Tuning Molecular Vibrational Energy Flow within an Aromatic Scaffold via Anharmonic Coupling.

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.

Energy Transport across Interfaces in Biomolecular Systems.

Energy transport during chemical reactions or following photoexcitation in systems of biological molecules is mediated by numerous interfaces that separate chemical groups and molecules. Describing and predicting energy transport has been complicated by the inhomogeneous environment through which it occurs, and general rules are still lacking. We discuss recent work on identification of networks for vibrational energy transport in biomolecules and their environment, with focus on the nature of energy transfer across interfaces. Energy transport is influenced both by structure of the biomolecular system as well as by equilibrium fluctuations of nonbonded contacts between chemical groups, biomolecules, and water along the network. We also discuss recent theoretical and computational work on the related topic of thermal transport through molecular interfaces, with focus on systems important in biology as well as relevant experimental studies.

Vibrational States and Nitrile Lifetimes of Cyanophenylalanine Isotopomers in Solution.

Nitrile lifetimes and the structure of the vibrational state space of four isotopomers of cyanophenylalanine in solution are calculated. While the frequency of the nitrile of the four isotopomers decreases in the order 12C14N, 12C15N, 13C14N, and 13C15N, the lifetime varies nonmonotonically with the change in frequency. The vibrational properties of the molecules that control the lifetime are examined. The specific resonances that contribute to the lifetime are tuned by isotopic substitution, and the magnitudes of the anharmonic constants involved in the coupling of vibrations that mediate the lifetime of the nitrile vary with CN mass. The nature of the modes coupled to the nitrile varies, as the frequency of the nitrile changes with isotopic substitution. For some CN frequencies the modes coupled to the CN are rather localized to the ring, while at other frequencies the modes coupled to the CN are more delocalized. Comparison of the calculated frequencies and lifetimes with recent experimental measurements on these molecules is discussed.

Small Saccharides as a Blanket around Proteins: A Computational Study.

Saccharides stabilize proteins exposed to thermal fluctuations and stresses. While the effect of a layer of trehalose around a protein on the melting temperature has been well studied, its role as a thermal insulator remains unclear. We report calculations of thermalization in small saccharides, including glucose, galactose, lactose, and trehalose, and thermal transport through a trehalose layer between water and protein and between gold, such as a gold nanoparticle, and its cellular environment. The thermalization rates calculated for the saccharides provide information about the scope of applicability of approaches that can be used to predict thermal conduction in these systems, specifically where Fourier's law breaks down and where a Landauer approach is suitable. We find that trehalose serves as an excellent molecular insulator over a wide range of temperatures.

Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study.

We investigate by molecular simulations thermodynamic properties of hydration water and protein, the sensitivity of hydrogen bonds to change in temperature, and hydration water distribution at varying levels of hydration of a hyperactive antifreeze protein, DAFP-1. Hydration water coverage of the protein and partial thermodynamic properties of the hydration water are heterogeneous, different for the water near the ice-binding site (IBS) and the rest of the protein, particularly at low levels of hydration. Overall, we find the partial specific heat of water to be larger at low hydration levels than in the fully hydrated limit, with the separation corresponding roughly to one hydration layer. Differences in the specific heat in the low- and fully hydrated regions are accounted for by the varying sensitivity of water-water and water-protein hydrogen bonds to change in temperature as a function of hydration, most strikingly near the IBS. Using values computed for the specific heat, we estimate the partial entropy of the water and protein. We find the partial entropy of DAFP-1 to be greater in the fully hydrated limit than at low levels of hydration, whereas the partial entropy of water is somewhat smaller.

Influence of thermalization on thermal conduction through molecular junctions: Computational study of PEG oligomers.

Thermalization in molecular junctions and the extent to which it mediates thermal transport through the junction are explored and illustrated with computational modeling of polyethylene glycol (PEG) oligomer junctions. We calculate rates of thermalization in the PEG oligomers from 100 K to 600 K and thermal conduction through PEG oligomer interfaces between gold and other materials, including water, motivated in part by photothermal applications of gold nanoparticles capped by PEG oligomers in aqueous and cellular environments. Variation of thermalization rates over a range of oligomer lengths and temperatures reveals striking effects of thermalization on thermal conduction through the junction. The calculated thermalization rates help clarify the scope of applicability of approaches that can be used to predict thermal conduction, e.g., where Fourier's law breaks down and where a Landauer approach is suitable. The rates and nature of vibrational energy transport computed for PEG oligomers are compared with available experimental results.

Thermalization and Thermal Transport in Molecules.

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.

Asymmetric energy flow in liquid alkylbenzenes: A computational study.

Ultrafast IR-Raman experiments on substituted benzenes [B. C. Pein et al., J. Phys. Chem. B 117, 10898-10904 (2013)] reveal that energy can flow more efficiently in one direction along a molecule than in others. We carry out a computational study of energy flow in the three alkyl benzenes, toluene, isopropylbenzene, and t-butylbenzene, studied in these experiments, and find an asymmetry in the flow of vibrational energy between the two chemical groups of the molecule due to quantum mechanical vibrational relaxation bottlenecks, which give rise to a preferred direction of energy flow. We compare energy flow computed for all modes of the three alkylbenzenes over the relaxation time into the liquid with energy flow through the subset of modes monitored in the time-resolved Raman experiments and find qualitatively similar results when using the subset compared to all the modes.