1
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Dodia M, Rouxel JR, Cho D, Zhang Y, Keefer D, Bonn M, Nagata Y, Mukamel S. Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer. J Chem Theory Comput 2024; 20:4254-4264. [PMID: 38727197 DOI: 10.1021/acs.jctc.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
We propose an X-ray Raman pump-X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information about the entire molecular ensemble. A combination of molecular dynamics and ab initio quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, we extracted solvation shell dynamics.
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Affiliation(s)
- Mayank Dodia
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Jérémy R Rouxel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Daeheum Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yu Zhang
- Ames National Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Daniel Keefer
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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2
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Hoang Ngoc Minh T, Kim J, Pireddu G, Chubak I, Nair S, Rotenberg B. Electrical noise in electrolytes: a theoretical perspective. Faraday Discuss 2023; 246:198-224. [PMID: 37409620 DOI: 10.1039/d3fd00026e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Seemingly unrelated experiments such as electrolyte transport through nanotubes, nano-scale electrochemistry, NMR relaxometry and surface force balance measurements, all probe electrical fluctuations: of the electric current, the charge and polarization, the field gradient (for quadrupolar nuclei) and the coupled mass/charge densities. The fluctuations of such various observables arise from the same underlying microscopic dynamics of the ions and solvent molecules. In principle, the relevant length and time scales of these dynamics are encoded in the dynamic structure factors. However, modelling the latter for frequencies and wavevectors spanning many orders of magnitude remains a great challenge to interpret the experiments in terms of physical processes such as solvation dynamics, diffusion, electrostatic and hydrodynamic interactions between ions, interactions with solid surfaces, etc. Here, we highlight the central role of the charge-charge dynamic structure factor in the fluctuations of electrical observables in electrolytes and offer a unifying perspective over a variety of complementary experiments. We further analyze this quantity in the special case of an aqueous NaCl electrolyte, using simulations with explicit ions and an explicit or implicit solvent. We discuss the ability of the standard Poisson-Nernst-Planck theory to capture the simulation results, and how the predictions can be improved. We finally discuss the contributions of ions and water to the total charge fluctuations. This work illustrates an ongoing effort towards a comprehensive understanding of electrical fluctuations in bulk and confined electrolytes, in order to enable experimentalists to decipher the microscopic properties encoded in the measured electrical noise.
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Affiliation(s)
- Thê Hoang Ngoc Minh
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France.
| | - Jeongmin Kim
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France.
| | - Giovanni Pireddu
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France.
| | - Iurii Chubak
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France.
| | - Swetha Nair
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France.
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France.
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
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3
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Schöller A, Woodcock HL, Boresch S. Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes. Molecules 2023; 28:4006. [PMID: 37241747 PMCID: PMC10222338 DOI: 10.3390/molecules28104006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Non-equilibrium work switching simulations and Jarzynski's equation are a reliable method for computing free energy differences, ΔAlow→high, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecular mechanical (QM/MM) description of a system of interest. Despite the inherent parallelism, the computational cost of this approach can quickly become very high. This is particularly true for systems where the core region, the part of the system to be described at different levels of theory, is embedded in an environment such as explicit solvent water. We find that even for relatively simple solute-water systems, switching lengths of at least 5 ps are necessary to compute ΔAlow→high reliably. In this study, we investigate two approaches towards an affordable protocol, with an emphasis on keeping the switching length well below 5 ps. Inserting a hybrid charge intermediate state with modified partial charges, which resembles the charge distribution of the desired high level, makes it possible to obtain reliable calculations with 2 ps switches. Attempts using step-wise linear switching paths, on the other hand, did not lead to improvement, i.e., a faster convergence for all systems. To understand these findings, we analyzed the solutes' properties as a function of the partial charges used and the number of water molecules in direct contact with the solute, and studied the time needed for water molecules to reorient themselves upon a change in the solute's charge distribution.
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Affiliation(s)
- Andreas Schöller
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währingerstr. 42, A-1090 Vienna, Austria
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250, USA;
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria
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4
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Abstract
The theory of electron transfer reactions establishes the conceptual foundation for redox solution chemistry, electrochemistry, and bioenergetics. Electron and proton transfer across the cellular membrane provide all energy of life gained through natural photosynthesis and mitochondrial respiration. Rates of biological charge transfer set kinetic bottlenecks for biological energy storage. The main system-specific parameter determining the activation barrier for a single electron-transfer hop is the reorganization energy of the medium. Both harvesting of light energy in natural and artificial photosynthesis and efficient electron transport in biological energy chains require reduction of the reorganization energy to allow fast transitions. This review article discusses mechanisms by which small values of the reorganization energy are achieved in protein electron transfer and how similar mechanisms can operate in other media, such as nonpolar and ionic liquids. One of the major mechanisms of reorganization energy reduction is through non-Gibbsian (nonergodic) sampling of the medium configurations on the reaction time. A number of alternative mechanisms, such as electrowetting of active sites of proteins, give rise to non-parabolic free energy surfaces of electron transfer. These mechanisms, and nonequilibrium population of donor-acceptor vibrations, lead to a universal phenomenology of separation between the Stokes shift and variance reorganization energies of electron transfer.
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Affiliation(s)
- Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA.
