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14 Feb 2010

Volume 132, Issue 6, Articles (06xxxx)

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J. Chem. Phys. 132, 064101 (2010); http://dx.doi.org/10.1063/1.3298862 (16 pages)

Patrice Koehl and Marc Delarue
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back to top Theoretical Methods and Algorithms

AQUASOL: An efficient solver for the dipolar Poisson–Boltzmann–Langevin equation

Patrice Koehl and Marc Delarue

J. Chem. Phys. 132, 064101 (2010); http://dx.doi.org/10.1063/1.3298862 (16 pages) | Cited 1 time

Online Publication Date: 8 February 2010

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The Poisson–Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson–Boltzmann–Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE solver. While both methods are not guaranteed to converge, numerical evidences suggest that they do and that their convergence is also superlinear. Both variants are significantly faster than the solver based on the exact Jacobian, with a much smaller memory footprint. All three methods have been implemented in a new code named AQUASOL, which is freely available.
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82.30.Nr Association, addition, insertion, cluster formation
82.20.Wt Computational modeling; simulation
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
02.60.Lj Ordinary and partial differential equations; boundary value problems

On the linear response and scattering of an interacting molecule-metal system

David J. Masiello and George C. Schatz

J. Chem. Phys. 132, 064102 (2010); http://dx.doi.org/10.1063/1.3308624 (8 pages) | Cited 8 times

Online Publication Date: 8 February 2010

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A many-body Green’s function approach to the microscopic theory of plasmon-enhanced spectroscopy is presented within the context of localized surface-plasmon resonance spectroscopy and applied to investigate the coupling between quantum-molecular and classical-plasmonic resonances in monolayer-coated silver nanoparticles. Electronic propagators or Green’s functions, accounting for the repeated polarization interaction between a single molecule and its image in a nearby nanoscale metal, are explicitly computed and used to construct the linear-response properties of the combined molecule-metal system to an external electromagnetic perturbation. Shifting and finite lifetime of states appear rigorously and automatically within our approach and reveal an intricate coupling between molecule and metal not fully described by previous theories. Self-consistent incorporation of this quantum-molecular response into the continuum-electromagnetic scattering of the molecule-metal target is exploited to compute the localized surface-plasmon resonance wavelength shift with respect to the bare metal from first principles.
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71.15.-m Methods of electronic structure calculations
73.20.Mf Collective excitations (including excitons, polarons, plasmons and other charge-density excitations)
73.22.-f Electronic structure of nanoscale materials and related systems

Statistical model for small clusters transforming from one isomer to another

Xiao-Jing Han, Yin Wang, Zheng-Zhe Lin, Wenxian Zhang, Jun Zhuang, and Xi-Jing Ning

J. Chem. Phys. 132, 064103 (2010); http://dx.doi.org/10.1063/1.3298584 (6 pages) | Cited 3 times

Online Publication Date: 8 February 2010

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Based on the fact that the kinetic energy of one atom in small cluster still obeys the Boltzmann distribution, a statistical model is developed to predict the time consumed by a small cluster transforming from one isomer to another and is tested by vast molecular dynamics simulations of C12 isomers transformation in helium gas at high temperatures (2000–3500 K). Extrapolating the model to lower temperatures, we found that the time for the most probable isomer of C12 formed at 2500 K turning into the most stable one is more than 1012 years at room temperature.
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36.40.-c Atomic and molecular clusters
31.15.xv Molecular dynamics and other numerical methods

Assessment of an analytical density matrix derived from a modified Colle–Salvetti approach to the electron gas

Sébastien Ragot

J. Chem. Phys. 132, 064104 (2010); http://dx.doi.org/10.1063/1.3314220 (9 pages) | Cited 1 time

Online Publication Date: 8 February 2010

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The Ragot–Cortona model of local correlation energy [ S. Ragot and P. Cortona, J. Chem. Phys. 121, 7671 (2004) ] revisits the initial approach of Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975) ] in order to reinstate the kinetic contribution Tc to the total correlation energy Ec. In this work, the one-electron reduced density matrix underlying the amended model is fully derived in closed form. By construction, the said density matrix is parameter-free but not N-representable, owing to approximations used in the Ragot–Cortona approach. However, the resulting density matrix is shown to have formally correct short- and long-range expansions. Furthermore, its momentum-space counterpart qualitatively agrees with known parametrized momentum distributions except at small momenta, where the disagreement reflects the nonrepresentability of the model and restricts to a small fraction of the slowest electrons only.
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31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
05.30.Fk Fermion systems and electron gas

A Chebychev propagator with iterative time ordering for explicitly time-dependent Hamiltonians

