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New features of molecular wires can be observed when they are irradiated by laser fields. These effects can be achieved by periodically oscillating fields but also by short laser pulses. The theoretical foundation used for these investigations is a density-matrix formalism where the full system is partitioned into a relevant part and a thermal fermionic bath. The derivation of a quantum master equation, either based on a time-convolutionless or time-convolution projection-operator approach, incorporates the interaction with time-dependent laser fields nonperturbatively and is valid at low temperatures for weak system-bath coupling. From the population dynamics the electrical current through the molecular wire is determined. This theory including further extensions is used for the determination of electron transport through molecular wires. As examples, we show computations of coherent destruction of tunneling in asymmetric periodically driven quantum systems, alternating currents and the suppression of the directed current by using a short laser pulse. [ABSTRACT FROM AUTHOR]

The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter ξ. Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a β-turn motif and restraining ξ to a region of the conformational space that extends from the α-helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact α helix. Sampling of this conformation is, however, marginal when the range of ξ values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized. [ABSTRACT FROM AUTHOR]

We first show that a simple scaling of fluctuation coordinates defined in terms of a given reference point gives the conventional virial estimator in discretized path integral, where different choices of the reference point lead to different forms of the estimator (e.g., centroid virial). The merit of this procedure is that it allows a finite-difference evaluation of the virial estimator with respect to temperature, which totally avoids the need of higher-order potential derivatives. We apply this procedure to energy and heat-capacity calculations of the (H2)22 and Ne13 clusters at low temperature using the fourth-order Takahashi-Imada [J. Phys. Soc. Jpn. 53, 3765 (1984)] and Suzuki [Phys. Lett. A 201, 425 (1995)] propagators. This type of calculation requires up to third-order potential derivatives if analytical virial estimators are used, but in practice only first-order derivatives suffice by virtue of the finite-difference scheme above. From the application to quantum clusters, we find that the fourth-order propagators do improve upon the primitive approximation, and that the choice of the reference point plays a vital role in reducing the variance of the virial estimator. [ABSTRACT FROM AUTHOR]

In this work we focus on the dynamics of macromolecular networks formed by end-linking identical polymer stars. The resulting macromolecular network can then be viewed as consisting of spacers which connect branching points (the cores of the stars). We succeed in analyzing exactly, in the framework of the generalized Gaussian model, the eigenvalue spectrum of such networks. As applications we focus on several topologies, such as regular networks and dendrimers; furthermore, we compare the results to those found for regular hyperbranched structures. In so doing, we also consider situations in which the beads of the cores differ from the beads of the spacers. The analytical procedure which we use involves an exact real-space renormalization, which allows to relate the star network to a (much simpler) network, in which each star is reduced to its core. It turns out that the eigenvalue spectrum of the star-polymer structure consists of two parts: one follows in terms of polynomial equations from the relaxation spectrum of the corresponding renormalized structure, while the second part involves the motion of the spacer chains themselves. Finally, we show exemplarily the situation for copolymeric dendrimers, calculate their spectra, and from them their storage and the loss moduli. [ABSTRACT FROM AUTHOR]

Quantum coherent vibrational relaxation of an impurity strongly coupled to its solid host is demonstrated through four-wave mixing measurements to infer sustained coherence in the bath, which is recognized as a superposition of macroscopically distinct states. [ABSTRACT FROM AUTHOR]

Two-color resonant two-photon mass-analyzed threshold ionization (MATI) spectroscopy was used to record the vibrationally resolved cation spectra of the selected rotamers of p-n-propylphenol. The adiabatic ionization energies of the trans, gauche-A, and gauche-B rotamers are determined to be 65 283±5, 65 385±5, and 65 369±5 cm-1, which are less than that of phenol by 3342, 3240, and 3256 cm-1, respectively. This suggests that the n-propyl substitution causes a greater degree in lowering the energy level in the cationic than the neutral ground state. Analysis on the MATI spectra of the selected rotamers of p-n-propylphenol cation shows that the relative orientation of the p-n-alkyl group has little effect on the in-plane ring vibrations. However, the low-frequency C3H7 bending vibrations appear to be active only for the two gauche forms of the cation. