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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2022-04-20 DOI: 10.1146/annurev-physchem-082720-123928
Sarah E Biehn, Steffen Lindert
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.
蛋白质结构的知识对于我们理解生物功能是至关重要的,并且经常用于药物发现。确定蛋白质三维原子坐标的高分辨率技术是可用的。然而,这些方法经常受到实验挑战的限制,如样本数量、目标大小和效率。结构质谱法(MS)是一种快速且相对容易地阐明蛋白质结构特征的技术。需要将稀疏的MS数据转换为与数据一致的蛋白质模型的计算技术。这篇综述采用了尖端的计算方法,从质谱数据预测蛋白质结构,如化学交联,氢-氘交换,羟基自由基蛋白质足迹,有限的蛋白质水解,离子迁移率和表面诱导解离。此外,我们还讨论了用稀疏MS数据预测蛋白质结构的未来方向。
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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 Q1 CHEMISTRY, PHYSICAL 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

Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.

结合量子力学和经典描述的多尺度模型是一种非常流行的模拟复杂系统性质和过程的策略。许多替代配方已经被开发出来,它们现在可以在所有最广泛使用的量子化学包中使用。然而,它们在光驱动过程研究中的应用是最近才出现的,一些方法和数值问题还有待解决。这对于这些模型的可极化公式来说尤其如此,我们在这里回顾一下最近的进展。具体来说,我们确定并描述了极化公式引入激发态动力学模拟和激发态能量和电子转移过程建模的最重要的特性。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2021-04-20 Epub Date: 2021-02-12 DOI: 10.1146/annurev-physchem-090419-044828
Hiroshi Masuhara, Ken-Ichi Yuyama

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.

当强烈的1064纳米连续波激光紧紧聚焦在溶液表面时,它会对分子、聚合物和纳米颗粒(NPs)施加光力。最初,分子和NPs在焦点内聚集成一个单一的组件,激光在组件中散射和传播。扩展的激光进一步将它们困在组件的边缘,产生一个比表面聚焦大得多的组件。氨基酸和无机离子化合物经历结晶和晶体生长,聚苯乙烯NPs形成同心圆或六边形填充的周期性阵列和盘状结构,Au NPs表现出组装和蜂群,其中NPs像一群蜜蜂一样波动。这些依赖于激光偏振的现象被称为溶液表面的光演化聚集,本文对其动力学和机制进行了阐述。介绍了卤化铅钙钛矿、超分子和聚集诱导发射增强活性分子的光阱组装方法,并讨论了今后的基础研究方向。
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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 Q1 CHEMISTRY, PHYSICAL 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

Lateral organization in the plane of the plasma membrane is an important driver of biological processes. The past dozen years have seen increasing experimental support for the notion that lipid organization plays an important role in modulating this heterogeneity. Various biophysical mechanisms rooted in the concept of liquid-liquid phase separation have been proposed to explain diverse experimental observations of heterogeneity in model and cell membranes with distinct but overlapping applicability. In this review, we focus on the evidence for and the consequences of the hypothesis that the plasma membrane is poised near an equilibrium miscibility critical point. Critical phenomena explain certain features of the heterogeneity observed in cells and model systems but also go beyond heterogeneity to predict other interesting phenomena, including responses to perturbations in membrane composition.

质膜平面上的横向组织是生物过程的重要驱动力。在过去的十几年中,越来越多的实验支持了脂质组织在调节这种异质性中起重要作用的观点。基于液-液相分离概念的各种生物物理机制被提出来解释模型和细胞膜异质性的不同实验观察,具有不同但重叠的适用性。在这篇综述中,我们集中在证据和假设的后果,质膜是平衡混相临界点附近。临界现象解释了在细胞和模型系统中观察到的异质性的某些特征,但也超越了异质性来预测其他有趣的现象,包括对膜成分扰动的响应。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2021-04-20 Epub Date: 2021-12-04 DOI: 10.1146/annurev-physchem-090519-124238
Robert Benny Gerber
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.
这是一个在理论化学领域的职业生涯的故事,在这个领域由于计算能力的显著增长而发生了巨大的变化。同样,我也有幸在我的职业生涯中指导过那些极具天赋的研究生和博士后。它包括对我的伟大导师的回忆,以及与实验家和理论家的令人兴奋的合作,我的大部分研究都建立在这些合作的基础上。这是一个关于我参与的令人兴奋的科学学科发展的描述:振动光谱学,分子反应机制和动力学,例如,在大气化学中,以及新的外来分子的预测,特别是稀有气体分子。从我的第一个项目到我现在的工作,我的科学生涯给我带来了研究的兴奋和魅力。多么美妙的追求啊!
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2021-04-20 Epub Date: 2021-01-27 DOI: 10.1146/annurev-physchem-090319-054423
Ruth M Lynden-Bell

I describe some of the science that I have been involved in during the last 60 years and the changes in equipment that made it possible. Starting with an interest in spectroscopy and measurement of NMR parameters, I moved to work on theoretical aspects of spin systems and infrared and Raman line shapes. This morphed into using the new technique of computer simulation to study such problems. The last half of my working life has concentrated on the application of computer simulation to a number of problems culminating in pioneering investigations of the behavior of ionic liquids.

