Structural transitions in the 309-atom magic number Lennard-Jones cluster

The thermal behavior of the 309-atom Lennard-Jones cluster, whose structure is a complete Mackay icosahedron, has been studied by parallel tempering Monte Carlo simulations. Surprisingly for a magic number cluster, the heat capacity shows a very pronounced peak before melting, which is attributed to several coincident structural transformation processes. The main transformation is somewhat akin to surface roughening and involves a cooperative condensation of vacancies and adatoms that leads to the formation of pits and islands one or two layers thick on the Mackay icosahedron. The second transition in order of importance involves a whole scale transformation of the cluster structure and leads to a diverse set of twinned structures that are assemblies of face-centered-cubic tetrahedra with six atoms along their edges, i.e., one atom more than the edges of the 20 tetrahedra that make up the 309-atom Mackay icosahedron. A surface reconstruction of the icosahedron from a Mackay to an anti-Mackay overlayer is also observed, but with a lower probability.     

Computer simulation studies of the influence of side alkyl chain on glass transition behavior of carbazole trimer

In this work,all-atom molecular dynamics simulations were employed to study the influence of the side alkyl chain on glass transition behavior of several carbazole trimers(CT) in a temperature range from 423 to 183 K.The glass transition temperatures were obtained from the break in the slope of the volume-temperature curves and found to agree with the experimental values.The short time dynamics of four CT molecules were probed by usingvelocity autocorrelation functions and mean-square displacements.The current studies showed that the dynamics of CT systems can be easily interpreted through the cage effect.Furthermore,the investigation of the torsional autocorrelation function and P_(2-state)/P_(3-state) functions showed that the rotational barriers of side chains can slow down the conformational relaxation and lead to stronger temperature dependence of conformational relaxation.The relaxation time,characteristic time of P_(2-state)(t) and P_(3-state)(t) functions were all found to have Arrhenius-type temperature dependence.     

Communication: a minimal model for the diffusion-relaxation backbone dynamics of proteins

We present a model for the local diffusion-relaxation dynamics of the C(α)-atoms in proteins describing both the diffusive short-time dynamics and the asymptotic long-time relaxation of the position autocorrelation functions. The relaxation rate spectra of the latter are represented by shifted gamma distributions, where the standard gamma distribution describes anomalous slow relaxation in macromolecular systems of infinite size and the shift accounts for a smallest local relaxation rate in macromolecules of finite size. The resulting autocorrelation functions are analytic for any time t ≥ 0. Using results from a molecular dynamics simulation of lysozyme, we demonstrate that the model fits the position autocorrelation functions of the C(α)-atoms exceptionally well and reveals moreover a strong correlation between the residue's solvent-accessible surface and the fitted model parameters.     

Relaxation processes of the structural rearrangement of clusters in liquids: 1,2-ethanediol, 1,2-propanediol, and 1,2,6-hexanetriol

The dielectric relaxation spectra (DRS) of 1,2-ethanediol, 1,2-propanediol, and 1,2,6-gexanetriol are analyzed in terms of the Dissado-Hill (DH) model in a wide range of temperatures, with all parameters required for calculating the cluster dipole moments being determined within the DH molecular model itself. The dependence of the equilibrium and relaxation properties of DRS on the hydrocarbon radical length and the number of OH groups is studied. The dipole moments of the clusters are calculated. It is shown how the roles of the processes of intracluster rearrangement are redistributed due to the break of hydrogen bonds and fluctuation processes of synchronous exchange of molecules between the clusters.     

