1
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Yu Q, Li X, Shen C, Yu Z, Guan J, Zheng J. Blue-Shifted and Broadened Fluorescence Enhancement by Visible and Mode-Selective Infrared Double Excitations. J Phys Chem A 2024; 128:2912-2922. [PMID: 38572812 DOI: 10.1021/acs.jpca.3c07060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Mode-selective vibrational excitations to modify the electronic states of fluorescein dianion in methanol solutions are carried out with a femtosecond visible pulse synchronized with a tunable high-power, narrow-band picosecond infrared (IR) pulse. In this work, simultaneous intensity enhancement, peak blueshift, and line width broadening of fluorescence are observed in the visible/IR double resonance experiments. Comprehensive investigations on the modulation mechanism with scanning the vibrational excitation frequencies, tuning the time delay between the two excitation pulses, theoretical calculations, and nonlinear and linear spectroscopic measurements suggest that the fluorescence intensity enhancement is caused by the increase of the Franck-Condon factor induced by the vibrational excitations at the electronic ground state. Various enhancement effects are observed as vibrations initially excited by the IR photons relax to populate the vibrational modes of lower frequencies. The peak blueshift and line width broadening are caused by both increasing the Franck-Condon factors among different subensembles because of IR pre-excitation and the long-lived processes induced by the initial IR excitation. The results demonstrate that the fluorescence from the visible/IR double resonance experiments is not a simple sum frequency effect, and vibrational relaxations can produce profound effects modifying luminescence.
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Affiliation(s)
- Qirui Yu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Xinmao Li
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Chengzhen Shen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhihao Yu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Jianxin Guan
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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2
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Feid C, Luma L, Fischer T, Löffler JG, Grebenovsky N, Wachtveitl J, Heckel A, Bredenbeck J. Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer. Angew Chem Int Ed Engl 2024; 63:e202317047. [PMID: 38103205 DOI: 10.1002/anie.202317047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/18/2023]
Abstract
Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient. Here, we introduce two novel donor ncAAs based on an iminothioindoxyl (ITI) chromophore. The dimethylamino-ITI (DMA-ITI) and julolidine-ITI (J-ITI) moieties overcome the limitation of AzAla with a 50 times higher Vis extinction coefficient. While ITI moieties are known for ultrafast photoswitching, DMA-ITI and J-ITI exclusively form a hot ground state on the sub-ps timescale instead, which is essential for their usage as vibrational energy donor. In VET measurements of donor-sensor dipeptides we investigate the performance of the new donors. We observe 20 times larger signals compared to the established AzAla donor, which opens unprecedented possibilities for the study of VET in proteins.
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Affiliation(s)
- Carolin Feid
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Larita Luma
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
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3
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Hassani M, Mallon CJ, Monzy JN, Schmitz AJ, Brewer SH, Fenlon EE, Tucker MJ. Inhibition of vibrational energy flow within an aromatic scaffold via heavy atom effect. J Chem Phys 2023; 158:224201. [PMID: 37309893 PMCID: PMC10275622 DOI: 10.1063/5.0153760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
The regulation of intramolecular vibrational energy redistribution (IVR) to influence energy flow within molecular scaffolds provides a way to steer fundamental processes of chemistry, such as chemical reactivity in proteins and design of molecular diodes. Using two-dimensional infrared (2D IR) spectroscopy, changes in the intensity of vibrational cross-peaks are often used to evaluate different energy transfer pathways present in small molecules. Previous 2D IR studies of para-azidobenzonitrile (PAB) demonstrated that several possible energy pathways from the N3 to the cyano-vibrational reporters were modulated by Fermi resonance, followed by energy relaxation into the solvent [Schmitz et al., J. Phys. Chem. A 123, 10571 (2019)]. In this work, the mechanisms of IVR were hindered via the introduction of a heavy atom, selenium, into the molecular scaffold. This effectively eliminated the energy transfer pathway and resulted in the dissipation of the energy into the bath and direct dipole-dipole coupling between the two vibrational reporters. Several structural variations of the aforementioned molecular scaffold were employed to assess how each interrupted the energy transfer pathways, and the evolution of 2D IR cross-peaks was measured to assess the changes in the energy flow. By eliminating the energy transfer pathways through isolation of specific vibrational transitions, through-space vibrational coupling between an azido (N3) and a selenocyanato (SeCN) probe is facilitated and observed for the first time. Thus, the rectification of this molecular circuitry is accomplished through the inhibition of energy flow using heavy atoms to suppress the anharmonic coupling and, instead, favor a vibrational coupling pathway.
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Affiliation(s)
- Majid Hassani
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | | | - Judith N. Monzy
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Andrew J. Schmitz
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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4
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Chenchiliyan M, Kübel J, Ooi SA, Salvadori G, Mennucci B, Westenhoff S, Maj M. Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy. J Chem Phys 2023; 158:085103. [PMID: 36859103 DOI: 10.1063/5.0135268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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Affiliation(s)
- Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
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5
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Cho M. Molecular photothermal effects on time-resolved IR spectroscopy. J Chem Phys 2022; 157:124201. [DOI: 10.1063/5.0108826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Time-resolved IR pump-probe (IR-PP) and two-dimensional IR (2D-IR) spectroscopy are valuable techniques for studying various ultrafast chemical and biological processes in solutions. The time-dependent changes of nonlinear IR signals reflecting fast molecular processes such as vibrational energy transfer and chemical exchange provide invaluable information on the rates and mechanisms of solvation dynamics and structural transitions of multi-species vibrationally interacting molecular systems. However, due to the intrinsic difficulties in distinguishing the contributions of molecule-specific processes to the time-resolved IR signals from those resulting from local heating, it becomes challenging to interpret time-resolved IR-PP and 2D-IR spectra exhibiting transient growing-in spectral components and cross-peaks unambiguously. Here, theoretical considerations of various effects of vibrational coupling, energy transfer, chemical exchange, the generation of hot ground states, molecular photothermal process, and their combinations on the lineshapes and time-dependent intensities of IR-PP spectra and 2D-IR diagonal and cross-peaks are presented. We anticipate that the present work will help researchers using IR pump-probe and 2D-IR techniques to distinguish local heating-induced photothermal signals from genuine nonlinear IR signals.
