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14 Sep 2011

Volume 135, Issue 10, Articles (10xxxx)

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J. Chem. Phys. 135, 104301 (2011); http://dx.doi.org/10.1063/1.3625959 (8 pages)

Timur R. Galeev, Constantin Romanescu, Wei-Li Li, Lai-Sheng Wang, and Alexander I. Boldyrev
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Communication: Are metallic glasses different from other glasses? A closer look at their high frequency dynamics

P. Bruna, G. Baldi, E. Pineda, J. Serrano, J. B. Suck, D. Crespo, and G. Monaco

J. Chem. Phys. 135, 101101 (2011); http://dx.doi.org/10.1063/1.3640002 (4 pages)

Online Publication Date: 8 September 2011

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Using high resolution inelastic x-ray scattering we studied the collective dynamics of the Pd77Si16.5Cu6.5 metallic glass, focusing on the energy-momentum region where the boson peak appears. The dispersion relation and the width of the acoustic excitations are determined showing how the longitudinal acoustic modes maintain their dispersive character for frequencies well above the boson peak frequencies. Moreover, we prove that close to these frequencies there is a softening of the apparent sound speed indicating a failure of the Debye continuum approximation at the boson peak frequencies and challenging previous results on other metallic glasses.
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78.70.Ck X-ray scattering
61.43.Fs Glasses
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Communication: Rationale for a new class of double-hybrid approximations in density-functional theory

Julien Toulouse, Kamal Sharkas, Eric Brémond, and Carlo Adamo

J. Chem. Phys. 135, 101102 (2011); http://dx.doi.org/10.1063/1.3640019 (3 pages) | Cited 4 times

Online Publication Date: 8 September 2011

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We provide a rationale for a new class of double-hybrid approximations introduced by Brémond and Adamo [J. Chem. Phys. 135, 024106 (2011)]10.1063/1.3604569 which combine an exchange-correlation density functional with Hartree-Fock exchange weighted by λ and second-order Møller-Plesset (MP2) correlation weighted by λ3. We show that this double-hybrid model can be understood in the context of the density-scaled double-hybrid model proposed by Sharkas et al. [J. Chem. Phys. 134, 064113 (2011)]10.1063/1.3544215, as approximating the density-scaled correlation functional Ec[n1/λ] by a linear function of λ, interpolating between MP2 at λ = 0 and a density-functional approximation at λ = 1. Numerical results obtained with the Perdew-Burke-Ernzerhof density functional confirms the relevance of this double-hybrid model.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.xr Self-consistent-field methods
31.15.xp Perturbation theory
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Communication: Stabilization of radical anions with weakly bound electron in condensed media: A case study of diacetonyl radical anion

Elizaveta V. Saenko, Dimitri N. Laikov, Irina A. Baranova, and Vladimir I. Feldman

J. Chem. Phys. 135, 101103 (2011); http://dx.doi.org/10.1063/1.3638690 (4 pages)

Online Publication Date: 12 September 2011

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The radical anion resulting from electron capture by diacetonyl molecule has been characterized by EPR and optical absorption spectroscopy in glassy ether matrices at 77 K. In non-polar alkane glasses this species was not observed under the same conditions, which confirms the crucial role of matrix interactions in stabilizing this species. Calculations at the MP2 level show the vertical detachment energy to increase gradually from roughly zero for a bare anion to ∼1 eV for the complex involving six ether molecules.
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34.70.+e Charge transfer
33.20.Kf Visible spectra
33.20.Lg Ultraviolet spectra
33.35.+r Electron resonance and relaxation
33.80.Eh Autoionization, photoionization, and photodetachment
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NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface

Trond S. Ingebrigtsen, Søren Toxvaerd, Ole J. Heilmann, Thomas B. Schrøder, and Jeppe C. Dyre

J. Chem. Phys. 135, 104101 (2011); http://dx.doi.org/10.1063/1.3623585 (9 pages)

Online Publication Date: 8 September 2011

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An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine precision. Nevertheless, just as for NVE algorithms, stabilizers are needed for very long runs in order to compensate for the accumulation of numerical errors that eventually lead to “entropic drift” of the potential energy towards higher values. A modification of the basic NVU algorithm is introduced that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE algorithm have identical radial distribution functions for the Lennard-Jones liquid.
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61.20.Ja Computer simulation of liquid structure
65.20.Jk Studies of thermodynamic properties of specific liquids
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NVU dynamics. II. Comparing to four other dynamics

