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7 Mar 2013

Volume 138, Issue 9, Articles (09xxxx)

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J. Chem. Phys. 138, 094501 (2013); http://dx.doi.org/10.1063/1.4793314 (6 pages)

Yansun Yao and Dennis D. Klug
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Communication: Importance sampling including path correlation in semiclassical initial value representation calculations for time correlation functions

Feng Pan and Guohua Tao

J. Chem. Phys. 138, 091101 (2013); http://dx.doi.org/10.1063/1.4794191 (4 pages)

Online Publication Date: 4 March 2013

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Full semiclassical (SC) initial value representation (IVR) for time correlation functions involves a double phase space average over a set of two phase points, each of which evolves along a classical path. Conventionally, the two initial phase points are sampled independently for all degrees of freedom (DOF) in the Monte Carlo procedure. Here, we present an efficient importance sampling scheme by including the path correlation between the two initial phase points for the bath DOF, which greatly improves the performance of the SC-IVR calculations for large molecular systems. Satisfactory convergence in the study of quantum coherence in vibrational relaxation has been achieved for a benchmark system-bath model with up to 21 DOF.
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31.15.xg Semiclassical methods
02.50.-r Probability theory, stochastic processes, and statistics
02.70.Uu Applications of Monte Carlo methods
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back to top Theoretical Methods and Algorithms

Localized saddle-point search and application to temperature-accelerated dynamics

Yunsic Shim, Nathan B. Callahan, and Jacques G. Amar

J. Chem. Phys. 138, 094101 (2013); http://dx.doi.org/10.1063/1.4793218 (7 pages)

Online Publication Date: 1 March 2013

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We present a method for speeding up temperature-accelerated dynamics (TAD) simulations by carrying out a localized saddle-point (LSAD) search. In this method, instead of using the entire system to determine the energy barriers of activated processes, the calculation is localized by only including a small chunk of atoms around the atoms directly involved in the transition. Using this method, we have obtained N-independent scaling for the computational cost of the saddle-point search as a function of system size N. The error arising from localization is analyzed using a variety of model systems, including a variety of activated processes on Ag(100) and Cu(100) surfaces, as well as multiatom moves in Cu radiation damage and metal heteroepitaxial growth. Our results show significantly improved performance of TAD with the LSAD method, for the case of Ag/Ag(100) annealing and Cu/Cu(100) growth, while maintaining a negligibly small error in energy barriers.
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72.15.Rn Localization effects (Anderson or weak localization)
81.40.Gh Other heat and thermomechanical treatments
61.82.Bg Metals and alloys

Applicability of the wide-band limit in DFT-based molecular transport calculations

C. J. O. Verzijl, J. S. Seldenthuis, and J. M. Thijssen

J. Chem. Phys. 138, 094102 (2013); http://dx.doi.org/10.1063/1.4793259 (10 pages)

Online Publication Date: 1 March 2013

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Transport properties of molecular junctions are notoriously expensive to calculate with ab initio methods, primarily due to the semi-infinite electrodes. This has led to the introduction of different approximation schemes for the electrodes. For the most popular metals used in experiments, such as gold, the wide-band limit (WBL) is a particularly efficient choice. In this paper, we investigate the performance of different WBL schemes relative to more sophisticated approaches including the fully self-consistent non-equilibrium Green's function method. We find reasonably good agreement between all schemes for systems in which the molecule (and not the metal-molecule interface) dominates the transport properties. Moreover, our implementation of the WBL requires negligible computational effort compared to the ground-state density-functional theory calculation of a molecular junction. We also present a new approximate but efficient scheme for calculating transport with a finite bias. Provided the voltage drop occurs primarily inside the molecule, this method provides results in reasonable agreement with fully self-consistent calculations.
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72.10.Bg General formulation of transport theory

Recycling random numbers in the stochastic simulation algorithm

Christian A. Yates and Guido Klingbeil

J. Chem. Phys. 138, 094103 (2013); http://dx.doi.org/10.1063/1.4792207 (6 pages)

Online Publication Date: 1 March 2013

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The stochastic simulation algorithm (SSA) was introduced by Gillespie and in a different form by Kurtz. Since its original formulation there have been several attempts at improving the efficiency and hence the speed of the algorithm. We briefly discuss some of these methods before outlining our own simple improvement, the recycling direct method (RDM), and demonstrating that it is capable of increasing the speed of most stochastic simulations. The RDM involves the statistically acceptable recycling of random numbers in order to reduce the computational cost associated with their generation and is compatible with several of the pre-existing improvements on the original SSA. Our improvement is also sufficiently simple (one additional line of code) that we hope will be adopted by both trained mathematical modelers and experimentalists wishing to simulate their model systems.
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82.20.Uv Stochastic theories of rate constants
02.50.Ey Stochastic processes
02.50.Fz Stochastic analysis
05.10.Gg Stochastic analysis methods (Fokker-Planck, Langevin, etc.)
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
82.20.Db Transition state theory and statistical theories of rate constants

