Heat flow in proteins: computation of thermal transport coefficients

The rate of vibrational energy transfer and thermal transport coefficients are computed for two structurally distinct proteins, green fluorescent protein (GFP) and myoglobin. The computation of thermal transport coefficients exploits the scaling of the energy diffusion coefficient with the vibrational mode frequency of a protein. Near 300 K we find that vibrational energy transfer due to anharmonicity contributes substantially to thermal transport because of the localization of many thermally accessible normal modes. The thermal diffusivity for the beta-barrel GFP is larger than that for myoglobin, particularly at low temperature due to a mean free path for vibrational energy propagation that is twice as large at low frequency. Vibrational energy transfer is also faster in GFP than in myoglobin for most vibrational modes.     

Assessment and prediction of thermal transport at solid-self-assembled monolayer junctions

Self-assembled monolayers (SAMs) have recently garnered much interest due to their unique electrical, chemical, and thermal properties. Several studies have focused on thermal transport across solid-SAM junctions, demonstrating that interface conductance is largely insensitive to changes in SAM length. In the present study, we have investigated the vibrational spectra of alkanedithiol-based SAMs as a function of the number of methylene groups forming the molecular backbone via Hartree-Fock methods. In the case of Au-alkanedithiol junctions, it is found that despite the addition of nine new vibrational modes per added methylene group, only one of these modes falls below the maximum phonon frequency of Au. In addition, the alkanedithiol one-dimensional density of normal modes (modes per unit energy per unit length) is nearly constant regardless of chain length, explaining the observed insensitivity. Furthermore, we developed a diffusive transport model intended to predict interface conductance at solid-SAM junctions. It is shown that this predictive model is in an excellent agreement with prior experimental data available in the literature.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.     

Influence of the host on vibronic relaxation: a study of free-base porphin in a series of n-alkanes by photochemical hole-burning

Photochemical hole-burning is used to determine the relaxation times of vibronic bands of the S₁ ← S₀ transition to free-base porphin in different substitutional sites of n-hexane, n-heptane, n-octane and n-decane at 1.6 K. The vibronic relaxation depends strongly on site and host. A correlation between the n-alkane chain length and the vibronic relaxation time is observed.     

Ballistic energy transport along PEG chains: distance dependence of the transport efficiency

Dual-frequency relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy was used to investigate energy transport in polyethylene glycol (PEG) oligomers of different length, having 0, 4, 8, and 12 repeating units and end-labeled with azido and succinimide ester moieties (azPEGn). The energy transport initiated by excitation of the N≡N stretching mode of the azido group in azPEGn in CCl(4) at ca. 2100 cm(-1) was recorded by probing the C=O stretching modes (reporters) of the succinimide ester moiety. Sensitive to the excess energy delivered to the reporter modes, RA 2DIR permits observation of both the through-bond and through-solvent energy transport contributions. The cross-peak data involving the reporter modes with different thermal sensitivity and the data for mixtures of compounds permitted concluding that through-bond energy transport is the dominant mechanism for most cross peaks in all four azPEGn compounds. The through-bond energy transport time, evaluated as the waiting time at which the cross peak maximum is reached, was found to be linearly dependent on the chain length of up to 60 ?, suggesting a ballistic energy transport regime. The through-bond energy transport speed determined from the chain-length dependence of T(max) in CCl(4) is found to be ca. 450 m s(-1). The cross-peak amplitude at the maximum decays exponentially with the chain length; a characteristic decay distance is found to be 15.7 ± 1 ?. The cross-peak amplitude at zero waiting time, determined by the end-to-end distance distribution, is found to decay with the chain length (L) as ～L(-1.4), which is close to predictions of the free flight chain model. The match indicates that the end-group interaction does not strongly perturb the end-to-end distribution, which is close to the ideal random coil distribution with the Gaussian probability density.     

Experimental and theoretical study of the rovibrational relaxation of CH4 and CD4 by Ar

Experimental results are reported for the vibrational relaxation of the lowest bending modes of CH₄ and CD₄ br Ar in the temperature range of 140–376 K. Theoretical calculations are carried out in the framework of the semiclassical coupled-states approximation using asymptotic expressions of (3j) symbols and a first-order perturbation treatment. The confrontation of experimental and theoretical rate constants confirms the crucial role of rotational energy transfer upon the vibrational relaxation transfer.     

