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21 Apr 2008

Volume 128, Issue 15, Articles (15xxxx)

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Competing sigmatropic shift rearrangements in excited allyl radicals

D. Stranges, P. O’Keeffe, G. Scotti, R. Di Santo, and P. L. Houston

J. Chem. Phys. 128, 151101 (2008); http://dx.doi.org/10.1063/1.2907714 (4 pages) | Cited 3 times

Online Publication Date: 16 April 2008

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The competition between rearrangement of the excited allyl radical via a 1,3 sigmatropic shift versus sequential 1,2 shifts has been observed and characterized using isotopic substitution, laser excitation, and molecular beam techniques. Both rearrangements produce a 1-propenyl radical that subsequently dissociates to methyl plus acetylene. The 1,3 shift and 1,2 shift mechanisms are equally probable for CH2CHCH2, whereas the 1,3 shift is favored by a factor of 1.6 in CH2CDCH2. The translational energy distributions for the methyl and acetylene products of these two mechanisms are substantially different. Both of these allyl dissociation channels are minor pathways compared to hydrogen atom loss.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.30.Qt Isomerization and rearrangement
82.50.-m Photochemistry
82.20.Hf Product distribution

Dynamics of molecular diffusion of rhodamine 6G in silica nanochannels

Y. Y. Kievsky, B. Carey, S. Naik, N. Mangan, D. ben-Avraham, and I. Sokolov

J. Chem. Phys. 128, 151102 (2008); http://dx.doi.org/10.1063/1.2908875 (5 pages) | Cited 9 times

Online Publication Date: 16 April 2008

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We describe a method to study diffusion of rhodamine 6G dye in single silica nanochannels using arrays of silica nanochannels. Dynamics of the molecules inside single nanochannel is found from the change of the dye concentration in solution with time. A 108 decrease in the dye diffusion coefficient relative to water was observed. In comparison to single fluorescent molecule studies, the presented method does not require fluorescence of the diffusing molecules.
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66.30.Pa Diffusion in nanoscale solids
66.30.Dn Theory of diffusion and ionic conduction in solids
61.46.-w Structure of nanoscale materials
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back to top Theoretical Methods and Algorithms

An atomic orbital-based reformulation of energy gradients in second-order Møller–Plesset perturbation theory

Sabine Schweizer, Bernd Doser, and Christian Ochsenfeld

J. Chem. Phys. 128, 154101 (2008); http://dx.doi.org/10.1063/1.2906127 (8 pages) | Cited 8 times

Online Publication Date: 15 April 2008

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A fully atomic orbital (AO)-based reformulation of second-order Møller–Plesset perturbation theory (MP2) energy gradients is introduced, which provides the basis for reducing the computational scaling with the molecular size from the fifth power to linear. Our formulation avoids any transformation between the AO and the molecular orbital (MO) basis and employs pseudodensity matrices similar to the AO-MP2 energy expressions within the Laplace scheme for energies. The explicit computation of perturbed one-particle density matrices emerging in the new AO-based gradient expression is avoided by reformulating the Z-vector method of Handy and Schaefer [J. Chem. Phys. 81, 5031 (1984)] within a density matrix-based scheme.
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31.15.xp Perturbation theory

Cooperativity between two types of hydrogen bond in H3C–HCN–HCN and H3C–HNC–HNC complexes

Qingzhong Li, Xiulin An, Feng Luan, Wenzuo Li, Baoan Gong, Jianbo Cheng, and Jiazhong Sun

J. Chem. Phys. 128, 154102 (2008); http://dx.doi.org/10.1063/1.2898499 (6 pages) | Cited 22 times

Online Publication Date: 16 April 2008

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Hydrogen-bonded clusters, H3C–HCN, HCN–HCN, H3C–HCN–HCN, H3C–HNC, HNC–HNC, and H3C–HNC–HNC, have been studied by using ab initio calculations. The optimized structures, harmonic vibrational frequencies, and interaction energies are calculated at the MP2 level with aug-cc-pVTZ basis set. The cooperative effects in the properties of these complexes are investigated quantitatively. A cooperativity contribution of around 10% relative to the total interaction energy was found in the H3C–HCN–HCN complex. In the case of H3C–HNC–HNC complex, the cooperativity contribution is about 15%. The cooperativity contribution in the single-electron hydrogen bond is larger than that in the hydrogen bond of HCN–HCN and HNC–HNC complexes. NMR chemical shifts, charge transfers, and topological parameters also support such conclusions.
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31.15.ae Electronic structure and bonding characteristics
36.40.Jn Reactivity of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
33.25.+k Nuclear resonance and relaxation
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants

Explicitly correlated RMP2 for high-spin open-shell reference states

Gerald Knizia and Hans-Joachim Werner

J. Chem. Phys. 128, 154103 (2008); http://dx.doi.org/10.1063/1.2889388 (12 pages) | Cited 47 times

Online Publication Date: 16 April 2008

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We present an explicitly correlated version of the high-spin open-shell RMP2 method. The theory is derived in a unitarily invariant form, which is suitable for the insertion of local approximations. It is demonstrated that the rapid basis set convergence of closed-shell MP2-F12 is also achieved in RMP2-F12, and similar Ansätze and approximations can be employed. All integrals are computed using efficient density fitting approximations, and many-electron integrals are avoided using resolution of the identity approximations. The performance of the method is demonstrated by benchmark calculations on a large set of ionization potentials, electron affinities and atomization energies. Using triple-zeta basis sets RMP2-F12 yields results that are closer to the basis set limit than standard RMP2 with augmented quintuple-zeta basis sets for all properties. Different variants of perturbative corrections for the open-shell Hartree–Fock treatment are described and tested.
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31.15.xr Self-consistent-field methods
32.50.+d Fluorescence, phosphorescence (including quenching)

Nonadiabatic electron wavepacket dynamics of molecules in an intense optical field: An ab initio electronic state study

Takehiro Yonehara and Kazuo Takatsuka

J. Chem. Phys. 128, 154104 (2008); http://dx.doi.org/10.1063/1.2904867 (13 pages) | Cited 6 times

Online Publication Date: 16 April 2008

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A theory of quantum electron wavepacket dynamics that nonadiabatically couples with classical nuclear motions in intense optical fields is studied. The formalism is intended to track the laser-driven electron wavepackets in terms of the linear combination of configuration-state functions generated with ab initio molecular orbitals. Beginning with the total quantum Hamiltonian for electrons and nuclei in the vector potential of classical electromagnetic field, we reduce the Hamiltonian into a mixed quantum-classical representation by replacing the quantum nuclear momentum operators with the classical counterparts. This framework gives equations of motion for electron wavepackets in an intense laser field through the time dependent variational principle. On the other hand, a generalization of the Newtonian equations provides a matrix form of forces acting on the nuclei for nonadiabatic dynamics. A mean-field approximation to the force matrix reduces this higher order formalism to the semiclassical Ehrenfest theory in intense optical fields. To bring these theories into a practical quantum chemical package for general molecules, we have implemented the relevant ab initio algorithms in it. Some numerical results in the level of the semiclassical Ehrenfest-type theory with explicit use of the nuclear kinematic (derivative) coupling and the velocity form for the optical interaction are presented.
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33.80.-b Photon interactions with molecules
31.15.A- Ab initio calculations
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Turbo charging time-dependent density-functional theory with Lanczos chains

