Volume 134, Issue 1, 07 January 2011
Index of content:

Firstprinciples molecular dynamics simulations are used to investigate the chemical response of acetaldehyde molecules (MeCHO) to compression and decompression between (0001) surfaces of αalumina (Al_{2}O_{3}), with pressures reaching approximately 40 GPa. The results demonstrate that the MeCHO molecules are transformed into other chemical species through a range of chemical processes involving the formation of C–O and C–C bonds between MeCHO monomers as well as proton transfer. The mechanistic details of a representative set of the observed reactions are elucidated through analysis of maximally localized Wannier functions. Analysis of the changes in structure demonstrates that the main role of compression is to reduce the distances between MeCHO molecules to facilitate the formation of C–O bonds. Additional examination of the electronic structure demonstrates that the surface plays a role in facilitating proton transfer by both rendering hydrogen atoms in adsorbed MeCHO molecules more acidic and by acting as a proton acceptor. In addition, adsorption of the MeCHO molecules on the surface renders the sp^{2}carbon atoms in these molecules more electrophilic, which promotes the formation of C–C and C–O bonds. It is suggested that the reaction products may be beneficial in the context of wear inhibition. Comparison of the surface structure before compression and after decompression demonstrates that the aldehydes and reaction products are capable of inhibiting irreversible changes in the structure as long as there is at least a monolayer coverage of these species. As a whole, the study sheds light on the chemical behavior of the aldehydes in response to uniaxial compression in nanoscopic contacts that likely applies to other molecules containing carbonyl groups and other metal oxide surfaces.
 COMMUNICATIONS


Communication: Universal Markovian reduction of Brownian particle dynamics
View Description Hide DescriptionNonMarkovian processes can often be turned Markovian by enlarging the set of variables. Here we show, by an explicit construction, how this can be done for the dynamics of a Brownian particle obeying the generalized Langevin equation. Given an arbitrary bath spectral density , we introduce an orthogonal transformation of the bath variables into effective modes, leading stepwise to a semiinfinite chain with nearestneighbor interactions. The transformation is uniquely determined by and defines a sequence of residual spectral densities describing the interaction of the terminal chain mode, at each step, with the remaining bath. We derive a simple oneterm recurrence relation for this sequence and show that its limit is the quasiOhmic expression provided by the Rubin model of dissipation. Numerical calculations show that, irrespective of the details of , convergence is fast enough to be useful in practice for an effective Ohmic reduction of the dissipative dynamics.

Communication: Critical dynamics and nuclear relaxation in lipid bilayers
View Description Hide DescriptionMembrane composition fluctuations affect deuterium nuclear magnetic relaxation in lipid bilayers. The time dependence of the fluctuations depends on lipiddiffusion. Near a miscibilitycritical point this diffusion involves an advective hydrodynamic coupling to the aqueous phase. The corresponding diffusion coefficient depends on both the critical length and the fluctuation wavelength. We calculate the effects of these dynamics on transverse deuterium nuclear relaxation in the 0.1^{o}–10^{o} range above the critical temperature.

Communication: Heavy atom quantum diffraction by scattering from surfaces
View Description Hide DescriptionTypically one expects that when a heavy particle collides with a surface, the scatteredangular distribution will follow classical mechanics. The heavy mass usually assures that the coherence length of the incident particle in the direction of the propagation of the particle (the parallel direction) will be much shorter than the characteristic lattice length of the surface, thus leading to a classical description. Recent work on molecular interferometry has shown that extreme collimation of the beam creates a perpendicular coherence length which is sufficiently long so as to observe interference of very heavy species passing through a grating. Here we show, using quantum mechanical simulations, that the same effect will lead to quantum diffraction of heavy particles colliding with a surface. The effect is robust with respect to the incident energy, the angle of incidence, and the mass of the particle.