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Affiliation(s)
- Minhaeng Cho
- Chemistry, Korea University, Korea, Republic of (South Korea)
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6
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Leong TX, Collins BK, Dey Baksi S, Mackin RT, Sribnyi A, Burin AL, Gladysz JA, Rubtsov IV. Tracking Energy Transfer across a Platinum Center. J Phys Chem A 2022; 126:4915-4930. [PMID: 35881911 PMCID: PMC9358659 DOI: 10.1021/acs.jpca.2c02017] [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] [Indexed: 12/02/2022]
Abstract
![]()
Rigid, conjugated alkyne bridges serve as important components
in various transition-metal complexes used for energy conversion,
charge separation, sensing, and molecular electronics. Alkyne stretching
modes have potential for modulating charge separation in donor–bridge–acceptor
compounds. Understanding the rules of energy relaxation and energy
transfer across the metal center in such compounds can help optimize
their electron transfer switching properties. We used relaxation-assisted
two-dimensional infrared spectroscopy to track energy transfer across
metal centers in platinum complexes featuring a triazole-terminated
alkyne ligand of two or six carbons, a perfluorophenyl ligand, and
two tri(p-tolyl)phosphine ligands. Comprehensive
analyses of waiting-time dynamics for numerous cross and diagonal
peaks were performed, focusing on coherent oscillation, energy transfer,
and cooling parameters. These observables augmented with density functional
theory computations of vibrational frequencies and anharmonic force
constants enabled identification of different functional groups of
the compounds. Computations of vibrational relaxation pathways and
mode couplings were performed, and two regimes of intramolecular energy
redistribution are described. One involves energy transfer between
ligands via high-frequency modes; the transfer is efficient only if
the modes involved are delocalized over both ligands. The energy transport
pathways between the ligands are identified. Another regime involves
redistribution via low-frequency delocalized modes, which does not
lead to interligand energy transport.
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Affiliation(s)
- Tammy X Leong
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Brenna K Collins
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sourajit Dey Baksi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Robert T Mackin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Artem Sribnyi
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - John A Gladysz
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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7
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Dereka B, Lewis NHC, Zhang Y, Hahn NT, Keim JH, Snyder SA, Maginn EJ, Tokmakoff A. Exchange-Mediated Transport in Battery Electrolytes: Ultrafast or Ultraslow? J Am Chem Soc 2022; 144:8591-8604. [PMID: 35470669 DOI: 10.1021/jacs.2c00154] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the mechanisms of charge transport in batteries is important for the rational design of new electrolyte formulations. Persistent questions about ion transport mechanisms in battery electrolytes are often framed in terms of vehicular diffusion by persistent ion-solvent complexes versus structural diffusion through the breaking and reformation of ion-solvent contacts, i.e., solvent exchange events. Ultrafast two-dimensional (2D) IR spectroscopy can probe exchange processes directly via the evolution of the cross-peaks on picosecond time scales. However, vibrational energy transfer in the absence of solvent exchange gives rise to the same spectral signatures, hiding the desired processes. We employ 2D IR on solvent resonances of a mixture of acetonitrile isotopologues to differentiate chemical exchange and energy-transfer dynamics in a comprehensive series of Li+, Mg2+, Zn2+, Ca2+, and Ba2+ bis(trifluoromethylsulfonyl)imide electrolytes from the dilute to the superconcentrated regime. No exchange phenomena occur within at least 100 ps, regardless of the ion identity, salt concentration, and presence of water. All of the observed spectral dynamics originate from the intermolecular energy transfer. These results place the lower experimental boundary on the ion-solvent residence times to several hundred picoseconds, much slower than previously suggested. With the help of MD simulations and conductivity measurements on the Li+ and Zn2+ systems, we discuss these results as a continuum of vehicular and structural modalities that vary with concentration and emphasize the importance of collective electrolyte motions to ion transport. These results hold broadly applicable to many battery-relevant ions and solvents.
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Affiliation(s)
- Bogdan Dereka
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Nicholas H C Lewis
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yong Zhang
- Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nathan T Hahn
- Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Material, Physical and Chemical Sciences Center, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Jonathan H Keim
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Scott A Snyder
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Edward J Maginn
- Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andrei Tokmakoff
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Joint Center for Energy Storage Research, Argonne National Laboratory, Lemont, Illinois 60439, United States
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8
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Cohn B, Sufrin S, Chuntonov L. Ultrafast vibrational excitation transfer on resonant antenna lattices revealed by two-dimensional infrared spectroscopy. J Chem Phys 2022; 156:121101. [DOI: 10.1063/5.0082161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
High-quality lattice resonances in arrays of infrared antennas operating in an open-cavity regime form polariton states by means of strong coupling to molecular vibrations. We studied polaritons formed by carbonyl stretching modes of (poly)methyl methacrylate on resonant antenna arrays using femtosecond 2DIR spectroscopy. At a normal incidence of excitation light, doubly degenerate antenna-lattice resonances (ALRs) form two polariton states: a lower polariton and an upper polariton. At an off-normal incidence geometry of 2DIR experiments, the ALR degeneracy is lifted and, consequently, the polariton energies are split. We spectrally resolved and tracked the time-dependent evolution of a cross-peak signal associated with the excitation of reservoir states and the unidirectional transfer of the excess energy to lower polaritons. Bi-exponential decay of the cross-peak suggests that a reversible energy exchange between the bright and dark lower polaritons occurs with a characteristic transfer time of ∼200 fs. The cross-peak signal further decays within ∼800 fs, which is consistent with the relaxation time of the carbonyl stretching vibration and with the dephasing time of the ALR. An increase in the excitation pulse intensity leads to saturation of the cross-peak amplitude and a modification of the relaxation dynamics. Using quantum-mechanical modeling, we found that the kinetic scheme that captures all the experimental observations implies that only the bright lower polariton accepts the energy from the reservoir, suggesting that transfer occurs via a mechanism involving dipole–dipole interaction. An efficient reservoir-to-polariton transfer can play an important role in developing novel room-temperature quantum optical devices in the mid-infrared wavelength region.
