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21 Apr 2010

Volume 132, Issue 15, Articles (15xxxx)

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J. Chem. Phys. 132, 154302 (2010); http://dx.doi.org/10.1063/1.3352553 (9 pages)

Nandini Mukherjee and Richard N. Zare
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Communications: Explicitly correlated second-order Møller–Plesset perturbation method for extended systems

Toru Shiozaki and So Hirata

J. Chem. Phys. 132, 151101 (2010); http://dx.doi.org/10.1063/1.3396079 (4 pages) | Cited 4 times

Online Publication Date: 15 April 2010

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A formalism for the second-order Møller–Plesset perturbation method employing basis functions that depend explicitly on electron-electron distances (the MP2-R12 or F12 method) is derived and implemented into computer codes for extended systems periodic in one dimension. The excitation amplitudes on these functions are held fixed at values that satisfy the first-order cusp condition. Necessary many-electron integrals over Gaussian-type functions involving Slater-type geminals are evaluated by means of the resolution-of-the-identity approximation with a complementary auxiliary basis set. These integrals and thus the final correlation energy are shown to have the correct size dependence. The valence MP2 correlation energy of polyethylene near the complete basis-set limit is obtained and shown to be considerably greater in magnitude than the value obtained without the R12 treatment.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
36.20.Hb Configuration (bonds, dimensions)
31.15.xr Self-consistent-field methods
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
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back to top Theoretical Methods and Algorithms

Fully relativistic calculations of NMR shielding tensors using restricted magnetically balanced basis and gauge including atomic orbitals

Stanislav Komorovský, Michal Repiský, Olga L. Malkina, and Vladimir G. Malkin

J. Chem. Phys. 132, 154101 (2010); http://dx.doi.org/10.1063/1.3359849 (8 pages) | Cited 11 times

Online Publication Date: 15 April 2010

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A recently developed relativistic four-component density functional method for calculation of nuclear magnetic resonance (NMR) shielding tensors using restricted magnetically balanced basis sets for the small component (mDKS-RMB) was extended to incorporate the gauge including atomic orbitals (GIAO) approach. The combined method eliminates a strong dependence of the results, calculated with a finite basis set, on the choice of the gauge origin for the magnetic potential of a uniform external magnetic field. Benchmark relativistic calculations have been carried out for xenon dimer and the HX series (X = F, Cl, Br, I), where spin-orbit effects are known to be very pronounced for hydrogen shieldings. Our results clearly demonstrate that shieldings calculated at the four-component level with a common gauge (i.e., without GIAO, IGLO, or similar methods to treat the gauge problem) depend dramatically on the choice of the common gauge. The GIAO approach solves the problem in fully relativistic calculations as it does in the nonrelativistic case.
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33.25.+k Nuclear resonance and relaxation
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.15.E- Density-functional theory

Polymer length distributions for catalytic polymerization within mesoporous materials: Non-Markovian behavior associated with partial extrusion

Da-Jiang Liu, Hung-Ting Chen, Victor S.-Y. Lin, and J. W. Evans

J. Chem. Phys. 132, 154102 (2010); http://dx.doi.org/10.1063/1.3361663 (11 pages) | Cited 1 time

Online Publication Date: 15 April 2010

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We analyze a model for polymerization at catalytic sites distributed within parallel linear pores of a mesoporous material. Polymerization occurs primarily by reaction of monomers diffusing into the pores with the ends of polymers near the pore openings. Monomers and polymers undergo single-file diffusion within the pores. Model behavior, including the polymer length distribution, is determined by kinetic Monte Carlo simulation of a suitable atomistic-level lattice model. While the polymers remain within the pore, their length distribution during growth can be described qualitatively by a Markovian rate equation treatment. However, once they become partially extruded, the distribution is shown to exhibit non-Markovian scaling behavior. This feature is attributed to the long-tail in the “return-time distribution” for the protruding end of the partially extruded polymer to return to the pore, such return being necessary for further reaction and growth. The detailed form of the scaled length distribution is elucidated by application of continuous-time random walk theory.
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82.35.-x Polymers: properties; reactions; polymerization
05.40.Fb Random walks and Levy flights
82.20.Wt Computational modeling; simulation
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Vy Homogeneous catalysis in solution, polymers and zeolites
82.20.Db Transition state theory and statistical theories of rate constants

Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer

Karol Kowalski, Sriram Krishnamoorthy, Oreste Villa, Jeff R. Hammond, and Niranjan Govind

J. Chem. Phys. 132, 154103 (2010); http://dx.doi.org/10.1063/1.3385315 (11 pages) | Cited 18 times

Online Publication Date: 16 April 2010

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The completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] has proven to be a reliable tool in describing vertical excitation energies in small and medium size molecules. In order to reduce the high numerical cost of the genuine CR-EOMCCSD(T) method and make noniterative CR-EOMCCSD(T) approaches applicable to large molecular systems, two active-space variants of this formalism [the CR-EOMCCSd(t)-II and CR-EOMCCSd(t)-III methods], based on two different choices of the subspace of triply excited configurations employed to construct noniterative correction, are introduced. In calculations for green fluorescent protein (GFP) and free-base porphyrin, where the CR-EOMCCSD(T) results are available, we show good agreement between the active-space CR-EOMCCSD(T) (variant II) and full CR-EOMCCSD(T) excitation energies. For the oligoporphyrin dimer (P2TA) active-space CR-EOMCCSD(T) results provide reasonable agreement with experimentally inferred data. For all systems considered we demonstrated that the active-space CR-EOMCCSD(T) corrections lower the EOMCCSD (iterative equation-of-motion coupled-cluster method with singles and doubles) excitation energies by 0.2 and 0.3 eV, which leads to a better agreement with experiment. We also discuss the quality of basis sets used and compare EOMCC excitation energies with excitation energies obtained with other methods. In particular, we demonstrate that for GFP and FBP Sadlej’s TZP and cc-pVTZ basis sets lead to a similar quality of the EOMCC results. The performance of the CR-EOMCCSD(T) implementation is discussed from the point of view of timings of iterative parts and scalability of the most expensive, N7, part of the calculation. In the latter case the scalability across 34 008 processors is reported.
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31.15.bw Coupled-cluster theory
36.20.Kd Electronic structure and spectra

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

Stefan Grimme, Jens Antony, Stephan Ehrlich, and Helge Krieg

J. Chem. Phys. 132, 154104 (2010); http://dx.doi.org/10.1063/1.3382344 (19 pages) | Cited 266 times

Online Publication Date: 16 April 2010

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The method of dispersion correction as an add-on to standard Kohn–Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%–40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
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31.15.em Corrections for core-spin polarization, surface effects, etc.
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
68.43.Mn Adsorption kinetics
68.43.Bc Ab initio calculations of adsorbate structure and reactions

Multireference Mukherjee’s coupled cluster method with triexcitations in the linked formulation: Efficient implementation and applications

Kiran Bhaskaran-Nair, Ondřej Demel, and Jiří Pittner

J. Chem. Phys. 132, 154105 (2010); http://dx.doi.org/10.1063/1.3376053 (12 pages) | Cited 23 times

Online Publication Date: 19 April 2010

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We have formulated the multireference Mukherjee’s coupled clusters method with triexcitations (MR MkCCSDT) in the linked version and implemented it in the ACES II program package. The assessment of the new method has been performed on the first three electronic states of the oxygen molecule, on studies of singlet-triplet gap in methylene and twisted ethylene, where a comparison with other multireference CC treatments and with experimental data is available. The MR MkCCSDT results show accuracy comparable to which can be achieved with CCSDT in single reference cases. Comparison of the previously developed MkCCSD(T) method with MkCCSDT as a reference suggests, that MkCCSD(T) might be a promising candidate for an accurate treatment of systems where the static correlation plays an important role, at least for situations where small model spaces are sufficient.
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31.15.bw Coupled-cluster theory
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Time reversible molecular dynamics algorithms with holonomic bond constraints in the NPH and NPT ensembles using molecular scaling

