Structure and Dynamics of Methyl-substituted Beryllocene: [Be(C5Me5)2]

In this paper we study theoretically the molecular structure of [Be(C₅Me₅)₂], with special interest in similarities and differences found in the computed geometric parameters, depending on the treatment of the electron correlation used. Given the low energy differences found between the different configurations studied (less than 4 kcal mol⁻¹), and the high fluxionality found in experimental studies for this compound, we analyzed the dynamics of the system by means of first principles molecular dynamics calculations. A complex dynamics is found and analyzed in terms of two molecular rearrangement processes: 1,2-sigmatropic intraring rearrangement and a ring inversion mechanism that interchanges the roles (with regard to their coordination to the central Be atom) of the two rings.Dedicated to Dr. Jeal Paul Malrieu on occasion of his 65th birthday.     

Bifurcation phenomena near homoclinic systems: A two-parameter analysis

The bifurcations of periodic orbits in a class of autonomous three-variable, nonlinear-differential-equation systems possessing a homoclinic orbit associated with a saddle focus with eigenvalues ( ±i,), where ¦/¦ < 1 (Sil'nikov's condition), are studied in a two-parameter space. The perturbed homoclinic systems undergo a countable set of tangent bifurcations followed by period-doubling bifurcations leading to periodic orbits which may be attractors if ¦/¦ < 1/2. The accumulation rate of the critical parameter values at the homoclinic system is exp(-2¦/¦). A global mechanism for the onset of homoclinicity in strongly contractive flows is analyzed. Cusp bifurcations with bistability and hysteresis phenomena exist locally near the onset of homoclinicity. A countable set of these cusp bifurcations with scaling properties related to the eigenvalues±i of the stationary state are shown to occur in infinitely contractive flows. In the two-parameter space, the periodic orbit attractor domain exhibits a spiral structure globally, around the set of homoclinic systems, in which all the different periodic orbits are continuously connected.     

The solvation of Li and Na in acetonitrile from ab initio-derived many-body ion–solvent potentials

Several Li⁺- and Na⁺-acetonitrile models were derived from ab initio calculations at the counterpoise-corrected MP2/TZV++(d,p) level for distorted ion-(MeCN)_n clusters with n=1, 4 and 6. Two different many-body ion-acetonitrile models were constructed: an effective three-body potential for use with the six-site effective pair model of Böhm et al., and an effective polarizable many-body model. The polarizable acetonitrile model used in the latter model is a new empirical model which was also derived in the present paper. Mainly for comparative purposes, two ion-acetonitrile pair potentials were also constructed from the ab initio cluster calculations: one pure pair potential and one effective pair potential. Using all these potential models, MD simulations in the NPT ensemble were performed for the pure acetonitrile liquid and for Li⁺(MeCN) and Na⁺(MeCN) solutions with 1 ion in 512 solvent molecules and with a simulation time of at least 120 ps per system. Thermodynamic properties, solvation-shell structure and the self-diffusion coefficient of the ions and of the solvent molecules were calculated and compared between the different models and with experimental data, where available. The Li⁺ ion is found to be four-coordinated when the new many-body potentials are used, in contrast to the six-coordinated structure obtained for the pure pair and effective pair potentials. The coordination number of Na⁺ is close to six for all the models derived here, although the coordination number becomes slightly smaller with the many-body potentials. For both ions, the solvent molecules in the first shell point their nitrogen ends towards the cation, while in the second shell the opposite orientation is the most common.     

The phases of polymers as determined by NMR

Nuclear magnetic resonance (NMR) spectroscopy has been used to study the morphology and dynamics in semicrystalline polymers. Dynamics may be observed through NMR relaxation rates that are sensitive to motions in the 1–10⁸ Hz range, or through modulation of anisotropic magnetic interactions, such as the chemical shift and dipole-dipole interactions. Morphological structure may be inferred through NMR measurements of polymer dynamics or investigated directly through studies of the magnetic interactions. Here, we discuss the study of morphological structure in semicrystalline polymers using NMR, and review results on poly(ethylene terephthalate) that address the question of the number of phases in this semicrystalline polymer.This work was funded by the Office of Naval Research.     

Vibrational frequencies and structural determination of phosphirane

The normal mode frequencies and corresponding vibrational assignments of phosphirane in are examined theoretically using the GAUSSIAN 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of nine types of motion (C–C stretch, P–C stretch C–H stretch, P–H stretch, CH₂ scissors, CH₂ wag, CH₂ rock, CH₂ twist, and P–H wag) predicted by a group theoretical analysis. Comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors are derived. Predicted infrared and Raman intensities are reported.     

Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Absolute line intensity measurements of hot bands for carbonyl sulfide at 12 microm

Using diode-laser spectroscopy, the intensities of 58 lines of the v(1) + v(1/2) - v(1/2) band and 36 lines of the 2v(1) - v(1) band of OCS have been measured. The corresponding band strengths S(0)(v) and the vibrational transition dipoles micro(v) have been derived through least squares fitting of these individual intensities. The band strengths values have been determined with a precision better than 2.5%.     

Nonequilibrium Brownian dynamics simulations of shear thinning in concentrated colloidal suspensions

The effect of interparticle forces on shear thinning in concentrated aqueous and nonaqueous colloidal suspensions was studied using nonequilibrium Brownian dynamics. Hydrodynamic interactions among particles were neglected. Systems of 108 particles were studied at volume fractions of 0.2 and 0.4. For the nonaqueous systems, shear thinning could be correlated with the gradual breakup of small flocs present because of the weak, attractive secondary minimum in the interparticle potential. At the highest shear rate for=0.4, the particles were organized into a hexagonally packed array of strings. For the strongly repulsive aqueous systems, the viscosity appeared to be a discontinuous function of the shear rate. For=0.4, this discontinuity coincided with a transition from a disordered state to a lamellar structure for the suspension.     

Phase separation dynamics in driven diffusive systems

We study phase separation dynamics in a driven diffusive system. Our simulations are based on the Cahn-Hilliard equation with an additional flux term due to an external field. We study the dynamical scaling parallel and perpendicular to the field. A crossover is observed from isotropic domains at early times to extremely anisotropic domains at later times. We find that the inverse interfacial density (an isotropic measure of the domain size) increases ast , with =1/3, from early times independent of the field strength, even though we do not observe dynamical scaling during these times. Our results indicate that a growth exponent =1/3 may be more universal than previously expected. We analyze the dynamics in terms of surface driven instabilities and one-dimensional solitary waves.     

Phenomenology of nonlocal cellular automata

Dynamical systems with nonlocal connections have potential applications to economic and biological systems. This paper studies the dynamics of nonlocal cellular automata. In particular, all two-state, three-input nonlocal cellular automata are classified according to the dynamical behavior starting from random initial configurations and random wirings, although it is observed that sometimes a rule can have different dynamical behaviors with different wirings. The nonlocal cellular automata rule space is studied using a mean-field parametrization which is ideal for the situation of random wiring. Nonlocal cellular automata can be considered as computers carrying out computation at the level of each component. Their computational abilities are studied from the point of view of whether they contain many basic logical gates. In particular, I ask the question of whether a three-input cellular automaton rule contains the three fundamental logical gates: two-input rules AND and OR, and one-input rule NOT. A particularly interesting edge-of-chaos nonlocal cellular automaton, the rule 184, is studied in detail. It is a system of coupled selectors or multiplexers. It is also part of the Fredkin's gate—a proposed fundamental gate for conservative computations. This rule exhibits irregular fluctuations of density, large coherent structures, and long transient times.