The Journal of chemical physics最新文献_第9页

A local mode study of ring puckering effects in the infrared spectra of cyclopentane. 环戊烷红外光谱中起皱效应的局部模态研究。

The Journal of chemical physics Pub Date : 2022-05-10 DOI: 10.1063/5.0095010

E. Sibert, P. Bernath

引用次数: 1

Femtosecond-to-millisecond mid-IR spectroscopy of photoactive yellow protein uncovers structural micro-transitions of the chromophore's protonation mechanism. 光活性黄色蛋白的飞秒-毫秒中红外光谱揭示了发色团质子化机制的结构微跃迁。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0091918

L. V. van Wilderen, L. Blankenburg, J. Bredenbeck

{"title":"Femtosecond-to-millisecond mid-IR spectroscopy of photoactive yellow protein uncovers structural micro-transitions of the chromophore's protonation mechanism.","authors":"L. V. van Wilderen, L. Blankenburg, J. Bredenbeck","doi":"10.1063/5.0091918","DOIUrl":"https://doi.org/10.1063/5.0091918","url":null,"abstract":"Protein structural dynamics can span many orders of magnitude in time. Photoactive yellow protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-infrared spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to the formation of the partially unfolded signaling state pB. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a few hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist the ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117088846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

DFT investigations of KTiOPO4Mx (M = K, Na, and Li) anodes for alkali-ion battery. 用于碱性离子电池的 KTiOPO4Mx（M = K、Na 和 Li）阳极的 DFT 研究。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.2139/ssrn.4035322

Jiajia Huang, Xu Cai, Yanli Li, Zhongpu Fang, Yi Li, Wei-hui Lin, Shuping Huang, Yongfan Zhang

引用次数: 4

OptiBoost: A method for choosing a safe and efficient boost for the bond-boost method in accelerated molecular dynamics simulations with hyperdynamics. OptiBoost:一种在超动力学加速分子动力学模拟中为bond-boost方法选择安全有效的boost的方法。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0088521

Jianming Cui, K. Fichthorn

引用次数: 2

Temporal and chirp effects of laser pulses on the spectral line shape in sum-frequency generation vibrational spectroscopy. 和频产生振动光谱中激光脉冲的时间和啁啾效应对谱线形状的影响。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0088506

Hui Wang, Xiao-Hua Hu, Hong-fei Wang

{"title":"Temporal and chirp effects of laser pulses on the spectral line shape in sum-frequency generation vibrational spectroscopy.","authors":"Hui Wang, Xiao-Hua Hu, Hong-fei Wang","doi":"10.1063/5.0088506","DOIUrl":"https://doi.org/10.1063/5.0088506","url":null,"abstract":"Assignment and interpretation of the sum-frequency generation vibrational spectra (SFG-VS) depend on the ability to measure and understand the factors affecting the SFG-VS spectral line shape accurately and reliably. In the past, the formulation of the polarization selection rules for SFG-VS and the development of the sub-wavenumber high-resolution broadband SFG-VS (HR-BB-SFG-VS) have provided solutions for many of these needs. However, despite these advantages, HR-BB-SFG-VS have not been widely adopted. The majority of SFG measurements so far still relies on the picosecond (ps) scanning SFG-VS or the conventional broadband SFG-VS (BB-SFG-VS) with the spectral resolution around (mostly above) 10 cm-1, which also results in less ideal spectral line shape in the SFG spectra due to the temporal and chirp effects of the laser pulses used in experiment. In this study, the temporal and the chirp effects of laser pulses with different profiles in the SFG experiment on the measured SFG-VS spectral line shape are examined through spectral simulation. In addition, the experimental data of a classical model system, i.e., octadecyltrichlorosilane monolayer on glass, obtained from the ps scanning SFG-VS, the BB-SFG-VS, and the HR-BB-SFG-VS measurements are directly compared and examined. These results show that temporal and chirp effects are often significant in the conventional BB-SFG-VS, resulting in line shape distortions and peak position shifts besides spectral broadening. Such temporal and chirp effects are less significant in the ps scanning SFG-VS. For the HR-BB-SFG-VS, spectral broadening and temporal and chirp effects are insignificant, making HR-BB-SFG-VS the choice for accurate and reliable measurement and analysis of SFG-VS.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129694734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Rotational excitation of NS+ by H2 revisited: A new global potential energy surface and rate coefficients. H2对NS+的旋转激发:一个新的全局势能面和速率系数。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0089745

C. Bop, Y. Kalugina, F. Lique

{"title":"Rotational excitation of NS+ by H2 revisited: A new global potential energy surface and rate coefficients.","authors":"C. Bop, Y. Kalugina, F. Lique","doi":"10.1063/5.0089745","DOIUrl":"https://doi.org/10.1063/5.0089745","url":null,"abstract":"Due to the lack of specific collisional data, the abundance of NS+ in cold dense interstellar clouds was determined using collisional rate coefficients of CS as a substitute. To better understand the chemistry of sulfur in the interstellar medium, further abundance modeling using the actual NS+ collisional rate coefficients is needed. For this purpose, we have computed the first full 4D potential energy surface of the NS+-H2 van der Waals complex using the explicitly correlated coupled cluster approach with single, double, and non-iterative triple excitation in conjunction with the augmented-correlation consistent-polarized valence triple zeta basis set. The potential energy surface exhibits a global minimum of 848.24 cm-1 for a planar configuration of the complex. The long-range interaction energy, described using multipolar moments, is sensitive to the orientation of H2 up to radial distances of ∼50 a0. From this new interaction potential, we derived excitation cross sections, induced by collision with ortho- and para-H2, for the 15 low-lying rotational levels of NS+ using the quantum mechanical close-coupling approach. By thermally averaging these data, we determined downward rate coefficients for temperatures up to 50 K. By comparing them with the previous NS+-H2 data, we demonstrated that reduced dimensional approaches are not suited for this system. In addition, we found that the CS collisional data underestimate our results by up to an order of magnitude. The differences clearly indicate that the abundance of NS+, in cold dense clouds retrieved from observational spectra, must be reassessed using these new collisional rate coefficients.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128085881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Polymer informatics for QSPR prediction of tensile mechanical properties. Case study: Strength at break. 聚合物信息学用于拉伸力学性能的QSPR预测。案例研究:休息时的力量。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0087392