Trond S. Ingebrigtsen, Søren Toxvaerd, Thomas B. Schrøder, and Jeppe C. Dyre

J. Chem. Phys. 135, 104102 (2011); http://dx.doi.org/10.1063/1.3623586 (7 pages)

Online Publication Date: 8 September 2011

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In the companion paper [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, “NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface,” J. Chem. Phys. (in press)] an algorithm was developed for tracing out a geodesic curve on the constant-potential-energy hypersurface. Here, simulations of NVU dynamics are compared to results for four other dynamics, both deterministic and stochastic. First, NVU dynamics is compared to the standard energy-conserving Newtonian NVE dynamics by simulations of the Kob-Andersen binary Lennard-Jones liquid, its WCA version (i.e., with cut-off's at the pair potential minima), and the Lennard-Jones Gaussian liquid. We find identical results for all quantities probed: radial distribution functions, incoherent intermediate scattering functions, and mean-square displacement as function of time. Arguments are presented for the equivalence of NVU and NVE dynamics in the thermodynamic limit; in particular, to leading order in 1/N these two dynamics give identical time-autocorrelation functions. In the final part of the paper, NVU dynamics is compared to Monte Carlo dynamics, to a diffusive dynamics of small-step random walks on the constant-potential-energy hypersurface, and to Nosmath-Hoover NVT dynamics. If time is scaled for the two stochastic dynamics to make single-particle diffusion constants identical to that of NVE dynamics, the simulations show that all five dynamics are equivalent at low temperatures except at short times.
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05.70.Ce Thermodynamic functions and equations of state
02.40.Hw Classical differential geometry
02.50.Ey Stochastic processes

Quadratically convergent algorithm for orbital optimization in the orbital-optimized coupled-cluster doubles method and in orbital-optimized second-order Møller-Plesset perturbation theory

Uğur Bozkaya, Justin M. Turney, Yukio Yamaguchi, Henry F. Schaefer, III, and C. David Sherrill

J. Chem. Phys. 135, 104103 (2011); http://dx.doi.org/10.1063/1.3631129 (17 pages) | Cited 1 time

Online Publication Date: 8 September 2011

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Using a Lagrangian-based approach, we present a more elegant derivation of the equations necessary for the variational optimization of the molecular orbitals (MOs) for the coupled-cluster doubles (CCD) method and second-order Møller-Plesset perturbation theory (MP2). These orbital-optimized theories are referred to as OO-CCD and OO-MP2 (or simply “OD” and “OMP2” for short), respectively. We also present an improved algorithm for orbital optimization in these methods. Explicit equations for response density matrices, the MO gradient, and the MO Hessian are reported both in spin-orbital and closed-shell spin-adapted forms. The Newton-Raphson algorithm is used for the optimization procedure using the MO gradient and Hessian. Further, orbital stability analyses are also carried out at correlated levels. The OD and OMP2 approaches are compared with the standard MP2, CCD, CCSD, and CCSD(T) methods. All these methods are applied to H2O, three diatomics, and the O4+ molecule. Results demonstrate that the CCSD and OD methods give nearly identical results for H2O and diatomics; however, in symmetry-breaking problems as exemplified by O4+, the OD method provides better results for vibrational frequencies. The OD method has further advantages over CCSD: its analytic gradients are easier to compute since there is no need to solve the coupled-perturbed equations for the orbital response, the computation of one-electron properties are easier because there is no response contribution to the particle density matrices, the variational optimized orbitals can be readily extended to allow inactive orbitals, it avoids spurious second-order poles in its response function, and its transition dipole moments are gauge invariant. The OMP2 has these same advantages over canonical MP2, making it promising for excited state properties via linear response theory. The quadratically convergent orbital-optimization procedure converges quickly for OMP2, and provides molecular properties that are somewhat different than those of MP2 for most of the test cases considered (although they are similar for H2O). Bond lengths are somewhat longer, and vibrational frequencies somewhat smaller, for OMP2 compared to MP2. In the difficult case of O4+, results for several vibrational frequencies are significantly improved in going from MP2 to OMP2.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
33.15.Dj Interatomic distances and angles
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Mt Rotation, vibration, and vibration-rotation constants

