1
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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Mendis KC, Li X, Valdiviezo J, Banziger SD, Zhang P, Ren T, Beratan DN, Rubtsov IV. Electron transfer rate modulation with mid-IR in butadiyne-bridged donor-bridge-acceptor compounds. Phys Chem Chem Phys 2024; 26:1819-1828. [PMID: 38168814 DOI: 10.1039/d3cp03175f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Controlling electron transfer (ET) processes in donor-bridge-acceptor (DBA) compounds by mid-IR excitation can enhance our understanding of the ET dynamics and may find practical applications in molecular sensing and molecular-scale electronics. Alkyne moieties are attractive to serve as ET bridges, as they offer the possibility of fast ET and present convenient vibrational modes to perturb the ET dynamics. Yet, these bridges introduce complexity because of the strong torsion angle dependence of the ET rates and transition dipoles among electronic states and a shallow torsion barrier. In this study, we implemented ultrafast 3-pulse laser spectroscopy to investigate how the ET from the dimethyl aniline (D) electron donor to the N-isopropyl-1,8-napthalimide (NAP) electron acceptor can be altered by exciting the CC stretching mode (νCC) of the butadiyne bridge linking the donor and acceptor. The electron transfer was initiated by electronically exciting the acceptor moiety at 400 nm, followed by vibrational excitation of the alkyne, νCC, and detecting the changes in the absorption spectrum in the visible spectral region. The experiments were performed at different delay times t1 and t2, which are the delays between UV-mid-IR and mid-IR-Vis pulses, respectively. Two sets of torsion-angle conformers were identified, one featuring a very fast mean ET time of 0.63 ps (group A) and another featuring a slower mean ET time of 4.3 ps (group B), in the absence of the mid-IR excitation. TD-DFT calculations were performed to determine key torsion angle dependent molecular parameters, including the electronic and vibrational transition dipoles, transition frequencies, and electronic couplings. To describe the 3-pulse data, we developed a kinetic model that includes a locally excited, acceptor-based S2 state, a charge separated S1 state, and their vibrationally excited counterparts, with either excited νCC (denoted as S1Atr, S1Btr, S2Atr, and S2Btr, where tr stands for the excited triplet bond, νCC) or excited daughter modes of the νCC relaxation (S1Ah, S1Bh, S2Ah, and S2Bh, where h stands for vibrationally hot species). The kinetic model was solved analytically, and the species-associated spectra (SAS) were determined numerically using a matrix approach, treating first the experiments with longer t1 delays and then using the already determined SAS for modeling the experiments with shorter t1 delays. Strong vibronic coupling of νCC and of vibrationally hot states makes the analysis complicated. Nevertheless, the SAS were identified and the ET rates of the vibrationally excited species, S2Atr, S2Btr and S2Bh, were determined. The results show that the ET rate for the S2A species is ca. 1.2-fold slower when the νCC mode is excited. The ET rate for species S2B is slower by ca. 1.3-fold if the compound is vibrationally hot and is essentially unchanged when the νCC mode is excited. The SAS determined for the tr and h species resemble the SAS for their respective precursor species in the 2-pulse transient absorption experiments, which validates the procedure used and the results.
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Affiliation(s)
- Kasun C Mendis
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
| | - Xiao Li
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
| | - Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Susannah D Banziger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Tong Ren
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
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3
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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4
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Wilcken R, Nishida J, Triana JF, John-Herpin A, Altug H, Sharma S, Herrera F, Raschke MB. Antenna-coupled infrared nanospectroscopy of intramolecular vibrational interaction. Proc Natl Acad Sci U S A 2023; 120:e2220852120. [PMID: 37155895 PMCID: PMC10193936 DOI: 10.1073/pnas.2220852120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
Many photonic and electronic molecular properties, as well as chemical and biochemical reactivities are controlled by fast intramolecular vibrational energy redistribution (IVR). This fundamental ultrafast process limits coherence time in applications from photochemistry to single quantum level control. While time-resolved multidimensional IR-spectroscopy can resolve the underlying vibrational interaction dynamics, as a nonlinear optical technique it has been challenging to extend its sensitivity to probe small molecular ensembles, achieve nanoscale spatial resolution, and control intramolecular dynamics. Here, we demonstrate a concept how mode-selective coupling of vibrational resonances to IR nanoantennas can reveal intramolecular vibrational energy transfer. In time-resolved infrared vibrational nanospectroscopy, we measure the Purcell-enhanced decrease of vibrational lifetimes of molecular vibrations while tuning the IR nanoantenna across coupled vibrations. At the example of a Re-carbonyl complex monolayer, we derive an IVR rate of (25±8) cm-1 corresponding to (450±150) fs, as is typical for the fast initial equilibration between symmetric and antisymmetric carbonyl vibrations. We model the enhancement of the cross-vibrational relaxation based on intrinsic intramolecular coupling and extrinsic antenna-enhanced vibrational energy relaxation. The model further suggests an anti-Purcell effect based on antenna and laser-field-driven vibrational mode interference which can counteract IVR-induced relaxation. Nanooptical spectroscopy of antenna-coupled vibrational dynamics thus provides for an approach to probe intramolecular vibrational dynamics with a perspective for vibrational coherent control of small molecular ensembles.