Trond Ingebrigtsen, Ole J. Heilmann, Søren Toxvaerd, and Jeppe C. Dyre

J. Chem. Phys. 132, 154106 (2010); http://dx.doi.org/10.1063/1.3363609 (8 pages) | Cited 2 times

Online Publication Date: 19 April 2010

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A modification of the constrained equations of motion of Kalibaeva et al. [Mol. Phys. 101, 765 (2003) ] in the NPH and NPT ensembles is presented. The modified equations of motion are discretized using central-difference techniques, and the derived integrators are time reversible and conserve the invariant phase space measure. The constraint algorithm builds on the work of Toxvaerd et al. [J. Chem. Phys. 131, 064102 (2009) ] in the NVE and NVT ensembles: it thus conserves the holonomic bond constraints at the finite machine precision level in the NPH and NPT ensembles. The algorithms were tested on a system of n = 320 ortho-terphenyl molecules, arriving at the target temperature and pressure in a low and high pressure state. Isobaric heat capacities in the NPH and NPT ensembles were calculated for comparison using the fluctuation formulas as well as the thermodynamic definition. The heat capacities agree within the estimated uncertainties.
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31.15.xv Molecular dynamics and other numerical methods
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Fm Bond strengths, dissociation energies

Large-scale simulations of fluctuating biological membranes

Andrea Pasqua, Lutz Maibaum, George Oster, Daniel A. Fletcher, and Phillip L. Geissler

J. Chem. Phys. 132, 154107 (2010); http://dx.doi.org/10.1063/1.3382349 (6 pages) | Cited 1 time

Online Publication Date: 20 April 2010

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We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each ≈ 25 nm2 patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic association, multiparticle interactions suppress the exposure of each sphere’s equator to its implicit solvent surroundings. The requirement of high equatorial density stabilizes two-dimensional structures without necessitating crystalline order, allowing us to match both the elasticity and fluidity of natural lipid membranes. We illustrate the model’s versatility and realism by characterizing a membrane’s response to a prodding nanorod.
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87.16.D- Membranes, bilayers, and vesicles
87.16.A- Theory, modeling, and simulations
87.16.dm Mechanical properties and rheology

High-order expansion of T2×t2 Jahn–Teller potential-energy surfaces in tetrahedral molecules

Daniel Opalka and Wolfgang Domcke

J. Chem. Phys. 132, 154108 (2010); http://dx.doi.org/10.1063/1.3382912 (14 pages) | Cited 12 times

Online Publication Date: 20 April 2010

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Methods from Jahn–Teller theory and invariant theory have been combined for the construction of analytic diabatic potential-energy surfaces of triply degenerate states in tetrahedral molecules. The potentials of a threefold degenerate electronic state of T2 symmetry, subject to the T2×t2 or T2×(t2+t2) Jahn–Teller effect in a three-dimensional or six-dimensional space of nuclear coordinates, respectively, are considered. The permutation symmetry of four identical nuclei is taken into account in the polynomial expansion of the diabatic surfaces. Symmetry adapted polynomials up to high orders are explicitly given and a simple combinatorial scheme was developed to express terms of arbitrary order as products of a small number of polynomials which are invariant under the permutation of identical nuclei. The method is applied to the methane cation in its triply degenerate ground state. The parameters of the analytic surfaces have been fitted to accurate ab initio data calculated at the full-valence CASSCF/MRCI/cc-pVTZ level. A three-sheeted six-dimensional analytic potential-energy surface of the 2T2 ground state of CH4+ is reported, which involves terms up to eighth order in the degenerate stretching coordinate, up to 12th order in the degenerate bending coordinate, and up to fourth order in the stretch-bend coupling.
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31.50.Bc Potential energy surfaces for ground electronic states
31.30.-i Corrections to electronic structure
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.15.xr Self-consistent-field methods
31.15.ve Electron correlation calculations for atoms and ions: ground state
02.10.De Algebraic structures and number theory

Conical intersections in triplet excited states of methylene from the anti-Hermitian contracted Schrödinger equation