Extension of the KLI approximation toward the exact optimized effective potential

G. J. Iafrate and J. B. Krieger

J. Chem. Phys. 138, 094104 (2013); http://dx.doi.org/10.1063/1.4792365 (8 pages)

Online Publication Date: 1 March 2013

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The integral equation for the optimized effective potential (OEP) is utilized in a compact form from which an accurate OEP solution for the spin-unrestricted exchange-correlation potential, Vxcσ, is obtained for any assumed orbital-dependent exchange-correlation energy functional. The method extends beyond the Krieger-Li-Iafrate (KLI) approximation toward the exact OEP result. The compact nature of the OEP equation arises by replacing the integrals involving the Green's function terms in the traditional OEP equation by an equivalent first-order perturbation theory wavefunction often referred to as the “orbital shift” function. Significant progress is then obtained by solving the equation for the first order perturbation theory wavefunction by use of Dalgarno functions which are determined from well known methods of partial differential equations. The use of Dalgarno functions circumvents the need to explicitly address the Green's functions and the associated problems with “sum over states” numerics; as well, the Dalgarno functions provide ease in dealing with inherent singularities arising from the origin and the zeros of the occupied orbital wavefunctions. The Dalgarno approach for finding a solution to the OEP equation is described herein, and a detailed illustrative example is presented for the special case of a spherically symmetric exchange-correlation potential. For the case of spherical symmetry, the relevant Dalgarno function is derived by direct integration of the appropriate radial equation while utilizing a user friendly method which explicitly treats the singular behavior at the origin and at the nodal singularities arising from the zeros of the occupied states. The derived Dalgarno function is shown to be an explicit integral functional of the exact OEP Vxcσ, thus allowing for the reduction of the OEP equation to a self-consistent integral equation for the exact exchange-correlation potential; the exact solution to this integral equation can be determined by iteration with the natural zeroth order correction given by the KLI exchange-correlation potential. Explicit analytic results are provided to illustrate the first order iterative correction beyond the KLI approximation. The derived correction term to the KLI potential explicitly involves spatially weighted products of occupied orbital densities in any assumed orbital-dependent exchange-correlation energy functional; as well, the correction term is obtained with no adjustable parameters. Moreover, if the equation for the exact optimized effective potential is further iterated, one can obtain the OEP as accurately as desired.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.V- Electron correlation calculations for atoms, ions and molecules

Spin filtering in molecular junction: Magnetoresistance evaluation from wave-function calculations

Martin Vérot, Serguei A. Borshch, and Vincent Robert

J. Chem. Phys. 138, 094105 (2013); http://dx.doi.org/10.1063/1.4793318 (7 pages)

Online Publication Date: 1 March 2013

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The conductance of magnetic molecules opens new ways to probe the electronic structure of correlated systems. Based on a 2-electron/2-molecular orbital prototype system, the current-potential characteristics is inspected as a function of the differential magnetization of the electrodes sandwiching the molecule within a multideterminantal framework. The bias-dependent magnetoresistance effect along the junction reflects the nature and energetics of the different multiplets, obtained within the multiconfigurational wave-function approach. From the wave-function description, a modulation of the magnetoresistance ratio is anticipated and both direct and inverse regimes are observed depending on the electronic structure of the junction.
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85.65.+h Molecular electronic devices
72.20.My Galvanomagnetic and other magnetotransport effects
75.60.Ej Magnetization curves, hysteresis, Barkhausen and related effects

Types of single particle symmetry breaking in transition metal oxides due to electron correlation

Lucas K. Wagner

J. Chem. Phys. 138, 094106 (2013); http://dx.doi.org/10.1063/1.4793531 (6 pages)

Online Publication Date: 5 March 2013

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Very accurate wave functions are calculated for small transition metal oxide molecules. These wave functions are decomposed using reduced density matrices to study the underlying correlation of electrons. The correlation is primarily of left-right type between the transition metals and the oxygen atoms, which is mediated by excitations from the nominal single Slater ground state into antibonding and d-type orbitals. In a localized representation, this correlation manifests itself in a 2-electron hopping term that is off-diagonal. This term is of similar magnitude to the commonly considered Hubbard-type on-site interaction.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
33.15.Fm Bond strengths, dissociation energies

