1
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Islam MM, Nawagamuwage SU, Parshin IV, Richard MC, Burin AL, Rubtsov IV. Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy. J Am Chem Soc 2023; 145:26363-26373. [PMID: 37982703 DOI: 10.1021/jacs.3c10178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an azido moiety and a cyano or carboxylic acid moiety, connected by an alkyl chain of different lengths, was synthesized. FTIR data and molecular dynamics calculations indicated that the test compounds in a bilayer are oriented so that the cyano or carboxylic acid moiety is located in the lipid head-group region, while the azido group stays inside the bilayer at the depth determined by its alkyl chain length. We found that the asymmetric stretching mode of the azido group (νN3) can serve as a reporter of the membrane interior dynamics. FTIR and two-dimensional infrared (2DIR) studies were performed at different temperatures, ranging from 22 to 45 °C, covering the Lβ-Lα phase transition temperature of dipalmitoylphosphatidylcholine (∼41 °C). The width of the νN3 peak was found to be very sensitive to the phase transition and to the temperature in general. We introduced an order parameter, SN3, which characterizes restrictions to motion inside the bilayer. 2DIR spectra of νN3 showed different extents of inhomogeneity at different depths in the bilayer, with the smallest inhomogeneity in the middle of the leaflet. The spectral diffusion dynamics of the N3 peak was found to be dependent on the depth of the N3 group location in the bilayer. The obtained results enhance our understanding of the bilayer dynamics and can be extended to investigate membranes with more complex compositions.
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Affiliation(s)
- Md Muhaiminul Islam
- 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
| | - Margaret C Richard
- 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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2
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Chen R, Dinpajooh M, Nitzan A. Quantum bath augmented stochastic nonequilibrium atomistic simulations for molecular heat conduction. J Chem Phys 2023; 159:134110. [PMID: 37800644 DOI: 10.1063/5.0168117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023] Open
Abstract
Classical molecular dynamics (MD) has been shown to be effective in simulating heat conduction in certain molecular junctions since it inherently takes into account some essential methodological components which are lacking in the quantum Landauer-type transport model, such as many-body full force-field interactions, anharmonicity effects and nonlinear responses for large temperature biases. However, the classical MD reaches its limit in the environments where the quantum effects are significant (e.g. with low-temperatures substrates, presence of extremely high frequency molecular modes). Here, we present an atomistic simulation methodology for molecular heat conduction that incorporates the quantum Bose-Einstein statistics into an "effective temperature" in the form of a modified Langevin equation. We show that the results from such a quasi-classical effective temperature MD method deviates drastically when the baths temperature approaches zero from classical MD simulations and the results converge to the classical ones when the bath approaches the high-temperature limit, which makes the method suitable for full temperature range. In addition, we show that our quasi-classical thermal transport method can be used to model the conducting substrate layout and molecular composition (e.g. anharmonicities, high-frequency modes). Anharmonic models are explicitly simulated via the Morse potential and compared to pure harmonic interactions to show the effects of anharmonicities under quantum colored bath setups. Finally, the chain length dependence of heat conduction is examined for one-dimensional polymer chains placed in between quantum augmented baths.
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Affiliation(s)
- Renai Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87544, USA
| | - Mohammadhasan Dinpajooh
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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3
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Abstract
ConspectusWhen molecular vibrational modes strongly couple to virtual states of photonic modes, new molecular vibrational polariton states are formed, along with a large population of dark reservoir modes. The polaritons are much like the bonding and antibonding molecular orbitals when atomic orbitals form molecular bonds, while the dark modes are like nonbonding orbitals. Because the polariton states are half-matter and half-light, whose energy is shifted from the parental states, polaritons are predicted to modify chemistry under thermally activated conditions, leading to an exciting and emerging field known as polariton chemistry that could potentially shift paradigms in chemistry. Despite several published results supporting this concept, the chemical physics and mechanism of polariton chemistry remain elusive. One reason for this challenge is that previous works cannot differentiate polaritons from dark modes. This limitation makes delineating the contributions to chemistry from polaritons and dark states difficult. However, this level of insight is critical for developing a solid mechanism for polariton chemistry to design and predict the outcome of strong coupling with any given reaction. My group addressed the challenge of differentiating the dynamics of polaritons and dark modes by ultrafast two-dimensional infrared (2D IR) spectroscopy. Specifically, (1) we found that polaritons can facilitate intra- and intermolecular vibrational energy transfer, opening a pathway to control vibrational energy flow in liquid-phase molecular systems, and (2) by studying a single-step isomerization event, we verified that indeed polaritons can modify chemical dynamics under strong coupling conditions, but in contrast, the dark modes behave like uncoupled molecules and do not change the dynamics. This finding confirmed the central concept of polariton chemistry: polaritons modify the potential energy landscape of reactions. The result also clarified the role of dark modes, which lays a critical foundation for designing cavities for future polariton chemistry. Aside from using 2D IR spectroscopy to study polariton chemistry, we also used the same technique to develop molecular polaritons into a potential quantum simulation platform. We demonstrated that polaritons have Rabi oscillations, and using a checkerboard cavity design, we showed that polaritons could have large nonlinearity across space. We further used the checkerboard polaritons to simulate coherence transfer and visualize it. A unidirectional coherence transfer was observed, indicating non-Hermitian dynamics. The highlighted efforts in this Account provide a solid understanding of the capability of polaritons for chemistry and quantum information science. I conclude this Account by discussing a few challenges for moving polariton chemistry toward being predictable and making the polariton quantum platform a complement to existing systems.