 ARTICLES


Theoretical Methods and Algorithms

Efficient numerical method for locating Feshbach resonances of ultracold molecules in external fields
View Description Hide DescriptionCollision properties of atoms and molecules in low temperature gases can be controlled by applying an external magnetic or electric field. The external field shifts the energy levels of the colliding particles, which gives rise to Feshbach resonances modifying the scattering cross sections. The resonances occur at particular magnitudes of the external field, where a bound state of the collision complex is degenerate with a scattering state. The positions of the resonances in the external field are usually identified by computing either the scattering cross sections or the bound states of the collision complex as functions of the external field magnitude. We propose a more efficient method for locating Feshbach resonances that requires neither of these computations. In particular, we show that the positions of Feshbach resonances can be identified by computing the logderivative of the total wave function in a classically allowed region as a function of the external field strength. This procedure is particularly useful for locating narrow Feshbach resonances that may be hard to identify with the other methods.

Generalized CCTDSCF and LCSA: The systemenergy representation
View Description Hide DescriptionTypical (sub)systembath quantum dynamical problems are often investigated by means of (approximate) reduced equations of motion. Wavepacket approaches to the dynamics of the whole system have gained momentum in recent years and there is hope that properly designed approximations to the wavefunction will allow one to correctly describe the subsystem evolution. The continuousconfiguration timedependent selfconsistent field (CCTDSCF) and local coherentstate approximation (LCSA) methods, for instance, use a simple Hartree product of bath singleparticlefunctions for each discrete variable representation (DVR) state introduced in the Hilbert space of the subsystem. Here we focus on the above two methods and replace the DVR states with the eigenstates of the subsystem Hamiltonian, i.e., we adopt an energylocal representation for the subsystem. We find that stable and semiquantitative results are obtained for a number of dissipative problems, at the same (small) computational cost of the original methods. Furthermore, we find that both methods give very similar results, thus suggesting that coherentstates are well suited to describe (local) bath states. As a whole, present results highlight the importance of the system basisset in the selectedmulticonfiguration expansion of the wavefunction. They suggest that accurate and yet computationally cheap methods may be simply obtained from CCTDSCF/LCSA by letting the subsystem states be variationally optimized.

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances
View Description Hide DescriptionMultiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice, the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.

Optimization of Monte Carlo trial moves for protein simulations
View Description Hide DescriptionClosed rigidbody rotations of residue segments under bondangle restraints are simple and effective Monte Carlo moves for searching the conformational space of proteins. The efficiency of these moves is examined here as a function of the number of moving residues and the magnitude of their displacement. It is found that the efficiency of folding and equilibrium simulations can be significantly improved by tailoring the distribution of the number of moving residues to the simulation temperature. In general, simulations exploring compact conformations are more efficient when the average number of moving residues is smaller. It is also demonstrated that the moves do not require additional restrictions on the magnitude of the rotation displacements and perform much better than other rotation moves that do not restrict the bond angles a priori. As an example, these results are applied to the replica exchange method. By assigning distributions that generate a smaller number of moving residues to lower temperature replicas, the simulation times are decreased as long as the higher temperature replicas are effective.

Flattening a puckered cyclohexasilane ring by suppression of the pseudoJahn–Teller effect
View Description Hide DescriptionWe report the experimental and theoretical characterization of neutral Si_{6}X_{12} (X = Cl, Br) molecules that contain D _{ 3d } distorted sixmember siliconrings due to a pseudoJahn–Teller (PJT) effect. Calculations show that filling the intervenient molecular orbitals with electron pairs of adduct suppresses the PJT effect in Si_{6}X_{12}, with the Si_{6}ring becoming planar (D _{ 6h }) upon complex formation. The stabilizing role of electrostatic and covalent interactions between positively charged silicon atoms and chlorine atoms of the subject [Si_{6}Cl_{14}]^{2} dianionic complexes is discussed. The reaction of Si_{6}Cl_{12} with a Lewis base (e.g., Cl^{}) to give planar [Si_{6}Cl_{14}]^{2} dianionic complexes presents an experimental proof that suppression of the PJT effect is an effective strategy in restoring high Si_{6}ring symmetry. Additionally, the proposed pathway for the PJT suppression has been proved by the synthesis and characterization of novel compounds containing planar Si_{6}ring, namely, [^{n}Bu_{4}N]_{2}[Si_{6}Cl_{12}I_{2}], [^{n}Bu_{4}N]_{2}[Si_{6}Br_{14}], and [^{n}Bu_{4}N]_{2}[Si_{6}Br_{12}I_{2}]. This work represents the first demonstration that PJT effect suppression is useful in the rational design of materials with novel properties.

A partialpropensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays
View Description Hide DescriptionSeveral realworld systems, such as gene expression networks in biological cells, contain coupled chemical reactions with a time delay between reaction initiation and completion. The nonMarkovian kinetics of such reactionnetworks can be exactly simulated using the delay stochastic simulation algorithm (dSSA). The computational cost of dSSA scales with the total number of reactions in the network. We reduce this cost to scale at most with the smaller number of species by using the concept of partial reaction propensities. The resulting delay partialpropensity direct method (dPDM) is an exact dSSA formulation for wellstirred systems of coupled chemical reactions with delays. We detail dPDM and present a theoretical analysis of its computational cost. Furthermore, we demonstrate the implications of the theoretical cost analysis in two prototypical benchmark applications. The dPDM formulation is shown to be particularly efficient for strongly coupled reactionnetworks, where the number of reactions is much larger than the number of species.

Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Fulldimensional quantum dynamics calculations of H_{2}–H_{2} collisions
View Description Hide DescriptionWe report quantum dynamics calculations of rotational and vibrational energy transfer in collisions between two paraH molecules over collisionenergies spanning from the ultracold limit to thermal energies. Results obtained using a recent fulldimensional –Hpotential energy surface (PES) developed by Hinde [J. Chem. Phys. 128, 154308 (2008)] are compared with those derived from the Boothroyd, Martin, Keogh, and Peterson (BMKP) PES [J. Chem. Phys. 116, 666 (2002)]. For vibrational relaxation of by collisions with H as well as rotational excitations in collisions between ground state molecules, the PES of Hinde is found to yield results in better agreement with available experimental data. A highly efficient nearresonant energy transfer mechanism that conserves internal rotational angular momentum and was identified in our previous study of the system [Phys. Rev. A 77, 030704(R) (2008)] using the BMKP PES is also found to be reproduced by the Hinde PES, demonstrating that the process is largely insensitive to the details of the PES. In the absence of the nearresonance mechanism, vibrational relaxation is driven by the anisotropy of the potential energy surface. Based on a comparison of results obtained using the Hinde and BMKP PESs with available experimental data, it appears that the Hinde PES provides a more accurate description of rotational and vibrational transitions in –Hcollisions, at least for vibrational quantum numbers v ⩽ 1.

Infrared spectroscopy of Sc^{+}(H_{2}O) and Sc^{2+}(H_{2}O) via argon complex predissociation: The charge dependence of cation hydration
View Description Hide DescriptionSingly and doubly charged scandium–water ionmolecule complexes are produced in a supersonic molecular beam by laser vaporization. These ions are mass analyzed and size selected in a specially designed reflectron timeofflight spectrometer. To probe their structure, vibrational spectroscopy is measured for these complexes in the O–H stretching region using infrared laser photodissociation and the method of rare gas atom predissociation, also known as “tagging.” The O–H stretches in these systems are shifted to lower frequency than those for the free water molecule, and the intensity of the symmetric stretch band is strongly enhanced relative to the asymmetric stretch. These effects are more prominent for the doubly charged ions. Partially resolved rotational structure for the Sc^{+}(H_{2}O)Ar complex shows that the H–O–H bond angle is larger than it is in the free water molecule. Fragmentation and spectral patterns indicate that the coordination of the Sc^{2+} ion is filled with six ligands (one water and five argons).