A general nuclear motion Hamiltonian and non-internal curvilinear coordinates

D. Strobusch and Ch. Scheurer

J. Chem. Phys. 138, 094107 (2013); http://dx.doi.org/10.1063/1.4793627 (11 pages)

Online Publication Date: 5 March 2013

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An exact Hamiltonian for nuclear motions in general curvilinear coordinates is derived. It is demonstrated how this Hamiltonian transforms into well-established expressions, such as the Wilson Howard Hamiltonian or the Meyer Günthard Hamiltonian, if the general coordinates are restricted to be rectilinear or internal. Furthermore, a compact expression for the Hamiltonian expressed in non-internal curvilinear coordinates is provided, which makes this coordinate class available for applications in a simple way, since only the Jacobian matrix with respect to the rotating frame coordinates must be calculated. An example, employing a water model potential, exemplifies how different coordinate systems from all three coordinate classes (rectilinear, internal, and non-internal) lead to vibrational spectra, which are in excellent agreement. Thereby, the applicability of the general Hamiltonian is demonstrated and also its correctness is confirmed.
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33.20.Tp Vibrational analysis
31.15.X- Alternative approaches

Electronic transition dipole moments and dipole oscillator strengths within Fock-space multi-reference coupled cluster framework: An efficient and novel approach

Debarati Bhattacharya, Nayana Vaval, and Sourav Pal

J. Chem. Phys. 138, 094108 (2013); http://dx.doi.org/10.1063/1.4793277 (9 pages)

Online Publication Date: 5 March 2013

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Within the Fock-space multi-reference coupled cluster framework, we have evaluated the electronic transition dipole moments, which determine absorption intensities. These depend on matrix elements between two different wave functions (e.g., ground state to the excited state). We present two different ways, to calculate these transition moments. In the first method, we construct the ground and excited state wave functions with the normal exponential ansatz of Fock-space coupled cluster method and then calculate the relevant off-diagonal matrix elements. In the second approach, we linearize the exponential form of the wave operator which will generate the left vector, by use of Lagrangian formulation. The right vector is obtained from the exponential ansatz. In order to relate the transition moments to oscillator strengths, excitation energies need to be evaluated. The excitation energies are obtained from the Fock-space multi-reference framework. The transition dipole moments of the ground to a few excited states, together with the oscillator strengths of a few molecules, are presented.
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31.15.bw Coupled-cluster theory
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.70.Fd Absolute and relative line and band intensities

A second-order unconstrained optimization method for canonical-ensemble density-functional methods

Cecilie R. Nygaard and Jeppe Olsen

J. Chem. Phys. 138, 094109 (2013); http://dx.doi.org/10.1063/1.4791571 (12 pages)

Online Publication Date: 5 March 2013

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A second order converging method of ensemble optimization (SOEO) in the framework of Kohn-Sham Density-Functional Theory is presented, where the energy is minimized with respect to an ensemble density matrix. It is general in the sense that the number of fractionally occupied orbitals is not predefined, but rather it is optimized by the algorithm. SOEO is a second order Newton-Raphson method of optimization, where both the form of the orbitals and the occupation numbers are optimized simultaneously. To keep the occupation numbers between zero and two, a set of occupation angles is defined, from which the occupation numbers are expressed as trigonometric functions. The total number of electrons is controlled by a built-in second order restriction of the Newton-Raphson equations, which can be deactivated in the case of a grand-canonical ensemble (where the total number of electrons is allowed to change). To test the optimization method, dissociation curves for diatomic carbon are produced using different functionals for the exchange-correlation energy. These curves show that SOEO favors symmetry broken pure-state solutions when using functionals with exact exchange such as Hartree-Fock and Becke three-parameter Lee-Yang-Parr. This is explained by an unphysical contribution to the exact exchange energy from interactions between fractional occupations. For functionals without exact exchange, such as local density approximation or Becke Lee-Yang-Parr, ensemble solutions are favored at interatomic distances larger than the equilibrium distance. Calculations on the chromium dimer are also discussed. They show that SOEO is able to converge to ensemble solutions for systems that are more complicated than diatomic carbon.
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31.15.E- Density-functional theory

Efficient softest mode finding in transition states calculations

Jing Leng, Weiguo Gao, Cheng Shang, and Zhi-Pan Liu

J. Chem. Phys. 138, 094110 (2013); http://dx.doi.org/10.1063/1.4792644 (8 pages)

Online Publication Date: 6 March 2013

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Transition states are fundamental to understanding the reaction dynamics qualitatively in chemical physics. To date various methods of first principle location of the transition states have been developed. In the absence of the knowledge of the final structure, the softest-mode following method climbs up to a transition state without calculating the Hessian matrix. One weakness of this kind of approaches is that the number of rotations to determine the softest mode is usually unpredictable. In this paper, we propose a locally optimal search direction finding algorithm, namely LOR, which is an extension of the traditional conjugate gradient method without additional calculations of the forces. We also show that the translation of forces improves the numerical stability. Experiments for the Baker test system show that the proposed algorithm is much faster than the original dimer conjugate gradient method.
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82.20.Db Transition state theory and statistical theories of rate constants