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Affiliation(s)
- Roland Wilcken
- Department of Physics, and JILA, University of Colorado, Boulder, CO80309
| | - Jun Nishida
- Department of Physics, and JILA, University of Colorado, Boulder, CO80309
| | - Johan F. Triana
- Department of Physics, Universidad de Santiago de Chile, Estación Central917022, Chile
| | - Aurelian John-Herpin
- Institute of Bioengineering, École Polytechnique Fédéral de Lausanne, Lausanne1015, Switzerland
| | - Hatice Altug
- Institute of Bioengineering, École Polytechnique Fédéral de Lausanne, Lausanne1015, Switzerland
| | - Sandeep Sharma
- Department of Chemistry, University of Colorado, Boulder, CO80309
| | - Felipe Herrera
- Department of Physics, Universidad de Santiago de Chile, Estación Central917022, Chile
- Millennium Institute for Research in Optics, Concepción4030000, Chile
| | - Markus B. Raschke
- Department of Physics, and JILA, University of Colorado, Boulder, CO80309
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5
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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
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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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6
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022; 61:e202200648. [PMID: 35226765 PMCID: PMC9401566 DOI: 10.1002/anie.202200648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 11/10/2022]
Abstract
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
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Affiliation(s)
- Jan G. Löffler
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Erhan Deniz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Carolin Feid
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Valentin G. Franz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Jens Bredenbeck
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
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7
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Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan G. Löffler
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Erhan Deniz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Carolin Feid
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Valentin G. Franz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 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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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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Maitra A, Sarkar S, Leitner DM, Dawlaty JM. Electric Fields Influence Intramolecular Vibrational Energy Relaxation and Line Widths. J Phys Chem Lett 2021; 12:7818-7825. [PMID: 34378946 DOI: 10.1021/acs.jpclett.1c02238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Intramolecular vibrational energy relaxation (IVR) is fundamentally important to chemical dynamics. We show that externally applied electric fields affect IVR and vibrational line widths by changing the anharmonic couplings and frequency detunings between modes. We demonstrate this effect in benzonitrile for which prior experimental results show a decrease in vibrational line width as a function of applied electric field. We identify three major channels for IVR that depend on electric field. In the dominant channel, the electric field affects the frequency detuning, while in the other two channels, variation of anharmonic couplings as a function of field is the underlying mechanism. Consistent with experimental results, we show that the combination of all channels gives rise to reduced line widths with increasing electric field in benzonitrile. Our results are relevant for controlling IVR with external or internal fields and for gaining a more complete interpretation of line widths of vibrational Stark probes.
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Affiliation(s)
- Anwesha Maitra
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0001, United States
| | - Sohini Sarkar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0001, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89519, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0001, United States
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10
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Nawagamuwage SU, Qasim LN, Zhou X, Leong TX, Parshin IV, Jayawickramarajah J, Burin AL, Rubtsov IV. Competition of Several Energy-Transport Initiation Mechanisms Defines the Ballistic Transport Speed. J Phys Chem B 2021; 125:7546-7555. [PMID: 34185993 PMCID: PMC8287563 DOI: 10.1021/acs.jpcb.1c03986] [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: 11/30/2022]
Abstract
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The ballistic regime
of vibrational energy transport in oligomeric
molecular chains occurs with a constant, often high, transport speed
and high efficiency. Such a transport regime can be initiated by exciting
a chain end group with a mid-infrared (IR) photon. To better understand
the wavepacket formation process, two chemically identical end groups,
azido groups with normal, 14N3-, and isotopically
substituted, 15N3-, nitrogen atoms, were tested
for wavepacket initiation in compounds with alkyl chains of n = 5, 10, and 15 methylene units terminated with a carboxylic
acid (-a) group, denoted as 14N3Cn-a and 15N3Cn-a. The transport
was initiated by exciting the azido moiety stretching mode, the νN≡N tag, at 2100 cm–1 (14N3Cn-a) or 2031 cm–1 (15N3Cn-a). Opposite to the
expectation, the ballistic transport speed was found to decrease upon 14N3 → 15N3 isotope
editing. Three mechanisms of the transport initiation of a vibrational
wavepacket are described and analyzed. The first mechanism involves
the direct formation of a wavepacket via excitation with IR photons
of several strong Fermi resonances of the tag mode with the νN=N + νN–C combination state
while each of the combination state components is mixed with delocalized
chain states. The second mechanism relies on the vibrational relaxation
of an end-group-localized tag into a mostly localized end-group state
that is strongly coupled to multiple delocalized states of a chain
band. Harmonic mixing of νN=N of the azido
group with CH2 wagging states of the chain permits a wavepacket
formation within a portion of the wagging band, suggesting a fast
transport speed. The third mechanism involves the vibrational relaxation
of an end-group-localized mode into chain states. Two such pathways
were found for the νN≡N initiation: The νN=N mode relaxes efficiently into the twisting band
states and low-frequency acoustic modes, and the νN–C mode relaxes into the rocking band states and low-frequency acoustic
modes. The contributions of the three initiation mechanisms in the
ballistic energy transport initiated by νN≡N tag are quantitatively evaluated and related to the experiment.