A molecular Debye-Hückel theory and its applications to electrolyte solutions

Tiejun Xiao and Xueyu Song

J. Chem. Phys. 135, 104104 (2011); http://dx.doi.org/10.1063/1.3632052 (14 pages)

Online Publication Date: 9 September 2011

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In this report, a molecular Debye-Hückel theory for ionic fluids is developed. Starting from the macroscopic Maxwell equations for bulk systems, the dispersion relation leads to a generalized Debye-Hückel theory which is related to the dressed ion theory in the static case. Due to the multi-pole structure of dielectric function of ionic fluids, the electric potential around a single ion has a multi-Yukawa form. Given the dielectric function, the multi-Yukawa potential can be determined from our molecular Debye-Hückel theory, hence, the electrostatic contributions to thermodynamic properties of ionic fluids can be obtained. Applications to binary as well as multi-component primitive models of electrolyte solutions demonstrated the accuracy of our approach. More importantly, for electrolyte solution models with soft short-ranged interactions, it is shown that the traditional perturbation theory can be extended to ionic fluids successfully just as the perturbation theory has been successfully used for short-ranged systems.
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82.45.Gj Electrolytes
41.20.Cv Electrostatics; Poisson and Laplace equations, boundary-value problems
61.25.Em Molecular liquids

Local pressure components and surface tension of spherical interfaces. Thermodynamic versus mechanical definitions. I. A mesoscale modeling of droplets

Aziz Ghoufi and Patrice Malfreyt

J. Chem. Phys. 135, 104105 (2011); http://dx.doi.org/10.1063/1.3632991 (10 pages) | Cited 1 time

Online Publication Date: 9 September 2011

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We report mesoscale simulations of spherical drops to investigate the surface tension and mechanical properties. The Monte Carlo simulations are performed with the multibody potential commonly used in the many-body dissipative particle dynamics simulations. We establish here the calculation of the local normal and transverse components of the pressure tensor via the perturbation volume within the thermodynamic route. The different profiles of these components are compared to those calculated using the mechanical approach. To complete the mesoscale modeling of drops, we investigate the curvature dependence of the surface tension in order to calculate the Tolman's length, which is found to be negative.
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68.03.Cd Surface tension and related phenomena
47.55.dr Interactions with surfaces

Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling

Anna-Pitschna E. Kunz, Haiyan Liu, and Wilfred F. van Gunsteren

J. Chem. Phys. 135, 104106 (2011); http://dx.doi.org/10.1063/1.3629450 (21 pages)

Online Publication Date: 9 September 2011

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A method to enhance sampling of a small subset of Nh particular degrees of freedom of a system of Nh + Nl degrees of freedom is presented. It makes use of adiabatically decoupling these degrees of freedom by increasing their mass followed by either increasing their temperature or reducing their interaction or the force acting on them. The appropriate statistical-mechanical expressions for use of these methods in simulation studies are derived. As long as the subset of mass-increased degrees of freedom is small compared to the total number of degrees of freedom of the system, sampling of this subset of degrees of freedom can be much enhanced at the cost of a slight perturbation of the configurational distribution. This is illustrated for a test system of 1000 SPC, simple point charge, water molecules at 300 K and a density of 997 kg m−3. Various fractions Nh/(Nh + Nl) of water molecules were adiabatically decoupled to different degrees. The size of the diffusion coefficient of these decoupled water molecules was used as a measure for how much the sampling was enhanced and the average potential energy per water molecule was used as a measure of how much the configurational distribution of the system gets distorted. A variety of parameter values was investigated and it was found that for Nh/(Nh + Nl) ⩽ 0.1 the diffusion of the Nh molecules could be enhanced by factors up to 35 depending on the method, the ratio Nh/(Nh + Nl), the extent of adiabatic decoupling, and the temperature or force scaling factors, at the cost of a slight perturbation of the configurational distribution.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.xv Molecular dynamics and other numerical methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
31.50.-x Potential energy surfaces

Ion-orbital coupling in Car-Parrinello calculations of hydrogen-bond vibrational dynamics: Case study with the NH3–HCl dimer

