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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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Szymczak JJ, Hofmann FD, Meuwly M. Structure and dynamics of solvent shells around photoexcited metal complexes. Phys Chem Chem Phys 2013; 15:6268-77. [DOI: 10.1039/c3cp44465a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gansmüller A, Concistrè M, McLean N, Johannessen OG, Marín-Montesinos I, Bovee-Geurts PHM, Verdegem P, Lugtenburg J, Brown RCD, Degrip WJ, Levitt MH. Towards an interpretation of 13C chemical shifts in bathorhodopsin, a functional intermediate of a G-protein coupled receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1350-7. [PMID: 19265671 DOI: 10.1016/j.bbamem.2009.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
Abstract
Photoisomerization of the membrane-bound light receptor protein rhodopsin leads to an energy-rich photostate called bathorhodopsin, which may be trapped at temperatures of 120 K or lower. We recently studied bathorhodopsin by low-temperature solid-state NMR, using in situ illumination of the sample in a purpose-built NMR probe. In this way we acquired (13)C chemical shifts along the retinylidene chain of the chromophore. Here we compare these results with the chemical shifts of the dark state chromophore in rhodopsin, as well as with the chemical shifts of retinylidene model compounds in solution. An earlier solid-state NMR study of bathorhodopsin found only small changes in the (13)C chemical shifts upon isomerization, suggesting only minor perturbations of the electronic structure in the isomerized retinylidene chain. This is at variance with our recent measurements which show much larger perturbations of the (13)C chemical shifts. Here we present a tentative interpretation of our NMR results involving an increased charge delocalization inside the polyene chain of the bathorhodopsin chromophore. Our results suggest that the bathochromic shift of bathorhodopsin is due to modified electrostatic interactions between the chromophore and the binding pocket, whereas both electrostatic interactions and torsional strain are involved in the energy storage mechanism of bathorhodopsin.
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Affiliation(s)
- Axel Gansmüller
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, England, UK
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Nibbering ETJ, Fidder H, Pines E. ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics. Annu Rev Phys Chem 2005; 56:337-67. [PMID: 15796704 DOI: 10.1146/annurev.physchem.56.092503.141314] [Citation(s) in RCA: 257] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.
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Affiliation(s)
- Erik T J Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany.
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Sakmar TP, Menon ST, Marin EP, Awad ES. Rhodopsin: insights from recent structural studies. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2002; 31:443-84. [PMID: 11988478 DOI: 10.1146/annurev.biophys.31.082901.134348] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
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Affiliation(s)
- Thomas P Sakmar
- Howard Hughes Medical Institute, Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, NY 10021, USA.
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Ujj L, Coates CG, Kelly JM, Kruger PE, McGarvey JJ, Atkinson GH. Picosecond Coherent Vibrational Spectroscopy (CARS) of a DNA-Intercalating Ru Complex. J Phys Chem B 2002. [DOI: 10.1021/jp012450z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laszlo Ujj
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Chemistry, Queens University, Belfast, Northern Ireland, Department of Chemistry, Trinity College, University of Dublin, Dublin, Ireland, and Department of Physics, University of West Florida, Pensacola, Florida 32514
| | - Colin G. Coates
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Chemistry, Queens University, Belfast, Northern Ireland, Department of Chemistry, Trinity College, University of Dublin, Dublin, Ireland, and Department of Physics, University of West Florida, Pensacola, Florida 32514
| | - John M. Kelly
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Chemistry, Queens University, Belfast, Northern Ireland, Department of Chemistry, Trinity College, University of Dublin, Dublin, Ireland, and Department of Physics, University of West Florida, Pensacola, Florida 32514
| | - Paul E. Kruger
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Chemistry, Queens University, Belfast, Northern Ireland, Department of Chemistry, Trinity College, University of Dublin, Dublin, Ireland, and Department of Physics, University of West Florida, Pensacola, Florida 32514
| | - John J. McGarvey
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Chemistry, Queens University, Belfast, Northern Ireland, Department of Chemistry, Trinity College, University of Dublin, Dublin, Ireland, and Department of Physics, University of West Florida, Pensacola, Florida 32514
| | - George H. Atkinson
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Chemistry, Queens University, Belfast, Northern Ireland, Department of Chemistry, Trinity College, University of Dublin, Dublin, Ireland, and Department of Physics, University of West Florida, Pensacola, Florida 32514
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Abstract
The crystal structure of rod cell visual pigment rhodopsin was recently solved at 2.8-A resolution. A critical evaluation of a decade of structure-function studies is now possible. It is also possible to begin to explain the structural basis for several unique physiological properties of the vertebrate visual system, including extremely low dark noise levels as well as high gain and color detection. The ligand-binding pocket of rhodopsin is remarkably compact, and several apparent chromophore-protein interactions were not predicted from extensive mutagenesis or spectroscopic studies. The transmembrane helices are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The helix movement model of receptor activation, which might apply to all G protein-coupled receptors (GPCRs) of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor is remarkable for a carboxy-terminal helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. Thus the cytoplasmic surface appears to be approximately the right size to bind to the transducin heterotrimer in a one-to-one complex. Future high-resolution structural studies of rhodopsin and other GPCRs will form a basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