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5
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Hu K, Wang X, Li T. Explicit Projection of Stokes Shifts onto Solvent Motion in an Aqueous Liquid and Linear Response Theory. J Phys Chem B 2022; 126:9168-9175. [PMID: 36342144 DOI: 10.1021/acs.jpcb.2c05012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We investigate the molecular origin of the fluorescence Stokes shift in an aqueous liquid. By examining the speed of energy change, the solvation response function is explicitly projected onto the translational and rotational motions of water molecules for both nonequilibrium relaxation and equilibrium fluctuations. Molecular dynamics simulations of a tryptophan solution show that these two processes have highly consistent dynamics, not only for the total response function but also for the decomposed components in terms of specific molecular movements. We found that the rotational mode governs the relaxation of the Stokes shift, whereas the translational mode contributes non-negligibly with slower dynamics. This consistency implies the similarity of the underlying translational and rotational movements of water molecules as the system is far away from and at equilibrium, supporting the validity of the linear response theory at the molecular level. The decomposition methodology is also applicable to a rigid solvent.
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Affiliation(s)
- Kai Hu
- School of Physics, Xidian University, Xi'an 710071, People's Republic of China
| | - Xiaofang Wang
- School of Physics, Xidian University, Xi'an 710071, People's Republic of China
| | - Tanping Li
- School of Physics, Xidian University, Xi'an 710071, People's Republic of China
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6
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Ghosh S, Puranik M. Initial Excited State Dynamics of Lumichrome upon Ultraviolet Excitation. Photochem Photobiol 2022; 98:1270-1283. [PMID: 35380739 DOI: 10.1111/php.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
Lumichrome (LC) is the major photodegradation product of biologically important flavin cofactors. Since LC serves as a structural comparison to the flavins; understanding excited states of LC is fundamentally important to establish a connection with photophysics of different flavins, such as lumiflavin (LF), riboflavin (RF), flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Herein, we deduce the initial excited state structural dynamics of LC using UV resonance Raman (UVRR) intensity analysis. The UVRR spectra at wavelengths across the 260 nm absorption band of LC were measured and resulting Raman excitation profiles and absorption spectrum were self consistently simulated using a time-dependent wave packet formalism to extract the initial excited state structural and solvent broadening parameters. These results are compared with those obtained for other flavins following UV excitations. We find that LC undergoes a very distinct instantaneous charge redistribution than flavins, which is attributed to the extended π-conjugation present in flavins but missing in LC. The homogeneous broadening linewidth of LC appears to be lower than that of LF, while the inhomogeneous broadening values are comparable, indicating greater solvent interaction with excited flavin on ultrafast timescale compared to LC, whereas on longer timescale these interactions are almost similar.
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Affiliation(s)
- Sudeb Ghosh
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411 008, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411 008, India
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7
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Li Y, Qing L, Yu H, Peng Y, Xu X, Li P, Zhao S. Dynamical density functional theory for solvation dynamics in polar solvent: Heterogeneous effect of solvent orientation. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Petersen J, Møller KB, Hynes JT, Rey R. Ultrafast Rotational and Translational Energy Relaxation in Neat Liquids. J Phys Chem B 2021; 125:12806-12819. [PMID: 34762424 DOI: 10.1021/acs.jpcb.1c08014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The excess energy flow pathways during rotational and translational relaxation induced by rotational or translational excitation of a single molecule of and within each of four different neat liquids (H2O, MeOH, CCl4, and CH4) are studied using classical molecular dynamics simulations and energy flux analysis. For all four liquids, the relaxation processes for both types of excitation are ultrafast, but the energy flow is significantly faster for the polar, hydrogen-bonded (H-bonded) liquids H2O and MeOH. Whereas the majority of the initial excess energy is transferred into hindered rotations (librations) for rotational excitation in the H-bonded liquids, an almost equal efficiency for transfer to translational and rotational motions is observed in the nonpolar, non-H-bonded liquids CCl4 and CH4. For translational excitation, transfer to translational motions dominates for all liquids. In general, the energy flows are quite local; i.e., more than 70% of the energy flows directly to the first solvent shell molecules, reaching almost 100% for CCl4 and CH4. Finally, the determined validity of linear response theory for these nonequilibrium relaxation processes is quite solvent-dependent, with the deviation from linear response most marked for rotational excitation and for the nonpolar liquids.
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Affiliation(s)
- Jakob Petersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs. Lyngby, Denmark
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs. Lyngby, Denmark
| | - James T Hynes
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Rossend Rey
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
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9
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Brian D, Sun X. Linear-Response and Nonlinear-Response Formulations of the Instantaneous Marcus Theory for Nonequilibrium Photoinduced Charge Transfer. J Chem Theory Comput 2021; 17:2065-2079. [PMID: 33687212 DOI: 10.1021/acs.jctc.0c01250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Instantaneous Marcus theory (IMT) offers a way for capturing the time-dependent charge transfer (CT) rate coefficient in nonequilibrium photoinduced CT processes, where the system was photoexcited from its equilibrated ground state vertically to the excitonic state, followed by an electronic transition to the CT state. As derived from the linearized semiclassical nonequilibrium Fermi's golden rule (LSC NE-FGR), the original IMT requires expensive all-atom nonequilibrium molecular dynamics (NEMD) simulations. In this work, we propose computationally efficient linear-response and nonlinear-response formulations for IMT rate calculations, which only require equilibrium molecular dynamics simulations. The linear- and nonlinear-response IMT methods were tested to predict the transient behavior in the photoinduced CT dynamics of the carotenoid-porphyrin-C60 molecular triad solvated in explicit tetrahydrofuran. Our result demonstrated that the nonlinear-response IMT is in excellent agreement with the benchmark NEMD for all cases investigated here, whereas the linear-response IMT predicts the correct trend for all cases but overestimates the transient CT rate in one case involving a significant nonequilibrium relaxation. This mild breakdown of linear-response IMT is due to neglecting the higher-order terms in the exact nonlinear-response IMT. Taking advantage of time translational symmetry, the linear- and nonlinear-response approaches were demonstrated to be able to reduce the computational cost by 80% and 60% compared with NEMD simulations, respectively. Thus, we highly recommend the readily applicable and accurate nonlinear-response IMT approach for simulating nonequilibrium CT processes in complex molecular systems in the condensed phase.
