Annual review of physical chemistry最新文献_第8页

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":"73 ","pages":"1-19"},"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

Multiscale Models for Light-Driven Processes. 光驱动过程的多尺度模型。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-02-09 DOI: 10.1146/annurev-physchem-090419-104031

Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Giovanni Granucci, Benedetta Mennucci

引用次数: 16

Optical Force-Induced Chemistry at Solution Surfaces. 溶液表面的光力诱导化学。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-02-12 DOI: 10.1146/annurev-physchem-090419-044828

Hiroshi Masuhara, Ken-Ichi Yuyama

{"title":"Optical Force-Induced Chemistry at Solution Surfaces.","authors":"Hiroshi Masuhara, Ken-Ichi Yuyama","doi":"10.1146/annurev-physchem-090419-044828","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090419-044828","url":null,"abstract":"When an intense 1,064-nm continuous-wave laser is tightly focused at solution surfaces, it exerts an optical force on molecules, polymers, and nanoparticles (NPs). Initially, molecules and NPs are gathered into a single assembly inside the focus, and the laser is scattered and propagated through the assembly. The expanded laser further traps them at the edge of the assembly, producing a single assembly much larger than the focus along the surface. Amino acids and inorganic ionic compounds undergo crystallization and crystal growth, polystyrene NPs form periodic arrays and disklike structures with concentric circles or hexagonal packing, and Au NPs demonstrate assembling and swarming, in which the NPs fluctuate like a group of bees. These phenomena that depend on laser polarization are called optically evolved assembling at solution surfaces, and their dynamics and mechanisms are elucidated in this review. As a promising application in materials science, the optical trapping assembly of lead halide perovskites, supramolecules, and aggregation-induced emission enhancement-active molecules is demonstrated and future directions for fundamental study are discussed.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"72 ","pages":"565-589"},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25354891","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: 15

Critical Phenomena in Plasma Membrane Organization and Function. 质膜组织与功能中的关键现象。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2020-12-01 DOI: 10.1146/annurev-physchem-090419-115951

Thomas R Shaw, Subhadip Ghosh, Sarah L Veatch

引用次数: 27

My Trajectory in Molecular Reaction Dynamics and Spectroscopy. 我的分子反应动力学和光谱学轨迹。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-12-04 DOI: 10.1146/annurev-physchem-090519-124238

Robert Benny Gerber

{"title":"My Trajectory in Molecular Reaction Dynamics and Spectroscopy.","authors":"Robert Benny Gerber","doi":"10.1146/annurev-physchem-090519-124238","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090519-124238","url":null,"abstract":"This is the story of a career in theoretical chemistry during a time of dramatic changes in the field due to phenomenal growth in the availability of computational power. It is likewise the story of the highly gifted graduate students and postdoctoral fellows that I was fortunate to mentor throughout my career. It includes reminiscences of the great mentors that I had and of the exciting collaborations with both experimentalists and theorists on which I built much of my research. This is an account of the developments of exciting scientific disciplines in which I was involved: vibrational spectroscopy, molecular reaction mechanisms and dynamics, e.g., in atmospheric chemistry, and the prediction of new, exotic molecules, in particular noble gas molecules. From my very first project to my current work, my career in science has brought me the excitement and fascination of research. What a wonderful pursuit! Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 20, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"72 ","pages":"1-34"},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-090519-124238","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38674497","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: 0

My Life in Changing Times: New Ideas and New Techniques. 我的生活在变化的时代:新思想和新技术。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-27 DOI: 10.1146/annurev-physchem-090319-054423

Ruth M Lynden-Bell

引用次数: 0

Multiconfiguration Pair-Density Functional Theory. 多组态对密度泛函理论。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 DOI: 10.1146/annurev-physchem-090419-043839

