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7 Jan 2011

Volume 134, Issue 1, Articles (01xxxx)

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J. Chem. Phys. 134, 014702 (2011); http://dx.doi.org/10.1063/1.3528980 (14 pages)

Sarah M. Haw and Nicholas J. Mosey
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Communication: Universal Markovian reduction of Brownian particle dynamics

R. Martinazzo, B. Vacchini, K. H. Hughes, and I. Burghardt

J. Chem. Phys. 134, 011101 (2011); http://dx.doi.org/10.1063/1.3532408 (4 pages)

Online Publication Date: 3 January 2011

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Non-Markovian 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 J0, we introduce an orthogonal transformation of the bath variables into effective modes, leading stepwise to a semi-infinite chain with nearest-neighbor interactions. The transformation is uniquely determined by J0 and defines a sequence math of residual spectral densities describing the interaction of the terminal chain mode, at each step, with the remaining bath. We derive a simple one-term recurrence relation for this sequence and show that its limit is the quasi-Ohmic expression provided by the Rubin model of dissipation. Numerical calculations show that, irrespective of the details of J0, convergence is fast enough to be useful in practice for an effective Ohmic reduction of the dissipative dynamics.
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05.40.Jc Brownian motion
02.30.Hq Ordinary differential equations
02.50.Ga Markov processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
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Communication: Critical dynamics and nuclear relaxation in lipid bilayers

Harden McConnell

J. Chem. Phys. 134, 011102 (2011); http://dx.doi.org/10.1063/1.3529955 (4 pages)

Online Publication Date: 5 January 2011

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Membrane composition fluctuations affect deuterium nuclear magnetic relaxation in lipid bilayers. The time dependence of the fluctuations depends on lipid diffusion. Near a miscibility critical 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 0.1o–10o range above the critical temperature.
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87.16.dj Dynamics and fluctuations
87.15.hj Transport dynamics
87.15.M- Spectra of biomolecules
87.14.Cc Lipids
82.56.Pp NMR of biomolecules
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Communication: Heavy atom quantum diffraction by scattering from surfaces

Jeremy M. Moix and Eli Pollak

J. Chem. Phys. 134, 011103 (2011); http://dx.doi.org/10.1063/1.3528120 (4 pages)

Online Publication Date: 6 January 2011

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Typically one expects that when a heavy particle collides with a surface, the scattered angular 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.
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34.35.+a Interactions of atoms and molecules with surfaces
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
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back to top Theoretical Methods and Algorithms

Efficient numerical method for locating Feshbach resonances of ultracold molecules in external fields

Yury V. Suleimanov and Roman V. Krems

J. Chem. Phys. 134, 014101 (2011); http://dx.doi.org/10.1063/1.3512627 (5 pages)

Online Publication Date: 4 January 2011

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Collision 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 log-derivative 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.
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31.50.Df Potential energy surfaces for excited electronic states
34.50.Cx Elastic; ultracold collisions

Generalized CC-TDSCF and LCSA: The system-energy representation

Sergio López-López, Mathias Nest, and Rocco Martinazzo

J. Chem. Phys. 134, 014102 (2011); http://dx.doi.org/10.1063/1.3518418 (8 pages)

Online Publication Date: 5 January 2011

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Typical (sub)system-bath 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 continuous-configuration time-dependent self-consistent field (CC-TDSCF) and local coherent-state approximation (LCSA) methods, for instance, use a simple Hartree product of bath single-particle-functions 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 energy-local 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 coherent-states are well suited to describe (local) bath states. As a whole, present results highlight the importance of the system basis-set in the selected-multiconfiguration expansion of the wavefunction. They suggest that accurate and yet computationally cheap methods may be simply obtained from CC-TDSCF/LCSA by letting the subsystem states be variationally optimized.
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31.15.xr Self-consistent-field methods