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Affiliation(s)
- Wei Xiong
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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4
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Mizutani Y, Mizuno M. Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale. J Chem Phys 2022; 157:240901. [PMID: 36586981 DOI: 10.1063/5.0116734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.
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Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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5
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Wang JJ, Gong J, McGaughey AJH, Segal D. Simulations of heat transport in single-molecule junctions: Investigations of the thermal diode effect. J Chem Phys 2022; 157:174105. [PMID: 36347668 DOI: 10.1063/5.0125714] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the objective of understanding microscopic principles governing thermal energy flow in nanojunctions, we study phononic heat transport through metal-molecule-metal junctions using classical molecular dynamics (MD) simulations. Considering a single-molecule gold-alkanedithiol-gold junction, we first focus on aspects of method development and compare two techniques for calculating thermal conductance: (i) The Reverse Nonequilibrium MD (RNEMD) method, where heat is inputted and extracted at a constant rate from opposite metals. In this case, the thermal conductance is calculated from the nonequilibrium temperature profile that is created at the junction. (ii) The Approach-to-Equilibrium MD (AEMD) method, with the thermal conductance of the junction obtained from the equilibration dynamics of the metals. In both methods, simulations of alkane chains of a growing size display an approximate length-independence of the thermal conductance, with calculated values matching computational and experimental studies. The RNEMD and AEMD methods offer different insights, and we discuss their benefits and shortcomings. Assessing the potential application of molecular junctions as thermal diodes, alkane junctions are made spatially asymmetric by modifying their contact regions with the bulk, either by using distinct endgroups or by replacing one of the Au contacts with Ag. Anharmonicity is built into the system within the molecular force-field. We find that, while the temperature profile strongly varies (compared with the gold-alkanedithiol-gold junctions) due to these structural modifications, the thermal diode effect is inconsequential in these systems-unless one goes to very large thermal biases. This finding suggests that one should seek molecules with considerable internal anharmonic effects for developing nonlinear thermal devices.
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Affiliation(s)
- Jonathan J Wang
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
| | - Jie Gong
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Alan J H McGaughey
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Dvira Segal
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
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6
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Leong TX, Collins BK, Dey Baksi S, Mackin RT, Sribnyi A, Burin AL, Gladysz JA, Rubtsov IV. Tracking Energy Transfer across a Platinum Center. J Phys Chem A 2022; 126:4915-4930. [PMID: 35881911 PMCID: PMC9358659 DOI: 10.1021/acs.jpca.2c02017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Rigid, conjugated alkyne bridges serve as important components
in various transition-metal complexes used for energy conversion,
charge separation, sensing, and molecular electronics. Alkyne stretching
modes have potential for modulating charge separation in donor–bridge–acceptor
compounds. Understanding the rules of energy relaxation and energy
transfer across the metal center in such compounds can help optimize
their electron transfer switching properties. We used relaxation-assisted
two-dimensional infrared spectroscopy to track energy transfer across
metal centers in platinum complexes featuring a triazole-terminated
alkyne ligand of two or six carbons, a perfluorophenyl ligand, and
two tri(p-tolyl)phosphine ligands. Comprehensive
analyses of waiting-time dynamics for numerous cross and diagonal
peaks were performed, focusing on coherent oscillation, energy transfer,
and cooling parameters. These observables augmented with density functional
theory computations of vibrational frequencies and anharmonic force
constants enabled identification of different functional groups of
the compounds. Computations of vibrational relaxation pathways and
mode couplings were performed, and two regimes of intramolecular energy
redistribution are described. One involves energy transfer between
ligands via high-frequency modes; the transfer is efficient only if
the modes involved are delocalized over both ligands. The energy transport
pathways between the ligands are identified. Another regime involves
redistribution via low-frequency delocalized modes, which does not
lead to interligand energy transport.