Optical Stark spectroscopy of the (000)←(000) system of copper hydroxide
View Description Hide DescriptionThe (000)←(000) band system of a cold beam of CuOH has been studied fieldfree and in the presence of a static electric field. The Stark tuning of the lowJ levels of the (000) state were analyzed to give a value of 3.968(32) D for the acomponent of the permanent electric dipole moment,μ _{ a }. An upper limit of 0.3 D for μ _{ a }() is established from the lack of observable Stark tuning for the lowJ levels of the (000) state. The experimental value for μ _{ a }() is compared to theoretical predictions and other Cucontaining molecules. A molecular orbital correlation diagram is used to rationalize the large change in μ _{ a } upon excitation. The electronegativity of OH was determined to be 2.81 from a comparison of the determined μ _{ a } with the experimental μ values for CuF, CuO, and CuS.

The decay mechanism of photoexcited guanine − A nonadiabatic dynamics study
View Description Hide DescriptionAb initiosurface hopping dynamics calculations were performed for the biologically relevant tautomer of guanine in gas phase excited into the first ππ* state. The results show that the complete population of UVexcited molecules returns to the ground state following an exponential decay within ∼220 fs. This value is in good agreement with the experimentally obtained decay times of 148 and 360 fs. No fraction of the population remains trapped in the excited states. The internal conversion occurs in the ππ* state at two related types of conical intersections strongly puckered at the C2 atom. Only a small population of about 5% following an alternative pathway via a nπ* state was found in the dynamics.

Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study
View Description Hide DescriptionThe solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical/molecular mechanical (QM/MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM/MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorptionspectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorptionspectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorptionspectrum. In the solvent effect, the variation in C–C bond length has the largest contribution on the absorptionspectrum from the solute molecule. For the solvent effect on the absorptionspectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.

Excess entropy scaling of transport properties in networkforming ionic melts (SiO and BeF)
View Description Hide DescriptionThe regime of validity of Rosenfeld excess entropy scaling of diffusivity and viscosity is examined for two tetrahedral, networkforming ionic melts (BeF and SiO) using molecular dynamics simulations. With decrease in temperature, onset of local caging behavior in the diffusionaldynamics is shown to be accompanied by a significant increase in the effect of threebody and higherorder particle correlations on the excess entropy, diffusivity, ionic conductivity, and entropytransport relationships. The signature of caging effects on the Rosenfeld entropy scaling of transport properties is a distinctly steeper dependence of the logarithm of the diffusivity on the excess entropy in ionic melts. This is shown to be true also for a binary LennardJones glassformer, based on available results in the literature. Our results suggest that the onset of a landscapeinfluenced regime in the dynamics is correlated with this characteristic departure from Rosenfeld scaling. The breakdown of the Nernst–Einstein relation in the ionic melts can also be correlated with the emerging cooperative dynamics.

Reentrant kinetic arrest and elasticity of concentrated suspensions of spherical and nonspherical repulsive and attractive colloids
View Description Hide DescriptionWe have designed and studied a new experimental colloidal system to probe how the weak shape anisotropy of uniaxial particles and variable repulsive (Coulombic) and attractive (van der Waals) forces influence slow dynamics, shear elasticity, and kinetic vitrification in dense suspensions. The introduction of shape anisotropy dramatically delays kinetic vitrification and reduces the shear elastic modulus of colloidal diatomics relative to their chemically identical spherical analogs. Tuning the interparticle interaction from repulsive, to nearly hard, to attractive by increasing suspension ionic strength reveals a nonmonotonic reentrant dynamical phase behavior (glass–fluid–gel) and a rich variation of the shear modulus. The experimental results are quantitatively confronted with recent predictions of ideal mode coupling and activated barrier hopping theories of kinetic arrest and elasticity, and good agreement is generally found with a couple of exceptions. The systems created may have interesting materials science applications such as flowable ultrahigh volume fraction suspensions, or responsive fluids that can be reversibly switched between a flowing liquid and a solid nonequilibrium state based on in situ modification of suspension ionic strength.

Resonant Raman spectra of diindenoperylene thin films
View Description Hide DescriptionResonant and preresonant Raman spectra obtained on diindenoperylene (DIP) thin films are interpreted with calculations of the deformation of a relaxed excited molecule with density functional theory(DFT). The comparison of excited state geometries based on timedependent DFT or on a constrained DFT scheme with observed absorption spectra of dissolved DIP reveals that the deformation pattern deduced from constrained DFT is more reliable. Most observed Raman peaks can be assigned to calculated symmetric breathing modes of DIP or their combinations. As the position of one of the laser lines used falls into a highly structured absorption band, we have carefully analyzed the Raman excitation profile arising from the frequency dependence of the dielectric tensor. This procedure gives Raman cross sections in good agreement with the observed relative intensities, both in the fully resonant and in the preresonant case.