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

Joseph A. Morrone, Thomas E. Markland, Michele Ceriotti, and B. J. Berne

J. Chem. Phys. 134, 014103 (2011); http://dx.doi.org/10.1063/1.3518369 (11 pages)

Online Publication Date: 7 January 2011

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Multiple 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.
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61.20.Ja Computer simulation of liquid structure
05.40.Ca Noise
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Optimization of Monte Carlo trial moves for protein simulations

Marcos R. Betancourt

J. Chem. Phys. 134, 014104 (2011); http://dx.doi.org/10.1063/1.3515960 (13 pages)

Online Publication Date: 7 January 2011

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Closed rigid-body rotations of residue segments under bond-angle 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.
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87.15.ak Monte Carlo simulations
36.20.Hb Configuration (bonds, dimensions)
36.20.Ey Conformation (statistics and dynamics)
87.14.E- Proteins
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.H- Dynamics of biomolecules
02.60.Pn Numerical optimization

Flattening a puckered cyclohexasilane ring by suppression of the pseudo-Jahn–Teller effect

Konstantin Pokhodnya, Christopher Olson, Xuliang Dai, Douglas L. Schulz, Philip Boudjouk, Alina P. Sergeeva, and Alexander I. Boldyrev

J. Chem. Phys. 134, 014105 (2011); http://dx.doi.org/10.1063/1.3516179 (5 pages)

Online Publication Date: 7 January 2011

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We report the experimental and theoretical characterization of neutral Si6X12 (X = Cl, Br) molecules that contain D3d distorted six-member silicon rings due to a pseudo-Jahn–Teller (PJT) effect. Calculations show that filling the intervenient molecular orbitals with electron pairs of adduct suppresses the PJT effect in Si6X12, with the Si6 ring becoming planar (D6h) upon complex formation. The stabilizing role of electrostatic and covalent interactions between positively charged silicon atoms and chlorine atoms of the subject [Si6Cl14]2- dianionic complexes is discussed. The reaction of Si6Cl12 with a Lewis base (e.g., Cl-) to give planar [Si6Cl14]2- dianionic complexes presents an experimental proof that suppression of the PJT effect is an effective strategy in restoring high Si6 ring symmetry. Additionally, the proposed pathway for the PJT suppression has been proved by the synthesis and characterization of novel compounds containing planar Si6 ring, namely, [nBu4N]2[Si6Cl12I2], [nBu4N]2[Si6Br14], and [nBu4N]2[Si6Br12I2]. This work represents the first demonstration that PJT effect suppression is useful in the rational design of materials with novel properties.
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31.30.-i Corrections to electronic structure
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)

A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays

Rajesh Ramaswamy and Ivo F. Sbalzarini

J. Chem. Phys. 134, 014106 (2011); http://dx.doi.org/10.1063/1.3521496 (8 pages) | Cited 1 time

Online Publication Date: 7 January 2011

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Several real-world systems, such as gene expression networks in biological cells, contain coupled chemical reactions with a time delay between reaction initiation and completion. The non-Markovian kinetics of such reaction networks 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 partial-propensity direct method (dPDM) is an exact dSSA formulation for well-stirred 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 reaction networks, where the number of reactions is much larger than the number of species.
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87.15.R- Reactions and kinetics
82.39.Rt Reactions in complex biological systems
87.16.-b Subcellular structure and processes
87.10.Mn Stochastic modeling
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Full-dimensional quantum dynamics calculations of H2–H2 collisions

N. Balakrishnan, G. Quéméner, R. C. Forrey, R. J. Hinde, and P. C. Stancil

J. Chem. Phys. 134, 014301 (2011); http://dx.doi.org/10.1063/1.3511699 (9 pages) | Cited 3 times

Online Publication Date: 3 January 2011

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We report quantum dynamics calculations of rotational and vibrational energy transfer in collisions between two para-H2 molecules over collision energies spanning from the ultracold limit to thermal energies. Results obtained using a recent full-dimensional H2–H2 potential 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 H2(v = 1,j = 0) by collisions with H2(v = 0,j = 0) as well as rotational excitations in collisions between ground state H2 molecules, the PES of Hinde is found to yield results in better agreement with available experimental data. A highly efficient near-resonant energy transfer mechanism that conserves internal rotational angular momentum and was identified in our previous study of the H2–H2 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 near-resonance 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 H2–H2 collisions, at least for vibrational quantum numbers v ⩽ 1.
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34.50.Ez Rotational and vibrational energy transfer
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
33.15.Mt Rotation, vibration, and vibration-rotation constants