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecules bonded between two metal contacts form the simplest possible molecular devices. Coupled by the molecule, the left and right contact-based states form symmetric and antisymmetric pairs near the Fermi level. We relate the size of the resulting energy splitting ΔE to the symmetry and degree of delocalization of the coupling molecular orbital. Qualitative trends in molecular conductances are then estimated from the variations in ΔE. We examine benzenedithiol and other molecules of interest in transport. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We discuss a coarse-grained approach to the computation of rare events in the context of grand canonical Monte Carlo (GCMC) simulations of self-assembly of surfactant molecules into micelles. The basic assumption is that the computational system dynamics can be decomposed into two parts—fast (noise) and slow (reaction coordinates) dynamics, so that the system can be described by an effective, coarse-grained Fokker–Planck (FP) equation. While such an assumption may be valid in many circumstances, an explicit form of FP equation is not always available. In our computations we bypass the analytic derivation of such an effective FP equation. The effective free energy gradient and the state-dependent magnitude of the random noise, which are necessary to formulate the effective Fokker–Planck equation, are obtained from ensembles of short bursts of microscopic simulations with judiciously chosen initial conditions. The reaction coordinate in our micelle formation problem is taken to be the size of a cluster of surfactant molecules. We test the validity of the effective FP description in this system and reconstruct a coarse-grained free energy surface in good agreement with full-scale GCMC simulations. We also show that, for very small clusters, the cluster size ceases to be a good reaction coordinate for a one-dimensional effective description. We discuss possible ways to improve the current model and to take higher-dimensional coarse-grained dynamics into account.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present a Monte Carlo algorithm that allows simulations where portions of the system of variable size are moved. The algorithm requires the definition of an augmented space that contains information on the bonding between components of the system and is updated as the simulation proceeds. With this method it is possible to incorporate, within the same simulation, processes involving motion of smaller and larger portions of a given system. The algorithm is presented in general terms and illustrated for a simple one-dimensional lattice model. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The paper develops a theory of electron transfer with torsionally induced non-Condon (NC) effects. The starting point of the theory is a generalized spin-boson Hamiltonian, where an additional torsional oscillator bilinearly coupled to other bath modes causes a sinusoidal NC modulation. We derive closed form time dependent nonadiabatic rate expressions for both sudden and relaxed initial conditions, which are applicable for general spectral densities and energetic condition. Under the assumption that the torsional motion is not correlated with the polaronic shift of the bath, simple stationary limit rate expression is obtained. Model calculations of this rate expression illustrate the effects of torsional quantization and gating on the driving force and temperature dependences of the electron transfer rate. The classical limit of the rate expression consists of three Marcus-type terms, and is shown to agree very well with the exact numerical result.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Time-divergence in linear and nonlinear classical response functions can be removed by taking a phase-space average within the quantized uncertainty volume O(hn) around the microcanonical energy surface. For a quasiperiodic system, the replacement of the microcanonical distribution density in the classical response function with the quantized uniform distribution density results in agreement of quantum and classical expressions through Heisenberg’s correspondence principle: each matrix element 〈u|α(t)|v〉 corresponds to the (u-v)th Fourier component of α(t) evaluated along the classical trajectory with mean action (Ju+Jv)/2. Numerical calculations for one- and two-dimensional systems show good agreement between quantum and classical results. The generalization to the case of N degrees of freedom is made. Thus, phase-space averaging within the quantized uncertainty volume provides a useful way to establish the classical-quantum correspondence for the linear and nonlinear response functions of a quasiperiodic system. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We report on the progress of our implementation of the configuration-selecting multireference configuration interaction method on massively parallel architectures with distributed memory, which now permits the treatment of Hilbert spaces of dimension O(1012). Of these about 50 000 000 can be selected in the variational subspace. We provide scaling data for the running time of the code for the IBM/SP3 and the CRAY-T3E. We present benchmark results for two selected applications: the energetics of the isomers of dinitrosoethylene and the benchmark results for the ring closure reaction of enediyene.