James W. Snyder, Adam E. Rothman, Jonathan J. Foley, and David A. Mazziotti

J. Chem. Phys. 132, 154109 (2010); http://dx.doi.org/10.1063/1.3394020 (7 pages) | Cited 7 times

Online Publication Date: 20 April 2010

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A conical intersection in triplet excited states of methylene is computed through the direct calculation of two-electron reduced density matrices (2-RDMs) from solutions of the anti-Hermitian contracted Schrödinger equation (ACSE). The study synthesizes recent extensions of the ACSE method for the treatment of excited states [ G. Gidofalvi and D. A. Mazziotti, Phys. Rev. A 80, 022507 (2009) ] and arbitrary-spin states [ A. E. Rothman, J. J. Foley, and D. A. Mazziotti, Phys. Rev. A 80, 052508 (2009) ]. We compute absolute energies of the 1 3B1, 1 3A2, and 2 3B1 states of methylene (CH2) and the location of the conical intersection along the 1 3A2−2 3B1 potential-energy surfaces. To treat multireference correlation, we seed the ACSE with an initial 2-RDM from a multiconfiguration self-consistent field (MCSCF) calculation. The ACSE produces energies that significantly improve upon those from MCSCF and second-order multireference many-body perturbation theory, and the 2-RDMs from the ACSE nearly satisfy necessary N-representability conditions. Comparison of the results from augmented double-zeta and triple-zeta basis sets demonstrates the importance of augmented (or diffuse) functions for determining the location of the conical intersection.
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31.50.Df Potential energy surfaces for excited electronic states
31.15.xr Self-consistent-field methods

Constructing smooth potentials of mean force, radial distribution functions, and probability densities from sampled data

Ramses van Zon and Jeremy Schofield

J. Chem. Phys. 132, 154110 (2010); http://dx.doi.org/10.1063/1.3366523 (13 pages) | Cited 1 time

Online Publication Date: 21 April 2010

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In this paper a method of obtaining smooth analytical estimates of probability densities, radial distribution functions, and potentials of mean force from sampled data in a statistically controlled fashion is presented. The approach is general and can be applied to any density of a single random variable. The method outlined here avoids the use of histograms, which require the specification of a physical parameter (bin size) and tend to give noisy results. The technique is an extension of the Berg–Harris method [ B. A. Berg and R. C. Harris, Comput. Phys. Commun. 179, 443 (2008) ], which is typically inaccurate for radial distribution functions and potentials of mean force due to a nonuniform Jacobian factor. In addition, the standard method often requires a large number of Fourier modes to represent radial distribution functions, which tends to lead to oscillatory fits. It is shown that the issues of poor sampling due to a Jacobian factor can be resolved using a biased resampling scheme, while the requirement of a large number of Fourier modes is mitigated through an automated piecewise construction approach. The method is demonstrated by analyzing the radial distribution functions in an energy-discretized water model. In addition, the fitting procedure is illustrated on three more applications for which the original Berg–Harris method is not suitable, namely, a random variable with a discontinuous probability density, a density with long tails, and the distribution of the first arrival times of a diffusing particle to a sphere, which has both long tails and short-time structure. In all cases, the resampled, piecewise analytical fit outperforms the histogram and the original Berg–Harris method.
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34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
05.10.-a Computational methods in statistical physics and nonlinear dynamics
02.70.Ns Molecular dynamics and particle methods

Wannier-ridge states of He and H− with symmetries 3Pe and 1Do and the validity of classification schemata

Spyros I. Themelis

J. Chem. Phys. 132, 154111 (2010); http://dx.doi.org/10.1063/1.3385316 (7 pages) | Cited 1 time

Online Publication Date: 21 April 2010

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High lying doubly excited Wannier-ridge states of He and H− with symmetries 3Pe and 1Do are studied and energies and intrinsic characteristics of their wave functions are reported. Energies of these states associated with the hydrogenic threshold up to N = 20 are presented and, wherever available, we compare them to other calculations. Proposed classification schemata for these states by approximate collective quantum numbers are examined.
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31.10.+z Theory of electronic structure, electronic transitions, and chemical binding
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries

Sandeep Tyagi, Mehmet Süzen, Marcello Sega, Marcia Barbosa, Sofia S. Kantorovich, and Christian Holm

J. Chem. Phys. 132, 154112 (2010); http://dx.doi.org/10.1063/1.3376011 (9 pages) | Cited 4 times

Online Publication Date: 21 April 2010

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Simulating coarse-grained models of charged soft-condensed matter systems in presence of dielectric discontinuities between different media requires an efficient calculation of polarization effects. This is almost always the case if implicit solvent models are used near interfaces or large macromolecules. We present a fast and accurate method (ICC⋆) that allows to simulate the presence of an arbitrary number of interfaces of arbitrary shape, each characterized by a different dielectric permittivity in one-, two-, and three-dimensional periodic boundary conditions. The scaling behavior and accuracy of the underlying electrostatic algorithms allow to choose the most appropriate scheme for the system under investigation in terms of precision and computational speed. Due to these characteristics the method is particularly suited to include nonplanar dielectric boundaries in coarse-grained molecular dynamics simulations.
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77.22.Ch Permittivity (dielectric function)
77.22.Ej Polarization and depolarization

