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21 Jun 2010

Volume 132, Issue 23, Articles (23xxxx)

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J. Chem. Phys. 132, 234501 (2010); http://dx.doi.org/10.1063/1.3435213 (10 pages)

S. Yang, D. Z. Xu, Z. Song, and C. P. Sun
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Communications: Is quantum chemical treatment of biopolymers accurate? Intramolecular basis set superposition error (BSSE)

Roman M. Balabin

J. Chem. Phys. 132, 231101 (2010); http://dx.doi.org/10.1063/1.3442466 (4 pages) | Cited 13 times

Online Publication Date: 16 June 2010

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The accuracy of quantum chemical treatment of biopolymers by means of density functional theory is brought into question in terms of intramolecular basis set superposition error (BSSE). Secondary structure forms—β-strands (C5; fully extended conformation), repeated γ-turns (C7), 310-helices (C10), and α-helices (C13)—of homopolypeptides (polyglycine and polyalanine) are used as representative examples. The studied molecules include Ace(Gly)5NH2, Ace(Gly)10NH2, Ace(Ala)5NH2, and Ace(Ala)10NH2. The counterpoise correction procedure was found to produce reliable estimations for the BSSE values (other methods of BSSE correction are discussed). The calculations reported here used the B3LYP, PBE0 (PBE1PBE), and BMK density functionals with different basis sets [from 6-31G(d) to 6-311+G(3df,3pd)] to estimate the influence of basis set size on intramolecular BSSE. Calculation of BSSE was used to determine the deviation of the current results from the complete basis set limit. Intramolecular BSSE was found to be nonadditive with respect to biopolymer size, in contrast to claims in recent literature. The error, which is produced by a basis set superposition, was found to exceed 4 kcal mol−1 when a medium-sized basis set was used. This indicates that this error has the same order of magnitude as the relative energy differences of secondary structure elements of biopolymers. This result makes all recent reports on the gas-phase stability of homopolypeptides and their analogs questionable.
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87.15.ag Quantum calculations
87.15.bd Secondary structure
36.20.Hb Configuration (bonds, dimensions)
31.15.E- Density-functional theory
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Communications: Accurate and efficient approximations to explicitly correlated coupled-cluster singles and doubles, CCSD-F12

Christof Hättig, David P. Tew, and Andreas Köhn

J. Chem. Phys. 132, 231102 (2010); http://dx.doi.org/10.1063/1.3442368 (4 pages) | Cited 25 times

Online Publication Date: 16 June 2010

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We propose a novel explicitly correlated coupled-cluster singles and doubles method CCSD(F12∗), which retains the accuracy of CCSD-F12 while the computational costs are only insignificantly larger than those for a conventional CCSD calculation.
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31.15.bw Coupled-cluster theory
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Communications: The fractional Stokes–Einstein equation: Application to water

Kenneth R. Harris

J. Chem. Phys. 132, 231103 (2010); http://dx.doi.org/10.1063/1.3455342 (3 pages) | Cited 2 times

Online Publication Date: 21 June 2010

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Previously [ K. R. Harris, J. Chem. Phys. 131, 054503 (2009) ] it was shown that both real and model liquids fit the fractional form of the Stokes–Einstein relation [fractional Stokes–Einstein (FSE)] over extended ranges of temperature and density. For example, the self-diffusion coefficient and viscosity of the Lennard-Jones fluid fit the relation (D/T) = (1/η)t with t = (0.921±0.003) and a range of molecular and ionic liquids for which high pressure data are available behave similarly, with t values between 0.79 and 1. At atmospheric pressure, normal and heavy water were also found to fit FSE from 238 to 363 K and from 242 to 328 K, respectively, but with distinct transitions in the supercooled region at about 258 and 265 K, respectively, from t = 0.94 (high temperature) to 0.67 (low temperature). Here the recent self-diffusion data of Yoshida et al. [J. Chem. Phys. 129, 214501 (2008)] for the saturation line are used to extend the high temperature fit to FSE to 623 K for both isotopomers. The FSE transition temperature in bulk water can be contrasted with much lower values reported in the literature for confined water.
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66.10.cg Mass diffusion, including self-diffusion, mutual diffusion, tracer diffusion, etc.
66.20.-d Viscosity of liquids; diffusive momentum transport
61.20.Gy Theory and models of liquid structure
64.70.Ja Liquid-liquid transitions
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Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory

