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28 Jun 2008

Volume 128, Issue 24, Articles (24xxxx)

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Announcement: Online manuscript submission and peer review via Peer X-Press

Mark M. Cassar

J. Chem. Phys. 128, 240201 (2008); http://dx.doi.org/10.1063/1.2952652 (1 page)

Online Publication Date: 26 June 2008

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A generalized Poisson equation and short-range self-interaction energies

Sergey A. Varganov, Andrew T. B. Gilbert, and Peter M. W. Gill

J. Chem. Phys. 128, 241101 (2008); http://dx.doi.org/10.1063/1.2945298 (4 pages) | Cited 3 times

Online Publication Date: 24 June 2008

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We generalize the Poisson equation to attenuated Newtonian potentials. If the attenuation is at least exponential, the equation provides a local mapping between the density and its potential. We use this to derive several density functionals for the short-range self-interaction energy.
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02.30.Jr Partial differential equations
02.60.Lj Ordinary and partial differential equations; boundary value problems

A 140 GHz prepolarizer for dissolution dynamic nuclear polarization

S. Jannin, A. Comment, F. Kurdzesau, J. A. Konter, P. Hautle, B. van den Brandt, and J. J. van der Klink

J. Chem. Phys. 128, 241102 (2008); http://dx.doi.org/10.1063/1.2951994 (4 pages) | Cited 29 times

Online Publication Date: 25 June 2008

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Apart from their very classical use to build polarized targets for particle physics, the methods of dynamic nuclear polarization (DNP) have more recently found application for sensitivity enhancement in high-resolution NMR, both in the solid and in the liquid state. It is often thought that the possible signal enhancement in such applications deteriorates when the DNP is performed at higher fields. We show that for a dissolution-DNP method that uses conventional (2,2,6,6-tetramethylpiperidine 1-oxyl) radicals as the paramagnetic agent, this is not the case for fields up to 5 T.
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76.70.Fz Double nuclear magnetic resonance (DNMR), dynamical nuclear polarization
76.60.-k Nuclear magnetic resonance and relaxation
64.75.Bc Solubility

Absolute level-resolved reactive and inelastic rate constants in Li+Li2∗

Steven Coppage, Paula Matei, and Brian Stewart

J. Chem. Phys. 128, 241103 (2008); http://dx.doi.org/10.1063/1.2951992 (4 pages) | Cited 2 times

Online Publication Date: 30 June 2008

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We have used nuclear parity-changing collisions to obtain absolute level-to-level rate constants for reactive scattering in a triatomic system with identical nuclei. We have determined rate constants for the system 7Li2∗(A 1Σu+)(vi = 2,ji = 19)+7Li→7Li+7Li2∗(A 1Σu+)(vf,jf), from laser-induced fluorescence spectra of lithium vapor in a heat pipe oven. Parity-preserving collisions yielded measurements of absolute rotationally and vibrationally inelastic rate constants as well. We compare the reactive rate constants with statistical prior distributions and the inelastic results with previously measured results on the Ne+7Li2∗ system.
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34.50.Ez Rotational and vibrational energy transfer
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.50.Dq Fluorescence and phosphorescence spectra
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back to top Theoretical Methods and Algorithms

Time-dependent density-functional theory in the projector augmented-wave method

Michael Walter, Hannu Häkkinen, Lauri Lehtovaara, Martti Puska, Jussi Enkovaara, Carsten Rostgaard, and Jens Jørgen Mortensen

J. Chem. Phys. 128, 244101 (2008); http://dx.doi.org/10.1063/1.2943138 (10 pages) | Cited 12 times

Online Publication Date: 23 June 2008

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We present the implementation of the time-dependent density-functional theory both in linear-response and in time-propagation formalisms using the projector augmented-wave method in real-space grids. The two technically very different methods are compared in the linear-response regime where we found perfect agreement in the calculated photoabsorption spectra. We discuss the strengths and weaknesses of the two methods as well as their convergence properties. We demonstrate different applications of the methods by calculating excitation energies and excited state Born–Oppenheimer potential surfaces for a set of atoms and molecules with the linear-response method and by calculating nonlinear emission spectra using the time-propagation method.
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31.15.E- Density-functional theory
31.50.Df Potential energy surfaces for excited electronic states
43.35.Ud Thermoacoustics, high temperature acoustics, photoacoustic effect