We conclude that the third mechanism dominates the transport in alkane
chains of 5–15 methylene units initiated with the νN≡N tag and the wavepacket generated predominantly at
the CH2 twisting band. The isotope effect of the transport
speed is attributed to a larger contribution of the faster wavepackets
for 14N3Cn-a or to the different
breadth of the wavepacket within the twisting band. The study offers
a systematic description of different transport initiation mechanisms
and discusses the requirements and features of each mechanism. Such
analysis will be useful for designing novel materials for energy management.
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Affiliation(s)
| | - Layla N Qasim
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Tammy X Leong
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V Parshin
- 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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11
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Behera J, Bandyopadhyay M. Environment-dependent vibrational heat transport in molecular junctions: Rectification, quantum effects, vibrational mismatch. Phys Rev E 2021; 104:014148. [PMID: 34412343 DOI: 10.1103/physreve.104.014148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Vibrational heat transport in molecular junctions is a central issue in different contemporary research areas such as chemistry, materials science, mechanical engineering, thermoelectrics, and power generation. Our model system consists of a chain of molecules which are sandwiched between two solids that are maintained at different temperatures. We employ a quantum self-consistent reservoir model, which is built on a generalized quantum Langevin equation, to investigate quantum effects and far from equilibrium conditions on thermal conduction at nanoscale. The present self-consistent reservoir model can easily mimic the phonon-phonon scattering mechanisms. Different thermal environments are modeled as (i) Ohmic, (ii) sub-Ohmic, and (iii) super-Ohmic environments, and their effects are demonstrated for the thermal rectification properties of the system with spring graded or mass graded features. The behavior of heat current across molecular junctions as a function of chain length, temperature gradient, and phonon scattering rates are studied. Further, our analysis reveals the effects of vibrational mismatch between the solids phonon spectra on heat transfer characteristics in molecular junctions for different thermal environments.
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Affiliation(s)
- Jayasmita Behera
- SBS, I.I.T. Bhubaneswar, Argul, Jatni, Khurda, Odisha 752050, India
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12
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Procacci B, Rutherford SH, Greetham GM, Towrie M, Parker AW, Robinson CV, Howle CR, Hunt NT. Differentiation of bacterial spores via 2D-IR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119319. [PMID: 33360210 DOI: 10.1016/j.saa.2020.119319] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF2 windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H2O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.
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Affiliation(s)
- Barbara Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Camilla V Robinson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Christopher R Howle
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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13
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Rubtsova NI, Lin Z, Mackin RT, Rubtsov IV. How Intramolecular Vibrational Energy Transport Changes with Rigidity and Polarity of the Environment? HIGH ENERGY CHEMISTRY 2020. [DOI: 10.1134/s0018143920060120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Marzolf DR, McKenzie AM, O’Malley MC, Ponomarenko NS, Swaim CM, Brittain TJ, Simmons NL, Pokkuluri PR, Mulfort KL, Tiede DM, Kokhan O. Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2143. [PMID: 33126541 PMCID: PMC7693585 DOI: 10.3390/nano10112143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4-8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.
