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Annual review of physical chemistry最新文献

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Vibrational Sum-Frequency Generation Hyperspectral Microscopy for Molecular Self-Assembled Systems. 分子自组装系统的振动和频率产生高光谱显微镜。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-13 DOI: 10.1146/annurev-physchem-090519-050510
Haoyuan Wang, Wei Xiong
{"title":"Vibrational Sum-Frequency Generation Hyperspectral Microscopy for Molecular Self-Assembled Systems.","authors":"Haoyuan Wang,&nbsp;Wei Xiong","doi":"10.1146/annurev-physchem-090519-050510","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090519-050510","url":null,"abstract":"<p><p>In this review, we discuss the recent developments and applications of vibrational sum-frequency generation (VSFG) microscopy. This hyperspectral imaging technique can resolve systems without inversion symmetry, such as surfaces, interfaces and noncentrosymmetric self-assembled materials, in the spatial, temporal, and spectral domains. We discuss two common VSFG microscopy geometries: wide-field and confocal point-scanning. We then introduce the principle of VSFG and the relationships between hyperspectral imaging with traditional spectroscopy, microscopy, and time-resolved measurements. We further highlight crucial applications of VSFG microscopy in self-assembled monolayers, cellulose in plants, collagen fibers, and lattice self-assembled biomimetic materials. In these systems, VSFG microscopy reveals relationships between physical properties that would otherwise be hidden without being spectrally, spatially, and temporally resolved. Lastly, we discuss the recent development of ultrafast transient VSFG microscopy, which can spatially measure the ultrafast vibrational dynamics of self-assembled materials. The review ends with an outlook on the technical challenges of and scientific potential for VSFG microscopy.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38749446","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: 8
Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale. 低温超分辨率荧光和电子显微镜在纳米尺度上的相关性。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-13 DOI: 10.1146/annurev-physchem-090319-051546
Peter D Dahlberg, W E Moerner
{"title":"Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale.","authors":"Peter D Dahlberg,&nbsp;W E Moerner","doi":"10.1146/annurev-physchem-090319-051546","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090319-051546","url":null,"abstract":"<p><p>We review the emerging method of super-resolved cryogenic correlative light and electron microscopy (srCryoCLEM). Super-resolution (SR) fluorescence microscopy and cryogenic electron tomography (CET) are both powerful techniques for observing subcellular organization, but each approach has unique limitations. The combination of the two brings the single-molecule sensitivity and specificity of SR to the detailed cellular context and molecular scale resolution of CET. The resulting correlative data is more informative than the sum of its parts. The correlative images can be used to pinpoint the positions of fluorescently labeled proteins in the high-resolution context of CET with nanometer-scale precision and/or to identify proteins in electron-dense structures. The execution of srCryoCLEM is challenging and the approach is best described as a method that is still in its infancy with numerous technical challenges. In this review, we describe state-of-the-art srCryoCLEM experiments, discuss the most pressing challenges, and give a brief outlook on future applications.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8877847/pdf/nihms-1779529.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38749866","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: 38
Quantitative Mass Spectrometry Imaging of Biological Systems. 生物系统的定量质谱成像。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-13 DOI: 10.1146/annurev-physchem-061020-053416
Daisy Unsihuay, Daniela Mesa Sanchez, Julia Laskin
{"title":"Quantitative Mass Spectrometry Imaging of Biological Systems.","authors":"Daisy Unsihuay, Daniela Mesa Sanchez, Julia Laskin","doi":"10.1146/annurev-physchem-061020-053416","DOIUrl":"10.1146/annurev-physchem-061020-053416","url":null,"abstract":"<p><p>Mass spectrometry imaging (MSI) is a powerful, label-free technique that provides detailed maps of hundreds of molecules in complex samples with high sensitivity and subcellular spatial resolution. Accurate quantification in MSI relies on a detailed understanding of matrix effects associated with the ionization process along with evaluation of the extraction efficiency and mass-dependent ion losses occurring in the analysis step. We present a critical summary of approaches developed for quantitative MSI of metabolites, lipids, and proteins in biological tissues and discuss their current and future applications.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8161172/pdf/nihms-1699190.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38749868","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: 0
