Annual review of physical chemistry最新文献_第5页

3D Super-Resolution Fluorescence Imaging of Microgels. 微凝胶的三维超分辨率荧光成像。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2023-04-24 DOI: 10.1146/annurev-physchem-062422-022601

Oleksii Nevskyi, Dominik Wöll

引用次数: 3

Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing. 由机器学习、图形处理单元和云计算实现的交互量子化学。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2023-04-24 DOI: 10.1146/annurev-physchem-061020-053438

Umberto Raucci, Hayley Weir, Sukolsak Sakshuwong, Stefan Seritan, Colton B Hicks, Fabio Vannucci, Francesco Rea, Todd J Martínez

{"title":"Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing.","authors":"Umberto Raucci, Hayley Weir, Sukolsak Sakshuwong, Stefan Seritan, Colton B Hicks, Fabio Vannucci, Francesco Rea, Todd J Martínez","doi":"10.1146/annurev-physchem-061020-053438","DOIUrl":"https://doi.org/10.1146/annurev-physchem-061020-053438","url":null,"abstract":"Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units-accelerated quantum chemistry in the cloud, artificial intelligence-driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9335376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 2

Ultrafast Dynamics of Photosynthetic Light Harvesting: Strategies for Acclimation Across Organisms. 光合光收获的超快动态:跨生物驯化策略。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2023-04-24 DOI: 10.1146/annurev-physchem-083122-111318

Olivia C Fiebig, Dvir Harris, Dihao Wang, Madeline P Hoffmann, Gabriela S Schlau-Cohen

{"title":"Ultrafast Dynamics of Photosynthetic Light Harvesting: Strategies for Acclimation Across Organisms.","authors":"Olivia C Fiebig, Dvir Harris, Dihao Wang, Madeline P Hoffmann, Gabriela S Schlau-Cohen","doi":"10.1146/annurev-physchem-083122-111318","DOIUrl":"https://doi.org/10.1146/annurev-physchem-083122-111318","url":null,"abstract":"Photosynthetic light harvesting exhibits near-unity quantum efficiency. The high efficiency is achieved through a series of energy and charge transfer steps within a network of pigment-containing proteins. Remarkably, high efficiency is conserved across many organisms despite differences in the protein structures and organization that allow each organism to respond to its own biological niche and the stressors within. In this review, we highlight recent progress toward understanding how organisms maintain optimal light-harvesting ability by acclimating to their environment. First, we review the building blocks of photosynthetic light harvesting, energy transfer, and time-resolved spectroscopic techniques. Then, we explore how three classes of photosynthetic organisms-purple bacteria, cyanobacteria, and green plants-optimize their light-harvesting apparatuses to their particular environment. Overall, research has shown that photosynthetic energy transfer is robust to changing environmental conditions, with each organism utilizing its own strategies to optimize photon capture in its particular biological niche.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9359773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 2

Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy. 用位点特异性激子耦合二聚体探针光谱研究局部DNA主链构象和构象紊乱。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2023-04-24 Epub Date: 2023-01-25 DOI: 10.1146/annurev-physchem-090419-041204

Andrew H Marcus, Dylan Heussman, Jack Maurer, Claire S Albrecht, Patrick Herbert, Peter H von Hippel

{"title":"Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy.","authors":"Andrew H Marcus, Dylan Heussman, Jack Maurer, Claire S Albrecht, Patrick Herbert, Peter H von Hippel","doi":"10.1146/annurev-physchem-090419-041204","DOIUrl":"10.1146/annurev-physchem-090419-041204","url":null,"abstract":"The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded-double-stranded DNA (ssDNA-dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA-dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2 dimer probes. With the application of these methods, the (iCy3)2 dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein-DNA complex assembly and function.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10590263/pdf/nihms-1938226.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9352275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 3

Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development. 水系统中的多体效应:相互作用分析技术和力场发展之间的协同作用。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2023-04-24 DOI: 10.1146/annurev-physchem-062422-023532

Joseph P Heindel, Kristina M Herman, Sotiris S Xantheas

{"title":"Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development.","authors":"Joseph P Heindel, Kristina M Herman, Sotiris S Xantheas","doi":"10.1146/annurev-physchem-062422-023532","DOIUrl":"https://doi.org/10.1146/annurev-physchem-062422-023532","url":null,"abstract":"Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born-Oppenheimer potential energy surface. In particular, we focus on ab initio-based force fields that aim to explicitly reproduce many-body terms and are fitted to high-level electronic structure results. These force fields generally incorporate many-body effects through (a) parameterization of distributed multipoles, (b) explicit fitting of the MBE, (c) inclusion of many-atom features in a neural network, and (d) coarse-graining of many-body terms into an effective two-body term. We also discuss the emerging use of the MBE to improve the accuracy and speed of ab initio molecular dynamics.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 4

Photochemical Upconversion. 光化学上转换。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2023-04-24 DOI: 10.1146/annurev-physchem-092722-104952

