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Dynamical Reweighting for Biased Rare Event Simulations. 有偏差的罕见事件模拟的动态重权重。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 DOI: 10.1146/annurev-physchem-083122-124538
Bettina G Keller, Peter G Bolhuis
{"title":"Dynamical Reweighting for Biased Rare Event Simulations.","authors":"Bettina G Keller, Peter G Bolhuis","doi":"10.1146/annurev-physchem-083122-124538","DOIUrl":"10.1146/annurev-physchem-083122-124538","url":null,"abstract":"<p><p>Dynamical reweighting techniques aim to recover the correct molecular dynamics from a simulation at a modified potential energy surface. They are important for unbiasing enhanced sampling simulations of molecular rare events. Here, we review the theoretical frameworks of dynamical reweighting for modified potentials. Based on an overview of kinetic models with increasing level of detail, we discuss techniques to reweight two-state dynamics, multistate dynamics, and path integrals. We explore the natural link to transition path sampling and how the effect of nonequilibrium forces can be reweighted. We end by providing an outlook on how dynamical reweighting integrates with techniques for optimizing collective variables and with modern potential energy surfaces.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"75 1","pages":"137-162"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465674","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
Phenomenology of Intermediate Molecular Dynamics at Metal-Oxide Interfaces. 金属-氧化物界面的中间分子动力学现象学。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 DOI: 10.1146/annurev-physchem-062123-022921
Tanja Cuk
{"title":"Phenomenology of Intermediate Molecular Dynamics at Metal-Oxide Interfaces.","authors":"Tanja Cuk","doi":"10.1146/annurev-physchem-062123-022921","DOIUrl":"10.1146/annurev-physchem-062123-022921","url":null,"abstract":"<p><p>Reaction intermediates buried within a solid-liquid interface are difficult targets for physiochemical measurements. They are inherently molecular and locally dynamic, while their surroundings are extended by a periodic lattice on one side and the solvent dielectric on the other. Challenges compound on a metal-oxide surface of varied sites and especially so at its aqueous interface of many prominent reactions. Recently, phenomenological theory coupled with optical spectroscopy has become a more prominent tool for isolating the intermediates and their molecular dynamics. The following article reviews three examples of the SrTiO<sub>3</sub>-aqueous interface subject to the oxygen evolution from water: reaction-dependent component analyses of time-resolved intermediates, a Fano resonance of a mode at the metal-oxide-water interface, and reaction isotherms of metastable intermediates. The phenomenology uses parameters to encase what is unknown at a microscopic level to then circumscribe the clear and macroscopically tuned trends seen in the spectroscopic data.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"75 1","pages":"457-481"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465725","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
Submicrometer Particle Impact Dynamics and Chemistry. 亚微米粒子撞击动力学与化学。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 DOI: 10.1146/annurev-physchem-083122-122157
Sally E Burke, Robert E Continetti
{"title":"Submicrometer Particle Impact Dynamics and Chemistry.","authors":"Sally E Burke, Robert E Continetti","doi":"10.1146/annurev-physchem-083122-122157","DOIUrl":"10.1146/annurev-physchem-083122-122157","url":null,"abstract":"<p><p>Experimental studies of the collision phenomena of submicrometer particles is a developing field. This review examines the range of phenomena that can be observed with new experimental approaches. The primary focus is on single-particle impact studies enabled by charge detection mass spectrometry (CDMS) implemented using the Aerosol Impact Spectrometer (AIS) at the University of California, San Diego. The AIS combines electrospray ionization, aerodynamic lens techniques, CDMS, and an electrostatic linear accelerator to study the dynamics of particle impact over a wide range of incident velocities. The AIS has been used for single-particle impact experiments on positively charged particles of diverse composition, including polystyrene latex spheres, tin particles, and ice grains, over a wide range of impact velocities. Detection schemes based on induced charge measurements and time-of-flight mass spectrometry have enabled measurements of the impact inelasticity through the determination of the coefficient of restitution, measurements of the angular distributions of scattered submicrometer particles, and the chemical composition and dissociation of solute molecules in hypervelocity ice grain impacts.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"75 1","pages":"67-88"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465728","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