Mamadou Ndong, Hillel Tal-Ezer, Ronnie Kosloff, and Christiane P. Koch

J. Chem. Phys. 132, 064105 (2010); http://dx.doi.org/10.1063/1.3312531 (12 pages) | Cited 2 times

Online Publication Date: 9 February 2010

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A propagation method for time-dependent Schrödinger equations with an explicitly time-dependent Hamiltonian is developed where time ordering is achieved iteratively. The explicit time dependence of the time-dependent Schrödinger equation is rewritten as an inhomogeneous term. At each step of the iteration, the resulting inhomogeneous Schrödinger equation is solved with the Chebychev propagation scheme presented in the work of M. Ndong et al. [J. Chem. Phys. 130, 124108 (2009) ]. The iteratively time-ordering Chebychev propagator is shown to be robust, efficient, and accurate and compares very favorably with all other available propagation schemes.
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03.65.Ge Solutions of wave equations: bound states
02.60.-x Numerical approximation and analysis

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories

John S. Perkyns, Gillian C. Lynch, Jesse J. Howard, and B. Montgomery Pettitt

J. Chem. Phys. 132, 064106 (2010); http://dx.doi.org/10.1063/1.3299277 (13 pages) | Cited 2 times

Online Publication Date: 9 February 2010

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Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko–Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.
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87.15.rs Dissociation
82.30.-b Specific chemical reactions; reaction mechanisms
87.14.E- Proteins
36.20.-r Macromolecules and polymer molecules
02.30.Rz Integral equations
31.15.xv Molecular dynamics and other numerical methods

Alcohol solubility in a lipid bilayer: Efficient grand-canonical simulation of an interfacially active molecule

Jocelyn M. Rodgers, Michael Webb, and Berend Smit

J. Chem. Phys. 132, 064107 (2010); http://dx.doi.org/10.1063/1.3314289 (10 pages) | Cited 3 times

Online Publication Date: 11 February 2010

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We derive a new density-biased Monte Carlo technique which preserves detailed balance and improves the convergence of grand-canonical simulations of a species with a strong preference for an interfacial region as compared to the bulk. This density-biasing technique is applied to the solubility of “alcohol” molecules in a mesoscopic model of the lipid bilayer, a system which has anesthetic implications but is poorly understood.
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87.16.D- Membranes, bilayers, and vesicles
87.85.J- Biomaterials
87.16.af Monte Carlo calculations
87.14.Cc Lipids

Genetic algorithm optimization of laser pulses for molecular quantum state excitation

Sitansh Sharma, Harjinder Singh, and Gabriel G. Balint-Kurti

J. Chem. Phys. 132, 064108 (2010); http://dx.doi.org/10.1063/1.3314223 (10 pages) | Cited 1 time

Online Publication Date: 12 February 2010

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Conventionally optimal control theory has been used in the theoretical design of laser pulses through the direct variation in the electric field of the laser pulse as a function of time. This often leads to designed laser pulses which contain a broad and seemingly arbitrary frequency structure that varies in time in a manner which may be difficult to realize experimentally. In contrast, the experimental design of laser pulses has used a genetic algorithm (GA) approach, varying only those laser parameters actually available to the experimentalist. We investigate in this paper the possibility of using GA optimization methods in the theoretical design of laser pulses to bring about quantum state transitions in molecules. This allows us to select only a small limited number of parameters to vary and to choose these parameters so that they correspond to those available to the experimentalist. In the paper we apply our methods to the vibrational-rotational excitation of the HF molecule. We choose a small limited number of frequencies and vary only the associated electric field amplitudes and pulse envelopes. We show that laser pulses designed in this way can lead to very high transition probabilities.
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42.50.-p Quantum optics
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
33.20.Vq Vibration-rotation analysis
42.60.Jf Beam characteristics: profile, intensity, and power; spatial pattern formation

Quantitative prediction of gas-phase math and math nuclear magnetic shielding constants

Eric Prochnow and Alexander A. Auer

J. Chem. Phys. 132, 064109 (2010); http://dx.doi.org/10.1063/1.3310282 (7 pages) | Cited 2 times

Online Publication Date: 12 February 2010

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High-level ab initio benchmark calculations of the math and math NMR chemical shielding constants for a representative set of molecules are presented. The computations have been carried out at the Hartree–Fock self-consistent field (HF-SCF), density functional theory (DFT) (B-P86 and B3-LYP), second-order Møller–Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), and CCSD augmented by a perturbative treatment of triple excitations [CCSD(T)] level of theory using basis sets of triple zeta quality or better. The influence of the geometry, the treatment of electron correlation, as well as basis set and zero-point vibrational effects on the shielding constants are discussed and the results are compared to gas-phase experimental shifts. As for the first time a study using high-level post-HF methods is carried out for a second-row element, we also propose a family of basis sets suitable for the computation of math shielding constants. The mean deviations observed for math and math are 0.9 [CCSD(T)/13s9p4d3f] and −3.3 ppm [CCSD(T)/15s12p4d3f2g], respectively, when corrected for zero-point vibrational effects. Results obtained at the DFT level of theory are of comparable accuracy to MP2 for math and of comparable accuracy to HF-SCF for math. However, they are not improved by inclusion of zero-point vibrational effects. The PN molecule is an especially interesting case with exceptionally large electron correlation effects on shielding constants beyond MP2 which, therefore, represents an excellent example for further benchmark studies.
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31.15.A- Ab initio calculations
31.30.-i Corrections to electronic structure
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
33.25.+k Nuclear resonance and relaxation
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.bw Coupled-cluster theory
33.15.Bh General molecular conformation and symmetry; stereochemistry

