Journal of Chemical Physics最新文献_第2页

Double Mpemba effect in the cooling of trapped colloids. 被困胶体冷却过程中的双重姆彭巴效应。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0225749

Isha Malhotra, Hartmut Löwen

引用次数: 0

Dynamics of hydride anion and acetyloxyl radical production by electron attachment to acetic acid. 乙酸电子附着产生氢化物阴离子和乙酰氧自由基的动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0226252

M Hasan, Th Weber, M Centurion, D S Slaughter

引用次数: 0

Effect of load-resisting force on photoisomerization mechanism of a single second generation light-driven molecular rotary motor. 负载阻力对单个第二代光驱动分子旋转电机光异构化机理的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0216074

Xiaojuan Pang, Kaiyue Zhao, Deping Hu, Quanjie Zhong, Ningbo Zhang, Chenwei Jiang

{"title":"Effect of load-resisting force on photoisomerization mechanism of a single second generation light-driven molecular rotary motor.","authors":"Xiaojuan Pang, Kaiyue Zhao, Deping Hu, Quanjie Zhong, Ningbo Zhang, Chenwei Jiang","doi":"10.1063/5.0216074","DOIUrl":"10.1063/5.0216074","url":null,"abstract":"A pivotal aspect of molecular motors is their capability to generate load capacity from a single entity. However, few studies have directly characterized the load-resisting force of a single light-driven molecular motor. This research provides a simulation analysis of the load-resisting force for a highly efficient, second-generation molecular motor developed by Feringa et al. We investigate the M-to-P photoinduced nonadiabatic molecular dynamics of 9-(2,3-dihydro-2-methyl-1H-benz[e]inden-1-ylidene)-9H-fluorene utilizing Tully's surface hopping method at the semi-empirical OM2/MRCI level under varying load-resisting forces. The findings indicate that the quantum yield remains relatively stable under forces up to 0.003 a.u., with the photoisomerization mechanism functioning typically. Beyond this threshold, the quantum yield declines, and an alternative photoisomerization mechanism emerges, characterized by an inversion of the central double bond's twisting direction. The photoisomerization process stalls when the force attains a critical value of 0.012 a.u. Moreover, the average lifetime of the excited state oscillates around that of the unperturbed system. The quantum yield and mean lifetime of the S1 excited state in the absence of external force are recorded at 0.54 and 877.9 fs, respectively. In addition, we analyze a time-dependent fluorescence radiation spectrum, confirming the presence of a dark state and significant vibrations, as previously observed experimentally by Conyard et al.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466491","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

Exploring the molecular pathways of the activation process in PPARγ recurrent bladder cancer mutants. 探索 PPARγ 复发性膀胱癌突变体激活过程的分子途径。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0232041

Vinícius M de Oliveira, Caique C Malospirito, Fernando B da Silva, Natália B Videira, Marieli M G Dias, Murilo N Sanches, Vitor B P Leite, Ana Carolina M Figueira

{"title":"Exploring the molecular pathways of the activation process in PPARγ recurrent bladder cancer mutants.","authors":"Vinícius M de Oliveira, Caique C Malospirito, Fernando B da Silva, Natália B Videira, Marieli M G Dias, Murilo N Sanches, Vitor B P Leite, Ana Carolina M Figueira","doi":"10.1063/5.0232041","DOIUrl":"10.1063/5.0232041","url":null,"abstract":"The intricate involvement of Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) in glucose homeostasis and adipogenesis is well-established. However, its role in cancer, particularly luminal bladder cancer, remains debated. The overexpression and activation of PPARγ are implicated in tumorigenesis. Specific gain-of-function mutations (M280I, I290M, and T475M) within the ligand-binding domain of PPARγ are associated with bladder cancer and receptor activation. The underlying molecular pathways prompted by these mutations remain unclear. We employed a dual-basin structure-based model (db-SBM) to explore the conformational dynamics between the inactive and active states of PPARγ and examined the effects of the M280I, I290M, and T475M mutations. Our findings, consistent with the existing literature, reveal heightened ligand-independent transcriptional activity in the I290M and T475M mutants. Both mutants showed enhanced stabilization of the active state compared to the wild-type receptor, with the I290M mutation promoting a specific transition route, making it a prime candidate for further study. Electrostatic analysis identified residues K303 and E488 as pivotal in the I290M activation cascade. Biophysical assays confirmed that disrupting the K303-E488 interaction reduced the thermal stabilization characteristic of the I290M mutation. Our study demonstrates the predictive capabilities of combining simulation and cheminformatics methods, validated by biochemical experiments, to gain insights into molecular activation mechanisms and identify target residues for protein modulation.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501165","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

