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7 Oct 2008

Volume 129, Issue 13, Articles (13xxxx)

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Conformational dependence of DNA ballistic conductivity

E. B. Starikov, A. Quintilla, K. H. Lee, and W. Wenzel

J. Chem. Phys. 129, 131101 (2008); http://dx.doi.org/10.1063/1.2985612 (5 pages) | Cited 1 time

Online Publication Date: 7 October 2008

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With the atomistic Kubo–Verges method we calculate the ballistic conductance of various conformers of DNA (A,B,Z), as well as intermediate and composite conformations, using experimental structures and model complexes. For duplexes with 6 and 15 base pairs, we find that the valence band conductivity near the Fermi edge varies dramatically between the different conformations, most notably for the B-to-Z transition. The latter conductivity differences are largely unchanged both in the presence and in the absence of trimethylthiol linkers between DNA and gold electrodes in vacuo, but become much less drastic when explicit molecular dynamics and water-counterion surrounding of B- and Z-DNA are taken into account. Based on atomistic structural models, we argue that changes in the electrostatic energy in the presence of an applied external electric field can induce conformational switching that may be exploited in novel DNA-based memory devices of high packing density.
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87.14.gk DNA
87.15.-v Biomolecules: structure and physical properties
87.15.Pc Electronic and electrical properties
73.23.Ad Ballistic transport
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back to top Theoretical Methods and Algorithms

Calculating interaction energies in transition metal complexes with local electron correlation methods

J. Grant Hill and James A. Platts

J. Chem. Phys. 129, 134101 (2008); http://dx.doi.org/10.1063/1.2982790 (5 pages) | Cited 2 times

Online Publication Date: 1 October 2008

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The results of density fitting and local approximations applied to the calculation of transition metal–ligand binding energies using second order Møller–Plesset perturbation theory are reported. This procedure accurately reproduces counterpoise corrected binding energies from the canonical method for a range of test complexes. While counterpoise corrections for basis set superposition error are generally small, this procedure can be time consuming, and in some cases gives rise to unphysical dissociation of complexes. In circumventing this correction, a local treatment of electron correlation offers major efficiency savings with little loss of accuracy. The use of density fitting for the underlying Hartree–Fock calculations is also tested for sample Ru complexes, leading to further efficiency gains but essentially no loss in accuracy.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Computing conformational free energy by deactivated morphing

Sanghyun Park, Albert Y. Lau, and Benoît Roux

J. Chem. Phys. 129, 134102 (2008); http://dx.doi.org/10.1063/1.2982170 (8 pages) | Cited 3 times

Online Publication Date: 1 October 2008

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Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called “deactivated morphing,” in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity.
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87.15.hp Conformational changes
36.20.Ey Conformation (statistics and dynamics)
36.20.Hb Configuration (bonds, dimensions)
87.15.A- Theory, modeling, and computer simulation

A family of model Kohn–Sham potentials for exact exchange

Viktor N. Staroverov

J. Chem. Phys. 129, 134103 (2008); http://dx.doi.org/10.1063/1.2982791 (6 pages) | Cited 11 times

Online Publication Date: 2 October 2008

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The exact-exchange Kohn–Sham potential is partitioned into Slater’s averaged exchange charge potential and a correction. A family of nonempirical approximations to the correction term is proposed based on the known second-order gradient expansion of the exact potential. By taking the uniform electron gas limit of the correction term and using alternative definitions of the average relative electron momentum that are motivated by analysis of the Negele–Vautherin density matrix expansion, we recover the “modified Slater potential” of Harbola and Sen and the much more accurate Becke–Johnson approximation [ J. Chem. Phys. 124, 221101 (2006) ]. Inclusion of an explicit gradient-dependent term in the Becke–Johnson model yields an even more realistic approximation, as demonstrated by comparing the shapes of these potentials and integrated exchange energies for a series of atoms.
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31.15.ej Spin-density functionals
31.15.eg Exchange-correlation functionals (in current density functional theory)

