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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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Lee Y, Oang KY, Kim D, Ihee H. A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:031301. [PMID: 38706888 PMCID: PMC11065455 DOI: 10.1063/4.0000249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.
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Affiliation(s)
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Korea Atomic Energy Research Institute (KAERI), Daejeon 34057, South Korea
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3
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Yoneda Y, Kuramochi H. Rapid-Scan Resonant Two-Dimensional Impulsive Stimulated Raman Spectroscopy of Excited States. J Phys Chem A 2023. [PMID: 37289973 DOI: 10.1021/acs.jpca.3c02489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photochemical reactions occur in the electronically excited state, which is effectively represented by a multidimensional potential energy surface (PES) with a vast degree of freedom of nuclear coordinates. The elucidation of the intricate shape of the PES constitutes an important topic in the field of photochemistry and has long been studied both experimentally and theoretically. Recently, fully time-domain resonant two-dimensional Raman spectroscopy has emerged as a potentially powerful tool to provide unique information about the coupling between vibrational manifolds in the excited state. However, the wide application of this technique has been significantly hampered by the technical difficulties associated with experimental implementation and remains challenging. Herein, we demonstrate time-domain resonant two-dimensional impulsive stimulated Raman spectroscopy (2D-ISRS) of excited states using sub-10 fs pulses based on the rapid scan of the time delay, which facilitates the efficient collection of time-domain vibrational signals with high sensitivity. As a proof-of-principle experiment, we performed 2D-ISRS of 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene) in solution. Through 2D Fourier transformation of the high-quality time-time oscillatory signal, we obtained a 2D frequency-frequency correlation map of excited-state TIPS-pentacene in the broad frequency window of 0-2000 cm-1. The data clearly resolve a number of cross peaks that signify the correlations among excited-state vibrational manifolds. The high capability of the rapid-scan-based 2D-ISRS spectrometer presented in this study enables the systematic investigation of various photochemical reaction systems, thereby further promoting the understanding and applications of this new multidimensional spectroscopy.
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Affiliation(s)
- Yusuke Yoneda
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Hikaru Kuramochi
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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4
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Codescu MA, Kunze T, Weiß M, Brehm M, Kornilov O, Sebastiani D, Nibbering ETJ. Ultrafast Proton Transfer Pathways Mediated by Amphoteric Imidazole. J Phys Chem Lett 2023; 14:4775-4785. [PMID: 37186569 DOI: 10.1021/acs.jpclett.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Imidazole, being an amphoteric molecule, can act both as an acid and as a base. This property enables imidazole, as an essential building block, to effectively facilitate proton transport in high-temperature proton exchange membrane fuel cells and in proton channel transmembrane proteins, enabling those systems to exhibit high energy conversion yields and optimal biological function. We explore the amphoteric properties of imidazole by following the proton transfer exchange reaction dynamics with the bifunctional photoacid 7-hydroxyquinoline (7HQ). We show with ultrafast ultraviolet-mid-infrared pump-probe spectroscopy how for imidazole, in contrast to expectations based on textbook knowledge of acid-base reactivity, the preferential reaction pathway is that of an initial proton transfer from 7HQ to imidazole, and only at a later stage a transfer from imidazole to 7HQ, completing the 7HQ tautomerization reaction. An assessment of the molecular distribution functions and first-principles calculations of proton transfer reaction barriers reveal the underlying reasons for our observations.
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Affiliation(s)
- Marius-Andrei Codescu
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489 Berlin, Germany
| | - Thomas Kunze
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Moritz Weiß
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Brehm
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Oleg Kornilov
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489 Berlin, Germany
| | - Daniel Sebastiani
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Erik T J Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, 12489 Berlin, Germany
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5
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Glotz G, Püschmann S, Haas M, Gescheidt G. Direct detection of photo-induced reactions by IR: from Brook rearrangement to photo-catalysis. Photochem Photobiol Sci 2023:10.1007/s43630-023-00406-4. [PMID: 36933157 DOI: 10.1007/s43630-023-00406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
In situ IR detection of photoreactions induced by the light of LEDs at appropriate wavelengths provides a simple, cost-effective, and versatile method to get insight into mechanistic details. In particular, conversions of functional groups can be selectively followed. Overlapping UV-Vis bands or fluorescence from the reactants and products and the incident light do not obstruct IR detection. Compared with in situ photo-NMR, our setup does not require tedious sample preparation (optical fibers) and offers a selective detection of reactions, even at positions where 1H-NMR lines overlap or 1H resonances are not clear-cut. We illustrate the applicability of our setup following the photo-Brook rearrangement of (adamant-1-yl-carbonyl)-tris(trimethylsilyl)silane, address photo-induced α-bond cleavage (1-hydroxycyclohexyl phenyl ketone), study photoreduction using tris(bipyridine)ruthenium(II), investigate photo-oxygenation of double bonds with molecular oxygen and the fluorescent 2,4,6-triphenylpyrylium photocatalyst, and address photo-polymerization. With the LED/FT-IR combination, reactions can be qualitatively followed in fluid solution, (highly) viscous environments, and in the solid state. Viscosity changes during the reaction (e.g., during a polymerization) do not obstruct the method.
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Affiliation(s)
- Gabriel Glotz
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria.
| | - Sabrina Püschmann
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Michael Haas
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010, Graz, Austria
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6
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Ghosh R, Datta S, Mora AK, Modak B, Nath S, Palit DK. Dynamics of hydrogen bond reorganization in the S1(ππ*) state of 9-Anthracenecarboxaldehyde. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Bailey-Darland S, Krueger TD, Fang C. Ultrafast Spectroscopies of Nitrophenols and Nitrophenolates in Solution: From Electronic Dynamics and Vibrational Structures to Photochemical and Environmental Implications. Molecules 2023; 28:601. [PMID: 36677656 PMCID: PMC9866910 DOI: 10.3390/molecules28020601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Nitrophenols are a group of small organic molecules with significant environmental implications from the atmosphere to waterways. In this work, we investigate a series of nitrophenols and nitrophenolates, with the contrasting ortho-, meta-, and para-substituted nitro group to the phenolic hydroxy or phenolate oxygen site (2/3/4NP or NP-), implementing a suite of steady-state and time-resolved spectroscopic techniques that include UV/Visible spectroscopy, femtosecond transient absorption (fs-TA) spectroscopy with probe-dependent and global analysis, and femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations. The excitation-dependent (400 and 267 nm) electronic dynamics in water and methanol, for six protonated or deprotonated nitrophenol molecules (three regioisomers in each set), enable a systematic investigation of the excited-state dynamics of these functional "nanomachines" that can undergo nitro-group twisting (as a rotor), excited-state intramolecular or intermolecular proton transfer (donor-acceptor, ESIPT, or ESPT), solvation, and cooling (chromophore) events on molecular timescales. In particular, the meta-substituted compound 3NP or 3NP- exhibits the strongest charge-transfer character with FSRS signatures (e.g., C-N peak frequency), and thus, does not favor nitroaromatic twist in the excited state, while the ortho-substituted compound 2NP can undergo ESIPT in water and likely generate nitrous acid (HONO) after 267 nm excitation. The delineated mechanistic insights into the nitro-substituent-location-, protonation-, solvent-, and excitation-wavelength-dependent effects on nitrophenols, in conjunction with the ultraviolet-light-induced degradation of 2NP in water, substantiates an appealing discovery loop to characterize and engineer functional molecules for environmental applications.
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8
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Donaldson PM. Spectrophotometric Concentration Analysis Without Molar Absorption Coefficients by Two-Dimensional-Infrared and Fourier Transform Infrared Spectroscopy. Anal Chem 2022; 94:17988-17999. [PMID: 36516397 PMCID: PMC9798376 DOI: 10.1021/acs.analchem.2c04287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
A spectrophotometric method for determining relative concentrations of infrared (IR)-active analytes with unknown concentration and unknown molar absorption coefficient is explored. This type of method may be useful for the characterization of complex/heterogeneous liquids or solids, the study of transient species, and for other scenarios where it might be difficult to gain concentration information by other means. Concentration ratios of two species are obtained from their IR absorption and two-dimensional (2D)-IR diagonal bleach signals using simple ratiometric calculations. A simple calculation framework for deriving concentration ratios from spectral data is developed, extended to IR-pump-probe signals, and applied to the calculation of transition dipole ratios. Corrections to account for the attenuation of the 2D-IR signal caused by population relaxation, spectral overlap, wavelength-dependent pump absorption, inhomogeneous broadening, and laser intensity variations are described. A simple formula for calculating the attenuation of the 2D-IR signal due to sample absorption is deduced and by comparison with 2D-IR signals at varying total sample absorbance found to be quantitatively accurate. 2D-IR and Fourier transform infrared spectroscopy of two carbonyl containing species acetone and N-methyl-acetamide dissolved in D2O are used to experimentally confirm the validity of the ratiometric calculations. Finally, to address ambiguities over units and scaling of 2D-IR signals, a physical unit of 2D-IR spectral amplitude in mOD/c m - 1 is proposed.