Infrared spectroscopy of Sc+(H2O) and Sc2+(H2O) via argon complex predissociation: The charge dependence of cation hydration

P. D. Carnegie, B. Bandyopadhyay, and M. A. Duncan

J. Chem. Phys. 134, 014302 (2011); http://dx.doi.org/10.1063/1.3515425 (9 pages) | Cited 2 times

Online Publication Date: 3 January 2011

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Singly and doubly charged scandium–water ion-molecule complexes are produced in a supersonic molecular beam by laser vaporization. These ions are mass analyzed and size selected in a specially designed reflectron time-of-flight 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+(H2O)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 Sc2+ ion is filled with six ligands (one water and five argons).
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33.80.Gj Diffuse spectra; predissociation, photodissociation
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Dj Interatomic distances and angles
33.20.Ea Infrared spectra

Optical Stark spectroscopy of the math1A′′(000)←math1A′(000) system of copper hydroxide

Fang Wang and Timothy C. Steimle

J. Chem. Phys. 134, 014303 (2011); http://dx.doi.org/10.1063/1.3517057 (7 pages) | Cited 2 times

Online Publication Date: 7 January 2011

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The math1A′′(000)←math1A′(000) band system of a cold beam of CuOH has been studied field-free and in the presence of a static electric field. The Stark tuning of the low-J levels of the math1A′(000) state were analyzed to give a value of 3.968(32) D for the a-component of the permanent electric dipole moment, μa. An upper limit of 0.3 D for μa(math1A′′) is established from the lack of observable Stark tuning for the low-J levels of the math1A′′(000) state. The experimental value for μa(math1A′) is compared to theoretical predictions and other Cu-containing molecules. A molecular orbital correlation diagram is used to rationalize the large change in μa upon excitation. The electronegativity of OH was determined to be 2.81 from a comparison of the determined μa with the experimental μ values for CuF, CuO, and CuS.
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33.57.+c Magneto-optical and electro-optical spectra and effects
31.50.Df Potential energy surfaces for excited electronic states
32.30.Jc Visible and ultraviolet spectra
33.20.Lg Ultraviolet spectra
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

The decay mechanism of photoexcited guanine − A nonadiabatic dynamics study

Mario Barbatti, Jaroslaw J. Szymczak, Adélia J. A. Aquino, Dana Nachtigallová, and Hans Lischka

J. Chem. Phys. 134, 014304 (2011); http://dx.doi.org/10.1063/1.3521498 (5 pages)

Online Publication Date: 7 January 2011

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Ab initio surface 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 UV-excited 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.
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87.15.M- Spectra of biomolecules
87.15.ap Molecular dynamics simulation
36.20.Ey Conformation (statistics and dynamics)
87.15.R- Reactions and kinetics
87.15.H- Dynamics of biomolecules
31.15.ag Excitation energies and lifetimes; oscillator strengths
back to top 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

Tetsuya Sakata, Yukio Kawashima, and Haruyuki Nakano

J. Chem. Phys. 134, 014501 (2011); http://dx.doi.org/10.1063/1.3506616 (11 pages)

Online Publication Date: 3 January 2011

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The 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 absorption spectrum 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 absorption spectrum, 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 absorption spectrum. In the solvent effect, the variation in C–C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.
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31.70.Dk Environmental and solvent effects
33.15.Dj Interatomic distances and angles
31.15.xv Molecular dynamics and other numerical methods
03.65.-w Quantum mechanics
31.15.xp Perturbation theory
33.70.Jg Line and band widths, shapes, and shifts