Atomic approximation to the projection on electronic states in the Douglas-Kroll-Hess approach to the relativistic Kohn-Sham method

Alexei V. Matveev and Notker Rösch

J. Chem. Phys. 128, 244102 (2008); http://dx.doi.org/10.1063/1.2940352 (12 pages) | Cited 6 times

Online Publication Date: 23 June 2008

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We suggest an approximate relativistic model for economical all-electron calculations on molecular systems that exploits an atomic ansatz for the relativistic projection transformation. With such a choice, the projection transformation matrix is by definition both transferable and independent of the geometry. The formulation is flexible with regard to the level at which the projection transformation is approximated; we employ the free-particle Foldy–Wouthuysen and the second-order Douglas-Kroll-Hess variants. The (atomic) infinite-order decoupling scheme shows little effect on structural parameters in scalar-relativistic calculations; also, the use of a screened nuclear potential in the definition of the projection transformation shows hardly any effect in the context of the present work. Applications to structural and energetic parameters of various systems (diatomics AuH, AuCl, and Au2, two structural isomers of Ir4, and uranyl dication UO22+ solvated by 3-6 water ligands) show that the atomic approximation to the conventional second-order Douglas-Kroll-Hess projection (ADKH) transformation yields highly accurate results at substantial computational savings, in particular, when calculating energy derivatives of larger systems. The size-dependence of the intrinsic error of the ADKH method in extended systems of heavy elements is analyzed for the atomization energies of Pdn clusters (n ⩽ 116).
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31.10.+z Theory of electronic structure, electronic transitions, and chemical binding
31.15.X- Alternative approaches
36.40.Cg Electronic and magnetic properties of clusters

Probability distributions of molecular observables computed from Markov models

Frank Noé

J. Chem. Phys. 128, 244103 (2008); http://dx.doi.org/10.1063/1.2916718 (13 pages) | Cited 35 times

Online Publication Date: 23 June 2008

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Molecular dynamics (MD) simulations can be used to estimate transition rates between conformational substates of the simulated molecule. Such an estimation is associated with statistical uncertainty, which depends on the number of observed transitions. In turn, it induces uncertainties in any property computed from the simulation, such as free energy differences or the time scales involved in the system’s kinetics. Assessing these uncertainties is essential for testing the reliability of a given observation and also to plan further simulations in such a way that the most serious uncertainties will be reduced with minimal effort. Here, a rigorous statistical method is proposed to approximate the complete statistical distribution of any observable of an MD simulation provided that one can identify conformational substates such that the transition process between them may be modeled with a memoryless jump process, i.e., Markov or Master equation dynamics. The method is based on sampling the statistical distribution of Markov transition matrices that is induced by the observed transition events. It allows physically meaningful constraints to be included, such as sampling only matrices that fulfill detailed balance, or matrices that produce a predefined equilibrium distribution of states. The method is illustrated on μs MD simulations of a hexapeptide for which the distributions and uncertainties of the free energy differences between conformations, the transition matrix elements, and the transition matrix eigenvalues are estimated. It is found that both constraints, detailed balance and predefined equilibrium distribution, can significantly reduce the uncertainty of some observables.
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87.15.ap Molecular dynamics simulation
36.20.Ey Conformation (statistics and dynamics)
87.14.ef Peptides

Comparative ab initio studies on the molecular structure and spectroscopic properties of FeF2: Single reference versus multireference methods

