Influence of vibrational energy flow on isomerization of flexible molecules: Incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization

Agbo, Johnson K.; Leitner, David M.; Evans, David A.; Wales, David J.

doi:10.1063/1.2011399

Cited by 24 publications

(16 citation statements)

References 27 publications

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“…Control of vibrational energy transfer in molecules affects chemical processes, e.g. reaction pathways, bond breaking processes, and folding dynamics [33]. Finally, we propose building technological devices based on heat flow, in analogy with electron current devices [34].…”

Section: Discussionmentioning

confidence: 99%

“…The coefficients λ n,j are the effective system-bath interaction parameters that depend on the level index and the reservoir mode, see Appendix A. The Hamiltonian (33) is similar to that defined in Eqs. ( 4)- (13), except that the L and R system-baths couplings appear as multiplicative rather than additive factors in the interaction term, implying non-separable transport at the two contacts [23].…”

Section: Strong System-bath Couplingmentioning

confidence: 99%

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Heat flow in nonlinear molecular junctions: Master equation analysis

2006

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We investigate the heat conduction properties of molecular junctions comprising anharmonic interactions. We find that nonlinear interactions can lead to novel phenomena: negative differential thermal conductance and heat rectification. Based on analytically solvable models we derive an expression for the heat current that clearly reflects the interplay between anharmonic interactions, strengths of coupling to the thermal reservoirs, and junction asymmetry. This expression indicates that negative differential thermal conductance shows up when the molecule is strongly coupled to the thermal baths, even in the absence of internal molecular nonlinearities. In contrast, diode like behavior is expected for a highly anharmonic molecule with an inherent structural asymmetry.Anharmonic interactions are also necessary for manifesting Fourier type transport. We briefly present an extension of our model system that can lead to this behavior.

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Section: Discussionmentioning

confidence: 99%

Section: Strong System-bath Couplingmentioning

confidence: 99%

Heat flow in nonlinear molecular junctions: Master equation analysis

2006

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“…Thermalization in molecules has been the focus of considerable attention, 87,91, in part because it mediates chemical reaction kinetics, [143][144][145][146][147][148][149][150][151][152][153][154] and thermalization appears to be largely complete on the scale of peptides. [155][156][157][158][159][160][161] In practice a region, A, is a residue or a cofactor such as a heme, or perhaps a cluster of water molecules in the protein.…”

Section: Locating Energy Transport Network Communication Mapsmentioning

confidence: 99%

Mapping Energy Transport Networks in Proteins

Leitner

Yamato

2018

Reviews in Computational Chemistry

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INTRODUCTIONThe response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. [1][2][3] In recent years ultrafast X-ray studies have provided ever more detailed information about the evolution of protein structural change following ligand photolysis, 4-5 and time-resolved IR and Raman techniques, e.g., have provided detailed pictures of the nature and rate of energy transport in peptides and proteins, [6][7][8][9][10][11] including recent advances in identifying transport through individual amino acids of several heme proteins. [12][13][14] Computational tools to locate energy transport pathways in proteins have also been advancing. 15 Energy transport pathways in proteins have since some time been identified by molecular dynamics (MD) simulations, [16][17] and more recent efforts have focused on the development of coarse graining approaches, 18-29 some of which have exploited analogies to thermal transport in other molecular materials. [30][31][32][33][34][35] With the identification of pathways in proteins and protein 2 complexes, network analysis has been applied to locate residues that control protein dynamics and possibly allostery, [36][37][38] where chemical reactions at one binding site mediate reactions at distance sites of the protein. In this chapter we review approaches for locating computationally energy transport networks in proteins. We present background into energy and thermal transport in condensed phase and macromolecules that underlies the approaches we discuss before turning to a description of the approaches themselves. We also illustrate the application of the computational methods for locating energy transport networks and simulating energy dynamics in proteins with several examples.One of the themes that we address in this chapter is the difference between energy transport in condensed phase generally and in a folded polymer such as a protein specifically. While the approaches that we present and detail are based on linearresponse theory for transport, we apply them to a system, a protein, where energy transport occurs highly anisotropically.We are mainly concerned with the characterization of such anisotropic transport, not simply the calculation of transport coefficients for a particular object, though that information can also be calculated starting with the approaches we present. The focus here then is on local energy transport coefficients, such as local energy conductivities and diffusivities, as discussed below, and how these local transport properties connect into a network that mediates energy dynamics in the protein. It is the network of such local energy transport coefficients that, once identified and located, can be used to model the global energy dynamics in a protein, as we describe.That energy transport pathways exist, i.e., energy does not simply flow isotropically through a globular protein, is an inherent property of the geometry of a 3 folded protein, [62][63][64][65][66][67][68][69][70] which i...

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“…Numerous other reactions where the standard TST predictions break down have been reviewed recently [ 9 ]. The recognition that chemical reactions are more complex than can be captured by traditional theories based on equilibrium statistical mechanics, and the development of new approaches to this problem, accounting for complex dynamics in the VSS of a molecule, continue to be an active research topic [ 44 , 45 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 ]. We have also reviewed here some recent work examining the role of thermalization in thermal conduction in molecular junctions.…”

Section: Discussionmentioning

confidence: 99%

Molecules and the Eigenstate Thermalization Hypothesis

Leitner

2018

Entropy

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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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Influence of vibrational energy flow on isomerization of flexible molecules: Incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization

Cited by 24 publications

References 27 publications

Heat flow in nonlinear molecular junctions: Master equation analysis

Heat flow in nonlinear molecular junctions: Master equation analysis

Mapping Energy Transport Networks in Proteins

Molecules and the Eigenstate Thermalization Hypothesis

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