S. W. Ong, B. X. B. Lee, and H. C. Kang

J. Chem. Phys. 135, 104107 (2011); http://dx.doi.org/10.1063/1.3633273 (9 pages)

Online Publication Date: 9 September 2011

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We have performed Car-Parrinello molecular dynamics (CPMD) calculations of the hydrogen-bonded NH3–HCl dimer. Our main aim is to establish how ionic-orbital coupling in CPMD affects the vibrational dynamics in hydrogen-bonded systems by characterizing the dependence of the calculated vibrational frequencies upon the orbital mass in the adiabatic limit of Car-Parrinello calculations. We use the example of the NH3–HCl dimer because of interest in its vibrational spectrum, in particular the magnitude of the frequency shift of the H–Cl stretch due to the anharmonic interactions when the hydrogen bond is formed. We find that an orbital mass of about 100 a.u. or smaller is required in order for the ion-orbital coupling to be linear in orbital mass, and the results for which can be accurately extrapolated to the adiabatic limit of zero orbital mass. We argue that this is general for hydrogen-bonded systems, suggesting that typical orbital mass values used in CPMD are too high to accurately describe vibrational dynamics in hydrogen-bonded systems. Our results also show that the usual application of a scaling factor to the CPMD frequencies to correct for the effects of orbital mass is not valid. For the dynamics of the dimer, we find that the H–Cl stretch and the N–H–Cl bend are significantly coupled, suggesting that it is important to include the latter degree of freedom in quantum dynamical calculations. Results from our calculations with deuterium-substitution show that both these degrees of freedom have significant anharmonic interactions. Our calculated frequency for the H–Cl stretch using the Becke-exchange Lee-Yang-Parr correlation functional compares reasonably well with a previous second-order Møller-Plesset calculation with anharmonic corrections, although it is low compared to the experimental value for the dimer trapped in a neon-matrix.
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33.20.Tp Vibrational analysis
31.15.E- Density-functional theory
31.15.xv Molecular dynamics and other numerical methods
31.15.xp Perturbation theory
33.15.Fm Bond strengths, dissociation energies

Relativistic Jahn-Teller effects in the photoelectron spectra of tetrahedral P4, As4, Sb4, and Bi4

Daniel Opalka, Leonid V. Poluyanov, and Wolfgang Domcke

J. Chem. Phys. 135, 104108 (2011); http://dx.doi.org/10.1063/1.3629779 (10 pages)

Online Publication Date: 9 September 2011

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The group-V tetrahedral cluster cations P4+, As 4+, Sb 4+, and Bi 4+ are known to exhibit exceptionally strong Jahn-Teller (JT) effects of electrostatic origin in their 2E ground states and 2T2 excited states. It has been predicted that there exist, in addition, JT couplings of relativistic origin (arising from the spin-orbit (SO) operator) in 2E and 2T2 states of tetrahedral systems, which should become relevant for the heavier elements. In the present work, the JT and SO couplings in the group-V tetramer cations have been analyzed with ab initio relativistic electronic structure calculations. The vibronic line spectra and the band shapes of the photoelectron spectra were simulated with time-dependent quantum wave-packet methods. The results provide insight into the interplay of electrostatic and relativistic JT couplings and SO splittings in the complex photoelectron spectra of these systems.
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31.30.-i Corrections to electronic structure
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
36.40.Mr Spectroscopy and geometrical structure of clusters
32.80.Fb Photoionization of atoms and ions
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions

Single mode phonon energy transmission in functionalized carbon nanotubes

Jonghoon Lee, Vikas Varshney, Ajit K. Roy, and Barry L. Farmer

J. Chem. Phys. 135, 104109 (2011); http://dx.doi.org/10.1063/1.3633514 (8 pages) | Cited 1 time

Online Publication Date: 9 September 2011

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Although the carbon nanotube (CNT) features superior thermal properties in its pristine form, the chemical functionalization often required for many applications of CNT inevitably degrades the structural integrity and affects the transport of energy carriers. In this article, the effect of the side wall functionalization on the phonon energy transmission along the symmetry axis of CNT is studied using the phonon wave packet method. Three different functional groups are studied: methyl (–CH3), vinyl (–C2H3), and carboxyl (–COOH). We find that, near Γ point of the Brillouin zone, acoustic phonons show ideal transmission, while the transmission of the optical phonons is strongly suppressed. A positive correlation between the energy transmission coefficient and the phonon group velocity is observed for both acoustic and optical phonon modes. On comparing the transmission due to functional groups with equivalent point mass defects on CNT, we find that the chemistry of the functional group, rather than its molecular mass, has a dominant role in determining phonon scattering, hence the transmission, at the defect sites.
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63.22.Gh Nanotubes and nanowires