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Affiliation(s)
- Daniel R. Marzolf
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Aidan M. McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Matthew C. O’Malley
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Nina S. Ponomarenko
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - Coleman M. Swaim
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Tyler J. Brittain
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Natalie L. Simmons
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA;
| | | | - Karen L. Mulfort
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - David M. Tiede
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
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15
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Sharony I, Chen R, Nitzan A. Stochastic simulation of nonequilibrium heat conduction in extended molecular junctions. J Chem Phys 2020; 153:144113. [PMID: 33086795 DOI: 10.1063/5.0022423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Understanding phononic heat transport processes in molecular junctions is a central issue in the developing field of nanoscale heat conduction. Here, we present a Langevin dynamics simulation framework to investigate heat transport processes in molecular junctions at and beyond the linear response regime and apply it to saturated and unsaturated linear hydrocarbon chains connecting two gold substrates. Thermal boundary conditions represented by Markovian noise and damping are filtered through several (up to four) gold layers to provide a realistic and controllable bath spectral density. Classical simulations using the full universal force field are compared with quantum calculations that use only the harmonic part of this field. The close agreement found at about room temperature between these very different calculations suggests that heat transport at such temperatures is dominated by lower frequency vibrations whose dynamics is described well by classical mechanics. The results obtained for alkanedithiol molecules connecting gold substrates agree with previous quantum calculations based on the Landauer formula and match recent experimental measurements [e.g., thermal conductance around 20 pW/K for alkanedithiols in single-molecule junctions (SMJs)]. Heat conductance simulations on polyynes of different lengths illuminate the effects of molecular conjugation on thermal transport. The difference between alkanes and polyynes is not large but correlates with the larger rigidity and stronger mode localization that characterize the polyyne structure. This computational approach has been recently used [R. Chen, I. Sharony, and A. Nitzan, J. Phys. Chem. Lett. 11, 4261-4268 (2020)] to unveil local atomic heat currents and phononic interference effect in aromatic-ring based SMJs.
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Affiliation(s)
- Inon Sharony
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Renai Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Abraham Nitzan
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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16
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Chalyavi F, Schmitz AJ, Fetto NR, Tucker MJ, Brewer SH, Fenlon EE. Extending the vibrational lifetime of azides with heavy atoms. Phys Chem Chem Phys 2020; 22:18007-18013. [PMID: 32749405 DOI: 10.1039/d0cp02814b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of novel vibrational reporters (VRs), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (<2 ps) have limited their full potential. Herein we report that the vibrational lifetimes of azides can be increased by attaching them to heavy atoms and by using heavy 15N isotopes. Three group 14 atom triphenyl azides (Ph3CN3, Ph3SiN3, Ph3SnN3), and their triple-15N isotopomers, were synthesized in good yields. Tributyltin azide and its heavy isotopomer (Bu3Sn15N3) were also prepared to probe the effect of molecular scaffolding. The extinction coefficients for the natural abundance azides were determined, ranging from 900 to 1500 M-1 cm-1. The vibrational lifetimes of all azides were measured by pump-probe IR spectroscopy and each showed a major component with a short-to-moderate vibrational lifetime and a minor component with a much longer vibrational lifetime. Based on these results, the lifetime, aka the observation window, of an azide reporter can be extended from ∼2 ps to as long as ∼300 ps by a combination of isotopic labeling and heavy atom effect. 2D IR measurements of these compounds further confirmed the ability to observe these azide transitions at much longer timescales showing their utility to capture dynamic processes from tens to hundreds of picoseconds.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Natalie R Fetto
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA.
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA. ,
| | - Edward E Fenlon
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA. ,
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17
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Mackin RT, Leong TX, Rubtsova NI, Burin AL, Rubtsov IV. Low-Temperature Vibrational Energy Transport via PEG Chains. J Phys Chem Lett 2020; 11:4578-4583. [PMID: 32437615 DOI: 10.1021/acs.jpclett.0c01273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We used relaxation-assisted two-dimensional infrared spectroscopy to study the temperature dependence (10-295 K) of end-to-end energy transport across end-decorated PEG oligomers of various chain lengths. The excess energy was introduced by exciting the azido end-group stretching mode at 2100 cm-1 (tag); the transport was recorded by observing the asymmetric C═O stretching mode of the succinimide ester end group at 1740 cm-1. The overall transport involves diffusive steps at the end groups and a ballistic step through the PEG chain. We found that at lower temperatures the through-chain energy transport became faster, while the end-group diffusive transport time and the tag lifetime increase. The modeling of the transport using a quantum Liouville equation linked the observations to the reduction of decoherence rate and an increase of the mean-free-path for the vibrational wavepacket. The energy transport at the end groups slowed down at low temperatures due to the decreased number and efficiency of the anharmonic energy redistribution pathways.
