the short timescale to accurately model the system. Due to the disparate timescales, such simulations require excessive amounts of computational time before the behavior on the long timescale can be observed. To resolve this problem, we use singular perturbation theory to develop a proximity-based reaction condition that enables us to ignore all fast reactions and directly reproduce non-mass action kinetics at long timescales. To demonstrate our approach, we implement simulations of a specific third order reaction with kinetics reminiscent of the prototypical Michaelis-Menten system.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675944","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

2D-IR spectroscopy of azide-labeled carbohydrates in H2O. H2O 中叠氮标记碳水化合物的二维红外光谱。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0225308

P Gasse, T Stensitzki, H M Müller-Werkmeister

{"title":"2D-IR spectroscopy of azide-labeled carbohydrates in H2O.","authors":"P Gasse, T Stensitzki, H M Müller-Werkmeister","doi":"10.1063/5.0225308","DOIUrl":"https://doi.org/10.1063/5.0225308","url":null,"abstract":"Carbohydrates constitute one of the key classes of biomacromolecules, yet vibrational spectroscopic studies involving carbohydrates remain scarce as spectra are highly congested and lack significant marker vibrations. Recently, we introduced and characterized a thiocyanate-labeled glucose [Gasse et al., J. Chem. Phys. 158, 145101 (2023)] demonstrating 2D-IR spectroscopy of carbohydrates using vibrational probes. Here, we build on that work and test azide groups as alternative for studies of carbohydrates to expand the available set of local probes. Many common carbohydrates with different azide labeling positions, such as galactose, glucose, or lactose, are readily available due to their application in click chemistry and hence do not require additional complex synthesis strategies. In this work, we have characterized azide-labeled glucose,, galactose, acetylglucosamine and lactose in water using IR and 2D-IR spectroscopy to test their potential for future applications in studies of carbohydrate-protein interactions. Our findings indicate that their absorption profiles and vibrational dynamics are primarily determined by the labeling position on the ring. However, we also observe additional variations between samples with the same labeling position. Furthermore, we demonstrate that their usage remains feasible at biologically relevant concentrations, highlighting their potential to probe more complex biological processes, i.e., enzymatic catalysis.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675943","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

Investigation of cross-association behavior in water-ethanol solutions: A combined computational-ATR spectroscopy study. 水-乙醇溶液中交叉结合行为的研究：计算-ATR 光谱联合研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0226699

Evangelos Drougkas, Carsten F Frøstrup, Henrik G Bohr, Michael Bache, Georgios M Kontogeorgis, Xiaodong Liang

{"title":"Investigation of cross-association behavior in water-ethanol solutions: A combined computational-ATR spectroscopy study.","authors":"Evangelos Drougkas, Carsten F Frøstrup, Henrik G Bohr, Michael Bache, Georgios M Kontogeorgis, Xiaodong Liang","doi":"10.1063/5.0226699","DOIUrl":"10.1063/5.0226699","url":null,"abstract":"The water/ethanol system possesses complexities at the molecular level, which render its description a difficult task. For the elucidation of the system's hydrogen bonding features that are the key factors in its complex behavior, we conduct a Density Functional Theory analysis on relevant water/ethanol clusters inside implicit solvent cavities for the determination of the ethanol donor hydrogen bond strength. We record Attenuated Total Reflectance spectra of water/ethanol-OD solutions and utilize our density and refractive index measurements for post-processing. The application of the Badger-Bauer rule reveals a minimum in the strength of the ethanol donor hydrogen bond for a composition of xwater = 0.74. We attempt to analyze further this result by estimating the effect of the implicit solvent on the ethanol donor hydrogen bond strength, finding it to be incremental. A brief analysis of different cluster conformations is carried out to determine the cooperativity conditions that can potentially explain the observed minimum in the ethanol donor hydrogen bond strength. These observations are related to notions of microheterogeneity in water/alcohol mixtures and provide context toward a more elaborate picture of association in heteroclusters.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666447","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

Two-molecule theory of polyethylene liquids. 聚乙烯液体的双分子理论。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0242204

Huimin Li, James P Donley, David T Wu, John G Curro, Caleb A Tormey

{"title":"Two-molecule theory of polyethylene liquids.","authors":"Huimin Li, James P Donley, David T Wu, John G Curro, Caleb A Tormey","doi":"10.1063/5.0242204","DOIUrl":"10.1063/5.0242204","url":null,"abstract":"Two-molecule theory refers to a class of microscopic, self-consistent field theories for the radial distribution function in classical molecular liquids. The version examined here can be considered as one of the very few formally derived closures to the reference interaction site model (RISM) equation. The theory is applied to polyethylene liquids, computing their equilibrium structural and thermodynamic properties at melt densities. The equation for the radial distribution function, which is represented as an average over the accessible states of two molecules in an external field that mimics the effects of the other molecules in the liquid, is computed by Monte Carlo simulation along with the intramolecular structure function. An improved direct sampling algorithm is utilized to speed the equilibration. Polyethylene chains of 24 and 66 united atom CH2 units are studied. The results are compared to full, many-chain molecular dynamics (MD) simulations and self-consistent polymer-RISM (PRISM) theory with the atomic Percus-Yevick (PY) closure under the same conditions. It is shown that the two-molecule theory produces results that are close to those of MD and is thus able to overcome defects of PRISM-PY theory and predict more accurate liquid structure at both short and long ranges. Predictions for the equation of state are also discussed.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667617","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 of a 4-nitrothiophenol monolayer to rapid heating studied by vibrational sum frequency spectroscopy. 通过振动和频谱研究 4-硝基苯硫酚单层对快速加热的响应。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-11-21 DOI: 10.1063/5.0231489

Matthias Linke, Joshua Multhaup, Eckart Hasselbrink

引用次数: 0