Prachi Sharma, Jie J Bao, Donald G Truhlar, Laura Gagliardi

{"title":"Multiconfiguration Pair-Density Functional Theory.","authors":"Prachi Sharma, Jie J Bao, Donald G Truhlar, Laura Gagliardi","doi":"10.1146/annurev-physchem-090419-043839","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090419-043839","url":null,"abstract":"Kohn-Sham density functional theory with the available exchange-correlation functionals is less accurate for strongly correlated systems, which require a multiconfigurational description as a zero-order function, than for weakly correlated systems, and available functionals of the spin densities do not accurately predict energies for many strongly correlated systems when one uses multiconfigurational wave functions with spin symmetry. Furthermore, adding a correlation functional to a multiconfigurational reference energy can lead to double counting of electron correlation. Multiconfiguration pair-density functional theory (MC-PDFT) overcomes both obstacles, the second by calculating the quantum mechanical part of the electronic energy entirely by a functional, and the first by using a functional of the total density and the on-top pair density rather than the spin densities. This allows one to calculate the energy of strongly correlated systems efficiently with a pair-density functional and a suitable multiconfigurational reference function. This article reviews MC-PDFT and related background information.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"72 ","pages":"541-564"},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38893284","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: 18

Spectroscopy and Scattering Studies Using Interpolated Ab Initio Potentials. 利用插值从头算电位的光谱学和散射研究。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-27 DOI: 10.1146/annurev-physchem-090519-051837

Ernesto Quintas-Sánchez, Richard Dawes

{"title":"Spectroscopy and Scattering Studies Using Interpolated Ab Initio Potentials.","authors":"Ernesto Quintas-Sánchez, Richard Dawes","doi":"10.1146/annurev-physchem-090519-051837","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090519-051837","url":null,"abstract":"The Born-Oppenheimer potential energy surface (PES) has come a long way since its introduction in the 1920s, both conceptually and in predictive power for practical applications. Nevertheless, nearly 100 years later-despite astonishing advances in computational power-the state-of-the-art first-principles prediction of observables related to spectroscopy and scattering dynamics is surprisingly limited. For example, the water dimer, (H2O)2, with only six nuclei and 20 electrons, still presents a formidable challenge for full-dimensional variational calculations of bound states and is considered out of reach for rigorous scattering calculations. The extremely poor scaling of the most rigorous quantum methods is fundamental; however, recent progress in development of approximate methodologies has opened the door to fairly routine high-quality predictions, unthinkable 20 years ago. In this review, in relation to the workflow of spectroscopy and/or scattering studies, we summarize progress and challenges in the component areas of electronic structure calculations, PES fitting, and quantum dynamical calculations.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"72 ","pages":"399-421"},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38872100","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: 3

Demystifying the Diffuse Vibrational Spectrum of Aqueous Protons Through Cold Cluster Spectroscopy. 用冷簇光谱学揭开水质子扩散振动谱的神秘面纱。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-03-01 DOI: 10.1146/annurev-physchem-061020-053456

Helen J Zeng, Mark A Johnson

引用次数: 13

First-Principles Insights into Plasmon-Induced Catalysis. 等离子体诱导催化的第一性原理。

IF 14.7 1区化学

Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-12-02 DOI: 10.1146/annurev-physchem-061020-053501

John Mark P Martirez, Junwei Lucas Bao, Emily A Carter

{"title":"First-Principles Insights into Plasmon-Induced Catalysis.","authors":"John Mark P Martirez, Junwei Lucas Bao, Emily A Carter","doi":"10.1146/annurev-physchem-061020-053501","DOIUrl":"https://doi.org/10.1146/annurev-physchem-061020-053501","url":null,"abstract":"The size- and shape-controlled enhanced optical response of metal nanoparticles (NPs) is referred to as a localized surface plasmon resonance (LSPR). LSPRs result in amplified surface and interparticle electric fields, which then enhance light absorption of the molecules or other materials coupled to the metallic NPs and/or generate hot carriers within the NPs themselves. When mediated by metallic NPs, photocatalysis can take advantage of this unique optical phenomenon. This review highlights the contributions of quantum mechanical modeling in understanding and guiding current attempts to incorporate plasmonic excitations to improve the kinetics of heterogeneously catalyzed reactions. A range of first-principles quantum mechanics techniques has offered insights, from ground-state density functional theory (DFT) to excited-state theories such as multireference correlated wavefunction methods. Here we discuss the advantages and limitations of these methods in the context of accurately capturing plasmonic effects, with accompanying examples.","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"72 ","pages":"99-119"},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-061020-053501","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38677990","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: 25