Analytical theory of finite-size effects in mechanical desorption of a polymer chain

A. M. Skvortsov, L. I. Klushin, G. J. Fleer, and F. A. M. Leermakers

J. Chem. Phys. 132, 064110 (2010); http://dx.doi.org/10.1063/1.3308626 (15 pages) | Cited 5 times

Online Publication Date: 12 February 2010

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We discuss a unique system that allows exact analytical investigation of first- and second-order transitions with finite-size effects: mechanical desorption of an ideal lattice polymer chain grafted with one end to a solid substrate with a pulling force applied to the other end. We exploit the analogy with a continuum model and use accurate mapping between the parameters in continuum and lattice descriptions, which leads to a fully analytical partition function as a function of chain length, temperature (or adsorption strength), and pulling force. The adsorption-desorption phase diagram, which gives the critical force as a function of temperature, is nonmonotonic and gives rise to re-entrance. We analyze the chain length dependence of several chain properties (bound fraction, chain extension, and heat capacity) for different cross sections of the phase diagram. Close to the transition a single parameter (the product of the chain length N and the deviation from the transition point) describes all thermodynamic properties. We discuss finite-size effects at the second-order transition (adsorption without force) and at the first-order transition (mechanical desorption). The first-order transition has some unusual features: The heat capacity in the transition region increases anomalously with temperature as a power law, metastable states are completely absent, and instead of a bimodal distribution there is a flat region that becomes more pronounced with increasing chain length. The reason for this anomaly is the absence of an excess surface energy for the boundary between adsorbed and stretched coexisting phases (this boundary is one segment only): The two states strongly fluctuate in the transition point. The relation between mechanical desorption and mechanical unzipping of DNA is discussed.
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36.20.Fz Constitution (chains and sequences)
68.43.Nr Desorption kinetics
61.25.hk Polymer melts and blends
65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Theoretical study for the reaction of CH3CN with O(math)

Jingyu Sun, Yizhen Tang, Xiujuan Jia, Fang Wang, Hao Sun, Jingdong Feng, Xiumei Pan, Lizhu Hao, and Rongshun Wang

J. Chem. Phys. 132, 064301 (2010); http://dx.doi.org/10.1063/1.3292570 (13 pages) | Cited 3 times

Online Publication Date: 8 February 2010

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The low-lying triplet and singlet potential energy surfaces of the O(math)+CH3CN reaction have been studied at the G3(MP2)//B3LYP/6-311+G(d,p) level. On the triplet surface, six kinds of pathways are revealed, namely, direct hydrogen abstraction, C-addition/elimination, N-addition/elimination, substitution, insertion, and H-migration. Multichannel Rice–Ramsperger–Kassel–Marcus theory and transition-state theory are employed to calculate the overall and individual rate constants over a wide range of temperatures and pressures. It is predicted that the direct hydrogen abstraction and C-addition/elimination on triplet potential energy surface are dominant pathways. Major predicted end products include CH3+NCO and CH2CN+OH. At atmospheric pressure with Ar and N2 as bath gases, CH3C(O)N (IM1) formed by collisional stabilization is dominated at T<700 K, whereas CH3 and NCO produced by C-addition/elimination pathway are the major products at the temperatures between 800 and 1500 K; the direct hydrogen abstraction leading to CH2CN+OH plays an important role at higher temperatures in hydrocarbon combustion chemistry and flames, with estimated contribution of 64% at 2000 K. Furthermore, the calculated rate constants are in good agreement with available experimental data over the temperature range 300–600 K. The kinetic isotope effect has also been calculated for the triplet O(math)+CH3CN reaction. On the singlet surface, the atomic oxygen can easily insert into C–H or C–C bonds of CH3CN, forming the insertion intermediates s-IM8(HOCH2CN) and s-IM5(CH3OCN) or add to the carbon atom of CN group in CH3CN, forming the addition intermediate s-IM1(CH3C(O)N); both approaches were found to be barrierless. It is indicated that the singlet reaction exhibits a marked difference from the triplet reaction. This calculation is useful to simulate experimental investigations of the O(math)+CH3CN reaction in the singlet state surface.
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82.20.Kh Potential energy surfaces for chemical reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.30.Nr Association, addition, insertion, cluster formation
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Tr Kinetic isotope effects including muonium