Dario Rocca, Ralph Gebauer, Yousef Saad, and Stefano Baroni

J. Chem. Phys. 128, 154105 (2008); http://dx.doi.org/10.1063/1.2899649 (14 pages) | Cited 30 times

Online Publication Date: 16 April 2008

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We introduce a new implementation of time-dependent density-functional theory which allows the entire spectrum of a molecule or extended system to be computed with a numerical effort comparable to that of a single standard ground-state calculation. This method is particularly well suited for large systems and/or large basis sets, such as plane waves or real-space grids. By using a superoperator formulation of linearized time-dependent density-functional theory, we first represent the dynamical polarizability of an interacting-electron system as an off-diagonal matrix element of the resolvent of the Liouvillian superoperator. One-electron operators and density matrices are treated using a representation borrowed from time-independent density-functional perturbation theory, which permits us to avoid the calculation of unoccupied Kohn–Sham orbitals. The resolvent of the Liouvillian is evaluated through a newly developed algorithm based on the nonsymmetric Lanczos method. Each step of the Lanczos recursion essentially requires twice as many operations as a single step of the iterative diagonalization of the unperturbed Kohn–Sham Hamiltonian. Suitable extrapolation of the Lanczos coefficients allows for a dramatic reduction of the number of Lanczos steps necessary to obtain well converged spectra, bringing such number down to hundreds (or a few thousands, at worst) in typical plane-wave pseudopotential applications. The resulting numerical workload is only a few times larger than that needed by a ground-state Kohn–Sham calculation for a same system. Our method is demonstrated with the calculation of the spectra of benzene, C60 fullerene, and of chlorophyll a.
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31.15.E- Density-functional theory
36.40.-c Atomic and molecular clusters
31.15.xp Perturbation theory

Quantum trajectories in complex space: One-dimensional stationary scattering problems

Chia-Chun Chou and Robert E. Wyatt

J. Chem. Phys. 128, 154106 (2008); http://dx.doi.org/10.1063/1.2850743 (10 pages) | Cited 9 times

Online Publication Date: 16 April 2008

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One-dimensional time-independent scattering problems are investigated in the framework of the quantum Hamilton–Jacobi formalism. The equation for the local approximate quantum trajectories near the stagnation point of the quantum momentum function is derived, and the first derivative of the quantum momentum function is related to the local structure of quantum trajectories. Exact complex quantum trajectories are determined for two examples by numerically integrating the equations of motion. For the soft potential step, some particles penetrate into the nonclassical region, and then turn back to the reflection region. For the barrier scattering problem, quantum trajectories may spiral into the attractors or from the repellers in the barrier region. Although the classical potentials extended to complex space show different pole structures for each problem, the quantum potentials present the same second-order pole structure in the reflection region. This paper not only analyzes complex quantum trajectories and the total potentials for these examples but also demonstrates general properties and similar structures of the complex quantum trajectories and the quantum potentials for one-dimensional time-independent scattering problems.
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03.65.Nk Scattering theory
03.65.Ge Solutions of wave equations: bound states

Solving the electron-nuclear Schrödinger equation of helium atom and its isoelectronic ions with the free iterative-complement-interaction method

Hiroyuki Nakashima and Hiroshi Nakatsuji

J. Chem. Phys. 128, 154107 (2008); http://dx.doi.org/10.1063/1.2904562 (7 pages) | Cited 12 times

Online Publication Date: 17 April 2008

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Our previous paper [ J. Chem. Phys. 127, 224104 (2007) ] revealed that the Schrödinger equation in the fixed-nucleus approximation could be very accurately solved for helium atom and its isoelectronic ions (Z = 1–10) with the free iterative-complement-interaction (ICI) method combined with the variation principle. In this report, the quantum effect of nuclear motion has further been variationally considered by the free ICI formalism for the Hamiltonian including mass-polarization operator. We obtained −2.903 304 557 729 580 294 733 816 943 892 697 752 659 273 965 a.u. for helium atom, which is over 40 digits in accuracy, similarly to the previous result for the fixed-nucleus level. Similar accuracy was also obtained for the helium isoelectronic ions. The present results may be regarded to be the nonrelativistic limits. We have further analyzed the physics of the free ICI wave function by applying it to an imaginary atom called “eneon,” [e−e10+e−]8+, in which both of the quantum effect of nuclear motion and the three-particle collisions are differently important from the helium and its isoelectronic ions. This revealed the accurate physics automatically generated by the free ICI formalism.
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31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
31.15.xt Variational techniques

Solving the electron and electron-nuclear Schrödinger equations for the excited states of helium atom with the free iterative-complement-interaction method