Benoît Roux and Haibo Yu

J. Chem. Phys. 132, 234101 (2010); http://dx.doi.org/10.1063/1.3436632 (13 pages) | Cited 5 times

Online Publication Date: 15 June 2010

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Quasichemical theory (QCT) provides a framework that can be used to partition the influence of the solvent surrounding an ion into near and distant contributions. Within QCT, the solvation properties of the ion are expressed as a sum of configurational integrals comprising only the ion and a small number of solvent molecules. QCT adopts a particularly simple form if it is assumed that the clusters undergo only small thermal fluctuations around a well-defined energy minimum and are affected exclusively in a mean-field sense by the surrounding bulk solvent. The fluctuations can then be integrated out via a simple vibrational analysis, leading to a closed-form expression for the solvation free energy of the ion. This constitutes the primitive form of quasichemical theory (pQCT), which is an approximate mathematical formulation aimed at reproducing the results from the full many-body configurational averages of statistical mechanics. While the results from pQCT from previous applications are reasonable, the accuracy of the approach has not been fully characterized and its range of validity remains unclear. Here, a direct test of pQCT for a set of ion models is carried out by comparing with the results of free energy simulations with explicit solvent. The influence of the distant surrounding bulk on the cluster comprising the ion and the nearest solvent molecule is treated both with a continuum dielectric approximation and with free energy perturbation molecular dynamics simulations with explicit solvent. The analysis shows that pQCT can provide an accurate framework in the case of a small cation such as Li+. However, the approximation encounters increasing difficulties when applied to larger cations such as Na+, and particularly for K+. This suggests that results from pQCT should be interpreted with caution when comparing ions of different sizes.
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82.30.Nr Association, addition, insertion, cluster formation
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
82.20.Wt Computational modeling; simulation

Ab initio floating occupation molecular orbital-complete active space configuration interaction: An efficient approximation to CASSCF

Petr Slavíček and Todd J. Martínez

J. Chem. Phys. 132, 234102 (2010); http://dx.doi.org/10.1063/1.3436501 (10 pages) | Cited 4 times

Online Publication Date: 15 June 2010

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We have implemented a complete active space configuration interaction method (CASCI) based on floating occupation molecular orbitals (FOMOs) at the ab initio level. The performance of this FOMO-CASCI method was investigated for potential applications in photochemistry and photodynamics. We found that FOMO-CASCI often represents a good approximation to the state-averaged complete active space self-consistent field (SA-CASSCF) method. FOMO-CASCI is therefore an attractive alternative for use in ab initio photodynamics. The method is more efficient and more stable than SA-CASSCF. We also discuss some problematic cases for the FOMO-CASCI approach. Possible extensions of the FOMO-CASCI approach are discussed briefly.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Interlaced P3M algorithm with analytical and ik-differentiation