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Affiliation(s)
- Tammy X Leong
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Brenna K Collins
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sourajit Dey Baksi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Robert T Mackin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Artem Sribnyi
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - John A Gladysz
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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7
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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
![]()
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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8
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Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids. Nat Commun 2021; 12:3284. [PMID: 34078890 PMCID: PMC8172543 DOI: 10.1038/s41467-021-23591-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
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9
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Leong TX, Qasim LN, Mackin RT, Du Y, Pascal RA, Rubtsov IV. Unidirectional coherent energy transport via conjugated oligo(p-phenylene) chains. J Chem Phys 2021; 154:134304. [PMID: 33832250 DOI: 10.1063/5.0046932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We discovered a way to funnel high-frequency vibrational quanta rapidly and unidirectionally over large distances using oligo(p-phenylene) chains. After mid-IR photon photoexcitation of a -COOH end group, the excess energy is injected efficiently into the chain, forming vibrational wavepackets that propagate freely along the chain. The transport delivers high-energy vibrational quanta with a range of transport speeds reaching 8.6 km/s, which exceeds the speed of sound in common metals (∼5 km/s) and polymers (∼2 km/s). Efficiencies of energy injection into the chain and transport along the chain are found to be very high and dependent on the extent of conjugation across the structure. By tuning the degree of conjugation via electronic doping of the chain, the transport speed and efficiency can be controlled. The study opens avenues for developing materials with controllable energy transport properties for heat management, schemes with efficient energy delivery to hard-to-reach regions, including transport against thermal gradients, and ways for initiating chemical reactions remotely.
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Affiliation(s)
- Tammy X Leong
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Layla N Qasim
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Robert T Mackin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Yuchen Du
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Robert A Pascal
- 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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10
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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: 11] [Impact Index Per Article: 2.8] [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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11
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Boulatov A, Burin AL. Crucial effect of transverse vibrations on the transport through polymer chains. J Chem Phys 2020; 153:134102. [PMID: 33032425 DOI: 10.1063/5.0018591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The low temperature transport of electron, or vibrational or electronic exciton toward polymer chains, turns out to be dramatically sensitive to its interaction with transverse acoustic vibrations. We show that this interaction leads to a substantial polaron effect and decoherence, which are generally stronger than those associated with longitudinal vibrations. For site-dependent interactions, transverse phonons form subohmic bath leading to the quantum phase transition accompanied by full suppression of the transport at zero temperature and fast decoherence characterized by temperature dependent rate k2 ∝ T3/4 at low temperature, while k2 ∝ T2 for site-independent interactions. The latter dependence was used to interpret recent measurements of temperature dependent vibrational energy transport in polyethylene glycol oligomers.
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Affiliation(s)
- Alexei Boulatov
- National Research University Higher School of Economics, 11 Pokrovsky Blvd., Moscow 101000, Russia
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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12
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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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13
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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14
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Heyne K, Kühn O. Infrared Laser Excitation Controlled Reaction Acceleration in the Electronic Ground State. J Am Chem Soc 2019; 141:11730-11738. [DOI: 10.1021/jacs.9b02600] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Karsten Heyne
- Department of Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Oliver Kühn
- Institute of Physics, University of Rostock, Albert Einstein-Strasse 23-24, 18059 Rostock, Germany
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15
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Liu M, Kawauchi T, Iyoda T, Piotrowiak P. Vibrational Cooling in Oligomeric Viologens of Different Sizes and Topologies. J Phys Chem B 2019; 123:1847-1854. [PMID: 30724560 DOI: 10.1021/acs.jpcb.8b12165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrational cooling was investigated in a set of homologous dimers and trimers with methyl viologen repeat units (MV2+). The rapid, <500 fs decay of the D1 excited state of monoreduced viologen (MV+•) via a conical intersection allows the preparation of a vibrationally hot D0 ground state with a large excess energy of 1.7 eV, which is equivalent to the initial effective temperature of ∼800 K. Pump-probe spectroscopy was used to monitor the disappearance of the characteristic D0 → D1 hot absorption band, which appears at longer wavelengths than the steady-state spectrum of "cold" MV+• in equilibrium with the solvent. It is assumed that the vibrational excitation of the ground is initially confined to the same monoreduced viologen repeat unit, which was optically excited to the localized electronic D1 state, although some degree of redistribution may occur already in the excited state. The observed cooling rates depend on the size and topology of the oligomer, with the linear trimer exhibiting significantly faster thermalization than the branched one. The experimental results were corroborated by molecular dynamics simulations carried out in the harmonic approximation. The dynamics of the thermal equilibration in these systems appears to be consistent with primarily ballistic initial propagation of the vibrational excess energy over distances as large as ∼4 nm and suggests the presence of interference between the equivalent pathways in the branched trimer.