The metal-insulator transition in dimerized Hückel chains

Antonio Monari, Gian Luigi Bendazzoli, and Stefano Evangelisti

J. Chem. Phys. 129, 134104 (2008); http://dx.doi.org/10.1063/1.2987702 (10 pages) | Cited 7 times

Online Publication Date: 2 October 2008

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The metal-insulator transition is investigated in the case of linear chains described by a one-electron Hückel Hamiltonian. In these systems, the transition is a consequence of a dimerization of the chain bond length, which induces a similar dimerization of the hopping integral. Three indicators of the chain character are considered: The highest occupied molecular orbital–lowest unoccupied molecular orbital gap, the polarizability, and the localization tensor. In the case of even open chains, the behavior of the large chains depends in a crucial way on the alternating structure of the hopping integrals. If the ending atoms of the chain are weakly bonded to their neighbors, the energy spectrum of the Hamiltonian shows two quasidegenerated eigenvalues, and all the indicators would predict a (spurious) metallic behavior. It is shown that if the corresponding eigenvectors are removed from the Hamiltonian, the ordinary insulating behavior of alternating chains is recovered.
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71.30.+h Metal-insulator transitions and other electronic transitions

Multireference Fock-space coupled-cluster and equation-of-motion coupled-cluster theories: The detailed interconnections

Monika Musial and Rodney J. Bartlett

J. Chem. Phys. 129, 134105 (2008); http://dx.doi.org/10.1063/1.2982788 (12 pages) | Cited 20 times

Online Publication Date: 2 October 2008

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The multireference Fock-space coupled-cluster (FS-CC) equations constructed via the effective Hamiltonian approach are reduced to those obtained through a partitioning technique for the matrix diagonalization. This allows finding a better route to solve the FS-CC equations for the (1,1) sector by the direct diagonalization of the properly constructed matrix, which is identical to that obtained with the intermediate Hamiltonian approach. The detailed connections with the equation-of-motion CC (EOM-CC) approach also provides alternative routes for studying the higher-sectors of Fock space, and for the treatment of properties other than the energy. The approach studied in this work is formulated at the CC singles, doubles (CCSD) and CC singles, doubles, triples (CCSDT) level. The performance of the method is illustrated by numerical examples for the C2, C2H4, and H2CO molecules in comparison with the EOM-CC method and available experimental data.
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31.15.bw Coupled-cluster theory

Quantum Drude friction for time-dependent density functional theory

Daniel Neuhauser and Kenneth Lopata

J. Chem. Phys. 129, 134106 (2008); http://dx.doi.org/10.1063/1.2985650 (10 pages) | Cited 6 times

Online Publication Date: 2 October 2008

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Friction is a desired property in quantum dynamics as it allows for localization, prevents backscattering, and is essential in the description of multistage transfer. Practical approaches for friction generally involve memory functionals or interactions with system baths. Here, we start by requiring that a friction term will always reduce the energy of the system; we show that this is automatically true once the Hamiltonian is augmented by a term of the form ∫a(q;n0)[∂j(q,t)/∂t]⋅J(q)dq, which includes the current operator times the derivative of its expectation value with respect to time, times a local coefficient; the local coefficient will be fitted to experiment, to more sophisticated theories of electron-electron interaction and interaction with nuclear vibrations and the nuclear background, or alternately, will be artificially constructed to prevent backscattering of energy. We relate this term to previous results and to optimal control studies, and generalize it to further operators, i.e., any operator of the form ∫a(q;n0)[∂c(q,t)/∂t]⋅C(q)dq (or a discrete sum) will yield friction. Simulations of a small jellium cluster, both in the linear and highly nonlinear excitation regime, demonstrate that the friction always reduces energy. The energy damping is essentially double exponential; the long-time decay is almost an order of magnitude slower than the rapid short-time decay. The friction term stabilizes the propagation (split-operator propagator here), therefore increasing the time-step needed for convergence, i.e., reducing the overall computational cost. The local friction also allows the simulation of a metal cluster in a uniform jellium as the energy loss in the excitation due to the underlying corrugation is accounted for by the friction. We also relate the friction to models of coupling to damped harmonic oscillators, which can be used for a more sophisticated description of the coupling, and to memory functionals. Our results open the way to very simple finite grid description of scattering and multistage conductance using time-dependent density functional theory away from the linear regime, just as absorbing potentials and self-energies are useful for noninteracting systems and leads.
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81.40.Pq Friction, lubrication, and wear
62.20.Qp Friction, tribology, and hardness
61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.10.Ca Electron gas, Fermi gas