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Affiliation(s)
- Bar Cohn
- Schulich Faculty of Chemistry, Technion – Israel Institute of Technology, Haifa 3200003, Israel
- Solid State Institute, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Shmuel Sufrin
- Solid State Institute, Technion – Israel Institute of Technology, Haifa 3200003, Israel
- Faculty of Mechanical Engineering, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry, Technion – Israel Institute of Technology, Haifa 3200003, Israel
- Solid State Institute, Technion – Israel Institute of Technology, Haifa 3200003, Israel
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9
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Deniz E, Löffler JG, Kondratiev A, Thun AR, Shen Y, Wille G, Bredenbeck J. High-precision background correction and artifact suppression for ultrafast spectroscopy by quasi-simultaneous measurements in a split-sample cell. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:033001. [PMID: 35364971 DOI: 10.1063/5.0079958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Alternating acquisition of background and sample spectra is often employed in conventional Fourier-transform infrared spectroscopy or ultraviolet-visible spectroscopy for accurate background subtraction. For example, for solvent background correction, typically a spectrum of a cuvette with solvent is measured and subtracted from a spectrum of a cuvette with solvent and solute. Ultrafast spectroscopies, though, come with many peculiarities that make the collection of well-matched, subtractable background and sample spectra challenging. Here, we present a demountable split-sample cell in combination with a modified Lissajous scanner to overcome these challenges. It allows for quasi-simultaneous measurements of background and sample spectra, mitigating the effects of drifts of the setup and maintaining the beam and sample geometry when swapping between background and sample measurements. The cell is moving between subsequent laser shots to refresh the excited sample volume. With less than 45 μl of solution for 150 μm optical thickness, sample usage is economical. Cell assembly is a key step and covered in an illustrated protocol.
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Affiliation(s)
- E Deniz
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - J G Löffler
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - A Kondratiev
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - A R Thun
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Y Shen
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - G Wille
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - J Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
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10
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Abstract
Coherent multidimensional spectroscopy has been widely used to study the structure and dynamics of chemical and biological systems. Each ultrashort pulse from a single mode-locked laser is split into multiple pulses by beam splitters. Their arrival times at a given molecular sample are controlled with mechanical time-delay generators for time-resolved measurements of molecular responses. Such nonlinear vibrational, electronic, or vibrational-electronic spectroscopy can now be carried out with multiple mode-locked lasers with highly stabilized repetition and sometimes carrier-envelope-offset frequencies. By precisely controlling the repetition frequencies of multiple mode-locked lasers, one can achieve automatic delay time scanning, known as asynchronous optical sampling, to investigate various relaxation processes associated with photochemical or photobiological phenomena at one sweep in time. In this Perspective, the current developments and applications of multiple mode-locked laser-based techniques to time-resolved nonlinear spectroscopy of chromophores in condensed phases are discussed. The author's perspective on this approach is also presented.
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Affiliation(s)
- Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
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11
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Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids. Nat Commun 2021; 12:3284. [PMID: 34078890 PMCID: PMC8172543 DOI: 10.1038/s41467-021-23591-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
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12
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El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. J Chem Phys 2021; 154:124201. [PMID: 33810651 DOI: 10.1063/5.0039969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Guillaume Le Breton
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luuk J G W van Wilderen
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
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13
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Boulatov A, Burin AL. Crucial effect of transverse vibrations on the transport through polymer chains. J Chem Phys 2020; 153:134102. [PMID: 33032425 DOI: 10.1063/5.0018591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The low temperature transport of electron, or vibrational or electronic exciton toward polymer chains, turns out to be dramatically sensitive to its interaction with transverse acoustic vibrations. We show that this interaction leads to a substantial polaron effect and decoherence, which are generally stronger than those associated with longitudinal vibrations. For site-dependent interactions, transverse phonons form subohmic bath leading to the quantum phase transition accompanied by full suppression of the transport at zero temperature and fast decoherence characterized by temperature dependent rate k2 ∝ T3/4 at low temperature, while k2 ∝ T2 for site-independent interactions. The latter dependence was used to interpret recent measurements of temperature dependent vibrational energy transport in polyethylene glycol oligomers.
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Affiliation(s)
- Alexei Boulatov
- National Research University Higher School of Economics, 11 Pokrovsky Blvd., Moscow 101000, Russia
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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14
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Chuntonov L, Rubtsov IV. Surface-enhanced ultrafast two-dimensional vibrational spectroscopy with engineered plasmonic nano-antennas. J Chem Phys 2020; 153:050902. [DOI: 10.1063/5.0013956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute, Technion – Israel Institute of Technology, Haifa 3200003, Israel
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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15
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Guan J, Wei R, Prlj A, Peng J, Lin K, Liu J, Han H, Corminboeuf C, Zhao D, Yu Z, Zheng J. Direct Observation of Aggregation‐Induced Emission Mechanism. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jianxin Guan
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Rong Wei
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Antonio Prlj
- Laboratory for Computational Molecular Design École polytechnique fédérale de Lausanne Lausanne Switzerland
| | - Jie Peng
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Kun‐Han Lin
- Laboratory for Computational Molecular Design École polytechnique fédérale de Lausanne Lausanne Switzerland
| | - Jitian Liu
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Han Han
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design École polytechnique fédérale de Lausanne Lausanne Switzerland
| | - Dahui Zhao
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Zhihao Yu
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
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16
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Guan J, Wei R, Prlj A, Peng J, Lin KH, Liu J, Han H, Corminboeuf C, Zhao D, Yu Z, Zheng J. Direct Observation of Aggregation-Induced Emission Mechanism. Angew Chem Int Ed Engl 2020; 59:14903-14909. [PMID: 32441469 DOI: 10.1002/anie.202004318] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/03/2020] [Indexed: 12/30/2022]
Abstract
The mechanism of aggregation-induced emission, which overcomes the common aggregation-caused quenching problem in organic optoelectronics, is revealed by monitoring the real time structural evolution and dynamics of electronic excited state with frequency and polarization resolved ultrafast UV/IR spectroscopy and theoretical calculations. The formation of Woodward-Hoffmann cyclic intermediates upon ultraviolet excitation is observed in dilute solutions of tetraphenylethylene and its derivatives but not in their respective solid. The ultrafast cyclization provides an efficient nonradiative relaxation pathway through crossing a conical intersection. Without such a reaction mechanism, the electronic excitation is preserved in the molecular solids and the molecule fluoresces efficiently, aided by the very slow intermolecular charge and energy transfers due to the well separated molecular packing arrangement. The mechanisms can be general for tuning the properties of chromophores in different phases for various important applications.
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Affiliation(s)
- Jianxin Guan
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Rong Wei
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Antonio Prlj
- Laboratory for Computational Molecular Design, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Jie Peng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Kun-Han Lin
- Laboratory for Computational Molecular Design, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Jitian Liu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Han Han
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Dahui Zhao
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Zhihao Yu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
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17
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Leitner DM, Yamato T. Recent developments in the computational study of protein structural and vibrational energy dynamics. Biophys Rev 2020; 12:317-322. [PMID: 32124240 DOI: 10.1007/s12551-020-00661-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/23/2020] [Indexed: 12/11/2022] Open
Abstract
Recent developments in the computational study of energy transport in proteins are reviewed, including advances in both methodology and applications. The concept of energy exchange network (EEN) is discussed, and a recent calculation of EENs for the allosteric protein FixL is reviewed, which illustrates how residues and protein regions involved in the allosteric transition can be identified. Recent work has examined relations between EENs and protein dynamics as well as structure. We review some of the computational studies carried out on several proteins that explore connections between energy conductivity across polar contacts in proteins and between proteins and water and equilibrium dynamics of the contacts, and we discuss some of the recent experimental work that addresses this topic.