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Affiliation(s)
- Robert T Mackin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Tammy X Leong
- 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
| | - 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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18
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Chen R, Sharony I, Nitzan A. Local Atomic Heat Currents and Classical Interference in Single-Molecule Heat Conduction. J Phys Chem Lett 2020; 11:4261-4268. [PMID: 32375004 DOI: 10.1021/acs.jpclett.0c00471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We consider interference effects in vibrational heat conduction across single-molecule junctions. Previous theoretical descriptions of such effects have relied on the quantum Landauer-type expression for heat transport by harmonic molecules, and such observations are sometimes termed "quantum interference". Here we demonstrate via classical atomistic simulations of heat conduction in benzenedithiol single-molecule junctions that the room-temperature effect is essentially classical. In fact, classical simulations and quantum evaluation of room-temperature heat conduction in these systems yield similar results. Simulations of para-, meta-, and ortho-connected benzenedithiols between gold substrates yield conductions in the order para > ortho > meta, which is similar to trends found in the electronic conduction of these structures. The (essentially classical) interference origin of this ordering is indicated by the similarity of the quantum and classical behaviors of these systems.
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Affiliation(s)
- Renai Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Inon Sharony
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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19
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Chen X, Cui Y, Gobeze HB, Kuroda DG. Assessing the Location of Ionic and Molecular Solutes in a Molecularly Heterogeneous and Nonionic Deep Eutectic Solvent. J Phys Chem B 2020; 124:4762-4773. [PMID: 32421342 PMCID: PMC7304071 DOI: 10.1021/acs.jpcb.0c02482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Deep
eutectic solvents (DES) are emerging sustainable designer
solvents viewed as greener and better alternatives to ionic liquids.
Nonionic DESs possess unique properties such as viscosity and hydrophobicity
that make them desirable in microextraction applications such as oil-spill
remediation. This work builds upon a nonionic DES, NMA–LA DES,
previously designed by our group. The NMA–LA DES presents a
rich nanoscopic morphology that could be used to allocate solutes
of different polarities. In this work, the possibility of solvating
different solutes within the nanoscopically heterogeneous molecular
structure of the NMA–LA DES is investigated using ionic and
molecular solutes. In particular, the localized vibrational transitions
in these solutes are used as reporters of the DES molecular structure
via vibrational spectroscopy. The FTIR and 2DIR data suggest that
the ionic solute is confined in a polar and continuous domain formed
by NMA, clearly sensing the direct effect of the change in NMA concentration.
In the case of the molecular nonionic and polar solute, the data indicates
that the solute resides in the interface between the polar and nonpolar
domains. Finally, the results for the nonpolar and nonionic solute
(W(CO)6) are unexpected and less conclusive. Contrary to
its polarity, the data suggest that the W(CO)6 resides
within the NMA polar domain of the DES, probably by inducing a domain
restructuring in the solvent. However, the data are not conclusive
enough to discard the possibility that the restructuring comprises
not only the polar domain but also the interface. Overall, our results
demonstrate that the NMA–LA DES has nanoscopic domains with
affinity to particular molecular properties, such as polarity. Thus,
the presented results have a direct implication to separation science.
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Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yaowen Cui
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Habtom B Gobeze
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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20
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Hume S, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. 2D-Infrared Spectroscopy of Proteins in Water: Using the Solvent Thermal Response as an Internal Standard. Anal Chem 2020; 92:3463-3469. [PMID: 31985198 PMCID: PMC7145279 DOI: 10.1021/acs.analchem.9b05601] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Ultrafast
two-dimensional infrared (2D-IR) spectra can now be obtained
in a matter of seconds, opening up the possibility of high-throughput
screening applications of relevance to the biomedical and pharmaceutical
sectors. Determining quantitative information from 2D-IR spectra recorded
on different samples and different instruments is however made difficult
by variations in beam alignment, laser intensity, and sample conditions.
Recently, we demonstrated that 2D-IR spectroscopy of the protein amide
I band can be performed in aqueous (H2O) rather than deuterated
(D2O) solvents, and we now report a method that uses the
magnitude of the associated thermal response of H2O as
an internal normalization standard for 2D-IR spectra. Using the water
response, which is temporally separated from the protein signal, to
normalize the spectra allows significant reduction of the impact of
measurement-to-measurement fluctuations on the data. We demonstrate
that this normalization method enables creation of calibration curves
for measurement of absolute protein concentrations and facilitates
reproducible difference spectroscopy methodologies. These advances
make significant progress toward the robust data handling strategies
that will be essential for the realization of automated spectral analysis
tools for large scale 2D-IR screening studies of protein-containing
solutions and biofluids.