Electron correlation via frozen Gaussian dynamics

Peter Elliott and Neepa T. Maitra

J. Chem. Phys. 135, 104110 (2011); http://dx.doi.org/10.1063/1.3630134 (13 pages)

Online Publication Date: 9 September 2011

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We investigate the accuracy and efficiency of the semiclassical frozen Gaussian method in describing electron dynamics in real time. Model systems of two soft-Coulomb-interacting electrons are used to study correlated dynamics under non-perturbative electric fields, as well as the excitation spectrum. The results show that a recently proposed method that combines exact-exchange with semiclassical correlation to propagate the one-body density-matrix holds promise for electron dynamics in many situations that either wavefunction or density-functional methods have difficulty describing. The results also however point out challenges in such a method that need to be addressed before it can become widely applicable.
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31.15.ve Electron correlation calculations for atoms and ions: ground state

A general-order local coupled-cluster method based on the cluster-in-molecule approach

Zoltán Rolik and Mihály Kállay

J. Chem. Phys. 135, 104111 (2011); http://dx.doi.org/10.1063/1.3632085 (18 pages) | Cited 1 time

Online Publication Date: 12 September 2011

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A general-order local coupled-cluster (CC) method is presented which has the potential to provide accurate correlation energies for extended systems. Our method combines the cluster-in-molecule approach of Li and co-workers [J. Chem. Phys. 131, 114109 (2009)]10.1063/1.3218842 with the frozen natural orbital (NO) techniques widely used for the cost reduction of correlation methods. The occupied molecular orbitals (MOs) are localized, and for each occupied MO a local subspace of occupied and virtual orbitals is constructed using approximate Møller–Plesset NOs. The CC equations are solved and the correlation energies are calculated in the local subspace for each occupied MO, while the total correlation energy is evaluated as the sum of the individual contributions. The size of the local subspaces and the accuracy of the results can be controlled by varying only one parameter, the threshold for the occupation number of NOs which are included in the subspaces. Though our local CC method in its present form scales as the fifth power of the system size, our benchmark calculations show that it is still competitive for the CC singles and doubles (CCSD) and the CCSD with perturbative triples [CCSD(T)] approaches. For higher order CC methods, the reduction in computation time is more pronounced, and the new method enables calculations for considerably bigger molecules than before with a reasonable loss in accuracy. We also demonstrate that the independent calculation of the correlation contributions allows for a higher order description of the chemically more important segments of the molecule and a lower level treatment of the rest delivering further significant savings in computer time.
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31.15.bw Coupled-cluster theory
31.15.vn Electron correlation calculations for diatomic molecules
31.15.vq Electron correlation calculations for polyatomic molecules
31.15.xp Perturbation theory

Amplitude equations for breathing spiral waves in a forced reaction-diffusion system

Pushpita Ghosh and Deb Shankar Ray

J. Chem. Phys. 135, 104112 (2011); http://dx.doi.org/10.1063/1.3632992 (7 pages)

Online Publication Date: 12 September 2011

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Based on a multiple scale analysis of a forced reaction-diffusion system leading to amplitude equations, we explain the existence of spiral wave and its photo-induced spatiotemporal behavior in chlorine dioxide-iodine-malonic acid system. When the photo-illumination intensity is modulated, breathing of spiral is observed in which the period of breathing is identical to the period of forcing. We have also derived the condition for breakup and suppression of spiral wave by periodic illumination. The numerical simulations agree well with our analytical treatment.
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05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
05.45.-a Nonlinear dynamics and chaos
02.60.Cb Numerical simulation; solution of equations

Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins

Jaydeep P. Bardhan

J. Chem. Phys. 135, 104113 (2011); http://dx.doi.org/10.1063/1.3632995 (8 pages)

Online Publication Date: 12 September 2011

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We study the energetics of burying charges, ion pairs, and ionizable groups in a simple protein model using nonlocal continuum electrostatics. Our primary finding is that the nonlocal response leads to markedly reduced solvent screening, comparable to the use of application-specific protein dielectric constants. Employing the same parameters as used in other nonlocal studies, we find that for a sphere of radius 13.4 Å containing a single +1e charge, the nonlocal solvation free energy varies less than 18 kcal/mol as the charge moves from the surface to the center, whereas the difference in the local Poisson model is ∼35 kcal/mol. Because an ion pair (salt bridge) generates a comparatively more rapidly varying Coulomb potential, energetics for salt bridges are even more significantly reduced in the nonlocal model. By varying the central parameter in nonlocal theory, which is an effective length scale associated with correlations between solvent molecules, nonlocal-model energetics can be varied from the standard local results to essentially zero; however, the existence of the reduction in charge-burial penalties is quite robust to variations in the protein dielectric constant and the correlation length. Finally, as a simple exploratory test of the implications of nonlocal response, we calculate glutamate pKa shifts and find that using standard protein parameters (εprotein = 2–4), nonlocal results match local-model predictions with much higher dielectric constants. Nonlocality may, therefore, be one factor in resolving discrepancies between measured protein dielectric constants and the model parameters often used to match titration experiments. Nonlocal models may hold significant promise to deepen our understanding of macromolecular electrostatics without substantially increasing computational complexity.
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87.15.Pc Electronic and electrical properties
87.14.E- Proteins
87.15.R- Reactions and kinetics

Optimal diabatic bases via thermodynamic bounds

Sina Yeganeh and Troy Van Voorhis

J. Chem. Phys. 135, 104114 (2011); http://dx.doi.org/10.1063/1.3626566 (9 pages)

Online Publication Date: 13 September 2011

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Describing kinetic processes within a perturbation theory approach such as Fermi's golden rule requires an understanding of the initial and final states of the system. A number of different methods have been proposed for obtaining these diabatic-like states, but a robust criterion for evaluating their accuracy has not been established. Here, we approach the problem of determining the most appropriate set of diabatic states for use in incoherent rate expressions. We develop a method that rotates an initial set of diabats into an optimized set beginning with a zeroth-order diabatic Hamiltonian and choosing the rotation that minimizes the effect of non-diabatic terms on the thermodynamic free energy. The Gibbs-Bogoliubov (GB) bound on the Helmholtz free energy is thus used as the diabatic criterion. We first derive the GB free energy for a two site system and then find an expression general for any electronic system Hamiltonian. Efficient numerical methods are used to perform the minimization subject to orthogonality constraints, and we examine the resulting diabats for system Hamiltonians in various parameter regimes. The transition from localized to delocalized states is clearly seen in these calculations, and some interesting features are discussed.
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05.70.Ce Thermodynamic functions and equations of state

Mechanisms of kinetic trapping in self-assembly and phase transformation

Michael F. Hagan, Oren M. Elrad, and Robert L. Jack

J. Chem. Phys. 135, 104115 (2011); http://dx.doi.org/10.1063/1.3635775 (13 pages) | Cited 2 times

Online Publication Date: 14 September 2011

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In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions.
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87.14.E- Proteins
87.15.hg Dynamics of intermolecular interactions
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
05.20.Dd Kinetic theory

Electric field effects on nuclear magnetic shielding of the 1:1 and 2:1 (homo and heterochiral) complexes of XOOX′ (X, X′ = H, CH3) with lithium cation and their chiral discrimination

Ibon Alkorta, José Elguero, Patricio F. Provasi, Gabriel I. Pagola, and Marta B. Ferraro

J. Chem. Phys. 135, 104116 (2011); http://dx.doi.org/10.1063/1.3632086 (9 pages)

Online Publication Date: 14 September 2011

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The set of 1:1 and 2:1 complexes of XOOX′ (X, X′ = H, CH3) with lithium cation has been studied to determine if they are suitable candidates for chiral discrimination in an isotropic medium via nuclear magnetic resonance spectroscopy. Conventional nuclear magnetic resonance is unable to distinguish between enantiomers in the absence of a chiral solvent. The criterion for experimental detection is valuated by the isotropic part of nuclear shielding polarisability tensors, related to a pseudoscalar of opposite sign for two enantiomers. The study includes calculations at coupled Hartree-Fock and density functional theory schemes for 17O nucleus in each compound. Additional calculations for 1H are also included for some compounds. A huge static homogeneous electric field, perpendicular to the magnetic field of the spectromer, as big as ≈1.7 × 108 V m−1 should be applied to observe a shift of ≈1 ppm for 17O magnetic shielding in the proposed set of complexes.
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31.30.-i Corrections to electronic structure
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.25.+k Nuclear resonance and relaxation
31.15.E- Density-functional theory