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this study we have introduced a formulation of time-dependent density functional theory (TDDFT) based on a noncollinear exchange-correlation potential. This formulation is a generalization of conventional TDDFT. The form of this formulation is exactly the same as that of the conventional TDDFT for the excitation energies of transitions that do not involve spin flips. In addition, this noncollinear TDDFT formulation allows for spin-flip transitions. This feature makes it possible to resolve more fully excited state spin multiplets, while for closed-shell systems, the spin-flip transitions will result in singlet-triplet excitations and this excitation energy calculated from this formulation of TDDFT is exactly the same as that from ordinary TDDFT. This formulation is applied to the dissociation of H2 in its 1Σg+ ground state and 1Σu+ and 3Σu- excited states with 3Σu- (Ms=+1) as the reference state and the multiplets splitting of some atoms.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Potential curves for the ground and the first lowest excited states of the MHe (where M={Li,Na,K,Rb,Cs,Fr}) exciplexes are calculated using the density functional theory (DFT) formalism. Relativistic calculations are carried out with and without spin-orbit (SO) coupling effect, using a zeroth order regular approximation (ZORA) approach. The depth De and position Re parameters of the potential curves for the case without spin-orbit effect are presented and compared with other works. Potential curves for Li-He, Cs-He, and Fr-He without spin-orbit effect and Cs-He with the spin-orbit effect are shown. A bond analysis is presented too, since the central interest of the study of the exciplexes is the nature and the existence of the bonding states that are the origin of emission spectra observed experimentally for these systems. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A new dynamical definition of the effective colloidal charge, especially suitable for the Monte Carlo and Molecular-dynamics simulations, is proposed. It is shown that for aqueous colloidal suspensions containing monovalent counterions the “dynamical” effective charge agrees perfectly with the “statistical” effective charge calculated using the Alexander prescription. In the case of multivalent ions, the effective charge behaves in a qualitatively different way from the predictions of the Poisson–Boltzmann theory.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

An analytical potential energy curve is developed from high quality ab initio calculations for the He+Li- interaction. The HeLi- electrostatic complex is found to have an Re of 18.5 bohrs and a De of 0.974 cm-1. Numerical solution of the rovibrational Schrödinger equation with this potential indicates two bound levels, (v,J)=(0,0) and (0,1), for all naturally occurring isotopologs (i.e., 4He7Li-, 4He6Li-, 3He7Li-, and 3He6Li-). For the common isotopolog, 4He7Li-, a D0 of 0.207 cm-1 and an R0 of 26.5 bohrs is determined. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Dispersed fluorescence (DF) spectra of 1-propoxy, 1-butoxy, 2-propoxy, and 2-butoxy radicals have been observed under supersonic jet cooling conditions by pumping different vibronic bands of the B-X laser induced fluorescence excitation spectrum. The DF spectra were recorded for both conformers of 1-propoxy, three conformers of the possible five of 1-butoxy, the one possible conformer of 2-propoxy, and two conformers of the possible three of 2-butoxy. Analysis of the spectra yields the energy separations of the vibrationless levels of the ground X and low-lying à electronic state as well as their vibrational frequencies. In all cases, the vibrational structure of the DF spectra is dominated by a CO stretch progression yielding the νCO stretching frequency for the X state and in most cases for the à state. In addition to the experimental work, quantum chemical calculations were carried out to aid the assignment of the vibrational levels of the X state and for some conformers the à state as well. Geometry optimizations of the different conformers of the isomers were performed and their energy differences in the ground states were determined. The results of the calculation of the energy separations of the close-lying X and à states of the different conformations are provided for comparison with the experimental observations.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The expression for driving force is presented for multicomponent gas hydrate nucleation in an aqueous phase. The derivation includes working equations for predicting the composition of a hydrate nucleus. The results for driving force in multicomponent systems show a significant effect of the composition of the hydrate nucleus. All past work assume a fixed composition based on the three-phase equilibrium point independent of subcooling and supersaturation. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The association of an excess electron with scavengers in nonpolar solvents is considered assuming that the free electron performs the free diffusion during the lifetime between sequential places of temporary localization. The reaction of a free electron during this motion is at first taken into account along with a tunneling of the localized electron. When the mean step length between sequential localizations is short the reaction of the excess electron is diffusional and the free state contribution to the total reaction rate is negligible. In the opposite case, when this reaction becomes essentially hopping, the corresponding rate is significantly accelerated due to a faster diffusion of the free electron. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Density fingering of the chlorite-tetrathionate reaction has been studied experimentally in a Hele-Shaw cell. The initially emerging cellular structure transforms into a single cell with constant—asymmetric and symmetric—shape in narrow reaction vessels. The interactions of fingers in wider Hele-Shaw cells lead to the coarsening of the patterns, however, splitting of fingers is observed as well. The long time evolution has been quantitatively described by the change in the mixing length, i.e., the amplitude of the patterns, and by the power-averaged cell number of the structures.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A lattice simulation of a model diblock copolymer melt is presented. In a series of simulation experiments an 8-8 diblock melt is quenched from an athermal state to 47 lower temperatures. A set of simulation boxes, 30×32×30, 40×32×60, 50×32×30, and 60×32×30, is used in order to explore the size effects. Energy, specific heat, copolymer end-to-end distance, lamellar spacing, and the degree of interfacial ordering are reported. For all sizes considered, the low-temperature interfacial ordering is noticeable.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The viscoelastic properties of dendrimers of generation 1–4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The formation of a pore in a membrane requires a considerable rearrangement of the amphiphilic molecules about to form the bilayer edge surrounding the pore, and hence is accompanied by a steep increase of the free energy. Recent rupture and conductance experiments suggest that this reshuffling process is also responsible for a small energy barrier that stabilizes “prepores” with diameters of less than 1 nm, rendering both the opening and closing of pores an activated process. We use the potential of mean constraint force method to study this free energy profile, as a function of pore radius, in a coarse grained bilayer model. The calculations show that the free energy rises by (15–20) kT during pore opening, making it an extremely rare nucleation event. Although we do not observe a barrier to pore closure, the results do make the existence of such a barrier plausible. For larger pores we find a smooth transition to Litster’s model, from which a line tension coefficient of about 3.7×10-11 J m-1 is deduced.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this study, the thermal stability of a designed α/β protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7–9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (α helix and β hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

An analytical potential energy curve is developed from high quality ab initio calculations for the He+Li- interaction. The HeLi- electrostatic complex is found to have an Re of 18.5 bohrs and a De of 0.974 cm-1. Numerical solution of the rovibrational Schrödinger equation with this potential indicates two bound levels, (v,J)=(0,0) and (0,1), for all naturally occurring isotopologs (i.e., 4He7Li-, 4He6Li-, 3He7Li-, and 3He6Li-). For the common isotopolog, 4He7Li-, a D0 of 0.207 cm-1 and an R0 of 26.5 bohrs is determined. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The formalism developed in Part I [K. L. Ivanov, N. N. Lukzen, A. A. Kipriyanov, and A. B. Doktorov, Phys. Chem. Chem. Phys. 6, 1706 (2004)] of the present contribution is extended to treat the reacting particles with internal quantum states. Initial spatial correlations of reactants are considered in the framework of this formalism as well. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of semiflexible polymers depends not only on the details of the disorder but also on the ease with which polymers can bend. The interplay of these two effects can lead to the delocalization of a localized polymer with an increase in either the disorder density or the stiffness. Our theory provides a general criterion for the delocalization of polymers with varying degrees of flexibility and allows us to propose a phase diagram for the highly folded (localized) states of semiflexible polymers as a function of the disorder strength and chain rigidity. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Using a homologous series of n-alkanes as a model system, we compare the predictions of a lattice Born-Green-Yvon (BGY) theory and a continuum BGY theory with experimental results. We find that both theories are capable of describing the fluid properties and critical points of alkanes ranging from heptamers (n-C7) to nonadecamers (n-C19). We probe the connection between the lattice and continuum BGY models and extend our discussion to include a sampling of other lattice and continuum treatments. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Variational approach based on the diabatic variational transition state theory optimization is extended and applied to the calculation of the radiationless transition rate for asymmetric high-barrier normal and inverted crossings. Scaling argument is employed to derive an analytic expression for the renormalized frequency as a function of the asymmetry of the crossing and of the dissipation strength for the particular case of Ohmic dissipation (Debye relaxation). The effect of the asymmetry of the crossing on the physical parameters and on the radiationless transition rate is explored. The effective adiabaticity parameter increases with the increasing asymmetry of the crossing in the normal region and decreases with the increasing asymmetry in the inverted region. The physical behavior of the radiationless transition rate in the normal and inverted regions is qualitatively different in the strong dissipation (Smoluchowski) limit. In the inverted region the rate exhibits stretched exponential decay as a function of the dissipation strength reflecting adiabatic suppression in the strong dissipation limit. The accuracy of the approach decreases with the increasing (decreasing) asymmetry of the crossing in the normal (inverted) region and breaks down in the activationless case. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A method to alter the inertial response of generic degrees of freedom is presented. A Hamiltonian acts on the inertial response of a set of independent configurational observables by the introduction of a kinetic bias. The method finds its natural application in reducing the spreading of arbitrary modes in a complex system. The resulting compressed spectrum allows a more efficient sampling of configurational space. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present potential energy surfaces for the He-N2H+ system adiabatically corrected for the zero-point motion along the intermolecular stretching vibrations v1=0 and v1=1. The potentials are extended to shorter He-N2H+ separations which makes them useful for scattering calculations. Close coupling calculations of the spinless S matrices for the rotational excitation of N2H+ by He are presented, and recoupling techniques to obtain collisional excitation cross sections between the N2H+ hyperfine levels are used. The propensity rules between hyperfine levels are investigated for the case where two nuclear spins are involved. It is found that the only well defined propensity rule is ΔF=ΔF1=Δj and that calculations are required in order to obtain the relative intensities of the two-spin hyperfine cross sections. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Ultrafast time-resolved infrared absorption studies of aqueous chlorine dioxide (OClO) photochemistry are reported. Following photoexcitation at 401 nm, the evolution in optical density at frequencies between 1000 to 1100 cm-1 is monitored to investigate vibrational energy deposition and relaxation along the asymmetric-stretch coordinate following the reformation of ground-state OClO via geminate recombination of the primary photofragments. The measured kinetics are compared to two proposed models for the vibrational-relaxation dynamics along the asymmetric-stretch coordinate. This comparison demonstrates that the perturbation model derived from molecular dynamics studies is capable of qualitatively reproducing the observed kinetics, where the collisional model employed in previous UV-pump, visible probe experiments demonstrates poor agreement with experiment. The ability of the perturbation model to reproduce the optical-density evolution observed in these studies demonstrates that for aqueous OClO, frequency dependence of the solvent–solute coupling is important in defining the level-dependent vibrational relaxation rates along the asymmetric-stretch coordinate. The absence of optical-density evolution corresponding to the population of higher vibrational levels (n>8) along the asymmetric-stretch coordinate suggests that following geminate recombination, energy is initially deposited into a local Cl–O stretch, with the relaxation of vibrational energy from this coordinate providing for delayed vibrational excitation of the asymmetric- and symmetric-stretch coordinates relative to geminate recombination, as previously observed. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We investigated dissociation of X-(H2O)n (X=Cl, I, n=13–31) by the impact onto a (La0.7Ce0.3)B6(100) surface at a collision energy Ecol of 1–5 eV per water molecule in a tandem time-of-flight mass spectrometer equipped with a translation-energy analyzer. The mechanism of the dissociation was elucidated on the basis of the measurements of the mass spectrum and the translational energies of the product anions, X-(H2O)m (m=0–4), scattered from the surface. It was concluded that (1) the parent cluster anion impacted on the surface undergoes dissociation on the surface under quasiequilibrium with its characteristic time varying with Ecol and n, and (2) the total collision energy introduced is partitioned preferentially to the translational motions of the products on the surface and to the rotational, the vibrational, and the lattice vibrational motions (surface) in this order. The quasiequilibrium model is applicable, even at the collision energy as low as 1 eV, because the translational modes are found to be statistically distributed while the other modes are not much populated by dynamical and energetics limitation. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Adsorption of H2, C2H2, C2H4, and CO onto a Si(100)-(2×1) surface has been treated theoretically using Si12n-3H8n+4 (n=1–4) clusters. The energy density analysis (EDA) proposed by Nakai has been adopted to examine surface-molecule interactions for different cluster sizes. EDA results for the largest model cluster Si45H36 have shown that the adsorption-induced energy density variation in Si atoms decays with distance from the adsorption site. Analysis of this decay, which can be carried out using the EDA technique, is important because it enables verification of the reliability of the model cluster used. In the cases of H2, C2H2, C2H4, and CO adsorption onto the Si(100)-(2×1) surface, it is found that at least a Si21H20 cluster is necessary to treat the surface-molecule interaction with chemical accuracy. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The observed macroscopic anisotropic properties such as the components of infrared (IR) absorbances of liquid crystals are expressed in terms of the order parameters of the long molecular axis, molecular, and phase biaxiality. The order parameters of the organo-siloxane tetrapode liquid crystal of zero dendritic order (G0) in its nematic and smectic phases have been determined using results of the polarized IR spectroscopic measurements on a planar homogenously and hometropic aligned cells. The spatial components of the absorbances for the vibrational bands (in the mesogenic unit, terminal chains, and spacer) have been measured and analyzed. For the laboratory reference system, the apparent orientational order parameter S of the mesogen unit shows a significant drop in the transition from the nematic to the smectic phase while the phase biaxiality order parameter P increases to almost 0.4 in the smectic phase. This result shows that the director is tilted out of the sample plane in the smectic phase. The molecular biaxiality parameter D is found to be positive both for the nematic and smectic phases. This suggests that the carbonyl dipoles are oriented close to the tilt plane. For the vibrational bands in the chains, low values of S and D indicative of their low orientational order are obtained. As a result of the interaction among the molecules in the tilted smectic phases, the transition dipoles show positive correlations for the transversal and negative for the longitudinal dipoles. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation and analysis based upon the many-body potential energy landscape (PEL) are employed to characterize single molecule reorientation and structural relaxation, and their interrelation, in deeply supercooled liquid CS2. The rotational mechanism changes from small-step Debye diffusion to sudden large angle reorientation (SLAR) as the temperature falls below the mode-coupling temperature Tc. The onset of SLAR is explained in terms of the PEL; it is an essential feature of low-T rotational dynamics, along with the related phenomena of dynamic heterogeneity and the bifurcation of slow and fast relaxation processes. A long trajectory in which the system is initially trapped in a low energy local minimum, and eventually escapes, is followed in detail, both on the PEL and in real space. During the trapped period, “return” dynamics occurs, always leading back to the trap. Structural relaxation is identified with irreversible escape to a new trap. These processes lead to weak and strong SLAR, respectively; strong SLAR is a clear signal of structural relaxation. Return dynamics involves small groups of two to four molecules, while a string-like structure composed of all the active groups participates in the escape. It is proposed that, rather than simple, nearly instantaneous, one-dimensional barrier crossings, relaxation involves activation of the system to the complex, multidimensional region on the borders of the basins of attraction of the minima for an extended period. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

An experimental method suitable for reproducible results has been used to investigate dewetting behavior of thin films of solvent-laden polymer. This solvent-driven dewetting enables one to change spreading coefficient by an order of magnitude that is not readily realizable in thermal dewetting and to study polar interactions that have not been fully exploited experimentally. While the film instability is similar to that found in thermal dewetting, the rim instability is quite different. Two different types of the rim instability have been found. With a polar solvent, the rim instability changes from one type to another with increasing film thickness whereas the unstable rim becomes stable for an apolar solvent. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We have carried out first principles plane wave density-functional theory calculations to study the adsorption of CO molecule on a clean and unreconstructed Cu (110) surface at 1/12 monolayer coverage and have investigated the subsequent oxidation by preadsorbed oxygen atoms. As found experimentally, the CO adsorbs perpendicular to the surface plane through the carbon atom; the top site was found to be the most favorable position for CO adsorption although the short-bridge site is only slightly less stable. Surprisingly, for a sparely oxidized surface with O atoms adsorbed in hollow sites the coadsorption energy is slightly negative for only the above two CO sites which have therefore been used as starting points to explore the energy surface of the oxidation reaction. We have confirmed the existence of bent CO2 surface intermediate as previously suggested from experimental studies. Using the nudged elastic band method, we have characterized a two step reaction which involves the formation of this intermediate. The results suggest that the rate determining step of the oxidation reaction is the formation of the intermediate and the energy barrier (200 meV) is close to although smaller than experimentally estimated values. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The energetics and dynamics of double proton transfer (DPT) is investigated theoretically for the Watson-Crick conformation of the guanine-cytosine (GC) base pair. Using semiempirical density functional theory the isolated and DNA-embedded GC pair is considered. Differences in the energetics and dynamics of DPT thus addresses the question of how relevant studies of isolated base pairs are for the understanding of processes occurring in DNA. Two-dimensional potential energy surfaces involving the transferring hydrogen atoms and the proton donors and acceptors are presented for both systems. The DPT reaction is accompanied by a contraction of the distance between the two bases with virtually identical energetic barriers being 18.8 and 18.7 kcal/mol for the isolated and DNA-embedded system, respectively. However, the transition state for DPT in the DNA-embedded GC pair is offset by 0.1 Å to larger N-H separation compared to the isolated GC pair. Using activated ab initio molecular dynamics, DPT is readily observed for the isolated base pair with a minimal amount of 21.4 kcal/mol of initial average kinetic energy along the DPT normal mode vector. On a time scale of ≈100 fs DPT has occurred and the excess energy is redistributed. For the DNA-embedded GC pair considerably more kinetic energy is required (30.0 kcal/mol) for DPT and the process is completed within one hydrogen vibration. The relevance of studies of isolated base pairs and base pair analogs in regard of reactions or properties involving DNA is discussed. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We introduce and apply a variant of a dynamic self-consistent field simulation in two dimensions to predict the structure of interfaces between a nematic and an amorphous polymer compatibilized by a diblock copolymer. First, we investigate the effect of the nematic order on the polymer polymer interface without compatibilizer. Then we include the compatibilizer and consider two interfacial setups previously used in experiments, i.e., the bilayer setup and the trilayer setup. In the bilayer setup the diblock copolymer is mixed into the amorphous homopolymer and migrates to the interface in the course of the simulation forming a layered structure. We compare the amount of copolymer at the interface for initial concentrations of the copolymer below and above the critical micelle concentration. In the trilayer setup the initial thickness of the diblock copolymer is varied. The resulting interfacial morphology evolves in the competition between the lamellar structure induced by the interface and a micellar structure, which is intrinsic to the copolymer. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Newly developed exchange-correlation functionals in density functional theory (DFT) have been applied to describe conjugation effects in organic molecules. The performance of the various approaches is assessed through the calculation of torsion energy profiles and their critical comparison with available experimental data. Our results indicate that the OPTX-B95 exchange-correlation functional as well as its corresponding hybrid versions perform better than the well-established BLYP or B3LYP schemes when dealing with π-conjugated molecules. In contrast, the recently introduced VSXC functional is not as reliable as other DFT methods for the systems examined here. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A Monte Carlo study is made of the mean-square radius of gyration 〈S2〉 for the freely rotating chain with such fictitious excluded-volume interactions that the Lennard-Jones 6-12 potentials at the Θ temperature act only between the fourth-through (3+Δ)th-neighbor beads (Δ>=1) along the chain. The behavior of the asymptotic value (/n)∞ of the ratio 〈S2〉/n as a function of the number n of bonds in the chain in the limit of n→∞ is examined as a function of Δ. It is shown that the approach of (/n)∞ to its value for the real unperturbed chain with Δ=∞ is so slow that the interactions between even up to about 100th-neighbor beads should be taken into account in order to reproduce nearly its dimension. The result implies that the unperturbed polymer chain dimension as experimentally observed at the Θ temperature depends not only on short-range interactions but also to a considerable extent on the long-range excluded-volume interactions, and that the asymptotic value C∞ of the characteristic ratio Cn for the rotational isomeric state model in the limit of n→∞, which is determined only by the very local conformational energy, cannot be directly compared with the corresponding experimental value. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The stability of closed shell bimetallic magic clusters MAu4 (M=Ti and Zr) is investigated theoretically through ab initio molecular orbital calculations. Both these clusters have tetrahedral structures and are found to be associated with large values of the ionization potential, HOMO-LUMO gap as well as the binding energies, which are characteristic of the magic clusters. However, the cluster–cluster interaction energy corresponding to a dimer formation is found to be unusually high (∼5–7 eV) in contradiction to the usual properties of a magic cluster and is attributed to a 3-center–2-electron M–Au–M type bridge bonding as well as aurophilic attraction. Gross geometrical features of the individual clusters are, however, mostly retained in the dimer, thus satisfying the basic requirements for the cluster-assembled materials. This work would have important implications in the design of novel cluster-based nanomaterials for various nanoscale applications.