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Affiliation(s)
- Paul M. Donaldson
- Central Laser Facility, RCaH, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, DidcotOX11 0QX, U.K.
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9
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Knorr J, Sülzner N, Geissler B, Spies C, Grandjean A, Kutta RJ, Jung G, Nuernberger P. Ultrafast transient absorption and solvation of a super-photoacid in acetoneous environments. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2022; 21:2179-2192. [PMID: 36178669 DOI: 10.1007/s43630-022-00287-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/08/2022] [Indexed: 12/13/2022]
Abstract
The phenomenon of photoacidity, i.e., an increase in acidity by several orders of magnitude upon electronic excitation, is frequently encountered in aromatic alcohols capable of transferring a proton to a suitable acceptor. A promising new class of neutral super-photoacids based on pyranine derivatives has been shown to exhibit pronounced solvatochromic effects. To disclose the underlying mechanisms contributing to excited-state proton transfer (ESPT) and the temporal characteristics of solvation and ESPT, we scrutinize the associated ultrafast dynamics of the strongest photoacid of this class, namely tris(1,1,1,3,3,3-hexafluoropropan-2-yl)8-hydroxypyrene-1,3,6-trisulfonate, in acetoneous environment, thereby finding experimental evidence for ESPT even under these adverse conditions for proton transfer. Juxtaposing results from time-correlated single-photon counting and femtosecond transient absorption measurements combined with a complete decomposition of all signal components, i.e., absorption of ground and excited states as well as stimulated emission, we disclose dynamics of solvation, rotational diffusion, and radiative relaxation processes in acetone and identify the relevant steps of ESPT along with the associated time scales.
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Affiliation(s)
- Johannes Knorr
- Physikalische Chemie II, Ruhr-Universität Bochum, 44780, Bochum, Germany.,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Paul-Gordan-Straße 6, 91052, Erlangen, Germany
| | - Niklas Sülzner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany.,Physikalische Chemie II, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Bastian Geissler
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstraße 31, 95053, Regensburg, Germany.,Physikalische Chemie II, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Christian Spies
- Biophysikalische Chemie, Universität des Saarlandes, 66123, Saarbrücken, Germany.,Physikalische Chemie II, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Alexander Grandjean
- Biophysikalische Chemie, Universität des Saarlandes, 66123, Saarbrücken, Germany
| | - Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstraße 31, 95053, Regensburg, Germany
| | - Gregor Jung
- Biophysikalische Chemie, Universität des Saarlandes, 66123, Saarbrücken, Germany
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstraße 31, 95053, Regensburg, Germany. .,Physikalische Chemie II, Ruhr-Universität Bochum, 44780, Bochum, Germany.
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10
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Liu A, Chow M, Wildman A, Frisch MJ, Hammes-Schiffer S, Li X. Simultaneous Optimization of Nuclear-Electronic Orbitals. J Phys Chem A 2022; 126:7033-7039. [PMID: 36154137 DOI: 10.1021/acs.jpca.2c05172] [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
Accurate modeling of important nuclear quantum effects, such as nuclear delocalization, zero-point energy, and tunneling, as well as non-Born-Oppenheimer effects, requires treatment of both nuclei and electrons quantum mechanically. The nuclear-electronic orbital (NEO) method provides an elegant framework to treat specified nuclei, typically protons, on the same level as the electrons. In conventional electronic structure theory, finding a converged ground state can be a computationally demanding task; converging NEO wavefunctions, due to their coupled electronic and nuclear nature, is even more demanding. Herein, we present an efficient simultaneous optimization method that uses the direct inversion in the iterative subspace method to simultaneously converge wavefunctions for both the electrons and quantum nuclei. Benchmark studies show that the simultaneous optimization method can significantly reduce the computational cost compared to the conventional stepwise method for optimizing NEO wavefunctions for multicomponent systems.
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Affiliation(s)
- Aodong Liu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mathew Chow
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Michael J Frisch
- Gaussian Incorporated, 340 Quinnipiac Street, Bldg 40, Wallingford, Connecticut 06492, United States
| | | | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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11
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Morzan UN, Díaz Mirón G, Grisanti L, González Lebrero MC, Kaminski Schierle GS, Hassanali A. Non-Aromatic Fluorescence in Biological Matter: The Exception or the Rule? J Phys Chem B 2022; 126:7203-7211. [PMID: 36128666 DOI: 10.1021/acs.jpcb.2c04280] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While in the vast majority of cases fluorescence in biological matter has been attributed to aromatic or conjugated groups, peptides associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, or Huntington's, have been recently shown to display an intrinsic visible fluorescence even in the absence of aromatic residues. This has called the attention of researchers from many different fields, trying to understand the origin of this peculiar behavior and, at the same time, motivating the search for novel strategies to control the optical properties of new biophotonic materials. Today, after nearly 15 years of its discovery, there is a growing consensus about the mechanism underlying this phenomenon, namely, that electronic interactions between non-optically active molecules can result in supramolecular assemblies that are fluorescent. Despite this progress, many aspects of this phenomenon remain uncharted territory. In this Perspective, we lay down the state-of-the-art in the field highlighting the open questions from both experimental and theoretical fronts in this fascinating emerging area of non-aromatic fluorescence.
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Affiliation(s)
- Uriel N Morzan
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Gonzalo Díaz Mirón
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | - Luca Grisanti
- Division of Theoretical Physics, Ruđer Bos̆cković Institute, Bijenic̆ka cesta 54, 10000 Zagreb, Croatia
| | - Mariano C González Lebrero
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | | | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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12
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Fusco G, Bemporad F, Chiti F, Dobson CM, De Simone A. The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes. Front Mol Biosci 2022; 9:981312. [PMID: 36158582 PMCID: PMC9490001 DOI: 10.3389/fmolb.2022.981312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins from hyperthermophilic organisms are evolutionary optimised to adopt functional structures and dynamics under conditions in which their mesophilic homologues are generally inactive or unfolded. Understanding the nature of such adaptation is of crucial interest to clarify the underlying mechanisms of biological activity in proteins. Here we measured NMR residual dipolar couplings of a hyperthermophilic acylphosphatase enzyme at 80°C and used these data to generate an accurate structural ensemble representative of its native state. The resulting energy landscape was compared to that obtained for a human homologue at 37°C, and additional NMR experiments were carried out to probe fast (15N relaxation) and slow (H/D exchange) backbone dynamics, collectively sampling fluctuations of the two proteins ranging from the nanosecond to the millisecond timescale. The results identified key differences in the strategies for protein-protein and protein-ligand interactions of the two enzymes at the respective physiological temperatures. These include the dynamical behaviour of a β-strand involved in the protection against aberrant protein aggregation and concerted motions of loops involved in substrate binding and catalysis. Taken together these results elucidate the structure-dynamics-function relationship associated with the strategies of thermal adaptation of protein molecules.
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Affiliation(s)
- Giuliana Fusco
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco Bemporad
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | | | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
- *Correspondence: Alfonso De Simone,
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13
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Maiti S, Mitra S, Johnson CA, Gronborg KC, Garrett-Roe S, Donaldson PM. pH Jumps in a Protic Ionic Liquid Proceed by Vehicular Proton Transport. J Phys Chem Lett 2022; 13:8104-8110. [PMID: 35997534 PMCID: PMC9442784 DOI: 10.1021/acs.jpclett.2c01457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The dynamics of excess protons in the protic ionic liquid (PIL) ethylammonium formate (EAF) have been investigated from femtoseconds to microseconds using visible pump mid-infrared probe spectroscopy. The pH jump following the visible photoexcitation of a photoacid (8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt, HPTS) results in proton transfer to the formate of the EAF. The proton transfer predominantly (∼70%) occurs over picoseconds through a preformed hydrogen-bonded tight complex between HPTS and EAF. We investigate the longer-range and longer-time-scale proton-transport processes in the PIL by obtaining the ground-state conjugate base (RO-) dynamics from the congested transient-infrared spectra. The spectral kinetics indicate that the protons diffuse only a few solvent shells from the parent photoacid before recombining with RO-. A kinetic isotope effect of nearly unity (kH/kD ≈ 1) suggests vehicular transfer and the transport of excess protons in this PIL. Our findings provide comprehensive insight into the complete photoprotolytic cycle of excess protons in a PIL.