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Affiliation(s)
- David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, NV, 89557, USA.
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
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18
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Schmitz AJ, Pandey HD, Chalyavi F, Shi T, Fenlon EE, Brewer SH, Leitner DM, Tucker MJ. Tuning Molecular Vibrational Energy Flow within an Aromatic Scaffold via Anharmonic Coupling. J Phys Chem A 2019; 123:10571-10581. [PMID: 31735035 DOI: 10.1021/acs.jpca.9b08010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
From guiding chemical reactivity in synthesis or protein folding to the design of energy diodes, intramolecular vibrational energy redistribution harnesses the power to influence the underlying fundamental principles of chemistry. To evaluate the ability to steer these processes, the mechanism and time scales of intramolecular vibrational energy redistribution through aromatic molecular scaffolds have been assessed by utilizing two-dimensional infrared (2D IR) spectroscopy. 2D IR cross peaks reveal energy relaxation through an aromatic scaffold from the azido- to the cyano-vibrational reporters in para-azidobenzonitrile (PAB) and para-(azidomethyl)benzonitrile (PAMB) prior to energy relaxation into the solvent. The rates of energy transfer are modulated by Fermi resonances, which are apparent by the coupling cross peaks identified within the 2D IR spectrum. Theoretical vibrational mode analysis allowed the determination of the origins of the energy flow, the transfer pathway, and a direct comparison of the associated transfer rates, which were in good agreement with the experimental results. Large variations in energy-transfer rates, approximately 1.9 ps for PAB and 23 ps for PAMB, illustrate the importance of strong anharmonic coupling, i.e., Fermi resonance, on the transfer pathways. In particular, vibrational energy rectification is altered by Fermi resonances of the cyano- and azido-modes allowing control of the propensity for energy flow.
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Affiliation(s)
- Andrew J Schmitz
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Hari Datt Pandey
- Department of Chemistry , University of California , Riverside , California 92521 , United States
| | - Farzaneh Chalyavi
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Tianjiao Shi
- Department of Chemistry , Franklin & Marshall College , Lancaster , Pennsylvania 17604-3003 , United States
| | - Edward E Fenlon
- Department of Chemistry , Franklin & Marshall College , Lancaster , Pennsylvania 17604-3003 , United States
| | - Scott H Brewer
- Department of Chemistry , Franklin & Marshall College , Lancaster , Pennsylvania 17604-3003 , United States
| | - David M Leitner
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
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19
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Heyne K, Kühn O. Infrared Laser Excitation Controlled Reaction Acceleration in the Electronic Ground State. J Am Chem Soc 2019; 141:11730-11738. [DOI: 10.1021/jacs.9b02600] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Karsten Heyne
- Department of Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Oliver Kühn
- Institute of Physics, University of Rostock, Albert Einstein-Strasse 23-24, 18059 Rostock, Germany
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20
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Kim IP, Benderskii VA. Sol–Gel Transition-Accompanied Radical Polymerization Initiated by Two Primary Radicals. HIGH ENERGY CHEMISTRY 2019. [DOI: 10.1134/s001814391903007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Ghosh A, Prasad AK, Chuntonov L. Two-Dimensional Infrared Spectroscopy Reveals Molecular Self-Assembly on the Surface of Silver Nanoparticles. J Phys Chem Lett 2019; 10:2481-2486. [PMID: 30978284 DOI: 10.1021/acs.jpclett.9b00530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The conformation of molecules, peptides, and proteins, self-assembled into structured monolayers on the surface of metal nanoparticles (NPs), can strongly affect their properties and use in chemical or nanobiomedical applications. Elucidating molecular conformations on the NP surface is highly challenging, and the microscopic details mostly remain elusive. Using polarization-selective third-order two-dimensional ultrafast infrared spectroscopy, we revealed the highly ordered intermolecular structure of γ-tripeptide glutathione on the surface of silver NPs in aqueous solution. Glutathione is an antioxidant thiol abundant in living cells; it is extensively used in NP chemistry and related research. We identified conditions where the interaction of glutathione with the NP surface facilitates formation of a β-sheet-like structure enclosing the NPs. A spectroscopic signature associated with the assembly of β-sheets into an amyloid fibril-like structure was also observed. Remarkably, the interaction with the metal surface promotes formation of a fibril-like structure by a small peptide involving only two amino acids.
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Affiliation(s)
- Anup Ghosh
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Amit K Prasad
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
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22
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Baumann T, Hauf M, Schildhauer F, Eberl KB, Durkin PM, Deniz E, Löffler JG, Acevedo‐Rocha CG, Jaric J, Martins BM, Dobbek H, Bredenbeck J, Budisa N. Ortsaufgelöste Beobachtung von Schwingungsenergietransfer durch ein genetisch codiertes ultraschnelles Heizelement. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tobias Baumann
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Matthias Hauf
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Fabian Schildhauer
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Katharina B. Eberl
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Patrick M. Durkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Erhan Deniz
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Jan G. Löffler
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | | | - Jelena Jaric
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
- Derzeitige Adresse: Hospira Zagreb d.o.o.a Pfizer company Prudnicka cesta 60 10291 Prigorje Brdovecko Kroatien
| | - Berta M. Martins
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Unter den Linden 6 10099 Berlin Deutschland
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Unter den Linden 6 10099 Berlin Deutschland
| | - Jens Bredenbeck
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
- Department of ChemistryUniversity of Manitoba 44 Dysart Rd R3T 2N2 Winnipeg MB Kanada
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23
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Baumann T, Hauf M, Schildhauer F, Eberl KB, Durkin PM, Deniz E, Löffler JG, Acevedo-Rocha CG, Jaric J, Martins BM, Dobbek H, Bredenbeck J, Budisa N. Site-Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater. Angew Chem Int Ed Engl 2019; 58:2899-2903. [PMID: 30589180 DOI: 10.1002/anie.201812995] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 12/22/2022]
Abstract
Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site-selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site-specific incorporation of the non-canonical amino acid β-(1-azulenyl)-l-alanine (AzAla) through genetic code expansion. As an exception to Kasha's rule, AzAla undergoes ultrafast internal conversion and heating after S1 excitation while upon S2 excitation, it serves as a fluorescent label. We equipped PDZ3, a protein interaction domain of postsynaptic density protein 95, with this ultrafast heater at two distinct positions. We indeed observed VET from the incorporation sites in the protein to a bound peptide ligand on the picosecond timescale by ultrafast IR spectroscopy. This approach based on genetically encoded AzAla paves the way for detailed studies of VET and its role in a wide range of proteins.