Dry Deposition of Atmospheric Aerosols: Approaches, Observations, and Mechanisms. 大气气溶胶的干沉降:方法、观测和机制。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-20 DOI: 10.1146/annurev-physchem-090519-034936
Delphine K Farmer, Erin K Boedicker, Holly M DeBolt
{"title":"Dry Deposition of Atmospheric Aerosols: Approaches, Observations, and Mechanisms.","authors":"Delphine K Farmer,&nbsp;Erin K Boedicker,&nbsp;Holly M DeBolt","doi":"10.1146/annurev-physchem-090519-034936","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090519-034936","url":null,"abstract":"<p><p>Aerosols are liquid or solid particles suspended in the atmosphere, typically with diameters on the order of nanometers to microns. These particles impact air quality and the radiative balance of the planet. Dry deposition is a key process for the removal of aerosols from the atmosphere and plays an important role in controlling the lifetime of atmospheric aerosols. Dry deposition is driven by turbulence and shows a strong dependence on particle size. This review summarizes the mechanisms behind aerosol dry deposition, including measurement approaches, field observations, and modeling studies. We identify several gaps in the literature, including deposition over the cryosphere (i.e., snow and ice surfaces) and the ocean; in addition, we highlight new techniques to measure black carbon fluxes. While recent advances in aerosol instrumentation have enhanced our understanding of aerosol sources and chemistry, dry deposition and other loss processes remain poorly investigated.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38842057","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: 29
Molecular Simulation of Electrode-Solution Interfaces. 电极-溶液界面的分子模拟。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2021-04-20 Epub Date: 2021-01-04 DOI: 10.1146/annurev-physchem-090519-024042
Laura Scalfi, Mathieu Salanne, Benjamin Rotenberg
{"title":"Molecular Simulation of Electrode-Solution Interfaces.","authors":"Laura Scalfi,&nbsp;Mathieu Salanne,&nbsp;Benjamin Rotenberg","doi":"10.1146/annurev-physchem-090519-024042","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090519-024042","url":null,"abstract":"<p><p>Many key industrial processes, from electricity production, conversion, and storage to electrocatalysis or electrochemistry in general, rely on physical mechanisms occurring at the interface between a metallic electrode and an electrolyte solution, summarized by the concept of an electric double layer, with the accumulation/depletion of electrons on the metal side and of ions on the liquid side. While electrostatic interactions play an essential role in the structure, thermodynamics, dynamics, and reactivity of electrode-electrolyte interfaces, these properties also crucially depend on the nature of the ions and solvent, as well as that of the metal itself. Such interfaces pose many challenges for modeling because they are a place where quantum chemistry meets statistical physics. In the present review, we explore the recent advances in the description and understanding of electrode-electrolyte interfaces with classical molecular simulations, with a focus on planar interfaces and solvent-based liquids, from pure solvent to water-in-salt electrolytes.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39126537","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: 39
High-Field Dynamic Nuclear Polarization. 高场动态核极化。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2020-04-20 Epub Date: 2020-02-19 DOI: 10.1146/annurev-physchem-071119-040222
Björn Corzilius
{"title":"High-Field Dynamic Nuclear Polarization.","authors":"Björn Corzilius","doi":"10.1146/annurev-physchem-071119-040222","DOIUrl":"https://doi.org/10.1146/annurev-physchem-071119-040222","url":null,"abstract":"<p><p>Dynamic nuclear polarization (DNP) is one of the most prominent methods of sensitivity enhancement in nuclear magnetic resonance (NMR). Even though solid-state DNP under magic-angle spinning (MAS) has left the proof-of-concept phase and has become an important tool for structural investigations of biomolecules as well as materials, it is still far from mainstream applicability because of the potentially overwhelming combination of unique instrumentation, complex sample preparation, and a multitude of different mechanisms and methods available. In this review, I introduce the diverse field and history of DNP, combining aspects of NMR and electron paramagnetic resonance. I then explain the general concepts and detailed mechanisms relevant at high magnetic field, including solution-state methods based on Overhauser DNP but with a greater focus on the more established MAS DNP methods. Finally, I review practical considerations and fields of application and discuss future developments.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2020-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-071119-040222","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37658205","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: 47