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Affiliation(s)
- Mengdi Liu
- Department of Chemistry , Rutgers University-Newark , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Takehiro Kawauchi
- Department of Materials Chemistry, Faculty of Science and Technology , Ryukoku University , 1-5 Yokotani , Oe-cho, Seta, Otsu , Shiga 520-2194 , Japan
| | - Tomokazu Iyoda
- Harris Science Research Institute , Doshisha University , 1-3 Tatara Miyakodani , Kyotanabe , Kyoto 610-0394 , Japan
| | - Piotr Piotrowiak
- Department of Chemistry , Rutgers University-Newark , 73 Warren Street , Newark , New Jersey 07102 , United States
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16
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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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17
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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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18
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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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19
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Varner C, Zhou X, Saxman ZK, Leger JD, Jayawickramarajah J, Rubtsov IV. Azido alkanes as convenient reporters for mobility within lipid membranes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Bailey JO, Singleton DA. Failure and Redemption of Statistical and Nonstatistical Rate Theories in the Hydroboration of Alkenes. J Am Chem Soc 2017; 139:15710-15723. [PMID: 29029560 PMCID: PMC5831723 DOI: 10.1021/jacs.7b07175] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Our previous work found that canonical forms of transition state theory incorrectly predict the regioselectivity of the hydroboration of propene with BH3 in solution. In response, it has been suggested that alternative statistical and nonstatistical rate theories can adequately account for the selectivity. This paper uses a combination of experimental and theoretical studies to critically evaluate the ability of these rate theories, as well as dynamic trajectories and newly developed localized statistical models, to predict quantitative selectivities and qualitative trends in hydroborations on a broader scale. The hydroboration of a series of terminally substituted alkenes with BH3 was examined experimentally, and a classically unexpected trend is that the selectivity increases as the alkyl chain is lengthened far from the reactive centers. Conventional and variational transition state theories can predict neither the selectivities nor the trends. The canonical competitive nonstatistical model makes somewhat better predictions for some alkenes but fails to predict trends, and it performs poorly with an alkene chosen to test a specific prediction of the model. Added nonstatistical corrections to this model make the predictions worse. Parametrized Rice-Ramsperger-Kassel-Marcus (RRKM)-master equation calculations correctly predict the direction of the trend in selectivity versus alkene size but overpredict its magnitude, and the selectivity with large alkenes remains unpredictable with any parametrization. Trajectory studies in explicit solvent can predict selectivities without parametrization but are impractical for predicting small changes in selectivity. From a lifetime and energy analysis of the trajectories, "localized RRKM-ME" and "competitive localized noncanonical" rate models are suggested as steps toward a general model. These provide the best predictions of the experimental observations and insight into the selectivities.