Alexey Neelov and Christian Holm

J. Chem. Phys. 132, 234103 (2010); http://dx.doi.org/10.1063/1.3430521 (15 pages) | Cited 4 times

Online Publication Date: 15 June 2010

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The interlacing technique of Hockney and Eastwood is extended to the particle-particle, particle-mesh (P3M) algorithm with analytical and ik-differentiation that computes the approximate Coulomb forces between N point particles in a periodic box. Interlacing means that one makes two separate computations of the reciprocal-space Ewald force, using two grids shifted with respect to each other by half of the diagonal of the grid subcell, and then takes the average of the two forces. The resulting algorithms compare favorably against their own noninterlaced versions and against the interlaced smooth particle-mesh Ewald algorithm. In our tests, the accuracy of the interlaced P3M methods was usually more than an order of magnitude higher than that of the other particle-mesh algorithms with the same parameter values. This accuracy gain can be converted into a speedup if the parameters of the algorithm are changed. Interlacing allows one to increase the grid spacing by up to a factor of 2 while keeping the same accuracy. A priori error estimates for the new algorithms are constructed, and the removal of the spurious self-force term is discussed. The success of interlacing is shown to be due to the fact that it suppresses the aliasing effects in the forces. It should be easy to incorporate the interlaced P3M algorithms into an existing simulation package, since this only requires a minor modification of the particle-mesh Ewald part of the code.
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34.10.+x General theories and models of atomic and molecular collisions and interactions (including statistical theories, transition state, stochastic and trajectory models, etc.)
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
02.60.Jh Numerical differentiation and integration
02.70.Dh Finite-element and Galerkin methods

Coulomb explosion in dicationic noble gas clusters: A genetic algorithm-based approach to critical size estimation for the suppression of Coulomb explosion and prediction of dissociation channels

Subhajit Nandy, Pinaki Chaudhury, and S. P. Bhattacharyya

J. Chem. Phys. 132, 234104 (2010); http://dx.doi.org/10.1063/1.3439690 (8 pages)

Online Publication Date: 16 June 2010

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We present a genetic algorithm based investigation of structural fragmentation in dicationic noble gas clusters, Arn+2, Krn+2, and Xen+2, where n denotes the size of the cluster. Dications are predicted to be stable above a threshold size of the cluster when positive charges are assumed to remain localized on two noble gas atoms and the Lennard-Jones potential along with bare Coulomb and ion-induced dipole interactions are taken into account for describing the potential energy surface. Our cutoff values are close to those obtained experimentally [ P. Scheier and T. D. Mark, J. Chem. Phys. 11, 3056 (1987) ] and theoretically [ J. G. Gay and B. J. Berne, Phys. Rev. Lett. 49, 194 (1982) ]. When the charges are allowed to be equally distributed over four noble gas atoms in the cluster and the nonpolarization interaction terms are allowed to remain unchanged, our method successfully identifies the size threshold for stability as well as the nature of the channels of dissociation as function of cluster size. In Arn2+, for example, fissionlike fragmentation is predicted for n = 55 while for n = 43, the predicted outcome is nonfission fragmentation in complete agreement with earlier work [ Golberg et al., J. Chem. Phys. 100, 8277 (1994) ].
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36.40.Qv Stability and fragmentation of clusters
36.40.Wa Charged clusters
34.20.Gj Intermolecular and atom-molecule potentials and forces
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
31.50.-x Potential energy surfaces

Time-dependent transport through molecular junctions

San-Huang Ke, Rui Liu, Weitao Yang, and Harold U. Baranger

J. Chem. Phys. 132, 234105 (2010); http://dx.doi.org/10.1063/1.3435351 (6 pages) | Cited 4 times

Online Publication Date: 16 June 2010

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We investigate transport properties of molecular junctions under two types of bias—a short time pulse or an ac bias—by combining a solution for Green’s functions in the time domain with electronic structure information coming from ab initio density functional calculations. We find that the short time response depends on lead structure, bias voltage, and barrier heights both at the molecule-lead contacts and within molecules. Under a low frequency ac bias, the electron flow either tracks or leads the bias signal (resistive or capacitive response) depending on whether the junction is perfectly conducting or not. For high frequency, the current lags the bias signal due to the kinetic inductance. The transition frequency is an intrinsic property of the junctions.
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85.65.+h Molecular electronic devices
02.30.-f Function theory, analysis