Victor G. Solomonik, John F. Stanton, and James E. Boggs

J. Chem. Phys. 128, 244104 (2008); http://dx.doi.org/10.1063/1.2939574 (9 pages) | Cited 4 times

Online Publication Date: 23 June 2008

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The electronic excitation energies, molecular geometry, quadratic force fields, and vibrational frequencies in the ground math and low-lying excited math and math electronic states of iron difluoride are studied at sophisticated levels of theory. Two families of basis sets, nonrelativistic and Douglas–Kroll–Hess relativistic, are used that range in quality from triple-ζ to quintuple-ζ. These are augmented by additional diffuse functions (on fluorine atoms) and tight functions (on all atoms) for the description of core-valence correlation and utilized to determine complete basis set molecular properties. The quality of electron correlation treatment using conventional single reference coupled cluster methods CCSD and CCSD(T) is compared to that attained at the multiconfigurational quasidegenerate second-order perturbation theory (CASSCF+MCQDPT2) and the electron attachment equation-of-motion coupled cluster (EOMEA-CCSD) levels. Spin-orbit coupling effects are studied by the SO-MCQDPT2 method using the full Breit–Pauli spin-orbit operator. Effects of spin contamination in the coupled cluster molecular calculations are carefully analyzed. Results of the single reference CCSD(T) and multireference calculations are found to be in a remarkable agreement. The calculations indicate that the EOMEA-CC approach provides a suitable tool for an accurate treatment of FeF2 and other systems where delicate electron correlation effects have to be carefully dealt with. The inclusion of relativistic effects is shown to be necessary for an accurate description of the molecular geometry and excitation energies of FeF2. The results of calculations are in good agreement with the experimental data available. The predicted FeF2 molecular properties are compared to those of the related FeF3.
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31.15.ae Electronic structure and bonding characteristics
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.vq Electron correlation calculations for polyatomic molecules
33.20.Tp Vibrational analysis
31.15.bw Coupled-cluster theory
33.15.Mt Rotation, vibration, and vibration-rotation constants

Integrated computational approach to vibrationally resolved electronic spectra: Anisole as a test case

Julien Bloino, Malgorzata Biczysko, Orlando Crescenzi, and Vincenzo Barone

J. Chem. Phys. 128, 244105 (2008); http://dx.doi.org/10.1063/1.2943140 (15 pages) | Cited 11 times

Online Publication Date: 24 June 2008

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A new general and effective procedure to compute Franck–Condon spectra from first principles is exploited to elucidate the subtle features of the vibrationally resolved optical spectra of anisole. Methods based on the density functional theory and its time-dependent extension for electronic excited states [B3LYP/6-311+G(d,p) and TD-B3LYP/6-311+G(d,p)] have been applied to geometry optimizations and harmonic frequency calculations. Perturbative anharmonic frequencies [ J. Chem. Phys. 122, 014108 (2005) ] have been calculated for the ground state, and the Duschinsky matrix elements have been used to evaluate the corresponding anharmonic corrections for the first excited electronic state. The relative energetics of both electronic states has been refined by single point calculations at the coupled clusters (CC) level with the aug-cc-pVDZ basis set. Theoretical spectra have been evaluated using a new optimized implementation for the effective computation of Franck–Condon factors. The remarkable agreement between theoretical and experimental spectra allowed for revision of some assignments of fundamental vibrations in the S1 state of anisole.
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33.20.Tp Vibrational analysis
31.15.bw Coupled-cluster theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.ee Time-dependent density functional theory
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.15.Mt Rotation, vibration, and vibration-rotation constants

Dynamic correlations with time-dependent quantum Monte Carlo

Ivan P. Christov

J. Chem. Phys. 128, 244106 (2008); http://dx.doi.org/10.1063/1.2943674 (7 pages) | Cited 4 times

Online Publication Date: 24 June 2008

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In this paper, we solve quantum many-body problem by propagating ensembles of trajectories and guiding waves in physical space. We introduce the “effective potential” correction within the recently proposed time-dependent quantum Monte Carlo methodology to incorporate the nonlocal quantum correlation effects between the electrons. The associated correlation length is calculated by adaptive kernel density estimation over the walker distribution. The general formalism is developed and tested on one-dimensional helium atom in laser field of different intensities and carrier frequencies. Good agreement with exact results for the atomic ionization is obtained.
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02.50.Ng Distribution theory and Monte Carlo studies
32.80.Fb Photoionization of atoms and ions

Rototranslational sum rules for electromagnetic hypershielding at the nuclei and related atomic Cartesian derivatives of the optical rotatory power