Excess entropy scaling of transport properties in network-forming ionic melts (SiO2 and BeF2)

Manish Agarwal, Murari Singh, B. Shadrack Jabes, and Charusita Chakravarty

J. Chem. Phys. 134, 014502 (2011); http://dx.doi.org/10.1063/1.3521488 (7 pages) | Cited 3 times

Online Publication Date: 3 January 2011

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The regime of validity of Rosenfeld excess entropy scaling of diffusivity and viscosity is examined for two tetrahedral, network-forming ionic melts (BeF2 and SiO2) using molecular dynamics simulations. With decrease in temperature, onset of local caging behavior in the diffusional dynamics is shown to be accompanied by a significant increase in the effect of three-body and higher-order particle correlations on the excess entropy, diffusivity, ionic conductivity, and entropy-transport 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 Lennard-Jones glassformer, based on available results in the literature. Our results suggest that the onset of a landscape-influenced 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.
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66.10.C- Diffusion and thermal diffusion
66.10.Ed Ionic conduction
66.20.Cy Theory and modeling of viscosity and rheological properties, including computer simulation
66.20.Ej Studies of viscosity and rheological properties of specific liquids
61.20.Ja Computer simulation of liquid structure
65.20.-w Thermal properties of liquids

Re-entrant kinetic arrest and elasticity of concentrated suspensions of spherical and nonspherical repulsive and attractive colloids

Ryan C. Kramb, Rui Zhang, Kenneth S. Schweizer, and Charles F. Zukoski

J. Chem. Phys. 134, 014503 (2011); http://dx.doi.org/10.1063/1.3509393 (11 pages) | Cited 3 times

Online Publication Date: 4 January 2011

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We 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 re-entrant 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.
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82.70.Kj Emulsions and suspensions
81.40.Jj Elasticity and anelasticity, stress-strain relations
62.20.de Elastic moduli

Resonant Raman spectra of diindenoperylene thin films

R. Scholz, L. Gisslén, B.-E. Schuster, M. B. Casu, T. Chassé, U. Heinemeyer, and F. Schreiber

J. Chem. Phys. 134, 014504 (2011); http://dx.doi.org/10.1063/1.3514709 (11 pages)

Online Publication Date: 4 January 2011

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Resonant 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 time-dependent 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 Ag-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.
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78.30.Jw Organic compounds, polymers
68.55.-a Thin film structure and morphology
78.66.Qn Polymers; organic compounds
81.40.Lm Deformation, plasticity, and creep
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
78.20.Ci Optical constants (including refractive index, complex dielectric constant, absorption, reflection and transmission coefficients, emissivity)

The structure of molten AgCl, AgI and their eutectic mixture as studied by molecular dynamics simulations of polarizable ion model potentials

Olga Alcaraz, Vicente Bitrián, and Joaquim Trullàs

J. Chem. Phys. 134, 014505 (2011); http://dx.doi.org/10.1063/1.3506867 (9 pages)

Online Publication Date: 5 January 2011

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The structure of molten AgCl, AgI, and their eutectic mixture Ag(Cl0.43I0.57) 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 initio molecular dynamics.
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61.20.Ja Computer simulation of liquid structure
61.25.-f Studies of specific liquid structures

A fundamental measure theory for the sticky hard sphere fluid

Hendrik Hansen-Goos and J. S. Wettlaufer

J. Chem. Phys. 134, 014506 (2011); http://dx.doi.org/10.1063/1.3528226 (8 pages)

Online Publication Date: 6 January 2011

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We 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 Φ SHS 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.
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65.20.De General theory of thermodynamic properties of liquids, including computer simulation

Putting the squeeze on cavities in liquids: Quantifying pressure effects on solvation using simulations and scaled-particle theory