A time-dependent semiempirical approach to determining excited states

Lizette A. Bartell, Michael R. Wall, and Daniel Neuhauser

J. Chem. Phys. 132, 234106 (2010); http://dx.doi.org/10.1063/1.3453683 (6 pages) | Cited 5 times

Online Publication Date: 16 June 2010

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We study a time-dependent semiempirical method to determine excitation energies, TD-PM3. This semiempirical method allows large molecules to be treated. A Linear-response Chebyshev approach yields the TD-PM3 spectrum very efficiently. Spectra and excitation energies were tested by comparing it with the results obtained using TD-DFT (Time Dependent-Density Functional Theory), using both small and large basis sets. They were also compared to PM3-CI, Time Dependent-Hartree Fock using the STO-3G basis set, and to experiment. TD-PM3 results generally match better the large-basis set calculations than the small-basis TD-DFT do; excitation energies are almost always accurate to within about 20% or less, except for a few small molecules. Accuracy improves as the molecules get larger.
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31.15.xp Perturbation theory

An algebraic proof of generalized Wick theorem

Liguo Kong, Marcel Nooijen, and Debashis Mukherjee

J. Chem. Phys. 132, 234107 (2010); http://dx.doi.org/10.1063/1.3439395 (8 pages) | Cited 4 times

Online Publication Date: 16 June 2010

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The multireference normal order theory, introduced by Kutzelnigg and Mukherjee [J. Chem. Phys. 107, 432 (1997)] , is defined explicitly, and an algebraic proof is given for the corresponding contraction rules for a product of any two normal ordered operators. The proof does not require that the contractions be cumulants, so it is less restricted. In addition, it follows from the proof that the normal order theory and corresponding contraction rules hold equally well if the contractions are only defined up to a certain level. These relaxations enable us to extend the original normal order theory. As a particular example, a quasi-normal-order theory is developed, in which only one-body contractions are present. These contractions are based on the one-particle reduced density matrix.
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02.50.-r Probability theory, stochastic processes, and statistics

Modeling diffusion in restricted systems using the heat kernel expansion

Bahman Ghadirian, Tim Stait-Gardner, Reynaldo Castillo, and William S. Price

J. Chem. Phys. 132, 234108 (2010); http://dx.doi.org/10.1063/1.3451124 (10 pages)

Online Publication Date: 17 June 2010

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The averaged return-to-origin probability of finding a diffusing particle within a volume or in the neighborhood of the surface of a bounded region can be separated into a volume and a surface integral of the corresponding probability densities. However with the usual treatments (e.g., the commonly encountered diffusion propagator approach) there is no clear method to separate the integration of the diffusion propagators in each domain. Here we propose a general procedure based on applying the heat kernel expansion in restricted diffusion problems for the Green’s function of the diffusion equation on an arbitrary region with an arbitrary boundary condition. We apply this method to the treatment of surface reaction rate in a sphere subject to the reflecting boundary condition. We determine that the rate of diffusion of a particle from the interior to the surface of the sphere changes by the square root of time plus some extra correction terms. Further, we are able to relate the diffusion propagator to the invariant properties of the region. Also in this approach we investigate how the heat kernel expansion can be applied to the problem of determining the return-to-origin probability, where we obtain a more precise result for the expansion of this probability in the case of a sphere. The advantage of this method lies in its generality and applicability to any geometrical boundary configuration and any kind of boundary condition.
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05.60.-k Transport processes
02.30.-f Function theory, analysis
02.50.Cw Probability theory

Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids

O. Anatole von Lilienfeld and Alexandre Tkatchenko

J. Chem. Phys. 132, 234109 (2010); http://dx.doi.org/10.1063/1.3432765 (11 pages) | Cited 11 times

Online Publication Date: 17 June 2010

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We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod–Teller–Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed “on the fly” from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang–Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He–Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine-d(CG)2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
36.20.-r Macromolecules and polymer molecules