Disparate product distributions observed in Mo(3−x)WxOy− (x = 0–3; y = 3–9) reactions with D2O and CO2

David W. Rothgeb, Ekram Hossain, Jennifer E. Mann, and Caroline Chick Jarrold

J. Chem. Phys. 132, 064302 (2010); http://dx.doi.org/10.1063/1.3313927 (10 pages) | Cited 6 times

Online Publication Date: 9 February 2010

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Results of gas phase reactivity studies on group six transition metal suboxide clusters, Mo3Oy−, Mo2WOy−, MoW2Oy−, and W3Oy− (Mo(3−x)WxOy−, x = 0–3; y = ca. 3–9) with both D2O and CO2 are reported. Sequential oxidation for the more reduced species, Mo(3−x)WxOy−+D2O/CO2→Mo(3−x)WxOy+1−+D2/CO, and dissociative addition for certain species, Mo(3−x)WxOy−+D2O/CO2→Mo(3−x)WxOy+1D2−/Mo(3−x)WxOy+1CO−, is evident in the product distributions observed in mass spectrometric measurements. Reactions with D2O proceed at a rate that is on the order of 102 higher than for CO2. The pattern of reaction products reveals composition-dependent chemical properties of these group six unary and binary clusters. At the core of this variation is the difference in Mo–O and W–O bond energies, the latter of which is significantly higher. This results in a larger thermodynamic drive to higher oxidation states in clusters with more tungsten atoms. However, addition products for more oxidized W-rich clusters are not observed, while they are observed for the more Mo-rich clusters. This is attributed to the following: In the higher oxides (e.g., y = 8), addition reactions require distortion of local metal-oxygen bonding, and will necessarily have higher activation barriers for W–O bonds, since the vibrational potentials will be narrower. The binary (x = 1,2) clusters generally show sequential oxidation to higher values of y. This again is attributed to higher W–O bond energy, the result being that stable binary structures have W atoms in higher oxidation states, and Mo centers both in more reduced states and sterically unhindered. The reduced Mo center provides a locus of higher reactivity. An unusual result that is not readily explained is the chemically inert behavior of Mo3O6−.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.30.Nr Association, addition, insertion, cluster formation
82.20.Hf Product distribution
82.80.Ms Mass spectrometry (including SIMS, multiphoton ionization and resonance ionization mass spectrometry, MALDI)
36.40.Jn Reactivity of clusters

Cooperative and diminutive hydrogen bonding in Y⋯HCN⋯HCN and NCH⋯Y⋯HCN trimers (Y = BF,CO,N2)

Sean A. C. McDowell and A. David Buckingham

J. Chem. Phys. 132, 064303 (2010); http://dx.doi.org/10.1063/1.3297894 (5 pages) | Cited 5 times

Online Publication Date: 11 February 2010

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A computational study of the cooperative effect of hydrogen bonding in Y⋯HCN⋯HCN and its diminutive effect in NCH⋯Y⋯HCN (Y = BF,CO,N2) linear complexes relative to the Y⋯HCN dimer was undertaken at the MP2/6-311++G(2d,2p) level of theory. It was found that the additional hydrogen bond in Y⋯HCN⋯HCN leads to an enhanced Y⋯HCN dissociation energy, extended H–C bond length, and larger redshift of the H–C stretch relative to Y⋯HCN, while opposite features are observed in NCH⋯Y⋯HCN. The cooperativity is diminished as the hardness of the Y atom directly bonded to the HCN molecule increases. A particularly interesting result is that the small bond contraction and blueshift associated with the H–C bond in BF⋯HCN is converted to a small bond extension and redshift on the formation of the BF⋯HCN⋯HCN trimer.
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33.20.Tp Vibrational analysis
33.70.Jg Line and band widths, shapes, and shifts
31.15.xp Perturbation theory
33.15.Fm Bond strengths, dissociation energies
33.15.Dj Interatomic distances and angles
33.15.Mt Rotation, vibration, and vibration-rotation constants

Argon nucleation in a cryogenic supersonic nozzle

Somnath Sinha, Ashutosh Bhabhe, Hartawan Laksmono, Judith Wölk, Reinhard Strey, and Barbara Wyslouzil