Vibrational relaxation in the group IVA trimethylmetal chlorides

The temperature dependence of the polarized and depolarized Raman spectra of the ν₂, ν₄, ν₆ and ν₇ modes were measured for t-butyl chloride and the analogous group IVA trimethylmetal chrlorides (silicon, germanium and tin). Analysis of the lineshapes revealed that isotropic second moments and vibrational relaxation times for a given mode remained approximately constant through the series. This tranferability of relaxation parameters between molecules extended to modulation times calculated from the Kubo formalism. The above results are in contrast to earlier studies on molecules of dissimilar structure. They provide some preliminary evidence that the mechanism of vibrational relaxation may be the same for equivalent modes in members of the series.     

Electronic and Vibrational Coherence Dynamics in a Cyanine Dye Studied Using a Few‐Cycle Pulsed Laser

We report the relaxation times of electronic and vibrational coherence in the cyanine dye 1,1′,3,3,3′,3′‐hexamethyl‐4,4′,5,5′‐dibenzo‐2,2′‐indotricarbocyanine, measured using a 7.1 fs pulsed laser. The vibrational phase relaxation times are found to be between 380 and 680 fs in the ground and lowest excited singlet states. The vibrational dephasing times of the 294, 446, and 736 cm^?1 modes are relatively long among the six modes associated with excited‐state wave packets. The slower relaxations are explained in terms of a coupled triplet of vibrational modes, which preserves coherence by forming a tightly bound group to satisfy the condition of circa conservation of vibrational energy. Using data from the negative‐time range (i.e., when the probe pulse precedes the pump pulse), the electronic phase relaxation time is found to be 31±1 fs. The dynamic vibrational mode in the excited state (1171 cm^?1), detected in the positive‐time range, is also studied from the negative‐time traces under the same experimental conditions.     

Vibrational relaxation of ethylene oxide and ethylene oxide-rare-gas mixtures

The collision-induced vibrational energy relaxation of ethylene oxide (C₂H₄O) was studied by means of laser-induced fluorescence. The time-dependent population of the vibrational modes v₃ and v₅/v₁₂ was measured after excitation of CH-stretching vibrations near 3000 cm^?1. Rate constants for the vibrational energy transfer by collisions with C₂H₄O and the rare gases are deduced, and a simplified model for the vibrational relaxation of C₂H₄O is discussed.     

Author index to volume 53

The triplet-state EPR spectra of photosynthetic bacteria reported in the literature exhibit a unique spin polarization pattern, previously attributed to intermolecular processes such as electron transfer. We show here that another, purely intramolecular, model can also account for the observed spin polarization. New experimental results, obtained for a porphyrin triplet state, are used to illustrate the proposed interpretation.     

Vibrational kinetics in HeCO reacting discharges

Combined measurements of vibrational distributions (N_υ) of CO and CO₂ yields (β) in HeCO discharges have been performed at different residence times in radiofrequency discharges. The experimental results on N_υ have been obtained by IR emission spectroscopy and on β by gas-chromatographic and mass-spectrometric techniques. A theoretical model including the most important relaxation channels of the vibrational energy has been set up and coupled to the plasma chemistry describing the rate of formation of species such as CO₂, C, and O. Theoretical and experimental results are in good agreement, emphasizing the role of a vibrational mechanism in dissociating CO in HeCO mixtures.     