Methods for finding transition states on reduced potential energy surfaces

Steven K. Burger and Paul W. Ayers

J. Chem. Phys. 132, 234110 (2010); http://dx.doi.org/10.1063/1.3445772 (7 pages) | Cited 5 times

Online Publication Date: 17 June 2010

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Three new algorithms are presented for determining transition state (TS) structures on the reduced potential energy surface, that is, for problems in which a few important degrees of freedom can be isolated. All three methods use constrained optimization to rapidly find the TS without an initial Hessian evaluation. The algorithms highlight how efficiently the TS can be located on a reduced surface, where the rest of the degrees of freedom are minimized. The first method uses a nonpositive definite quasi-Newton update for the reduced degrees of freedom. The second uses Shepard interpolation to fit the Hessian and starts from a set of points that bound the TS. The third directly uses a finite difference scheme to calculate the reduced degrees of freedom of the Hessian of the entire system, and searches for the TS on the full potential energy surface. All three methods are tested on an epoxide hydrolase cluster, and the ring formations of cyclohexane and cyclobutenone. The results indicate that all the methods are able to converge quite rapidly to the correct TS, but that the finite difference approach is the most efficient.
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31.50.Df Potential energy surfaces for excited electronic states
02.70.Bf Finite-difference methods
02.60.Ed Interpolation; curve fitting
31.15.xf Finite-difference schemes
36.40.Cg Electronic and magnetic properties of clusters

Correlation energy of two electrons in a ball

Pierre-François Loos and Peter M. W. Gill

J. Chem. Phys. 132, 234111 (2010); http://dx.doi.org/10.1063/1.3455706 (6 pages) | Cited 7 times

Online Publication Date: 17 June 2010

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We study the ground-state correlation energy Ec of two electrons of opposite spin confined within a D-dimensional ball (D ≥ 2) of radius R. In the high-density regime, we report accurate results for the exact and restricted Hartree–Fock energy, using a Hylleraas-type expansion for the former and a simple polynomial basis set for the latter. By investigating the exact limiting correlation energy Ec(0) = limR→0Ec for various values of D, we test our recent conjecture [ P.-F. Loos and P. M. W. Gill, J. Chem. Phys. 131, 241101 (2009) ] that in the large-D limit, Ec(0) ∼ −δ2/8 for any spherically symmetric confining external potential, where δ = 1/(D−1).
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31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.xr Self-consistent-field methods

Replication of noise-sustained autocatalytic chemical structures

Gonzalo G. Izús, Roberto R. Deza, and Alejandro D. Sánchez

J. Chem. Phys. 132, 234112 (2010); http://dx.doi.org/10.1063/1.3432622 (7 pages) | Cited 2 times

Online Publication Date: 17 June 2010

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Autocatalytic systems in a differential-flow reactor may undergo a differential-flow-induced chemical instability toward a convectively unstable regime, in which noise-sustained structures may appear. This is the case of a system with Gray–Scott kinetics in a packed-bed reactor, as reported in [ B. von Haeften and G. Izús, Phys. Rev. E 67, 056207 (2003) ]. In this work, two identical copies of such a system are coupled in master-slave configuration and submitted to independent spatiotemporal Gaussian white noise sources. Numerical simulation of two-dimensional reactors with uniform and Poiseuille flows reveals that the slave system replicates to a very high degree of precision and the convective patterns arising in the master one due to the presence of noise. The quality of this synchronization is assessed through several measures. A convective instability in the synchronization manifold is theoretically predicted and numerically confirmed.
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82.40.Ck Pattern formation in reactions with diffusion, flow and heat transfer
47.54.-r Pattern selection; pattern formation
82.40.Np Temporal and spatial patterns in surface reactions
47.70.Fw Chemically reactive flows

Structural manifestation of the delocalization error of density functional approximations: C4N+2 rings and C20 bowl, cage, and ring isomers