Vincent Liégeois, Benoît Champagne, and Paolo Lazzeretti

J. Chem. Phys. 128, 244107 (2008); http://dx.doi.org/10.1063/1.2943139 (10 pages) | Cited 2 times

Online Publication Date: 25 June 2008

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Two molecular properties, the nuclear electromagnetic hypershielding (ψγ,αβ′I) and the gradient of the electric dipole–magnetic dipole polarizability (∇IγGαβ′), have been calculated using the time-dependent Hartree–Fock method. Provided the Hellmann–Feynman theorem is satisfied, these quantities are equivalent and are related through the ∇IγGαβ′ = eZIψγ,αβ′I relation, where ZI is the atomic number of atom I and e the magnitude of the electron charge. In such a case, the determination of the nuclear electromagnetic hypershielding presents the computational advantage over the evaluation of the gradient of Gαβ′ of requiring only the knowledge of nine mixed second-order derivatives of the density matrix with respect to both electric and magnetic fields (Dα,β(−ω,ω)) instead of the 3N (N is the number of atoms) derivatives of the density matrix with respect to the Cartesian coordinates (DIγ). It is shown here for the H2O2 molecule that very large basis sets such as the aug-cc-pVQZ or the R12 basis are required to satisfy the Hellmann–Feynman theorem. These basis set requirements have been substantiated by considering the corresponding rototranslational sum rules. The origin dependence of the rototranslational sum rules for the gradient of Gαβ′ has then been theoretically described and verified for the H2O2 molecule.
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33.20.Sn Rotational analysis
31.15.xr Self-consistent-field methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Mt Rotation, vibration, and vibration-rotation constants

Quantum initial condition sampling for linearized density matrix dynamics: Vibrational pure dephasing of iodine in krypton matrices

Z. Ma and D. F. Coker

J. Chem. Phys. 128, 244108 (2008); http://dx.doi.org/10.1063/1.2944270 (18 pages) | Cited 10 times

Online Publication Date: 25 June 2008

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This paper reviews the linearized path integral approach for computing time dependent properties of systems that can be approximated using a mixed quantum-classical description. This approach is applied to studying vibrational pure dephasing of ground state molecular iodine in a rare gas matrix. The Feynman–Kleinert optimized harmonic approximation for the full system density operator is used to sample initial conditions for the bath degrees of freedom. This extremely efficient approach is compared to alternative initial condition sampling techniques at low temperatures where classical initial condition sampling yields dephasing rates that are nearly an order of magnitude too slow compared to quantum initial condition sampling and experimental results.
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33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods

Roberto Gaspari and Arnaldo Rapallo

J. Chem. Phys. 128, 244109 (2008); http://dx.doi.org/10.1063/1.2936843 (15 pages)

Online Publication Date: 26 June 2008

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In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the “numerical experiment” provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum trajectory, with great savings in computational time required. This offers a theoretical bridge between the experimental static and dynamical properties of polymers.
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36.20.Ey Conformation (statistics and dynamics)
36.20.Fz Constitution (chains and sequences)
36.20.Ng Vibrational and rotational structure, infrared and Raman spectra
61.41.+e Polymers, elastomers, and plastics

Improved configuration space sampling: Langevin dynamics with alternative mobility

C. D. Chau, G. J. A. Sevink, and J. G. E. M. Fraaije

J. Chem. Phys. 128, 244110 (2008); http://dx.doi.org/10.1063/1.2943313 (9 pages) | Cited 1 time

Online Publication Date: 26 June 2008

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We present a new and efficient method for determining optimal configurations of a large number (N) of interacting particles. We use a coarse-grained stochastic Langevin equation in the overdamped limit to describe the dynamics of this system and replace the standard mobility by an effective space dependent inverse Hessian correlation matrix. Due to the analogy of the drift term in the Langevin equation and the update scheme in Newton’s method, we expect accelerated dynamics or improved convergence in the convex part of the potential energy surface Φ. The stochastic noise term, however, is not only essential for proper thermodynamic sampling but also allows the system to access transition states in the concave parts of Φ. We employ a Broyden–Fletcher–Goldfarb–Shannon method for updating the local mobility matrix. Quantitative analysis for one and two dimensional systems shows that the new method is indeed more efficient than standard methods with constant effective friction. Due to the construction, our effective mobility adapts high values/low friction in configurations which are less optimal and low values/high friction in configurations that are more optimal.
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82.20.Kh Potential energy surfaces for chemical reactions
82.20.Db Transition state theory and statistical theories of rate constants

