Journal of Chemical Physics最新文献_第2页

Effect of hard confinement on the phase state and dynamics of 1-propanol/water mixtures. 硬约束对1-丙醇/水混合物相态和动力学的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-28 DOI: 10.1063/5.0268637

Vasileios Moschos, Martin Steinhart, Hans-Jürgen Butt, George Floudas

引用次数: 0

Characterization of the hemithioindigo photoswitch and its derivatives with x-ray photoabsorption and photoemission spectroscopies. 半硫靛蓝光开关及其衍生物的x射线光吸收和光发射光谱表征。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-28 DOI: 10.1063/5.0271164

L Oberti, L Avaldi, P Bolognesi, M Bonanomi, R Borrego-Varillas, C Callegari, L Carlini, J Chiarinelli, E Ciekalski, M Coreno, M Devetta, M Di Fraia, M Garavelli, M Goffe, C Grazioli, F Montorsi, K C Prince, R Richter, F Segatta, S Waldmannstetter, G Cerullo, H Dube, O Plekan, D Faccialà, C Vozzi, A Nenov

{"title":"Characterization of the hemithioindigo photoswitch and its derivatives with x-ray photoabsorption and photoemission spectroscopies.","authors":"L Oberti, L Avaldi, P Bolognesi, M Bonanomi, R Borrego-Varillas, C Callegari, L Carlini, J Chiarinelli, E Ciekalski, M Coreno, M Devetta, M Di Fraia, M Garavelli, M Goffe, C Grazioli, F Montorsi, K C Prince, R Richter, F Segatta, S Waldmannstetter, G Cerullo, H Dube, O Plekan, D Faccialà, C Vozzi, A Nenov","doi":"10.1063/5.0271164","DOIUrl":"https://doi.org/10.1063/5.0271164","url":null,"abstract":"In this study, we investigate the electronic structure of hemithioindigo-hemistilbene (HTI) photoswitches and their functionalized derivatives, HTI-OMe and HTI-SMe, using x-ray photoemission spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy. HTI compounds are known for their high quantum yield, thermal bistability, and rapid photoisomerization, making them promising candidates for applications in molecular motors, optical materials, and photocatalysis. Our analysis, supported by first-principles simulations, reveals how the conjugation of heteroatoms within the π-system affects the core-level chemical shifts and ionization intensities in XPS, while NEXAFS probes the influence of substituents on virtual molecular orbitals and energy transitions. In particular, the comparison between different functionalized HTIs allowed us to evaluate the effect of electronic relaxation following core-level photoionization and photo-excitation. These results provide a detailed understanding of the influence of functionalization on the electron distribution of HTI compounds, providing a robust foundation for the study and control of ultrafast charge transfer and photoswitching mechanisms in these molecular systems.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528180","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

Extending Badger's rule. II. The relationship between energy and vibrational spectra in hydrogen bonds. 扩展獾的规则。2。氢键中能量与振动谱的关系。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-28 DOI: 10.1063/5.0263484

Garrett D Santis, Sotiris S Xantheas

{"title":"Extending Badger's rule. II. The relationship between energy and vibrational spectra in hydrogen bonds.","authors":"Garrett D Santis, Sotiris S Xantheas","doi":"10.1063/5.0263484","DOIUrl":"https://doi.org/10.1063/5.0263484","url":null,"abstract":"We describe the energetic-spectral relationship between the energy of a hydrogen bond (EHB) and the redshift in the vibrational frequency of the covalent hydrogen bond donor (ΔωHB). The relationship was derived by convoluting expressions relating EHB and ΔωHB to the covalent bond distance of the hydrogen bond donor (ΔrHB), while ensuring balanced treatment of the exchange repulsion. We relied on reduced parts of the potential energy surfaces (PESs) of six hydrogen bonded dimers, namely, NH3-NH3, H2O-H2O, HF-HF, H2O-NH3, HF-H2O, and HF-NH3 derived from ab initio electronic structure calculations to fit the parameters of the model and validated its performance for extended parts of the PESs that include non-linear hydrogen bonds. The developed model suggests a novel relationship of a strength of 4.5 kcal/mol per 100 cm-1 redshift in the covalent donor (D-H) vibrational frequency, while non-linear effects become important for redshifts >200 cm-1. The single descriptor (ΔωHB), which is measurable either experimentally via gas-phase spectroscopy or theoretically via electronic structure calculations, was able to predict the experimental or calculated hydrogen bond energies of typical hydrogen bonded dimers using the developed relationship.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528181","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