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Affiliation(s)
- Sourav Maiti
- Central
Laser Facility, RCaH, STFC-Rutherford Appleton
Laboratory, Harwell Science
and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Sunayana Mitra
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Clinton A. Johnson
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kai C. Gronborg
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Sean Garrett-Roe
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Paul M. Donaldson
- Central
Laser Facility, RCaH, STFC-Rutherford Appleton
Laboratory, Harwell Science
and Innovation Campus, Didcot OX11 0QX, United Kingdom
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14
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Boulanger SA, Chen C, Myasnyanko IN, Baranov MS, Fang C. Fluorescence Modulation of ortho-Green Fluorescent Protein Chromophores Following Ultrafast Proton Transfer in Solution. J Phys Chem B 2022; 126:5081-5093. [PMID: 35786966 DOI: 10.1021/acs.jpcb.2c03812] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photophysical and photochemical properties of the green fluorescent protein (GFP) chromophore and derivatives underlie their bioimaging applications. To date, ultrafast spectroscopic tools represent the key for unraveling fluorescence mechanisms toward rational design of this powerful biomimetic framework. To correlate the excited-state intramolecular proton transfer (ESIPT) with chromophore emission properties, we implement experimental and computational tool sets to elucidate real-time electronic and structural dynamics of two archetypal ortho-GFP chromophores (o-HBDI and o-LHBDI) possessing an intramolecular hydrogen bond to undergo efficient ESIPT, only differing in a bridge-bond constraint. Using excited-state femtosecond stimulated Raman spectroscopy (FSRS), a low-frequency phenolic (P)-ring-deformation mode (∼562 cm-1) was uncovered to accompany ESIPT. The tautomerized chromophore undergoes either rapid P-ring isomerization to reach the ground state with essentially no fluorescence for o-HBDI or enhanced (up to an impressive 180-fold in acetonitrile) and solvent-polarity-dependent fluorescence by P-ring locking in o-LHBDI. The significant dependence of the fluorescence enhancement ratio on solvent viscosity confirms P-ring isomerization as the dominant nonradiative decay pathway for o-HBDI. This work provides crucial insights into the dynamic solute-solvent electrostatic and steric interactions, enabling the application-specific improvement of ESIPT-capable molecules as versatile fluorescence-based sensors and imaging agents from large Stokes shift emission to brighter probes in physiological environments.
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Affiliation(s)
- Sean A Boulanger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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15
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Böckmann H, Horstmann JG, Razzaq AS, Wippermann S, Ropers C. Mode-selective ballistic pathway to a metastable electronic phase. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:045102. [PMID: 35991705 PMCID: PMC9385219 DOI: 10.1063/4.0000162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Exploiting vibrational excitation for the dynamic control of material properties is an attractive goal with wide-ranging technological potential. Most metal-to-insulator transitions are mediated by few structural modes and are, thus, ideal candidates for selective driving toward a desired electronic phase. Such targeted navigation within a generally multi-dimensional potential energy landscape requires microscopic insight into the non-equilibrium pathway. However, the exact role of coherent inertial motion across the transition state has remained elusive. Here, we demonstrate mode-selective control over the metal-to-insulator phase transition of atomic indium wires on the Si(111) surface, monitored by ultrafast low-energy electron diffraction. We use tailored pulse sequences to individually enhance or suppress key phonon modes and thereby steer the collective atomic motion within the potential energy surface underlying the structural transformation. Ab initio molecular dynamics simulations demonstrate the ballistic character of the structural transition along the deformation vectors of the Peierls amplitude modes. Our work illustrates that coherent excitation of collective modes via exciton-phonon interactions evades entropic barriers and enables the dynamic control of materials functionality.
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Affiliation(s)
| | | | | | - Stefan Wippermann
- Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf 40237, Germany
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16
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Liu Y, Sun T, Zhou L, Zhao Y, Chen Q, Shen X, Lv H, Xu H. Ultrafast time-resolved polarization-dependent investigations on the dynamics in the Ã2B2 state of NO2 molecules. Chemphyschem 2022; 23:e202200221. [PMID: 35687037 DOI: 10.1002/cphc.202200221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/10/2022] [Indexed: 11/09/2022]
Abstract
We perform time-resolved polarization-dependent study on ultrafast dynamics in the à 2 B 2 state of NO 2 . A linearly-polarized 400 nm femtosecond laser is used to resonantly pump NO 2 to its first excited state à 2 B 2 , and the time-dependent ionic yields produced via strong field ionization at 800 nm are measured under different laser polarizations. The yield ratios measured with the lasers perpendicular and parallel to each other first decrease then increase as the wave packet evolves on the excited state, with a minimum ratio at the delay time of 180 fs, which can be attributed to the evolution time in the à 2 B 2 state. The behavior of the time-resolved ionization in elliptically polarized laser field is also investigated and discussed. Our study indicates that the time-resolved polarization-dependent studies will shed some light on and pave the way to understand ultrafast dynamics in molecular excited states.
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Affiliation(s)
- Yang Liu
- Jilin University Institute of Atomic and Molecular Physics, Jilin, CHINA
| | - Tian Sun
- Jilin University Institute of Atomic and Molecular Physics, Jilin, CHINA
| | | | - Yiwen Zhao
- Jilin University Institute of Atomic and Molecular Physics, Jilin, CHINA
| | - Qi Chen
- Jilin University Institute of Atomic and Molecular Physics, Jilin, CHINA
| | - Xingchen Shen
- Jilin University Institute of Atomic and Molecular Physics, Jilin, CHINA
| | - Hang Lv
- Jilin University Institute of Atomic and Molecular Physics, Jilin, Qianjin Street, 130012, Changchun, CHINA
| | - Haifeng Xu
- Jilin University Institute of Atomic and Molecular Physics, Jilin, CHINA
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17
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Töpfer K, Upadhyay M, Meuwly M. Quantitative molecular simulations. Phys Chem Chem Phys 2022; 24:12767-12786. [PMID: 35593769 PMCID: PMC9158373 DOI: 10.1039/d2cp01211a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022]
Abstract
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular interactions. The present perspective provides an overview of the present status of quantitative atomistic simulations from colleagues' and our own efforts for gas- and solution-phase processes and for the dynamics on surfaces. Particular attention is paid to direct comparison with experiment. An outlook discusses present challenges and future extensions to bring such dynamics simulations even closer to reality.
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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18
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Photoacid-induced aqueous acid-base reactions probed by femtosecond infrared spectroscopy. Photochem Photobiol Sci 2022; 21:1419-1431. [PMID: 35526216 DOI: 10.1007/s43630-022-00232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/13/2022] [Indexed: 10/18/2022]
Abstract
Acid-base reactions involving an excited photoacid have typically been investigated at high base concentrations, but the mechanisms at low base concentrations require clarification. Herein, the dynamics of acid-base reactions induced by an excited photoacid, pyranine (DA), were investigated in the presence of azide ion (N3-) in D2O solution using femtosecond infrared spectroscopy. Specifically, the spectral characteristics of four species (DA, electronically excited DA (DA*), the conjugate base of DA* (A*-), and the conjugate base of DA (A-)) were probed in the spectral region of 1400-1670 cm-1 in the time range of 1 ps-1 μs. This broad timescale encompassed all the acid-base reactions initiated by photoexcitation at 400 nm; thus, reactions related to both DA* and A- could be probed. Furthermore, changes in the populations of N3- and DN3 were monitored using the absorption bands at 2042 and 2133 cm-1, respectively. Following excitation, approximately half of DA* relaxed to DA with a time constant of 0.44 ± 0.04 ns. The remainder underwent an acid-base reaction to produce A*-, which relaxed to A- with a time constant of 3.9 ± 0.3 ns. The acid-base reaction proceeded via two paths, namely, proton exchange with the added base or simple deuteron release to D2O (protolysis). Notably, all the acid-base reactions were well described by the rate constant at the steady-state limit. Thus, although the acid-base reactions at low base concentrations (< 0.1 M) were diffusion controlled, they could be described using a simple rate equation.
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19
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Sülzner N, Geissler B, Grandjean A, Jung G, Nuernberger P. Excited‐state Proton Transfer Dynamics of a Super‐Photoacid in Acetone‐Water Mixtures. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Niklas Sülzner
- Ruhr-Universitat Bochum Lehrstuhl für Theoretische Chemie GERMANY
| | - Bastian Geissler
- Universitat Regensburg Institut für Physikalische und Theoretische Chemie GERMANY
| | | | - Gregor Jung
- Universitat des Saarlandes Biophysikalische Chemie GERMANY
| | - Patrick Nuernberger
- Universitat Regensburg Institut für Physikalische und Theoretische Chemie Universitätsstraße 31 93053 Regensburg GERMANY
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20
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Dhamija S, Bhutani G, Jayachandran A, De AK. A Revisit on Impulsive Stimulated Raman Spectroscopy: Importance of Spectral Dispersion of Chirped Broadband Probe. J Phys Chem A 2022; 126:1019-1032. [PMID: 35142494 DOI: 10.1021/acs.jpca.1c10566] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The usefulness of a chirped broadband probe and spectral dispersion to obtain Raman spectra under nonresonant/resonant impulsive excitation is revisited. A general methodology is presented that inherently takes care of phasing the time-domain low-frequency oscillations without probe pulse compression and retrieves the absolute phase of the oscillations. As test beds, neat solvents (CCl4, CHCl3, and CH2Cl2) are used. Observation of periodic intensity modulation along detection wavelengths for particular modes is explained using a simple electric field interaction picture. This method is extended to diatomic molecule (iodine) and polyatomic molecules (Nile blue and methylene blue) to assign vibrational frequencies in ground/excited electronic state that are supported by density functional theory calculations. A comparison between frequency-domain and time-domain counterparts, i.e., stimulated Raman scattering and impulsive stimulated Raman scattering using degenerate pump-probe pairs is presented, and most importantly, it is shown how impulsive stimulated Raman scattering using chirped broadband probe retains unique advantages offered by both.