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Affiliation(s)
- Dominikus Brian
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
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10
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Biasin E, Fox ZW, Andersen A, Ledbetter K, Kjær KS, Alonso-Mori R, Carlstad JM, Chollet M, Gaynor JD, Glownia JM, Hong K, Kroll T, Lee JH, Liekhus-Schmaltz C, Reinhard M, Sokaras D, Zhang Y, Doumy G, March AM, Southworth SH, Mukamel S, Gaffney KJ, Schoenlein RW, Govind N, Cordones AA, Khalil M. Direct observation of coherent femtosecond solvent reorganization coupled to intramolecular electron transfer. Nat Chem 2021; 13:343-349. [PMID: 33589787 DOI: 10.1038/s41557-020-00629-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/14/2020] [Indexed: 01/31/2023]
Abstract
It is well known that the solvent plays a critical role in ultrafast electron-transfer reactions. However, solvent reorganization occurs on multiple length scales, and selectively measuring short-range solute-solvent interactions at the atomic level with femtosecond time resolution remains a challenge. Here we report femtosecond X-ray scattering and emission measurements following photoinduced charge-transfer excitation in a mixed-valence bimetallic (FeiiRuiii) complex in water, and their interpretation using non-equilibrium molecular dynamics simulations. Combined experimental and computational analysis reveals that the charge-transfer excited state has a lifetime of 62 fs and that coherent translational motions of the first solvation shell are coupled to the back electron transfer. Our molecular dynamics simulations identify that the observed coherent translational motions arise from hydrogen bonding changes between the solute and nearby water molecules upon photoexcitation, and have an amplitude of tenths of ångströms, 120-200 cm-1 frequency and ~100 fs relaxation time. This study provides an atomistic view of coherent solvent reorganization mediating ultrafast intramolecular electron transfer.
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Affiliation(s)
- Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| | - Zachary W Fox
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Amity Andersen
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kathryn Ledbetter
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kasper S Kjær
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Julia M Carlstad
- Department of Chemistry, University of Washington, Seattle, WA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James D Gaynor
- Department of Chemistry, University of Washington, Seattle, WA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA
| | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kiryong Hong
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gas Metrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Thomas Kroll
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jae Hyuk Lee
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | | | - Marco Reinhard
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dimosthenis Sokaras
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Yu Zhang
- Department of Chemistry, Physics, and Astronomy, University of California, Irvine, CA, USA.,Q-Chem, Pleasanton, CA, USA
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anne Marie March
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Shaul Mukamel
- Department of Chemistry, Physics, and Astronomy, University of California, Irvine, CA, USA
| | - Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Robert W Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Niranjan Govind
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Amy A Cordones
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| | - Munira Khalil
- Department of Chemistry, University of Washington, Seattle, WA, USA.
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11
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Fujii K, Nakano H, Sato H, Kimura Y. Experimental observation of the unique solvation process along multiple solvation coordinates of photodissociated products. Phys Chem Chem Phys 2021; 23:4569-4579. [PMID: 33616585 DOI: 10.1039/d0cp06588a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical reaction dynamics in solution are closely related to solvation dynamics, and understanding solvent responses remains a crucial issue in chemistry and chemical biology. In this study, we experimentally and computationally investigated the solvation dynamics along different solvation coordinates of the same molecule: the electronically excited state and ground state of the p-aminophenylthiyl radical generated by the photodissociation of bis(p-aminophenyl)disulfide. Time profiles of the peak shifts from the transient absorption and emission spectra after photodissociation were extracted to discuss the solvent reorganization process in various ionic liquids (ILs) with different viscosities. The absorption peak position of the radical followed common solvation dynamics, shifting to a lower energy with time due to reorganization of the surrounding solvent molecules in response to the charge redistribution and molecular volume change caused by photodissociation. On the other hand, the emission band of the radical did not show a meaningful spectral shift with time. It was also found that the solvation time in the ground state was not strongly dependent on the solvent viscosity. These experimental results deviate from the conventional dynamic Stokes shift theory. To discuss the experimental results, non-equilibrium molecular dynamics simulations were conducted. The spectral shift obtained by MD simulations indicated the existence of a large solvation energy change and solvation dynamics around the radical after the photodissociation. On the other hand, the electronic excitation of the radical brought about a relatively smaller solvation energy change, especially at the long delay time after the photodissociation. These differences might be one of the reasons for the unique experimentally observed solvation dynamics.
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Affiliation(s)
- Kaori Fujii
- Department of Applied Chemistry, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan.
| | - Hiroshi Nakano
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto Daigaku Katsura, Kyoto 615-8510, Japan
| | - Yoshifumi Kimura
- Department of Applied Chemistry, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan.
