Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the "inherent structure entropy." The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics.     

Improved transition path sampling methods for simulation of rare events

The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.     

A simple model of entropy relaxation for explaining effective activation energy behavior below the glass transition temperature

Strong changes in relaxation rates observed at the glass transition region are frequently explained in terms of a physical singularity of the molecular motions. We show that the unexpected trends and values for activation energy and preexponential factor of the relaxation time tau, obtained at the glass transition from the analysis of the thermally stimulated current signal, result from the use of the Arrhenius law for treating the experimental data obtained in nonstationary experimental conditions. We then demonstrate that a simple model of structural relaxation based on a time dependent configurational entropy and Adam-Gibbs relaxation time is sufficient to explain the experimental behavior, without invoking a kinetic singularity at the glass transition region. The pronounced variation of the effective activation energy appears as a dynamic signature of entropy relaxation that governs the change of relaxation time in nonstationary conditions. A connection is demonstrated between the peak of apparent activation energy measured in nonequilibrium dielectric techniques, with the overshoot of the dynamic specific heat that is obtained in calorimetry techniques.     

Freezing-in and production of entropy in vitrification

Following the classical concepts developed by Simon [Z. Anorg. Allg. Chem. 203, 219 (1931)], vitrification in the cooling of glass-forming melts is commonly interpreted as the transformation of a thermodynamically (meta)stable equilibrium system into a frozen-in, thermodynamically nonequilibrium system, the glass. Hereby it is assumed that the transformation takes place at some well-defined sharp temperature, the glass transition temperature Tg. However, a more detailed experimental and theoretical analysis shows that the transition to a glass proceeds in a broader temperature range, where the characteristic times of change of temperature, tauT=-(TT), and relaxation times, tau, of the system to the respective equilibrium states are of similar order of magnitude. In this transition interval, the interplay of relaxation and change of external control parameters determines the value of the structural order parameters. In addition, irreversible processes take place in the transition interval, resulting both in an entropy freezing-in as well as in an irreversible increase of entropy and, as a result, in significant changes of all other thermodynamic parameters of the vitrifying systems. The effect of entropy production on glass transition and on the properties of glasses is analyzed here for the first time. In this analysis, the structural order-parameter concept as developed by de Donder and van Rysselberghe [Thermodynamic Theory of Affinity (Stanford University Press, Stanford, 1936)] and Prigogine and Defay [Chemical Thermodynamics (Longmans, London, 1954)] is employed. In the framework of this approach we obtain general expressions for the thermodynamic properties of vitrifying systems such as heat capacity, enthalpy, entropy, and Gibbs' free energy, and for the entropy production. As one of the general conclusions we show that entropy production has a single maximum upon cooling and two maxima upon heating in the glass transition interval. The theoretical concepts developed allow us to explain in addition to the thermodynamic parameters also specific features of the kinetic parameters of glass-forming melts such as the viscosity. Experimental results are presented which confirm the theoretical conclusions. Further experiments are suggested, allowing one to test several additional predictions of the theory.     

Mid-IR spectra of different conformers of phenylalanine in the gas phase

The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between experiment and theory is generally found to be very good, however strong discrepancies exist when -NH2 out-of-plane vibrations are involved. The relative energies of the minima as well as of some transition states connecting the minima are explored at the CCSD(T) level. Most transition states are found to be less than 2000 cm(-1) above the lowest energy structure. A simple model to describe the observed conformer abundances based on quasi-equilibria near the barriers is presented and it appears to describe the experimental observation reasonably well. In addition, the vibrations of one of the conformers are investigated using the correlation-corrected vibrational self-consistent field method.     

On the molecular mobility in amorphous polymers, inorganic glasses, and amorphous metal alloys in the glass transition range

The transition of kinetic units (atoms or groups of atoms) in amorphous media from one quasi-equilibrium state to another is determined by fluctuations of both energy and entropy of the system. In the glass transition range of liquids and polymers, the entropic mechanism plays a determining role: the fluctuation of packing of particles turns out to be more important than accumulation of energy. Above the glass transition range, the energy mechanism begins to play a dominant role. The procedure that is currently used to calculate the constant for the Bartenev equation, which relates the relaxation time to the cooling rate at the glass transition temperature, leads to overestimated values. A procedure for the calculation of this parameter was proposed with allowance for the temperature dependence of the entropy of activation in the region of the liquid-glass transition. The use of this equation in the relaxation spectrometry of amorphous polymers, inorganic glasses, and amorphous metal alloys is discussed.     