Henry S. Ashbaugh and Thomas M. Truskett

J. Chem. Phys. 134, 014507 (2011); http://dx.doi.org/10.1063/1.3510522 (10 pages) | Cited 1 time

Online Publication Date: 6 January 2011

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Extensive molecular simulations of the Lennard-Jones 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 scaled-particle 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 solute surfaces, counteracting the dewetting that is observed at lower pressures along the solvent saturation curve. Decomposing the excess chemical potential of cavities into volume and surface-area 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 pressure-induced 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 solute surface, 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 pressure-dependent solvation processes in water are made by using the revised theory to analyze previously published simulation data.
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61.20.Ja Computer simulation of liquid structure
61.25.Em Molecular liquids
65.20.-w Thermal properties of liquids
68.08.Bc Wetting

Study of dielectric relaxations of anhydrous trehalose and maltose glasses

Hyun-Joung Kwon, Jeong-Ah Seo, Hyung Kook Kim, and Yoon-Hwae Hwang

J. Chem. Phys. 134, 014508 (2011); http://dx.doi.org/10.1063/1.3517217 (6 pages) | Cited 1 time

Online Publication Date: 7 January 2011

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We investigated the frequency dependent dielectric relaxation behaviors of anhydrous trehalose and maltose glasses in the temperature range which covers a supercooled and glassy states. In addition to the α-, Johari-Goldstein (JG) β-, and γ-relaxations in a typical glass forming system, we observed an extra relaxation process between JG β- and γ-relaxations in the dielectric loss spectra. We found that the unknown extra relaxation is a unique property of disaccharide which might originate from the intramolecular motion of flexible glycosidic bond. We also found that the temperature dependence of the JG β-relaxation time changes at 0.95Tg and it might be universal.
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77.22.Gm Dielectric loss and relaxation
61.43.Fs Glasses

Experimental and theoretical study of two-photon absorption in nitrofuran derivatives: Promising compounds for photochemotherapy

L. De Boni, D. S. Correa, D. L. Silva, P. J. Gonçalves, S. C. Zilio, G. G. Parra, I. E. Borissevitch, S. Canuto, and C. R. Mendonca

J. Chem. Phys. 134, 014509 (2011); http://dx.doi.org/10.1063/1.3514911 (5 pages) | Cited 1 time

Online Publication Date: 7 January 2011

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We report experimental and theoretical studies of the two-photon absorption spectrum of two nitrofuran derivatives: nitrofurantoine, (1-(5-nitro-2-furfurilideneamine)-hidantoine) and quinifuryl, 2-(5′-nitro-2′-furanyl)ethenyl-4-{N-[4′-(N,N-diethylamino)-1′-methylbutyl]carbamoyl} quinoline. Both molecules are representative of a family of 5-nitrofuran-ethenyl-quinoline drugs that have been demonstrated to display high toxicity to various species of transformed cells in the dark. We determine the two-photon absorption cross-section for both compounds, from 560 to 880 nm, which present peak values of 64 GM for quinifuryl and 20 GM for nitrofurantoine (1 GM = 1×10−50cm4.s.photon−1). Besides, theoretical calculations employing the linear and quadratic response functions were carried out at the density functional theory level to aid the interpretations of the experimental results. The theoretical results yielded oscillator strengths, two-photon transition probabilities, and transition energies, which are in good agreement with the experimental data. A higher number of allowed electronic transitions was identified for quinifuryl in comparison to nitrofurantoine by the theoretical calculations. Due to the planar structure of both compounds, the differences in the two-photon absorption cross-section values are a consequence of their distinct conjugation lengths.
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33.80.-b Photon interactions with molecules
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
31.15.E- Density-functional theory