F. Cravero, M. Díaz, I. Ponzoni

{"title":"Polymer informatics for QSPR prediction of tensile mechanical properties. Case study: Strength at break.","authors":"F. Cravero, M. Díaz, I. Ponzoni","doi":"10.1063/5.0087392","DOIUrl":"https://doi.org/10.1063/5.0087392","url":null,"abstract":"The artificial intelligence-based prediction of the mechanical properties derived from the tensile test plays a key role in assessing the application profile of new polymeric materials, especially in the design stage, prior to synthesis. This strategy saves time and resources when creating new polymers with improved properties that are increasingly demanded by the market. A quantitative structure-property relationship (QSPR) model for tensile strength at break is presented in this work. The QSPR methodology applied here is based on machine learning tools, visual analytics methods, and expert-in-the-loop strategies. From the whole study, a QSPR model composed of five molecular descriptors that achieved a correlation coefficient of 0.9226 is proposed. We applied visual analytics tools at two levels of analysis: a more general one in which models are discarded for redundant information metrics and a deeper one in which a chemistry expert can make decisions on the composition of the model in terms of subsets of molecular descriptors, from a physical-chemical point of view. In this way, with the present work, we close a contribution cycle to polymer informatics, providing QSPR models oriented to the prediction of mechanical properties related to the tensile test.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"74 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124806944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

How do external forces related to mass and charge affect the structures and dynamics of an ionic liquid? 与质量和电荷有关的外力如何影响离子液体的结构和动力学?

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0091322

Yongji Guan, Ryan Clark, F. Philippi, Xiaoping Zhang, T. Welton

{"title":"How do external forces related to mass and charge affect the structures and dynamics of an ionic liquid?","authors":"Yongji Guan, Ryan Clark, F. Philippi, Xiaoping Zhang, T. Welton","doi":"10.1063/5.0091322","DOIUrl":"https://doi.org/10.1063/5.0091322","url":null,"abstract":"Ionic liquids (ILs) are novel promising materials widely used in various fields. Their structures and properties can be tuned by means of external perturbations, thus further broadening their applications. Herein, forces proportional to atomic mass (mass-related field) and atomic charge (electric field) are applied in molecular dynamics simulations to the IL 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide to investigate the origin of the resulting changes in structures and dynamics. The results show that both electric and mass-related fields cause the ion cages to expand and deform, eventually leading to their breakdown to produce a transformation of ILs from the cage structure to a channel-like structure, which results in faster self-diffusion of ions in the directions of the applied force and to a lesser extent other directions. Further comparison of electric and mass-related fields demonstrates that only the electric fields reorientate cations to produce a hydrodynamically favored conformation in the force direction, which shows faster diffusion. The cis isomer of the anion is preferred in the presence of the electric fields, whereas applying the forces proportional to mass does not change the anion conformer equilibrium significantly. The results presented in this work aid in the understanding of how ions adjust their structures to adapt to external perturbations and facilitate the application of ILs as electrolytes.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129640226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Note: Reproducibility of potential energy surfaces of organic/metal interfaces on the example of PTCDA on Ag(111). 注:以Ag(111)上PTCDA为例，有机/金属界面势能面再现性。

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0094163

Lukas Hörmann, A. Jeindl, O. Hofmann

引用次数: 1

Xanthophyll-cycle based model of the rapid photoprotection of Nannochloropsis in response to regular and irregular light/dark sequences. 基于叶黄素循环的纳米叶绿体对规则和不规则光/暗序列的快速光保护模型

The Journal of chemical physics Pub Date : 2022-05-09 DOI: 10.1063/5.0089335

Audrey H. Short, Thomas P Fay, Thien Crisanto, Johanna Hall, Collin J. Steen, K. Niyogi, David T. Limmer, G. Fleming

{"title":"Xanthophyll-cycle based model of the rapid photoprotection of Nannochloropsis in response to regular and irregular light/dark sequences.","authors":"Audrey H. Short, Thomas P Fay, Thien Crisanto, Johanna Hall, Collin J. Steen, K. Niyogi, David T. Limmer, G. Fleming","doi":"10.1063/5.0089335","DOIUrl":"https://doi.org/10.1063/5.0089335","url":null,"abstract":"We explore the photoprotection dynamics of Nannochloropsis oceanica using time-correlated single photon counting under regular and irregular actinic light sequences. The varying light sequences mimic natural conditions, allowing us to probe the real-time response of non-photochemical quenching (NPQ) pathways. Durations of fluctuating light exposure during a fixed total experimental time and prior light exposure of the algae are both found to have a profound effect on NPQ. These observations are rationalized with a quantitative model based on the xanthophyll cycle and the protonation of LHCX1. The model is able to accurately describe the dynamics of non-photochemical quenching across a variety of light sequences. The combined model and observations suggest that the accumulation of a quenching complex, likely zeaxanthin bound to a protonated LHCX1, is responsible for the gradual rise in NPQ. Additionally, the model makes specific predictions for the light sequence dependence of xanthophyll concentrations that are in reasonable agreement with independent chromatography measurements taken during a specific light/dark sequence.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124225476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10