High pressure structural and lattice dynamics study of α-In2Se3. α-In2Se3的高压结构和晶格动力学研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0266372

Shiyu Feng, Baihong Sun, Wenting Lu, Haikai Zou, Chenxin Wei, Qian Zhang, Bihan Wang, Martin Kunz, Hirokazu Kadobayashi, Azkar Saeed Ahmad, Elad Koren, Elissaios Stavrou

引用次数: 0

Long timescale solvation dynamics and confinement: The case of non-ionic deep eutectic solvents of lauric acid and N-methylacetamide. 长时间尺度溶剂化动力学和约束：月桂酸和n-甲基乙酰胺非离子型深共晶溶剂的情况。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0261957

Laura X Sepulveda-Montaño, Johan F Galindo, Daniel G Kuroda

{"title":"Long timescale solvation dynamics and confinement: The case of non-ionic deep eutectic solvents of lauric acid and N-methylacetamide.","authors":"Laura X Sepulveda-Montaño, Johan F Galindo, Daniel G Kuroda","doi":"10.1063/5.0261957","DOIUrl":"https://doi.org/10.1063/5.0261957","url":null,"abstract":"Microscopic segregation and molecular heterogeneities in complex liquids are the result of the interplay between different intermolecular forces, all of which contribute to the energy landscape of the system. A consequence of the intricate energy landscape is the nontrivial effect on the solvation dynamics. Here, the impact of molecular heterogeneities on the solvation dynamics is studied using infrared spectroscopies and molecular dynamics simulations. In particular, this study focuses on the dynamical effect of nanoscopic heterogeneities present in deep eutectic solvents (DESs) composed of lauric acid (LA) and N-methylacetamide (NMA). To this end, a molecular probe containing a carbon triple bond is used as an infrared reporter. The results show that the vibrational probe is likely to be located in the NMA polar domains. Furthermore, the probe solvation dynamics derived from the 2DIR spectra presents a slowdown of its timescale with increasing LA concentration in the DES. Kubo modeling of the probe solvation dynamics shows a correlation between the amplitude of its long time component and the presence of molecular heterogeneities in the sample. Semiclassical modeling of the vibrational line shape of the triple bond stretch demonstrates that the heterogeneities affect the whole solvation dynamics of the system through the amplitudes of the frequency fluctuations. Molecular dynamics simulations confirm the experimental results and their interpretation by showing a slowdown of the solvation dynamics when the LA heterogeneities are present. Overall, the study presents a molecular framework to explain the effect of confinement created by nanoscopic LA heterogeneities on the solvation dynamics of the system.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325910","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

A Gaussian kernel Monte Carlo resampling method to construct smooth free energy surface from discrete simulation data. 用高斯核蒙特卡罗重采样方法从离散仿真数据中构造光滑自由能面。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0273521