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Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Fabian Schildhauer
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Katharina B Eberl
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Patrick M Durkin
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Erhan Deniz
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Jan G Löffler
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | | | - Jelena Jaric
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,Present address: Hospira Zagreb d.o.o., a Pfizer company, Prudnicka cesta 60, 10291, Prigorje Brdovecko, Croatia
| | - Berta M Martins
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,Department of Chemistry, University of Manitoba, 44 Dysart Rd, R3T 2N2, Winnipeg, MB, Canada
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24
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Porter TM, Wang J, Li Y, Xiang B, Salsman C, Miller JS, Xiong W, Kubiak CP. Direct observation of the intermediate in an ultrafast isomerization. Chem Sci 2019; 10:113-117. [PMID: 30713623 PMCID: PMC6333165 DOI: 10.1039/c8sc03258k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/05/2018] [Indexed: 11/21/2022] Open
Abstract
Using a combination of two-dimensional infrared (2D IR) and variable temperature Fourier transform infrared (FTIR) spectroscopies the rapid structural isomerization of a five-coordinate ruthenium complex is investigated. In methylene chloride, three exchanging isomers were observed: (1) square pyramidal equatorial, (1); (2) trigonal bipyramidal, (0); and (3) square pyramidal apical, (2). Exchange between 1 and 0 was found to be an endergonic process (ΔH = 0.84 (0.08) kcal mol-1, ΔS = 0.6 (0.4) eu) with an isomerization time constant of 4.3 (1.5) picoseconds (ps, 10-12 s). Exchange between 0 and 2 however was found to be exergonic (ΔH = -2.18 (0.06) kcal mol-1, ΔS = -5.3 (0.3) eu) and rate limiting with an isomerization time constant of 6.3 (1.6) ps. The trigonal bipyramidal complex was found to be an intermediate, with an activation barrier of 2.2 (0.2) kcal mol-1 and 2.4 (0.2) kcal mol-1 relative to the equatorial and apical square pyramidal isomers respectively. This study provides direct validation of the mechanism of Berry pseudorotation - the pairwise exchange of ligands in a five-coordinate complex - a process that was first described over fifty years ago. This study also clearly demonstrates that the rate of pseudorotation approaches the frequency of molecular vibrations.
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Affiliation(s)
- Tyler M Porter
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
| | - Jiaxi Wang
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
| | - Yingmin Li
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
| | - Bo Xiang
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
| | - Catherine Salsman
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
| | - Joel S Miller
- Department of Chemistry , University of Utah , 315 South 1400 East, Room 2124 , Salt Lake City , Utah 84112-0850 , USA
| | - Wei Xiong
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
| | - Clifford P Kubiak
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , California 92093-0358 , USA . ;
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25
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Zhang Y, Chen X, Zheng B, Guo X, Pan Y, Chen H, Li H, Min S, Guan C, Huang KW, Zheng J. Structural analysis of transient reaction intermediate in formic acid dehydrogenation catalysis using two-dimensional IR spectroscopy. Proc Natl Acad Sci U S A 2018; 115:12395-12400. [PMID: 30455307 PMCID: PMC6298111 DOI: 10.1073/pnas.1809342115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The molecular structure of a catalytically active key intermediate is determined in solution by employing 2D IR spectroscopy measuring vibrational cross-angles. The formate intermediate (2) in the formic acid dehydrogenation reaction catalyzed by a phosphorus-nitrogen PN3P-Ru catalyst is elucidated. Our spectroscopic studies show that the complex features a formate ion directly attached to the Ru center as a ligand, and a proton added to the imine arm of the dearomatized PN3P* ligand. During the catalytic process, the imine arms are not only reversibly protonated and deprotonated, but also interacting with the protic substrate molecules, effectively serving as the local proton buffer to offer remarkable stability with a turnover number (TON) over one million.
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Affiliation(s)
- Yufan Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, 100871 Beijing, China
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Xin Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, 100871 Beijing, China
| | - Bin Zheng
- King Abdullah University of Science and Technology Catalysis Center, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
| | - Xunmin Guo
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, 100871 Beijing, China
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Yupeng Pan
- King Abdullah University of Science and Technology Catalysis Center, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology , 23955-6900 Thuwal, Saudi Arabia
| | - Hailong Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, 100871 Beijing, China
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Huaifeng Li
- King Abdullah University of Science and Technology Catalysis Center, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology , 23955-6900 Thuwal, Saudi Arabia
| | - Shixiong Min
- King Abdullah University of Science and Technology Catalysis Center, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology , 23955-6900 Thuwal, Saudi Arabia
| | - Chao Guan
- King Abdullah University of Science and Technology Catalysis Center, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology , 23955-6900 Thuwal, Saudi Arabia
| | - Kuo-Wei Huang
- King Abdullah University of Science and Technology Catalysis Center, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia;
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology , 23955-6900 Thuwal, Saudi Arabia
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, 100871 Beijing, China;
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26
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Cohn B, Engelman B, Goldner A, Chuntonov L. Two-Dimensional Infrared Spectroscopy with Local Plasmonic Fields of a Trimer Gap-Antenna Array. J Phys Chem Lett 2018; 9:4596-4601. [PMID: 30044640 DOI: 10.1021/acs.jpclett.8b01937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Half-wavelength plasmonic antennas tuned to resonance with molecular vibrational excitations have been demonstrated to enhance 2DIR signals by multiple orders of magnitude. We design doubly degenerate in-plane plasmonic normal modes of the symmetric trimer gap-antenna, which have orthogonal dipole moments excited by light of the appropriate polarization, to localize the enhanced field into the antenna's gap. Vibrational excitations serve as sensitive probes of the plasmonic fields. 2DIR spectroscopy of thin molecular films indicates that molecules emitting enhanced signals experience an electric field with a direction independent of the excitation laser pulse polarization. Our results illustrate the trade-off between the large signal amplification in molecules close to the antenna surface by resonant plasmons, where the direction of the enhanced fields follows metal surface boundary conditions, and the associated limitations for the polarization-selective spectroscopy. The ultrafast quantum dynamics reported by the enhanced signals is not affected by its interaction with plasmonic excitation.