Analysis of uncertainties in polymer viscoelastic properties obtained from equilibrium computer simulations

We critically evaluate the uncertainties in the stress autocorrelation function obtained from equilibrium molecular dynamics simulation of model polymer melts. This quantity is central to evaluating transport properties, e.g., the complex modulus and the viscosity. In contrast to the intuitive expectation that simulations have to be run five to six orders of magnitude longer than the chain relaxation time to reduce uncertainties to acceptable levels, our analysis shows that the majority of the uncertainty is associated with rapidly oscillating bonded interactions. These fluctuations occur on time scales which are approximately 10(4) times shorter than the relaxation time of a chain of length 80. Consequently, the effects of these oscillations on the stress autocorrelation function can be dramatically reduced by (i) conducting long simulations (typically 10(6) times longer than the bond relaxation times or only 10(2) chain relaxation times) and (ii) by performing running averages with time windows whose time scales are much longer than these oscillations. Conducting such long simulations also allows for the accurate determination of the melt viscosity and the low-frequency complex modulus, but performing running averages do not impact these quantities since they are time integrals of the stress autocorrelation function.     

Dynamic light scattering in liquid and supercooled diphenylmethane

We use a dynamic light scattering technique to measure both polarized (VV) and depolarized (VH) spectra of liquid diphenylmethane (DPM) between 288 and 362 K, covering both normal and supercooled liquid ranges. Our results allow extracting information on structural relaxation processes, rotational motions, rotation-translation couplings, and molecular reorientation phenomena in liquid DPM. The VV spectra are modeled according to the microscopic theory of Wang, which assumes that a structural relaxation process dominates the spectrum. We find that the relaxation time of the structural relaxation in DPM follows an Arrhenius behavior. The Rayleigh dip was observed in the VH spectra, which are described using the Andersen-Pecora theory. Our results are discussed in terms of the rotation-translation coupling parameter, which we find independent of temperature over the experimental range. The collective reorientation time also follows an Arrhenius behavior with temperature. Finally, we calculate the hydrodynamic volumes for the reorientation process from geometric molecular models in two hydrodynamic limits: slip and stick boundary conditions. Our results suggest that the DMP molecule reorientates in quasi-slipping conditions in the bulk liquid.     

Secondary and primary relaxations in hyperbranched polyglycerol: a comparative study in the frequency and time domains

The non-Debye relaxation behavior of hyperbranched polyglycerol was investigated by broadband dielectric spectroscopy. A thorough study of the relaxations was carried out paying special attention to truncation effects on deconvolutions of overlapping processes. Hyperbranched polyglycerol exhibits two relaxations in the glassy state named in increasing order of frequency beta and gamma processes. The study of the evolution of these two fast processes with temperature in the time retardation spectra shows that the beta absorption is swallowed by the alpha in the glass-liquid transition, the gamma absorption being the only relaxation that remains operative in the liquid state. In heating, a temperature is reached at which the alpha absorption vanishes appearing the alphagamma relaxation. Two characteristics of alpha absorptions, decrease of the dielectric strength with increasing temperature and rather high activation energy, are displayed by the alphagamma process. Williams' ansatz seems to hold for these topologically complex macromolecules.     

单分子层受限冰-水共存界线毛细波与固-液相变动力学

冰-水界面动力学性质在冰形核、生长、表界面熔化中扮演核心角色,长期以来一直被广泛关注.然而,受限水体系中冰-水界面的动力学性质却鲜有报道.本工作利用平衡态分子动力学模拟方法和受限固-液两相平衡模拟技术,对两种水模型(恒定偶极矩、可极化)描述的单分子层受限冰-水两相平衡体系中的一维固-液界线开展研究.通过对一维受限冰-水...     

Theoretical study of the adsorption and dissociation of oxygen on Pt(111) in the presence of homogeneous electric fields

The effect of homogeneous electric fields on the adsorption energies of atomic and molecular oxygen and the dissociation activation energy of molecular oxygen on Pt(111) were studied by density functional theory (DFT). Positive electric fields, corresponding to positively charged surfaces, reduce the adsorption energies of the oxygen species on Pt(111), whereas negative fields increase the adsorption energies. The magnitude of the energy change for a given field is primarily determined by the static surface dipole moment induced by adsorption. On 10-atom Pt(111) clusters, the adsorption energy of atomic oxygen decreased by ca. 0.25 eV in the presence of a 0.51 V/A (0.01 au) electric field. This energy change, however, is heavily dependent on the number of atoms in the Pt(111) cluster, as the static dipole moment decreases with cluster size. Similar calculations with periodic slab models revealed a change in energy smaller by roughly an order of magnitude relative to the 10-atom cluster results. Calculations with adsorbed molecular oxygen and its transition state for dissociation showed similar behavior. Additionally, substrate relaxation in periodic slab models lowers the static dipole moment and, therefore, the effect of electric field on binding energy. The results presented in this paper indicate that the electrostatic effect of electric fields at fuel cell cathodes may be sufficiently large to influence the oxygen reduction reaction kinetics by increasing the activation energy for dissociation.     