Xubin Li, Tianming Qu, Lianqing Zheng, Wei Yang

{"title":"A Gaussian kernel Monte Carlo resampling method to construct smooth free energy surface from discrete simulation data.","authors":"Xubin Li, Tianming Qu, Lianqing Zheng, Wei Yang","doi":"10.1063/5.0273521","DOIUrl":"10.1063/5.0273521","url":null,"abstract":"Constructing a free energy surface based on discrete molecular simulation data is a common practice in computational chemistry and biophysics. As a general strategy, histogram-based methods have substantial limitations in producing smooth free energy surfaces from sparse samples. Most histogram-free methods allow for possible smooth global free energy surface mapping but likely lead to significantly compromised local features. This issue is particularly severe when both the global shape and the local free energy transition need to be quantitatively depicted, as often aimed for in general ensemble simulation studies. In this work, we introduce a Gaussian kernel Monte Carlo (GKMC) resampling method to robustly construct a smooth free energy surface from discrete simulation data. In GKMC resampling, the target free energy surface is mapped as the sum of local Gaussian basis functions; the height of each Gaussian basis function is recursively obtained through MC resampling of the simulation data. In this work, the GKMC resampling method is illustrated based on the data from a generalized orthogonal space tempering simulation study of deca-alanine peptide conformational changes in aqueous solution. As revealed in the case study, smooth free energy surfaces that can accurately represent simulated probability distributions could be robustly generated through the GKMC resampling strategy. Because data noise can be effectively removed, local free energy features could be displayed in an informative way. Notably, without impacting the global free energy shape, local free energy smoothness can be conveniently adjusted via the choice of the Gaussian kernel function width. As demonstrated, GKMC resampling is a robust approach for high-quality free energy surface construction.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Formally exact fluorescence spectroscopy simulations for mesoscale molecular aggregates with N0 scaling. 正式精确荧光光谱模拟中尺度分子聚集体与N0标度。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0268435

Tarun Gera, Alexia Hartzell, Lipeng Chen, Alexander Eisfeld, Doran I G B Raccah

引用次数: 0

Tunable layer-specific polarizability in twisted multilayer graphene flakes capped with hexagonal boron nitride. 六方氮化硼覆盖的扭曲多层石墨烯片的可调层特定极化率。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0268147

Xian Wang, Wenfeng Guang, Yunpeng Lu

{"title":"Tunable layer-specific polarizability in twisted multilayer graphene flakes capped with hexagonal boron nitride.","authors":"Xian Wang, Wenfeng Guang, Yunpeng Lu","doi":"10.1063/5.0268147","DOIUrl":"10.1063/5.0268147","url":null,"abstract":"Twisted multilayer graphene (TMG) capped with hexagonal boron nitride (hBN) exhibits distinctive electronic phenomena under a vertical electric field. However, the dielectric constant alone is insufficient to comprehensively characterize the dielectric properties of low-dimensional materials, posing challenges for accurately measuring and controlling their field response. To address this, we develop a site-specific polarizability decomposition approach based on first-principles calculations, enabling the separation of intra- and interlayer polarizabilities in TMG@hBN. This method is applied to 2580 constructed configurations of TMG flakes with and without hBN encapsulation. Our findings reveal that intralayer polarizability dominates the overall magnitude, while the interlayer component governs its variation with twist angle. hBN encapsulation enhances interlayer polarizability while reducing its twist-angle dependence. For both TMG and TMG@hBN, the inner graphene layers exhibit negligible γ, which quantifies the layer-specific interlayer charge transfer response to an external field, while significant γ values emerge in the outermost graphene layers (γGra) and hBN (γBN). Interestingly, γGra and γBN exhibit opposite signs in non-equivalent layers, and γGra reverses between pristine TMG and TMG@hBN. Compared to TMG, γGra in TMG@hBN is suppressed, with variations strongly dependent on thickness, twist angle, and stacking patterns, particularly when nitrogen atoms align over phenyl ring centers. In addition to the well-known Bernal-stacked structure, notable changes in interlayer polarizability and γGra are also observed in slightly misaligned (AA)N-stacked structures with the exceptional twist angle (θp). This scalable method enables layer-resolved analysis of intra- and interlayer contributions, offering new insights for tuning electric field responses and optimizing graphene-based optoelectronic devices.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333157","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

Machine learning short-ranged many-body interactions in colloidal systems using descriptors based on Voronoi cells. 基于Voronoi细胞的胶体系统描述符的机器学习短程多体相互作用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0267835

