Pub Date : 2024-06-01Epub Date: 2024-06-14DOI: 10.1146/annurev-physchem-090722-010230
Xiaobing Chen, Ziareena A Al-Mualem, Carlos R Baiz
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.
{"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":null,"pages":null},"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}
Pub Date : 2024-06-01Epub Date: 2024-06-14DOI: 10.1146/annurev-physchem-070623-034225
Megan A Steves, Changdong He, Ke Xu
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.
{"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":null,"pages":null},"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}
Pub Date : 2024-06-01DOI: 10.1146/annurev-physchem-062123-024417
Yinuo Yang, Shuhao Zhang, Kavindri D Ranasinghe, Olexandr Isayev, Adrian E Roitberg
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.
{"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":null,"pages":null},"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}
Pub Date : 2024-06-01DOI: 10.1146/annurev-physchem-042018-052515
Joel D Eaves
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.
{"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":null,"pages":null},"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}
Pub Date : 2024-06-01DOI: 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
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.
{"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":null,"pages":null},"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}
Pub Date : 2024-06-01Epub Date: 2024-06-14DOI: 10.1146/annurev-physchem-090722-125031
Connor J Clarke, Jan R R Verlet
Gas-phase anions present an ideal playground for the exploration of excited-state dynamics. They offer control in terms of the mass, extent of solvation, internal temperature, and conformation. The application of a range of ion sources has opened the field to a vast array of anionic systems whose dynamics are important in areas ranging from biology to star formation. Here, we review recent experimental developments in the field of anion photodynamics, demonstrating the detailed insight into photodynamical and electron-capture processes that can be uncovered. We consider the electronic and nuclear ultrafast dynamics of electronically bound excited states along entire reaction coordinates; electronically unbound states showing that photochemical concepts, such as chromophores and Kasha's rule, are transferable to electron-driven chemistry; and nonvalence states that straddle the interface between bound and unbound states. Finally, we consider likely developments that are sure to keep the field of anion dynamics buoyant and impactful.
{"title":"Dynamics of Anions: From Bound to Unbound States and Everything In Between.","authors":"Connor J Clarke, Jan R R Verlet","doi":"10.1146/annurev-physchem-090722-125031","DOIUrl":"10.1146/annurev-physchem-090722-125031","url":null,"abstract":"<p><p>Gas-phase anions present an ideal playground for the exploration of excited-state dynamics. They offer control in terms of the mass, extent of solvation, internal temperature, and conformation. The application of a range of ion sources has opened the field to a vast array of anionic systems whose dynamics are important in areas ranging from biology to star formation. Here, we review recent experimental developments in the field of anion photodynamics, demonstrating the detailed insight into photodynamical and electron-capture processes that can be uncovered. We consider the electronic and nuclear ultrafast dynamics of electronically bound excited states along entire reaction coordinates; electronically unbound states showing that photochemical concepts, such as chromophores and Kasha's rule, are transferable to electron-driven chemistry; and nonvalence states that straddle the interface between bound and unbound states. Finally, we consider likely developments that are sure to keep the field of anion dynamics buoyant and impactful.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139566199","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}
Pub Date : 2024-06-01Epub Date: 2024-06-14DOI: 10.1146/annurev-physchem-090722-010849
Lucy M Ziurys
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 NH2COCH3, CH3OCH3, CH3COOCH3, and CH2(OH)CHO. Carbon (C) is also carried in the fullerenes C60 and C70, 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.
{"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":null,"pages":null},"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}
Large strides have been made in designing an ever-increasing set of modern organic materials of high functionality and thus, often, of high complexity, including semiconducting polymers, organic ferroelectrics, light-emitting small molecules, and beyond. Here, we review how broadly applied thermal analysis methodologies, especially differential scanning calorimetry, can be utilized to provide unique information on the assembly and solid-state structure of this extensive class of materials, as well as the phase behavior of intrinsically intricate multicomponent systems. Indeed, highly relevant insights can be gained that are useful, e.g., for further materials-discovery activities and the establishment of reliable processing protocols, in particular if combined with X-ray diffraction techniques, spectroscopic tools, and scanning electron microscopy enabled by vapor-phase infiltration staining. We, hence, illustrate that insights far richer than simple melting point- and glass-transition identification can be obtained with differential scanning calorimetry, rendering it a critical methodology to understand complex matter, including functional macromolecules and blends.