Method specific Cholesky decomposition: Coulomb and exchange energies

Linus Boman, Henrik Koch, and Alfredo Sánchez de Merás

J. Chem. Phys. 129, 134107 (2008); http://dx.doi.org/10.1063/1.2988315 (14 pages) | Cited 11 times

Online Publication Date: 2 October 2008

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We present a novel approach to the calculation of the Coulomb and exchange contributions to the total electronic energy in self consistent field and density functional theory. The numerical procedure is based on the Cholesky decomposition and involves decomposition of specific Hadamard product matrices that enter the energy expression. In this way, we determine an auxiliary basis and obtain a dramatic reduction in size as compared to the resolution of identity (RI) method. Although the auxiliary basis is determined from the energy expression, we have complete control of the errors in the gradient or Fock matrix. Another important advantage of this method specific Cholesky decomposition is that the exchange energy and Fock matrix can be evaluated with a linear scaling effort contrary to the RI method or standard Cholesky decomposition of the two-electron integral matrix. The methods presented show the same scaling properties as the so-called local density fitting methods, but with full error control.
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34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
31.15.xr Self-consistent-field methods
31.15.eg Exchange-correlation functionals (in current density functional theory)

Active-space two-electron reduced-density-matrix method: Complete active-space calculations without diagonalization of the N-electron Hamiltonian

Gergely Gidofalvi and David A. Mazziotti

J. Chem. Phys. 129, 134108 (2008); http://dx.doi.org/10.1063/1.2983652 (8 pages) | Cited 23 times

Online Publication Date: 3 October 2008

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Molecular systems in chemistry often have wave functions with substantial contributions from two-or-more electronic configurations. Because traditional complete-active-space self-consistent-field (CASSCF) methods scale exponentially with the number N of active electrons, their applicability is limited to small active spaces. In this paper we develop an active-space variational two-electron reduced-density-matrix (2-RDM) method in which the expensive diagonalization is replaced by a variational 2-RDM calculation where the 2-RDM is constrained by approximate N-representability conditions. Optimization of the constrained 2-RDM is accomplished by large-scale semidefinite programming [ Mazziotti, Phys. Rev. Lett. 93, 213001 (2004) ]. Because the computational cost of the active-space 2-RDM method scales polynomially as ra6 where ra is the number of active orbitals, the method can be applied to treat active spaces that are too large for conventional CASSCF. The active-space 2-RDM method performs two steps: (i) variational calculation of the 2-RDM in the active space and (ii) optimization of the active orbitals by Jacobi rotations. For large basis sets this two-step 2-RDM method is more efficient than the one-step, low-rank variational 2-RDM method [ Gidofalvi and Mazziotti, J. Chem. Phys. 127, 244105 (2007) ]. Applications are made to HF, H2O, and N2 as well as n-acene chains for n = 2–8. When n>4, the acenes cannot be treated by conventional CASSCF methods; for example, when n = 8, CASSCF requires optimization over approximately 1.47×1017 configuration state functions. The natural occupation numbers of the n-acenes show the emergence of bi- and polyradical character with increasing chain length.
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31.15.X- Alternative approaches
02.10.-v Logic, set theory, and algebra
02.30.-f Function theory, analysis

Phase-space averaging and natural branching of nuclear paths for nonadiabatic electron wavepacket dynamics