J. Chem. Phys. 132, 064304 (2010); http://dx.doi.org/10.1063/1.3299273 (11 pages) | Cited 9 times

Online Publication Date: 11 February 2010

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We have measured pressures p and temperatures T corresponding to the maximum nucleation rate of argon in a cryogenic supersonic nozzle apparatus where the estimated nucleation rates are J = 1017±1 cm−3 s−1. As T increases from 34 to 53 K, p increases from 0.47 to 8 kPa. Under these conditions, classical nucleation theory predicts nucleation rates of 11–13 orders of magnitude lower than the observed rates while mean field kinetic nucleation theory predicts the observed rates within 1 order of magnitude. The current data set appears consistent with the measurements of Iland et al. [ J. Chem. Phys. 127, 154506 (2007) ] in the cryogenic nucleation pulse chamber. Combining the two data sets suggests that classical nucleation theory fails because it overestimates both the critical cluster size and the excess internal energy of the critical clusters.
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36.40.Ei Phase transitions in clusters
64.60.qj Studies of nucleation in specific substances
64.70.F- Liquid-vapor transitions
FREE

Exploring the mechanisms of H atom loss in simple azoles: Ultraviolet photolysis of pyrazole and triazole

Graeme A. King, Thomas A. A. Oliver, Michael G. D. Nix, and Michael N. R. Ashfold

J. Chem. Phys. 132, 064305 (2010); http://dx.doi.org/10.1063/1.3292644 (13 pages) | Cited 8 times

Online Publication Date: 12 February 2010

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The photophysics of gas phase pyrazole (C3N2H4) and 2H-1,2,3-triazole (C2N3H3) molecules following excitation at wavelengths in the range 230 nm ≥ λphot ≥ 193.3 nm has been investigated using the experimental technique of H (Rydberg) atom photofragment translational spectroscopy. The findings are compared with previous studies of pyrrole (C4N1H5) and imidazole (C3N2H4), providing a guide to H atom loss dynamics in simple N-containing heterocycles. CASPT2 theoretical methods have been employed to validate these findings. Photoexcitation of pyrazole at the longest wavelengths studied is deduced to involve π∗←π excitation, but photolysis at λphot ≤ 214 nm is characterized by rapid N–H bond fission on a mathσ∗ potential energy surface. The eventual pyrazolyl radical products are formed in a range of vibrational levels associated with both the ground (math2) and first excited (math1) electronic states as a result of nonadiabatic coupling at large N–H bond lengths. The excitation energy of the lowest mathσ∗ state of pyrazole is found to be significantly higher in energy than that of pyrrole and imidazole. Similar studies of 2H-1,2,3-triazole reveal that the lowest mathσ∗ state is yet higher in energy and not accessible following excitation at λphot ≥ 193.3 nm. The N–H bond strength of pyrazole is determined as 37 680±40 cm−1, significantly greater than that of the N–H bonds in pyrrole and imidazole. The correlation between the photochemistry of azoles and the number and position of nitrogen atoms within the ring framework is discussed in terms of molecular symmetry and orbital electron density. A photodissociation channel yielding H atoms with low kinetic energies is also clearly evident in both pyrazole and 2H-1,2,3-triazole. Companion studies of pyrazole-d1 suggest that these slow H atoms arise primarily from the N–H site, following π∗←π excitation, and subsequent internal conversion and/or unintended multiphoton absorption processes.
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82.50.Hp Processes caused by visible and UV light
82.20.Kh Potential energy surfaces for chemical reactions
82.80.Gk Analytical methods involving vibrational spectroscopy
78.40.Me Organic compounds and polymers
71.20.Rv Polymers and organic compounds
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)

Probing the structural evolution of CuN−, N = 9–20, through a comparison of computed electron removal energies and experimental photoelectron spectra

M. Yang, F. Yang, K. A. Jackson, and J. Jellinek

J. Chem. Phys. 132, 064306 (2010); http://dx.doi.org/10.1063/1.3300128 (6 pages) | Cited 3 times

Online Publication Date: 12 February 2010

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Computed electron removal energies for CuN− clusters, N = 9–20, are presented for the three lowest-energy isomers obtained from extensive, unbiased searches for the minimum energy structure at each size. The density functional theory (DFT) computations make use of a scheme introduced by Jellinek and Acioli (JA) [J. Chem. Phys. 118, 7783 (2003) ] that obtains electron removal energies from DFT orbital energies using corrections based on DFT total energies. The computed removal energies are compared with the measured photoelectron spectra (PES) for CuN−. The patterns of computed removal energies are shown to be isomer specific for clusters in this size range. By matching the computed removal energies to the observed PES, the isomers responsible for the PES are identified. The results of the JA scheme are compared to those obtained using other DFT-based methods.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.60.+q Photoelectron spectra
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)