The structure of molten AgCl, AgI and their eutectic mixture as studied by molecular dynamics simulations of polarizable ion model potentials
View Description Hide DescriptionThe structure of molten AgCl, AgI, and their eutectic mixture Ag(Cl_{0.43}I_{0.57}) is studied by means of molecular dynamics simulations of polarizable ion model potentials. The corresponding static coherent structure factors reproduce quite well the available neutron scattering data. The qualitative behavior of the simulated partial structure factors and radial distribution functions for molten AgCl and AgI is that predicted by the reverse Monte Carlo modeling of the experimental data. The AgI results are also in qualitative agreement with those calculated from ab initiomolecular dynamics.

A fundamental measure theory for the sticky hard sphere fluid
View Description Hide DescriptionWe construct a density functional theory(DFT) for the sticky hard sphere (SHS) fluid which, like Rosenfeld's fundamental measure theory (FMT) for the hard sphere fluid [Y. Rosenfeld, Phys. Rev. Lett. 63, 980 (1989)], is based on a set of weighted densities and an exact result from scaled particle theory (SPT). It is demonstrated that the excess free energy density of the inhomogeneous SHS fluid is uniquely defined when (a) it is solely a function of the weighted densities from Kierlik and Rosinberg's version of FMT [E. Kierlik and M. L. Rosinberg, Phys. Rev. A 42, 3382 (1990)], (b) it satisfies the SPT differential equation, and (c) it yields any given direct correlation function (DCF) from the class of generalized Percus–Yevick closures introduced by Gazzillo and Giacometti [J. Chem. Phys. 120, 4742 (2004)]. The resulting DFT is shown to be in very good agreement with simulation data. In particular, this FMT yields the correct contact value of the density profiles with no adjustable parameters. Rather than requiring higher order DCFs, such as perturbative DFTs, our SHS FMT produces them. Interestingly, although equivalent to Kierlik and Rosinberg's FMT in the case of hard spheres, the set of weighted densities used for Rosenfeld's original FMT is insufficient for constructing a DFT which yields the SHS DCF.

Putting the squeeze on cavities in liquids: Quantifying pressure effects on solvation using simulations and scaledparticle theory
View Description Hide DescriptionExtensive molecular simulations of the LennardJones fluid are performed to examine the response of the excess chemical potential of cavitylike solutes to applied pressure.Solutes as large as ten times the solvent diameter are considered. The simulations are analyzed using the revised scaledparticle theory developed by Ashbaugh and Pratt to evaluate the thermodynamics of cavity solvation and curvature dependent interfacial properties well into the compressed liquid portion of the solvent phase diagram. The revised theory provides a quantitatively accurate description of the solvent–solute contact correlation function for all solutes and state points considered. The main structural effect of increasing pressure is to push the solvent molecules up against the solutesurfaces, counteracting the dewetting that is observed at lower pressures along the solvent saturation curve. Decomposing the excess chemical potential of cavities into volume and surfacearea contributions shows that pressure differentially affects the interfacial free energies of molecular versus macroscopic solutes. The interfacial free energy of surfaces of molecular dimension monotonically decreases with applied pressure, while that of surfaces larger than a small cluster of solvent molecules exhibit a maximum with increasing pressure, which may play a role in pressureinduced disaggregation of molecular assemblies. Moreover, since the pressure dependence of the interfacial free energy is thermodynamically linked to the excess adsorption of solvent on the solutesurface, the former is potentially a measurable macroscopic indicator of microscopic wetting/dewetting phenomena, implicated in hydrophobic interactions between macroscopic hydrophobic particles. Finally, some inferences about pressuredependent solvation processes in water are made by using the revised theory to analyze previously published simulation data.