Hiroyuki Nakashima, Yuh Hijikata, and Hiroshi Nakatsuji

J. Chem. Phys. 128, 154108 (2008); http://dx.doi.org/10.1063/1.2904871 (10 pages) | Cited 11 times

Online Publication Date: 17 April 2008

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Very accurate variational calculations with the free iterative-complement-interaction (ICI) method for solving the Schrödinger equation were performed for the 1sNs singlet and triplet excited states of helium atom up to N = 24. This is the first extensive applications of the free ICI method to the calculations of excited states to very high levels. We performed the calculations with the fixed-nucleus Hamiltonian and moving-nucleus Hamiltonian. The latter case is the Schrödinger equation for the electron-nuclear Hamiltonian and includes the quantum effect of nuclear motion. This solution corresponds to the nonrelativistic limit and reproduced the experimental values up to five decimal figures. The small differences from the experimental values are not at all the theoretical errors but represent the physical effects that are not included in the present calculations, such as relativistic effect, quantum electrodynamic effect, and even the experimental errors. The present calculations constitute a small step toward the accurately predictive quantum chemistry.
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31.15.xt Variational techniques
31.15.vj Electron correlation calculations for atoms and ions: excited states
03.65.Ge Solutions of wave equations: bound states
02.60.-x Numerical approximation and analysis
02.30.Xx Calculus of variations

Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte Carlo

Andreas Hellander

J. Chem. Phys. 128, 154109 (2008); http://dx.doi.org/10.1063/1.2897976 (7 pages) | Cited 1 time

Online Publication Date: 17 April 2008

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A quasi-Monte Carlo method for the simulation of discrete time Markov chains is applied to the simulation of biochemical reaction networks. The continuous process is formulated as a discrete chain subordinate to a Poisson process using the method of uniformization. It is shown that a substantial reduction of the number of trajectories that is required for an accurate estimation of the probability density functions (PDFs) can be achieved with this technique. The method is applied to the simulation of two model problems. Although the technique employed here does not address the typical stiffness of biochemical reaction networks, it is useful when computing the PDF by replication. The method can also be used in conjuncture with hybrid methods that reduce the stiffness.
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87.15.R- Reactions and kinetics
87.15.ak Monte Carlo simulations

Monte Carlo free energy calculations using electronic structure methods

Daniel R. Matusek, Sébastien Osborne, and Alain St-Amant

J. Chem. Phys. 128, 154110 (2008); http://dx.doi.org/10.1063/1.2890725 (13 pages) | Cited 2 times

Online Publication Date: 17 April 2008

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The molecular mechanics-based importance sampling function (MMBIF) algorithm [ R. Iftimie, D. Salahub, D. Wei, and J. Schofield, J. Chem. Phys. 113, 4852 (2000) ] is extended to incorporate semiempirical electronic structure methods in the secondary Markov chain, creating a fully quantum mechanical Monte Carlo sampling method for simulations of reactive chemical systems which, unlike the MMBIF algorithm, does not require the generation of a system-specific force field. The algorithm is applied to calculating the potential of mean force for the isomerization reaction of HCN using thermodynamic integration. Constraints are implemented in the sampling using a modification of the SHAKE algorithm, including that of a fixed, arbitrary reaction coordinate. Simulation results show that sampling efficiency with the semiempirical secondary potential is often comparable in quality to force fields constructed using the methods suggested in the original MMBIF work. The semiempirical based importance sampling method presented here is a useful alternative to MMBIF sampling as it can be applied to systems for which no suitable MM force field can be constructed.
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71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations

Nonadiabatic couplings from time-dependent density functional theory. II. Successes and challenges of the pseudopotential approximation