Quantitative prediction of gas-phase 19F nuclear magnetic shielding constants

Michael E. Harding, Michael Lenhart, Alexander A. Auer, and Jürgen Gauss

J. Chem. Phys. 128, 244111 (2008); http://dx.doi.org/10.1063/1.2943145 (10 pages) | Cited 18 times

Online Publication Date: 27 June 2008

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Benchmark calculations of 19F nuclear magnetic shielding constants are presented for a set of 28 molecules. Near-quantitative accuracy (ca. 2 ppm deviation from experiment) is achieved if (1) electron correlation is adequately treated by employing the coupled-cluster singles and doubles (CCSD) model augmented by a perturbative correction for triple excitations [CCSD(T)], (2) large (uncontracted) basis sets are used, (3) gauge-including atomic orbitals are used to ensure gauge-origin independence, (4) calculations are performed at accurate equilibrium geometries [obtained from CCSD(T)/cc-pVTZ calculations correlating all electrons], and (5) vibrational averaging and temperature corrections via second-order vibrational perturbation theory (VPT2) are included. For the CCSD(T)/13s9p4d3f calculations corrected for vibrational effects, mean and standard deviation from experiment are −1.9 and 1.6 ppm, respectively. Less elaborate theoretical treatments result in larger errors. Consideration of relative shifts can reduce the mean deviation (through an appropriately chosen reference compound), but does not change the standard deviation. Density-functional theory calculations of absolute and relative 19F nuclear magnetic shielding constants are found to be, at best, as accurate as the corresponding Hartree–Fock self-consistent-field calculations and are not improved by consideration of vibrational effects. Molecular systems containing fluorine-oxygen, fluorine-nitrogen, and fluorine-fluorine bonds are found to be more challenging than the other investigated molecules for the considered theoretical methods.
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31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods
31.15.xp Perturbation theory
32.70.Jz Line shapes, widths, and shifts

Hartree–Fock orbitals significantly improve the reaction barrier heights predicted by semilocal density functionals

Benjamin G. Janesko and Gustavo E. Scuseria

J. Chem. Phys. 128, 244112 (2008); http://dx.doi.org/10.1063/1.2940738 (4 pages) | Cited 13 times

Online Publication Date: 27 June 2008

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Semilocal density functional theory predictions for the barrier heights of representative hydrogen transfer, heavy-atom transfer, and nucleophilic substitution reactions are significantly improved in non-self-consistent calculations using Hartree–Fock orbitals. Orbitals from hybrid calculations yield related improvements. These results provide insight into compensating for one-electron self-interaction error in semilocal density functional theory.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Hf Product distribution

Simple coupled-cluster singles and doubles method with perturbative inclusion of triples and explicitly correlated geminals: The CCSDmath model

Edward F. Valeev and T. Daniel Crawford

J. Chem. Phys. 128, 244113 (2008); http://dx.doi.org/10.1063/1.2939577 (12 pages) | Cited 50 times

Online Publication Date: 27 June 2008

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To approach the complete basis set limit of the “gold-standard” coupled-cluster singles and doubles plus perturbative triples [CCSD(T)] method, we extend the recently proposed perturbative explicitly correlated coupled-cluster singles and doubles method, CCSDmath [ E. F. Valeev, Phys. Chem. Chem. Phys. 8, 106 (2008) ], to account for the effect of connected three-electron correlations. The natural choice of the zeroth-order Hamiltonian produces a perturbation expansion with rigorously separable second-order energy corrections due to the explicitly correlated geminals and conventional triple and higher excitations. The resulting CCSDmath energy is defined as a sum of the standard CCSD(T) energy and an amplitude-dependent geminal correction. The method is technically very simple: Its implementation requires no modification of the standard CCSD(T) program and the formal cost of the geminal correction is small. We investigate the performance of the open-shell version of the CCSDmath method as a possible replacement of the standard complete-basis-set CCSD(T) energies in the high accuracy extrapolated ab initio thermochemistry model of Stanton et al. [J. Chem. Phys. 121, 11599 (2004) ]. Correlation contributions to the heat of formation computed with the new method in an aug-cc-pCVXZ basis set have mean absolute basis set errors of 2.8 and 1.0 kJ/mol when X is T and Q, respectively. The corresponding errors of the standard CCSD(T) method are 9.1, 4.0, and 2.1 kJ/mol when X = T, Q, and 5. Simple two-point basis set extrapolations of standard CCSD(T) energies perform better than the explicitly correlated method for absolute correlation energies and atomization energies, but no such advantage found when computing heats of formation. A simple Schwenke-type two-point extrapolation of the CCSDmath/aug-cc-pCVXZ energies with X = T,Q yields the most accurate heats of formation found in this work, in error on average by 0.5 kJ/mol and at most by 1.7 kJ/mol.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
31.15.ag Excitation energies and lifetimes; oscillator strengths
82.20.Db Transition state theory and statistical theories of rate constants
82.60.Cx Enthalpies of combustion, reaction, and formation
31.15.vj Electron correlation calculations for atoms and ions: excited states