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Affiliation(s)
- Shaina Dhamija
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Garima Bhutani
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Ajay Jayachandran
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Arijit K De
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
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21
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Time-resolved infrared absorption spectroscopy applied to photoinduced reactions: how and why. Photochem Photobiol Sci 2022; 21:557-584. [DOI: 10.1007/s43630-022-00180-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
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22
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Liu Y, Wang H, Qu S, Li Y, Yang B, Zhao D. Theoretical calculation on excited state hydrogen bond kinetics of PRODAN derivative 2b molecule in methanol solution. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Krueger TD, Fang C. Elucidating Inner Workings of Naturally Sourced Organic Optoelectronic Materials with Ultrafast Spectroscopy. Chemistry 2021; 27:17736-17750. [PMID: 34545971 DOI: 10.1002/chem.202102766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 01/18/2023]
Abstract
Recent advances in sustainable optoelectronics including photovoltaics, light-emitting diodes, transistors, and semiconductors have been enabled by π-conjugated organic molecules. A fundamental understanding of light-matter interactions involving these materials can be realized by time-resolved electronic and vibrational spectroscopies. In this Minireview, the photoinduced mechanisms including charge/energy transfer, electronic (de)localization, and excited-state proton transfer are correlated with functional properties encompassing optical absorption, fluorescence quantum yield, conductivity, and photostability. Four naturally derived molecules (xylindein, dimethylxylindein, alizarin, indigo) with ultrafast spectral insights showcase efficient energy dissipation involving H-bonding networks and proton motions, which yield high photostability. Rational design principles derived from such investigations could increase the efficiency for light harvesting, triplet formation, and photosensitivity for improved and versatile optoelectronic performance.
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Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331-4003, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331-4003, USA
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24
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Gutiérrez-Arzaluz L, Nadinov I, Healing G, Czaban-Jóźwiak J, Jia J, Huang Z, Zhao Y, Shekhah O, Schanze KS, Eddaoudi M, Mohammed OF. Ultrafast Aggregation-Induced Tunable Emission Enhancement in a Benzothiadiazole-Based Fluorescent Metal-Organic Framework Linker. J Phys Chem B 2021; 125:13298-13308. [PMID: 34846146 DOI: 10.1021/acs.jpcb.1c08889] [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
Aggregation-induced emission enhancement (AIEE) is a process recently exploited in solid-state materials and organic luminophores, and it is explained by tight-molecular packaging. However, solution-phase AIEE and its formation mechanism have not been widely explored. This work investigated AIEE phenomena in two donor-acceptor-donor-type benzodiazole-based molecules (the organic building block in metal-organic frameworks) with an acetylene and phenyl π-conjugated backbone tapered with a carboxylic acid group at either end. This was done using time-resolved electronic and vibrational spectroscopy in conjunction with time-dependent density functional theory (TD-DFT) calculations. Fluorescence up-conversion spectroscopy and time-correlated single-photon counting conclusively showed an intramolecular charge transfer-driven aggregate emission enhancement. This is shown by a red spectral shift of the emission spectra as well as an increase in the fluorescence lifetime from 746 ps at 1.0 × 10-11 to 2.48 ns at 2.0 × 10-3 M. The TD-DFT calculations showed that a restricted intramolecular rotation mechanism is responsible for the enhanced emission. The femtosecond infrared (IR) transient absorption results directly revealed the structural dynamics of aggregate formation, as evident from the evolution of the C≡C vibrational marker mode of the acetylene unit upon photoexcitation. Moreover, the IR data clearly indicated that the aggregation process occurred over a time scale of 10 ps, which is consistent with the fluorescence up-conversion results. Interestingly, time-resolved results and DFT calculations clearly demonstrated that both acetylene bonds and the sulfur atom are the key requirements to achieve such a controllable aggregation-induced fluorescence enhancement. The finding of the work not only shows how slight changes in the chemical structure of fluorescent chromophores could make a tremendous change in their optical behavior but also prompts a surge of research into a profound understanding of the mechanistic origins of this phenomenon. This may lead to the discovery of new chemical strategies that aim to synthesize novel chromophores with excellent optical properties for light-harvesting applications.
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Affiliation(s)
- Luis Gutiérrez-Arzaluz
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Issatay Nadinov
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - George Healing
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Justyna Czaban-Jóźwiak
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.,Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jiangtao Jia
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.,Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Zhiyuan Huang
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.,Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yan Zhao
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Osama Shekhah
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.,Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Kirk S Schanze
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Mohamed Eddaoudi
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.,Functional Materials Design, Discovery and Development Research Group (FMD3), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Omar F Mohammed
- Advanced Membranes and Porous Materials (AMPM) Center, Physical Sciences and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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25
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Rodrigues NDN, Woolley JM, Krokidi KM, Tesa-Serrate MA, Turner MAP, Hine NDM, Stavros VG. Effects of substituent position on aminobenzoate relaxation pathways in solution. Phys Chem Chem Phys 2021; 23:23242-23255. [PMID: 34632473 DOI: 10.1039/d1cp03759e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The negative effects of ultraviolet radiation (UVR) on human skin have led to the widespread use of sunscreens, i.e. skincare products containing UV filters to absorb, reflect or otherwise block UVR. The mechanisms by which UV filters dissipate energy following photoexcitation, i.e. their photodynamics, can crucially determine a molecule's performance as a sunscreen UV filter. In this work, we evaluate the effects of substituent position on the in-solution relaxation pathways of two derivates of methyl anthranilate (an ortho compound that is a precursor to the UV filter meradimate), meta- and para-methyl anthranilate, m-MA and p-MA, respectively. The photodynamics of m-MA were found to be sensitive to solvent polarity: its emission spectra show larger Stokes shifts with increasing polarity, and both the fluorescence quantum yield and lifetimes for m-MA increase in polar solvents. While the Stokes shifts for p-MA are much milder and more independent of solvent environment than those of m-MA, we find its fluorescence quantum yields to be sensitive not only to solvent polarity but to the hydrogen bonding character of the solvent. In both cases (m- and p-MA) we have found common computational methods to be insufficient to appropriately model the observed spectroscopic data, likely due to an inability to account for explicit solvent interactions, a known challenge in computational chemistry. Therefore, apart from providing insight into the photodynamics of anthranilate derivatives, the work presented here also provides a case study that may be of use to theoretical chemists looking to improve and develop explicit solvent computational methods.
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Affiliation(s)
- Natércia D N Rodrigues
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, UK. .,Lipotec SAU, Calle Isaac Peral, 17 Pol. Ind. Camí Ral, 08850 Barcelona, Spain
| | - Jack M Woolley
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, UK.
| | | | | | - Matthew A P Turner
- University of Warwick, Department of Chemistry, Coventry, CV4 7AL, UK. .,University of Warwick, Department of Physics, Coventry, CV4 7AL, UK
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26
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Macaluso V, Hashem S, Nottoli M, Lipparini F, Cupellini L, Mennucci B. Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics. J Phys Chem B 2021; 125:10282-10292. [PMID: 34476939 PMCID: PMC8450903 DOI: 10.1021/acs.jpcb.1c05753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Indexed: 01/02/2023]
Abstract
Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
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Affiliation(s)
| | | | - Michele Nottoli
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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27
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Wustelt P, Oppermann F, Mhatre S, Kübel M, Sayler AM, Lein M, Gräfe S, Paulus GG. Laser-Driven Anharmonic Oscillator: Ground-State Dissociation of the Helium Hydride Molecular Ion by Midinfrared Pulses. PHYSICAL REVIEW LETTERS 2021; 127:043202. [PMID: 34355921 DOI: 10.1103/physrevlett.127.043202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/06/2021] [Accepted: 04/27/2021] [Indexed: 06/13/2023]
Abstract
The vibrational motion of molecules represents a fundamental example of an anharmonic oscillator. Using a prototype molecular system, HeH^{+}, we demonstrate that appropriate laser pulses make it possible to drive the nuclear motion in the anharmonic potential of the electronic ground state, increasing its energy above the potential barrier and facilitating dissociation by purely vibrational excitation. We find excellent agreement between the frequency-dependent response of the helium hydride molecular cation to both classical and quantum mechanical simulations, thus removing any ambiguities through electronic excitation. Our results provide access to the rich dynamics of anharmonic quantum oscillator systems and pave the way to state-selective control schemes in ground-state chemistry by the adequate choice of the laser parameters.
