Simulation of electronic and geometric degrees of freedom using a kink-based path integral formulation: application to molecular systems

A kink-based path integral method, previously applied to atomic systems, is modified and used to study molecular systems. The method allows the simultaneous evolution of atomic and electronic degrees of freedom. The results for CH4, NH3, and H2O demonstrate this method to be accurate for both geometries and energies. A comparison with density functional theory (DFT) and second-order Moller-Plesset (MP2) level calculations show the path integral approach to produce energies in close agreement with MP2 energies and geometries in close agreement with both DFT and MP2 results.     

Ab initio centroid path integral molecular dynamics: application to vibrational dynamics of diatomic molecular systems

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.     

Metal-organic framework nanosheets: a class of glamorous low-dimensional materials with distinct structural and chemical natures

Metal-organic framework nanosheets have gained great attention because of the diversified structures, tunable chemical functionalities, large surface area and ultrathin thickness. In this review, we introduce the recent progress in the favorable applications for catalysis, sensing, energy storage and gas separation, which has significantly addressed the advantages of the nanosheets. A summary of nanosheet fabrication approaches is put forward to establish a comprehension on the origin of the MOF nanosheets. And at last but not the least, we present the concerns on the challenges and opportunities of these materials from our perspectives.     

Thermodynamic properties of small rare gas clusters by path integral Monte Carlo simulations: a preliminary study

A strategy for reducing the risk of non-ergodic simulations in Monte Carlo calculations of the thermodynamic properties of clusters is discussed with the support of some examples. The results obtained attest the significance of the approach for the low-temperature regime, as non-ergodic sampling of potential energy surfaces is a particularly insidious occurrence. Fourier path integral Monte Carlo techniques for taking into account quantum effects are adopted, in conjunction with suitable tricks for improving the procedure reliability. Applications are restricted to Lennard-Jones clusters of rare-gas systems.     

Moderately and strongly supercooled liquids: a temperature-derivative study of the primary relaxation time scale

The primary relaxation time scale tau(T) derived from the glass forming supercooled liquids (SCLs) is discussed within ergodic-cluster Gaussian statistics, theoretically justified near and above the glass-transformation temperature T(g). An analysis is given for the temperature-derivative data by Stickel et al. on the steepness and the curvature of tau(T). Near the mode-coupling-theory (MCT) crossover T(c), these derivatives separate by a kink and a jump, respectively, the moderately and strongly SCL states. After accounting for the kink and the jump, the steepness remains a piecewise conitnuous function, a material-independent equation for the three fundamental characteristic temperatures, T(g), T(c), and the Vogel-Fulcher-Tamman (VFT) T(0), is found. Both states are described within the heterostructured model of solidlike clusters parametrized in a self-consistent manner by a minimum set of observable parameters: the fragility index, the MCT slowing-down exponent, and the chemical excess potential of Adam and Gibbs model (AGM). Below the Arrhenius temperature, the dynamically and thermodynamically stabilized clusters emerge with a size of around of seven to nine and two to three molecules above and close to T(g) and T(c), respectively. On cooling, the main transformation of the moderately into the strongly supercooled state is due to rebuilding of the cluster structure, and is attributed to its rigidity, introduced through the cluster compressibility. It is shown that the validity of the dynamic AGM (dynamically equivalent to the standard VFT form) is limited by the strongly supercooled state (T(g) < T < T(c)) where the superrigid cooperative rearranging regions are shown to be well-chosen parametrized solidlike clusters. Extension of the basic parameter set by the observable kinetic and diffusive exponents results in prediction of a subdiffusion relaxation regime in SCLs that is distinct from that established for amorphous polymers.     

Pair formation and global ordering of strongly interacting ferrocolloid mixtures: an integral equation study

Using the reference hypernetted chain (RHNC) integral equation theory and an accompanying stability analysis we investigate the structural and phase behaviors of model bidisperse ferrocolloids based on correlations of the homogeneous isotropic high-temperature phase. Our model consists of two species of dipolar hard spheres (DHSs) which dipole moments are proportional to the particle volume. At small packing fractions our results indicate the onset of chain formation, where the (more strongly coupled) A species behaves essentially as a one-component DHS fluid in a background of B particles. At high packing fractions, on the other hand, the RHNC theory indicates the appearance of isotropic-to-ferromagnetic transitions (volume ratios close to one) and demixing transitions (smaller volume ratios). However, contrary with the related case of monodisperse DHS mixtures previously studied by us [Phys. Rev. E 70, 031201 (2004)], none of the present bidisperse systems exhibit demixing within the isotropic phase, rather we observe coupled ferromagnetic/demixing phase transitions.     