Ab initio characterization of the Ca–HCl van der Waals complex

Jacek Koput and Jan Makarewicz

J. Chem. Phys. 132, 064307 (2010); http://dx.doi.org/10.1063/1.3318467 (10 pages) | Cited 1 time

Online Publication Date: 12 February 2010

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The equilibrium structure and three-dimensional potential energy surface of the Ca–HCl van der Waals complex in its ground electronic state have been determined from accurate ab initio calculations using the coupled-cluster method, CCSD(T), in conjunction with basis sets of quadruple- and quintuple-zeta quality. The core-electron correlation, high-order valence-electron correlation, and scalar relativistic effects were investigated. The Ca–HCl complex was confirmed to be linear at equilibrium, with the vibrationless dissociation energy (into Ca and HCl) De of 287 cm−1. The vibration-rotation energy levels of various Ca–HCl isotopomers were predicted using the variational method. The predicted spectroscopic constants can be useful in a further analysis of high-resolution vibration-rotation spectra of the Ca–HCl complex.
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31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
33.20.Vq Vibration-rotation analysis
31.50.Bc Potential energy surfaces for ground electronic states
31.15.bw Coupled-cluster theory
31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.xt Variational techniques

The barrier height, unimolecular rate constant, and lifetime for the dissociation of HN2

Uğur Bozkaya, Justin M. Turney, Yukio Yamaguchi, and Henry F. Schaefer

J. Chem. Phys. 132, 064308 (2010); http://dx.doi.org/10.1063/1.3310285 (13 pages) | Cited 5 times

Online Publication Date: 12 February 2010

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Although never spectroscopically identified in the laboratory, hydrogenated nitrogen (HN2) is thought to be an important species in combustion chemistry. The classical barrier height (10.6±0.2 kcal mol−1) and exothermicity (3.6±0.2 kcal mol−1) for the HN2→N2+H reaction are predicted by high level ab initio quantum mechanical methods [up to CCSDT(Q)]. Total energies are extrapolated to the complete basis set limit applying the focal point analysis. Zero-point vibrational energies are computed using fundamental (anharmonic) frequencies obtained from a quartic force field. Relativistic and diagonal Born–Oppenheimer corrections are also taken into account. The quantum mechanical barrier with these corrections is predicted to be 6.4±0.2 kcal mol−1 and the reaction exothermicity to be 8.8±0.2 kcal mol−1. The importance of these parameters for the thermal NOx decomposition (De-NOx) process is discussed. The unimolecular rate constant for dissociation of the HN2 molecule and its lifetime are estimated by canonical transition-state theory and Rice–Ramsperger–Kassel–Marcus theory. The lifetime of the HN2 molecule is here estimated to be 2.8×10−10 s at room temperature. Our result is in marginal agreement with the latest experimental kinetic modeling studies (τ = 1.5×10−8 s), albeit consistent with the very rough experimental upper limit (τ<0.5 μs). For the dissociation reaction, kinetic isotope effects are investigated. Our analysis demonstrates that the DN2 molecule has a longer lifetime than the HN2 molecule. Thus, DN2 might be more readily identified experimentally. The ionization potential of the HN2 molecule is determined by analogous high level ab initio methods and focal point analysis. The adiabatic IP of HN2 is predicted to be 8.19±0.05 eV, in only fair agreement with the experimental upper limit of 7.92 eV deduced from sychrothon-radiation-based photoionization mass spectrometry.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
82.20.Pm Rate constants, reaction cross sections, and activation energies
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
82.20.Tr Kinetic isotope effects including muonium
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Spectroscopic investigation of OCS (p-H2)n (n = 1–16) complexes inside helium droplets: Evidence for superfluid behavior

Slava Grebenev, Boris G. Sartakov, J. Peter Toennies, and Andrey F. Vilesov

J. Chem. Phys. 132, 064501 (2010); http://dx.doi.org/10.1063/1.3274509 (19 pages) | Cited 6 times

Online Publication Date: 11 February 2010

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Up to 16 parahydrogen and orthodeuterium molecules have been assembled around an OCS carbonyl sulfide chromophore molecule inside the pure math and mixed math/math droplets at temperatures of 0.38 and 0.15 K, respectively. The infrared spectra of the resulting complexes exhibit a sequence of rotationally resolved vibrational ν3 bands in the vicinity of 2060 cm−1, which are sufficiently separated to assign them to clusters with specific numbers of attached molecules for n = 1–16. The present article contains the first complete analysis of the spectra for n = 2–8 and a full documentation of the results for n = 8–15 briefly described in a short report [ Europhys. Lett. 83, 66008 (2008) ]. Distinct rotational Q-branches are observed for all OCS-(o-D2)n clusters at the He droplet temperatures of 0.38 K and 0.15 K, indicating that the (o-D2)n shell rotates nearly freely about the molecular OCS axis. In the case of OCS-(p-H2)n at 0.38 K, the Q-branch is seen for most n, with the exception of n = 5, 6 and n = 12. At 0.15 K, the Q-branch has disappeared for all n ≥ 11, indicating that the axial rotations are no longer active. Previously, the absence of a Q-branch for n = 5 and 6 was explained by the high group symmetry of the bosonic p-H2 rigid (donut) rings around the OCS molecule. This model, however, fails in explaining the disappearance of the Q-branch for n ≥ 11. In essential agreement with recent path-integral Monte Carlo calculations, the observed phenomenon is attributed to the onset of superfluidity in the multiring p-H2 shell and the related permutations of bosonic p-H2 molecules. A floppy shell model, which accounts for the effect of tunneling and exchange of molecules within the clusters, is able to explain the postulated superfluid behavior of the p-H2 shell at low temperatures. Within this model the activation of states of low axial symmetry is responsible for the appearance of the Q-branch at higher temperatures.
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33.20.Ea Infrared spectra
67.60.-g Mixtures of 3He and 4He
33.20.Tp Vibrational analysis
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis

Quantum instanton evaluations of surface diffusion, interior migration, and surface-subsurface transport for H/Ni

Wenji Wang and Yi Zhao

J. Chem. Phys. 132, 064502 (2010); http://dx.doi.org/10.1063/1.3317475 (10 pages)

Online Publication Date: 11 February 2010

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The quantum instanton approximation is extended to investigate dynamical processes of hydrogen on surface, from surface to subsurface, and between interior sites in nickel lattice. The path integral Monte Carlo and adaptive umbrella sampling techniques are employed to manipulate the quantum instanton formula. The free energy profiles along reaction paths, temperature dependence of free energies, and rates as well as diffusion coefficients are calculated for each process. The results manifest that the motions of nickel atoms beneath the surface have little effect on the hydrogen diffusion on Ni(111), and the hydrogen at the fcc binding site is much easier to get into bulk nickel than the one at the hcp site. The temperature dependence of free energy profiles also reveals that the hydrogen in the subsurface octahedral vacancy and interior tetrahedral vacancy becomes unstable at low temperatures, which proposes a temperature dependence of reaction mechanism. In addition, the relaxations of the lattices dramatically lower the free energy barriers except for the process of the hydrogen diffusion on Ni(111). The quantum motions of the lattice atoms affect the free energies little at 300 K, but they hinder the rates by 20%–40% compared with the classical motions of lattice atoms.
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68.35.Fx Diffusion; interface formation
65.40.G- Other thermodynamical quantities
61.72.jd Vacancies

A comparative ab initio study of neutral and charged kink solitons on conjugated carbon chains

M. L. Mayo and Yu. N. Gartstein

J. Chem. Phys. 132, 064503 (2010); http://dx.doi.org/10.1063/1.3314726 (8 pages)

Online Publication Date: 12 February 2010

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The ground state of odd-N polyynic oligomers CNH2 features kink solitons in carbon-carbon bond-length alternation (BLA) patterns. We perform a systematic first-principles computational study of neutral and singly charged kinks in long oligomers addressing relationships between BLA patterns, electron energy gaps, and accompanying distributions of spin and charge densities, both in vacuum and in the screening solvent environment. A quantitative comparison is made of the results derived with four different ab initio methods: from pure density-functional theory to pure Hartree–Fock (HF) and including two popular hybrid density functionals, B3LYP and BHandHLYP. A clear correlation is demonstrated between the derived spatial extent of kinks and the amount of HF exchange used in the functionals. For charged kinks, we find a substantial difference in the behavior of charge and spin densities.
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31.15.ae Electronic structure and bonding characteristics
31.15.ej Spin-density functionals
31.15.xr Self-consistent-field methods
33.15.Dj Interatomic distances and angles

Thermodynamic stability of soft-core Lennard-Jones fluids and their mixtures

D. M. Heyes

J. Chem. Phys. 132, 064504 (2010); http://dx.doi.org/10.1063/1.3319510 (8 pages) | Cited 1 time

Online Publication Date: 12 February 2010

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Thermodynamic stability of model single component and binary mixture fluids is considered with the Fisher–Ruelle (FR) stability criteria, which apply in the thermodynamic limit, and molecular dynamics (MD) simulation for finite periodic systems. Two soft-core potential forms are considered, ϕ6,1(r) = 4[1/(a+r6)2−1/(a+r6)] and ϕ2,3(r) = 4[1/(a+r2)6−1/(a+r2)3], where r is the separation between the particle centers. According to FR these are unstable in the thermodynamic limit if a>ac = 1/2 and a>ac = (7/32)1/3, respectively. MD simulations with single-component particles show, however, that this transition on typical simulation times is more gradual for finite periodic systems with variation in a on either side of ac. For a<ac, asymmetric density fluctuations are stabilized by the periodic boundary conditions. Also for binary mixtures of (stable) Lennard-Jones and ϕ2,3 particles, phase separation into regions richer in one component than the other was observed for a<ac. Binary systems with interactions similar to a model polymer-colloid fluid in the “depletion” limit equilibrated particularly slowly for a>ac, with the unstable component in the mixture breaking up into many long-lived microdroplets which conferred apparent equilibrium thermodynamic behavior (i.e., negligible N-dependence of the average potential energy per particle) in this period.
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65.20.Jk Studies of thermodynamic properties of specific liquids
64.75.-g Phase equilibria
47.11.Mn Molecular dynamics methods
61.20.Ja Computer simulation of liquid structure
82.60.Hc Chemical equilibria and equilibrium constants
64.75.Gh Phase separation and segregation in model systems (hard spheres, Lennard-Jones, etc.)

