质子在水性和生物分子体系中的溶剂化与传输：计算机模拟的见解
Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.
作者信息
Swanson Jessica M J, Maupin C Mark, Chen Hanning, Petersen Matt K, Xu Jiancong, Wu Yujie, Voth Gregory A
机构信息
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850, USA.
出版信息
J Phys Chem B. 2007 May 3;111(17):4300-14. doi: 10.1021/jp070104x. Epub 2007 Apr 13.
Abstract
The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article, various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water.
摘要
水介质中的过量质子在许多基础化学过程（如酸碱化学）和生物过程（如生物能量学和酶催化）中起着关键作用。因此，了解水合质子对于化学、生物学和材料科学至关重要。尽管对其进行了200多年的深入研究，但过量质子的溶剂化和传输至今仍然神秘、令人惊讶，甚至可能被误解。在这篇专题文章中，将描述通过计算机建模和模拟来解决这一问题的各种努力。将展示计算机模拟在一些重要且有趣的系统中的应用，突出电荷离域和Grotthuss穿梭的作用，这是一种在许多方面对于水中过量质子而言独一无二的现象。
相似文献
1
Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.质子在水性和生物分子体系中的溶剂化与传输：计算机模拟的见解
J Phys Chem B. 2007 May 3;111(17):4300-14. doi: 10.1021/jp070104x. Epub 2007 Apr 13.
2
Computer simulation of proton solvation and transport in aqueous and biomolecular systems.质子在水性和生物分子体系中的溶剂化作用与输运的计算机模拟。
Acc Chem Res. 2006 Feb;39(2):143-50. doi: 10.1021/ar0402098.
3
The curious case of the hydrated proton.水合质子的奇案。
Acc Chem Res. 2012 Jan 17;45(1):101-9. doi: 10.1021/ar200140h. Epub 2011 Aug 22.
4
Hydrated Excess Protons Can Create Their Own Water Wires.水合过量质子可形成自身的水线。
J Phys Chem B. 2015 Jul 23;119(29):9212-8. doi: 10.1021/jp5095118. Epub 2014 Nov 12.
5
Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane nafion.质子传导聚合物膜Nafion亲水口袋中的过量质子溶剂化和离域。
J Phys Chem B. 2005 Mar 10;109(9):3727-30. doi: 10.1021/jp044535g.
6
An improved multistate empirical valence bond model for aqueous proton solvation and transport.一种用于水合质子溶剂化和传输的改进多态经验价键模型。
J Phys Chem B. 2008 Jan 17;112(2):467-82. doi: 10.1021/jp076658h. Epub 2007 Nov 14.
7
Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion.全氟磺酸膜Nafion中水合质子的溶剂化作用及传输特性
J Phys Chem B. 2006 Sep 21;110(37):18594-600. doi: 10.1021/jp062719k.
8
Hydrated excess proton at water-hydrophobic interfaces.水-疏水性界面处的水合过量质子。
J Phys Chem B. 2009 Apr 2;113(13):4017-30. doi: 10.1021/jp805304j.
9
A modified two-state empirical valence bond model for proton transport in aqueous solutions.一种用于水溶液中质子传输的改进型双态经验价键模型。
J Chem Phys. 2015 Jul 7;143(1):014501. doi: 10.1063/1.4926394.
10
Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects.沿短杆菌肽通道的质子传输的真实模拟：证明溶剂化效应的重要性。
J Phys Chem B. 2005 Jan 13;109(1):583-92. doi: 10.1021/jp0465783.
引用本文的文献
1
Structural and ion transport characteristics of transparent proton conducting biopolymer electrolytes based on chitosan and cold water fish skin gelatin.基于壳聚糖和冷水鱼皮明胶的透明质子传导生物聚合物电解质的结构与离子传输特性
Sci Rep. 2025 Aug 19;15(1):30475. doi: 10.1038/s41598-025-15193-4.
2
Acid-Base Chemistry of Short Hydrogen Bonds: A Tale of Schrödinger's Cat in Glutamine-Derived Crystals.短氢键的酸碱化学：谷氨酰胺衍生晶体中的薛定谔猫的故事
J Phys Chem Lett. 2025 Aug 21;16(33):8588-8595. doi: 10.1021/acs.jpclett.5c01499. Epub 2025 Aug 13.
3
An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection.硅藻光捕获复合体中意想不到的水通道：对光捕获与光保护转换的启示
ACS Phys Chem Au. 2024 Aug 21;5(1):47-61. doi: 10.1021/acsphyschemau.4c00069. eCollection 2025 Jan 22.