Minimizing memory as an objective for coarse-graining

Nicholas Guttenberg, James F. Dama, Marissa G. Saunders, Gregory A. Voth, Jonathan Weare, and Aaron R. Dinner

J. Chem. Phys. 138, 094111 (2013); http://dx.doi.org/10.1063/1.4793313 (10 pages)

Online Publication Date: 6 March 2013

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Coarse-graining a molecular model is the process of integrating over degrees of freedom to obtain a reduced representation. This process typically involves two separate but related steps, selection of the coordinates comprising the reduced system and modeling their interactions. Both the coordinate selection and the modeling procedure present challenges. Here, we focus on the former. Typically, one seeks to integrate over the fast degrees of freedom and retain the slow degrees of freedom. Failure to separate timescales results in memory. With this motivation, we introduce a heuristic measure of memory and show that it can be used to compare competing coordinate selections for a given modeling procedure. We numerically explore the utility of this heuristic for three systems of increasing complexity. The first example is a four-particle linear model, which is exactly solvable. The second example is a sixteen-particle nonlinear model; this system has interactions that are characteristic of molecular force fields but is still sufficiently simple to permit exhaustive numerical treatment. The third example is an atomic-resolution representation of a protein, the class of models most often treated by relevant coarse-graining approaches; we specifically study an actin monomer. In all three cases, we find that the heuristic suggests coordinate selections that are physically intuitive and reflect molecular structure. The memory heuristic can thus serve as an objective codification of expert knowledge and a guide to sites within a model that requires further attention.
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87.15.B- Structure of biomolecules
33.15.Bh General molecular conformation and symmetry; stereochemistry
36.20.Ey Conformation (statistics and dynamics)
36.20.Hb Configuration (bonds, dimensions)
87.14.E- Proteins
87.15.A- Theory, modeling, and computer simulation

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

Andrea Cavalli, Carlo Camilloni, and Michele Vendruscolo

J. Chem. Phys. 138, 094112 (2013); http://dx.doi.org/10.1063/1.4793625 (5 pages)

Online Publication Date: 7 March 2013

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In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.
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87.15.ap Molecular dynamics simulation
87.64.kj NMR
87.15.B- Structure of biomolecules
87.15.M- Spectra of biomolecules
87.15.hp Conformational changes
87.14.E- Proteins

Bond energy decomposition analysis for subsystem density functional theory

S. Maya Beyhan, Andreas W. Götz, and Lucas Visscher

J. Chem. Phys. 138, 094113 (2013); http://dx.doi.org/10.1063/1.4793629 (10 pages)

Online Publication Date: 7 March 2013

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We employed an explicit expression for the dispersion (D) energy in conjunction with Kohn-Sham (KS) density functional theory and frozen-density embedding (FDE) to calculate interaction energies between DNA base pairs and a selected set of amino acid pairs in the hydrophobic core of a small protein Rubredoxin. We use this data to assess the accuracy of an FDE-D approach for the calculation of intermolecular interactions. To better analyze the calculated interaction energies we furthermore propose a new energy decomposition scheme that is similar to the well-known KS bond formation analysis [F. M. Bickelhaupt and E. J. Baerends, Rev. Comput. Chem. 15, 1 (2000)10.1002/9780470125922.ch1], but differs in the electron densities used to define the bond energy. The individual subsystem electron densities of the FDE approach sum to the total electron density which makes it possible to define bond energies in terms of promotion energies and an explicit interaction energy. We show that for the systems considered only a few freeze-and-thaw cycles suffice to reach convergence in these individual bond energy components, illustrating the potential of FDE-D as an efficient method to calculate intermolecular interactions.
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87.15.K- Molecular interactions; membrane-protein interactions
87.14.gk DNA
87.15.Pc Electronic and electrical properties

Oscillator strengths of electronic excitations with response theory using phase including natural orbital functionals