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Affiliation(s)
- Philipp Wustelt
- Institute of Optics and Quantum Electronics, Friedrich Schiller University Jena, D-07743 Jena, Germany
- Helmholtz Institute Jena, Fröbelstieg 3, 07743 Jena, Germany
| | - Florian Oppermann
- Institut für Theoretische Physik, Leibniz Universität Hannover, Appelstraße 2, 30167 Hannover, Germany
| | - Saurabh Mhatre
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Matthias Kübel
- Institute of Optics and Quantum Electronics, Friedrich Schiller University Jena, D-07743 Jena, Germany
- Helmholtz Institute Jena, Fröbelstieg 3, 07743 Jena, Germany
| | - A Max Sayler
- Institute of Optics and Quantum Electronics, Friedrich Schiller University Jena, D-07743 Jena, Germany
- Helmholtz Institute Jena, Fröbelstieg 3, 07743 Jena, Germany
| | - Manfred Lein
- Institut für Theoretische Physik, Leibniz Universität Hannover, Appelstraße 2, 30167 Hannover, Germany
| | - Stefanie Gräfe
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Gerhard G Paulus
- Institute of Optics and Quantum Electronics, Friedrich Schiller University Jena, D-07743 Jena, Germany
- Helmholtz Institute Jena, Fröbelstieg 3, 07743 Jena, Germany
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28
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Cercola R, Wong NGK, Rhodes C, Olijnyk L, Mistry NS, Hall LM, Berenbeim JA, Lynam JM, Dessent CEH. A "one pot" mass spectrometry technique for characterizing solution- and gas-phase photochemical reactions by electrospray mass spectrometry. RSC Adv 2021; 11:19500-19507. [PMID: 35479237 PMCID: PMC9033567 DOI: 10.1039/d1ra02581c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022] Open
Abstract
The characterization of new photochemical pathways is important to progress the understanding of emerging areas of light-triggered inorganic and organic chemistry. In this context, the development of platforms to perform routine characterization of photochemical reactions remains an important goal for photochemists. Here, we demonstrate a new instrument that can be used to characterise both solution-phase and gas-phase photochemical reactions through electrospray ionisation mass spectrometry (ESI-MS). The gas-phase photochemistry is studied by novel laser-interfaced mass spectrometry (LIMS), where the molecular species of interest is introduced to the gas-phase by ESI, mass-selected and then subjected to laser photodissociation in the ion-trap. On-line solution-phase photochemistry is initiated by LEDs prior to ESI-MS in the same instrument with ESI-MS again being used to monitor photoproducts. Two ruthenium metal carbonyls, [Ru(η5-C5H5)(PPh3)2CO][PF6] and [Ru(η5-C5H5)(dppe)CO][PF6] (dppe = 1,2-bis(diphenylphosphino)ethane) are studied using this methodology. We show that the gas-phase photofragmentation pathways observed for the ruthenium complexes via LIMS (i.e. loss of CO + PPh3 ligands from [Ru(η5-C5H5)(PPh3)2CO]+ and loss of just CO from [Ru(η5-C5H5)(dppe)CO]+) mirror the solution-phase photochemistry at 3.4 eV. The advantages of performing the gas-phase and solution-phase photochemical characterisations in a single instrument are discussed.
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Affiliation(s)
- Rosaria Cercola
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Natalie G K Wong
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Chris Rhodes
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Lorna Olijnyk
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Neetisha S Mistry
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Lewis M Hall
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Jacob A Berenbeim
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Jason M Lynam
- Department of Chemistry, University of York Heslington York YO10 5DD UK
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Jones T, Peters WK, Efimov A, Yarotski D, Trebino R, Bowlan P. Measuring an ultrashort, ultraviolet pulse in a slowly responding, absorbing medium. OPTICS EXPRESS 2021; 29:11394-11405. [PMID: 33984919 DOI: 10.1364/oe.417293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Frequency-resolved optical gating (FROG) is a common technique for measuring ultrashort laser pulses using an instantaneous, nonlinear-optical interaction as a fast time-gate to measure the pulse intensity and phase. But at high frequencies, materials are often absorbing and it is not always possible to find a medium with a fast nonlinear-optical response. Here we show that an ultrashort, ultraviolet (UV) pulse can be measured in a strongly absorbing medium, using the absorption as the nonlinear-optical time-gate. To do this, we build on our recent implementation of FROG, known as induced-grating cross-correlation FROG (IG XFROG), where an unknown, higher-frequency pulse creates a transient grating that is probed with a lower-frequency, more easily detectable reference pulse. We demonstrate this with an 800 nm reference pulse to characterize 400 nm or 267 nm pulses using ZnS as the nonlinear-optical medium, which is absorptive at and below 400 nm. By scanning the delay between the two UV pulses which create the transient grating, we show that the phase-sensitive instantaneous four-wave-mixing contribution to the nonlinear signal field can be detected and separated from the slower, incoherent part of the response. Measuring a spectrally-resolved cross-correlation in this way and then applying a simple model for the response of the medium, we show that a modified generalized projections (GP) phase-retrieval algorithm can be used to extract the pulse amplitude and phase. We test this approach by measuring chirped UV pulses centered at 400 nm and 267 nm. Since interband absorption (or even photoionization) is not strongly wavelength-dependent, we expect IG XFROG to be applicable deeper into the UV.
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30
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Kim JG, Choi EH, Lee Y, Ihee H. Femtosecond X-ray Liquidography Visualizes Wavepacket Trajectories in Multidimensional Nuclear Coordinates for a Bimolecular Reaction. Acc Chem Res 2021; 54:1685-1698. [PMID: 33733724 DOI: 10.1021/acs.accounts.0c00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ConspectusVibrational wavepacket motions on potential energy surfaces are one of the critical factors that determine the reaction dynamics of photoinduced reactions. The motions of vibrational wavepackets are often discussed in the interpretation of observables measured with various time-resolved vibrational or electronic spectroscopies but mostly in terms of the frequencies of wavepacket motions, which are approximated by normal modes, rather than the actual positions of the wavepacket. Although the time-dependent positions (that is, the trajectory) of wavepackets are hypothesized or drawn in imagined or calculated potential energy surfaces, it is not trivial to experimentally determine the trajectory of wavepackets, especially in multidimensional nuclear coordinates for a polyatomic molecule. Recently, we performed a femtosecond X-ray liquidography (solution scattering) experiment on a gold trimer complex (GTC), [Au(CN)2-]3, in water at X-ray free-electron lasers (XFELs) and elucidated the time-dependent positions of vibrational wavepackets from the Franck-Condon region to equilibrium structures on both excited and ground states in the course of the formation of covalent bonds between gold atoms.Bond making is an essential process in chemical reactions, but it is challenging to keep track of detailed atomic movements associated with bond making because of its bimolecular nature that requires slow diffusion of two reaction parties to meet each other. Bond formation in the solution phase has been elusive because the diffusion of the reactants limits the reaction rate of a bimolecular process, making it difficult to initiate and track the bond-making processes with an ultrafast time resolution. In principle, if the bimolecular encounter can be controlled to overcome the limitation caused by diffusion, the bond-making processes can be tracked in a time-resolved manner, providing valuable insight into the bimolecular reaction mechanism. In this regard, GTC offers a good model system for studying the dynamics of bond formation in solution. Au(I) atoms in GTC exhibit a noncovalent aurophilic interaction, making GTC an aggregate complex without any covalent bond. Upon photoexcitation of GTC, an electron is excited from an antibonding orbital to a bonding orbital, leading to the formation of covalent bonds among Au atoms. Since Au atoms in the ground state of GTC are located in close proximity within the same solvent cage, the formation of Au-Au covalent bonds occurs without its reaction rate being limited by diffusion through the solvent.Femtosecond time-resolved X-ray liquidography (fs-TRXL) data revealed that the ground state has an asymmetric bent structure. From the wavepacket trajectory determined in three-dimensional nuclear coordinates (two internuclear distances and one bond angle), we found that two covalent bonds are formed between three Au atoms of GTC asynchronously. Specifically, one covalent bond is formed first for the shorter Au-Au pair (of the asymmetric and bent ground-state structure) in 35 fs, and subsequently, the other covalent bond is formed for the longer Au-Au pair within 360 fs. The resultant trimer complex has a symmetric and linear geometry, implying the occurrence of bent-to-linear transformation concomitant with the formation of two equivalent covalent bonds, and exhibits vibrations that can be unambiguously assigned to specific normal modes based on the wavepacket trajectory, even without the vibrational frequencies provided by quantum calculation.