IR study of cross-strand coupling in a beta-hairpin peptide using isotopic labels

Model beta-hairpin peptides can be used to develop understanding of fundamental elements of beta-sheet secondary structure formation and stability. We have studied two 13C-labeled variants of a beta-hairpin peptide modified from a design originally proposed by Gellman: Arg-Tyr-Val-Glu-Val-Aib-Gly-Lys-Lys-Ile-Leu-Gln. (In this peptide, the two italicized residues form a beta-turn, while 13C-labels are on the amide C=O of Val3, Lys8 in HBG-L and Val3, Ile10 in HBG-S.) Both these peptides are labeled on opposite strands of the hairpin, but differ in the labeling pattern. One (HBG-L) forms a large (14-atom) H-bonded ring of labeled C=Os, while the other (HBG-S) forms a small (10-atom) H-bonded ring. These impact the amide I infrared spectra, with HBG-L having a 13C frequency and intensity higher than that of HBG-S, in good agreement with our spectral simulations based on quantum mechanically derived force fields. The thermal behavior of both peptides yields a broad thermal transition and lacks an isosbestic point. The 13C band for HBG-L has the largest intensity change with temperature, distinct from the 12C change and the HBG-S 13C change.     

Icosahedral to double-icosahedral shape transition of copper clusters

The lowest-energy isomers of Cu(N) clusters for N = 20-30 are identified using an unbiased search algorithm and density functional theory calculations. The low-energy structures over this size range are dominated by those based on a 13-atom icosahedral (I(h)) core and a 19-atom double icosahedron (DI(h)) core. A transition in the ground-state isomers from I(h)-based to DI(h)-based structures is predicted overt N = 21-23. We discuss this transition in the broader context of the growth pattern for Cu(N) over N = 2-30 that features regions of gradual evolution in which atoms successively add to the cluster surface, separated by sudden changes to a different structural organization and more compact shape. These transitions result from a competition between interatomic bonding energy and surface energy. The implications of this growth pattern for the further evolution of copper from microstructure to bulk are discussed.     

Quadrupole central transition 17O NMR spectroscopy of biological macromolecules in aqueous solution

We demonstrate a general nuclear magnetic resonance (NMR) spectroscopic approach in obtaining high-resolution (17)O (spin-5/2) NMR spectra for biological macromolecules in aqueous solution. This approach, termed quadrupole central transition (QCT) NMR, is based on the multiexponential relaxation properties of half-integer quadrupolar nuclei in molecules undergoing slow isotropic tumbling motion. Under such a circumstance, Redfield's relaxation theory predicts that the central transition, m(I) = +1/2 ? -1/2, can exhibit relatively long transverse relaxation time constants, thus giving rise to relatively narrow spectral lines. Using three robust protein-ligand complexes of size ranging from 65 to 240 kDa, we have obtained (17)O QCT NMR spectra with unprecedented resolution, allowing the chemical environment around the targeted oxygen atoms to be directly probed for the first time. The new QCT approach increases the size limit of molecular systems previously attainable by solution (17)O NMR by nearly 3 orders of magnitude (1000-fold). We have also shown that, when both quadrupole and shielding anisotropy interactions are operative, (17)O QCT NMR spectra display an analogous transverse relaxation optimized spectroscopy type behavior in that the condition for optimal resolution depends on the applied magnetic field. We conclude that, with the currently available moderate and ultrahigh magnetic fields (14 T and higher), this (17)O QCT NMR approach is applicable to a wide variety of biological macromolecules. The new (17)O NMR parameters so obtained for biological molecules are complementary to those obtained from (1)H, (13)C, and (15)N NMR studies.     

