Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Schade, Marco; Hamm, Peter

doi:10.1063/1.3185152

Cited by 32 publications

(39 citation statements)

References 44 publications

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“…As energy is then distributed over more degrees of freedom, thermalization of high-frequency modes will slightly lower the temperature of the simulation box as a whole, since its heat capacity is finite, explaining the slight overshooting of the CO kinetic energy. The interplay between energy transport through low-frequency modes and thermalization of high frequency modes has been described in detail in the context of small helices [38].…”

Section: B Molecular Dynamics Simulationsmentioning

confidence: 99%

Temperature Dependence of the Heat Diffusivity of Proteins

et al. 2011

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In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme protein, the sperm whale myoglobin double mutant L29W-S108L, and its dependence on temperature from 20 to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket) was used as the local thermometer. Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps)−1 at 20 K to (8 ps)−1 at 70 K. This temperature trend is opposite to what is expected, assuming that the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, nonequilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature-independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate-limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained. In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme-protein, the sperm whale myoglobin double mutant L29W-S108L, in dependence of temperature from 20 K to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket), was used as "local thermometer". Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps) −1 at 20 K to (8 ps) −1 at 70 K. This temperature trend is opposite to what is expected, assuming the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, non-equilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained.

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Section: B Molecular Dynamics Simulationsmentioning

confidence: 99%

Temperature Dependence of the Heat Diffusivity of Proteins

et al. 2011

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“…For simplicity, we choose a cascade-like connectivity of the localized states (like in Ref. [36]) with identical forward and backward rates, but, as shown analytically in the Appendix, the essential result of the paper also holds for much more complex distributions of modes within each site and for arbitrary rates. The dynamics of such a system can be described by set of coupled linear differential equations.…”

Section: Modelmentioning

confidence: 99%

“…Along the lines of our previous paper [36], a one-dimensional (1D) chain is defined, each consisting of one transporting mode and a set of localized ("parking") modes, as depicted in Fig. 1.…”

Section: Modelmentioning

confidence: 99%

“…However, since intra-site IVR is chain-length independent, the inter site propagation rate is expected to become rate limiting on some larger length scales. Due to the high computational costs of the quantum-mechanical simulations [36], we could not extend the system to length scales on which the expected transition between the intra-site-and inter-site-dominated regime occurs. In the present paper, we revisit the model and treat it on a much simpler level, which can be applied to much longer molecular chains, in order to closer investigate this transition.…”

Section: Introductionmentioning

confidence: 99%

“…To resolve the discrepancies between our experiments and the accompanying MD simulations [19], we have recently introduced a small toy model for simulating vibrational energy transport along linear chains in the presence of intrasite IVR [36]. The model was designed to mimic the normal mode distribution found in proteins (which is similar like in one-dimensional glasses), in which only a relatively small subset of low-frequency modes tend to delocalize over large distances and as such dominate vibrational energy transport [37][38][39][26][27][28][29]40].…”

Section: Introductionmentioning

confidence: 99%

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Transition from IVR limited vibrational energy transport to bulk heat transport

Schade

Hamm

2012

Chemical Physics

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In a previous paper (J. Chem. Phys. 131, 044511 (2009)), it has been shown that on ultrashort length and time scales, the speed of vibrational energy transport along a molecular chain is limited by intrasite vibrational relaxation rather than the actual inter site propagation. However, since intrasite vibrational relaxation is length independent, the inter site propagation rate is expected to become ratelimiting at some length scale, where propagation approaches the bulk limit. In the present paper, we investigate the transition between both regimes. The response of different types of modes may be very different at early times, depending on how much they contribute directly to energy transport. Surprisingly though, when averaging the energy content over all vibrational modes of the various chain sites, the complexity of the intrasite vibrational relaxation process is completely hidden so that energy transport on the nanoscale can be described by an effective propagation rate, that equals the bulk value, even at short times. Transition from IVR limited vibrational energy transport to bulk heat transport Marco Schade and Peter HammPhysikalisch-Chemisches Institut, Universität Zürich, Winterthurerstr. 190, Switzerland Abstract: In a previous paper (J. Chem. Phys. 131, 044511 (2009)), it has been shown that on ultrashort length and time scales, the speed of vibrational energy transport along a molecular chain is limited by intrasite vibrational relaxation rather than the actual inter site propagation. However, since intrasite vibrational relaxation is length independent, the inter site propagation rate is expected to become rate-limiting at some length scale, where propagation approaches the bulk limit. In the present paper, we investigate the transition between both regimes. The response of different types of modes may be very different at early times, depending on how much they contribute directly to energy transport. Surprisingly though, when averaging the energy content over all vibrational modes of the various chain sites, the complexity of the intrasite vibrational relaxation process is completely hidden so that energy transport on the nanoscale can be described by an effective propagation rate, that equals the bulk value, even at short times.

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Following the energy transfer in and out of a polyproline–peptide

et al. 2013

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The intramolecular and intermolecular vibrational energy flow in a polyproline peptide with a total number of nine amino acids in the solvent dimethyl sulfoxide is investigated using time-resolved infrared (IR) spectroscopy. Azobenzene covalently bound to a proline sequence containing nitrophenylalanine as a local sensor for vibrational excess energy serves as a heat source. Information on through-space distances in the polyproline peptides is obtained by independent Förster resonance energy transfer measurements. Photoexcitation of the azobenzene and subsequent internal conversion yield strong vibrational excitation of the molecule acting as a local heat source. The relaxation of excess heat, its transfer along the peptide and to the solvent is monitored by the response of the nitro-group in nitrophenylalanine acting as internal thermometer. After optical excitation, vibrational excess energy is observed via changes in the IR absorption spectra of the peptide. The nitrophenylalanine bands reveal that the vibrational excess energy flows in the peptide over distances of more than 20 Å and arrives delayed by up to 7 ps at the outer positions of the peptide. The vibrational excess energy is transferred to the surrounding solvent on a time scale of 10-20 ps. The experimental observations are analyzed by different heat conduction models. Isotropic heat conduction in three dimensions away from the azobenzene heat source is not able to describe the observations. One-dimensional heat dissipation along the polyproline peptide combined with a slower transversal heat transfer to the solvent surrounding well reproduces the observations.

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Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Cited by 32 publications

References 44 publications

Temperature Dependence of the Heat Diffusivity of Proteins

Temperature Dependence of the Heat Diffusivity of Proteins

Transition from IVR limited vibrational energy transport to bulk heat transport

Following the energy transfer in and out of a polyproline–peptide

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