The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics

Shenshen Wang, Tongye Shen, and Peter G. Wolynes

J. Chem. Phys. 134, 014510 (2011); http://dx.doi.org/10.1063/1.3518450 (16 pages) | Cited 2 times

Online Publication Date: 7 January 2011

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The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model of cytoskeletal structure treating it as an amorphous network of hard centers rigidly cross-linked by nonlinear elastic strings, neglecting the effects of motorization. Using simulations along with a self-consistent phonon method, we show that this minimal model exhibits diverse thermodynamically stable mechanical phases that depend on excluded volume, cross-link concentration, filament length, and stiffness. Within the framework set by the free energy functional formulation and making use of the random first order transition theory of structural glasses, we further estimate the characteristic densities for a kinetic glass transition to occur in this model system. Network connectivity strongly modulates the transition boundaries between various equilibrium phases, as well as the kinetic glass transition density.
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87.15.La Mechanical properties
87.80.-y Biophysical techniques (research methods)
87.85.jc Electrical, thermal, and mechanical properties of biological matter

Ions in solutions: Determining their polarizabilities from first-principles

John J. Molina, Sébastien Lectez, Sami Tazi, Mathieu Salanne, Jean-François Dufrêche, Jérôme Roques, Eric Simoni, Paul A. Madden, and Pierre Turq

J. Chem. Phys. 134, 014511 (2011); http://dx.doi.org/10.1063/1.3518101 (6 pages) | Cited 3 times

Online Publication Date: 7 January 2011

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Dipole polarizabilities of a series of ions in aqueous solutions are computed from first-principles. The procedure is based on the study of the linear response of the maximally localized Wannier functions to an applied external field, within density functional theory. For most monoatomic cations (Li+, Na+, K+, Rb+, Mg2+, Ca2+ and Sr2+) the computed polarizabilities are the same as in the gas phase. For Cs+ and a series of anions (F−, Cl−, Br− and I−), environmental effects are observed, which reduce the polarizabilities in aqueous solutions with respect to their gas phase values. The polarizabilities of H( aq )+, OH( aq )− have also been determined along an ab initio molecular dynamics simulation. We observe that the polarizability of a molecule instantaneously switches upon proton transfer events. Finally, we also computed the polarizability tensor in the case of a strongly anisotropic molecular ion, UO22+. The results of these calculations will be useful in building interaction potentials that include polarization effects.
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32.30.-r Atomic spectra
31.15.A- Ab initio calculations
34.70.+e Charge transfer
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
31.15.xv Molecular dynamics and other numerical methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

A simple methodology for analyzing association effects on response functions via Monte Carlo simulations

P. Gómez-Álvarez, A. Dopazo-Paz, L. Romaní, and D. González-Salgado

J. Chem. Phys. 134, 014512 (2011); http://dx.doi.org/10.1063/1.3524201 (10 pages)

Online Publication Date: 7 January 2011

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A simple methodology was developed to analyze association effects on the thermodynamic response functions for a pure self-associated fluid via Monte Carlo simulations. The procedure essentially involves expressing the residual energy and volume of the fluid in terms of these properties for two hypothetical fluids consisting of monomers and associated molecules, respectively. This allows the thermodynamic response functions to be expressed in a perturbative form as a combination of the values for the property in the monomeric fluid and the contribution of association (the perturbative term). The proposed methodology was used to determine both contributions to the isobaric heat capacity and to the temperature and pressure derivatives of the volume for OPLS methanol along the 50 MPa isobar from 220 to 1500 K. Based on the results, both terms exert a substantial influence on the isobaric heat capacity; by contrast, the association term for the volumetric properties is negligible. These results are consistent with those of a previous work involving simulations with the same model under identical thermodynamic conditions but a different approach. They are also compared with others previously reported in context. Moreover, a comprehensive study of the different types of clusters present in the fluid was performed and the results were related to thermodynamic properties. A strong correlation between the heat capacity of the monomeric fluid and this structural analysis was found.
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61.20.Qg Structure of associated liquids: electrolytes, molten salts, etc.
61.20.Ja Computer simulation of liquid structure
61.25.Em Molecular liquids
65.20.De General theory of thermodynamic properties of liquids, including computer simulation
82.60.Lf Thermodynamics of solutions
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