Takehiro Yonehara and Kazuo Takatsuka

J. Chem. Phys. 129, 134109 (2008); http://dx.doi.org/10.1063/1.2987302 (13 pages) | Cited 10 times

Online Publication Date: 3 October 2008

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We propose a simple and tractable method to treat quantum electron wavepacket dynamics that nonadiabatically couples with “classical” nuclear motions in mixed quantum-classical representation. The electron wavepacket is propagated inducing electronic-state mixing along our proposed paths. It has been shown in our previous studies that classical force working on nuclei in a nonadiabatic region is represented in a matrix form (called the force matrix), and the solutions of the Hamilton canonical equations of motion for nuclei based on this force matrix give rise to a cascade of infinitely many branching paths when solved simultaneously with electronic-state mixing. As a tractable approximation to these rigorous solutions, we here devise a method to provide much simpler nonadiabatic paths: (i) extract one or a few number of representative paths by taking an average over the paths in phase space (not averaging over the forces) that should be otherwise undergo the fine branching. (ii) After the nonadiabatic coupling becomes sufficiently small, let these paths naturally branch by running them with their own individual eigenforces (the eigenvalues of the force matrix). Since the eigenforces coincide with the forces of adiabatic potential energy surfaces in the limit of zero nonadiabatic coupling, these branching paths eventually run on one of possible adiabatic potential energy surfaces, converging to a classical path (Born–Oppenheimer path). The paths thus created are theoretically satisfactory in that they realize the coherent mixing of electronic states in the manner of quantum entanglement and yet eventually become consistent with the Born–Oppenheimer classical trajectories. We test the present method numerically with the use of two- and three-state systems that are extracted from ab initio calculations for the excited states of LiH molecule.
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31.50.Gh Surface crossings, non-adiabatic couplings
31.50.Df Potential energy surfaces for excited electronic states
31.15.ae Electronic structure and bonding characteristics

Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment

Hiroshi Fujisaki and Gerhard Stock

J. Chem. Phys. 129, 134110 (2008); http://dx.doi.org/10.1063/1.2985606 (10 pages) | Cited 10 times

Online Publication Date: 6 October 2008

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A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [ H. Fujisaki, Y. Zhang, and J. E. Straub, J. Chem. Phys. 124, 144910 (2006) ], second-order time-dependent perturbation theory is employed which includes the fluctuations of the parameters in the Hamiltonian within the vibrational adiabatic approximation. This means that the time-dependent vibrational frequencies along a molecular dynamics trajectory are obtained via a partial geometry optimization of the solute with fixed solvent and a subsequent normal mode calculation. Adopting the amide I mode of N-methylacetamide in heavy water as a test problem, it is shown that the inclusion of dynamic fluctuations may significantly change the vibrational energy relaxation. In particular, it is found that relaxation occurs in two phases, because for short times (≲200 fs) the spectral density appears continuous due to the frequency-time uncertainty relation, while at longer times the discrete nature of the bath becomes apparent. Considering the excellent agreement between theory and experiment, it is speculated if this behavior can explain the experimentally obtained biphasic relaxation the amide I mode of N-methylacetamide.
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34.50.Ez Rotational and vibrational energy transfer
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.xp Perturbation theory

Calculation of vibrational energy of molecule using coupled cluster linear response theory in bosonic representation: Convergence studies

Subrata Banik, Sourav Pal, and M. Durga Prasad

J. Chem. Phys. 129, 134111 (2008); http://dx.doi.org/10.1063/1.2982502 (9 pages) | Cited 5 times

Online Publication Date: 7 October 2008

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Vibrational excited state energies have been calculated using vibrational coupled cluster linear response theory (CCLRT). The method has been implemented on formaldehyde and water molecule. Convergence studies have been shown with varying the cluster operator from S4 to S6 as well as the excitation operator from four bosons to six bosons. A good agreement with full configuration interaction results has been observed with S6 truncation at coupled-cluster method level and six bosonic excitations at CCLRT level.
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31.15.bw Coupled-cluster theory
31.50.Df Potential energy surfaces for excited electronic states
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

Comparison of sampling efficiency between simulated tempering and replica exchange