Kinetic analysis of solid-state reactions: Evaluation of approximations to temperature integral and their applications

The temperature integral, which has no exact analytical solution, is involved in the analysis of the experiment data obtained under nonisothermal conditions. Some approximations for the temperature integral have been proposed in the literature for the determination of the kinetic parameters, in particular the activation energy. Those approximations are classified into two categories, that is, exponential and rational approximations. The precision of them for estimating the temperature integral was evaluated within a certain continuous range rather than at several discrete points. Some applications of the approximations in the kinetic methods were presented. The relative errors of the activation energy and pre-exponential factor with four rational approximations by employing model-fitting method were calculated. The relative errors of the activation energy for a series of conversion rate with four rational and four exponential approximations by employing linear integral isoconversional methods were evaluated.     

A line integral reaction path approximation for large systems via nonlinear constrained optimization: application to alanine dipeptide and the beta hairpin of protein G

A variation of the line integral method of Elber with self-avoiding walk has been implemented using a state of the art nonlinear constrained optimization procedure. The new implementation appears to be robust in finding approximate reaction paths for small and large systems. Exact transition states and intermediates for the resulting paths can easily be pinpointed with subsequent application of the conjugate peak refinement method [S. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992)] and unconstrained minimization, respectively. Unlike previous implementations utilizing a penalty function approach, the present implementation generates an exact solution of the underlying problem. Most importantly, this formulation does not require an initial guess for the path, which makes it particularly useful for studying complex molecular rearrangements. The method has been applied to conformational rearrangements of the alanine dipeptide in the gas phase and in water, and folding of the beta hairpin of protein G in water. In the latter case a procedure was developed to systematically sample the potential energy surface underlying folding and reconstruct folding pathways within the nearest-neighbor hopping approximation.     

Re-weighted random series path integral simulations of molecular clusters: Applications to lithium solvated by a mixed Stockmayer cluster

Nuclear quantum effects in finite temperature simulations of molecular clusters are determined by taking advantage of a recently developed method based on the Feynman Path Integral. The structural and thermodynamic properties, including the nuclear quantum effects are determined for three Stockmayer clusters. The ionic system contain a lithium ion solvated by six strong dipoles and 12 weaker ones. The presence of the ion in the mixed Stockmayer cluster drastically enhances the fluxional nature of the less polar components which occupy the second solvation layer, whereas the neutral counterpart has the effect of reducing it. The nuclear quantum effects are significant at room temperature and above for the solvated ionic system. These are attributable to two factors: (a) the lightness of the lithium ion and (b) the stiffness of the ion-dipole interactions. At 300 K, the difference between the fully converged quantum and the classical heat capacities is about 1.3 K_B for the ionic cluster. This difference is about 10 SDs obtained from 95% confidence estimates of the statistical fluctuations. Cubic convergence is confirmed for temperatures as low as 50 K by regression analysis. The nuclear quantum effects do not change the peak melting temperature of the cluster.     

Condensed-phase relaxation of multilevel quantum systems. II. Comparison of path integral calculations and second-order relaxation theory for a nondegenerate three-level system

An exactly solvable model of multisite condensed-phase vibrational relaxation was studied in Paper I (Peter, S.; Evans, D. G.; Coalson, R. D. J. Phys. Chem. B 2006, 110, 18758.), where it was shown that long-time steady-state site populations of a degenerate N-level system are not equal (hence, they are non-Boltzmann) and depend on the initial preparation of the system and the number of sites that it comprises. Here we consider a generalization of the model to the case of a nondegenerate three-level system coupled to a high-dimensional bath: such a model system has direct relevance to a large class of donor-bridge-acceptor electron transfer processes. Because the quantum dynamics of this system cannot be computed analytically, we compare numerically exact path integral calculations to the predictions of second-order time-local relaxation theory. For modest system-bath coupling strengths, the two sets of results are in excellent agreement. They show that non-Boltzmann long-time steady-state site populations are obtained when the level splitting is small but nonzero, whereas at larger values of the system bias (asymmetry) these populations become Boltzmann distributed.     