Signatures of coherent vibrational dynamics in ethylene carbonate. 碳酸乙烯酯中的相干振动动力学特征。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0216515

Luke Guerrieri, Sarah Hall, Brad M Luther, Amber T Krummel

引用次数: 0

Modeling of fluence-dependent hole-burned spectra and hole-growth kinetics using multiple two-level system model. 利用多两级系统模型模拟随通量变化的空穴燃烧光谱和空穴生长动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0222998

Tonu Reinot, Ryszard Jankowiak

{"title":"Modeling of fluence-dependent hole-burned spectra and hole-growth kinetics using multiple two-level system model.","authors":"Tonu Reinot, Ryszard Jankowiak","doi":"10.1063/5.0222998","DOIUrl":"https://doi.org/10.1063/5.0222998","url":null,"abstract":"Numerical formalism is presented that perfectly describes resonant low-temperature hole-burned spectra (including zero-phonon holes, ZPHs) and spectral hole-growth dynamics of Al-phthalocyanine tetrasulphonate embedded in hyperquenched glassy water films over more than seven orders of fluence magnitude (0.4 µJ/cm2-5.9 J/cm2). Frequency changes during spectral hole-burning (HB) are traditionally explained with the help of a single extrinsic two-level-system (TLSext) associated with impurity molecules. The new multiple two-level system (n-TLSext) models and data analysis presented in this work show that each chromophore in an amorphous medium can couple with multiple independent TLSext, which maintain perfect photo-memory, allowing a full return of the photoproduct to the initial (\"preburn\") state. Modeling reveals that the experimentally observed narrow photoproduct peak at higher energies, in close vicinity of the zero-phonon hole (ZPH), reflects a dynamical feature of the HB process populating so-called \"terminal\" states (states that do not interact with laser excitation). Within the n-TLSext model, each chromophore possesses multiple possibilities to create a photoproduct when in interaction with the burning laser, i.e., chromophores can interact with burning laser-light multiple times until reaching the terminal states. Due to phonon-assisted absorption, terminal states are typically at higher energies than the ZPH, in agreement with the hole burned spectra reported for many molecules embedded in various amorphous solids. However, many HB systems reveal both blue- (high-energy) and red-shifted (low-energy) antiholes (i.e., photoproducts). We suggest that future modeling of resonant holes in various proteins using our n-TLSext model will provide more insight on the complexity of the protein energy landscape.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501074","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

Dynamics of paramagnetic permanent chains and self-assembled clusters under a rapidly rotating magnetic field. 快速旋转磁场下顺磁性永久链和自组装团簇的动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0223442

Abdelkerim Hassan Hamid, David Gonzalez-Rodriguez, Hong Xu, Lydiane Bécu

{"title":"Dynamics of paramagnetic permanent chains and self-assembled clusters under a rapidly rotating magnetic field.","authors":"Abdelkerim Hassan Hamid, David Gonzalez-Rodriguez, Hong Xu, Lydiane Bécu","doi":"10.1063/5.0223442","DOIUrl":"https://doi.org/10.1063/5.0223442","url":null,"abstract":"We study experimentally and theoretically the dynamics of permanent paramagnetic chains and mixed clusters formed by permanent paramagnetic chains and paramagnetic particles under the influence of a time-varying magnetic field. First, we examine the dynamics of permanent chains at high frequencies (∼50 to 1000 Hz). These permanent chains exhibit continuous rotational motion with a frequency several orders of magnitude lower than that of the magnetic field. We develop a theoretical model that accurately describes the dependence of the rotational dynamics of chains on their length, as well as the amplitude and frequency of the external magnetic field in this high frequency regime. Next, we examine how cluster dynamics are affected by the presence of permanent chains. We show that the rotation of clusters composed of a high proportion of permanent chains is slowed down but remains qualitatively well described by the theoretical model we developed for homogeneous clusters of isotropic particles. We propose that the decrease in angular velocity for mixed clusters is due to the hardening of the cluster's 2D elastic modulus caused by the increase of the steric interaction parameter stemming from the presence of chemical links between particles in the chains.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501162","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