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

W. G. Noid, Jhih-Wei Chu, Gary S. Ayton, Vinod Krishna, Sergei Izvekov, Gregory A. Voth, Avisek Das, and Hans C. Andersen

J. Chem. Phys. 128, 244114 (2008); http://dx.doi.org/10.1063/1.2938860 (11 pages) | Cited 105 times

Online Publication Date: 27 June 2008

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Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarse-graining (MS-CG) method [ J. Phys. Chem. B 109, 2469 (2005) ; J. Chem. Phys. 123, 134105 (2005) ] for determining the effective interactions between CG sites using information from simulations of atomically detailed models. The present work develops a formal statistical mechanical framework for the MS-CG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the many-body potential of mean force (PMF) that governs the equilibrium distribution of positions of the CG sites for the MS-CG models. A CG model that employs such a PMF as a “potential energy function” will generate an equilibrium probability distribution of CG sites that is consistent with the atomically detailed model from which the PMF is derived. Consequently, the MS-CG method provides a formal multiscale bridge rigorously connecting the equilibrium ensembles generated with atomistic and CG models. The variational principle also suggests a class of practical algorithms for calculating approximations to this many-body PMF that are optimal. These algorithms use computer simulation data from the atomically detailed model. Finally, important generalizations of the MS-CG method are introduced for treating systems with rigid intramolecular constraints and for developing CG models whose equilibrium momentum distribution is consistent with that of an atomically detailed model.
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31.15.xt Variational techniques
31.15.xv Molecular dynamics and other numerical methods

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

W. G. Noid, Pu Liu, Yanting Wang, Jhih-Wei Chu, Gary S. Ayton, Sergei Izvekov, Hans C. Andersen, and Gregory A. Voth

J. Chem. Phys. 128, 244115 (2008); http://dx.doi.org/10.1063/1.2938857 (20 pages) | Cited 30 times

Online Publication Date: 27 June 2008

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The multiscale coarse-graining (MS-CG) method [ S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005) ] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+/NO3− ionic liquid are provided to illustrate the method.
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61.20.Ja Computer simulation of liquid structure
61.25.Em Molecular liquids
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Evidence of an isomeric pair in furan…HCl: Fourier transform infrared spectroscopy and ab initio calculations

P. Asselin, B. Madebène, P. Soulard, P. Reinhardt, and M. E. Alikhani

J. Chem. Phys. 128, 244301 (2008); http://dx.doi.org/10.1063/1.2944242 (7 pages) | Cited 5 times

Online Publication Date: 23 June 2008

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For the first time the coexistence of a σ- and a π-complex in the C4H4O:HCl system has been observed, in the same supersonic expansion of a molecular jet seeded with argon (or helium) or in a flow-cooled cell at 240 K. This is an exception to the third of the Legon–Miller rules which claims the σ-structure to be the only one to exist. On the grounds of energetic considerations and band contour simulations, two observed bands at 2787.7 and 2795.5 cm−1 of the νs HCl stretching frequency are assigned to the two complexes, recorded as Fourier transform infrared spectra with a resolution between 0.2 and 0.5 cm−1. Complementary calculations show that the use of the standard second-order Møller–Plesset perturbation theory may be erroneous for such a complex, due of the overestimation of the dispersion contribution with respect to the electrostatic term. It is finally established that only a balanced version of the second-order Møller–Plesset perturbation method, spin-component scaled-MP2, or a higher level of theory like a coupled-cluster approach, can provide a reliable energetic analysis for this complex.
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71.15.-m Methods of electronic structure calculations
33.20.Ea Infrared spectra
31.15.bw Coupled-cluster theory