我描述了我在过去60年里参与的一些科学研究,以及使其成为可能的设备的变化。从对光谱学和核磁共振参数测量的兴趣开始,我开始研究自旋系统和红外和拉曼线形状的理论方面。这演变为使用计算机模拟的新技术来研究这类问题。我的工作生涯的最后一半集中在计算机模拟在一些问题上的应用,最终在离子液体行为的开创性研究中达到高潮。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2021-04-20 DOI: 10.1146/annurev-physchem-090419-043839
Prachi Sharma, Jie J Bao, Donald G Truhlar, Laura Gagliardi

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.

具有交换相关泛函的Kohn-Sham密度泛函理论对强相关系统的准确性较低,强相关系统需要多构型描述为零阶函数,而弱相关系统则需要多构型描述,并且当使用具有自旋对称性的多构型波函数时,自旋密度的可用泛函不能准确预测许多强相关系统的能量。此外,在多构型参考能量中加入相关泛函可以导致电子相关的重复计数。多组态对密度泛函理论(MC-PDFT)克服了这两个障碍,第二个是完全通过一个泛函来计算电子能量的量子力学部分,第一个是使用总密度和上对密度的泛函而不是自旋密度。这允许人们用对密度泛函和合适的多构型参考函数有效地计算强相关系统的能量。本文综述了MC-PDFT及其相关背景资料。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2021-04-20 Epub Date: 2021-01-27 DOI: 10.1146/annurev-physchem-090519-051837
Ernesto Quintas-Sánchez, Richard Dawes

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.

波恩-奥本海默势能面(Born-Oppenheimer potential energy surface, PES)自20世纪20年代问世以来,无论是在概念上还是在实际应用中的预测能力方面,都取得了长足的进步。然而,近100年后,尽管计算能力取得了惊人的进步,但与光谱学和散射动力学有关的最先进的第一性原理预测却令人惊讶地有限。例如,水二聚体(H2O)2,只有6个原子核和20个电子,对于束缚态的全维变分计算仍然是一个巨大的挑战,并且被认为是严格的散射计算所无法达到的。最严格的量子方法的标度极差是根本问题;然而,近似方法发展的最新进展为相当常规的高质量预测打开了大门,这在20年前是不可想象的。本文就光谱学和/或散射研究的工作流程,总结了电子结构计算、PES拟合和量子动力学计算等组成领域的进展和挑战。
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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 Q1 CHEMISTRY, PHYSICAL Pub Date : 2021-04-20 Epub Date: 2021-03-01 DOI: 10.1146/annurev-physchem-061020-053456
Helen J Zeng, Mark A Johnson

The ease with which the pH is routinely determined for aqueous solutions masks the fact that the cationic product of Arrhenius acid dissolution, the hydrated proton, or H+(aq), is a remarkably complex species. Here, we review how results obtained over the past 30 years in the study of H+⋅(H2O)n cluster ions isolated in the gas phase shed light on the chemical nature of H+(aq). This effort has also revealed molecular-level aspects of the Grotthuss relay mechanism for positive-charge translocation in water. Recently developed methods involving cryogenic cooling in radiofrequency ion traps and the application of two-color, infrared-infrared (IR-IR) double-resonance spectroscopy have established a clear picture of how local hydrogen-bond topology drives the diverse spectral signatures of the excess proton. This information now enables a new generation of cluster studies designed to unravel the microscopic mechanics underlying the ultrafast relaxation dynamics displayed by H+(aq).

通常测定水溶液的pH值很容易,这掩盖了一个事实,即阿伦尼乌斯酸溶解的阳离子产物,水合质子,或H+(aq),是一个非常复杂的物质。在这里,我们回顾了过去30年来在气相分离H+⋅(H2O)n簇离子的研究中获得的结果如何揭示了H+(aq)的化学性质。这项工作还揭示了Grotthuss接力机制在水中正电荷转运的分子水平方面。最近发展的方法包括射频离子阱中的低温冷却和双色红外-红外(IR-IR)双共振光谱的应用,已经建立了局部氢键拓扑如何驱动多余质子的各种光谱特征的清晰图像。这些信息使得新一代的簇研究能够揭示H+(aq)显示的超快弛豫动力学背后的微观力学。
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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 Q1 CHEMISTRY, PHYSICAL 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

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.

金属纳米粒子(NPs)的尺寸和形状控制增强光学响应被称为局域表面等离子体共振(LSPR)。LSPRs导致放大的表面和粒子间电场,从而增强与金属NPs耦合的分子或其他材料的光吸收和/或在NPs本身内产生热载流子。当由金属NPs介导时,光催化可以利用这种独特的光学现象。这篇综述强调了量子力学建模在理解和指导当前尝试结合等离子体激发来改善多相催化反应动力学方面的贡献。从基态密度泛函理论(DFT)到激发态理论(如多参考相关波函数方法),一系列第一性原理量子力学技术提供了见解。本文讨论了这些方法在精确捕获等离子体效应方面的优点和局限性,并给出了相应的例子。
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引用次数: 25
期刊
Annual review of physical chemistry
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