R. van Meer, O. V. Gritsenko, K. J. H. Giesbertz, and E. J. Baerends

J. Chem. Phys. 138, 094114 (2013); http://dx.doi.org/10.1063/1.4793740 (12 pages)

Online Publication Date: 7 March 2013

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The key characteristics of electronic excitations of many-electron systems, the excitation energies ωα and the oscillator strengths fα, can be obtained from linear response theory. In one-electron models and within the adiabatic approximation, the zeros of the inverse response matrix, which occur at the excitation energies, can be obtained from a simple diagonalization. Particular cases are the eigenvalue equations of time-dependent density functional theory (TDDFT), time-dependent density matrix functional theory, and the recently developed phase-including natural orbital (PINO) functional theory. In this paper, an expression for the oscillator strengths fα of the electronic excitations is derived within adiabatic response PINO theory. The fα are expressed through the eigenvectors of the PINO inverse response matrix and the dipole integrals. They are calculated with the phase-including natural orbital functional for two-electron systems adapted from the work of Lmathwdin and Shull on two-electron systems (the phase-including Löwdin-Shull functional). The PINO calculations reproduce the reference fα values for all considered excitations and bond distances R of the prototype molecules H2 and HeH+ very well (perfectly, if the correct choice of the phases in the functional is made). Remarkably, the quality is still very good when the response matrices are severely restricted to almost TDDFT size, i.e., involving in addition to the occupied-virtual orbital pairs just (HOMO+1)-virtual pairs (R1) and possibly (HOMO+2)-virtual pairs (R2). The shape of the curves fα(R) is rationalized with a decomposition analysis of the transition dipole moments.
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33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
31.15.B- Approximate calculations
31.15.ee Time-dependent density functional theory
33.15.Dj Interatomic distances and angles
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
back to top Advanced Experimental Techniques

Comb-linked, cavity ring-down spectroscopy for measurements of molecular transition frequencies at the kHz-level

G.-W. Truong, D. A. Long, A. Cygan, D. Lisak, R. D. van Zee, and J. T. Hodges

J. Chem. Phys. 138, 094201 (2013); http://dx.doi.org/10.1063/1.4792372 (7 pages) | Cited 1 time

Online Publication Date: 4 March 2013

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We present a low uncertainty measurement technique for determining molecular transition frequencies. This approach is complementary to sub-Doppler saturation spectroscopies and is expected to enable new frequency measurements for a wide variety of molecular species with uncertainties at the kHz-level. The technique involves measurements of Doppler broadened lines using cavity ring-down spectroscopy whereby the probe laser is actively locked to the ring-down cavity and the spectrum frequencies are linked directly to an optical frequency comb that is referenced to an atomic frequency standard. As a demonstration we have measured the transition frequency of the (30012) ← (00001) P14e line of CO2 near 1.57 μm with a combined standard uncertainty of ∼9 kHz. This technique exhibits exceptional promise for measurements of transition frequencies and pressure shifting parameters of many weak absorbers, and indicates the potential for substantially improved measurements when compared to those obtained with conventional spectroscopic methods.
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33.70.Jg Line and band widths, shapes, and shifts

Restricted diffusion in annular geometrical pores

Bahman Ghadirian, Allan M. Torres, Nirbhay N. Yadav, and William S. Price

J. Chem. Phys. 138, 094202 (2013); http://dx.doi.org/10.1063/1.4793525 (11 pages)

Online Publication Date: 5 March 2013

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Nuclear magnetic resonance (NMR) diffusion (including diffusion MRI) experiments are only as powerful as the models used to analyse the NMR diffusion data. A major problem, especially with measurements on biological systems, is that the existing models are only very poor approximations of cellular shape. Here, diffusion propagators and pulsed gradient spin-echo attenuation equations are derived in the short gradient pulse limit for diffusion within the annular region of a concentric cylinder of finite length and, similarly, within the annular region of a concentric sphere. The models include the possibility of relaxation at the boundaries and, in the case of the concentric cylinder, having the cylinder arbitrarily oriented with respect to the direction of the applied field gradient. The two models are also of interest due to their direct analogy to optical double slit diffraction. Also expressions for the mean square displacements, which are very useful information for determining the diffusion coefficient within these complex geometries, are obtained as well as for the limiting cases of diffusion on cylindrical and spherical shells and in a ring.
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76.60.Lz Spin echoes
05.60.-k Transport processes
47.56.+r Flows through porous media
61.43.Gt Powders, porous materials

VUV photoionization of gas phase adenine and cytosine: A comparison between oven and aerosol vaporization