Tim Heaton-Burgess and Weitao Yang

J. Chem. Phys. 132, 234113 (2010); http://dx.doi.org/10.1063/1.3445266 (5 pages) | Cited 5 times

Online Publication Date: 18 June 2010

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The ground state structure of C4N+2 rings is believed to exhibit a geometric transition from angle alternation (N ≤ 2) to bond alternation (N>2). All previous density functional theory (DFT) studies on these molecules have failed to reproduce this behavior by predicting either that the transition occurs at too large a ring size, or that the transition leads to a higher symmetry cumulene. Employing the recently proposed perspective of delocalization error within DFT we rationalize this failure of common density functional approximations (DFAs) and present calculations with the rCAM-B3LYP exchange-correlation functional that show an angle-to-bond-alternation transition between C10 and C14. The behavior exemplified here manifests itself more generally as the well known tendency of DFAs to bias toward delocalized electron distributions as favored by Hückel aromaticity, of which the C4N+2 rings provide a quintessential example. Additional examples are the relative energies of the C20 bowl, cage, and ring isomers; we show that the results from functionals with minimal delocalization error are in good agreement with CCSD(T) results, in contrast to other commonly used DFAs. An unbiased DFT treatment of electron delocalization is a key for reliable prediction of relative stability and hence the structures of complex molecules where many structure stabilization mecahnisms exist.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.bw Coupled-cluster theory
33.15.Fm Bond strengths, dissociation energies
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.bu Semi-empirical and empirical calculations (differential overlap, Hückel, PPP methods, etc.)

Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration

Henk Eshuis, Julian Yarkony, and Filipp Furche

J. Chem. Phys. 132, 234114 (2010); http://dx.doi.org/10.1063/1.3442749 (9 pages) | Cited 19 times

Online Publication Date: 21 June 2010

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The random phase approximation (RPA) is an increasingly popular post-Kohn–Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller–Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [ A. Tajti et al., J. Chem. Phys. 121, 11599 (2004) ] and MOLEKEL [ F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998) ] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N4 log N) operations and O(N3) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30–40 grid points yield μH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn–Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [ J. Jung et al., Phys. Rev. B 70, 205107 (2004) ]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.xt Variational techniques
31.15.xr Self-consistent-field methods
02.30.Uu Integral transforms
31.15.E- Density-functional theory
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

Topology of cyclo-octane energy landscape

Shawn Martin, Aidan Thompson, Evangelos A. Coutsias, and Jean-Paul Watson

J. Chem. Phys. 132, 234115 (2010); http://dx.doi.org/10.1063/1.3445267 (7 pages) | Cited 1 time

Online Publication Date: 21 June 2010

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Understanding energy landscapes is a major challenge in chemistry and biology. Although a wide variety of methods have been invented and applied to this problem, very little is understood about the actual mathematical structures underlying such landscapes. Perhaps the most general assumption is the idea that energy landscapes are low-dimensional manifolds embedded in high-dimensional Euclidean space. While this is a very mild assumption, we have discovered an example of an energy landscape which is nonmanifold, demonstrating previously unknown mathematical complexity. The example occurs in the energy landscape of cyclo-octane, which was found to have the structure of a reducible algebraic variety, composed of the union of a sphere and a Klein bottle, intersecting in two rings.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

General no-go condition for stochastic pumping

Christian Maes, Karel Netočný, and Simi R. Thomas

J. Chem. Phys. 132, 234116 (2010); http://dx.doi.org/10.1063/1.3446811 (6 pages) | Cited 7 times

Online Publication Date: 21 June 2010

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The control of chemical dynamics requires understanding the effect of time-dependent transition rates between states of chemomechanical molecular configurations. Pumping refers to generating a net current, e.g., per period in the time dependence, through a cycle of consecutive states. The work of artificial machines or synthesized molecular motors depends on it. In this paper we give short and simple proofs of no-go theorems, some of which appeared before but here with essential extensions to non-Markovian dynamics, including the study of the diffusion limit. It allows to exclude certain protocols in the working of chemical motors where only the depth of the energy well is changed in time and not the barrier height between pairs of states. We also show how pre-existing steady state currents are, in general, modified with a multiplicative factor when this time dependence is turned on.
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82.20.Db Transition state theory and statistical theories of rate constants
82.30.-b Specific chemical reactions; reaction mechanisms
02.50.Ga Markov processes
33.15.Bh General molecular conformation and symmetry; stereochemistry
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Quantum-dynamical consequences of the permutation symmetry of methyl groups