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Affiliation(s)
- S T Menon
- Howard Hughes Medical Institute, Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York 10021, USA
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Degrip W, Rothschild K. Chapter 1 Structure and mechanism of vertebrate visual pigments. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Lyon LA, Keating CD, Fox AP, Baker BE, He L, Nicewarner SR, Mulvaney SP, Natan MJ. Raman spectroscopy. Anal Chem 1998; 70:341R-361R. [PMID: 9640107 DOI: 10.1021/a1980021p] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- L A Lyon
- Department of Chemistry, Pennsylvania State University, University Park 16802, USA
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Jäger F, Lou J, Nakanishi K, Ujj L, Atkinson GH. Vibrational Spectroscopy of a Picosecond, Structurally-Restricted Intermediate Containing a Seven-Membered Ring in the Room-Temperature Photoreaction of an Artificial Rhodopsin. J Am Chem Soc 1998. [DOI: 10.1021/ja972560c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Jäger
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Columbia University, New York, New York 10027
| | - Jihong Lou
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Columbia University, New York, New York 10027
| | - Koji Nakanishi
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Columbia University, New York, New York 10027
| | - L. Ujj
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Columbia University, New York, New York 10027
| | - G. H. Atkinson
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Columbia University, New York, New York 10027
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Ujj L, Jäger F, Atkinson GH. Vibrational spectrum of the lumi intermediate in the room temperature rhodopsin photo-reaction. Biophys J 1998; 74:1492-501. [PMID: 9512045 PMCID: PMC1299495 DOI: 10.1016/s0006-3495(98)77861-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The vibrational spectrum (650-1750 cm(-1)) of the lumi-rhodopsin (lumi) intermediate formed in the microsecond time regime of the room-temperature rhodopsin (RhRT) photoreaction is measured for the first time using picosecond time-resolved coherent anti-Stokes Raman spectroscopy (PTR/CARS). The vibrational spectrum of lumi is recorded 2.5 micros after the 3-ps, 500-nm excitation of RhRT. Complementary to Fourier transform infrared spectra recorded at Rh sample temperatures low enough to freeze lumi, these PTR/CARS results provide the first detailed view of the vibrational degrees of freedom of room-temperature lumi (lumiRT) through the identification of 21 bands. The exceptionally low intensity (compared to those observed in bathoRT) of the hydrogen out-of-plane (HOOP) bands, the moderate intensity and absolute positions of C-C stretching bands, and the presence of high-intensity C==C stretching bands suggest that lumiRT contains an almost planar (nontwisting), all-trans retinal geometry. Independently, the 944-cm(-1) position of the most intense HOOP band implies that a resonance coupling exists between the out-of-plane retinal vibrations and at least one group among the amino acids comprising the retinal binding pocket. The formation of lumiRT, monitored via PTR/CARS spectra recorded on the nanosecond time scale, can be associated with the decay of the blue-shifted intermediate (BSI(RT)) formed in equilibrium with the bathoRT intermediate. PTR/CARS spectra measured at a 210-ns delay contain distinct vibrational features attributable to BSI(RT), which suggest that the all-trans retinal in both BSI(RT) and lumiRT is strongly coupled to part of the retinal binding pocket. With regard to the energy storage/transduction mechanism in RhRT, these results support the hypothesis that during the formation of lumiRT, the majority of the photon energy absorbed by RhRT transfers to the apoprotein opsin.
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Affiliation(s)
- L Ujj
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson 85721-0041, USA
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F. Jäger,, Ujj L, Atkinson GH. Vibrational Spectrum of Bathorhodopsin in the Room-Temperature Rhodopsin Photoreaction. J Am Chem Soc 1997. [DOI: 10.1021/ja9715298] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- F. Jäger,
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - L. Ujj
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - G. H. Atkinson
- Contribution from the Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
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Weidlich O, Ujj L, Jäger F, Atkinson GH. Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy. Biophys J 1997; 72:2329-41. [PMID: 9129836 PMCID: PMC1184428 DOI: 10.1016/s0006-3495(97)78877-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.
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Affiliation(s)
- O Weidlich
- Department of Chemistry, University of Arizona, Tucson 85721, USA
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Jäger F, Ujj L, Atkinson GH, Sheves M, Livnah N, Ottolenghi M. Vibrational Spectrum of K-590 Containing 13C14,15 Retinal: Picosecond Time-Resolved Coherent Anti-Stokes Raman Spectroscopy of the Room Temperature Bacteriorhodopsin Photocycle. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961131i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | - M. Ottolenghi
- Department of Chemistry, Hebrew University, Jerusalem, Israel
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