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12
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Li Y, Zhao T, Qing L, Yu H, Xu X, Li P, Zhao S. Solvation dynamics in simple fluids: Effect of solute size and potential. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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13
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Cox SJ, Thorpe DG, Shaffer PR, Geissler PL. Assessing long-range contributions to the charge asymmetry of ion adsorption at the air-water interface. Chem Sci 2020; 11:11791-11800. [PMID: 34094413 PMCID: PMC8162909 DOI: 10.1039/d0sc01947j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Anions generally associate more favorably with the air–water interface than cations. In addition to solute size and polarizability, the intrinsic structure of the unperturbed interface has been discussed as an important contributor to this bias. Here we assess quantitatively the role that intrinsic charge asymmetry of water's surface plays in ion adsorption, using computer simulations to compare model solutes of various size and charge. In doing so, we also evaluate the degree to which linear response theory for solvent polarization is a reasonable approach for comparing the thermodynamics of bulk and interfacial ion solvation. Consistent with previous works on bulk ion solvation, we find that the average electrostatic potential at the center of a neutral, sub-nanometer solute at the air–water interface depends sensitively on its radius, and that this potential changes quite nonlinearly as the solute's charge is introduced. The nonlinear response closely resembles that of the bulk. As a result, the net nonlinearity of ion adsorption is weaker than in bulk, but still substantial, comparable to the apparent magnitude of macroscopically nonlocal contributions from the undisturbed interface. For the simple-point-charge model of water we study, these results argue distinctly against rationalizing ion adsorption in terms of surface potentials inherent to molecular structure of the liquid's boundary. Cations and anions have different affinities for the air-water interface. The intrinsic orientation of surface molecules suggests such an asymmetry, but the bias is dominated by solvent response that is spatially local and significantly nonlinear.![]()
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Affiliation(s)
- Stephen J Cox
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Dayton G Thorpe
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.,Department of Physics, University of California Berkeley CA 94720 USA
| | - Patrick R Shaffer
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Phillip L Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.,Department of Chemistry, University of California Berkeley CA 94720 USA
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14
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Rey R, Hynes JT. Solvation Dynamics in Water. 4. On the Initial Regime of Solvation Relaxation. J Phys Chem B 2020; 124:7668-7681. [PMID: 32790403 DOI: 10.1021/acs.jpcb.0c05706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is shown, by means of numerical and analytic work, that initial molecular momenta play little significant role in the initial fast solvation relaxation that follows electronic excitation of, and charge creation for, a standard model system of a solute in water. Instead, the nonequilibrium dynamics are predominantly described by noninertial "steering" by the torques directly generated by the newly created charge distribution. It is this process that largely overcomes inertia and drives the relaxation dynamics on a time scale of a few tens of femtoseconds in the key initial regime of the dynamics. These results are discussed in the context of commonly employed descriptions such as inertial, Gaussian, and underdamped dynamical behavior.
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Affiliation(s)
- Rossend Rey
- Departament de Fı́sica, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T Hynes
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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15
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Kirchberg H, Thorwart M. Time-Resolved Probing of the Nonequilibrium Structural Solvation Dynamics by the Time-Dependent Stokes Shift. J Phys Chem B 2020; 124:5717-5722. [PMID: 32515195 DOI: 10.1021/acs.jpcb.0c03990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The time-dependent fluorescence Stokes shift monitors the relaxation of the polarization of a polar solvent in the surroundings of a photoexcited solute molecule but also the structural variation of the solute following photoexcitation and the subsequent molecular charge redistribution. Here, we formulate a simple nonequilibrium quantum theory of solvation for an explicitly time-dependent continuous solvent. The time-dependent solvent induces nonequilibrium fluctuations on the solvent dynamics which are directly reflected in different time components in the time-dependent Stokes shift. We illustrate the structural dynamics in the presence of an explicitly time-dependent solvent by the example of a dynamically shrinking solute which leads to a bimodal Stokes shift. Interestingly, both contributions are mutually coupled. Furthermore, we can explain a prominent long-tail decay of the Stokes shift associated with slow structural dynamical variations.
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Affiliation(s)
- Henning Kirchberg
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstr. 9, 20355 Hamburg, Germany
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstr. 9, 20355 Hamburg, Germany
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16
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Abstract
We unravel the combined effects of confinement and surface interactions by studying the position dependent, time-resolved dynamic response functions in nano-containers of different shapes. Spectroscopic signatures are additionally studied through solvation dynamics by placing ionic and dipolar probes at varying distances from the enclosing surface. We find that the confined water molecules exhibit exotic dynamical features and stark differences from that in the bulk liquid. We employ atomistic molecular dynamics simulation to obtain the solvation time correlation function, non-Gaussian parameter, and non-linear response function that reveal the existence of heterogeneous and non-exponential dynamics with a strong sensitivity to both the size and the shape of the enclosure. Importantly, the slower long-time decay constant exhibits a non-monotonic spatial dependence. The initial ultrafast component is reminiscent of the same in the bulk, but it is found to have a different origin in the present systems. We perform shell-wise analyses to understand the microscopic origin of these observations and the range of the propagation of the surface induced effects.
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Affiliation(s)
- Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bengaluru, Karnataka, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bengaluru, Karnataka, India
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17
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Wang X, Guo J, Li T, Wei Z. To unravel the connection between the non-equilibrium and equilibrium solvation dynamics of tryptophan: success and failure of the linear response theory of fluorescence Stokes shift. RSC Adv 2020; 10:18348-18354. [PMID: 35517244 PMCID: PMC9053704 DOI: 10.1039/d0ra01227k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/15/2020] [Indexed: 11/21/2022] Open
Abstract
The connections between the non-equilibrium solvation dynamics upon optical transitions and the system's equilibrium fluctuations are explored in aqueous liquid. Linear response theory correlates time-dependent fluorescence with the equilibrium time correlation functions. In the previous work [T. Li, J. Chem. Theory Comput., 2017, 13, 1867], Stokes shift was explicitly decomposed into the contributions of various order time correlation functions on the excited state surface. Gaussian fluctuations of the solute-solvent interactions validate linear response theory. Correspondingly, the deviation of the Gaussian statistics causes the inefficiency of linear response evaluation. The above mechanism is thoroughly tested in this study. By employing molecular simulations, multiple non-equilibrium processes, not necessarily initiated from the ground state equilibrium minimum, were examined for tryptophan. Both the success and failure of linear response theory are found for this simple system and the mechanism is analyzed. These observations, assisted by the width dynamics, the initial state linear response approach, and the variation of the solvation structures, integrally verify the virtue of the excited state Gaussian statistics on the dynamics of Stokes shift.