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A new method for calculating the indirect nuclear spin–spin coupling constant within the regular approximation to the exact relativistic Hamiltonian is presented. The method is completely analytic in the sense that it does not employ numeric integration for the evaluation of relativistic corrections to the molecular Hamiltonian. It can be applied at the level of conventional wave function theory or density functional theory. In the latter case, both pure and hybrid density functionals can be used for the calculation of the quasirelativistic spin–spin coupling constants. The new method is used in connection with the infinite-order regular approximation with modified metric (IORAmm) to calculate the spin–spin coupling constants for molecules containing heavy elements. The importance of including exact exchange into the density functional calculations is demonstrated. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution. ©2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Two-color photon echo peak shift spectroscopy was used to study electronic coupling in a phthalocyanine homodimer. Two optical parametric amplifiers were used to produce pulses to excite the split lower states of LuPc[sub 2][sup -]. The existence of a two-color peak shift indicates the existence of correlation between these two dipole-allowed states. The nature of this correlation is discussed based on theoretical predictions of the interactions between exciton and charge resonance states. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

According to the definition in the text, the correlation energy of 1s[sub C][sup 2] of carbon atoms, the primary and secondary C–H bonding electron pairs in some CH[sub 3], CH[sub 2] fragments and CH[sub 3](CH[sub 2])[sub m]CH[sub 3] (m=1–5) linear alkane molecules are calculated and analyzed. The transferability of the correlation energies of these electron pairs in the linear alkanes is investigated. The results indicate that the correlation energy of 1s[sub C][sup 2] is perfectly transferable in the respective methyl and methylene groups, while the correlation energies of the primary and secondary C–H bonding electron pairs are approximately transferable in methyl and methylene groups. The analysis of the results of group correlation energy shows that both of the correlation energies of methyl and methylene groups are transferable in these linear alkanes. The correlation energies of methylene group in CH[sub 3](CH[sub 2])[sub m]CH[sub 3] (m=1–5) molecules are slightly decreasing showing a converging trend to a “standard” methylene group in linear alkanes. The excellent fitting relationship between the total correlation energy and the number of methylene groups of the linear alkanes shows that the total correlation energy is a linear function of the number of methylene groups, which means that the total correlation energies of large linear alkanes can be reproduced and predicted by counting the numbers of methylene groups. In this way, total correlation energy of large linear alkane molecule can be approximately calculated using this simple group additive scheme with substantial saving in computational time. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this article we consider the electronic diabatic presentation of a two-state system with the aim of earning insight regarding the distribution of conical intersections in a given region. In this process we revealed explicit relationship between the diabatic potentials and the locations of conical intersections. The study is accompanied with numerical examples as worked out for a model and ab initio potential energy surfaces of the Na+H[sub 2] system. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The role of fluctuations in both the density functional theory (DFT) and the field theory (FT) of nanosystems is studied. It turns out that although fluctuations are rigorously incorporated into the general formalism of DFT, they are often omitted in the choice of an approximate free energy functional that must be constructed in order to solve the basic integral equation appearing in DFT. Aside from the analytical discussion, it is demonstrated, in connection with a particular system (fluid in a nanopore) that the effects of fluctuation are missing when one of the most common functionals for this system is used. The demonstration involves a comparison of the results of Monte Carlo simulation with the predictions of DFT when this free energy functional is used. The applicability of FT and DFT in the context of the theory of nucleation is also discussed. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces “the hydrogen bond interaction region” in which a new parameter k[sub lp,H](R[sub lp,H]) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom–atom interaction, i.e., oxygen–oxygen, hydrogen–hydrogen, oxygen–hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H[sub 2]O)[sub n] (n=2–6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]