High-Energy X-ray Diffraction and MD Simulation Study on the Ion-Ion Interactions in 1-Ethyl-3-methylimidazolium Bis(fluorosulfonyl)amide

Ion-ion interactions or liquid structures in low-viscosity ionic liquid, 1-ethyl-3-methylimidazolium bis(fluorosulfonyl)amide, [C₂mIm⁺][FSA^?] were investigated by high-energy X-ray diffraction (HEXRD) experiments and molecular dynamics (MD) simulations. Experimental X-ray structure factor, S ^exp(q) obtained from the HEXRD was successfully deconvoluted into the intra- and the intermolecular components, S _intra ^exp (q) and S _inter ^exp (q), respectively, by taking into account the population of cis and trans conformers of the FSA anion to give the corresponding radial distribution functions, G _intra ^exp (r) and G _inter ^exp (r), respectively. The G _inter ^exp (r) exhibits the peaks at 3.5, 4.6 and 5.4 Å, which is well represented by theoretical radial distribution function, G _inter ^MD (r) obtained from MD simulations. From the space distribution function, SDF calculated by MD simulations, it was found that static structure (distance and orientation) of the nearest neighbor intermolecular interaction between cation and anion in [C₂mIm⁺][FSA^?] is similar to its analogous ionic liquid, [C₂mIm⁺][TFSA^?] where TFSA is bis(trifluoromethanesulfonyl)amide.     

Intramolecular vibrational energy redistribution in bridged azulene-anthracene compounds: ballistic energy transport through molecular chains

Intramolecular vibrational energy flow in excited bridged azulene-anthracene compounds is investigated by time-resolved pump-probe laser spectroscopy. The bridges consist of molecular chains and are of the type (CH(2))(m) with m up to 6 as well as (CH(2)OCH(2))(n) (n=1,2) and CH(2)SCH(2). After light absorption into the azulene S(1) band and subsequent fast internal conversion, excited molecules are formed where the vibrational energy is localized at the azulene side. The vibrational energy transfer through the molecular bridge to the anthracene side and, finally, to the surrounding medium is followed by probing the red edge of the azulene S(3) absorption band at 300 nm and/or the anthracene S(1) absorption band at 400 nm. In order to separate the time scales for intramolecular and intermolecular energy transfer, most of the experiments were performed in supercritical xenon where vibrational energy transfer to the bath is comparably slow. The intramolecular equilibration proceeds in two steps. About 15%-20% of the excitation energy leaves the azulene side within a short period of 300 fs. This component accompanies the intramolecular vibrational energy redistribution (IVR) within the azulene chromophore and it is caused by dephasing of normal modes contributing to the initial local excitation of the azulene side and extending over large parts of the molecule. Later, IVR in the whole molecule takes place transferring vibrational energy from the azulene through the bridge to the anthracene side and thereby leading to microcanonical equilibrium. The corresponding time constants tau(IVR) for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, tau(IVR) is constant at around 4-5 ps. Comparison with molecular dynamics simulations suggests that the coupling of these chains to the two chromophores limits the rate of intramolecular vibrational energy transfer. Inside the bridges the energy transport is essentially ballistic and, therefore, tau(IVR) is independent on the length.     

Vibrational energy relaxation in liquid N2CO mixtures

The vibrational energy relaxation rates of the liquid nitrogenCO system have been measured by optically pumping the collision-induced fundamental vibrational absorption band of liquid N₂ with the output of an HBr TEA laser. A radiatively dominated value of 56 ± 10 s is found for the intrinsic nitrogen relaxation time. The CO contribution to the decay rate is explained on the basis of a simple kinetic model and found also to be radiatively dominated at low CO concentrations. The importance of radiative trapping and energy transport in evaluating the lifetimes is demonstrated.     

On the excess-energy dependence of radiationless decay rate constants

The results of calculations of the dependence of the radiationless rate constant on the excess of excitation energy within the two-electronic states model under the weak coupling and statistical limits are presented. It is assumed that the exact molecular states for a given electronic configuration are global in character containing equal contributions from all degenerated vibrational levels at a given excitation energy due to intramolecular vibrational relaxation (IVR). The results of calculations indicate an important role of the low-frequency vibrational modes, the potential energy surfaces of which cross between the two electronic states involved into the radiationless process. The sharp increase of the rate constant is predicted for the excitation energy below the diabatic crossing point, followed by saturation at higher energies. The calculated rate constants for the T₁→S₀ intersystem crossing in pyrazine and benzene are in good agreement with experimental observations. Some comments concerning the “channel-three” phenomenon in benzene are presented.     

