Journal of Chemical Physics最新文献_第10页

Phase behavior and dissociation kinetics of lamins in a polymer model of progeria. 早衰症聚合物模型中层粘连蛋白的相行为和解离动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0265578

Hadiya Abdul Hameed, Jarosław Paturej, Aykut Erbaş

{"title":"Phase behavior and dissociation kinetics of lamins in a polymer model of progeria.","authors":"Hadiya Abdul Hameed, Jarosław Paturej, Aykut Erbaş","doi":"10.1063/5.0265578","DOIUrl":"https://doi.org/10.1063/5.0265578","url":null,"abstract":"One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery, known as the nuclear lamina, which provides rigidity and shape to the nucleus. Mutations in lamin proteins that alter the structure of the nuclear lamina underlie laminopathic diseases, including Hutchinson-Gilford Progeria Syndrome (HGPS). Experiments have shown that, compared to healthy cells, lamin supramolecular structures (e.g., protofilaments) assemble into a thicker lamina in HGPS, where they form highly stable nematic microdomains at the nuclear periphery, reminiscent of liquid crystals. This significantly alters the morphological and mechanical properties of the nucleus. In this study, we investigate the aggregation of lamin fibrous structures and their dissociation kinetics from the nuclear periphery by modeling them as coarse-grained, rod-like polymer chains confined within a rigid spherical shell. Our model reproduces the formation of multidirectional nematic domains at the nuclear surface and the reduced lamin dissociation observed in HGPS nuclei by adjusting lamin concentration, lamin-lamin (head-tail), and lamin-shell association strengths. While nematic phase formation requires relatively strong lamin-shell affinity under any non-vanishing inter-lamin attraction, the thickness of the lamina layer is primarily controlled by the head-tail association strength in the model. Furthermore, the unbinding kinetics of lamin chains from the lamina exhibit a concentration-dependent facilitated dissociation, suppressed by strong intra-lamin interactions, reminiscent of diseased nuclei. Overall, our calculations reveal the physical mechanisms by which mutations affecting native lamin interactions and concentration could lead to an abnormal nuclear lamina in laminopathic diseases.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973241","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

Photoelectron imaging spectroscopy of Ag3- in the S0 and S1 states. Ag3-在S0和S1态的光电子成像光谱。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0270711

Yuta Suzuki, Tasuku Nishizato, Kazuaki Matsumoto, Yuta Ushiki, Yuma Aoki, Akira Terasaki, Takuya Horio

{"title":"Photoelectron imaging spectroscopy of Ag3- in the S0 and S1 states.","authors":"Yuta Suzuki, Tasuku Nishizato, Kazuaki Matsumoto, Yuta Ushiki, Yuma Aoki, Akira Terasaki, Takuya Horio","doi":"10.1063/5.0270711","DOIUrl":"https://doi.org/10.1063/5.0270711","url":null,"abstract":"We explore laboratory-frame photoelectron angular distributions (LF-PADs) originating from the outermost two orbitals, σu [the highest occupied molecular orbital (HOMO)] and σg (HOMO-1), of the silver trimer anion (Ag3-) in the S0(1Σg+) state. The experiment was performed by our novel photoelectron imaging technique using a high-repetition-rate tunable laser [T. Horio et al., J. Chem. Phys. 162, 026101 (2025)]. The LF-PAD for σu is found to be highly energy-dependent in a photoelectron kinetic energy (PKE) range from 0 to 1.57 eV; an isotropic LF-PAD with an anisotropy parameter β ∼ 0 is observed at the detachment threshold, exemplifying the Wigner threshold law, whereas the β value decreases down to β = -0.4 at 0.46 eV, followed by an increase up to β = 0.6 at 1.57 eV, as PKE increases. A small dip discernible in the PKE range of 1.2-1.3 eV suggests an influence of the autodetachment process on the β value, which is via bound electronic state(s) embedded in the D0(2Σu+) + e- continuum. On the other hand, the LF-PAD for σg exhibits a strong anisotropy parallel to the laser polarization with β of ∼1 in 0-0.39 eV. These contrasted trends are qualitatively reproduced by theoretical modeling of LF-PAD that accounts for photoelectron partial waves allowed for each photodetachment process. Furthermore, two-photon detachment spectra via the excited S1(1Σu+) state are presented, where the relative band intensities for the two detachment channels, D0(2Σu+) + e- ← S1(1Σu+) and D1(2Σg+) + e- ← S1(1Σu+), are discussed in terms of their leading electronic configurations.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973244","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