Machine Learning for Molecular Simulation. 分子模拟的机器学习。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2020-04-20 Epub Date: 2020-02-24 DOI: 10.1146/annurev-physchem-042018-052331
Frank Noé, Alexandre Tkatchenko, Klaus-Robert Müller, Cecilia Clementi
{"title":"Machine Learning for Molecular Simulation.","authors":"Frank Noé,&nbsp;Alexandre Tkatchenko,&nbsp;Klaus-Robert Müller,&nbsp;Cecilia Clementi","doi":"10.1146/annurev-physchem-042018-052331","DOIUrl":"https://doi.org/10.1146/annurev-physchem-042018-052331","url":null,"abstract":"<p><p>Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML methods. Here we review recent ML methods for molecular simulation, with particular focus on (deep) neural networks for the prediction of quantum-mechanical energies and forces, on coarse-grained molecular dynamics, on the extraction of free energy surfaces and kinetics, and on generative network approaches to sample molecular equilibrium structures and compute thermodynamics. To explain these methods and illustrate open methodological problems, we review some important principles of molecular physics and describe how they can be incorporated into ML structures. Finally, we identify and describe a list of open challenges for the interface between ML and molecular simulation.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2020-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-042018-052331","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37672398","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: 430
Single-Molecule FRET of Intrinsically Disordered Proteins. 内在无序蛋白质的单分子FRET。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2020-04-20 Epub Date: 2020-02-25 DOI: 10.1146/annurev-physchem-012420-104917
Lauren Ann Metskas, Elizabeth Rhoades
{"title":"Single-Molecule FRET of Intrinsically Disordered Proteins.","authors":"Lauren Ann Metskas,&nbsp;Elizabeth Rhoades","doi":"10.1146/annurev-physchem-012420-104917","DOIUrl":"https://doi.org/10.1146/annurev-physchem-012420-104917","url":null,"abstract":"<p><p>Intrinsically disordered proteins (IDPs) are now widely recognized as playing critical roles in a broad range of cellular functions as well as being implicated in diverse diseases. Their lack of stable secondary structure and tertiary interactions, coupled with their sensitivity to measurement conditions, stymies many traditional structural biology approaches. Single-molecule Förster resonance energy transfer (smFRET) is now widely used to characterize the physicochemical properties of these proteins in isolation and is being increasingly applied to more complex assemblies and experimental environments. This review provides an overview of confocal diffusion-based smFRET as an experimental tool, including descriptions of instrumentation, data analysis, and protein labeling. Recent papers are discussed that illustrate the unique capability of smFRET to provide insight into aggregation-prone IDPs, protein-protein interactions involving IDPs, and IDPs in complex experimental milieus.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2020-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-012420-104917","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37676129","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: 37
The Exploration of Chemical Reaction Networks. 化学反应网络的探索。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2020-04-20 Epub Date: 2020-02-19 DOI: 10.1146/annurev-physchem-071119-040123
Jan P Unsleber, Markus Reiher
{"title":"The Exploration of Chemical Reaction Networks.","authors":"Jan P Unsleber,&nbsp;Markus Reiher","doi":"10.1146/annurev-physchem-071119-040123","DOIUrl":"https://doi.org/10.1146/annurev-physchem-071119-040123","url":null,"abstract":"<p><p>Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2020-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-071119-040123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37683128","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: 73
Low-Frequency Protein Motions Coupled to Catalytic Sites. 催化位点耦合的低频蛋白质运动。
IF 14.7 1区 化学
Annual review of physical chemistry Pub Date : 2020-04-20 DOI: 10.1146/annurev-physchem-050317-014308
Christopher M Cheatum
{"title":"Low-Frequency Protein Motions Coupled to Catalytic Sites.","authors":"Christopher M Cheatum","doi":"10.1146/annurev-physchem-050317-014308","DOIUrl":"https://doi.org/10.1146/annurev-physchem-050317-014308","url":null,"abstract":"<p><p>This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":14.7,"publicationDate":"2020-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-physchem-050317-014308","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37852186","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: 16
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