Heat rectification in molecular junctions

Heat conduction through molecular chains connecting two reservoirs at different temperatures can be asymmetric for forward and reversed temperature biases. Based on analytically solvable models and on numerical simulations we show that molecules rectify heat when two conditions are satisfied simultaneously: the interactions governing the heat conduction are nonlinear, and the junction has some structural asymmetry. We consider several simplified models where a two-level system (TLS) simulates a highly anharmonic vibrational mode, and asymmetry is introduced either through different coupling of the molecule to the contacts, or by considering internal molecular asymmetry. In the first case, we present analytical results for the asymmetric heat current flowing through a single anharmonic mode using different forms for the TLS-reservoirs coupling. We also demonstrate numerically, studying a realistic molecular model, that a uniform anharmonic molecular chain connecting asymmetrically two thermal reservoirs rectifies heat. This effect is stronger for longer chains, where nonlinear interactions dominate the transfer process. When asymmetry is related to the internal level structure of the molecule, numerical simulations reveal a nontrivial rectification behavior. We could still explain this behavior in terms of an effective system-bath coupling. Our study suggests that heat rectification is a fundamental characteristic of asymmetric nonlinear thermal conductors. This phenomenon is important for heat control in nanodevices and for understanding of energy flow in biomolecules.     

Exploring the effect of anharmonicity of molecular vibrations on thermodynamic properties

Thermodynamic properties of selected small and medium size molecules were calculated using harmonic and anharmonic vibrational frequencies. Harmonic vibrational frequencies were obtained by normal mode analysis, whereas anharmonic ones were calculated using the vibrational self-consistent field (VSCF) method. The calculated and available experimental thermodynamic data for zero point energy, enthalpy, entropy, and heat capacity are compared. It is found that the anharmonicity and coupling of molecular vibrations can play a significant role in predicting accurate thermodynamic quantities. Limitations of the current VSCF method for low frequency modes have been partially removed by following normal mode displacements in internal, rather than Cartesian, coordinates.     

Incoherent quasielastic neutron scattering study on the polymorphism of tristearin: dynamical properties of hydrocarbon chains

Dynamical properties of acyl chains in the three polymorphic phases alpha, beta', and beta of tristearin [C(3)H(5)(OCOC(17)H(35))3] have been studied by means of incoherent quasielastic neutron scattering (IQNS) using selectively deuterated samples. The mean square displacement of hydrogen atoms, , was estimated from the scattering vector Q dependence of the elastic scattering component under the harmonic approximation. It was shown that the temperature dependence of was significantly different between the three phases. There was no marked difference in between these phases up to 193 K, and the value increased linearly with temperature. Although the beta phase remained linear up to 293 K, the alpha and beta' phases started to show a nonlinear increase around 200 K, suggesting an anharmonic nature of molecular motions. The alpha phase exhibited the most conspicuous temperature dependence. These characteristics were ascribable to the difference in the lateral packing of acyl chains. Compared with the beta phase which has a tightly packed T// subcell, the beta' and alpha phases have looser O perpendicular and H subcells, respectively. The molecular motion in the alpha phase was analyzed using the model of uniaxial rotational diffusion in a onefold cosine potential. It has been clarified that the rotational fluctuation about the chain axis in the alpha phase is rather restricted compared with that in the rotator phase of n-alkanes.     

On the possible manifestation of harmonic-anharmonic dynamical transition in glassy media in electron paramagnetic resonance of nitroxide spin probes