Non-uniform Brillouin zone sampling for thermal transport in layered materials. 层状材料热输运的非均匀布里渊区采样。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0256384

Amey G Gokhale, Ankit Jain

引用次数: 0

Assessment of RPA and σ-functional methods for the calculation of dipole moments and static polarizabilities and hyperpolarizabilities. 偶极矩、静态极化率和超极化率的RPA和σ泛函计算方法的评价。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0267912

Raviraj Mandalia, Steffen Fauser, Egor Trushin, Andreas Görling

{"title":"Assessment of RPA and σ-functional methods for the calculation of dipole moments and static polarizabilities and hyperpolarizabilities.","authors":"Raviraj Mandalia, Steffen Fauser, Egor Trushin, Andreas Görling","doi":"10.1063/5.0267912","DOIUrl":"https://doi.org/10.1063/5.0267912","url":null,"abstract":"In the present paper, we assess the performance of methods based on the random phase approximation (RPA) and on σ-functionals for predicting static optical properties, i.e., dipole moment, polarizability, and first and second hyperpolarizability, of small- and medium-sized molecules, including chain-like systems. First, we provide accurate reference data by coupled-cluster singles, doubles, with perturbative triples calculations with sufficiently large basis sets. The RPA and σ-functional calculations are carried out post-self-consistently using input orbitals and eigenvalues from the hybrid density-functional calculation. The optimal fraction of exact non-local exchange in these calculations is found to be quite high, around 0.5-0.6 in RPA and around 0.8-1.0 in σ-functional methods. σ-functional methods, however, proved to be less sensitive than RPA methods with respect to the amount of exact non-local exchange used in the generation of their input data. σ-functional methods are shown to outperform in accuracy RPA methods and various other considered density-functional theory methods for static optical properties and, thus, are well-suited for the calculation of linear and non-linear optical properties.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019942","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

You reap what you sow: On the impact of nuclei morphology on seeded molecular dynamics simulations. 一分耕耘，一分收获：论核形态对种子分子动力学模拟的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0261353

Katarina E Blow, Gabriele C Sosso, David Quigley

{"title":"You reap what you sow: On the impact of nuclei morphology on seeded molecular dynamics simulations.","authors":"Katarina E Blow, Gabriele C Sosso, David Quigley","doi":"10.1063/5.0261353","DOIUrl":"https://doi.org/10.1063/5.0261353","url":null,"abstract":"Seeded molecular dynamics represents an increasingly popular approach to investigate crystal nucleation via computer simulations. This method involves the insertion of crystalline seeds into the supercooled liquid phase (often over a range of temperatures or sizes) in order to measure their evolution in time. When dealing with the prototypical scenario of crystal nucleation from Lennard-Jones melts, these seeds are artificially constructed to be approximately spherical fcc nuclei. In addition, the order parameter used to monitor the time evolution of a seed is typically chosen as the number of crystal-like atoms within it-consistent with the tenets of classical nucleation theory. However, evidence suggests that these artificially constructed seeds might be rather different from the crystalline nuclei formed during unbiased molecular dynamics simulations. In particular, previous studies of Lennard-Jones crystallization indicate that non-spherical, as well as bcc, nuclei might be involved with the nucleation process. In this work, we assess the impact of the choice of the initial crystalline nuclei in the context of seeded molecular dynamics by directly comparing two different classes of seeds. Specifically, we consider either crystalline nuclei extracted from \"brute force\" nucleation trajectories (\"unbiased seed\") or artificially constructed fcc spherical nuclei (\"constructed seeds\"). We show that the properties of these two classes of seeds, most notably their committor probability distributions, are markedly different. We also discuss the importance of choosing an appropriate order parameter for seeded molecular dynamics simulations and the implications of our results in the context of estimating crystal nucleation rates via computer simulations.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143982316","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