Structural and pathway complexity of beta-strand reorganization within aggregates of human transthyretin(105-115) peptide

Interstrand conformational rearrangements of human transthyretin peptide (TTR(105-115)) within dimeric aggregates were simulated by means of molecular dynamics (MD) with implicit solvation model for a total length of 48 micros. The conformations sampled in the MD simulations were clustered to identify free energy minima without any projections of free energy surface. A connected graph was constructed with nodes (=clusters) and edges corresponding to free energy minima and transitions between nodes, respectively. This connected graph which reflects the complexity of the free energy surface was used to extract the transition disconnectivity graph, which reflects the overall free energy barriers between pairs of free energy minima but does not contain information on transition paths. The routes of transitions between important free energy minima were obtained by further processing the original graph and the MD data. We have found that both parallel and antiparallel aggregates are populated. The parallel aggregates with different alignment patterns are separated by nonnegligible free energy barriers. Multiroutes exist in the interstrand conformational reorganization. Most visited routes do not dominant the kinetics, while less visited routes contribute a little each but they are numerous and their total contributions are actually dominant. There are various kinds of reptation motions, including those through a beta-bulge, side-chain aided reptation, and flipping or rotation of a hairpin formed by one strand.     

Gaussian excitations model for glass-former dynamics and thermodynamics

We describe a model for the thermodynamics and dynamics of glass-forming liquids in terms of excitations from an ideal glass state to a Gaussian manifold of configurationally excited states. The quantitative fit of this three parameter model to the experimental data on excess entropy and heat capacity shows that "fragile" behavior, indicated by a sharply rising excess heat capacity as the glass transition is approached from above, occurs in anticipation of a first-order transition--usually hidden below the glass transition--to a "strong" liquid state of low excess entropy. The distinction between fragile and strong behavior of glass formers is traced back to an order of magnitude difference in the Gaussian width of their excitation energies. Simple relations connect the excess heat capacity to the Gaussian width parameter, and the liquid-liquid transition temperature, and strong, testable, predictions concerning the distinct properties of energy landscape for fragile liquids are made. The dynamic model relates relaxation to a hierarchical sequence of excitation events each involving the probability of accumulating sufficient kinetic energy on a separate excitable unit. Super-Arrhenius behavior of the relaxation rates, and the known correlation of kinetic with thermodynamic fragility, both follow from the way the rugged landscape induces fluctuations in the partitioning of energy between vibrational and configurational manifolds. A relation is derived in which the configurational heat capacity, rather than the configurational entropy of the Adam-Gibbs equation, controls the temperature dependence of the relaxation times, and this gives a comparable account of the experimental observations without postulating a divergent length scale. The familiar coincidence of zero mobility and Kauzmann temperatures is obtained as an approximate extrapolation of the theoretical equations. The comparison of the fits to excess thermodynamic properties of laboratory glass formers, and to configurational thermodynamics from simulations, reveals that the major portion of the excitation entropy responsible for fragile behavior resides in the low-frequency vibrational density of states. The thermodynamic transition predicted for fragile liquids emerges from beneath the glass transition in case of laboratory water and the unusual heat capacity behavior observed for this much studied liquid can be closely reproduced by the model.     

Dynamically correlated regions and configurational entropy in supercooled liquids

When a liquid is cooled below its melting temperature, if crystallization is avoided, it forms a glass. This phenomenon, called glass transition, is characterized by a marked increase of viscosity, about 14 orders of magnitude, in a narrow temperature interval. The microscopic mechanism behind the glass transition is still poorly understood. However, recently, great advances have been made in the identification of cooperative rearranging regions, or dynamical heterogeneities, i.e., domains of the liquid whose relaxation is highly correlated. The growth of the size of these domains is now believed to be the driving mechanism for the increase of the viscosity. Recently a tool to quantify the size of these domains has been proposed. We apply this tool to a wide class of materials to investigate the correlation between the size of the heterogeneities and their configurational entropy, i.e., the number of states accessible to a correlated domain. We find that the relaxation time of a given system, apart from a material dependent prefactor, is a universal function of the configurational entropy of a correlated domain. As a consequence, we find that, at the glass transition temperature, the size of the domains and the configurational entropy per unit volume are anticorrelated, as originally predicted by the Adam-Gibbs theory. Finally, we use our data to extract some exponents defined in the framework of the random first-order theory, a recent quantitative theory of the glass transition.     