Continuous wave (cw) electron paramagnetic resonance (EPR) and echo-detected (ED) EPR were applied to study molecular motions of nitroxide spin probes in glassy glycerol and o-terphenyl. A linear decrease with increasing temperature of the total splitting in the cw EPR line shape was observed at low temperatures in both solvents. Above some temperature points the temperature dependencies become sharper. Within the model of molecular librations, this behavior is in qualitative and quantitative agreement with the numerical data on neutron scattering and Mossbauer absorption for molecular glasses and biomolecules, where temperature dependence of the mean-squared amplitude of the vibrational motion was obtained. In analogy with these data the departure from linear temperature dependence in cw EPR may be ascribed to the transition from harmonic to anharmonic motion (this transition is called dynamical transition). ED EPR spectra were found to change drastically above 195 K in glycerol and above 245 K in o-terphenyl, indicating the appearance of anisotropic transverse spin relaxation. This appearance may also be attributed to the dynamical transition as an estimation shows the anisotropic relaxation rates for harmonic and anharmonic librational motions and because these temperature points correspond well to those known from neutron scattering for these solvents. The low sensitivity of ED EPR to harmonic motion and its high sensitivity to the anharmonic one suggests that ED EPR may serve as a sensitive tool to detect dynamical transition in glasses and biomolecules.     

Calculation of the anharmonic effect on the main reactions referring to ethylbenzene combustion mechanism

About 11 reactions related to ethylbenzene are studied in this paper using transition state theory. The YL method proposed by Yao and Lin is utilized to calculate the anharmonic and the harmonic rate constants in these reaction processes in the temperature range of 300–4,000 K, energy diagram and the temperature dependence of the rate coefficients are also presented. The calculations indicate that the harmonic rate constants are larger than the anharmonic rate constants in most cases. Especially, there is a temperature junction between the high and low relationship between the anharmonic and harmonic rate constants in several reactions. Furthermore, the calculated values are in good agreement with other theoretical ones within the allowable error. Finally, the kinetic parameters and the thermodynamic parameters are calculated. To sum up, it can be concluded that the anharmonic effect in these reactions is very significant and cannot be ignored.     

A density functional theory based estimation of the anharmonic contributions to the free energy of a polypeptide helix

We have employed density functional theory to determine the temperature dependence of the intrinsic stability of an infinite poly-L-alanine helix. The most relevant helix types, i.e., the α- and the 3(10)-helix, and several unfolded conformations, which serve as reference for the stability analysis, have been included. For the calculation of the free energies for the various chain conformations we have explicitly included both, harmonic and anharmonic contributions. The latter have been calculated by means of a thermodynamic integration approach employing stochastic Langevin molecular dynamics, which is shown to provide a dramatic increase in the computational efficiency as compared to commonly employed deterministic molecular dynamics schemes. Employing this approach we demonstrate that the anharmonic part of the free energy amounts to the order of 0.1-0.4 kcal/mol per peptide unit for all analysed conformations. Although small, the anharmonic contribution stabilizes the helical conformations with respect to the fully extended structure.     

Effects of anharmonicity on nonadiabatic electron transfer: a model

The effect of anharmonicity in the intramolecular modes of a model system for exothermic intramolecular nonadiabatic electron transfer is probed by examining the dependence of the transition probability on the exoergicity. The Franck-Condon factor for the Morse potential is written in terms of the Gauss hypergeometric function both for a ground initial state and for the general case, and comparisons are made between the first-order perturbation theory results for transition probability for harmonic and Morse oscillators. These results are verified with quantum dynamical simulations using wave-packet propagations on a numerical grid. The transition-probability expression incorporating a high-frequency quantum mode and low-frequency medium mode is compared for Morse and harmonic oscillators in different temperature ranges and with various coarse-graining treatments of the delta function from the Fermi golden rule expression. We find that significant deviations from the harmonic approximation are expected for even moderately anharmonic quantum modes at large values of exoergicity. The addition of a second quantum mode of opposite displacement negates the anharmonic effect at small energy change, but in the inverted regime a significantly flatter dependence on exoergicity is predicted for anharmonic modes.     

Analysis of local anharmonicity using Gaussian model potentials and cartesian oscillator basis sets: example, HCN

This paper examines local anharmonic vibrations in molecules using an analysis that starts with an ab initio potential energy surface, fits a model potential constructed of Gaussian basis functions, and proceeds to a quantum mechanical analysis of the anharmonic modes using Cartesian harmonic oscillator basis functions in a variational calculation. The objective of this work is to suggest methods, with origins in nuclear and molecular (electronic) quantum mechanics, that should be useful for the accurate analysis of the local anharmonic motions of hydrogen, and perhaps other atoms or small molecular fragments, residing in molecularly complicated but otherwise harmonic environments.     