Cheng Zhang and Jianpeng Ma

J. Chem. Phys. 129, 134112 (2008); http://dx.doi.org/10.1063/1.2988339 (7 pages) | Cited 9 times

Online Publication Date: 7 October 2008

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We compared the sampling efficiency of simulated tempering and replica exchange. Our results indicate that simulated tempering is superior to replica exchange if the parameters for temperature transition in simulated tempering are adjusted to be proportional to the partition function. It is shown that, in simulated tempering, the rate of traversing energy space of different temperatures is much higher than that in replica exchange, especially in the case of low tempering frequency and/or larger temperature separations.
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81.40.Gh Other heat and thermomechanical treatments
02.50.-r Probability theory, stochastic processes, and statistics
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Optimal control of rotational motions in dissipative media

Adam Pelzer, S. Ramakrishna, and Tamar Seideman

J. Chem. Phys. 129, 134301 (2008); http://dx.doi.org/10.1063/1.2973633 (10 pages) | Cited 10 times

Online Publication Date: 2 October 2008

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We apply optimal control theory to explore and manipulate rotational wavepacket dynamics subject to a dissipative environment. In addition to investigating the extent to which nonadiabatic alignment can make a useful tool in the presence of decoherence and population relaxation, we use coherent rotational superpositions as a simple model to explore several general questions in the control of systems interacting with a bath. These include the extent to which a pure state can be created out of a statistical ensemble, the degree to which control theory can develop superposition states that resist dissipation, and the nature of environments that prohibits control. Our results illustrate the information content of control studies regarding the dissipative properties of the bath and point to the strategies that optimize different targets in wavepacket alignment in nonideal environments. As an interesting aside, the method is used to illustrate the limit where the coherence-based approach to molecular alignment converges to traditional incoherent approaches.
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33.15.Mt Rotation, vibration, and vibration-rotation constants

Nonadditive interactions in ns2 and spin-polarized ns metal atom trimers

Jacek Kłos, Piotr S. Żuchowski, Łukasz Rajchel, Grzegorz Chałasiński, and Małgorzata M. Szczęśniak

J. Chem. Phys. 129, 134302 (2008); http://dx.doi.org/10.1063/1.2982801 (9 pages) | Cited 7 times

Online Publication Date: 2 October 2008

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The origins of nonadditivity in the following groups of metal trimers are examined: alkali earth metals of the IIA group (Be, Mg, and Ca), Zn as a transition metal analog of this group, spin-polarized alkali metals from IA group (Li, Na, K), and the spin-polarized Cu as its transition metal analog. The nonadditive interactions in these trimers are analyzed using the following hierarchy of approximations: the Heitler–London, self-consistent field (SCF), and correlated levels of theory. The exchange nonadditivity, which is included at the Heitler–London level, constitutes a bulk of nonadditive interactions in these systems in their equilibrium structures. The SCF treatment reveals some unphysical characteristics. At the post-SCF levels of theory the multireference character of the wave function increases from atom to dimer to trimer. The role of configurations involving excitations ns-np increases in this sequence and it is the genuine nonadditive effect. There is also a dramatic change in the characteristics of the excited states upon formation of clusters. We use the parameters of these excited states to predict which complexes are bound by the unusually strong nonadditive interactions and which are not.
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31.15.xr Self-consistent-field methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.vn Electron correlation calculations for diatomic molecules

Millimeter-wave spectroscopy of CoNO Produced by UV laser photolysis of Co(CO)3NO

Ai Sakamoto, Masato Hayashi, Kensuke Harada, Takehiko Tanaka, and Keiichi Tanaka

J. Chem. Phys. 129, 134303 (2008); http://dx.doi.org/10.1063/1.2982783 (7 pages)

Online Publication Date: 2 October 2008

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The rotational spectrum of cobalt mononitrosyl (CoNO) produced by ultraviolet photolysis of Co(CO)3NO was observed in the millimeter-wave region. Seven rotational transitions in the ground state ranging from J = 6−5 to 12−11, with hyperfine splittings due to the Co nucleus (I = 7/2), were detected in a supersonic jet environment, while higher-frequency transitions in the range from J = 29−28 to 35−34 were measured in the ground, ν1, ν2, ν3, and 2ν2 vibrational states using a free-space absorption cell. It was confirmed from the observed spectral pattern that the CoNO molecule has a linear structure with the electronic ground state of 1Σ+ symmetry. The rotational lines in the 2ν2(Σ) and ν3 states were observed to be perturbed by Fermi resonance. The equilibrium rotational constant Be is determined to be 4682.207(15) MHz. The CoN bond length is derived to be 1.5842 Å assuming the NO bond length of 1.1823 Å. A large nuclear spin-rotation interaction constant, CI = 123.8(11) kHz, was determined, suggesting a 1Π electronic excited state lying close to the ground state.
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82.50.Hp Processes caused by visible and UV light
71.70.Jp Nuclear states and interactions