Controlling activated processes of nonadiabatically, periodically driven dynamical systems: a multiple scale perturbation approach

We arrive at the escape rate from a metastable state for a system of Brownian particles driven periodically by a space dependent, rapidly oscillating external perturbation (with frequency ω) in one dimension (one of the most important class of nonequilibrium system). Though the problem may seem to be time-dependent, and is poised on the extreme opposite side of adiabaticity, there exists a multiple scale perturbation theory ("Kapitza window") by means of which the dynamics can be treated in terms of an effective time-independent potential that is derived as an expansion in orders of 1/ω to the order ω(-3). The resulting time-independent equation is then used to calculate the escape rate of physical systems from a metastable state induced by external monochromatic field in the moderate-to-large damping limit and to investigate the effect of ω on the resulting rate in conjunction with the thermal energy. With large value of ω, we find that the environment with moderate-to-large damping impedes the escape process of the particle while high amplitude of the periodic driving force allows the particle to cross the barrier with a large escape rate. A comparison of our theoretical expression with numerical simulation gives a satisfactory agreement.     

Integrated fluidic systems on a nanometer scale and the study on behavior of liquids in small confinement

Nanofluidic systems and the studies on the behavior of liquids confined in nanometer-sized space are reviewed. Miniaturized chemical systems having nanometer-sized structures are fabricated by using advanced nanofabrication techniques. The size-confinement effect is expected to be applied in well-controlled chemical and biochemical analysis. While electroosmosis and electrokinetic migration in small-sized channels have been investigated extensively, there have been few reports on pressure-driven flow systems having nanometer-sized structures, which are widely used in laboratory-scale and micrometer-sized systems. In this review, fundamental technologies that can be used in integrated chemical analysis systems having nanometer-sized structures are introduced. In addition to the technological investigations, important topics in the fundamental research on the properties of liquids confined in nanometer-sized space are also presented.     

Global perspectives on the energy landscapes of liquids, supercooled liquids, and glassy systems: the potential energy landscape ensemble

In principle, all of the dynamical complexities of many-body systems are encapsulated in the potential energy landscapes on which the atoms move--an observation that suggests that the essentials of the dynamics ought to be determined by the geometry of those landscapes. But what are the principal geometric features that control the long-time dynamics? We suggest that the key lies not in the local minima and saddles of the landscape, but in a more global property of the surface: its accessible pathways. In order to make this notion more precise we introduce two ideas: (1) a switch to a new ensemble that deemphasizes the concept of potential barriers, and (2) a way of finding optimum pathways within this new ensemble. The potential energy landscape ensemble, which we describe in the current paper, regards the maximum accessible potential energy, rather than the temperature, as a control variable. We show here that while this approach is thermodynamically equivalent to the canonical ensemble, it not only sidesteps the idea of barriers it allows us to be quantitative about the connectivity of a landscape. We illustrate these ideas with calculations on a simple atomic liquid and on the Kob-Andersen [Phys. Rev. E 51, 4626 (1995)] of a glass-forming liquid, showing, in the process, that the landscape of the Kob-Anderson model appears to have a connectivity transition at the landscape energy associated with its empirical mode-coupling transition. We turn to the problem of finding the most efficient pathways through potential energy landscapes in our companion paper.     

Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments

Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, including single-molecule pulling experiments and analogous computer simulations. Challenges in collecting large data sets motivate the pursuit of efficient statistical estimators that maximize use of available information. Along these lines, Hummer and Szabo developed an estimator that combines data from multiple time slices along a driven nonequilibrium process to compute the potential of mean force. Here, we generalize their approach, pooling information from multiple time slices to estimate arbitrary equilibrium expectations. Our expression may be combined with estimators of path-ensemble averages, including existing optimal estimators that use data collected by unidirectional and bidirectional protocols. We demonstrate the estimator by calculating free energies, moments of the polymer extension, the thermodynamic metric tensor, and the thermodynamic length in a model single-molecule pulling experiment. Compared to estimators that only use individual time slices, our multiple time-slice estimators yield substantially smoother estimates and achieve lower variance for higher-order moments.     