An intraline of conical intersections for methylamine

C. Levi, G. J. Halász, Á. Vibók, I. Bar, Y. Zeiri, R. Kosloff, and M. Baer

J. Chem. Phys. 128, 244302 (2008); http://dx.doi.org/10.1063/1.2943143 (6 pages) | Cited 12 times

Online Publication Date: 23 June 2008

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In this article are considered the conical intersections (ci’s) related to the N–H bond in the methylamine, CH3NH2, molecule. The novel feature that was revealed is that the two lowest states 1A′ and 1A″ are coupled by a line of cis located in HC–NHH plane—a line that is formed by moving a single hydrogen on that plane while fixing the (six) other atoms. The validity of this line was proven first by studying the singularities of the (angular) nonadiabatic coupling terms and then by revealing the degeneracy points formed by the two interacting adiabatic potential energy surfaces (PESs). A theoretical analysis indicated that the line has to be a finite closed line. We also calculated the Berry phase for a contour that surrounds this line and found it to be 3.127 rad, namely, a value reasonably close to π. The existence of such lines of cis—instead of isolated cis (as exhibited by other n-atomic (n>3) molecules such as HNCO or C2H2)—may enhance significantly the transition rate from an upper adiabatic state to a lower one. There are also numerical advantages in such situations, that is, if such a line is properly placed in that plane (like in the present case) the wave-packet treatment of the nuclei can be carried out employing a single diabatic PES instead of having to consider two coupled PESs.
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31.50.Df Potential energy surfaces for excited electronic states
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.ae Electronic structure and bonding characteristics
31.15.V- Electron correlation calculations for atoms, ions and molecules

Formation of interstellar 2,4-pentadiynylidyne, HCCCCC(X 2Π), via the neutral-neutral reaction of ground state carbon atom, C(3P), with diacetylene, HCCCCH(X 1Σg+)

B. J. Sun, C. Y. Huang, H. H. Kuo, K. T. Chen, H. L. Sun, C. H. Huang, M. F. Tsai, C. H. Kao, Y. S. Wang, L. G. Gao, R. I. Kaiser, and A. H. H. Chang

J. Chem. Phys. 128, 244303 (2008); http://dx.doi.org/10.1063/1.2918367 (16 pages) | Cited 2 times

Online Publication Date: 23 June 2008

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The interstellar reaction of ground-state carbon atom with the simplest polyyne, diacetylene (HCCCCH), is investigated theoretically to explore probable routes to form hydrogen-deficient carbon clusters at ultralow temperature in cold molecular clouds. The isomerization and dissociation channels for each of the three collision complexes are characterized by utilizing the unrestricted B3LYP/6-311G(d,p) level of theory and the CCSD(T)/cc-pVTZ calculations. With facilitation of RRKM and variational RRKM rate constants at collision energies of 0–10 kcal/mol, the most probable paths, thus reaction mechanism, are determined. Subsequently, the corresponding rate equations are solved that the evolutions of concentrations of collision complexes, intermediates, and products versus time are obtained. As a result, the final products and yields are identified. This study predicts that three collision complexes, c1, c2, and c3, would produce a single final product, 2,4-pentadiynylidyne, HCCCCC(X 2Π), C5H (p1)+H, via the most stable intermediate, carbon chain HC5H (i4). Our investigation indicates the title reaction is efficient to form astronomically observed 2,4-pentadiynylidyne in cold molecular clouds, where a typical translational temperature is 10 K, via a single bimolecular gas phase reaction.
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95.30.Ft Molecular and chemical processes and interactions
98.38.Dq Molecular clouds, H2 clouds, dense clouds, and dark clouds
98.58.Db Molecular clouds, H2 clouds, dense clouds, and dark clouds
97.20.Li Giant and subgiant stars
95.30.Dr Atomic processes and interactions