Size-consistent variational approaches to nonlocal pseudopotentials: Standard and lattice regularized diffusion Monte Carlo methods revisited

Michele Casula, Saverio Moroni, Sandro Sorella, and Claudia Filippi

J. Chem. Phys. 132, 154113 (2010); http://dx.doi.org/10.1063/1.3380831 (9 pages) | Cited 3 times

Online Publication Date: 21 April 2010

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We propose improved versions of the standard diffusion Monte Carlo (DMC) and the lattice regularized diffusion Monte Carlo (LRDMC) algorithms. For the DMC method, we refine a scheme recently devised to treat nonlocal pseudopotential in a variational way. We show that such scheme—when applied to large enough systems—maintains its effectiveness only at correspondingly small enough time-steps, and we present two simple upgrades of the method which guarantee the variational property in a size-consistent manner. For the LRDMC method, which is size-consistent and variational by construction, we enhance the computational efficiency by introducing: (i) an improved definition of the effective lattice Hamiltonian which remains size-consistent and entails a small lattice-space error with a known leading term and (ii) a new randomization method for the positions of the lattice knots which requires a single lattice-space.
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71.15.Dx Computational methodology (Brillouin zone sampling, iterative diagonalization, pseudopotential construction)
31.15.xt Variational techniques
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Determination of the ionization and dissociation energies of the deuterium molecule (D2)

Jinjun Liu, Daniel Sprecher, Christian Jungen, Wim Ubachs, and Frédéric Merkt

J. Chem. Phys. 132, 154301 (2010); http://dx.doi.org/10.1063/1.3374426 (11 pages) | Cited 13 times

Online Publication Date: 15 April 2010

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The transition wave numbers from selected rovibrational levels of the EF 1Σg+(v = 0) state to selected np Rydberg states of ortho- and para-D2 located below the adiabatic ionization threshold have been measured at a precision better than 10−3 cm−1. Adding these wave numbers to the previously determined transition wave numbers from the X 1Σg+(v = 0, N = 0,1) states to the EF 1Σg+(v = 0, N = 0,1) states of D2 and to the binding energies of the Rydberg states calculated by multichannel quantum defect theory, the ionization energies of ortho- and para-D2 are determined to be 124 745.394 07(58) cm−1 and 124 715.003 77(75) cm−1, respectively. After re-evaluation of the dissociation energy of D2+ and using the known ionization energy of D, the dissociation energy of D2 is determined to be 36 748.362 86(68) cm−1. This result is more precise than previous experimental results by more than one order of magnitude and is in excellent agreement with the most recent theoretical value 36 748.3633(9) cm−1 [ K. Piszczatowski, G. Łach, M. Przybytek et al., J. Chem. Theory Comput. 5, 3039 (2009) ]. The ortho-para separation of D2, i.e., the energy difference between the N = 0 and N = 1 rotational levels of the X 1Σg+(v = 0) ground state, has been determined to be 59.781 30(95) cm−1.
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33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.15.Fm Bond strengths, dissociation energies
33.80.Eh Autoionization, photoionization, and photodetachment
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Mt Rotation, vibration, and vibration-rotation constants
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Preparation of polarized molecules using coherent infrared multicolor ladder excitation