Dynamics of water at the nanoscale hydrophobic confinement

Niharendu Choudhury

J. Chem. Phys. 132, 064505 (2010); http://dx.doi.org/10.1063/1.3319504 (5 pages) | Cited 2 times

Online Publication Date: 12 February 2010

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We investigate the effect of solute surface topology created by considering various intermolecular separations of the hydrophobic, paraffinlike plates on the dynamics of water confined between two such plates. The solute plates are made up of 5 n-C18H38 molecules arranged in parallel in such a way that all the carbon atoms of the paraffin molecule are lying on the same plane. Results are obtained from extensive molecular dynamics simulations of aqueous solutions of paraffinlike plates in the isothermal-isobaric ensemble. A strong dependence of the translational as well as vibrational dynamics of the confined water molecules on surface topology (intermolecular distance within the paraffinlike plate) has been observed. Analysis of mean squared displacement reveals anomalous nonlinear behavior of the water molecules in the nanoconfined environment.
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68.08.Bc Wetting
68.35.Ja Surface and interface dynamics and vibrations
02.70.Ns Molecular dynamics and particle methods
68.35.Dv Composition, segregation; defects and impurities
back to top Surfaces, Interfaces, and Materials

Confinement of Ar between two identical parallel semi-infinite walls

Salvador A. Sartarelli and Leszek Szybisz

J. Chem. Phys. 132, 064701 (2010); http://dx.doi.org/10.1063/1.3306449 (8 pages) | Cited 2 times

Online Publication Date: 11 February 2010

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The confinement of Ar in planar slits of two identical parallel semi-infinite walls of alkali metals, alkaline-earth metal Mg, and CO2 is investigated within the framework of the density functional theory. It is assumed that (1) the fluid atoms interact via a recently proposed effective attractive pair potential with strength, εff, which reproduces the experimental data of the surface tension of the liquid-vapor interface at the bulk coexistence curve, and (2) the adsorption on the walls is described by ab initio potentials characterized by a well depth, Wsf. In this way the systems were studied in the framework of a realistic approach. We found that for small coverages, the slit is always filled by forming two symmetric vapor films, one at each wall. For increasing coverage the behavior depends on the ratio Wsf/εff and the temperature T. In the case of alkali metals, we found at the triple point, Tt, of the adsorbate a regime of average density ρav∗ in which the ground state exhibits asymmetric density profiles, leading to the so-called spontaneous symmetry breaking (SSB) effect. The SSB appears at an average density ρsb1∗ and disappears at a higher average density ρsb2∗. When T is increased, the range of densities ρsb1∗ ≤ ρav∗ ≤ ρsb2∗ diminishes and eventually the SSB disappears at a critical temperature, Tsb, which coincides with the critical prewetting temperature Tcpw observed in the adsorption on a single wall. For T>Tcpw the slit is filled symmetrically up to the phase transition to capillary condensation. All these features are examined as a function of the strength of the substrate and the width of the slit. Furthermore, no SSB effect was found for Mg and CO2.
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68.03.Cd Surface tension and related phenomena
64.70.F- Liquid-vapor transitions
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
68.08.Bc Wetting

Thioglycolic acid on the gold (111) surface and Raman vibrational spectra

Jian-Ge Zhou, Quinton L. Williams, and Ruqian Wu

J. Chem. Phys. 132, 064702 (2010); http://dx.doi.org/10.1063/1.3319711 (8 pages)

Online Publication Date: 12 February 2010

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The interaction of thioglycolic acid (HSCH2COOH) with the Au(111) surface is investigated, and it is found that at the low coverage the molecule lies down on the substrate. If the mercaptan-hydrogen atom is eliminated, the resulting SCH2COOH molecule is randomly oriented on the surface. If the carboxylic acid group in the HSCH2COOH molecule is deprotonated instead, the HSCH2COO− molecule lies down on the surface. However, when the mercaptan-hydrogen atom in the HSCH2COO− molecule is removed, the resulting SCH2COO− molecule rises up to a certain level on the substrate. The calculated Raman vibrational spectra decipher which compounds and atomic displacements contribute to the corresponding frequencies. We thus propose a consistent mechanism for the deposition of thioglycolic acid on the Au(111) surface.
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68.43.Mn Adsorption kinetics
78.30.-j Infrared and Raman spectra
68.35.Ja Surface and interface dynamics and vibrations
68.43.Pq Adsorbate vibrations
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