Jiale Feng, Jessica Alves, Damon M de Clercq, Timothy W Schmidt

引用次数: 7

Intramolecular Vibrations in Excitation Energy Transfer: Insights from Real-Time Path Integral Calculations. 激发能量传递中的分子内振动:来自实时路径积分计算的见解。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2022-04-20 Epub Date: 2022-01-26 DOI: 10.1146/annurev-physchem-090419-120202

Sohang Kundu, Nancy Makri

{"title":"Intramolecular Vibrations in Excitation Energy Transfer: Insights from Real-Time Path Integral Calculations.","authors":"Sohang Kundu, Nancy Makri","doi":"10.1146/annurev-physchem-090419-120202","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090419-120202","url":null,"abstract":"Excitation energy transfer (EET) is fundamental to many processes in chemical and biological systems and carries significant implications for the design of materials suitable for efficient solar energy harvest and transport. This review discusses the role of intramolecular vibrations on the dynamics of EET in nonbonded molecular aggregates of bacteriochlorophyll, a perylene bisimide, and a model system, based on insights obtained from fully quantum mechanical real-time path integral results for a Frenkel exciton Hamiltonian that includes all vibrational modes of each molecular unit at finite temperature. Generic trends, as well as features specific to the vibrational characteristics of the molecules, are identified. Weak exciton-vibration (EV) interaction leads to compact, near-Gaussian densities on each electronic state, whose peak follows primarily a classical trajectory on a torus, while noncompact densities and nonlinear peak evolution are observed with strong EV coupling. Interaction with many intramolecular modes and increasing aggregate size smear, shift, and damp these dynamical features.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39950707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 23

Vibration-Cavity Polariton Chemistry and Dynamics. 振动腔极化化学与动力学。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2022-04-20 Epub Date: 2022-01-26 DOI: 10.1146/annurev-physchem-082620-014627

Adam D Dunkelberger, Blake S Simpkins, Igor Vurgaftman, Jeffrey C Owrutsky

引用次数: 45

Protein Structure Prediction with Mass Spectrometry Data. 用质谱数据预测蛋白质结构。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2022-04-20 DOI: 10.1146/annurev-physchem-082720-123928

Sarah E Biehn, Steffen Lindert

{"title":"Protein Structure Prediction with Mass Spectrometry Data.","authors":"Sarah E Biehn, Steffen Lindert","doi":"10.1146/annurev-physchem-082720-123928","DOIUrl":"https://doi.org/10.1146/annurev-physchem-082720-123928","url":null,"abstract":"Knowledge of protein structure is crucial to our understanding of biological function and is routinely used in drug discovery. High-resolution techniques to determine the three-dimensional atomic coordinates of proteins are available. However, such methods are frequently limited by experimental challenges such as sample quantity, target size, and efficiency. Structural mass spectrometry (MS) is a technique in which structural features of proteins are elucidated quickly and relatively easily. Computational techniques that convert sparse MS data into protein models that demonstrate agreement with the data are needed. This review features cutting-edge computational methods that predict protein structure from MS data such as chemical cross-linking, hydrogen-deuterium exchange, hydroxyl radical protein footprinting, limited proteolysis, ion mobility, and surface-induced dissociation. Additionally, we address future directions for protein structure prediction with sparse MS data. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9672978/pdf/nihms-1847175.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9682640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 14

Probing the Nature of the Transition-Metal-Boron Bonds and Novel Aromaticity in Small Metal-Doped Boron Clusters Using Photoelectron Spectroscopy. 利用光电子能谱研究小金属掺杂硼团簇中过渡金属-硼键的性质和新的芳构性。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2022-04-20 Epub Date: 2022-01-19 DOI: 10.1146/annurev-physchem-082820-113041

Teng-Teng Chen, Ling Fung Cheung, Lai-Sheng Wang

{"title":"Probing the Nature of the Transition-Metal-Boron Bonds and Novel Aromaticity in Small Metal-Doped Boron Clusters Using Photoelectron Spectroscopy.","authors":"Teng-Teng Chen, Ling Fung Cheung, Lai-Sheng Wang","doi":"10.1146/annurev-physchem-082820-113041","DOIUrl":"https://doi.org/10.1146/annurev-physchem-082820-113041","url":null,"abstract":"Photoelectron spectroscopy combined with quantum chemistry has been a powerful approach to elucidate the structures and bonding of size-selected boron clusters (Bn-), revealing a prevalent planar world that laid the foundation for borophenes. Investigations of metal-doped boron clusters not only lead to novel structures but also provide important information about the metal-boron bonds that are critical to understanding the properties of boride materials. The current review focuses on recent advances in transition-metal-doped boron clusters, including the discoveries of metal-boron multiple bonds and metal-doped novel aromatic boron clusters. The study of the RhB- and RhB2O- clusters led to the discovery of the first quadruple bond between boron and a transition-metal atom, whereas a metal-boron triplebond was found in ReB2O- and IrB2O-. The ReB4- cluster was shown to be the first metallaborocycle with Möbius aromaticity, and the planar ReB6- cluster was found to exhibit aromaticity analogous to metallabenzenes.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39831944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 5