Thermal Conductivities of Molecular Materials

Heat conduction is one of the most fundamental properties of a material. Knowledge of its magnitude and temperature dependence can be important in determining use limitations of a material. Experimental studies of heat conduction in molecular systems are summarized, with emphasis on N₂ and CBr₄, and placed in the context of our understanding of heat conduction mechanisms in solids.This revised version was published online in November 2005 with corrections to the Cover Date.     

A universal criterion of melting

Melting is analyzed dynamically as a problem of localization at a liquid-solid interface. A Lindemann-like criterion of melting is derived in terms of particular vibrational amplitudes, which turn out to equal a universal quotient (about one-tenth) of the molecular spacing, at the interface. The near universality of the Lindemann ratio apparently arises owing to strongly overdamped dynamics near melting, and despite the anharmonic interactions being system-specific. A similar criterion is derived for structural displacements in the bulk of the solid, in particular the premelted layer; the criterion is no longer strictly universal, but still depends only on the harmonic properties of the solid. We further compute the dependence of the magnitude of the elemental molecular translations, in deeply supercooled fluids, on the temperature and the high frequency elastic constants. We show explicitly that the surface tension between distinct liquid states, near the glass transition of a supercooled liquid, is nearly evenly split between entropic and energetic contributions.     

Modifying thermal transport in electrically conducting polymers: effects of stretching and combining polymer chains

If their thermal conductivity can be lowered, polyacetylene (PA) and polyaniline (PANI) offer examples of electrically conducting polymers that can have potential use as thermoelectrics. Thermal transport in such polymers is primarily influenced by bonded interactions and chain orientations relative to the direction of heat transfer. We employ molecular dynamics simulations to investigate two mechanisms to control the phonon thermal transport in PANI and PA, namely, (1) mechanical strain and (2) polymer combinations. The molecular configurations of PA and PANI have a significant influence on their thermal transport characteristics. The axial thermal conductivity increases when a polymer is axially stretched but decreases under transverse tension. Since the strain dependence of the thermal conductivity is related to the phonon scattering among neighboring polymer chains, this behavior is examined through Herman's orientation factor that quantifies the degree of chain alignment in a given direction. The conductivity is enhanced as adjacent chains become more aligned along the direction of heat conduction but diminishes when they are orthogonally oriented to it. Physically combining these polymers reduces the thermal conductivity, which reaches a minimum value for a 2:3 PANI/PA chain ratio.     

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions

The difference spectroscopy of the Raman optical activity (ROA) provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis on the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction (VCI), and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength (200-1800 cm(-1)) vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors (second dipole and polarizability derivatives) were found less important for the entire spectral profiles than the force field anharmonicities (third and fourth energy derivatives), except for a few weak combination bands which were dominated by the anharmonic tensor contributions.     

聚2,6—萘二甲酸乙二醇酯的光物理,光化学及电导

PEN-2,6的一些特殊性质(如刚性、耐热性和荧光性等)皆可归因于其芳香性和分子链的刚性。自1967年以来,人们采用多种方法、手段来研究这种功能材料,观察到了一些现象并作了相应的解释。本文所列举的关于PEN-2,6的工作主要集中在光物理、光化学和电导性能等方面。     

Four-component relativistic Kohn-Sham theory

A four-component relativistic implementation of Kohn-Sham theory for molecular systems is presented. The implementation is based on a nonredundant exponential parametrization of the Kohn-Sham energy, well suited to studies of molecular static and dynamic properties as well as of total electronic energies. Calculations are presented of the bond lengths and the harmonic and anharmonic vibrational frequencies of Au(2), Hg(2+)(2), HgAu(+), HgPt, and AuH. All calculations are based on the full four-component Dirac-Coulomb Hamiltonian, employing nonrelativistic local, gradient-corrected, and hybrid density functionals. The relevance of the Coulomb and Breit operators for the construction of relativistic functionals is discussed; it is argued that, at the relativistic level of density-functional theory and in the absence of a vector potential, the neglect of current functionals follows from the neglect of the Breit operator.     