Competition between Bailar and Ray-Dutt paths in conformational interconversion of tris-chelated complexes: a DFT study

Tris-chelated complexes of aluminum with α-isopropenyltropolonate and α-isopropyltropolonate ligands can be considered prototypical complexes for the study of internal rearrangements through prismatic transient structures. Such isomerization paths, known as Bailar and Ray-Dutt twists, have been suggested for these compounds on the basis of dynamic NMR study, but modern computational methodologies have never been applied to corroborate this finding. In this paper, we report a computational investigation about the internal isomerization processes of the mentioned complexes. Both the Bailar and Ray-Dutt twists have been found as possible reaction paths. The prismatic structures along each reaction path have been described as transition structures rather than intermediate and have been computationally characterized. A comparison between experimental and computational kinetic data has been performed.     

The fundamental syntopy of quasi-symmetric systems: Geometric criteria and the underlying syntopy of a nuclear configuration space

Point symmetry is a discrete concept; A nuclear configuration for a given stoichiometry either has or has not a particular point symmetry. By contrast, both static and dynamic properties of actual molecules exhibit continuous features. Using the formalism of fuzzy-set theory, we had previously proposed the concept of syntopy as a continuous extension of the symmetry concept for quasi-symmetric systems: This was based on an energetic criterion taking into account the energy costs of nuclear rearrangements. This extension of symmetry was necessarily dependent on the considered electronic state: For a given geometric arrangement of the nuclei, the energy cost of some rearrangement is dependent on the actual potential surface, that is, on the electronic state, in the Born–Oppenheimer approximation. In the extension of the syntopy model reported in the present work, we consider a syntopy criterion that is common to all electronic states. The syntopy thus defined—called the fundamental syntopy of the reduced nuclear configuration space—is independent of the potential surface and of the electronic state: It is defined only in terms of a geometric condition, which makes it more appropriate to rationalize mesoscopic structures. This new syntopy model provides a connection between all possible syntopies generated by the various potential-energy surfaces supported by the considered family of atomic nuclei. © 1993 John Wiley & Sons, Inc.     

Comparative study of measured and critically evaluated resonance integral to thermal cross section ratios,III

In the present paper, a tabulation is given of recommended Q₀-values [the ratio of the resonance integral (I₀) to the 2200 m·s^?1 cross-section (δ₀)] for 107 (n, γ) reactions of interest in NAA, including a revision and updating of formerly published results for 57 isotopes. The values were either critically evaluated from literature, or-in the majority of cases — experimentally determined according to the Cd-ratio method, with a correction for a non-ideal epithermal neutron flux distribution. These Q₀-measurements were performed at INW, Gent, at KFKI, Budapest, and occasionally at Risø. A comparison is made with results obtained by other workers or with values derived from δ₀'s and I₀'s quoted in recent compilations.     

Global perspectives on the energy landscapes of liquids, supercooled liquids, and glassy systems: geodesic pathways through the potential energy landscape

How useful it is to think about the potential energy landscape of a complex many-body system depends in large measure on how direct the connection is to the system's dynamics. In this paper we show that, within what we call the potential-energy-landscape ensemble, it is possible to make direct connections between the geometry of the landscape and the long-time dynamical behaviors of systems such as supercooled liquids. We show, in particular, that the onset of slow dynamics in such systems is governed directly by the lengths of their geodesics--the shortest paths through their landscapes within the special ensemble. The more convoluted and labyrinthine these geodesics are, the slower that dynamics is. Geodesics in the landscape ensemble have sufficiently well-defined characteristics that it is straightforward to search for them numerically, a point we illustrate by computing the geodesic lengths for an ordinary atomic liquid and a binary glass-forming atomic mixture. We find that the temperature dependence of the diffusion constants of these systems, including the precipitous drop as the glass-forming system approaches its empirical mode-coupling transition, is predicted quantitatively by the growth of the geodesic path lengths.