Determining landscape-based criteria for freezing of liquids

The correlation between statistical properties of the energy landscape and the number of accessible configurational states, as measured by the exponential of the excess entropy (e(Se)), are studied in the case of a simple Lennard-Jones-type liquid in the neighborhood of the thermodynamic freezing transition. The excess entropy Se is defined as the difference between the entropy of the liquid and that of the ideal gas under identical temperature and pressure conditions and is estimated using the pair correlation contribution, S2. Landscape properties associated with three categories of configurations are considered: instantaneous configurations, inherent saddles, and inherent minima. Landscape properties studied include the energy and the key parameters of the Hessian eigenvalue distribution as well as the mean distances between instantaneous configurations and the corresponding inherent saddles and minima. The signatures of the thermodynamic freezing transition are clearest in the case of inherent structure properties which show, as a function of e(S2), a pronounced change in slope in the vicinity of the solid-liquid coexistence. The mean distance between instantaneous and saddle configurations also shows a similar change in slope when the system crosses from the stable to the supercooled regime. In the case of inherent saddles, the minimum eigenvalue acts as a similar indicator of the thermodynamic freezing transition but the average and maximum eigenvalues do not carry similar signatures. In the case of instantaneous configurations, a weak indicator of the thermodynamic freezing transition is seen in the behavior of the fraction of negative curvature directions as a function of the exponential of the excess entropy.     

Computational study of iminium ion formation: effects of amine structure

Density functional calculations are used to explore the formation of iminium ions from secondary amines and acrolein and the subsequent reactivity of the resulting iminium ions. After establishing a feasible profile for this reaction in simulated experimental conditions, we focus on the effect of variation in amine structure on calculated barriers. This analysis shows that incorporation of a heteroatom (N or O) in the alpha-position to the reactive amine results in significantly reduced energy barriers, as does an electron-withdrawing group (carbonyl or thiocarbonyl) in the beta-position. Electron density analysis is used to monitor reactions at a detailed level, and to identify important intermolecular interactions at both minima and transition states. Barriers to reaction are linked to calculated proton affinities of secondary amines, suggesting that the relative ease of protonation-deprotonation of the amine is a key property of effective catalysts. Moreover, barriers for subsequent Diels-Alder reaction of iminium ions with cyclopentadiene are lower than for their formation, suggesting that formation may be the rate determining step in the catalytic cycle.     

Potential energy and free energy landscapes

Familiar concepts for small molecules may require reinterpretation for larger systems. For example, rearrangements between geometrical isomers are usually considered in terms of transitions between the corresponding local minima on the underlying potential energy surface, V. However, transitions between bulk phases such as solid and liquid, or between the denatured and native states of a protein, are normally addressed in terms of free energy minima. To reestablish a connection with the potential energy surface we must think in terms of representative samples of local minima of V, from which a free energy surface is projected by averaging over most of the coordinates. The present contribution outlines how this connection can be developed into a tool for quantitative calculations. In particular, stepping between the local minima of V provides powerful methods for locating the global potential energy minimum, and for calculating global thermodynamic properties. When the transition states that link local minima are also sampled we can exploit statistical rate theory to obtain insight into global dynamics and rare events. Visualizing the potential energy landscape helps to explain how the network of local minima and transition states determines properties such as heat capacity features, which signify transitions between free energy minima. The organization of the landscape also reveals how certain systems can reliably locate particular structures on the experimental time scale from among an exponentially large number of local minima. Such directed searches not only enable proteins to overcome Levinthal's paradox but may also underlie the formation of "magic numbers" in molecular beams, the self-assembly of macromolecular structures, and crystallization.     

An algorithm to find minimum free-energy paths using umbrella integration

The calculation of free-energy barriers by umbrella sampling and many other methods is hampered by the necessity for an a priori choice of the reaction coordinate along which to sample. We avoid this problem by providing a method to search for saddle points on the free-energy surface in many coordinates. The necessary gradients and Hessians of the free energy are obtained by multidimensional umbrella integration. We construct the minimum free-energy path by following the gradient down to minima on the free-energy surface. The change of free energy along the path is obtained by integrating out all coordinates orthogonal to the path. While we expect the method to be applicable to large systems, we test it on the alanine dipeptide in vacuum. The minima, transition states, and free-energy barriers agree well with those obtained previously with other methods.     