D. Touboul, F. Gaie-Levrel, G. A. Garcia, L. Nahon, L. Poisson, M. Schwell, and M. Hochlaf

J. Chem. Phys. 138, 094203 (2013); http://dx.doi.org/10.1063/1.4793734 (8 pages)

Online Publication Date: 5 March 2013

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We studied the single photon ionization of gas phase adenine and cytosine by means of vacuum ultraviolet synchrotron radiation coupled to a velocity map imaging electron/ion coincidence spectrometer. Both in-vacuum temperature-controlled oven and aerosol thermodesorption were successfully applied to promote the intact neutral biological species into the gas phase. The photoion yields are consistent with previous measurements. In addition, we deduced the threshold photoelectron spectra and the slow photoelectron spectra for both species, where the close to zero kinetic energy photoelectrons and the corresponding photoions are measured in coincidence. The photoionization close and above the ionization energies are found to occur mainly via direct processes. Both vaporization techniques lead to similar electronic spectra for the two molecules, which consist of broadbands due to the complex electronic structure of the cationic species and to the possible contribution of several neutral tautomers for cytosine prior to ionization. Accurate ionization energies are measured for adenine and cytosine at, respectively, 8.267 ± 0.005 eV and 8.66 ± 0.01 eV, and we deduce precise thermochemical data for the adenine radical cation. Finally, we performed an evaluation and a comparison of the two vaporization techniques addressing the following criteria: measurement precision, thermal fragmentation, sensitivity, and sample consumption. The aerosol thermodesorption technique appears as a promising alternative to vaporize large thermolabile biological compounds, where extended thermal decomposition or low sensitivity could be encountered when using a simple oven vaporization technique.
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87.15.mn Photoionization
33.80.Eh Autoionization, photoionization, and photodetachment
36.20.Kd Electronic structure and spectra
33.60.+q Photoelectron spectra
87.15.K- Molecular interactions; membrane-protein interactions
back to top Atoms, Molecules, and Clusters

Rovibronically selected and resolved two-color laser photoionization and photoelectron study of cobalt carbide cation

Huang Huang, Yih Chung Chang, Zhihong Luo, Xiaoyu Shi, Chow-Shing Lam, Kai-Chung Lau, and C. Y. Ng

J. Chem. Phys. 138, 094301 (2013); http://dx.doi.org/10.1063/1.4790707 (9 pages) | Cited 1 time

Online Publication Date: 1 March 2013

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We have conducted a two-color visible-ultraviolet (VIS-UV) resonance-enhanced laser photoionization efficiency and pulsed field ionization-photoelectron (PFI-PE) study of gaseous cobalt carbide (CoC) near its ionization onset in the total energy range of 61 200–64 510 cm−1. The cold gaseous CoC sample was prepared by a laser ablation supersonically cooled beam source. By exciting CoC molecules thus generated to single N′ rotational levels of the intermediate CoC*(2Σ+; v′) state using a VIS dye laser prior to UV laser photoionization, we have obtained N+ rotationally resolved PFI-PE spectra for the CoC+(X1Σ+; v+ = 0 and 1) ion vibrational bands free from interference by impurity species except Co atoms produced in the ablation source. The rotationally selected and resolved PFI-PE spectra have made possible unambiguous rotational assignments, yielding accurate values for the adiabatic ionization energy of CoC(X2Σ+), IE(CoC) = 62 384.3 ± 0.6 cm−1 (7.73467 ± 0.00007 eV), the vibrational frequency ωe+ = 985.6 ± 0.6 cm−1, the anharmonicity constant ωe+χe+ = 6.3 ± 0.6 cm−1, the rotational constants (Be+ = 0.7196 ± 0.0005 cm−1, αe+ = 0.0056 ± 0.0008 cm−1), and the equilibrium bond length re+ = 1.534 Å for CoC+(X1Σ+). The observation of the N+ = 0 level in the PFI-PE measurement indicates that the CoC+ ground state is of 1Σ+ symmetry. Large ΔN+ = N+ − N′ changes up to 6 are observed for the photoionization transitions CoC+(X1Σ+; v+ = 0–2; N+) ← CoC*(2Σ+; v′; N′ = 6, 7, 8, and 9). The highly precise energetic and spectroscopic data obtained in the present study have served as a benchmark for testing theoretical predictions based on state-of-the-art ab initio quantum calculations at the CCSDTQ/CBS level of theory as presented in the companion article.
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33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.60.+q Photoelectron spectra
33.15.Dj Interatomic distances and angles
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Vq Vibration-rotation analysis
33.80.Eh Autoionization, photoionization, and photodetachment

High-level ab initio predictions for the ionization energy, bond dissociation energies, and heats of formation of cobalt carbide (CoC) and its cation (CoC+)

Kai-Chung Lau, Yi Pan, Chow-Shing Lam, Huang Huang, Yih-Chung Chang, Zhihong Luo, Xiaoyu Shi, and C. Y. Ng