Determination of aqueous solubility of NaCl in molecular dynamics simulation using the Kirkwood-Buff method. 用Kirkwood-Buff方法测定NaCl水溶液溶解度的分子动力学模拟。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-07 DOI: 10.1063/5.0264104

Abhishek Chattopadhyay, Varun Mandalaparthy, Nico F A van der Vegt

{"title":"Determination of aqueous solubility of NaCl in molecular dynamics simulation using the Kirkwood-Buff method.","authors":"Abhishek Chattopadhyay, Varun Mandalaparthy, Nico F A van der Vegt","doi":"10.1063/5.0264104","DOIUrl":"https://doi.org/10.1063/5.0264104","url":null,"abstract":"Electrolyte solutions are central to a wide range of scientific and industrial applications, with ions in solution affecting properties as diverse as ion diffusion, solvation structure, and chemical potentials. However, accurately predicting the solubility of salts such as sodium chloride (NaCl) in molecular dynamics (MD) simulations is challenging. Existing methods, such as the direct coexistence method and the chemical potential route, provide insights but often require extensive computational resources or face limitations in reproducibility. In this study, we present an alternative approach using Kirkwood-Buff (KB) theory combined with MD simulations to estimate the solubility of NaCl. This \"KB method\" requires the calculation of ion-ion and ion-water Kirkwood-Buff integrals at different electrolyte concentrations based on a reference electrolyte chemical potential, yielding concentration-dependent chemical potentials. We calculated the solubility of five state-of-the-art NaCl models and found a clear link between ion pairing and solubility at low and moderately high electrolyte concentrations. Our results suggest that force fields with a mean number of contact ion pairs per ion between 0.014 and 0.025 in 1.0 molal aqueous electrolyte solution might be a good choice, offering valuable insights for future model refinement. By evaluating the computational efficiency of the KB method, we highlight its potential as a reliable tool to calculate the solubility of the future ion models.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020084","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

Longitudinal and transverse excitations: How nominally forbidden signals can be detected in autocorrelation functions relevant to liquids dynamics. 纵向和横向激励：如何在与液体动力学相关的自相关函数中检测名义上禁止的信号。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-07 DOI: 10.1063/5.0266698

Eleonora Guarini, Ubaldo Bafile, Daniele Colognesi, Alessandro Cunsolo, Alessio De Francesco, Ferdinando Formisano

{"title":"Longitudinal and transverse excitations: How nominally forbidden signals can be detected in autocorrelation functions relevant to liquids dynamics.","authors":"Eleonora Guarini, Ubaldo Bafile, Daniele Colognesi, Alessandro Cunsolo, Alessio De Francesco, Ferdinando Formisano","doi":"10.1063/5.0266698","DOIUrl":"https://doi.org/10.1063/5.0266698","url":null,"abstract":"This work provides evidence for the crucial role played by the self-part of functions as important as the dynamic structure factor S(Q, ω) and the spectrum of the transverse current autocorrelation CT(Q, ω) in studies of liquid dynamics. By using ab initio molecular dynamics simulations of liquid Ag, we show that a multimode representation also accounts very well for the simulated self-dynamic structure factor Sself(Q, ω), which provides insight on the single-particle dynamics. In particular, we provide a convincing proof that Sself(Q, ω) is responsible for the observation of transverse-like contributions in a longitudinal quantity such as S(Q, ω). It is particularly significant that an analogous situation was found when considering the transverse current. In fact, its self-part, CT,self(Q, ω), was shown to be accountable for the presence of longitudinal-like modes in a transverse quantity, such as CT(Q, ω). Due to the single-particle origin of the transverse signal in the dynamic structure factor, we also show that the apparent Q-dependence of transverse-like frequencies, as inferred from S(Q, ω), differs from the true dispersion of transverse excitations appropriately derived from CT(Q, ω).","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020165","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

Adsorption and reaction of 2-methylbenzimidazole molecules on a partially oxidized Cu(110) surface. 2-甲基苯并咪唑分子在部分氧化铜（110）表面的吸附和反应。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-07 DOI: 10.1063/5.0268988

Minlu Zhou, Xinle Lu, Rong Sun, Qinran Ding, Pengzhen Chen, Wen-Yi Tong, Chun-Gang Duan, Jun Zhang