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27
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28
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Pyles CG, Olson CM, Massari AM. Vibrational heavy atom effect controls relaxation and spectral diffusion in triphenyl hydride complexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Affiliation(s)
- Sean C. Edington
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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30
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Pandey HD, Leitner DM. Small Saccharides as a Blanket around Proteins: A Computational Study. J Phys Chem B 2018; 122:7277-7285. [DOI: 10.1021/acs.jpcb.8b04632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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31
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Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation. Nat Chem 2018; 10:126-131. [PMID: 29359754 DOI: 10.1038/nchem.2909] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 11/14/2017] [Indexed: 11/08/2022]
Abstract
Infrared (IR) excitation of vibrations that participate in the reaction coordinate of an otherwise thermally driven chemical reaction are believed to lead to its acceleration. Attempts at the practical realization of this concept have been hampered so far by competing processes leading to sample heating. Here we demonstrate, using femtosecond IR-pump IR-probe experiments, the acceleration of urethane and polyurethane formation due to vibrational excitation of the reactants for 1:1 mixtures of phenylisocyanate and cyclohexanol, and toluene-2,4-diisocyanate and 2,2,2-trichloroethane-1,1-diol, respectively. We measured reaction rate changes upon selective vibrational excitation with negligible heating of the sample and observed an increase of the reaction rate up to 24%. The observation is rationalized using reactant and transition-state structures obtained from quantum chemical calculations. We subsequently used IR-driven reaction acceleration to write a polyurethane square on sample windows using a femtosecond IR pulse.
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32
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Pindelska E, Sokal A, Kolodziejski W. Pharmaceutical cocrystals, salts and polymorphs: Advanced characterization techniques. Adv Drug Deliv Rev 2017; 117:111-146. [PMID: 28931472 DOI: 10.1016/j.addr.2017.09.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/21/2017] [Accepted: 09/14/2017] [Indexed: 12/11/2022]
Abstract
The main goal of a novel drug development is to obtain it with optimal physiochemical, pharmaceutical and biological properties. Pharmaceutical companies and scientists modify active pharmaceutical ingredients (APIs), which often are cocrystals, salts or carefully selected polymorphs, to improve the properties of a parent drug. To find the best form of a drug, various advanced characterization methods should be used. In this review, we have described such analytical methods, dedicated to solid drug forms. Thus, diffraction, spectroscopic, thermal and also pharmaceutical characterization methods are discussed. They all are necessary to study a solid API in its intrinsic complexity from bulk down to the molecular level, gain information on its structure, properties, purity and possible transformations, and make the characterization efficient, comprehensive and complete. Furthermore, these methods can be used to monitor and investigate physical processes, involved in the drug development, in situ and in real time. The main aim of this paper is to gather information on the current advancements in the analytical methods and highlight their pharmaceutical relevance.
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33
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Delor M, Archer SA, Keane T, Meijer AJHM, Sazanovich IV, Greetham GM, Towrie M, Weinstein JA. Directing the path of light-induced electron transfer at a molecular fork using vibrational excitation. Nat Chem 2017; 9:1099-1104. [DOI: 10.1038/nchem.2793] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/05/2017] [Indexed: 11/09/2022]
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34
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A Spin-Boson Screening approach for unraveling dominant vibrational energy transfer pathways in molecular materials. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.09.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Leger JD, Varner C, Rubtsov IV. Multi-mode heterodyned 5th-order infrared spectroscopy. J Chem Phys 2016; 145:154201. [DOI: 10.1063/1.4963815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joel D. Leger
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Clyde Varner
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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36
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El Khoury Y, Van Wilderen LJGW, Bredenbeck J. Ultrafast 2D-IR spectroelectrochemistry of flavin mononucleotide. J Chem Phys 2016; 142:212416. [PMID: 26049436 DOI: 10.1063/1.4916916] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We demonstrate the coupling of ultrafast two-dimensional infrared (2D-IR) spectroscopy to electrochemistry in solution and apply it to flavin mononucleotide, an important cofactor of redox proteins. For this purpose, we designed a spectroelectrochemical cell optimized for 2D-IR measurements in reflection and measured the time-dependent 2D-IR spectra of the oxidized and reduced forms of flavin mononucleotide. The data show anharmonic coupling and vibrational energy transfer between different vibrational modes in the two redox species. Such information is inaccessible with redox-controlled steady-state FTIR spectroscopy. The wide range of applications offered by 2D-IR spectroscopy, such as sub-picosecond structure determination, IR band assignment via energy transfer, disentangling reaction mixtures through band connectivity in the 2D spectra, and the measurement of solvation dynamics and chemical exchange can now be explored under controlled redox potential. The development of this technique furthermore opens new horizons for studying the dynamics of redox proteins.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main, Germany
| | - Luuk J G W Van Wilderen
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main, Germany
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37
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Yang F, Zhao J, Wang J. Two-Dimensional Infrared Study of (13)C-Natural Abundant Vibrational Transition Reveals Intramolecular Vibrational Redistribution Rather than Fluxional Exchange in Mn(CO)5Br. J Phys Chem B 2016; 120:1304-11. [PMID: 26836759 DOI: 10.1021/acs.jpcb.5b11310] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, molecular-symmetry enhanced (13)CO natural abundant isotopic infrared transition was identified in Mn(CO)5Br dissolved in CCl4 by FTIR spectroscopy. Diagonal and associated off-diagonal two-dimensional IR (2D IR) peaks of the (13)CO-species were found to be spectrally separated from the all-(12)CO species, allowing a direct probe of the (13)C natural abundant ensemble. Temperature-dependent FTIR experiment showed no evidence of ligand exchange in the metal carbonyl complex. Intramolecular vibrational redistribution dynamics among the CO stretching vibrational states were extracted using population-time dependent 2D IR diagonal and off-diagonal peaks for both radial mono-(13)CO and all-(12)CO isotopomers. This work demonstrates the potential use of natural abundant isotopic molecular species as a probe for revealing equilibrium and nonequilibrium structural dynamics in condensed-phase molecular systems.
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Affiliation(s)
- Fan Yang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, The Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, The Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, The Chinese Academy of Sciences , Beijing, 100190, People's Republic of China
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38
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Chuntonov L. 2D-IR spectroscopy of hydrogen-bond-mediated vibrational excitation transfer. Phys Chem Chem Phys 2016; 18:13852-60. [DOI: 10.1039/c6cp01640e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Inter-molecular vibrational energy transfer in the hydrogen-bonded complexes of methyl acetate and 4-cyanophenol is studied by dual-frequency 2D-IR spectroscopy.