Electron-impact ionization of water molecules at low impact energies. 低冲击能量下的水分子电子冲击电离。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0225885

A Tamin, S Houamer, T Khatir, L U Ancarani, C Dal Cappello

{"title":"Electron-impact ionization of water molecules at low impact energies.","authors":"A Tamin, S Houamer, T Khatir, L U Ancarani, C Dal Cappello","doi":"10.1063/5.0225885","DOIUrl":"10.1063/5.0225885","url":null,"abstract":"The electron-impact ionization of water molecules at low impact energies is investigated using a theoretical approach named M3CWZ. In this model, which considers exchange effects and post-collision interaction, the continuum electrons (incident, scattered, and ejected) are all described by a Coulomb wave that corresponds to distance-dependent charges generated from the molecular target properties. Triple differential cross-sections for low impact energy ionization of either the 1b1 or 3a1 orbitals are calculated for several geometrical and kinematical configurations, all in the dipole regime. The M3CWZ model is thoroughly tested with an extensive comparison with available theoretical results and COLTRIMS measurements performed at projectile energies of Ei = 81 eV [Ren et al., Phys. Rev. A 95, 022701 (2017)] and Ei = 65 eV [Zhou et al., Phys. Rev. A 104, 012817 (2021)]. Similar to other theoretical models, an overall good agreement with both sets of measured data is observed for the angular distributions. Our calculated cross-sections' magnitudes are also satisfactory when compared to the other theoretical results, as well as to the cross-normalized relative scale data at 81 eV impact energy. The 65 eV set of data, measured on an absolute scale, offers a further challenging task for theoretical descriptions, and globally the M3CWZ performs fairly well and comparably to other theories. The proposed approach with variable charges somehow allows to capture the main multicenter distortion effects while avoiding high computational costs.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466492","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 insights into the dynamical behavior of structurally modified water in aqueous deep eutectic solvents (ADES). 分子动力学洞察水性深共晶溶剂 (ADES) 中结构修饰水的动力学行为。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0223828

Arnab Sil, Sangeeta, Vishnu Poonia, Suman Das, Biswajit Guchhait

{"title":"Molecular dynamics insights into the dynamical behavior of structurally modified water in aqueous deep eutectic solvents (ADES).","authors":"Arnab Sil, Sangeeta, Vishnu Poonia, Suman Das, Biswajit Guchhait","doi":"10.1063/5.0223828","DOIUrl":"10.1063/5.0223828","url":null,"abstract":"Recent studies have demonstrated that the presence of water in deep eutectic solvents (DESs) significantly affects their dynamics, structure, and physical properties. Although the structural changes due to the addition of water are well understood, the microscopic dynamics of these changes have been rarely studied. Here, we performed molecular dynamics simulation of 30% (v/v) (∼0.57 molar fraction) water mixture of DES containing CH3CONH2 and NaSCN/KSCN at various salt fractions to understand the microscopic structure and dynamics of water. The simulated results reveal a heterogeneous environment for water molecules in aqueous DES (ADES), which is influenced by the nature of the cation. The diffusion coefficients of water in ADESs are significantly lower than that in neat water and concentrated aqueous NaSCN/KSCN solution. When Na+ ions are replaced by K+ ions in the ADES system, the diffusion coefficient increases, which is consistent with the measured nuclear magnetic resonance data. Self-dynamic structure factor for water and other simulated dynamic quantities, such as reorientation, hydrogen-bond, and residence time correlation functions, show markedly slower dynamics inside ADES than in the neat water and aqueous salt solution. Moreover, these dynamics become faster when Na+ ions in ADES are replaced by K+ ions. The results suggest that the structural environment of water in Na+-rich ADES is rigid due to the presence of cation-bound water and geometrically constrained water. The medium becomes less rigid as the KSCN fraction increases due to the relatively weaker interaction of K+ ions with water than Na+ ions, which accelerates the dynamical processes.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466494","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

Origin of unique electronic structures of single-atom alloys unraveled by interpretable deep learning. 可解释深度学习揭示单原子合金独特电子结构的起源

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-10-28 DOI: 10.1063/5.0232141

Yang Huang, Shih-Han Wang, Luke E K Achenie, Kamal Choudhary, Hongliang Xin

引用次数: 0