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Affiliation(s)
- Xiaofang Wang
- School of Physics and Optoelectronic Engineering, Xidian University Xi'an 710071 People's Republic of China
| | - Jirui Guo
- School of Physics and Optoelectronic Engineering, Xidian University Xi'an 710071 People's Republic of China
| | - Tanping Li
- School of Physics and Optoelectronic Engineering, Xidian University Xi'an 710071 People's Republic of China
| | - Zhiyi Wei
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences Beijing 100190 China
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18
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Guo J, Wang X, Li T, Wei Z. Linear Response Theory for Decomposition Energies of Stokes Shift in Proteins. J Phys Chem B 2020; 124:3540-3547. [PMID: 32212659 DOI: 10.1021/acs.jpcb.9b11519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In aqueous solution, fluorescence Stokes shift experiments monitor the relaxation of the solute-solvent interactions upon photon excitation of the solute chromophore. Linear response (LR) theory expects the identical dynamics between the Stokes shift and the system's spontaneous fluctuations. Whether this identity guarantees similar dynamics between the nonequilibrated and equilibrium processes for the decomposition energy of the Stokes shift is the main focus of this study. In our previous work [Li, T. J. Chem. Theory Comput. 2017, 13, 1867-1873], Stokes shift is properly correlated with various order time-correlation functions. As a continuation, its decomposition energy from the subsystem is further represented as the full summation of all of the cross-time correlation functions between the decomposition energy and the total solute-solvent interactions. Gaussian statistics of the total solute-solvent interactions ensure the same decay rates among the odd orders not only for the time-correlation functions but also for the cross-time correlation functions, validating the LR of the Stokes shift and the decompositions, respectively. The above mechanism is verified by molecular dynamics simulations in the protein Staphylococcus nuclease and is robust even as the decomposed energy associated with an individual residue exhibits typical non-Gaussian properties. Further examinations reveal the consistent molecular motions for a specific residue over the nonequilibrium and equilibrium processes, which are responsible for the nonequilibrium dynamics of the associated decomposed energy. Our results show the appropriateness of LR on finer molecular scales.
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Affiliation(s)
- Jirui Guo
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Xiaofang Wang
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Tanping Li
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Zhiyi Wei
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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19
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Hazra MK, Bagchi B. Non-linearity in dipolar solvation dynamics in water-ethanol mixture: Composition dependence of free energy landscape. J Chem Phys 2019; 151:084502. [DOI: 10.1063/1.5097751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Milan K. Hazra
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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20
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Fukuda A, Oroguchi T, Nakasako M. Dipole-dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme. Biochim Biophys Acta Gen Subj 2019; 1864:129406. [PMID: 31377191 DOI: 10.1016/j.bbagen.2019.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
The fluorescence intensity of tryptophan residues in hen egg-white lysozyme was measured up to 500 ps after the excitation by irradiation pulses at 290 nm. From the time-dependent variation of fluorescence intensity in a wavelength range of 320-370 nm, the energy relaxation in the dynamic Stokes shift was reconstructed as the temporal variation in wavenumber of the estimated fluorescence maximum. The relaxation was approximated by two exponential curves with decay constants of 1.2 and 26.7 ps. To interpret the relaxation, a molecular dynamics simulation of 75 ns was conducted for lysozyme immersed in a water box. From the simulation, the energy relaxation in the electrostatic interactions of each tryptophan residue was evaluated by using a scheme derived from the linear response theory. Dipole-dipole interactions between each of the Trp62 and Trp123 residues and hydration water molecules displayed an energy relaxation similar to that experimentally observed regarding time constants and magnitudes. The side chains of these residues were partly or fully exposed to the solvent. In addition, by inspecting the variation in dipole moments of the hydration water molecules around lysozyme, it was suggested that the observed relaxation could be attributed to the orientational relaxation of hydration water molecules participating in the hydrogen-bond network formed around each of the two tryptophan residues.
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Affiliation(s)
- Asahi Fukuda
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokihama 223-8522, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokihama 223-8522, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokihama 223-8522, Japan.
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21
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Chung S, Choi SM, Rhee YM. Exploring the Possibility of Excited State Keto‐Enolate Transformation of the Oxyluciferin‐Luciferase Complex with QM/MM Free Energy Simulations. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Seyoung Chung
- Department of ChemistryPohang University of Science and Technology (POSTECH) Pohang 37673 Korea
| | - Sun Mi Choi
- Department of ChemistryPohang University of Science and Technology (POSTECH) Pohang 37673 Korea
| | - Young Min Rhee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
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22
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Nandy A, Chakraborty S, Nandi S, Bhattacharyya K, Mukherjee S. Structure, Activity, and Dynamics of Human Serum Albumin in a Crowded Pluronic F127 Hydrogel. J Phys Chem B 2019; 123:3397-3408. [DOI: 10.1021/acs.jpcb.9b00219] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Somen Nandi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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23
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Heid E, Braun D. Fundamental limitations of the time-dependent Stokes shift for investigating protein hydration dynamics. Phys Chem Chem Phys 2019; 21:4435-4443. [DOI: 10.1039/c8cp07623e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the TDSS measured in protein systems, large protein contributions fully obscure hydration dynamics.