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Affiliation(s)
- Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute
- Technion – Israel Institute of Technology
- Haifa 32000
- Israel
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39
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Lukin L. Initial spatial distribution of geminate charge carriers photogenerated in doped conjugated polymers. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Rubtsova NI, Qasim LN, Kurnosov AA, Burin AL, Rubtsov IV. Ballistic Energy Transport in Oligomers. Acc Chem Res 2015; 48:2547-55. [PMID: 26305731 DOI: 10.1021/acs.accounts.5b00299] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of nanocomposite materials with desired heat management properties, including nanowires, layered semiconductor structures, and self-assembled monolayer (SAM) junctions, attracts broad interest. Such materials often involve polymeric/oligomeric components and can feature high or low thermal conductivity, depending on their design. For example, in SAM junctions made of alkane chains sandwiched between metal layers, the thermal conductivity can be very low, whereas the fibers of ordered polyethylene chains feature high thermal conductivity, exceeding that of many pure metals. The thermal conductivity of nanostructured materials is determined by the energy transport between and within each component of the material, which all need to be understood for optimizing the properties. For example, in the SAM junctions, the energy transport across the metal-chain interface as well as the transport through the chains both determine the overall heat conductivity, however, to separate these contributions is difficult. Recently developed relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy is capable of studying energy transport in individual molecules in the time domain. The transport in a molecule is initiated by exciting an IR-active group (a tag); the method records the influence of the excess energy on another mode in the molecule (a reporter). The energy transport time can be measured for different reporters, and the transport speed through the molecule is evaluated. Various molecules were interrogated by RA 2DIR: in molecules without repeating units (disordered), the transport mechanism was expected and found to be diffusive. The transport via an oligomer backbone can potentially be ballistic, as the chain offers delocalized vibrational states. Indeed, the transport regime via three tested types of oligomers, alkanes, polyethyleneglycols, and perfluoroalkanes was found to be ballistic, whereas the transport within the end groups was diffusive. Interestingly, the transport speeds via these chains were different. Moreover, the transport speed was found to be dependent on the vibrational mode initiating the transport. For the difference in the transport speeds to be explained, the chain bands involved in the wavepacket formation were analyzed, and specific optical bands of the chain were identified as the energy transporters. For example, the transport initiated in alkanes by the stretching mode of the azido end group (2100 cm(-1)) occurs predominantly via the CH2 twisting and wagging chain bands, but the transport initiated by the C=O stretching modes of the carboxylic acid or succinimide ester end groups occurs via C-C stretching and CH2 rocking bands of the alkane chain. Direct formation of the wavepacket within the CH2 twisting and wagging chain bands occurs when the transport is initiated by the N═N stretching mode (1270 cm-1) of the azido end-group. The transport via optical chain bands in oligomers involves rather large vibrational quanta (700-1400 cm(-1)), resulting in efficient energy delivery to substantial distances. Achieved quantitative description of various energy transport steps in oligomers, including the specific contributions of different chain bands, can result in a better understanding of the transport steps in nanocomposite materials, including SAM junctions, and lead towards designing systems for molecular electronics with a controllable energy transport speed.
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Affiliation(s)
- Natalia I. Rubtsova
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Layla N. Qasim
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Arkady A. Kurnosov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L. Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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41
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van Wilderen LJGW, Bredenbeck J. Von ultraschnellen Strukturbestimmungen bis zum Steuern von Reaktionen: mehrdimensionale gemischte IR/nicht-IR-Schwingungsspektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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42
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van Wilderen LJGW, Bredenbeck J. From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies. Angew Chem Int Ed Engl 2015; 54:11624-40. [PMID: 26394274 DOI: 10.1002/anie.201503155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/27/2022]
Abstract
Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential.
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Affiliation(s)
| | - Jens Bredenbeck
- Institute of Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main (Germany).
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43
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Rubtsova NI, Nyby CM, Zhang H, Zhang B, Zhou X, Jayawickramarajah J, Burin AL, Rubtsov IV. Room-temperature ballistic energy transport in molecules with repeating units. J Chem Phys 2015; 142:212412. [PMID: 26049432 DOI: 10.1063/1.4916326] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In materials, energy can propagate by means of two limiting regimes: diffusive and ballistic. Ballistic energy transport can be fast and efficient and often occurs with a constant speed. Using two-dimensional infrared spectroscopy methods, we discovered ballistic energy transport via individual polyethylene chains with a remarkably high speed of 1440 m/s and the mean free path length of 14.6 Å in solution at room temperature. Whereas the transport via the chains occurs ballistically, the mechanism switches to diffusive with the effective transport speed of 130 m/s at the end-groups attached to the chains. A unifying model of the transport in molecules is presented with clear time separation and additivity among the transport along oligomeric fragments, which occurs ballistically, and the transport within the disordered fragments, occurring diffusively. The results open new avenues for making novel elements for molecular electronics, including ultrafast energy transporters, controlled chemical reactors, and sub-wavelength quantum nanoseparators.