{"title":"Adsorption and reaction of 2-methylbenzimidazole molecules on a partially oxidized Cu(110) surface.","authors":"Minlu Zhou, Xinle Lu, Rong Sun, Qinran Ding, Pengzhen Chen, Wen-Yi Tong, Chun-Gang Duan, Jun Zhang","doi":"10.1063/5.0268988","DOIUrl":"https://doi.org/10.1063/5.0268988","url":null,"abstract":"N-Heterocyclic carbenes (NHCs) have emerged as a promising candidate for functionalizing and modifying metal surfaces. Despite extensive research, the influence of oxides, which frequently occur on metal surfaces, on the adsorption behavior of NHCs has received limited attention at the nanometric scale. In this study, the adsorption configurations and reactions of 2-methylbenzimidazole (MBI) molecules on a CuO/Cu(110) surface were investigated using scanning tunneling microscopy and non-contact atomic force microscopy (nc-AFM). Following the deposition of MBI molecules, Cu islands were observed, and the molecules predominantly adsorbed in a flat-lying configuration. Comparative experiments conducted on a bare Cu(110) surface indicate that the dehydrogenation of MBI molecules due to the cleavage of N-H bonds leads to CuO reduction and the release of Cu adatoms, which subsequently aggregate into islands. Upon annealing at 378 K, molecules adsorbed at the CuO strips assume a tilted flat-lying configuration, suggesting the formation of coordination bonds between nitrogen and copper atoms. On the copper regions, molecules assemble into double-chains, adopting an upright configuration. High-resolution nc-AFM images reveal a similarity between molecules in the double-chains and those at step edges, implying that Cu atoms are extracted from terraces to form slots where molecules preferentially occupy.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020864","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

Quantum electrodynamics formulation of multidimensional spectroscopy. 多维光谱的量子电动力学公式。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-07 DOI: 10.1063/5.0267953

Frank Schlawin

引用次数: 0

A strict and internally consistent diabatic representation for coupled N-state diatomics: A hybrid asymptotic-property-based diabatization method. 耦合n态双原子的严格和内部一致的非绝热表示：一种基于混合渐近性质的非绝热方法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-07 DOI: 10.1063/5.0260594

R P Brady

{"title":"A strict and internally consistent diabatic representation for coupled N-state diatomics: A hybrid asymptotic-property-based diabatization method.","authors":"R P Brady","doi":"10.1063/5.0260594","DOIUrl":"https://doi.org/10.1063/5.0260594","url":null,"abstract":"A robust regularization procedure for the radial non-adiabatic coupling (NAC) elements of the diatomic nuclear kinetic energy operator for the N-state diatomic problem is presented. This method ensures NACs are internally consistent with each other and with corresponding adiabatic properties, such as potentials or dipoles. Constructing a diabatic representation-where all components of the (radial) nuclear derivative couplings vanish-that is both physical and exactly equivalent to the adiabatic representation can be impossible due to inconsistencies between NACs and adiabatic properties. Such discrepancies arise from using different theory levels in ab initio molecular property calculations, convergence issues in quantum chemistry calculations, post-processing adjustments to computed property curves, and truncation errors when considering only a finite number of Born-Oppenheimer states. The presented regularization procedure leverages a hybrid asymptotic-property-based diabatization (HyAP), where the asymptotic behavior of diabatic properties is addressed and their smoothness maximized simultaneously. This is achieved through optimization of the trajectory of the adiabatic to diabatic transformation (AtDT) parameterized by the corresponding generator matrices (exponential mapping). The presented methodology is applied to the 3-state system of N2 [1Σ+1, 2Σ+1, and 3Σ+1] and the 4-state system of CH [CΣ+2, 2Σ+2, 3Σ+2, and 4Σ+2] via evolution of the AtDT, where a physical diabatization is achieved. The HyAP regularization, developed and tested for applications in spectroscopy, is guided by underlying electronic structure data to fulfill our pragmatic aim of constructing physical diabatic representations that effectively controls bound rovibronic molecular spectroscopy while remaining exactly equivalent to the adiabatic representation.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967499","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