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Affiliation(s)
- Samantha Hume
- Department of Physics, SUPA , University of Strathclyde , 107 Rottenrow East , Glasgow G4 0NG , U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Paul M Donaldson
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , U.K
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21
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Kendrick WJ, Jirásek M, Peeks MD, Greetham GM, Sazanovich IV, Donaldson PM, Towrie M, Parker AW, Anderson HL. Mechanisms of IR amplification in radical cation polarons. Chem Sci 2020; 11:2112-2120. [PMID: 34123299 PMCID: PMC8150116 DOI: 10.1039/c9sc05717j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 12/30/2022] Open
Abstract
Break down of the Born-Oppenheimer approximation is caused by mixing of electronic and vibrational transitions in the radical cations of some conjugated polymers, resulting in unusually intense vibrational bands known as infrared active vibrations (IRAVs). Here, we investigate the mechanism of this amplification, and show that it provides insights into intramolecular charge migration. Spectroelectrochemical time-resolved infrared (TRIR) and two-dimensional infrared (2D-IR) spectroscopies were used to investigate the radical cations of two butadiyne-linked conjugated porphyrin oligomers, a linear dimer and a cyclic hexamer. The 2D-IR spectra reveal strong coupling between all the IRAVs and the electronic π-π* polaron band. Intramolecular vibrational energy redistribution (IVR) and vibrational relaxation occur within ∼0.1-7 ps. TRIR spectra show that the transient ground state bleach (GSB) and excited state absorption (ESA) signals have anisotropies of 0.31 ± 0.07 and 0.08 ± 0.04 for the linear dimer and cyclic hexamer cations, respectively. The small TRIR anisotropy for the cyclic hexamer radical cation indicates that the vibrationally excited polaron migrates round the nanoring on a time scale faster than the measurement, i.e. within 0.5 ps, at 298 K. Density functional theory (DFT) calculations qualitatively reproduce the emergence of the IRAVs. The first singlet (S1) excited states of the neutral porphyrin oligomers exhibit similar IRAVs to the radical cations, implying that the excitons have similar electronic structures to polarons. Our results show that IRAVs originate from the strong coupling of charge redistribution to nuclear motion, and from the similar energies of electronic and vibrational transitions.
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Affiliation(s)
- William J Kendrick
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Oxford OX1 3TA UK
| | - Michael Jirásek
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Oxford OX1 3TA UK
| | - Martin D Peeks
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Oxford OX1 3TA UK
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council Didcot OX11 0QX UK
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council Didcot OX11 0QX UK
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council Didcot OX11 0QX UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council Didcot OX11 0QX UK
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council Didcot OX11 0QX UK
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Oxford OX1 3TA UK
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22
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Li X, Valdiviezo J, Banziger SD, Zhang P, Ren T, Beratan DN, Rubtsov IV. Symmetry controlled photo-selection and charge separation in butadiyne-bridged donor–bridge–acceptor compounds. Phys Chem Chem Phys 2020; 22:9664-9676. [DOI: 10.1039/d0cp01235a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer (ET) in donor–bridge–acceptor (DBA) compounds featuring alkyne bridges depends strongly on the torsion angle between the donor and acceptor.
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Affiliation(s)
- Xiao Li
- Department of Chemistry
- Tulane University
- New Orleans
- USA
| | | | | | - Peng Zhang
- Department of Chemistry
- Duke University
- Durham
- USA
| | - Tong Ren
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - David N. Beratan
- Department of Chemistry
- Duke University
- Durham
- USA
- Department of Physics, Duke University
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23
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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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24
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Chen X, Fulfer KD, Woodard KT, Kuroda DG. Structure and Dynamics of the Lithium-Ion Solvation Shell in Ureas. J Phys Chem B 2019; 123:9889-9898. [DOI: 10.1021/acs.jpcb.9b07623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kristen D. Fulfer
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Chemistry Program, Centre College, Danville, Kentucky 40422, United States
| | - Kaylee T. Woodard
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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25
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Cui Y, Rushing JC, Seifert S, Bedford NM, Kuroda DG. Molecularly Heterogeneous Structure of a Nonionic Deep Eutectic Solvent Composed of N-Methylacetamide and Lauric Acid. J Phys Chem B 2019; 123:3984-3993. [DOI: 10.1021/acs.jpcb.8b11732] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yaowen Cui
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeramie C. Rushing
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Soenke Seifert
- X-ray Sciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Nicholas M. Bedford
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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26
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Li J, Zhang Y, Zheng J. Intermolecular energy flows between surface molecules on metal nanoparticles. Phys Chem Chem Phys 2019; 21:4240-4245. [PMID: 30747170 DOI: 10.1039/c8cp05932b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three model systems are designed to investigate energy transport between molecules on metal nanoparticle surfaces. Energy is rapidly transferred from one carbon monoxide (CO) molecule to another CO molecule or an organic molecule on adjacent surface sites of 2 nm Pt particles within a few picoseconds. On the contrary, energy flow from a surface organic molecule to an adjacent CO molecule is significantly slower and, in fact, within experimental sensitivity and uncertainty the transfer is not observed. The energy transport on particle surfaces (about 2 km s-1) is almost ten times faster than inside a molecule (200 m s-1). The seemingly perplexing observations can be well explained by the combination of electron/vibration and vibration/vibration coupling mechanisms, which mediate molecular energy dynamics on metal nanoparticle surfaces: the strong electron/vibration coupling rapidly converts CO vibrational energy into heat that can be immediately sensed by nearby molecules; but the vibration/vibration coupling dissipates the vibrational excitation in the organic molecule as low-frequency intramolecular vibrations that may or may not couple to surface electronic motions.