Vibrational spectroscopy and relaxation of an anharmonic oscillator coupled to harmonic bath

The vibrational spectroscopy and relaxation of an anharmonic oscillator coupled to a harmonic bath are examined to assess the applicability of the time correlation function (TCF), the response function, and the semiclassical frequency modulation (SFM) model to the calculation of infrared (IR) spectra. These three approaches are often used in connection with the molecular dynamics simulations but have not been compared in detail. We also analyze the vibrational energy relaxation (VER), which determines the line shape and is itself a pivotal process in energy transport. The IR spectra and VER are calculated using the generalized Langevin equation (GLE), the Gaussian wavepacket (GWP) method, and the quantum master equation (QME). By calculating the vibrational frequency TCF, a detailed analysis of the frequency fluctuation and correlation time of the model is provided. The peak amplitude and width in the IR spectra calculated by the GLE with the harmonic quantum correction are shown to agree well with those by the QME though the vibrational frequency is generally overestimated. The GWP method improves the peak position by considering the zero-point energy and the anharmonicity although the red-shift slightly overshoots the QME reference. The GWP also yields an extra peak in the higher-frequency region than the fundamental transition arising from the difference frequency of the center and width oscillations of a wavepacket. The SFM approach underestimates the peak amplitude of the IR spectra but well reproduces the peak width. Further, the dependence of the VER rate on the strength of an excitation pulse is discussed.     

13-atom Ni-Al alloy clusters: Structures and dynamics

Structural and dynamical properties of model 13-atom Ni_nAl_m alloy clusters derived from a many-body potential are presented and discussed. Characterization of the structures corresponding to a given stoichiometric composition (i.e., chosen number of Ni and Al atoms) is carried out in terms of isomeric (geometric) forms and different distributions of the two types of atoms between the sites of a chosen isomer. We use the term homotops (“the same topography or geometry”) to label the structural forms that differ only by these distributions. The number and the energy spectra of the homotops are sensitive functions of the stoichiometric composition and isomeric form. Similarly to homogeneous clusters, alloy clusters undergo a solid-to-liquidlike transition as their energy is increased. Individual stages in the transition, such as isomerizations involving only surface atoms, isomerizations involving all atoms, surface melting (in a system as small as 13 atoms), and complete melting are identified and characterized. The actual occurrence of some or all of these stages in the meltinglike transition of a given cluster depends on the character of the energy spectra of its homotops, i.e., ultimately, on its stoichiometric composition. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 185–197, 1997     

Density matrix method and ultrafast processes

When femto-second (fs) time-resolved experiments are used to study ultrafast processes, quantum beat phenomena are often observed. In this paper, to analyze the fs time-resolved spectra, we will present the density matrix method, a powerful theoretical technique, which describes the dynamics of population and coherence of the system. How to employ it to study the pump-probe experiments and fs ultrafast processes is described. The ππ*→nπ* transition of pyrazine is used as an example to demonstrate the application of the density matrix method. Recently, Suzuki’s group have employed the 22 fs time resolution laser to study the dynamics of the ππ* state of pyrazine. In this case, conical intersection is commonly believed to play an important role in this non-adiabatic process. How to treat the effect of conical intersection on non-adiabatic processes and fs time-resolved spectra is presented. Another important ultrafast process, vibrational relaxation, which takes place in sub-ps and ps range and has never been carefully studied, is treated in this paper. The vibrational relaxation in water dimer is chosen to demonstrate the calculation. It should be noted that the vibrational relaxation of (H2O)2 has not been experimentally studied but it can be accomplished by the pump-probe experiments.     