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Affiliation(s)
- Jong Goo Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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31
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Aster A, Rumble C, Bornhof AB, Huang HH, Sakai N, Šolomek T, Matile S, Vauthey E. Long-lived triplet charge-separated state in naphthalenediimide based donor-acceptor systems. Chem Sci 2021; 12:4908-4915. [PMID: 34168763 PMCID: PMC8179635 DOI: 10.1039/d1sc00285f] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
1,4,5,8-Naphthalenediimides (NDIs) are widely used motifs to design multichromophoric architectures due to their ease of functionalisation, their high oxidative power and the stability of their radical anion. The NDI building block can be incorporated in supramolecular systems by either core or imide functionalization. We report on the charge-transfer dynamics of a series of electron donor-acceptor dyads consisting of a NDI chromophore with one or two donors linked at the axial, imide position. Photo-population of the core-centred π-π* state is followed by ultrafast electron transfer from the electron donor to the NDI. Due to a solvent dependent singlet-triplet equilibrium inherent to the NDI core, both singlet and triplet charge-separated states are populated. We demonstrate that long-lived charge separation in the triplet state can be achieved by controlling the mutual orientation of the donor-acceptor sub-units. By extending this study to a supramolecular NDI-based cage, we also show that the triplet charge-separation yield can be increased by tuning the environment.
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Affiliation(s)
- Alexander Aster
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Christopher Rumble
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Anna-Bea Bornhof
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Hsin-Hua Huang
- Department of Chemistry, University of Basel St. Johanns-Ring 19 Basel 4056 Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Tomáš Šolomek
- Department of Chemistry, University of Basel St. Johanns-Ring 19 Basel 4056 Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
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32
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Pirisi K, Nag L, Fekete Z, Iuliano JN, Tolentino Collado J, Clark IP, Pécsi I, Sournia P, Liebl U, Greetham GM, Tonge PJ, Meech SR, Vos MH, Lukacs A. Identification of the vibrational marker of tyrosine cation radical using ultrafast transient infrared spectroscopy of flavoprotein systems. Photochem Photobiol Sci 2021; 20:369-378. [PMID: 33721272 DOI: 10.1007/s43630-021-00024-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/09/2021] [Indexed: 11/29/2022]
Abstract
Tryptophan and tyrosine radical intermediates play crucial roles in many biological charge transfer processes. Particularly in flavoprotein photochemistry, short-lived reaction intermediates can be studied by the complementary techniques of ultrafast visible and infrared spectroscopy. The spectral properties of tryptophan radical are well established, and the formation of neutral tyrosine radicals has been observed in many biological processes. However, only recently, the formation of a cation tyrosine radical was observed by transient visible spectroscopy in a few systems. Here, we assigned the infrared vibrational markers of the cationic and neutral tyrosine radical at 1483 and 1502 cm-1 (in deuterated buffer), respectively, in a variant of the bacterial methyl transferase TrmFO, and in the native glucose oxidase. In addition, we studied a mutant of AppABLUF blue-light sensor domain from Rhodobacter sphaeroides in which only a direct formation of the neutral radical was observed. Our studies highlight the exquisite sensitivity of transient infrared spectroscopy to low concentrations of specific radicals.
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Affiliation(s)
- Katalin Pirisi
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary
| | - Lipsa Nag
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary
| | - James N Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | | | - Ian P Clark
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0QX, Oxon, UK
| | - Ildikó Pécsi
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary
| | - Pierre Sournia
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0QX, Oxon, UK
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Marten H Vos
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary.
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33
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Xia C, He X, Wang J, Wang W. Origin of subdiffusions in proteins: Insight from peptide systems. Phys Rev E 2020; 102:062424. [PMID: 33466075 DOI: 10.1103/physreve.102.062424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 11/07/2022]
Abstract
Subdiffusive kinetics are popular in proteins and peptides as observed in experiments and simulations. For protein systems with diverse interactions, are there multiple mechanisms to produce the common subdiffusion behavior? To approach this problem, long trajectories of two model peptides are simulated to study the mechanism of subdiffusion and the relations with their interactions. The free-energy profiles and the subdiffusive kinetics are observed for these two peptides. A hierarchical plateau analysis is employed to extract the features of the landscape from the mean square of displacement. The mechanism of subdiffusions can be postulated by comparing the exponents by simulations with those based on various models. The results indicate that the mechanisms of these two peptides are different and are related to the characteristics of their energy landscapes. The subdiffusion of the flexible peptide is mainly caused by depth distribution of traps on the energy landscape, while the subdiffusion of the helical peptide is attributed to the fractal topology of local minima on the landscape. The emergence of these different mechanisms reflects different kinetic scenarios in peptide systems though the peptides behave in a similar way of diffusion. To confirm these ideas, the transition networks between various conformations of these peptides are generated. Based on the network description, the controlled kinetics based only on the topology of the networks are calculated and compared with the results based on simulations. For the flexible peptide, the feature of controlled diffusion is distinct from that of simulation, and for the helical peptide, two kinds of kinetics have a similar exponent of subdiffusion. These results further exemplify the importance of the landscape topology in the kinetics of structural proteins and the effect of depth distribution of traps for the subdiffusion of disordered peptides.
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Affiliation(s)
- Chenliang Xia
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Xuefeng He
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Jun Wang
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Wei Wang
- School of Physics, Nanjing University, Nanjing 210093, People's Republic of China and National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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34
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Morzan UN, Videla PE, Soley MB, Nibbering ETJ, Batista VS. Vibronic Dynamics of Photodissociating ICN from Simulations of Ultrafast X‐Ray Absorption Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Condensed Matter Section The Abdus Salam International Center for Theoretical Physics Strada Costiera 11 34151 Trieste Italy
- Department of Chemistry Yale University P.O. Box 208107 New Haven CT 06520-8107 USA
| | - Pablo E. Videla
- Department of Chemistry Yale University P.O. Box 208107 New Haven CT 06520-8107 USA
- Energy Sciences Institute Yale University P.O. Box 27394 West Haven CT 06516-7394 USA
| | - Micheline B. Soley
- Department of Chemistry Yale University P.O. Box 208107 New Haven CT 06520-8107 USA
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
- Yale Quantum Institute Yale University P.O. Box 208334 New Haven CT 06520-8263 USA
| | - Erik T. J. Nibbering
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy Max Born Strasse 2A 12489 Berlin Germany
| | - Victor S. Batista
- Department of Chemistry Yale University P.O. Box 208107 New Haven CT 06520-8107 USA
- Energy Sciences Institute Yale University P.O. Box 27394 West Haven CT 06516-7394 USA
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35
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Morzan UN, Videla PE, Soley MB, Nibbering ETJ, Batista VS. Vibronic Dynamics of Photodissociating ICN from Simulations of Ultrafast X-Ray Absorption Spectroscopy. Angew Chem Int Ed Engl 2020; 59:20044-20048. [PMID: 32691867 PMCID: PMC7693200 DOI: 10.1002/anie.202007192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/23/2020] [Indexed: 11/07/2022]
Abstract
Ultrafast UV-pump/soft-X-ray-probe spectroscopy is a subject of great interest since it can provide detailed information about dynamical photochemical processes with ultrafast resolution and atomic specificity. Here, we focus on the photodissociation of ICN in the 1 Π1 excited state, with emphasis on the transient response in the soft-X-ray spectral region as described by the ab initio spectral lineshape averaged over the nuclear wavepacket probability density. We find that the carbon K-edge spectral region reveals a rich transient response that provides direct insights into the dynamics of frontier orbitals during the I-CN bond cleavage process. The simulated UV-pump/soft-X-ray-probe spectra exhibit detailed dynamical information, including a time-domain signature for coherent vibration associated with the photogenerated CN fragment.
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Affiliation(s)
- Uriel N. Morzan
- Condensed Matter SectionThe Abdus Salam International Center for Theoretical PhysicsStrada Costiera 1134151TriesteItaly
- Department of ChemistryYale UniversityP.O. Box 208107New HavenCT06520-8107USA
| | - Pablo E. Videla
- Department of ChemistryYale UniversityP.O. Box 208107New HavenCT06520-8107USA
- Energy Sciences InstituteYale UniversityP.O. Box 27394West HavenCT06516-7394USA
| | - Micheline B. Soley
- Department of ChemistryYale UniversityP.O. Box 208107New HavenCT06520-8107USA
- Department of Chemistry and Chemical BiologyHarvard University12 Oxford StreetCambridgeMA02138USA
- Yale Quantum InstituteYale UniversityP.O. Box 208334New HavenCT06520-8263USA
| | - Erik T. J. Nibbering
- Max Born Institute for Nonlinear Optics and Short Pulse SpectroscopyMax Born Strasse 2A12489BerlinGermany
| | - Victor S. Batista
- Department of ChemistryYale UniversityP.O. Box 208107New HavenCT06520-8107USA
- Energy Sciences InstituteYale UniversityP.O. Box 27394West HavenCT06516-7394USA
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36
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Whittock AL, Turner MAP, Coxon DJL, Woolley JM, Horbury MD, Stavros VG. Reinvestigating the Photoprotection Properties of a Mycosporine Amino Acid Motif. Front Chem 2020; 8:574038. [PMID: 33102444 PMCID: PMC7546825 DOI: 10.3389/fchem.2020.574038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/26/2020] [Indexed: 12/28/2022] Open
Abstract
With the growing concern regarding commercially available ultraviolet (UV) filters damaging the environment, there is an urgent need to discover new UV filters. A family of molecules called mycosporines and mycosporine-like amino acids (referred to as MAAs collectively) are synthesized by cyanobacteria, fungi and algae and act as the natural UV filters for these organisms. Mycosporines are formed of a cyclohexenone core structure while mycosporine-like amino acids are formed of a cyclohexenimine core structure. To better understand the photoprotection properties of MAAs, we implement a bottom-up approach by first studying a simple analog of an MAA, 3-aminocyclohex-2-en-1-one (ACyO). Previous experimental studies on ACyO using transient electronic absorption spectroscopy (TEAS) suggest that upon photoexcitation, ACyO becomes trapped in the minimum of an S1 state, which persists for extended time delays (>2.5 ns). However, these studies were unable to establish the extent of electronic ground state recovery of ACyO within 2.5 ns due to experimental constraints. In the present studies, we have implemented transient vibrational absorption spectroscopy (as well as complementary TEAS) with Fourier transform infrared spectroscopy and density functional theory to establish the extent of electronic ground state recovery of ACyO within this time window. We show that by 1.8 ns, there is >75% electronic ground state recovery of ACyO, with the remaining percentage likely persisting in the electronic excited state. Long-term irradiation studies on ACyO have shown that a small percentage degrades after 2 h of irradiation, plausibly due to some of the aforementioned trapped ACyO going on to form a photoproduct. Collectively, these studies imply that a base building block of MAAs already displays characteristics of an effective UV filter.