Using swarm intelligence for finding transition states and reaction paths

René Fournier, Satya Bulusu, Stephen Chen, and Jamie Tung

J. Chem. Phys. 135, 104117 (2011); http://dx.doi.org/10.1063/1.3633515 (11 pages)

Online Publication Date: 14 September 2011

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We describe an algorithm that explores potential energy surfaces (PES) and finds approximate reaction paths and transition states. A few (≈6) evolving atomic configurations (“climbers”) start near a local minimum M1 of the PES. The climbers seek a shallow ascent, low energy, path toward a saddle point S12, cross over to another valley of the PES, and climb down to a new minimum M2 that was not known beforehand. Climbers use both energy and energy derivatives to make individual decisions, and they use relative fitness to make team-based decisions. In sufficiently long runs, they keep exploring and may go through a sequence M1–S12–M2–S23–M3 … of minima and saddle points without revisiting any of the critical points. We report results on eight small test systems that highlight advantages and disadvantages of the method. We also investigated the PES of Li8, Al 7+, Ag7, and Ag2NH3 to illustrate potential applications of this new method.
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82.20.Db Transition state theory and statistical theories of rate constants
82.20.Kh Potential energy surfaces for chemical reactions
82.60.-s Chemical thermodynamics
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Valence isoelectronic substitution in the B8− and B9− molecular wheels by an Al dopant atom: Umbrella-like structures of AlB7− and AlB8−

Timur R. Galeev, Constantin Romanescu, Wei-Li Li, Lai-Sheng Wang, and Alexander I. Boldyrev

J. Chem. Phys. 135, 104301 (2011); http://dx.doi.org/10.1063/1.3625959 (8 pages)

Online Publication Date: 8 September 2011

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The structures and the electronic properties of two aluminum-doped boron clusters, AlB7− and AlB8−, were investigated using photoelectron spectroscopy and ab initio calculations. The photoelectron spectra of AlB7− and AlB8− are both broad, suggesting significant geometry changes between the ground states of the anions and the neutrals. Unbiased global minimum searches were carried out and the calculated vertical electron detachment energies were used to compare with the experimental data. We found that the Al atom does not simply replace a B atom in the parent B8− and B9− planar clusters in AlB7− and AlB8−. Instead, the global minima of the two doped-clusters are of umbrella shapes, featuring an Al atom interacting ionically with a hexagonal and heptagonal pyramidal B7 (C6v) and B8 (C7v) fragment, respectively. These unique umbrella-type structures are understood on the basis of the special stability of the quasi-planar B73− and planar B82− molecular wheels derived from double aromaticity.
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31.15.ae Electronic structure and bonding characteristics
33.60.+q Photoelectron spectra
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.80.Eh Autoionization, photoionization, and photodetachment
36.40.Cg Electronic and magnetic properties of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters

Characterization of the potential minimum of the F ′0u+(1D2) ion-pair state of Cl2 using (1 + 2′) optical-optical double resonance excitation and mass-resolved ion detection

Trevor Ridley, Robert J. Donovan, and Kenneth P. Lawley

J. Chem. Phys. 135, 104302 (2011); http://dx.doi.org/10.1063/1.3625956 (7 pages)

Online Publication Date: 8 September 2011

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Vibrational levels of the F′0u+(1D2), F0u   +(3P0), and D0u+(3P2) ion-pair states of 35Cl2 and 35Cl37Cl in the range 62 500–67 600 cm−1 have been observed using (1 + 2′) optical-optical double resonance excitation with mass-resolved ion detection. The strong F′0u+(1D2)/F0u   +(3P0) coupling has been modelled by a coupled two-state calculation. An optimized fit of the experimental data used an F′0u+(1D2) state potential with a Te of 65 177 cm−1 and an Re of ≈2.636 Å with a coupling constant of ≈430 cm−1. The calculation assigns the first observed members of the F′0u+(1D2) state progression of 35Cl2 and 35Cl37Cl at 64 998 and 65 094 cm−1, respectively, as transitions to v = 0.
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33.40.+f Multiple resonances (including double and higher-order resonance processes, such as double nuclear magnetic resonance, electron double resonance, and microwave optical double resonance)
33.80.Eh Autoionization, photoionization, and photodetachment
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

The visible spectrum of zirconium dioxide, ZrO2

Anh Le, Timothy C. Steimle, Varun Gupta, Corey A. Rice, John P. Maier, Sheng H. Lin, and Chih-Kai Lin