Interpretation of the TSDC fractional polarization experiments on the α‐relaxation of polymers

We report on the interpretation of the thermally stimulated depolarization current (TSDC) experiments, with partial polarization methods, on the dielectric α‐relaxation. The results obtained on polyvinyl acetate are rationalized on the basis of the Boltzmann superposition principle in combination with a Kohlrausch–Williams–Watts (KWW) time decay of the polarization (with the β exponent essentially temperature independent and equal to the value determined by conventional dielectric methods at T_g). From this analysis of the global TSDC spectrum we found a complex temperature dependence of the KWW relaxation time, which is Arrhenius‐like at the lowest temperatures but crosses over to the Vogel–Fulcher behavior observed above T_g in the temperature range of the TSDC peak. On the basis of these results, we found the way of predicting the TSDC spectra measured after partial polarization procedures. We found that, the distribution of activation energies and compensation behavior deduced by following the standard way of analysis are associated to the assumption of an Arrhenius‐like temperature dependence of the α‐relaxation time in the temperature range explored by TSDC. Therefore we conclude that both the distribution of activation energies and compensation behavior obtained by following the standard way of analysis do not give a proper physical picture of the α‐relaxation of glassy polymers around the glass‐transition temperature. Our results also show that the partial polarization TSDC methods are not able to give insight about the actual existence or not of a distribution of relaxation times at the origin of the nonexponentiality of the α‐relaxation of polymers. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2105–2113, 2000     

Dynamic light scattering study of salt effect on phase behavior of pig vitreous body and its microscopic implication

The salt effects on phase equilibrium and dynamical properties of pig vitreous body was studied by the macroscopic observation of the swelling behavior and dynamic light scattering under various conditions. It was found that the vitreous body collapses with maintaining the shape when the concentrations of salts (NaCl, CaCl2, and MgCl2) were changed. From the observations of the dynamics of light scattered by the pig vitreous body, intensity autocorrelation functions that revealed two diffusion coefficients, Dfast and Dslow were obtained. We developed the theory for describing the density fluctuation of the entities in the vitreous gel system with sodium hyaluronate filled in the meshes of the collagen fiber network. The dynamics of collagen and sodium hyaluronate explains two relaxation modes of the fluctuation. The diffusion coefficient of collagen obtained from Dfast and Dslow is very close to that in aqueous solution, which suggests the vitreous body is in the swollen state. Divergent behavior in the measured total scattered light intensities and diffusion coefficients upon varying the concentration of salt was observed. Namely, a slowing down of the dynamic modes accompanied by increased "static" scattered intensities was observed. This is indicative of the occurrence of a phase transition upon salt concentration.     

Picosecond observation of fluorescence from B4 states of diphenylpolyenes

Picosecond time-resolved fluorescence (TRF) spectroscopy has been used to study transient behavior in 1,6-diphenylhexa-1,3,5-triene (DPH) and 1,8-diphenylocta-1,3,5,7-tetraene (DPO). The observation is reported of short-lived fluorescence lying to shorter wavelengths than the literature spectra for these molecules. From the vibrational structure and the solvent shift of the DPO transient spectrum in benzene with respect to hexane, the pulse-limited feature can be assigned to fluorescence from vibrationally unrelaxed levels of the B_u state. In the DPH case, the relaxation time of the transient feature is greater than the laser pulse autocorrelation width, indicating that the decay of B_u state fluorescence may be limited by vibrational relaxation in the lowest excited (A_g) state.     

Microscopic simulations of molecular cluster decay: Does the carrier gas affect evaporation?

We develop a kinetic theory of cluster decay by considering the stochastic motion of molecules within an effective potential of mean force (PMF) due to the cluster. We perform molecular dynamics simulations on a 50-atom argon cluster to determine the mean radial force on a component atom and hence the confining potential of mean force. Comparisons between isolated clusters and clusters thermostatted through the presence of a 100-atom helium carrier gas show that the heat bath has only a slight effect upon the PMF. This confirms the validity of calculations of cluster properties using isolated cluster simulations. The PMF is used to calculate the atomic evaporation rate from these clusters, and results are compared with the predictions of the capillarity approximation together with detailed balance, both components of the classical theory of aerosol nucleation.