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Affiliation(s)
- Johnathan O. Bailey
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Daniel A. Singleton
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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21
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Chen R, Craven GT, Nitzan A. Electron-transfer-induced and phononic heat transport in molecular environments. J Chem Phys 2017; 147:124101. [DOI: 10.1063/1.4990410] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Renai Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104,
USA
| | - Galen T. Craven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104,
USA
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104,
USA
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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22
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Pandey HD, Leitner DM. Influence of thermalization on thermal conduction through molecular junctions: Computational study of PEG oligomers. J Chem Phys 2017; 147:084701. [DOI: 10.1063/1.4999411] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
| | - David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
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23
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Kraack JP, Kaech A, Hamm P. Molecule-specific interactions of diatomic adsorbates at metal-liquid interfaces. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044009. [PMID: 28396878 PMCID: PMC5367089 DOI: 10.1063/1.4978894] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/06/2017] [Indexed: 05/15/2023]
Abstract
Ultrafast vibrational dynamics of small molecules on platinum (Pt) layers in water are investigated using 2D attenuated total reflectance IR spectroscopy. Isotope combinations of carbon monoxide and cyanide are used to elucidate inter-adsorbate and substrate-adsorbate interactions. Despite observed cross-peaks in the CO spectra, we conclude that the molecules are not vibrationally coupled. Rather, strong substrate-adsorbate interactions evoke rapid (∼2 ps) vibrational relaxation from the adsorbate into the Pt layer, leading to thermal cross-peaks. In the case of CN, vibrational relaxation is significantly slower (∼10 ps) and dominated by adsorbate-solvent interactions, while the coupling to the substrate is negligible.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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24
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Kovács B, Kuş N, Tarczay G, Fausto R. Experimental Evidence of Long-Range Intramolecular Vibrational Energy Redistribution through Eight Covalent Bonds: NIR Irradiation Induced Conformational Transformation of E-Glutaconic Acid. J Phys Chem A 2017; 121:3392-3400. [PMID: 28423274 DOI: 10.1021/acs.jpca.7b00615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Long-range intramolecular vibrational energy redistribution (IVR) driven conformational changes were investigated in a matrix-isolated open-chain, asymmetrical dicarboxylic acid, E-glutaconic acid. Although the analysis was challenging due to the presence of multiple backbone conformers and short lifetimes of the prepared higher energy cis conformers, it was shown that the selective excitation of the O-H stretching overtone of one of the carboxylic groups can induce the conformational change (trans to cis) of the other carboxylic group, located at the other end of the E-glutaconic acid molecule. This is a direct proof that the IVR process can act through eight covalent bonds in a flexible molecule before the excess energy completely dissipates into the matrix. The lifetime of the prepared higher energy conformers (averaged over the different backbones) was measured to be 12 s.
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Affiliation(s)
- Benjámin Kovács
- Institute of Chemistry, Eötvös University , PO Box 32, H-1518 Budapest 112, Hungary
| | - Nihal Kuş
- CQC, Department of Chemistry, University of Coimbra , 3004-535 Coimbra, Portugal.,Department of Physics, Anadolu University , TR-26470 Eskişehir, Turkey
| | - György Tarczay
- Institute of Chemistry, Eötvös University , PO Box 32, H-1518 Budapest 112, Hungary
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra , 3004-535 Coimbra, Portugal
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25
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Craven GT, Nitzan A. Electron transfer at thermally heterogeneous molecule-metal interfaces. J Chem Phys 2017. [DOI: 10.1063/1.4971293] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Galen T. Craven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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26
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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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27
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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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28
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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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29
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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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30
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Abstract
Charge transfer is a fundamental process that underlies a multitude of phenomena in chemistry and biology. Recent advances in observing and manipulating charge and heat transport at the nanoscale, and recently developed techniques for monitoring temperature at high temporal and spatial resolution, imply the need for considering electron transfer across thermal gradients. Here, a theory is developed for the rate of electron transfer and the associated heat transport between donor-acceptor pairs located at sites of different temperatures. To this end, through application of a generalized multidimensional transition state theory, the traditional Arrhenius picture of activation energy as a single point on a free energy surface is replaced with a bithermal property that is derived from statistical weighting over all configurations where the reactant and product states are equienergetic. The flow of energy associated with the electron transfer process is also examined, leading to relations between the rate of heat exchange among the donor and acceptor sites as functions of the temperature difference and the electronic driving bias. In particular, we find that an open electron transfer channel contributes to enhanced heat transport between sites even when they are in electronic equilibrium. The presented results provide a unified theory for charge transport and the associated heat conduction between sites at different temperatures.
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Affiliation(s)
- Galen T Craven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104; School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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31
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Kurnosov AA, Rubtsov IV, Maksymov AO, Burin AL. Electronic torsional sound in linear atomic chains: Chemical energy transport at 1000 km/s. J Chem Phys 2016; 145:034903. [DOI: 10.1063/1.4958726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Arkady A. Kurnosov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Andrii O. Maksymov
- 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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