A theoretical study of the rovibrational levels of the bosonic van der Waals neon trimer

Moses Salci, Sergey B. Levin, Nils Elander, and Evgeny Yarevsky

J. Chem. Phys. 129, 134304 (2008); http://dx.doi.org/10.1063/1.2955736 (7 pages) | Cited 4 times

Online Publication Date: 2 October 2008

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The eigenenergies and root mean square radii of the rovibrational levels (J = 0–3) of the weakly bound bosonic van der Waals neon trimer were calculated using a full angular momentum three-dimensional finite element method. The differing results of three previous studies for zero angular momentum are discussed, explained, and compared with the results presented here.
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36.40.Cg Electronic and magnetic properties of clusters
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.A- Ab initio calculations
05.30.Jp Boson systems

Spectra of atomic sulfur 1D in transitions to autoionizing Rydberg states in the region of 75 800–89 500 cm−1

Wan-Chun Pan, I-Chia Chen, Tzu-Ping Huang, Jih-Young Yuh, and Yin-Yu Lee

J. Chem. Phys. 129, 134305 (2008); http://dx.doi.org/10.1063/1.2982804 (7 pages)

Online Publication Date: 3 October 2008

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We recorded photoionization spectra of sulfur atoms in transitions from state 1D in the range of 75 800–89 500 cm−1. Dissociation of CS2 after photolysis at 193 nm produced these sulfur atoms in a singlet excited state; they were then ionized with synchrotron radiation (NSRRC, beamline U9CGM) at resolution of up to 3 cm−1 and detected with a quadruple mass filter. Rydberg series 3s23p3(2D3/20)nd[3/2] and 3s23p3(2D5/20)ns[5/2] with n extending to 16 and 32, respectively, to limit 2D0 are assigned. New Rydberg series 3s23p3(2D3/20)nd[1/2]1, (2D5/20)nd[5/2], and (2D3/20)nd[5/2] with n from 5–9 for the former two series and 7–13 for the latter are assigned. A new Rydberg line at 85 335 cm−1 is assigned to 3s23p3(2D3/20)6d 1P.
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32.80.Zb Autoionization
32.80.Ee Rydberg states

R12-calibrated H2O–H2 interaction: Full dimensional and vibrationally averaged potential energy surfaces

Pierre Valiron, Michael Wernli, Alexandre Faure, Laurent Wiesenfeld, Claire Rist, Stanislav Kedžuch, and Jozef Noga

J. Chem. Phys. 129, 134306 (2008); http://dx.doi.org/10.1063/1.2988314 (14 pages) | Cited 26 times

Online Publication Date: 6 October 2008

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The potential energy surface of H2O–H2 is of great importance for quantum chemistry as a test case for H2O-molecule interactions. It is also required for a detailed understanding of important astrophysical processes, namely, the collisional excitation of water, including the pumping of water masers and the formation of molecular hydrogen on icy interstellar dust grains. We have calculated the interaction for H2O–H2 by performing both rigid-rotor (five-dimensional) and non-rigid-rotor (nine-dimensional) calculations using the coupled-cluster theory at the level of singles and doubles with perturbative corrections for triple excitations [CCSD(T)] with moderately large but thoroughly selected basis set. The resulting surface was further calibrated using high precision explicitly correlated CCSD(T)-R12 calculations on a subset of the rigid-rotor intermolecular geometries. The vibrationally averaged potential is presented in some details and is compared with the most recent rigid-rotor calculations. We explain, in particular, as to why vibrationally averaged rigid-rotor geometries are a better choice than equilibrium geometries. Our fit of the vibrationally averaged surface provides for the first time an accuracy of ∼ 3 cm−1 in the van der Waals minimum region of the interaction. The overall accuracy of the nine-dimensional surface and fit is lower but remains of the order of 3%–4% of the anisotropy in the domain spanned by the vibrational functions.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.xp Perturbation theory
95.30.Ft Molecular and chemical processes and interactions
98.58.Ca Interstellar dust grains; diffuse emission; infrared cirrus
31.15.bw Coupled-cluster theory