Nandini Mukherjee and Richard N. Zare

J. Chem. Phys. 132, 154302 (2010); http://dx.doi.org/10.1063/1.3352553 (9 pages) | Cited 2 times

Online Publication Date: 15 April 2010

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A density matrix treatment is presented for a general process of preparing polarized molecules through their coherent interaction with two or more infrared photons of different frequencies, each tuned to cause a transition between real levels. This process, which might be called infrared stimulated Raman adiabatic passage, allows complete population transfer to selected rotational-vibrational levels and controls the direction of the rotational angular momentum vector J of the molecule with the possibility of preparing higher moments of the J spatial distribution. HCl molecules in a supersonic molecular beam are considered as a candidate system. Theory predicts that under collision-free conditions two infrared laser pulses of microsecond duration and milliwatt power are able to achieve complete population transfer and alignment of HCl (v = 2, J = 2, and M = 0) for mutually parallel excitation and HCl (v = 2, J = 2, and M = ±1) for mutually perpendicular excitation. Orientation of the HCl (v = 2, J = 2, and M = ±2) can also be achieved using two circularly polarized pulses of the same helicity. For simplicity, our treatment ignores nuclear spin depolarization, which would be the case for molecules such as 12C16O and 12C16OO2. Polarized molecules in higher vibrational levels can be prepared using additional infrared pulses.
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33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.15.Mt Rotation, vibration, and vibration-rotation constants
37.20.+j Atomic and molecular beam sources and techniques
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.57.+c Magneto-optical and electro-optical spectra and effects

Direct determination of state-to-state rotational energy transfer rate constants via a Raman-Raman double resonance technique: ortho-acetylene in v2 = 1 at 155 K

José L. Doménech, Raúl Z. Martínez, Ángel Ramos, and Dionisio Bermejo

J. Chem. Phys. 132, 154303 (2010); http://dx.doi.org/10.1063/1.3374031 (12 pages) | Cited 5 times

Online Publication Date: 15 April 2010

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A new technique for the direct determination of state-to-state rotational energy transfer rate constants in the gas phase is presented. It is based on two sequential stimulated Raman processes: the first one prepares the sample in a single rotational state of an excited vibrational level, and the second one, using the high resolution quasi-continuous stimulated Raman-loss technique, monitors the transfer of population to other rotational states of the same vibrational level as a function of the delay between the pump and the probe stages. The technique is applied to the odd-J rotational states of v2 = 1 acetylene at 155 K. The experimental layout, data acquisition, retrieval procedures, and numerical treatment are described. The quantity and quality of the data are high enough to allow a direct determination of the state-to-state rate constant matrix from a fit of the experimental data, with the only conditions of detailed balance and of a closed number of states. The matrix obtained from this direct fit is also compared with those obtained using some common fitting and scaling laws.
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33.20.Sn Rotational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.40.+f Multiple resonances (including double and higher-order resonance processes, such as double nuclear magnetic resonance, electron double resonance, and microwave optical double resonance)
33.20.Tp Vibrational analysis
33.80.Wz Other multiphoton processes

A global search for the lowest energy isomer of C26

Jie An, Li-Hua Gan, Jian-Qiang Zhao, and Rui Li

J. Chem. Phys. 132, 154304 (2010); http://dx.doi.org/10.1063/1.3364801 (7 pages) | Cited 3 times

Online Publication Date: 15 April 2010

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The complete set of 2333 isomers of C26 fullerene composed of square, pentagonal, hexagonal, and heptagonal faces together with some noncage structures is investigated at the Hartree–Fock and density functional theory (DFT) levels. For the singlet states, a nonclassical isomer C26-10-01 with a square embedded is predicted by the DFT method as the lowest energy isomer, followed by the sole classical isomer C26-00-01. Further explorations reveal that the electronic ground state of C26-10-01 is triplet state in Cs symmetry, while that of C26-00-01 corresponds to its quintet in D3h symmetry. Both the total energies and nucleus independent chemical shift values at DFT level favor the classical isomer. It is found that both C26-00-01 and C26-10-01 possess high vertical electron affinity. The addition of electron(s) to C26-10-01 increases its aromatic character and encapsulation of Li atom into this cage is highly exothermic, indicating that it may be captured in the form of derivatives. To clarify the relative stabilities at elevated temperatures, the entropy contributions are taken into account based on the Gibbs free energy at the B3LYP/6-311+G∗ level. C26-10-01 behaves thermodynamically more stable than the classical isomer over a wide range of temperatures related to fullerene formation. The IR spectra of these two lowest energy isomers are simulated to facilitate their experimental identification.
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71.20.Tx Fullerenes and related materials; intercalation compounds
61.48.-c Structure of fullerenes and related hollow and planar molecular structures
78.30.Na Fullerenes and related materials
76.60.Cq Chemical and Knight shifts
71.15.Nc Total energy and cohesive energy calculations
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)