Thomas Grohmann and Monika Leibscher

J. Chem. Phys. 132, 234301 (2010); http://dx.doi.org/10.1063/1.3425880 (14 pages) | Cited 1 time

Online Publication Date: 15 June 2010

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We identify the nuclear spin isomers of nitromethane (CH3NO2) and discuss how symmetry arguments may be used to determine the spectrum and eigenfunctions of the spatial and spin-dependent Hamiltonians in an elegant way. Furthermore, we explore the effect of nuclear spin on the dynamics of the methyl group induced by a time-dependent magnetic field. We demonstrate that dipolar interactions between the protons can give rise to rotation of the methyl group and show within a one-dimensional model and first order time-dependent perturbation theory that the induced motion is unidirectional and nuclear-spin selective.
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33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.xp Perturbation theory
33.20.Sn Rotational analysis
36.20.Ng Vibrational and rotational structure, infrared and Raman spectra

Toward elucidating the mechanism of femtosecond pulse shaping control in photodynamics of molecules by velocity map photoelectron and ion imaging

Daniel Irimia and Maurice H. M. Janssen

J. Chem. Phys. 132, 234302 (2010); http://dx.doi.org/10.1063/1.3436720 (9 pages) | Cited 4 times

Online Publication Date: 15 June 2010

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The control of photofragmentation and ionization in a polyatomic molecule has been studied by femtosecond chirped laser pulse excitation and velocity map photoelectron and ion imaging. The experiments aimed at controlling and investigating the photodynamics in CH2BrCl using tunable chirped femtosecond pulses in the visible wavelength region 509–540 nm at maximum intensities of about 4×1013 W/cm2. We observe that the time-of-flight mass spectra as well as the photoelectron images can be strongly modified by manipulating the chirp parameter of ultrashort laser pulses. Specifically, a strong enhancement of the CH2Cl+/CH2BrCl+ ion ratio by a factor of five and changes in the photoelectron spectra are observed for positively chirped pulses centered near 520 nm. These changes are only observed within a narrow window of wavelengths around 520 nm and only for positively chirped pulses. From the combination of the photoelectron spectra and the ion recoil energy of the CH2Cl+ fragment we can deduce that the parent ionization and fragmentation is induced by a multiphoton excitation with five photons. The photoelectron images and the fragment ion images also provide the anisotropy (β-parameter) of the various electron bands and fragment ions. We conclude that multiphoton excitation of the highest occupied 22a′ and 8a″ CH2BrCl molecular orbitals of Br-character are both involved in the five-photon ionization, however, only excitation of the 22a′ orbital appears to be (mostly) involved in the chirped control dynamics leading to enhanced fragmentation to CH2Cl+(math A′)+Br(2P3/2). We propose that a wavepacket following or a time-delay resonance mechanism between the two-photon excited nx(Br,22a′)→(2A′) repulsive surface and the three-photon near-resonant nx(Br,22a′)→Rydberg(A′) state of the neutral CH2BrCl molecule is responsible for the enhanced excitation of the nx(Br,22a′) molecular orbital with up-chirped pulses. This leads to enhanced ionization to a configuration in the CH2BrCl+(math A′) continuum just above the dissociation limit of the CH2Cl++Br(2P3/2) channel, resulting in enhanced fragmentation.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.60.+q Photoelectron spectra
33.20.Kf Visible spectra
33.15.Ta Mass spectra
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)

The Fock space method of vibrational analysis

Christof Jung and Howard S. Taylor

J. Chem. Phys. 132, 234303 (2010); http://dx.doi.org/10.1063/1.3428618 (16 pages) | Cited 1 time

Online Publication Date: 15 June 2010

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A reformulation of a semiclassical theory that presently seems uniquely capable of interpreting generic complex multiresonant vibrational spectra is presented. Once given the spectroscopic Hamiltonian which reveals the set of possible resonant couplings and its eigenstates, the new and old formulations both yield without any further computation level by level dynamical assignments for the spectra. Computing a simple trajectory in phase space reveals the motions that when quantized yield the assigned levels. The reformulation introduces two new projected representations of the wave functions. The first is in action space and the second in angle space. The projected representations often allow the reduced angle space, where nodal searches are made, to be of lower dimension than formally occurred. In addition the action representation is a similarly lower dimension lattice representation whose discreteness and regularity allow higher reduced dimensions to be studied. The lattice representation is used to produce a significantly more complete and detailed assignment of the thiophosgene spectrum than previously published.
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33.20.Tp Vibrational analysis
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
03.65.Sq Semiclassical theories and applications