Chunping Hu, Hirotoshi Hirai, and Osamu Sugino

J. Chem. Phys. 128, 154111 (2008); http://dx.doi.org/10.1063/1.2900647 (9 pages) | Cited 9 times

Online Publication Date: 17 April 2008

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We present extensive calculations of nonadiabatic couplings (NACs) between the electronically ground and excited states of molecules, using time-dependent density functional theory (TDDFT) within (modified) linear response [ C. Hu et al. J. Chem. Phys. 127, 064103 (2007) ]. Our approach is implemented in the pseudopotential framework, with the consideration of nonlinear core corrections. The features of either the ordinary Jahn–Teller conical intersections in X3 (X = Li, Na, K, Cu, Ag, Au) trimers, or the elliptic Jahn–Teller conical intersections in NaH2, have been well reproduced. In particular, anticipated results for the H–H2 collision near the avoided crossing are obtained, showing appealing improvement over the first, real-time, TDDFT calculation. The other important type of intersections, Renner–Teller glancing intersection, has also been studied for several typical molecular systems (BH2, AlH2, CH2+, SiH2+), giving results in reasonable agreement with the theoretical model. Despite these successes, it is found that for some systems, including both Jahn–Teller and Renner–Teller systems, the pseudopotential scheme might give inaccurate results for some NAC components on nonhydrogen atoms. By trying different construction schemes of pseudopotentials, e.g., using local pseudopotentials, the results of NACs are found scheme-dependent and show improvement for some cases. Since there is much freedom in constructing ab initio nonlocal pseudopotentials, our findings on TDDFT calculation of NACs in the pseudopotential scheme might be helpful to give clues for constructing more “realistic” pseudopotentials.
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31.30.-i Corrections to electronic structure
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
34.50.-s Scattering of atoms and molecules
31.15.ee Time-dependent density functional theory
31.15.A- Ab initio calculations

Unbiased τ-leap methods for stochastic simulation of chemically reacting systems

Zhouyi Xu and Xiaodong Cai

J. Chem. Phys. 128, 154112 (2008); http://dx.doi.org/10.1063/1.2894479 (10 pages) | Cited 6 times

Online Publication Date: 17 April 2008

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The τ-leap method first developed by Gillespie [ D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001) ] can significantly speed up stochastic simulation of certain chemically reacting systems with acceptable losses in accuracy. Recently, several improved τ-leap methods, including the binomial, multinomial, and modified τ-leap methods, have been developed. However, in all these τ-leap methods, the mean of the number of times, Km, that the mth reaction channel fires during a leap is not equal to the true mean. Therefore, all existing τ-leap methods produce biased simulation results, which limit the simulation accuracy and speed. In this paper, we analyze the mean of Km based on the chemical master equation. Using this analytical result, we develop unbiased Poisson and binomial τ-leap methods. Moreover, we analyze the variance of Km, and then develop an unbiased Poisson/Gaussian/binomial τ-leap method to correct the errors in both the mean and variance of Km. Simulation results demonstrate that our unbiased τ-leap method can significantly improve simulation accuracy without sacrificing speed.
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82.30.-b Specific chemical reactions; reaction mechanisms
02.50.Fz Stochastic analysis
02.60.-x Numerical approximation and analysis

Towards fast computations of correlated vibrational wave functions: Vibrational coupled cluster response excitation energies at the two-mode coupling level

Peter Seidler, Mikkel Bo Hansen, and Ove Christiansen

J. Chem. Phys. 128, 154113 (2008); http://dx.doi.org/10.1063/1.2907860 (12 pages) | Cited 13 times

Online Publication Date: 18 April 2008

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An efficient implementation of vibrational coupled cluster theory with two-mode excitations and a two-mode Hamiltonian is described. The algorithm is shown to scale cubically with respect to the number of modes which is identical to the scaling of the corresponding vibrational configuration interaction algorithm. This is achieved through the use of special intermediates. The same algorithm can also be used in vibrational Møller–Plesset calculations. To improve performance, screening techniques have been implemented as well. Test calculations on polyaromatic hydrocarbons with up to 264 coupled modes and model systems with up to 1140 modes are used to illustrate the various features of the algorithm.
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31.15.bw Coupled-cluster theory
31.15.vq Electron correlation calculations for polyatomic molecules
33.15.Mt Rotation, vibration, and vibration-rotation constants

Coarse graining of master equations with fast and slow states

Simone Pigolotti and Angelo Vulpiani

J. Chem. Phys. 128, 154114 (2008); http://dx.doi.org/10.1063/1.2907242 (8 pages) | Cited 6 times

Online Publication Date: 18 April 2008

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We propose a general method for simplifying master equations by eliminating from the description rapidly evolving states. The physical recipe we impose is the suppression of these states and a renormalization of the rates of all the surviving states. In some cases, this decimation procedure can be analytically carried out and is consistent with other analytical approaches, such as in the problem of the random walk in a double well potential. We discuss the application of our method to nontrivial examples: diffusion in a lattice with defects and a model of an enzymatic reaction outside the steady state regime.
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87.15.R- Reactions and kinetics
82.39.Fk Enzyme kinetics
82.20.Wt Computational modeling; simulation