The structure of the NO(X 2Π)−N2 complex: A joint experimental-theoretical study

B. Wen, H. Meyer, and J. Kłos

J. Chem. Phys. 132, 154305 (2010); http://dx.doi.org/10.1063/1.3380666 (9 pages) | Cited 1 time

Online Publication Date: 16 April 2010

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We report the first measurement of the spectrum of the NO–N2 complex in the region of the first vibrational NO overtone transition. The origin band of the complex is blueshifted by 0.30 cm−1 from the corresponding NO monomer frequency. The observed spectrum consists of three bands assigned to the origin band, the excitation of one quantum of z-axis rotation and one associated hot band. The spacing of the bands and the rotational structure indicate a T-shaped vibrationally averaged structure with the NO molecule forming the top of the T. These findings are confirmed by high level ab initio calculations of the potential energy surfaces in planar symmetry. The deepest minimum is found for a T-shaped geometry on the A″-surface. As a result the sum potential also has the global minimum for this structure. The different potential surfaces show several additional local minima at slightly higher energies indicating that the complex most likely will perform large amplitude motion even in its ground vibrational state. Nevertheless, as suggested by the measured spectra, the complex must, on average, spend a substantial amount of time near the T-shaped configuration.
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33.20.Ea Infrared spectra
31.50.Bc Potential energy surfaces for ground electronic states
33.70.Jg Line and band widths, shapes, and shifts
31.15.A- Ab initio calculations
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Bh General molecular conformation and symmetry; stereochemistry

State-selected imaging studies of formic acid photodissociation dynamics

Cunshun Huang, Cuimei Zhang, and Xueming Yang

J. Chem. Phys. 132, 154306 (2010); http://dx.doi.org/10.1063/1.3386576 (6 pages) | Cited 5 times

Online Publication Date: 19 April 2010

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The photodissociation dynamics of formic acid have been studied using the velocity map ion imaging at the UV region. The measurements were made with resonance enhancement multiphoton ionization (REMPI) spectroscopy and dc slicing ion imaging. The OH REMPI spectrum from the photodissociation of formic acid at 244 nm has been recorded. The spectrum shows low rotational excitation (N ≤ 4). By fixing the probe laser at the specific rotational transitions, the resulting OH images from various dissociation wavelengths have been accumulated. The translational energy distributions derived from the OH images imply that about half of the available energies go to the photofragments internal excitation. The dissociation dynamics of formic acid were also discussed in view of the recent theoretical calculations.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
82.50.Hp Processes caused by visible and UV light
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.80.Eh Autoionization, photoionization, and photodetachment
33.20.Lg Ultraviolet spectra

Ab initio study of shock compressed oxygen

Cong Wang and Ping Zhang

J. Chem. Phys. 132, 154307 (2010); http://dx.doi.org/10.1063/1.3402497 (5 pages) | Cited 2 times

Online Publication Date: 20 April 2010

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Quantum molecular dynamic simulations are introduced to study the shock compressed oxygen. The principal Hugoniot points derived from the equation of state agree well with the available experimental data. With the increase in pressure, molecular dissociation is observed. Electron spin polarization determines the electronic structure of the system under low pressure, while it is suppressed at the pressure higher than 30 GPa. Particularly, nonmetal-metal transition and optical properties of shock compressed oxygen are also discussed.
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71.15.-m Methods of electronic structure calculations
62.50.Ef Shock wave effects in solids and liquids
72.25.-b Spin polarized transport
64.30.-t Equations of state of specific substances
71.30.+h Metal-insulator transitions and other electronic transitions

Identification of pseudodiatomic behavior in polyatomic bond dissociation: Reaction force analysis

Jane S. Murray, Alejandro Toro-Labbé, Soledad Gutiérrez-Oliva, and Peter Politzer

J. Chem. Phys. 132, 154308 (2010); http://dx.doi.org/10.1063/1.3397068 (6 pages) | Cited 1 time

Online Publication Date: 20 April 2010

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An interesting uniformity that has been observed for diatomic molecular dissociation has been demonstrated to apply to many single bonds in polyatomic molecules as well. The energy to reach a key point in the bond-breaking process, at which it changes from simply stretching to transition to products, is for most cases a nearly constant fraction of the dissociation energy. The point at which this change occurs corresponds to the minimum of the reaction force F(R) for the dissociation, F(R) being the negative gradient of the potential energy along the reaction coordinate. Thirty nine single bonds were analyzed at the B3PW91/6-31++G(3d,2p) level. Both adiabatic and vertical stretching were considered; those bonds for which these give essentially the same results are labeled “pseudodiatomic.”
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
33.15.Fm Bond strengths, dissociation energies
33.15.Dj Interatomic distances and angles
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Db Transition state theory and statistical theories of rate constants
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Two-dimensional freezing criteria for crystallizing colloidal monolayers