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Affiliation(s)
- Jiebo Li
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
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27
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Rubtsov IV, Burin AL. Ballistic and diffusive vibrational energy transport in molecules. J Chem Phys 2019; 150:020901. [PMID: 30646721 DOI: 10.1063/1.5055670] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Energy transport in molecules is essential for many areas of science and technology. Strong covalent bonds of a molecular backbone can facilitate the involvement of the molecule's high-frequency modes in energy transport, which, under certain conditions, makes the transport fast and efficient. We discuss such conditions and describe various transport regimes in molecules, including ballistic, diffusive, directed diffusion, and intermediate regime cases, in light of recently developed experimental and theoretical approaches.
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Affiliation(s)
- 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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28
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Moghaddasi Fereidani R, Segal D. Phononic heat transport in molecular junctions: Quantum effects and vibrational mismatch. J Chem Phys 2019; 150:024105. [DOI: 10.1063/1.5075620] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Roya Moghaddasi Fereidani
- Chemical Physics Theory Group, Department of Chemistry, and Centre for Quantum Information and Quantum Control, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
| | - Dvira Segal
- Chemical Physics Theory Group, Department of Chemistry, and Centre for Quantum Information and Quantum Control, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
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29
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Leitner DM. Molecules and the Eigenstate Thermalization Hypothesis. ENTROPY 2018; 20:e20090673. [PMID: 33265762 PMCID: PMC7513195 DOI: 10.3390/e20090673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 11/18/2022]
Abstract
We review a theory that predicts the onset of thermalization in a quantum mechanical coupled non-linear oscillator system, which models the vibrational degrees of freedom of a molecule. A system of N non-linear oscillators perturbed by cubic anharmonic interactions exhibits a many-body localization (MBL) transition in the vibrational state space (VSS) of the molecule. This transition can occur at rather high energy in a sizable molecule because the density of states coupled by cubic anharmonic terms scales as N3, in marked contrast to the total density of states, which scales as exp(aN), where a is a constant. The emergence of a MBL transition in the VSS is seen by analysis of a random matrix ensemble that captures the locality of coupling in the VSS, referred to as local random matrix theory (LRMT). Upon introducing higher order anharmonicity, the location of the MBL transition of even a sizable molecule, such as an organic molecule with tens of atoms, still lies at an energy that may exceed the energy to surmount a barrier to reaction, such as a barrier to conformational change. Illustrative calculations are provided, and some recent work on the influence of thermalization on thermal conduction in molecular junctions is also discussed.
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Affiliation(s)
- David M Leitner
- Department of Chemistry, University of Nevada, Reno, NV 89557, USA
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31
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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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32
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Affiliation(s)
- Lorenz S. Cederbaum
- Theoretische Chemie, Physikalisch–Chemisches Institut, Heidelberg University, Heidelberg, Germany
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33
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He X, Xu F, Yu P, Wu Y, Wang F, Zhao Y, Wang J. Solvent-dependent structural dynamics of an azido-platinum complex revealed by linear and nonlinear infrared spectroscopy. Phys Chem Chem Phys 2018; 20:9984-9996. [PMID: 29619447 DOI: 10.1039/c7cp08606g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The vibrational and anisotropic relaxation dynamics and structural dynamics of a potential anticancer prodrug, trans,trans,trans-[Pt(N3)2(OH)2(py)2], were investigated using time-resolved infrared pump-probe spectroscopy and ultrafast two-dimensional infrared (2D IR) spectroscopy. Herein, two representative bio-friendly solvents, H2O and DMSO, were used, in which the local structural and dynamical variations were monitored using the antisymmetric linear combination of the two N3 stretching vibrational modes as an infrared probe. It was found that the vibrational relaxation process of the N3 antisymmetric stretching (as) mode in H2O is two to three times faster than that in DMSO. The anisotropic relaxation process of the anticancer prodrug was observed to be hindered in DMSO; this indicated a tighter solvent environment around the sample molecule in this solvent. The vibrational frequency time correlation of the N3 antisymmetric stretching mode in H2O decays with a time constant of 1.94 ps, in agreement with the hydrogen bond formation and breaking times of water. In DMSO, the frequency time correlation of the N3 as mode decays on a much longer time scale; this further indicates its sensitivity to the out-layer DMSO structural dynamics, which are relatively static in the experimental time window.