A novel algorithm for creating coarse-grained, density dependent implicit solvent models

Erik C. Allen and Gregory C. Rutledge

J. Chem. Phys. 128, 154115 (2008); http://dx.doi.org/10.1063/1.2899729 (12 pages) | Cited 12 times

Online Publication Date: 18 April 2008

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Implicit solvent simulations are those in which solvent molecules are not explicitly simulated, and the solute-solute interaction potential is modified to compensate for the implicit solvent effect. Implicit solvation is well known in Brownian dynamics of dilute solutions but offers promise to speed up many other types of molecular simulations as well, including studies of proteins and colloids where the local density can vary considerably. This work examines implicit solvent potentials within a more general coarse-graining framework. While a pairwise potential between solute sites is relatively simple and ubiquitous, an additional parametrization based on the local solute concentration has the possibility to increase the accuracy of the simulations with only a marginal increase in computational cost. We describe here a method in which the radial distribution function and excess chemical potential of solute insertion for a system of Lennard–Jones particles are first measured in a fully explicit, all-particle simulation, and then reproduced across a range of solute particle densities in an implicit solvent simulation.
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61.20.Ja Computer simulation of liquid structure
87.14.E- Proteins
82.70.Dd Colloids

Extrapolating potential energy surfaces by scaling electron correlation: Isomerization of bicyclobutane to butadiene

Jesse J. Lutz and Piotr Piecuch

J. Chem. Phys. 128, 154116 (2008); http://dx.doi.org/10.1063/1.2904560 (12 pages) | Cited 9 times

Online Publication Date: 18 April 2008

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The recently proposed potential energy surface (PES) extrapolation scheme, which predicts smooth molecular PESs corresponding to larger basis sets from the relatively inexpensive calculations using smaller basis sets by scaling electron correlation energies [ A. J. C. Varandas and P. Piecuch, Chem. Phys. Lett. 430, 448 (2006) ], is applied to the PESs associated with the conrotatory and disrotatory isomerization pathways of bicyclo[1.1.0]butane to buta-1,3-diene. The relevant electronic structure calculations are performed using the completely renormalized coupled-cluster method with singly and doubly excited clusters and a noniterative treatment of connected triply excited clusters, termed CR-CC(2,3), which is known to provide a highly accurate description of chemical reaction profiles involving biradical transition states and intermediates. A comparison with the explicit CR-CC(2,3) calculations using the large correlation-consistent basis set of the cc-pVQZ quality shows that the cc-pVQZ PESs obtained by the extrapolation from the smaller basis set calculations employing the cc-pVDZ and cc-pVTZ basis sets are practically identical, to within fractions of a millihartree, to the true cc-pVQZ PESs. It is also demonstrated that one can use a similar extrapolation procedure to accurately predict the complete basis set (CBS) limits of the calculated PESs from the results of smaller basis set calculations at a fraction of the effort required by the conventional pointwise CBS extrapolations.
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82.30.Qt Isomerization and rearrangement
82.20.Kh Potential energy surfaces for chemical reactions
31.15.vj Electron correlation calculations for atoms and ions: excited states
31.15.bw Coupled-cluster theory

On the relationship between quantum control landscape structure and optimization complexity