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Affiliation(s)
- Esther Heid
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Daniel Braun
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
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24
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Honegger P, Heid E, Schmode S, Schröder C, Steinhauser O. Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect. RSC Adv 2019; 9:36982-36993. [PMID: 35539058 PMCID: PMC9075347 DOI: 10.1039/c9ra08008b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
The local changes in protein hydration dynamics upon encapsulation of the protein or macromolecular crowding are essential to understand protein function in cellular environments. We were able to obtain a spatially-resolved picture of the influence of confinement and crowding on the hydration dynamics of the protein ubiquitin by analyzing the time-dependent Stokes shift (TDSS), as well as the intermolecular Nuclear Overhauser Effect (NOE) at different sites of the protein by large-scale computer simulation of single and multiple proteins in water and confined in reverse micelles. Besides high advanced space resolved information on hydration dynamics we found a strong correlation of the change in NOE upon crowding or encapsulation and the change in the integral TDSS relaxation times in all investigated systems relative to the signals in a diluted protein solution. Changes in local protein hydration dynamics caused by encapsulation or crowding are reflected in the TDSS and the intermolecular NOE alike.![]()
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Stella Schmode
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
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25
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Prampolini G, Ingrosso F, Segalina A, Caramori S, Foggi P, Pastore M. Dynamical and Environmental Effects on the Optical Properties of an Heteroleptic Ru(II)–Polypyridine Complex: A Multilevel Approach Combining Accurate Ground and Excited State QM-Derived Force Fields, MD and TD-DFT. J Chem Theory Comput 2018; 15:529-545. [DOI: 10.1021/acs.jctc.8b01031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Francesca Ingrosso
- Université de Lorraine, CNRS, Laboratoire de Physique et Chimie Théoriques, F-54000 Nancy, France
| | - Alekos Segalina
- Université de Lorraine, CNRS, Laboratoire de Physique et Chimie Théoriques, F-54000 Nancy, France
| | - Stefano Caramori
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Luigi Borsari 46, I-44100, Ferrara, Italy
| | - Paolo Foggi
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino Florence, Italy
- INO−CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche, Largo Fermi 6, I-50125 Florence, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Mariachiara Pastore
- Université de Lorraine, CNRS, Laboratoire de Physique et Chimie Théoriques, F-54000 Nancy, France
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26
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Initial excited state structural dynamics of lumiflavin upon ultraviolet excitation. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Ahmed S, Pasti A, Fernández-Terán RJ, Ciardi G, Shalit A, Hamm P. Aqueous solvation from the water perspective. J Chem Phys 2018; 148:234505. [PMID: 29935500 DOI: 10.1063/1.5034225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The response of water re-solvating a charge-transfer dye (deprotonated Coumarin 343) after photoexcitation has been measured by means of transient THz spectroscopy. Two steps of increasing THz absorption are observed, a first ∼10 ps step on the time scale of Debye relaxation of bulk water and a much slower step on a 3.9 ns time scale, the latter of which reflecting heating of the bulk solution upon electronic relaxation of the dye molecules from the S1 back into the S0 state. As an additional reference experiment, the hydroxyl vibration of water has been excited directly by a short IR pulse, establishing that the THz signal measures an elevated temperature within ∼1 ps. This result shows that the first step upon dye excitation (10 ps) is not limited by the response time of the THz signal; it rather reflects the reorientation of water molecules in the solvation layer. The apparent discrepancy between the relatively slow reorientation time and the general notion that water is among the fastest solvents with a solvation time in the sub-picosecond regime is discussed. Furthermore, non-equilibrium molecular dynamics simulations have been performed, revealing a close-to-quantitative agreement with experiment, which allows one to disentangle the contribution of heating to the overall THz response from that of water orientation.
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Affiliation(s)
- Saima Ahmed
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Pasti
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Gustavo Ciardi
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Andrey Shalit
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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28
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Mukherjee S, Mondal S, Bagchi B. Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average. J Chem Phys 2018; 147:024901. [PMID: 28711050 DOI: 10.1063/1.4990693] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since the pioneering works of Pethig, Grant, and Wüthrich on a protein hydration layer, many studies have been devoted to find out if there are any "general and universal" characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform an atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at average properties but the distribution of relaxation times. We present results of calculations of distributions of residence times and rotational relaxation times for four different protein-water systems and compare them with the same quantities in the bulk. The distributions in the hydration layer are unusually broad and log-normal in nature due to the simultaneous presence of peptide backbones that form weak hydrogen bonds, hydrophobic amino acid side chains that form no hydrogen bond, and charged polar groups that form a strong hydrogen bond with the surrounding water molecules. The broad distribution is responsible for the non-exponential dielectric response and also agrees with large specific heat of the hydration water. Our calculations reveal that while the average time constant is just about 2-3 times larger than that of bulk water, it provides a poor representation of the real behaviour. In particular, the average leads to the erroneous conclusion that water in the hydration layer is bulk-like. However, the observed and calculated lower value of static dielectric constant of hydration layer remained difficult to reconcile with the broad distribution observed in dynamical properties. We offer a plausible explanation of these unique properties.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
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30
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Mondal S, Mukherjee S, Bagchi B. Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study. J Chem Phys 2018; 147:154901. [PMID: 29055291 DOI: 10.1063/1.4995420] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.
