Hydrogen Bonds and Heat Diffusion in α-Helices: A Computational Study

Phonon Transport in Supramolecular Polymers Regulated by Hydrogen Bonds

Supramolecular polymers hold promise in thermal management applications due to their multistability, high responsiveness, and cost-effectiveness. In this work, we successfully regulate phonon transport at the molecular level in supramolecular polymers by adjusting the strength of intermolecular hydrogen bonding. We synthesized three supramolecular polymer fibers with thermal conductivity differences of up to 289% based on melamine (M) and three simple positional isomers of hydroxybenzoic acid. Differential Scanning Calorimetry (DSC) measurement revealed discrepancies in thermal stability of the polymers, where structures with higher stability exhibited enhanced thermal conductivity. Fourier Transform Infrared Spectroscopy (FTIR) measurement and Density Functional Theory (DFT) calculations indicate that these differences arise from variations in hydrogen-bonding strengths at different bonding sites. Higher hydrogen-bonding strength leads to more stable thermal pathways, reduces phonon scattering, and increases thermal conductivity. Our findings provide valuable insights into controlling the thermal conductivity of polymer fibers, paving the way for applications in phonon-based thermal devices.

Thermal Energy Transport through Nonbonded Native Contacts in Protein

Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.

Intermolecular Protein-Water Coupling Impedes the Coupling Between the Amide A and Amide I Mode in Interfacial Proteins

The coupling between different vibrational modes in proteins is essential for chemical dynamics and biological functions and is linked to the propagation of conformational changes and pathways of allosteric communication. However, little is known about the influence of intermolecular protein-H2O coupling on the vibrational coupling between amide A (NH) and amide I (C═O) bands. Here, we investigate the NH/CO coupling strength in various peptides with different secondary structures at the lipid cell membrane/H2O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy (SFG-VS) in which a femtosecond infrared pump is used to excite the amide A band, and SFG-VS is used to probe transient spectral evolution in the amide A and amide I bands. Our results reveal that the NH/CO coupling strength strongly depends on the bandwidth of the amide I mode and the coupling of proteins with water molecules. A large extent of protein-water coupling significantly reduces the delocalization of the amide I mode along the peptide chain and impedes the NH/CO coupling strength. A large NH/CO coupling strength is found to show a strong correlation with the high energy transfer rate found in the light-harvesting proteins of green sulfur bacteria, which may understand the mechanism of energy transfer through a molecular system and assist in controlling vibrational energy transfer by engineering the molecular structures to achieve high energy transfer efficiency.

Hierarchically hydrogen-bonded graphene/polymer interfaces with drastically enhanced interfacial thermal conductance

Interfacial thermal transport is a critical physical process determining the performance of many material systems with small-scale features. Recently, self-assembled monolayers and polymer brushes have been widely used to engineer material interfaces presenting unprecedented properties. Here, we demonstrate that poly(vinyl alcohol) (PVA) monolayers with hierarchically arranged hydrogen bonds drastically enhance interfacial thermal conductance by a factor of 6.22 across the interface between graphene and poly(methyl methacrylate) (PMMA). The enhancement is tunable by varying the number of grafted chains and the density of hydrogen bonds in the unique hierarchical hydrogen bond network. The extraordinary enhancement results from a synergy of hydrogen bonds and other structural and thermal factors including molecular morphology, chain orientation, interfacial vibrational coupling and heat exchange. Two types of hydrogen bonds, i.e. PVA-PMMA hydrogen bonds and PVA-PVA hydrogen bonds, are analyzed and their effects on various structural and thermal properties are systematically investigated. These results are expected to provide new physical insights for interface engineering to achieve tunable thermal management and energy efficiency in a wide variety of systems involving polymers and biomaterials.

Allosteric communication pathways and thermal rectification in PDZ-2 protein: a computational study

Allosteric communication in proteins is a fundamental and yet unresolved problem of structural biochemistry. Previous findings, from computational biology ( Ota, N.; Agard, D. A. J. Mol. Biol. 2005 , 351 , 345 - 354 ), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures: heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (∼2.85 Å) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (∼2.60 Å), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science.

Tuning thermal conductivity of crystalline polymer nanofibers by interchain hydrogen bonding

Interchain hydrogen bonds enhance thermal conduction in crystalline polymer nanofibers by confining torsional motion of polymer chains and by increasing the group velocity of phonons.

Effects of the amino acid sequence on thermal conduction through β-sheet crystals of natural silk protein

Molecular mechanisms underpinning the thermal transport process through three types of β-sheets are studied to reveal the intrinsic sequence effects.