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Affiliation(s)
- Natalia I Rubtsova
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Clara M Nyby
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Hong Zhang
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Boyu Zhang
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Xiao Zhou
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | | | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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44
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Yue Y, Qasim LN, Kurnosov AA, Rubtsova NI, Mackin RT, Zhang H, Zhang B, Zhou X, Jayawickramarajah J, Burin AL, Rubtsov IV. Band-Selective Ballistic Energy Transport in Alkane Oligomers: Toward Controlling the Transport Speed. J Phys Chem B 2015; 119:6448-56. [DOI: 10.1021/acs.jpcb.5b03658] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuankai Yue
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Layla N. Qasim
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Arkady A. Kurnosov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Natalia I. Rubtsova
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Robert T. Mackin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Hong Zhang
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Boyu Zhang
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - Alexander L. Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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45
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Delor M, Sazanovich IV, Towrie M, Weinstein JA. Probing and Exploiting the Interplay between Nuclear and Electronic Motion in Charge Transfer Processes. Acc Chem Res 2015; 48:1131-9. [PMID: 25789559 DOI: 10.1021/ar500420c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Born-Oppenheimer approximation refers to the assumption that the nuclear and electronic wave functions describing a molecular system evolve and can be determined independently. It is now well-known that this approximation often breaks down and that nuclear-electronic (vibronic) coupling contributes greatly to the ultrafast photophysics and photochemistry observed in many systems ranging from simple molecules to biological organisms. In order to probe vibronic coupling in a time-dependent manner, one must use spectroscopic tools capable of correlating the motions of electrons and nuclei on an ultrafast time scale. Recent developments in nonlinear multidimensional electronic and vibrational spectroscopies allow monitoring both electronic and structural factors with unprecedented time and spatial resolution. In this Account, we present recent studies from our group that make use of different variants of frequency-domain transient two-dimensional infrared (T-2DIR) spectroscopy, a pulse sequence combining electronic and vibrational excitations in the form of a UV-visible pump, a narrowband (12 cm(-1)) IR pump, and a broadband (400 cm(-1)) IR probe. In the first example, T-2DIR is used to directly compare vibrational dynamics in the ground and relaxed electronic excited states of Re(Cl)(CO)3(4,4'-diethylester-2,2'-bipyridine) and Ru(4,4'-diethylester-2,2'-bipyridine)2(NCS)2, prototypical charge transfer complexes used in photocatalytic CO2 reduction and electron injection in dye-sensitized solar cells. The experiments show that intramolecular vibrational redistribution (IVR) and vibrational energy transfer (VET) are up to an order of magnitude faster in the triplet charge transfer excited state than in the ground state. These results show the influence of electronic arrangement on vibrational coupling patterns, with direct implications for vibronic coupling mechanisms in charge transfer excited states. In the second example, we show unambiguously that electronic and vibrational movement are coupled in a donor-bridge-acceptor complex based on a Pt(II) trans-acetylide design motif. Time-resolved IR (TRIR) spectroscopy reveals that the rate of electron transfer (ET) is highly dependent on the amount of excess energy localized on the bridge following electronic excitation. Using an adaptation of T-2DIR, we are able to selectively perturb bridge-localized vibrational modes during charge separation, resulting in the donor-acceptor charge separation pathway being completely switched off, with all excess energy redirected toward the formation of a long-lived intraligand triplet state. A series of control experiments reveal that this effect is mode specific: it is only when the high-frequency bridging C≡C stretching mode is pumped that radical changes in photoproduct yields are observed. These experiments therefore suggest that one may perturb electronic movement by stimulating structural motion along the reaction coordinate using IR light. These studies add to a growing body of evidence suggesting that controlling the pathways and efficiency of charge transfer may be achieved through synthetic and perturbative approaches aiming to modulate vibronic coupling. Achieving such control would represent a breakthrough for charge transfer-based applications such as solar energy conversion and molecular electronics.
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Affiliation(s)
- Milan Delor
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Igor V. Sazanovich
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, STFC, Chilton, Oxfordshire OX11 0QX, U.K
| | - Michael Towrie
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, STFC, Chilton, Oxfordshire OX11 0QX, U.K
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46
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Rubtsova NI, Rubtsov IV. Vibrational energy transport in molecules studied by relaxation-assisted two-dimensional infrared spectroscopy. Annu Rev Phys Chem 2015; 66:717-38. [PMID: 25747112 DOI: 10.1146/annurev-physchem-040214-121337] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review presents an overview of the relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy method for measuring structures and energy transport dynamics in molecules. The method strongly enhances the range of accessible distances compared to traditional 2DIR and offers new structural reporters, such as the energy transport time, cross-peak amplification factors, and connectivity patterns. The use of the method for assigning vibrational modes with various levels of delocalization is illustrated. RA 2DIR relies on vibrational energy transport in molecules; as such, the transport mechanism can be conveniently studied by the method. Applications to identify diffusive and ballistic energy transport are demonstrated.
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Affiliation(s)
- Natalia I Rubtsova
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
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47
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Leitner DM, Buchenberg S, Brettel P, Stock G. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. J Chem Phys 2015; 142:075101. [DOI: 10.1063/1.4907881] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Paul Brettel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Gerhard Stock
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
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48
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Kurnosov AA, Rubtsov IV, Burin AL. Communication: fast transport and relaxation of vibrational energy in polymer chains. J Chem Phys 2015; 142:011101. [PMID: 25573545 DOI: 10.1063/1.4905076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We investigate ballistic vibrational energy transport through optical phonon band in oligomeric chains in the presence of decoherence. An exact solution is obtained for the excitation density in the space-time representation in the continuous limit and this solution is used to characterize the energy transport time and intensity. Three transport mechanisms are identified such as ballistic, diffusive, and directed diffusive regimes, occurring at different distances and time scales. The crossover between the two diffusive regimes is continuous, while the switch between the ballistic and diffusive mechanisms occurs in a discontinuous manner in accord with the recent experimental results on energy transport in perfluoroalkanes.
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Affiliation(s)
- Arkady A Kurnosov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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49
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Yue Y, Grusenmeyer T, Ma Z, Zhang P, Schmehl RH, Beratan DN, Rubtsov IV. Electron transfer rate modulation in a compact Re(i) donor–acceptor complex. Dalton Trans 2015; 44:8609-16. [DOI: 10.1039/c4dt02145b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Excitation of the vibrational modes at the bipyridine ligand results in modulation of the electron transfer rate between the electron donating and accepting ligands in a Re(i) complex.
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Affiliation(s)
- Yuankai Yue
- Department of Chemistry
- Tulane University
- New Orleans
- USA
| | | | - Zheng Ma
- Departments of Chemistry
- Biochemistry
- and Physics
- Duke University
- Durham
| | - Peng Zhang
- Departments of Chemistry
- Biochemistry
- and Physics
- Duke University
- Durham
| | | | - David N. Beratan
- Departments of Chemistry
- Biochemistry
- and Physics
- Duke University
- Durham
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50
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Fedoseeva M, Delor M, Parker SC, Sazanovich IV, Towrie M, Parker AW, Weinstein JA. Vibrational energy transfer dynamics in ruthenium polypyridine transition metal complexes. Phys Chem Chem Phys 2015; 17:1688-96. [DOI: 10.1039/c4cp04166f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding vibrational energy propagation pathways during and following electron transfer in transition metal complexes, which are of interest for solar cell applications, can provide new insights on the interplay between electronic and vibrational movement within the molecule.
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Affiliation(s)
- Marina Fedoseeva
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
| | - Milan Delor
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
| | - Simon C. Parker
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
| | - Igor V. Sazanovich
- Central Laser Facility
- Research Complex at Harwell
- Rutherford Appleton Laboratory
- Harwell Science and Innovation Campus
- STFC
| | - Michael Towrie
- Central Laser Facility
- Research Complex at Harwell
- Rutherford Appleton Laboratory
- Harwell Science and Innovation Campus
- STFC
| | - Anthony W. Parker
- Central Laser Facility
- Research Complex at Harwell
- Rutherford Appleton Laboratory
- Harwell Science and Innovation Campus
- STFC
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