The permanent electric dipole moment of vanadium monosulfide

Xiujuan Zhuang and Timothy C. Steimle

J. Chem. Phys. 132, 234304 (2010); http://dx.doi.org/10.1063/1.3454722 (8 pages) | Cited 1 time

Online Publication Date: 16 June 2010

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A number of low-J lines of the C 4Σ−←X 4Σ− (0,0) band of a supersonic molecular beam sample of vanadium monosulfide (VS) have been recorded at a resolution of approximately 50 MHz by laser excitation spectroscopy. The electric field induced shift and splitting have been analyzed to give the permanent electric dipole moments μ of the C 4Σ−(υ = 0) and X 4Σ−(υ = 0) states as 2.38(13) and 5.16(5) D, respectively. An electrostatic model is used to predict μ for VS and VO. A molecular orbital correlation diagram is used to rationalize the trends in experimentally observed μ values of the 3d-monosulfides and 3d-monoxides. A comparison with theoretical predictions is made.
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33.20.Bx Radio-frequency and microwave spectra
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
37.20.+j Atomic and molecular beam sources and techniques
33.70.Jg Line and band widths, shapes, and shifts

Intermolecular potential energy surface of the water-carbon dioxide complex

Jan Makarewicz

J. Chem. Phys. 132, 234305 (2010); http://dx.doi.org/10.1063/1.3439693 (10 pages) | Cited 4 times

Online Publication Date: 16 June 2010

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A complete intermolecular potential energy surface (PES) of the H2O–CO2 complex has been constructed using a large scale ab initio calculations. This PES was sampled at 23 000 points of a five dimensional configuration space of the intermolecular coordinates. The interaction energy was calculated using the second order Møller–Plesset perturbation method in conjunction with the standard aug-cc-pVTZ basis set supplemented by bond functions. Single-point energy values were used to construct the analytical many-body representations of the PES that was further improved using a set of the interaction energy values calculated along the one-dimensional cuts of PES by employing the coupled cluster singles and doubles including connected triples method. The accurate data on the structure and energetics of the complex considered have been reported. The analysis of the PES determined revealed its complex structure. A few bifurcations were found on the minimum energy paths along the coordinates describing the radial and angular motions. For the torsional motion, four symmetrically equivalent potential barriers were found as a consequence of the bifurcations, so earlier models of this motion assuming two equivalent potential barriers were justified only for the lowest torsional states.
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31.50.-x Potential energy surfaces

High resolution mass analysis of N- and C-terminal negative ions resulting from resonance electron capture by aliphatic amino acids

Pavel V. Shchukin, Mars V. Muftakhov, Jeff Morré, Max L. Deinzer, and Yury V. Vasil’ev

J. Chem. Phys. 132, 234306 (2010); http://dx.doi.org/10.1063/1.3436719 (11 pages) | Cited 1 time

Online Publication Date: 16 June 2010

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High mass resolving power was applied to study resonance electron capture by glycine, alanine, and valine, and accurate mass measurements helped to distinguish between some negative ions having the same nominal masses. It was established that the C- and N-terminal negative ions of the same nominal masses were formed at different electron energies from different resonance states. The typical fragmentation pathways in deprotonated amino acids via loss of water initiated by collisional activation were not observed upon resonant electron capture by aliphatic amino acids. Instead, [M-18]− negative ions in the vicinity of 5 eV were found to be associated with simultaneous loss of either ammonia and a hydrogen atom or an amino group and a hydrogen molecule.
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87.15.M- Spectra of biomolecules
87.15.K- Molecular interactions; membrane-protein interactions
87.15.rs Dissociation
87.15.ht Ultrafast dynamics; charge transfer
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