在设计越来越多的高功能现代有机材料方面取得了长足进步,因此这些材料往往具有很高的复杂性,包括半导体聚合物、有机铁电体、发光小分子等。在此,我们回顾了如何利用广泛应用的热分析方法(尤其是差示扫描量热法)来提供有关这一大类材料的组装和固态结构的独特信息,以及内在错综复杂的多组分系统的相行为。事实上,结合 X 射线衍射技术、光谱工具和气相渗透染色扫描电子显微镜,可以获得非常有用的见解,例如有助于进一步的材料发现活动和建立可靠的加工协议。因此,我们说明,利用差示扫描量热法可以获得比简单的熔点和玻璃跃迁鉴定更丰富的见解,使其成为了解复杂物质(包括功能性大分子和混合物)的重要方法。物理化学年刊》第 75 卷的最终在线出版日期预计为 2024 年 4 月。修订后的预计日期请参见 http://www.annualreviews.org/page/journal/pubdates。
{"title":"Understanding Organic Photovoltaic Materials Using Simple Thermal Analysis Methodologies.","authors":"Aditi Khirbat, Oded Nahor, Sara Marina Barbier, Artem Levitsky, Jaime Martín, Gitti Frey, Natalie Stingelin","doi":"10.1146/annurev-physchem-070723-035427","DOIUrl":"10.1146/annurev-physchem-070723-035427","url":null,"abstract":"<p><p>Large strides have been made in designing an ever-increasing set of modern organic materials of high functionality and thus, often, of high complexity, including semiconducting polymers, organic ferroelectrics, light-emitting small molecules, and beyond. Here, we review how broadly applied thermal analysis methodologies, especially differential scanning calorimetry, can be utilized to provide unique information on the assembly and solid-state structure of this extensive class of materials, as well as the phase behavior of intrinsically intricate multicomponent systems. Indeed, highly relevant insights can be gained that are useful, e.g., for further materials-discovery activities and the establishment of reliable processing protocols, in particular if combined with X-ray diffraction techniques, spectroscopic tools, and scanning electron microscopy enabled by vapor-phase infiltration staining. We, hence, illustrate that insights far richer than simple melting point- and glass-transition identification can be obtained with differential scanning calorimetry, rendering it a critical methodology to understand complex matter, including functional macromolecules and blends.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995335","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}
Pub Date : 2024-06-01Epub Date: 2024-06-14DOI: 10.1146/annurev-physchem-090722-010601
Sergei Rudnizky, Peter J Murray, Clara H Wolfe, Taekjip Ha
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
{"title":"Single-Macromolecule Studies of Eukaryotic Genomic Maintenance.","authors":"Sergei Rudnizky, Peter J Murray, Clara H Wolfe, Taekjip Ha","doi":"10.1146/annurev-physchem-090722-010601","DOIUrl":"10.1146/annurev-physchem-090722-010601","url":null,"abstract":"<p><p>Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929662","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}
Pub Date : 2024-06-01Epub Date: 2024-06-14DOI: 10.1146/annurev-physchem-083122-121620
David T Limmer, Andreas W Götz, Timothy H Bertram, Gilbert M Nathanson
Atmospheric aerosols facilitate reactions between ambient gases and dissolved species. Here, we review our efforts to interrogate the uptake of these gases and the mechanisms of their reactions both theoretically and experimentally. We highlight the fascinating behavior of N2O5 in solutions ranging from pure water to complex mixtures, chosen because its aerosol-mediated reactions significantly impact global ozone, hydroxyl, and methane concentrations. As a hydrophobic, weakly soluble, and highly reactive species, N2O5 is a sensitive probe of the chemical and physical properties of aerosol interfaces. We employ contemporary theory to disentangle the fate of N2O5 as it approaches pure and salty water, starting with adsorption and ending with hydrolysis to HNO3, chlorination to ClNO2, or evaporation. Flow reactor and gas-liquid scattering experiments probe even greater complexity as added ions, organic molecules, and surfactants alter the interfacial composition and reaction rates. Together, we reveal a new perspective on multiphase chemistry in the atmosphere.
{"title":"Molecular Insights into Chemical Reactions at Aqueous Aerosol Interfaces.","authors":"David T Limmer, Andreas W Götz, Timothy H Bertram, Gilbert M Nathanson","doi":"10.1146/annurev-physchem-083122-121620","DOIUrl":"10.1146/annurev-physchem-083122-121620","url":null,"abstract":"<p><p>Atmospheric aerosols facilitate reactions between ambient gases and dissolved species. Here, we review our efforts to interrogate the uptake of these gases and the mechanisms of their reactions both theoretically and experimentally. We highlight the fascinating behavior of N<sub>2</sub>O<sub>5</sub> in solutions ranging from pure water to complex mixtures, chosen because its aerosol-mediated reactions significantly impact global ozone, hydroxyl, and methane concentrations. As a hydrophobic, weakly soluble, and highly reactive species, N<sub>2</sub>O<sub>5</sub> is a sensitive probe of the chemical and physical properties of aerosol interfaces. We employ contemporary theory to disentangle the fate of N<sub>2</sub>O<sub>5</sub> as it approaches pure and salty water, starting with adsorption and ending with hydrolysis to HNO<sub>3</sub>, chlorination to ClNO<sub>2</sub>, or evaporation. Flow reactor and gas-liquid scattering experiments probe even greater complexity as added ions, organic molecules, and surfactants alter the interfacial composition and reaction rates. Together, we reveal a new perspective on multiphase chemistry in the atmosphere.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":null,"pages":null},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139740206","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}