Ziren Wang (王梓任), Ahmed M. Alsayed, Arjun G. Yodh, and Yilong Han (韩一龙)

J. Chem. Phys. 132, 154501 (2010); http://dx.doi.org/10.1063/1.3372618 (8 pages) | Cited 5 times

Online Publication Date: 16 April 2010

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Video microscopy was employed to explore crystallization of colloidal monolayers composed of diameter-tunable microgel spheres. Two-dimensional (2D) colloidal liquids were frozen homogenously into polycrystalline solids, and four 2D criteria for freezing were experimentally tested in thermal systems for the first time: the Hansen–Verlet freezing rule, the Löwen–Palberg–Simon dynamical freezing criterion, and two other rules based, respectively, on the split shoulder of the radial distribution function and on the distribution of the shape factor of Voronoi polygons. Importantly, these freezing criteria, usually applied in the context of single crystals, were demonstrated to apply to the formation of polycrystalline solids. At the freezing point, we also observed a peak in the fluctuations of the orientational order parameter and a percolation transition associated with caged particles. Speculation about these percolated clusters of caged particles casts light on solidification mechanisms and dynamic heterogeneity in freezing.
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64.60.ah Percolation
82.50.Hp Processes caused by visible and UV light
82.50.-m Photochemistry
64.70.P- Glass transitions of specific systems
36.40.-c Atomic and molecular clusters
64.70.D- Solid-liquid transitions
64.70.dg Crystallization of specific substances
82.70.Dd Colloids

Asymmetric criticality in weakly compressible liquid mixtures

G. Pérez-Sánchez, P. Losada-Pérez, C. A. Cerdeiriña, J. V. Sengers, and M. A. Anisimov

J. Chem. Phys. 132, 154502 (2010); http://dx.doi.org/10.1063/1.3378626 (13 pages) | Cited 16 times

Online Publication Date: 16 April 2010

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The thermodynamics of asymmetric liquid-liquid criticality is updated by incorporating pressure effects into the complete-scaling formulation earlier developed for incompressible liquid mixtures [ C. A. Cerdeiriña et al., Chem. Phys. Lett. 424, 414 (2006) ; J. T. Wang et al., Phys. Rev. E 77, 031127 (2008) ]. Specifically, we show that pressure mixing enters into weakly compressible liquid mixtures as a consequence of the pressure dependence of the critical parameters. The theory is used to analyze experimental coexistence-curve data in the mole fraction–temperature, density-temperature, and partial density–temperature planes for a large number of binary liquid mixtures. It is shown how the asymmetry coefficients in the scaling fields are related to the difference in molecular volumes of the two liquid components. The work resolves the question of the so-called “best order parameter” discussed in the literature during the past decades.
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64.75.Cd Phase equilibria of fluid mixtures, including gases, hydrates, etc.
64.60.fd General theory of critical region behavior
64.60.fh Studies of specific substances in the critical region
61.25.Em Molecular liquids
61.20.Gy Theory and models of liquid structure
64.75.Ef Mixing

Correlation of the scaling exponent γ of the diffusivity-density function in viscous liquids with their elastic properties

Anthony N. Papathanassiou and Ilias Sakellis

J. Chem. Phys. 132, 154503 (2010); http://dx.doi.org/10.1063/1.3382645 (4 pages) | Cited 5 times

Online Publication Date: 16 April 2010

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Fundamental thermodynamical concepts and a solid-state point defect elastic model are used to formulate a diffusivity-density scaling function for viscous liquids. It is proved in a straightforward manner that the scaling exponent γ describing the density scaling of the diffusivity is related with the pressure derivative of the isothermal bulk modulus.
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66.20.-d Viscosity of liquids; diffusive momentum transport
62.10.+s Mechanical properties of liquids
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