A theoretical study of the N8 cubane to N8 pentalene isomerization reaction

The isomerization reaction of cubic N₈ to the planar bicyclic structure analogous to pentalene has been investigated using multiconfigurational self-consistent field and second-order perturbation theory (CASPT2). Comparative calculations using density functional theory have also been performed. Five local minima on the energy surface have been found, and the transition states between each two consecutive minima have been determined. The results show that all steps in the isomerization process, except one, can proceed via a set of transition states with moderately high energy barriers (10–20 kcal/mol). Received: 9 December 1996 / Accepted: 18 February 1997     

Archetypal energy landscapes: dynamical diagnosis

Recent studies have identified several motifs for potential energy surfaces corresponding to distinct dynamic and thermodynamic properties. The corresponding disconnectivity graphs were identified as "palm tree," "willow tree," and "banyan tree" patterns. In the present contribution we present a quantitative analysis of the relation between the topography and dynamics for each of these motifs. For the palm tree and willow tree forms we find that the arrangement of the stationary points in the monotonic sequences with respect to the global minimum is the most important factor in establishing the kinetic properties. However, the results are somewhat different for motifs involving a rough surface with several deep basins (banyan tree motif), with large barriers relative to the energy differences between minima. Here it is the size of the barrier for escape from the region relative to the barriers at the bottom that is most important. The present results may be helpful in distinguishing between the dynamics of "structure seeking" and "glass forming" systems.     

非晶态Co-B的局域电子结构的Xα原子簇计算

In the research on metallic glass, there are arguments against the "rigid band charge transfer", model which assumes a charge transfer from metalloid atoms to transition metal atoms to explain the experimental evidence of linear reduction of average atomic magnetic moment with the increasing concentration of metalloid atoms, but they could not explain the experimental relation of the reduction. In the present work, spin-polarized SCC-DV-X_a calculation for atomic clusters for metallic glass Co-B has been empoloyed to investigate the local electronic structure and magnetic property of the metallic glass. As opposed to the "rigid band charge transfer" model, calculation in the present work indicates that charge transfers from Co4s to both B and Co3d. It is found that there is Co3d4s-B2p hybird bonding in Co-B, which leads to the linear reduction of average atomic magnetic moment. Thus the explanation removes the above controversy.     

The theory of viscoelastic characteristics of a highly stretched macromolecule in single molecule AFM

The theory for the deformation of a model macromolecule stretched by its ends under the action of high constant and low periodic forces is constructed. The macromolecule is composed of monomer units in three conformational states. The proposed theory describes the regime of a severe stretching of a macromolecule extended to a length close to its contour length, when its extension proceeds via conformational transitions between different states of monomer units. The structural parameters of the monomer unit are found to correlate with viscoelastic characteristics, which are calculated from the experimental results on the deformation of an individual macromolecule obtained by the frequency atomic force microscopy. For a monomer unit with three conformations, the force dependences of viscoelastic characteristics (effective coefficients of elasticity and friction) can show one or two minima. When the experimental dependences of the above parameters show two minima, the monomer unit can have three or more equilibrium states. With the knowledge of the viscoelastic characteristics of a macromolecule, it is possible to unequivocally estimate all structural parameters of a monomer unit for its three-state conformational model. When the force dependence of viscoelastic characteristics show only one minimum, the monomer unit can have two or more states and analysis of the corresponding viscoelastic characteristics at the minimum makes it possible to select between two- and three-state conformational models. Then, for the three-state model, experimental data allow the prediction of only equilibrium parameters of the monomer unit (position of the minima and energy); dynamic parameters (positions and height of barriers between equilibrium states) remain indeterminate. The proposed theory is used for the interpretation of the viscoelastic characteristics of dextran obtained by single-molecule AFM experiments. The three-state conformational model of a dextran unit is shown to agree better with the experimental data than with the two-state conformational model.     

The use of “Boersma” type differential scanning calorimeters in the measurement of exothermic transitions

Questions have been raised about the suitability of the “Boersma” type differential scanning calorimeter for the measurement of exothermic transitions such as the crystallization of a metallic glass. However, it is demonstrated that provided the mass of the sample is kept lower than a certain value, which depends on the transition being studied (typically about 10–15 mg at a heating rate of 20 K min^? for a metallic glass), errors due to differences between actual sample temperature and that recorded by the instrument are negligible.     

Wetting of structured hydrophobic surfaces by water droplets

Super-hydrophobic surfaces may arise due to an interplay between the intrinsic, relatively high, contact angle of the more or less hydrophobic solid surface employed and the geometric features of the solid surface. In the present work, this relationship was investigated for a range of different surface geometries, making use of surface free energy minimization. As a rule, the free energy minima (and maxima) occur when the Laplace and Young conditions are simultaneously fulfilled. Special effort has been devoted to investigating the free energy barriers present between the Cassie-Baxter (heterogeneous wetting) and Wenzel (homogeneous wetting) modes. The predictions made on the basis of the model calculations compare favorably with experimental results presented in the literature.