J. Chem. Phys. 138, 094302 (2013); http://dx.doi.org/10.1063/1.4792718 (7 pages) | Cited 2 times

Online Publication Date: 1 March 2013

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The ionization energy (IE) of CoC and the 0 K bond dissociation energies (D0) and the heats of formation at 0 K (ΔH°f0) and 298 K (ΔH°f298) for CoC and CoC+ are predicted by the wavefunction based coupled-cluster theory with single, double, triple and quadruple excitations (CCSDTQ) and complete basis set (CBS) approach. The CCSDTQ/CBS calculations presented here involve the approximation to the CBS limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy, high-order correlation, core-valence (CV) electronic, spin-orbit coupling, and scalar relativistic effect corrections. The present calculations provide the correct symmetry, 1Σ+, for the ground state of CoC+. The CCSDTQ/CBS IE(CoC) = 7.740 eV is found in good agreement with the experimental IE value of 7.73467 ± 0.00007 eV, determined in a two-color laser photoion and pulsed field ionization-photoelectron study. This work together with the previous experimental and theoretical investigations support the conclusion that the CCSDTQ/CBS method is capable of providing reliable IE predictions for 3d-transition metal carbides, such as FeC, CoC, and NiC. Among the single-reference based coupled-cluster methods and multi-reference configuration interaction (MRCI) approach, the CCSDTQ and MRCI methods give the best predictions to the harmonic frequencies ωe (ωe+) = 956 (992) and 976 (1004) cm−1 and the bond lengths re (re+) = 1.560 (1.528) and 1.550 (1.522) Å, respectively, for CoC (CoC+) in comparison with the experimental values. The CCSDTQ/CBS calculations give the prediction of D0(Co+–C) − D0(Co–C) = 0.175 eV, which is also consistent with the experimental determination of 0.14630 ± 0.00014 eV. The theoretical results show that the CV and valence-valence electronic correlations beyond CCSD(T) wavefunction and the relativistic effect make significant contributions to the calculated thermochemical properties of CoC/CoC+. For the experimental D0 and ΔHof0 values of CoC/CoC+, which are not known experimentally, we recommend the following CCSDTQ/CBS predictions: ΔHof0(CoC) = 775.7 kJ/mol and ΔHof0(CoC+) = 1522.5 kJ/mol, ΔHof298(CoC) = 779.2 kJ/mol and ΔHo298(CoC+) = 1526.0 kJ/mol.
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31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
33.15.Fm Bond strengths, dissociation energies
31.15.bw Coupled-cluster theory
31.15.vj Electron correlation calculations for atoms and ions: excited states
33.20.Tp Vibrational analysis
33.15.Dj Interatomic distances and angles

The X1Σg+ ground state of Mg2 studied by Fourier-transform spectroscopy

H. Knöckel, S. Rühmann, and E. Tiemann

J. Chem. Phys. 138, 094303 (2013); http://dx.doi.org/10.1063/1.4792725 (10 pages) | Cited 1 time

Online Publication Date: 1 March 2013

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The A1Σu+ - X1Σg+ UV spectrum of Mg2 has been investigated with high resolution Fourier-transform spectroscopy. Mg2 vapor was created in a heat pipe. Various spectroscopic methods have been employed, such as conventional absorption spectroscopy with light from a broad band lamp and laser-induced fluorescence. The high resolution of the Fourier-transform spectrometer, together with computer aided evaluation methods of the spectra, yields precise transition frequencies. The new data and data available from earlier investigations are applied in direct potential fits of lower and upper electronic states. Various representations of potential energy curves for the ground state X1Σg+ have been employed and their benefits in terms of smallest number of parameters are discussed. Scattering lengths are derived for the homonuclear isotopologues and compared with previous results.
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33.20.Lg Ultraviolet spectra
33.50.Dq Fluorescence and phosphorescence spectra
31.30.Gs Hyperfine interactions and isotope effects
31.50.Bc Potential energy surfaces for ground electronic states
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

Site-specific analysis of dipole polarizabilities of heterogeneous systems: Iron-doped Sin (n = 1–14) clusters

Li Ma, Jianguang Wang, and Guanghou Wang

J. Chem. Phys. 138, 094304 (2013); http://dx.doi.org/10.1063/1.4793276 (9 pages)

Online Publication Date: 1 March 2013

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Following the recent work of decomposing the total dipole moment and polarizability of a homogeneous system into site-specific contributions, we extend the study to the heterogeneous systems of iron-doped Sin (n = 1–14) clusters by introducing a weighting function. The structure-/shape- and size-specific aspects of the dipole moments and polarizabilities of SinFe (n = 1–14) clusters are analyzed and compared with pure silicon clusters. It is shown that the polarizabilities associated with the individual constituent atoms vary considerably with the structure/shape of the cluster and the location of the atom or site within a given structure. For atoms at peripheral sites, the polarizabilities are substantially larger than atoms at the interior sites, and the more peripheral an atom is, the larger is its polarizability. The polarizability of the Fe atom in SinFe clusters decreases as the cluster size increases. This is related to the position of Fe atom in SinFe clusters and indicates significant screening of the interior of the cluster by its surface. The correlation between the anisotropy of the total polarizability and the anisotropy of the cluster shape is also analyzed. Comparing with pure Sin clusters, the polarizabilities of Si atoms are increased after Fe atom doping. The structures are more compact for SinFe than the same sizes of Sin+1 clusters and the polarizabilities of SinFe are smaller than Sin+1 for the sizes of n = 7–14.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Torsional electric dipole moment functions calculated for HOOH and ClOOCl