Rinske M Alkemade, Rastko Sknepnek, Frank Smallenburg, Laura Filion

{"title":"Machine learning short-ranged many-body interactions in colloidal systems using descriptors based on Voronoi cells.","authors":"Rinske M Alkemade, Rastko Sknepnek, Frank Smallenburg, Laura Filion","doi":"10.1063/5.0267835","DOIUrl":"https://doi.org/10.1063/5.0267835","url":null,"abstract":"Machine learning (ML) strategies are opening the door to faster computer simulations, allowing us to simulate more realistic colloidal systems. Since the interactions in colloidal systems are often highly many-body, stemming from, e.g., depletion and steric interactions, one of the challenges for these algorithms is capturing the many-body nature of these interactions. In this paper, we introduce a new ML-based strategy for fitting many-body interactions in colloidal systems where the many-body interaction is highly local. To this end, we develop Voronoi-based descriptors for capturing the local environment and fit the effective potential using a simple neural network. To test this algorithm, we consider a simple two-dimensional model for a colloid-polymer mixture, where the colloid-colloid interactions and colloid-polymer interactions are hard-disk like, while the polymers themselves interact as ideal gas particles. We find that a Voronoi-based description is sufficient to accurately capture the many-body nature of this system. Moreover, we find that the Pearson correlation function alone is insufficient to determine the predictive power of the network emphasizing the importance of additional metrics when assessing the quality of ML-based potentials.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325911","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

Revealing the importance of the C(1) position to modulate the photophysics and Z-scan responses of o-locked GFP chromophores. 揭示了C(1)位置在调节o锁定GFP发色团的光物理和z扫描响应中的重要性。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-06-21 DOI: 10.1063/5.0274692

Debasish Paul, Priyadarshi Sahoo, Amit Kumar Pradhan, Prasanta Kumar Datta, Arunava Sengupta, Umakanta Tripathy, Soumit Chatterjee

{"title":"Revealing the importance of the C(1) position to modulate the photophysics and Z-scan responses of o-locked GFP chromophores.","authors":"Debasish Paul, Priyadarshi Sahoo, Amit Kumar Pradhan, Prasanta Kumar Datta, Arunava Sengupta, Umakanta Tripathy, Soumit Chatterjee","doi":"10.1063/5.0274692","DOIUrl":"10.1063/5.0274692","url":null,"abstract":"Three novel ortho-locked (o-locked) green fluorescent protein (GFP) chromophores, which are also doubly locked, with a phenyl group at the C(1) of the imidazolinone ring and substituents with varying electronic effects at the C(9) of the benzylidene moiety, have been synthesized. All the chromophores show relatively weak but much red-shifted emissions compared to their methyl counterparts at C(1), as previously reported by us [D. Paul et al., J. Phys. Chem. B 129, 692-711 (2025)]. Quantum chemical calculations indicate that the excited state dynamics of the chromophores possess initial rotation of the phenyl, followed by proton transfer and geometry twisting. Fluorescence decays confirm an early time charge transfer from the benzylidene moiety to the electron-withdrawing substituents at C(9). The relaxation processes occur within a time range of hundreds of femtoseconds to a few picoseconds, subject to respective compounds. This study supports our earlier reported findings [D. Paul et al., J. Phys. Chem. B 129, 692-711 (2025)] that the electronic effect at C(9) significantly affects the quantum yields of o-locked GFP chromophore analogs. This study also shows that solvent viscosity and temperature play dominant roles in modulating the fluorescence intensities of o-locked GFP chromophores. Furthermore, these compounds display significantly superior nonlinear optical (NLO) properties than their methyl analogs [D. Paul et al., J. Phys. Chem. B 129, 692-711 (2025)]. These findings provide valuable insight regarding the correlation between the molecular structures of o-locked GFP chromophores and their spectroscopic nature and pave the way to structurally engineering improved fluorophores. In a nutshell, these chromophores with a phenyl group at C(1), with poor but highly red-shifted emission in solution, showing viscosity dependency on emission intensity, and high NLO properties, can be very useful in bio-imaging.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144336538","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