4
Femtosecond Electron-Transfer Dynamics across the DO/Cs/Cu(111) Interface: The Impact of Hydrogen Bonding.飞秒电子在DO/Cs/Cu(111)界面间的转移动力学：氢键的影响
J Phys Chem C Nanomater Interfaces. 2023 Nov 17;127(48):23467-23474. doi: 10.1021/acs.jpcc.3c06172. eCollection 2023 Dec 7.
5
-Heterocyclic Carbene Formation in the Ionic Liquid [EMIM][OAc]: Elucidating Solvation Effects with Reactive Molecular Dynamics Simulations.[EMIM][OAc]离子液体中杂环卡宾的形成：用反应分子动力学模拟阐明溶剂化效应。
J Phys Chem B. 2023 Jun 15;127(23):5317-5333. doi: 10.1021/acs.jpcb.3c02064. Epub 2023 Jun 6.
6
Search for a Grotthuss mechanism through the observation of proton transfer.通过观察质子转移来寻找一种Grotthuss机制。
Commun Chem. 2023 Apr 22;6(1):77. doi: 10.1038/s42004-023-00878-6.
7
Accurate p Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values.准确的 p 值计算在蛋白质中的反应分子动力学提供物理洞察到他们的价值观的静电起源。
J Phys Chem B. 2022 Sep 29;126(38):7321-7330. doi: 10.1021/acs.jpcb.2c04899. Epub 2022 Sep 15.
8
Comparison of proton transfer paths to the Q and Q sites of the Rb. sphaeroides photosynthetic reaction centers.比较质子转移路径到 Rb. sphaeroides 光合反应中心的 Q 和 Q 位点。
Photosynth Res. 2022 May;152(2):153-165. doi: 10.1007/s11120-022-00906-x. Epub 2022 Mar 28.
9
The Solvation-Induced Onsager Reaction Field Rather than the Double-Layer Field Controls CO Reduction on Gold.溶剂化诱导的昂萨格反应场而非双层场控制金表面的CO还原反应。
JACS Au. 2022 Jan 28;2(2):472-482. doi: 10.1021/jacsau.1c00512. eCollection 2022 Feb 28.
10
A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces.水辅助质子通过蛋白质和其他受限空间的定量范式。
Proc Natl Acad Sci U S A. 2021 Dec 7;118(49). doi: 10.1073/pnas.2113141118.
本文引用的文献
1
Aqueous Solution/Air Interfaces Probed with Sum Frequency Generation Spectroscopy.用和频振动光谱探测水溶液/空气界面
J Phys Chem B. 2002 May 30;106(21):5313-5324. doi: 10.1021/jp014466v.
2
Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster.质子在细胞色素C氧化酶d通路氢键网络中的过量储存：质子化水簇的鉴定。
J Am Chem Soc. 2007 Mar 14;129(10):2910-3. doi: 10.1021/ja067360s. Epub 2007 Feb 20.
3
Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules.用于有机分子的SCC-DFTB和基于NDDO的半经验分子轨道方法的比较。
J Phys Chem A. 2006 Dec 21;110(50):13551-9. doi: 10.1021/jp064544k.
4
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.溶液和酶中远程质子转移反应中的“质子空穴”：理论分析
J Am Chem Soc. 2006 Dec 20;128(50):16302-11. doi: 10.1021/ja065451j.
5
Spectroscopic studies of solvated hydrogen and hydroxide ions at aqueous surfaces.水溶液表面溶剂化氢离子和氢氧根离子的光谱研究。
J Am Chem Soc. 2006 Nov 15;128(45):14519-27. doi: 10.1021/ja063184b.
6
Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit.基于在完备基组极限下进行的从头算分子动力学研究常温液态水的结构
J Chem Phys. 2006 Oct 21;125(15):154507. doi: 10.1063/1.2354158.
7
Charge delocalization in proton channels, I: the aquaporin channels and proton blockage.质子通道中的电荷离域，I：水通道蛋白通道与质子阻断
Biophys J. 2007 Jan 1;92(1):46-60. doi: 10.1529/biophysj.106.091934. Epub 2006 Oct 20.
8
Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity.质子通道中的电荷离域，II：合成的LS2通道与质子选择性。
Biophys J. 2007 Jan 1;92(1):61-9. doi: 10.1529/biophysj.106.091942. Epub 2006 Oct 20.
9
Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.在膜蛋白细胞色素c氧化酶的高分辨率结构中鉴定保守的脂质/去污剂结合位点。
Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16117-22. doi: 10.1073/pnas.0606149103. Epub 2006 Oct 18.
10
Mechanisms of passive ion permeation through lipid bilayers: insights from simulations.脂质双分子层被动离子渗透机制：模拟研究的见解
J Phys Chem B. 2006 Oct 26;110(42):21327-37. doi: 10.1021/jp064192h.
Zotero 插件