Mark P. McGrath

J. Chem. Phys. 138, 094305 (2013); http://dx.doi.org/10.1063/1.4792364 (6 pages)

Online Publication Date: 1 March 2013

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The periodic torsional, electric dipole moment (EDM) functions μ(ϕ) = ∑m = 0pmcos (m + 1/2)ϕ, of the atmospherically significant molecules HOOH and ClOOCl, have been derived from calculations at the CCSD(T) (coupled-cluster singles and doubles model, plus a noniterative triples correction) level of electronic-structure theory with augmented, correlation-consistent basis sets extrapolated to the approximate complete basis set limit. The μ(ϕ) of HOOH, defined by {pm} = {3.0979, −0.0301, −0.0058} D, is used to calculate squared transition EDMs that compare well with those previously derived using the experimental torsional line intensities. The μ(ϕ) of ClOOCl, defined by μ(ϕ) = {1.1935, 0.1163, 0.1341, −0.0040, −0.0099} D, requires a longer Fourier expansion because, in the range of dihedral angles from the cis (ϕ = 0) to the trans (ϕ = π) transition structures, three inflection points are found for ClOOCl, but only one for HOOH. The permanent EDM calculated for HOOH, 1.754 D, is in close agreement with the value deduced from experiment. Compared to HOOH, the permanent EDM vector calculated for ClOOCl is directed analogously, but has a significantly smaller magnitude, 0.700 D.
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33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.20.Tp Vibrational analysis
31.15.bw Coupled-cluster theory
33.15.Bh General molecular conformation and symmetry; stereochemistry

Dissociation limit and dissociation dynamic of CF4+: Application of threshold photoelectron-photoion coincidence velocity imaging

Xiaofeng Tang, Xiaoguo Zhou, Manman Wu, Zhi Gao, Shilin Liu, Fuyi Liu, Xiaobin Shan, and Liusi Sheng

J. Chem. Phys. 138, 094306 (2013); http://dx.doi.org/10.1063/1.4792368 (9 pages)

Online Publication Date: 1 March 2013

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Dissociation of internal energy selected CF4+ ions in an excitation energy range of 15.40–19.60 eV has been investigated using threshold photoelectron-photoion coincidence (TPEPICO) velocity imaging. Only CF3+ fragment ions are observed in coincident mass spectra, indicating all the X2T1, A2T2, and B2E ionic states of CF4+ are fully dissociative. Both kinetic energy released distribution (KERD) and angular distribution in dissociation of CF4+ ions have been derived from three-dimensional TPEPICO time-sliced images. A parallel distribution of CF3+ fragments along the polarization vector of photon is observed for dissociation of CF4+ ions in all the low-lying electronic states. With the aid of F-loss potential energy curves, dissociation mechanisms of CF4+ ions in these electronic states have been proposed. CF4+ ions in both X2T1 and A2T2 states directly dissociate to CF3+ and F fragments along the repulsive C-F coordinate, while a two-step dissociation mechanism is suggested for B2E state: CF4+(B2E) ion first converts to the lower A2T2 state via internal conversion, then dissociates to CF3+ and F fragments along the steep A2T2 potential energy surface. In addition, an adiabatic appearance potential of AP0(CF3+/CF4) has also been established to be 14.71 ± 0.02 eV, which is very consistent with the recent calculated values.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Hf Product distribution
82.20.Kh Potential energy surfaces for chemical reactions

Rate coefficients and kinetic isotope effects of the X + CH4 → CH3 + HX (X = H, D, Mu) reactions from ring polymer molecular dynamics

Yongle Li, Yury V. Suleimanov, Jun Li, William H. Green, and Hua Guo

J. Chem. Phys. 138, 094307 (2013); http://dx.doi.org/10.1063/1.4793394 (9 pages) | Cited 1 time

Online Publication Date: 1 March 2013

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The thermal rate coefficients and kinetic isotope effects have been calculated using ring polymer molecular dynamics (RPMD) for the prototypical reactions between methane and several hydrogen isotopes (H, D, and Mu). The excellent agreement with the theoretical rate coefficients of the H + CH4 reaction obtained previously from a multi-configuration time-dependent Hartree calculation on the same potential energy surface provides strong evidence for the accuracy of the RPMD approach. These quantum mechanical rate coefficients are also in good agreement with the results obtained previously using the transition-state theory with semi-classical tunneling corrections for the H/D + CH4 reactions. However, it is shown that the RPMD rate coefficients for the ultralight Mu reaction with CH4 are significantly smaller than the experimental data, presumably suggesting inaccuracies in the potential energy surface and/or experimental errors. Significant discrepancies between the RPMD and transition-state theory results have also been found for this challenging system.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Tr Kinetic isotope effects including muonium
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Kh Potential energy surfaces for chemical reactions
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