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Affiliation(s)
- Xuemei He
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
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34
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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. Nat Chem 2017; 10:8-16. [DOI: 10.1038/nchem.2894] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/20/2017] [Indexed: 12/19/2022]
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35
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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36
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He X, Yu P, Zhao J, Wang J. Efficient Vibrational Energy Transfer through Covalent Bond in Indigo Carmine Revealed by Nonlinear IR Spectroscopy. J Phys Chem B 2017; 121:9411-9421. [DOI: 10.1021/acs.jpcb.7b06766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xuemei He
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory for Molecular Sciences, Molecular Reaction Dynamics
Laboratory, CAS Research/Education Center for Excellence in Molecular
Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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37
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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38
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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39
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Wright JC. Applications of the New Family of Coherent Multidimensional Spectroscopies for Analytical Chemistry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:45-70. [PMID: 28375700 DOI: 10.1146/annurev-anchem-061516-045349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A new family of vibrational and electronic spectroscopies has emerged, comprising the coherent analogs of traditional analytical methods. These methods are also analogs of coherent multidimensional nuclear magnetic resonance (NMR) spectroscopy. This new family is based on creating the same quantum mechanical superposition states called multiple quantum coherences (MQCs). NMR MQCs are mixtures of nuclear spin states that retain their quantum mechanical phase information for milliseconds. The MQCs in this new family are mixtures of vibrational and electronic states that retain their phases for picoseconds or shorter times. Ultrafast, high-intensity coherent beams rapidly excite multiple states. The excited MQCs then emit bright beams while they retain their phases. Time-domain methods measure the frequencies of the MQCs by resolving their phase oscillations, whereas frequency-domain methods measure the resonance enhancements of the output beam while scanning the excitation frequencies. The resulting spectra provide multidimensional spectral signatures that increase the spectroscopic selectivity required for analyzing complex samples.
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Affiliation(s)
- John C Wright
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706;
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40
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Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
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41
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Pandey HD, Leitner DM. Vibrational energy transport in molecules and the statistical properties of vibrational modes. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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42
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Fujisaki H, Yagi K, Kikuchi H, Takami T, Stock G. Vibrational energy transport in acetylbenzonitrile described by an ab initio-based quantum tier model. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Abstract
The nature and rate of thermal transport through molecular junctions depend on the length over which thermalization occurs. For junctions formed by alkane chains, in which thermalization occurs only slowly, measurements reveal that thermal resistance is controlled by bonding with the substrates, whereas fluorination can introduce thermal resistance within the molecules themselves, although the mechanism remains unclear. Here we present results of quantum-mechanical calculations of elastic and inelastic scattering rates, the length over which thermalization occurs, and thermal conductance in alkane and perfluoroalkane junctions. The contribution to thermalization of quantum effects that give rise to many-body localization (MBL) in isolated molecules is examined. While MBL does not occur due to dephasing, thermalization is typically too slow to establish local temperature if the same molecule in isolation exhibits MBL. The results indicate limitations on the applicability of classical molecular simulations in modeling thermal transport in molecular junctions.
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Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
| | - David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
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44
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Kraack JP, Hamm P. Surface-Sensitive and Surface-Specific Ultrafast Two-Dimensional Vibrational Spectroscopy. Chem Rev 2016; 117:10623-10664. [DOI: 10.1021/acs.chemrev.6b00437] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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45
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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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46
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Wright JC. Analytical chemistry, multidimensional spectral signatures, and the future of coherent multidimensional spectroscopy. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Shen YN, Jiang B, Ge CQ, Deng GH, Chen HL, Yang XM, Yuan KJ, Zheng JR. Intermolecular Vibrational Energy Transfers in Melts and Solutions. CHINESE J CHEM PHYS 2016. [DOI: 10.1063/1674-0068/29/cjcp1602028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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48
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Abstract
We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.
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Affiliation(s)
- Dvira Segal
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada;,
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49
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Straight SC, Paesani F. Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics. J Phys Chem B 2016; 120:8539-46. [DOI: 10.1021/acs.jpcb.6b02366] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shelby C. Straight
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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50
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Hithell G, Shaw DJ, Donaldson PM, Greetham GM, Towrie M, Burley GA, Parker AW, Hunt NT. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA. J Phys Chem B 2016; 120:4009-18. [PMID: 27079484 DOI: 10.1021/acs.jpcb.6b02112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.
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Affiliation(s)
- Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Daniel J Shaw
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Paul M Donaldson
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Gregory M Greetham
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Michael Towrie
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Anthony W Parker
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, U.K
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