Accurate theoretical IR and Raman spectrum of Al2O2 and Al2O3 molecules

The accurate harmonic vibration frequencies together with the infrared (IR) and Raman intensities of the most stable conformers of Al₂O₂ and Al₂O₃ molecules have been calculated by the density functional theory (DFT) method with B3LYP exchange–correlation potential and using a set of the augmented correlated consistent basis sets up to quintuple order. The anharmonic vibration frequencies of the non-linear Al₂O₂ molecule have also been calculated. The obtained equilibrium geometrical parameters, harmonic and anharmonic vibration frequencies along with the IR and Raman intensities good converge to their limits with increasing the size of the used basis set. A comparison of the calculated harmonic and anharmonic vibrational frequencies with the available experimental ones points out that the small differences between the calculated harmonic and experimental frequencies can be further substantially reduced when calculations of the anharmonic vibrational frequencies will be available for all types of molecular geometries.     

The properties of a single polymer chain in solvent confined in a slit: A molecular dynamics simulation

A single polymer chain in solvent confined in a slit formed by two parallel plates is studied by using molecular dynamics simulation method. The square radii of gyration and diffusion behaviors of polymers are greatly affected by the distance between the two plates, but they do not follow the same way. The chain size decays drastically with increasing h (h is the distance between two plates), until a basin occurs, and a universal h/〈R _g〉₀ dependence for polymer chains with different degrees of polymerization can be obtained. While, for the chain’s diffusion coefficient, it decays monotonously and there is no such basin-like behavior. Furthermore, we studied the radial distribution function of confined polymer chains to explain the reason why there is a difference for the decay behaviors between dynamic properties and static properties. Besides, we also give the degree of confinement dependence of the static scaling exponent for a single polymer chain. Our work provides an efficient way to estimate the dynamics and static properties of confined polymer chains, and also helps us to understand the behavior of polymer chains under confinement.     

Harmonic and anharmonic contributions to parity-violating vibrational frequency difference between enantiomers of chiral molecules

A general perturbative procedure for the computation of harmonic and anharmonic contributions to parity-violating vibrational shifts is introduced and applied to PHBrF and AsHBrF. The results point out the importance of both diagonal and off-diagonal anharmonic contributions and indicate that some parity-violating shift of AsHBrF approaches the resolution forecasted for next generation experiments. The proposed approach is sufficiently general and computationally effective to allow studies of similar and larger molecular systems.     

Molecular structure and vibrational spectra of 4-, 5-, 6-chloroindole

The molecular geometry, IR intensities, harmonic and anharmonic vibrational frequencies of 4-, 5-, 6-chloroindole in the ground state were calculated by DFT/B3LYP level of theory using the 6-31G (d, p) basis set. To give complete and reasonable vibrational assignments, the normal coordinate analysis has been performed for 4-chloroindole, 5-chloroindole and 6-chloroindole. The effect of position of chloro atom on the molecular properties (electron density, dipole moments and energies) of the indole aromatic system is examined on the basis of calculation data for 4-, 5- and 6-chloroindoles.     

The thermodynamic stability of clathrate hydrate. Encaging non-spherical propane molecules

The thermodynamic stability of a clathrate hydrate encaging non-spherical molecules has been investigated by examining the free energy of cage occupancy. In the present study, a generalized van der Waals and Platteeuw theory is extended to treat the rotational motion of guest molecules in clathrate hydrate cages. The vibrational free energy of both guest and host molecules is divided into harmonic and anharmonic contributions. The anharmonic free energy associated with the non-spherical nature of the guest molecules is evaluated as a perturbation from the spherical guest. Predicted thermodynamic properties are compared with measured values. It is shown that this anharmonic contribution is important in the free energy of the hindered rotation of the guests.     

Quaternion formulation of lattice dynamics of molecular crystals

The use of quaternions to specify rigid-molecule orientation is reviewed. Application of this formalism to lattice dynamics of molecular crystals is developed. Basic formulae for harmonic and anharmonic approximations are summarised.