Structures, energetics, vibrational spectra of NH4+(H2O)n = 4,6 clusters: Ab initio calculations and first principles molecular dynamics simulations

S. Karthikeyan, Jiten N. Singh, Mina Park, Rajesh Kumar, and Kwang S. Kim

J. Chem. Phys. 128, 244304 (2008); http://dx.doi.org/10.1063/1.2943671 (7 pages) | Cited 7 times

Online Publication Date: 24 June 2008

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Important structural isomers of NH4+(H2O)n = 4,6 have been studied by using density functional theory, Møller–Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH4+(H2O)n = 4,6 because otherwise wrong structures could be assigned for the most probable structures. For NH4+(H2O)6, the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car–Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH4+(H2O)4 and two lowest energy isomers of NH4+(H2O)6 explains each experimental IR spectrum.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.20.Tp Vibrational analysis
31.15.at Molecule transport characteristics; molecular dynamics; electronic structure of polymers
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Differential scattering of cold molecules in superimposed electric and magnetic fields

T. V. Tscherbul

J. Chem. Phys. 128, 244305 (2008); http://dx.doi.org/10.1063/1.2943197 (9 pages) | Cited 7 times

Online Publication Date: 25 June 2008

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We present a detailed theoretical study of differential cross sections for inelastic collisions of 2Σ molecules in the presence of superimposed electric and magnetic fields. Using rigorous quantum dynamical calculations, we show that the angular dependence of cross sections for Zeeman relaxation in collisions of CaD molecules with He atoms at low temperatures can be significantly modified by electric fields of less than 100 kV/cm. Our results suggest that the differential scattering cross sections are more sensitive to the electric field than the averaged integral cross sections. We show that the integral cross sections corresponding to a fixed orientation of the incoming collision flux may exhibit interference effects induced by electric fields.
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34.50.-s Scattering of atoms and molecules
33.57.+c Magneto-optical and electro-optical spectra and effects

Core molecule dependence of energy migration in phenylacetylene nanostar dendrimers: Ab initio molecular orbital–configuration interaction based quantum master equation study

Ryohei Kishi, Takuya Minami, Hitoshi Fukui, Hideaki Takahashi, and Masayoshi Nakano

J. Chem. Phys. 128, 244306 (2008); http://dx.doi.org/10.1063/1.2939244 (8 pages) | Cited 3 times

Online Publication Date: 25 June 2008

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The core molecule dependence of energy (exciton) migration in phenylacetylene nanostar dendrimers is investigated using the ab initio molecular orbital (MO)–configuration interaction based quantum master equation approach. We examine three kinds of core molecular species, i.e., benzene, anthracene, and pentacene, with different highest occupied MO–lowest unoccupied MO (HOMO-LUMO) gaps, which lead to different orbital interactions between the dendron parts and the core molecule. The nanostars bearing anthracene and pentacene cores are characterized by multistep exciton states with spatially well-segmented distributions: The exciton distributions of high-lying exciton states are spatially localized well in the periphery region, whereas those of low-lying exciton states are done in the core region. On the other hand, for the nanostar bearing benzene core, which also has multistep exciton states, the spatial exciton distributions of low-lying exciton states are delocalized over the dendron and the core regions. It is found that the former nanostars exhibit nearly complete exciton migration from the periphery to the core molecule in contrast to the latter one, in which significant exciton distribution remains in the dendron parts attached to the core after the exciton relaxation, although all these dendrimers exhibit fast exciton relaxation from the initially populated states. It is predicted from the analysis based on the MO correlation diagrams and the relative relaxation factor that the complete exciton migration to the core occurs not only when the HOMO-LUMO gap of the core molecule is nearly equal to that of the dendron parts attached to the core (anthracene case) but also when fairly smaller than that (pentacene case), whereas the complete migration is not achieved when the HOMO-LUMO gap of the core is larger than that of the dendron parts (benzene case). These results suggest that the fast and complete exciton migration of real dendrimers could be realized by adjusting the HOMO-LUMO gap of the core molecule to be smaller than that of dendron parts, although there exist more complicated relaxation processes as compared to simple dendritic aggregate models studied so far.
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31.15.vj Electron correlation calculations for atoms and ions: excited states
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
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