Katharine Moore, Michael Hsieh, and Herschel Rabitz

J. Chem. Phys. 128, 154117 (2008); http://dx.doi.org/10.1063/1.2907740 (12 pages) | Cited 11 times

Online Publication Date: 18 April 2008

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It has been widely observed in optimal control simulations and experiments that state preparation is surprisingly easy to achieve, regardless of the dimension N of the system Hilbert space. In contrast, simulations for the generation of targeted unitary transformations indicate that the effort increases exponentially with N. In order to understand such behavior, the concept of quantum control landscapes was recently introduced, where the landscape is defined as the physical objective, as a function of the control variables. The present work explores how the local structure of the control landscape influences the effectiveness and efficiency of quantum optimal control search efforts. Optimizations of state and unitary transformation preparation using kinematic control variables (i.e., the elements of the action matrix) are performed with gradient, genetic, and simplex algorithms. The results indicate that the search effort scales weakly, or possibly independently, with N for state preparation, while the search effort for the unitary transformation objective increases exponentially with N. Analysis of the mean path length traversed during a search trajectory through the space of action matrices and the local structure along this trajectory provides a basis to explain the difference in the scaling of the search effort with N for these control objectives. Much more favorable scaling for unitary transformation preparation arises upon specifying an initial action matrix based on state preparation results. The consequences of choosing a reduced number of control variables for state preparation is also investigated, showing a significant reduction in performance for using fewer than 2N−2 variables, which is consistent with the topological analysis of the associated landscape.
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03.67.Ac Quantum algorithms, protocols, and simulations
03.65.Ta Foundations of quantum mechanics; measurement theory

Higher excitations for an exponential multireference wavefunction Ansatz and single-reference based multireference coupled cluster Ansatz: Application to model systems H4, P4, and BeH2

Michael Hanrath

J. Chem. Phys. 128, 154118 (2008); http://dx.doi.org/10.1063/1.2899645 (10 pages) | Cited 27 times

Online Publication Date: 21 April 2008

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This article reports on the convergence of the exponential multireference wavefunction Ansatz (MRexpT) [ J. Chem. Phys. 123, 84102 (2005) ] and the single-reference based multireference coupled cluster Ansatz [ J. Chem. Phys. 94, 1229 (1991) ] with respect to higher cluster excitations. The approaches are applied to the H4, P4, and BeH2 model systems according to the recently published analysis by Evangelista et al. [J. Chem. Phys. 125, 154113 (2006) ]. The results show both MRexpT and SRMRCC to be highly accurate although SRMRCC shows problems due to its lack of Fermi vacuum invariance (symmetry breaking).
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31.50.Df Potential energy surfaces for excited electronic states
31.15.bw Coupled-cluster theory

Event-driven dynamics of rigid bodies interacting via discretized potentials

Ramses van Zon and Jeremy Schofield

J. Chem. Phys. 128, 154119 (2008); http://dx.doi.org/10.1063/1.2901173 (9 pages) | Cited 6 times

Online Publication Date: 21 April 2008

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A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The scheme is based on a discretization of an underlying continuous potential that effectively determines the times at which interaction energies change. As in most event-driven approaches, the method consists of specifying a means of computing the free motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion for the terraced potential. The latter two aspects are shown to be simply expressible in terms of the underlying smooth potential. Within this context, algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The method is illustrated on a system composed of rigid rods in which the constituents interact via a terraced potential that depends on the relative orientations of the rods.
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02.70.Ns Molecular dynamics and particle methods
45.40.-f Dynamics and kinematics of rigid bodies
45.20.da Forces and torques
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Benchmark calculations on the adiabatic ionization potentials of M–NH3 (M = Na,Al,Ga,In,Cu,Ag)

Shenggang Li, Kirk A. Peterson, and David A. Dixon

J. Chem. Phys. 128, 154301 (2008); http://dx.doi.org/10.1063/1.2834923 (12 pages) | Cited 4 times

Online Publication Date: 15 April 2008

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The ground states of the M–NH3 (M = Na,Al,Ga,In,Cu,Ag) complexes and their cations have been studied with density functional theory and coupled cluster [CCSD(T)] methods. The adiabatic ionization potentials (AIPs) of these complexes are calculated, and these are compared to results from high-resolution zero-electron kinetic energy photoelectron spectroscopy. By extrapolating the CCSD(T) energies to the complete basis set (CBS) limit and including the core-valence, scalar relativistic, spin-orbit, and zero-point corrections, the CCSD(T) method is shown to be able to predict the AIPs of these complexes to better than 6 meV or 0.15 kcal/mol. 27 exchange-correlation functionals, including one in the local density approximation, 13 in the generalized gradient approximation (GGA), and 13 with hybrid GGAs, were benchmarked in the calculations of the AIPs. The B1B95, mPW1PW91, B98, B97-1, PBE1PBE, O3LYP, TPSSh, and HCTH93 functionals give an average error of 0.1 eV for all the complexes studied, with the B98 functional alone yielding a maximum error of 0.1 eV. In addition, the calculated metal-ammonia harmonic stretching frequencies with the CCSD(T) method are in excellent agreement with their experimental values, whereas the B3LYP method tends to underestimate these stretching frequencies. The metal-ammonia binding energies were also calculated at the CCSD(T)/CBS level, and are in excellent agreement with the available experimental values considering the error limits, except for Ag–NH3 and Ag+–NH3, where the calculations predict stronger bond energies than measured by about 4 kcal/mol, just outside the experimental error bars of ±3 kcal/mol.
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33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.bw Coupled-cluster theory
31.30.jd Relativistic corrections due to negative-energy states or processes