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Affiliation(s)
- Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
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31
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Mondal S, Samajdar RN, Mukherjee S, Bhattacharyya AJ, Bagchi B. Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves. J Phys Chem B 2018; 122:2227-2242. [DOI: 10.1021/acs.jpcb.7b11928] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sayantan Mondal
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Rudra N. Samajdar
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Saumyak Mukherjee
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aninda J. Bhattacharyya
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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32
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Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
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34
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35
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Mondal S, Mukherjee S, Bagchi B. Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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36
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Mondal S, Puranik M. Sub-50 fs excited state dynamics of 6-chloroguanine upon deep ultraviolet excitation. Phys Chem Chem Phys 2017; 18:13874-87. [PMID: 27146198 DOI: 10.1039/c6cp01746k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The photophysical properties of natural nucleobases and their respective nucleotides are ascribed to the sub-picosecond lifetime of their first singlet states in the UV-B region (260-350 nm). Electronic transitions of the ππ* type, which are stronger than those in the UV-B region, lie at the red edge of the UV-C range (100-260 nm) in all isolated nucleobases. The lowest energetic excited states in the UV-B region of nucleobases have been investigated using a plethora of experimental and theoretical methods in gas and solution phases. The sub-picosecond lifetime of these molecules is not a general attribute of all nucleobases but specific to the five primary nucleobases and a few xanthine and methylated derivatives. To determine the overall UV photostability, we aim to understand the effect of more energetic photons lying in the UV-C region on nucleobases. To determine the UV-C initiated photophysics of a nucleobase system, we chose a halogen substituted purine, 6-chloroguanine (6-ClG), that we had investigated previously using resonance Raman spectroscopy. We have performed quantitative measurements of the resonance Raman cross-section across the Bb absorption band (210-230 nm) and constructed the Raman excitation profiles. We modeled the excitation profiles using Lee and Heller's time-dependent theory of resonance Raman intensities to extract the initial excited state dynamics of 6-ClG within 30-50 fs after photoexcitation. We found that imidazole and pyrimidine rings of 6-ClG undergo expansion and contraction, respectively, following photoexcitation to the Bb state. The amount of distortions of the excited state structure from that of the ground state structure is reflected by the total internal reorganization energy that is determined at 112 cm(-1). The contribution of the inertial component of the solvent response towards the total reorganization energy was obtained at 1220 cm(-1). In addition, our simulation also yields an instantaneous response of the first solvation shell within an ultrafast timescale of less than 30 fs following photoexcitation.
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Affiliation(s)
- Sayan Mondal
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
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37
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Mondal S, Puranik M. Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5'-Monophosphate in Three Singlet States. J Phys Chem B 2017; 121:7095-7107. [PMID: 28653848 DOI: 10.1021/acs.jpcb.7b05735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report measurement of resonance Raman (RR) spectra of guanosine-5'-monophosphate (GMP), a DNA nucleotide at excitation wavelengths throughout its ππ* absorption band (Bb) in the 210-230 nm range. From these data, we constructed wavelength-dependent Raman intensity excitation profiles (REPs) for all observed modes. These profiles and the absorption spectrum were then modeled using self-consistent simulations based on the time-dependent wave packet propagation formalism. We inferred the initial structural dynamics of GMP immediately after photoexcitation in terms of dimensionless displacements. The simulations also provide linewidth-broadening parameters that in turn report on the time scale of dynamics. We compared deduced structural changes in the purine ring upon photoabsorption into the Bb state with those deduced for the two lowest lying ππ* (La and Lb at 280 and 248 nm, respectively) excited states of GMP. We find that excitation to the Lb state lengthens C6-N1 and C2═N3 bonds, which lie along the formation coordinate of various oxidative adducts but Bb excitation does not. We also find that photoabsorption by the Bb state weakens the C8-N9 bond and thus might assist imidazole ring opening via cleavage of the same bond. Electronic excitation to different ππ* states of the guanine chromophore results in contrasting structural changes; although absorption by the La and Lb states induces expansion of pyrimidine and contraction of imidazole rings, excitation results in overall shrinkage of both the rings. Computed absolute changes in internal coordinates imply that photoexcitation to any of the three singlet states of GMP does not lead directly to the formation of a cation radical of guanine.
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Affiliation(s)
- Sayan Mondal
- Indian Institute of Science Education and Research , Pune 411008, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research , Pune 411008, India
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38
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Li T. Efficient Criterion To Evaluate Linear Response Theory in Optical Transitions. J Chem Theory Comput 2017; 13:1867-1873. [PMID: 28414910 DOI: 10.1021/acs.jctc.6b01083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of the Gaussian statistics on the solvation dynamics upon the photon excitation of the chromophore is deeply explored. The linear response theory for the fluorescence Stokes shift is investigated. An analytical formulism is presented to recast Stokes shift into the contributions of the equilibrium time correlation functions of the solute-solvent interactions on the excited-state surface, and the latter is further reformed and depicted by the time relaxation of the moment. As the first application of the formulism in the molecular dynamics simulations, it is verified that the efficiency of the linear response theory relies on the Gaussian characteristics of the dominant moments in terms of the Stokes shift, which is identified by the same relaxation dynamics between those moments and the linear order one. The comparisons between the above observations on the linearity of Stokes shift and the explanations in the literature are discussed. The key finding is the development of explicit criterion to measure the appropriateness of applying linear response theory.
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Affiliation(s)
- Tanping Li
- School of Physics and Optoelectronic Engineering, Xidian University , Xi'an, Shaanxi 710071, People's Republic of China
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39
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Schile AJ, Thompson WH. Tests for, origins of, and corrections to non-Gaussian statistics. The dipole-flip model. J Chem Phys 2017; 146:154109. [DOI: 10.1063/1.4981009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Addison J. Schile
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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40
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Kolář MH, Kubař T. Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer. J Phys Chem B 2017; 121:1520-1532. [PMID: 28121443 DOI: 10.1021/acs.jpcb.6b12109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.
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Affiliation(s)
- Michal H Kolář
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich , 52428 Jülich, Germany.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , 16610 Praha, Czech Republic
| | - Tomáš Kubař
- Institute of Physical Chemistry & Center for Functional Nanostructures, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
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41
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Rey R, Hynes JT. Solvation Dynamics in Liquid Water. III. Energy Fluxes and Structural Changes. J Phys Chem B 2017; 121:1377-1385. [PMID: 28095693 DOI: 10.1021/acs.jpcb.6b11805] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation-and in particular, hydration- relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent's spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible "inverse snowball" effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors' principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor.