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Affiliation(s)
- Abigail L Whittock
- Analytical Science Centre for Doctoral Training, Senate House, University of Warwick, Coventry, United Kingdom.,Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Matthew A P Turner
- Department of Chemistry, University of Warwick, Coventry, United Kingdom.,Molecular Analytical Science Centre for Doctoral Training, Senate House, University of Warwick, Coventry, United Kingdom.,Department of Physics, University of Warwick, Coventry, United Kingdom
| | - Daniel J L Coxon
- Department of Chemistry, University of Warwick, Coventry, United Kingdom.,Department of Physics, University of Warwick, Coventry, United Kingdom.,Diamond Science and Technology Centre for Doctoral Training, University of Warwick, Coventry, United Kingdom
| | - Jack M Woolley
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Michael D Horbury
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, United Kingdom
| | - Vasilios G Stavros
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
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37
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Konold PE, Arik E, Weißenborn J, Arents JC, Hellingwerf KJ, van Stokkum IHM, Kennis JTM, Groot ML. Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein. Nat Commun 2020; 11:4248. [PMID: 32843623 PMCID: PMC7447820 DOI: 10.1038/s41467-020-18065-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/31/2020] [Indexed: 11/27/2022] Open
Abstract
Femtosecond time-resolved crystallography (TRC) on proteins enables resolving the spatial structure of short-lived photocycle intermediates. An open question is whether confinement and lower hydration of the proteins in the crystalline state affect the light-induced structural transformations. Here, we measured the full photocycle dynamics of a signal transduction protein often used as model system in TRC, Photoactive Yellow Protein (PYP), in the crystalline state and compared those to the dynamics in solution, utilizing electronic and vibrational transient absorption measurements from 100 fs over 12 decades in time. We find that the photocycle kinetics and structural dynamics of PYP in the crystalline form deviate from those in solution from the very first steps following photon absorption. This illustrates that ultrafast TRC results cannot be uncritically extrapolated to in vivo function, and that comparative spectroscopic experiments on proteins in crystalline and solution states can help identify structural intermediates under native conditions. Protein structural dynamics can be studied by time-resolved crystallography (TRC) and ultrafast transient spectroscopic methods. Here, the authors perform electronic and vibrational transient absorption measurements to characterise the full photocycle of Photoactive Yellow Protein (PYP) both in the crystalline and solution state and find that the photocycle kinetics and structural intermediates of PYP deviate in the crystalline state, which must be taken into consideration when planning TRC experiments.
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Affiliation(s)
- Patrick E Konold
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Enis Arik
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Jörn Weißenborn
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Jos C Arents
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, 1098, XH, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, 1098, XH, Amsterdam, The Netherlands
| | - Ivo H M van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Marie Louise Groot
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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38
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Horstmann JG, Böckmann H, Wit B, Kurtz F, Storeck G, Ropers C. Coherent control of a surface structural phase transition. Nature 2020; 583:232-236. [PMID: 32641815 DOI: 10.1038/s41586-020-2440-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 03/31/2020] [Indexed: 11/09/2022]
Abstract
Active optical control over matter is desirable in many scientific disciplines, with prominent examples in all-optical magnetic switching1,2, light-induced metastable or exotic phases of solids3-8 and the coherent control of chemical reactions9,10. Typically, these approaches dynamically steer a system towards states or reaction products far from equilibrium. In solids, metal-to-insulator transitions are an important target for optical manipulation, offering ultrafast changes of the electronic4 and lattice11-16 properties. The impact of coherences on the efficiencies and thresholds of such transitions, however, remains a largely open subject. Here, we demonstrate coherent control over a metal-insulator structural phase transition in a quasi-one-dimensional solid-state surface system. A femtosecond double-pulse excitation scheme17-20 is used to switch the system from the insulating to a metastable metallic state, and the corresponding structural changes are monitored by ultrafast low-energy electron diffraction21,22. To govern the transition, we harness vibrational coherence in key structural modes connecting both phases, and observe delay-dependent oscillations in the double-pulse switching efficiency. Mode-selective coherent control of solids and surfaces could open new routes to switching chemical and physical functionalities, enabled by metastable and non-equilibrium states.
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Affiliation(s)
- Jan Gerrit Horstmann
- 4th Physical Institute, Solids and Nanostructures, University of Göttingen, Göttingen, Germany
| | - Hannes Böckmann
- 4th Physical Institute, Solids and Nanostructures, University of Göttingen, Göttingen, Germany
| | - Bareld Wit
- 4th Physical Institute, Solids and Nanostructures, University of Göttingen, Göttingen, Germany
| | - Felix Kurtz
- 4th Physical Institute, Solids and Nanostructures, University of Göttingen, Göttingen, Germany
| | - Gero Storeck
- 4th Physical Institute, Solids and Nanostructures, University of Göttingen, Göttingen, Germany
| | - Claus Ropers
- 4th Physical Institute, Solids and Nanostructures, University of Göttingen, Göttingen, Germany. .,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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39
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Karmakar S, Ambastha A, Jha A, Dharmadhikari A, Dharmadhikari J, Venkatramani R, Dasgupta J. Transient Raman Snapshots of the Twisted Intramolecular Charge Transfer State in a Stilbazolium Dye. J Phys Chem Lett 2020; 11:4842-4848. [PMID: 32460494 DOI: 10.1021/acs.jpclett.0c01124] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Optically triggered twisted intramolecular charge transfer (TICT) states in donor-acceptor chromophores form the molecular basis for designing bioimaging probes that sense polarity, microviscosity, and pH in vivo. However, a lack of predictive understanding of the "twist" localization precludes a rational design of TICT-based dyes. Here, using femtosecond stimulated Raman spectroscopy, we reveal a distinct Raman signature of the TICT state for a stilbazolium-class mitochondrial staining dye. Resonance-selective probing of 4-N,N-diethylamino-4″-N'-methyl-stilbazolium tosylate (DEST) tracks the excited-state structure of the dye as it relaxes to a TICT state on a picosecond time scale. The appearance of a remarkably blue-shifted C=C stretching mode at 1650 cm-1 in the TICT state is attributed to the "twist" of a single bond adjacent to the ethylenic π-bridge in the DEST backbone based on detailed electronic structure calculations and vibrational mode analysis. Our work demonstrates that the π-bridge, connecting the donor and acceptor moieties, influences the spatial location of the "twist" and offers a new perspective for designing organelle-specific probes through cogent tuning of backbone dynamics.
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Affiliation(s)
- Shreetama Karmakar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Abhinandan Ambastha
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ajay Jha
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Aditya Dharmadhikari
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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40
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Anand N, Nag P, Kanaparthi RK, Vennapusa SR. O-H vibrational motions promote sub-50 fs nonadiabatic dynamics in 3-hydroxypyran-4-one: interplay between internal conversion and ESIPT. Phys Chem Chem Phys 2020; 22:8745-8756. [PMID: 32282004 DOI: 10.1039/d0cp00741b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical study is used to explore the involvement of O-H vibrational motions in the S0 → S2 photoinduced dynamics of 3-hydroxypyran-4-one (3-HOX). Two transitions, S0 → S1 and S0 → S2, are attributed to the experimentally observed electronic absorption spectral features in the range of 3.5-5.5 eV. We compute model potential energy surfaces of vibronically coupled S1 (nπ*) and S2 (ππ*) states with the aid of extensive electronic structure calculations. The S1-S2 conical intersection is characterized in the O-H bend and O-H stretch vibrational coordinate space. Quantum wavepacket dynamics simulations reveal an ultrafast S2 → S1 internal conversion decay, where about 90% of the S2 population disappears within the first 50 fs of the propagation time. The participation of O-H vibrational motions in the early events of nonadiabatic dynamics is analyzed based on the time evolution of nuclear densities on S2. We discuss the implications of these observations to provide fundamental insights into the nonadiabatic excited-state intramolecular proton transfer in 3-HOX and its derivatives.