Chemical Kinetics in Microdroplets. 微滴中的化学动力学
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 Epub Date: 2024-06-14 DOI: 10.1146/annurev-physchem-052623-120718
Kevin R Wilson, Alexander M Prophet
{"title":"Chemical Kinetics in Microdroplets.","authors":"Kevin R Wilson, Alexander M Prophet","doi":"10.1146/annurev-physchem-052623-120718","DOIUrl":"10.1146/annurev-physchem-052623-120718","url":null,"abstract":"<p><p>Micrometer-sized compartments play significant roles in driving heterogeneous transformations within atmospheric and biochemical systems as well as providing vehicles for drug delivery and novel reaction environments for the synthesis of industrial chemicals. Many reports now indicate that reaction kinetics are accelerated under microconfinement, for example, in sprays, thin films, droplets, aerosols, and emulsions. These observations are dramatic, posing a challenge to our understanding of chemical reaction mechanisms with potentially significant practical consequences for predicting the complex chemistry in natural systems. Here we introduce the idea of kinetic confinement, which is intended to provide a conceptual backdrop for understanding when and why microdroplet reaction kinetics differ from their macroscale analogs.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"185-208"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929655","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
Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity. 脂质景观：用于解码膜复杂性的振动光谱学。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 Epub Date: 2024-06-14 DOI: 10.1146/annurev-physchem-090722-010230
Xiaobing Chen, Ziareena A Al-Mualem, Carlos R Baiz
{"title":"Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity.","authors":"Xiaobing Chen, Ziareena A Al-Mualem, Carlos R Baiz","doi":"10.1146/annurev-physchem-090722-010230","DOIUrl":"10.1146/annurev-physchem-090722-010230","url":null,"abstract":"<p><p>Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"283-305"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929657","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
Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. 活细胞中物理化学参数的单分子光谱和超分辨率绘图。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 Epub Date: 2024-06-14 DOI: 10.1146/annurev-physchem-070623-034225
Megan A Steves, Changdong He, Ke Xu
{"title":"Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells.","authors":"Megan A Steves, Changdong He, Ke Xu","doi":"10.1146/annurev-physchem-070623-034225","DOIUrl":"10.1146/annurev-physchem-070623-034225","url":null,"abstract":"<p><p>By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"163-183"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139740207","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
Machine Learning of Reactive Potentials. 反应电位的机器学习。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 DOI: 10.1146/annurev-physchem-062123-024417
Yinuo Yang, Shuhao Zhang, Kavindri D Ranasinghe, Olexandr Isayev, Adrian E Roitberg
{"title":"Machine Learning of Reactive Potentials.","authors":"Yinuo Yang, Shuhao Zhang, Kavindri D Ranasinghe, Olexandr Isayev, Adrian E Roitberg","doi":"10.1146/annurev-physchem-062123-024417","DOIUrl":"10.1146/annurev-physchem-062123-024417","url":null,"abstract":"<p><p>In the past two decades, machine learning potentials (MLPs) have driven significant developments in chemical, biological, and material sciences. The construction and training of MLPs enable fast and accurate simulations and analysis of thermodynamic and kinetic properties. This review focuses on the application of MLPs to reaction systems with consideration of bond breaking and formation. We review the development of MLP models, primarily with neural network and kernel-based algorithms, and recent applications of reactive MLPs (RMLPs) to systems at different scales. We show how RMLPs are constructed, how they speed up the calculation of reactive dynamics, and how they facilitate the study of reaction trajectories, reaction rates, free energy calculations, and many other calculations. Different data sampling strategies applied in building RMLPs are also discussed with a focus on how to collect structures for rare events and how to further improve their performance with active learning.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"75 1","pages":"371-395"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465675","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
Multielectron Dynamics in the Condensed Phase: Quantum Structure-Function Relationships. 凝聚相中的多电子动力学：量子结构-功能关系
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 DOI: 10.1146/annurev-physchem-042018-052515
Joel D Eaves