Theoretical investigation of the vibronic spectrum in the X 2Πu electronic state of C6+

Radomir Ranković, Stanka Jerosimić, and Miljenko Perić

J. Chem. Phys. 128, 154302 (2008); http://dx.doi.org/10.1063/1.2894312 (7 pages) | Cited 1 time

Online Publication Date: 15 April 2008

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In this study we employ the recently developed model for handling the Renner–Teller effect in Π electronic states of six-atomic molecules with linear equilibrium geometry to calculate the vibronic spectrum in the X 2Πu electronic state of the C6+ ion. The applied model Hamiltonian excludes the stretching vibrations and end-over-end rotations. On the other hand, it considers the interplay between the vibronic and spin-orbit couplings. The parameters determining the shape of the bending potential energy surfaces are computed by means of a Density functional theory, and the spin-orbit coupling constant by the Multireference CI program using state-averaged complete active space self-consistent field (SA-CASSCF) wavefunctions. The results of the present study are expected to motivate and help future experimental investigations on C6+.
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33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.50.-x Potential energy surfaces
31.15.xr Self-consistent-field methods

C5N− anion and new carbenic isomers of cyanodiacetylene: A matrix isolation IR study

Anne Coupeaud, Michał Turowski, Marcin Gronowski, Nathalie Piétri, Isabelle Couturier-Tamburelli, Robert Kołos, and Jean-Pierre Aycard

J. Chem. Phys. 128, 154303 (2008); http://dx.doi.org/10.1063/1.2894875 (6 pages) | Cited 4 times

Online Publication Date: 15 April 2008

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Products of the vacuum-UV photolysis of cyanodiacetylene (HC5N) in solid argon—the anion C5N−, imine HNC5, and the branched carbene C4(H)CN—have been identified by IR absorption spectroscopy, in addition to the already discovered isonitrile HC4NC. Spectral assignments were assisted by deuterium substitution experiments, by BD(T) calculations, and by the results of a recent density functional theory study.
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82.50.Hp Processes caused by visible and UV light
82.80.Gk Analytical methods involving vibrational spectroscopy
82.20.Db Transition state theory and statistical theories of rate constants

Density-functional study of structural and electronic properties of SinCn (n = 1–10) clusters

Jinyu Hou and Bin Song

J. Chem. Phys. 128, 154304 (2008); http://dx.doi.org/10.1063/1.2895051 (11 pages) | Cited 11 times

Online Publication Date: 15 April 2008

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Density-functional theory with generalized gradient approximation for the exchange-correlation potential has been used to calculate the structural and electronic structure of SinCn (n = 1–10) clusters. The geometries are found to undergo a structural change from two dimensional to three dimensional when the cluster size n equals 4. Cagelike structures are favored as the cluster size increases. A distinct segregation between the silicon and carbon atoms is observed for these clusters. It is found that the C atoms favor to form five-membered rings as the cluster size n increases. However, the growth motif for Si atoms is not observed. The SinCn clusters at n = 2, 6, and 9 are found to possess relatively higher stability. On the basis of the lowest-energy geometries obtained, the size dependence of cluster properties such as binding energy, HOMO-LUMO gap, Mulliken charge, vibrational spectrum, and ionization potential has been computed and analyzed. The bonding characteristics of the clusters are discussed.
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36.40.Mr Spectroscopy and geometrical structure of clusters
36.40.Cg Electronic and magnetic properties of clusters
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis
31.15.eg Exchange-correlation functionals (in current density functional theory)
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