Mode-specific pressure effects on the relaxation of an excited nitromethane molecule in an argon bath

The vibrational and rotational mode-specific relaxations of CH₃NO₂ with 50 kcal/mol of initial internal energy in an argon bath is computed at 300 K at pressures of 10-400 atm. This work uses archived information from our previously published [J. Chem. Phys. 142, 014303 (2015)] molecular dynamics simulations and employs our previous published [J. Chem. Phys. 151, 034303 (2019)] method for projecting time-dependent Cartesian velocities onto normal mode eigenvectors. The computed relaxations cover three types of energies: vibrational, rotational, and Coriolis. In general, rotational and Coriolis relaxations in all modes are initially fast followed by an orders of magnitude slower relaxation. For all modes, that slower relaxation rate is approximately comparable to the vibrational relaxation rate. For all three types of energies, there are small-scale mode-to-mode variations. Of particular prominence is the exceptionally fast relaxation shared in common by the external rotation about the C N axis, the internal hindered rotation of the CH₃ group relative to the NO₂ group, and the symmetric stretch of the CH₃ group.     

Infrared spectroscopy and intramolecular vibrational relaxation of c-C6F12 excited above the dissociation threshold

The IR spectrum of c-C₆F₁₂ at a vibrational energy of twice the dissociation threshold was investigated. Absorption of cw CO₂ laser radiation was measured at various frequencies. Our experimental conditions were chosen such that during absorption measurements all vibrational degrees of freedom were in equilibrium, the molecular rotation being at room temperature. The Boltzmann vibrational distribution allowed computer simulations of the spectrum to be made to determine the homogeneous contribution. The homogeneous half-width of the spectrum is γ=13±0.5 cm⁻¹ and the homogeneous spectrum of c-C₆F₁₂ at E= 60000 cm⁻¹ is non-Lorentzian. We attribute this to the influence of higher-order anharmonicities on the relaxation from the excited mode (v₂₇) to other modes in the molecule.     

Intermode vibrational crossing in CH3Br*

Subsequent to Q-switch CO₂-laser pumping of the v₆ band of CH₃Br, rate constants for activation and deactivation of other modes have been measured. v₁, v₄ and v₂, v₅ are populated in about 60 gas kinetic collissions, and v₃ in about 170 collissions. All modes decay at the same rate, corresponding to about 335 collissions. Measurements have also been made on deactivation of the various modes by rare gases. The results are discussed in terms of possible mechanisms and in comparison to those on CH₃F and CH₃Cl. Considerations based on available theories of vibrational relaxation seem to give considerable, though quantitatively imperfect, insight into energy transfer in these species.     

Diamondoids approach to electronic,structural, and vibrational properties of GeSi superlattice nanocrystals: a first-principles study

Germanium silicide diamondoids are used to determine electronic, structural, and vibrational properties of GeSi superlattice nanocrystals and bulk as their building block limit. Density functional theory at the generalized gradient approximation level of Perdew, Burke, and Ernzerhof (PBE) with 6-31G(d) basis including polarization functions is used to investigate the electronic structure of these diamondoids. The investigated molecules and diamondoids range from GeSiH₆ to Ge₆₃Si₆₃H₉₂. The variation of the energy gap is shown from nearly 7 eV toward bulk value which is slightly higher than the average of Si and Ge energy gaps. Variations of bond lengths, tetrahedral, and dihedral angles as the number of atoms increases are shown taking into account the effect of shape fluctuations. Localized and delocalized electronic charge distribution and bonds for these molecules are discussed. Vibrational radial breathing mode (RBM) converges from its initial molecular value at 332 cm^?1 to its bulk limit at 0 cm^?1 (blue shift). Longitudinal optical-highest reduced mass mode (HRMM) converges from its initial molecular value 332 cm^?1 to experimental bulk limit at 420.7 cm^?1 (red shift). Hydrogen vibrational modes are nearly constant in their frequencies as the size of diamondoids increases in contrast with lower frequency Ge–Si vibrational modes. GeSi diamondoids can be identified from surface hydrogen vibrational modes fingerprint, while the size of these diamondoids can be identified from Ge–Si vibrational modes.