{"title":"Multielectron Dynamics in the Condensed Phase: Quantum Structure-Function Relationships.","authors":"Joel D Eaves","doi":"10.1146/annurev-physchem-042018-052515","DOIUrl":"10.1146/annurev-physchem-042018-052515","url":null,"abstract":"<p><p>Quantum information promises dramatic advances in computing last seen in the digital revolution, but quantum hardware is fragile, noisy, and resource intensive. Chemistry has a role in developing new materials for quantum information that are robust to noise, scalable, and operable in ambient conditions. While molecular structure is the foundation for understanding mechanism and reactivity, molecular structure/quantum function relationships remain mostly undiscovered. Using singlet fission as a specific example of a multielectron process capable of producing long-lived spin-entangled electronic states at high temperatures, I describe how to exploit molecular structure and symmetry to gain quantum function and how some principles learned from singlet fission apply more broadly to quantum science.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"75 1","pages":"437-456"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465676","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
Spectroscopy in Nanoscopic Cavities: Models and Recent Experiments. 纳米空腔中的光谱学：模型与最新实验
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 DOI: 10.1146/annurev-physchem-083122-125525
Marc R Bourgeois, Feng Pan, C Praise Anyanwu, Austin G Nixon, Elliot K Beutler, Jennifer A Dionne, Randall H Goldsmith, David J Masiello
{"title":"Spectroscopy in Nanoscopic Cavities: Models and Recent Experiments.","authors":"Marc R Bourgeois, Feng Pan, C Praise Anyanwu, Austin G Nixon, Elliot K Beutler, Jennifer A Dionne, Randall H Goldsmith, David J Masiello","doi":"10.1146/annurev-physchem-083122-125525","DOIUrl":"10.1146/annurev-physchem-083122-125525","url":null,"abstract":"<p><p>The ability of nanophotonic cavities to confine and store light to nanoscale dimensions has important implications for enhancing molecular, excitonic, phononic, and plasmonic optical responses. Spectroscopic signatures of processes that are ordinarily exceedingly weak such as pure absorption and Raman scattering have been brought to the single-particle limit of detection, while new emergent polaritonic states of optical matter have been realized through coupling material and photonic cavity degrees of freedom across a wide range of experimentally accessible interaction strengths. In this review, we discuss both optical and electron beam spectroscopies of cavity-coupled material systems in weak, strong, and ultrastrong coupling regimes, providing a theoretical basis for understanding the physics inherent to each while highlighting recent experimental advances and exciting future directions.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"75 1","pages":"509-534"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465727","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
Prebiotic Astrochemistry from Astronomical Observations and Laboratory Spectroscopy. 从天文观测和实验室光谱学看前生物天体化学。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 Epub Date: 2024-06-14 DOI: 10.1146/annurev-physchem-090722-010849
Lucy M Ziurys
{"title":"Prebiotic Astrochemistry from Astronomical Observations and Laboratory Spectroscopy.","authors":"Lucy M Ziurys","doi":"10.1146/annurev-physchem-090722-010849","DOIUrl":"10.1146/annurev-physchem-090722-010849","url":null,"abstract":"<p><p>The discovery of more than 200 gas-phase chemical compounds in interstellar space has led to the speculation that this nonterrestrial synthesis may play a role in the origin of life. These identifications were possible because of laboratory spectroscopy, which provides the molecular fingerprints for astronomical observations. Interstellar chemistry produces a wide range of small, organic molecules in dense clouds, such as NH<sub>2</sub>COCH<sub>3</sub>, CH<sub>3</sub>OCH<sub>3</sub>, CH<sub>3</sub>COOCH<sub>3</sub>, and CH<sub>2</sub>(OH)CHO. Carbon (C) is also carried in the fullerenes C<sub>60</sub> and C<sub>70</sub>, which can preserve C-C bonds from circumstellar environments for future synthesis. Elusive phosphorus has now been found in molecular clouds, the sites of star formation, in the molecules PO and PN. Such clouds can collapse into solar systems, although the chemical/physical processing of the emerging planetary disk is uncertain. The presence of molecule-rich interstellar starting material, as well as the link to planetary bodies such as meteorites and comets, suggests that astrochemical processes set a prebiotic foundation.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"307-327"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929661","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
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