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Affiliation(s)
- Rossend Rey
- Departament de Física, Universitat Politècnica de Catalunya , Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Chemistry Department, Ecole Normale Supérieure-PSL Research University , Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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42
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Heid E, Moser W, Schröder C. On the validity of linear response approximations regarding the solvation dynamics of polyatomic solutes. Phys Chem Chem Phys 2017; 19:10940-10950. [DOI: 10.1039/c6cp08575j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gaussian statistics and linear response predictions of the nonequilibrium solvation dynamics are tested for numerous solute/solvent combinations.
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Affiliation(s)
- Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Wanda Moser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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43
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Mondal S, Puranik M. Ultrafast structural dynamics of photoexcited adenine. Phys Chem Chem Phys 2017; 19:20224-20240. [DOI: 10.1039/c7cp03092d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the La (260 nm) and Bb (210 nm) excited states.
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Affiliation(s)
- Sayan Mondal
- Indian Institute of Science Education and Research
- Pune – 411008
- India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research
- Pune – 411008
- India
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44
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Kumpulainen T, Lang B, Rosspeintner A, Vauthey E. Ultrafast Elementary Photochemical Processes of Organic Molecules in Liquid Solution. Chem Rev 2016; 117:10826-10939. [DOI: 10.1021/acs.chemrev.6b00491] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tatu Kumpulainen
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Bernhard Lang
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Arnulf Rosspeintner
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
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45
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Jumper CC, Arpin PC, Turner DB, McClure SD, Rather SR, Dean JC, Cina JA, Kovac PA, Mirkovic T, Scholes GD. Broad-Band Pump-Probe Spectroscopy Quantifies Ultrafast Solvation Dynamics of Proteins and Molecules. J Phys Chem Lett 2016; 7:4722-4731. [PMID: 27934206 DOI: 10.1021/acs.jpclett.6b02237] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond solvation dynamics. We report studies of a rhodamine dye in methanol and cryptophyte algae light-harvesting proteins in aqueous suspension. Broad-band impulsive excitation generates a vibrational wavepacket that oscillates on the excited-state potential energy surface, destructively interfering with itself at the minimum of the surface. This destructive interference gives rise to a node at a certain probe wavelength that varies with time. This reveals the Gibbs free-energy changes of the excited-state potential energy surface, which equates to the solvation time correlation function. This method captures the inertial solvent response of water (∼40 fs) and the bimodal inertial response of methanol (∼40 and ∼150 fs) and reveals how protein-buried chromophores are sensitive to the solvent dynamics inside and outside of the protein environment.
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Affiliation(s)
- Chanelle C Jumper
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Paul C Arpin
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, California State University, Chico , Chico, California 95929-0202, United States
| | - Daniel B Turner
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
| | - Scott D McClure
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Shahnawaz R. Rather
- Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
| | - Jacob C Dean
- Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
| | - Jeffrey A Cina
- Department of Chemistry and Biochemistry, and Oregon Center for Optical, Molecular, and Quantum Science, University of Oregon , Eugene, Oregon 97403, United States
| | - Philip A Kovac
- Department of Chemistry and Biochemistry, and Oregon Center for Optical, Molecular, and Quantum Science, University of Oregon , Eugene, Oregon 97403, United States
| | - Tihana Mirkovic
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Gregory D Scholes
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, Princeton University , Washington Road, Princeton, New Jersey 08544, United States
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46
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Rey R, Hynes JT. Solvation Dynamics in Water: 2. Energy Fluxes on Excited- and Ground-State Surfaces. J Phys Chem B 2016; 120:11287-11297. [DOI: 10.1021/acs.jpcb.6b08965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rossend Rey
- Departament
de Física, Universitat Politècnica de Catalunya, Campus
Nord B4-B5, Barcelona 08034, Spain
| | - James T. Hynes
- Department of Chemistry and
Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Ecole Normale Supérieure-PSL
Research
University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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47
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Shukla N, Pomarico E, Chen L, Chergui M, Othon CM. Retardation of Bulk Water Dynamics by Disaccharide Osmolytes. J Phys Chem B 2016; 120:9477-83. [DOI: 10.1021/acs.jpcb.6b07751] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nimesh Shukla
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Enrico Pomarico
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Lee Chen
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Christina M. Othon
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06457, United States
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48
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Ghosh C, Bhunia D, Ghosh S, Jana B, Ghosh S, Bhattacharyya K. Fluorescence Probing of Fluctuating Microtubule using a Covalent Fluorescent Probe: Effect of Taxol. ChemistrySelect 2016. [DOI: 10.1002/slct.201600353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Catherine Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Debmalya Bhunia
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Shirsendu Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Batakrishna Jana
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
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49
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Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path. J Phys Chem B 2016; 120:2281-90. [PMID: 26876428 DOI: 10.1021/acs.jpcb.5b12744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an ∼100 fs time scale, with the proton transfer (PT) event itself being very sudden (<10 fs). This transfer is preceded by the acid-base H-bond's compression, while the water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base ΔpKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale ∼120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3(+).
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Affiliation(s)
- Snehasis Daschakraborty
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Philip M Kiefer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yair Motro
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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50
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Schmollngruber M, Braun D, Steinhauser O. Combining non-equilibrium simulations and coarse-grained modelling allows for a fine-grained decomposition of solvation dynamics. Phys Chem Chem Phys 2016; 18:30954-30960. [DOI: 10.1039/c6cp06282b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The time-dependent Stokes shift is shown to be a localized and short-ranged effect in ionic liquids.
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Affiliation(s)
| | - Daniel Braun
- University of Vienna
- Department of Computational Biological Chemistry
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Department of Computational Biological Chemistry
- Austria
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