J. Chem. Phys. 135, 104303 (2011); http://dx.doi.org/10.1063/1.3632053 (11 pages)

Online Publication Date: 8 September 2011

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The electronic spectrum of a cold molecular beam of zirconium dioxide, ZrO2, has been investigated using laser induced fluorescence (LIF) in the region from 17 000 cm−1 to 18 800 cm−1 and by mass-resolved resonance enhanced multi-photon ionization (REMPI) spectroscopy from 17 000 cm−1–21 000 cm−1. The LIF and REMPI spectra are assigned to progressions in the math1B2(ν1, ν2, ν3) ← math1A1(0, 0, 0) transitions. Dispersed fluorescence from 13 bands was recorded and analyzed to produce harmonic vibrational parameters for the math1A1 state of ω1 = 898(1) cm−1, ω2 = 287(2) cm−1, and ω3 = 808(3) cm−1. The observed transition frequencies of 45 bands in the LIF and REMPI spectra produce origin and harmonic vibrational parameters for the math1B2 state of Te = 16 307(8) cm−1, ω1 = 819(3) cm−1, ω2 = 149(3) cm−1, and ω3 = 518(4) cm−1. The spectra were modeled using a normal coordinate analysis and Franck-Condon factor predictions. The structures, harmonic vibrational frequencies, and the potential energies as a function of bending angle for the math1B2 and math1A1 states are predicted using time-dependent density functional theory, complete active space self-consistent field, and related first-principle calculations. A comparison with isovalent TiO2 is made.
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33.20.Kf Visible spectra
33.20.Tp Vibrational analysis
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.80.Eh Autoionization, photoionization, and photodetachment
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods

Global ab initio potential energy surfaces for both the ground (math1A′) and excited (math1A′′) electronic states of HNO and vibrational states of the Renner-Teller math1A′′–math1A′system

Anyang Li, Huixian Han, and Daiqian Xie

J. Chem. Phys. 135, 104304 (2011); http://dx.doi.org/10.1063/1.3632994 (10 pages) | Cited 1 time

Online Publication Date: 8 September 2011

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The global potential energy surfaces for both the ground (math1A′) and excited (math1A′′) electronic states of the HNO molecule have been constructed by three-dimensional cubic spline interpolation of more than 17 000 ab initio points, which have been calculated at the internal contracted multi-reference configuration interaction level with the Davidson correction using an augmented correlation-consistent polarized valence quadruple zeta basis set. The low-lying vibrational energy levels for the two electronic states of HNO have also been calculated on our potential energy surfaces including the diagonal Renner-Teller terms. The calculated results have shown a good agreement with the experimental vibrational frequencies of HNO and its isotopomers.
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33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.vq Electron correlation calculations for polyatomic molecules
31.50.Bc Potential energy surfaces for ground electronic states
31.50.Df Potential energy surfaces for excited electronic states

Cluster cross sections from pickup measurements: Are the established methods consistent?

J. Fedor, V. Poterya, A. Pysanenko, and M. Fárník

J. Chem. Phys. 135, 104305 (2011); http://dx.doi.org/10.1063/1.3633474 (10 pages)

Online Publication Date: 8 September 2011

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Pickup of several molecules, H2O, HBr, and CH3OH, and Ar atoms on free ArN clusters has been investigated in a molecular beam experiment. The pickup cross sections of the clusters with known mean sizes, math ≈ 150 and 260 were measured by two independent methods: (i) the cluster beam velocity decrease due to the momentum transfer of the picked up molecules to the clusters, and (ii) Poisson distribution of a selected cluster fragment ion as a function of the pickup pressure. In addition, the pickup cross sections were calculated using molecular dynamics and Monte Carlo simulations. The simulations support the results of the velocity measurements. On the other hand, the Poisson distributions yield significantly smaller cross sections, inconsistent with the known ArN cluster sizes. These results are discussed in terms of: (i) an incomplete coagulation of guest molecules on the argon clusters when two or more molecules are picked up; and (ii) the fragmentation pattern of the embedded molecules and their clusters upon ionization on the Ar cluster. We conclude that the Poisson distribution method has to be cautiously examined, if conclusions should be drawn about the cluster cross section, or the mean cluster size math, and the number of picked up molecules.
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36.40.Jn Reactivity of clusters
36.40.Qv Stability and fragmentation of clusters
34.50.Gb Electronic excitation and ionization of molecules
31.15.xv Molecular dynamics and other numerical methods
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