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Affiliation(s)
- Neethu Anand
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O, Vithura, Thiruvananthapuram-695551, Kerala, India.
| | - Probal Nag
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O, Vithura, Thiruvananthapuram-695551, Kerala, India.
| | - Ravi Kumar Kanaparthi
- Department Of Chemistry, School Of Physical Sciences, Central University of Kerala, Tejaswini Hills, Periya, Kerala - 671320, India.
| | - Sivaranjana Reddy Vennapusa
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O, Vithura, Thiruvananthapuram-695551, Kerala, India.
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41
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Kim W, Kim T, Kang S, Hong Y, Würthner F, Kim D. Tracking Structural Evolution during Symmetry‐Breaking Charge Separation in Quadrupolar Perylene Bisimide with Time‐Resolved Impulsive Stimulated Raman Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Woojae Kim
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Taeyeon Kim
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Seongsoo Kang
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Yongseok Hong
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Frank Würthner
- Institut für Organische Chemie & Center for, Nanosystems Chemistry Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Dongho Kim
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
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42
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Kim W, Kim T, Kang S, Hong Y, Würthner F, Kim D. Tracking Structural Evolution during Symmetry‐Breaking Charge Separation in Quadrupolar Perylene Bisimide with Time‐Resolved Impulsive Stimulated Raman Spectroscopy. Angew Chem Int Ed Engl 2020; 59:8571-8578. [DOI: 10.1002/anie.202002733] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Woojae Kim
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Taeyeon Kim
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Seongsoo Kang
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Yongseok Hong
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
| | - Frank Würthner
- Institut für Organische Chemie & Center for, Nanosystems Chemistry Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Dongho Kim
- Department of Chemistry Spectroscopy Laboratory for Functional π-Electronic Systems Yonsei University 03722 Seoul Korea
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43
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Eng J, Penfold TJ. Understanding and Designing Thermally Activated Delayed Fluorescence Emitters: Beyond the Energy Gap Approximation. CHEM REC 2020; 20:831-856. [PMID: 32267093 DOI: 10.1002/tcr.202000013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
Abstract
In this article recent progress in the development of molecules exhibiting Thermally Activated Delayed Fluorescence (TADF) is discussed with a particular focus upon their application as emitters in highly efficient organic light emitting diodes (OLEDs). The key aspects controlling the desirable functional properties, e. g. fast intersystem crossing, high radiative rate and unity quantum yield, are introduced with a particular focus upon the competition between the key requirements needed to achieve high performance OLEDs. The design rules required for organic and metal organic materials are discussed, and the correlation between them outlined. Recent progress towards understanding the influence of the interaction between a molecule and its environment are explained as is the role of the mechanism for excited state formation in OLEDs. Finally, all of these aspects are combined to discuss the ability to implement high level design rules for achieving higher quality materials for commercial applications. This article highlights the significant progress that has been made in recent years, but also outlines the significant challenges which persist to achieve a full understanding of the TADF mechanism and improve the stability and performance of these materials.
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Affiliation(s)
- Julien Eng
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Thomas J Penfold
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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44
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Krueger TD, Boulanger SA, Zhu L, Tang L, Fang C. Discovering a rotational barrier within a charge-transfer state of a photoexcited chromophore in solution. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024901. [PMID: 32161777 PMCID: PMC7056454 DOI: 10.1063/1.5143441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/18/2020] [Indexed: 05/15/2023]
Abstract
Methylation occurs in a myriad of systems with protective and regulatory functions. 8-methoxypyrene-1,3,6-trisulfonate (MPTS), a methoxy derivative of a photoacid, serves as a model system to study effects of methylation on the excited state potential energy landscape. A suite of spectroscopic techniques including transient absorption, wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS), and fluorescence quantum yield measurements via steady-state electronic spectroscopy reveal the energy dissipation pathways of MPTS following photoexcitation. Various solvents enable a systematic characterization of the H-bonding interaction, viscosity, and dynamic solvation that influence the ensuing relaxation pathways. The formation of a charge-transfer state out of the Franck-Condon region occurs on the femtosecond-to-picosecond solvation timescale before encountering a rotational barrier. The rotational relaxation correlates with the H-bond donating strength of solvent, while the rotational time constant lengthens as solvent viscosity increases. Time-resolved excited-state FSRS, aided by quantum calculations, provides crucial structural dynamics knowledge and reveals the sulfonate groups playing a dominant role during solvation. Several prominent vibrational motions of the pyrene ring backbone help maneuver the population toward the more fluorescent state. These ultrafast correlated electronic and nuclear motions ultimately govern the fate of the photoexcited chromophore in solution. Overall, MPTS in water displays the highest probability to fluoresce, while the aprotic and more viscous dimethyl sulfoxide enhances the nonradiative pathways. These mechanistic insights may apply robustly to other photoexcited chromophores that do not undergo excited-state proton transfer or remain trapped in a broad electronic state and also provide design principles to control molecular optical responses with site-specific atomic substitution.
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Affiliation(s)
- Taylor D. Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Sean A. Boulanger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, USA
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45
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Pines E, Pines D, Gajst O, Huppert D. Reversible intermolecular-coupled-intramolecular (RICI) proton transfer occurring on the reaction-radius a of 2-naphthol-6,8-disulfonate photoacid. J Chem Phys 2020; 152:074205. [PMID: 32087655 DOI: 10.1063/1.5134760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Steady-state and time-resolved fluorescence techniques were employed to study the excited-state proton transfer (ESPT) from a reversibly dissociating photoacid, 2-naphthol-6,8-disulfonate (2N68DS). The reaction was carried out in water and in acetonitrile-water solutions. We find by carefully analyzing the geminate recombination dynamics of the photobase-proton pair that follows the ESPT reaction that there are two targets for the proton back-recombination reaction: the original O- dissociation site and the SO3 - side group at the 8 position which is closest to the proton OH dissociation site. This observation is corroborated in acetonitrile-water mixtures of χwater < 0.14, where a slow intramolecular ESPT occurs on a time scale of about 1 ns between the OH group and the SO3 - group via H-bonding water. The proton-transferred R*O- fluorescence band in mixtures of χwater < 0.14 where only intramolecular ESPT occurs is red shifted by about 2000 cm-1 from the free R*O- band in neat water. As the water content in the mixture increases above χwater = 0.14, the R*O- fluorescence band shifts noticeably to the blue region. For χwater > 0.23 the band resembles the free anion band observed in pure water. Concomitantly, the ESPT rate increases when χwater increases because the intermolecular ESPT to the solvent (bulk water) gradually prevails over the much slower intramolecular via the water-bridges ESPT process.
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Affiliation(s)
- Ehud Pines
- 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
| | - Oren Gajst
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dan Huppert
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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46
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Zilberg S. Design of Light‐Induced Molecular Switcher for the Driver of the Quantum Cellular Automata (QCA) Based on the Transition through the Intramolecular Charge Transfer (ICT) Structure. Isr J Chem 2020. [DOI: 10.1002/ijch.201900148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shmuel Zilberg
- Department of Chemical SciencesAriel University 40700 Ariel Israel
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47
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Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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48
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Jakob MA, Namboodiri M, Prandolini MJ, Laarmann T. Generation and characterization of tailored MIR waveforms for steering molecular dynamics. OPTICS EXPRESS 2019; 27:26979-26988. [PMID: 31674567 DOI: 10.1364/oe.27.026979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
The dream of physico-chemists to control molecular reactions with light beyond electronic excitations pushes the development of laser pulse shaping capabilities in the mid-infrared (MIR) spectral range. Here, we present a compact optical parametric amplifier platform for the generation and shaping of MIR laser pulses in the wavelength range between 8 μm and 15 μm. Opportunities for judiciously tailoring the electromagnetic waveform are investigated, demonstrating light field control with a spectral resolution of 59 GHz at a total spectral bandwidth of 5 THz. In experiments focusing on spectral amplitude manipulation these parameters result in a time window of 1.8 ps available for shaping the temporal pulse envelope and a phase modulation resolution of 100 mrad for several picosecond delays.
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49
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He X, Yang F, Li S, He X, Yu A, Chen J, Xu J, Wang J. Ultrafast Excited-State Intermolecular Proton Transfer in Indigo Oligomer. J Phys Chem A 2019; 123:6463-6471. [DOI: 10.1021/acs.jpca.9b06427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuemei He
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shuang Li
- Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, P. R. China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, P. R. China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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50
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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