Electronic spectroscopy of the jet-cooled arsenic dicarbide (C2As) free radical

Jie Wei, Robert A. Grimminger, Fumie X. Sunahori, and Dennis J. Clouthier

J. Chem. Phys. 129, 134307 (2008); http://dx.doi.org/10.1063/1.2988311 (7 pages) | Cited 8 times

Online Publication Date: 6 October 2008

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The 2Δr-math 2Πr band system of the jet-cooled arsenic dicarbide (C2As) free radical has been recorded by laser-induced fluorescence (LIF) techniques in the 685–588 nm region. The radical was produced in a pulsed electric discharge jet using a precursor mixture of AsCl3 vapor and methane in high pressure argon. A series of weak bands involving all three excited state vibrations was observed for both 12C2As and 13C2As. High-resolution spectra of the 2Π1/2 component of the 000 bands of both isotopomers were rotationally analyzed, leading to the conclusion that the upper state is 2Δ with a small spin-orbit splitting (A = 2.78 cm−1). Ground and excited state molecular structures of r0″(CC,ab initio) = 1.2933 Å, r0″(CAs) = 1.734(4) Å and r0′(CC,ab initio) = 1.2276 Å, r0′(CAs) = 1.830(3) Å were derived from the B values and our density functional predictions of the C–C bond lengths. Single vibronic level emission spectra were recorded for many of the LIF bands and these were used to obtain the ground state vibrational frequencies and spin-orbit splittings. These data were satisfactorily fitted to a Renner–Teller model which gave 12C2As parameters of ε = 0.695(8), ω1 = 1704.8(20) cm−1, ω2 = 161.6(8) cm−1, ω3 = 663.6(12) cm−1, and a spin-orbit constant A = 857.7(11) cm−1.
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33.50.Dq Fluorescence and phosphorescence spectra
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.50.Df Potential energy surfaces for excited electronic states
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure

Photoelectron spectroscopy and theoretical studies of [Com(pyrene)n]− (m = 1,2 and n = 1,2) complexes

Anil K. Kandalam, Puru Jena, Xiang Li, Soren N. Eustis, and Kit H. Bowen

J. Chem. Phys. 129, 134308 (2008); http://dx.doi.org/10.1063/1.2982786 (11 pages) | Cited 2 times

Online Publication Date: 6 October 2008

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Anion photoelectron spectroscopic experiments and density functional theory based calculations have been used to investigate the structural, electronic, and magnetic properties of neutral and anionic [Com(pyrene)n] (m,n = 1–2) complexes. The calculated electron affinities and vertical transition energies of Com(pyrene)n are in good agreement with the measured values. Our results provide clear evidence for dimerization of Co atoms and formation of sandwich structures in these complexes. While the calculated spin magnetic moments of neutral Co2(pyrene)n complexes suggest a preference for ferromagnetic coupling between Co atoms, the spin magnetic moment of Co atom in Co(pyrene) and Co(pyrene)2 complexes was reduced to 1μB.
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79.60.Fr Polymers; organic compounds
75.50.Dd Nonmetallic ferromagnetic materials
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
75.30.Cr Saturation moments and magnetic susceptibilities
71.20.Rv Polymers and organic compounds

Heteroborane analogs of silicon clusters: Experimental and theoretical studies on Bi2Si5 and Bi2Si5−

Xiang Li, Haopeng Wang, Andrej Grubisic, Di Wang, Kit H. Bowen, Miley Jackson, and Boggavarapu Kiran

J. Chem. Phys. 129, 134309 (2008); http://dx.doi.org/10.1063/1.2988727 (4 pages) | Cited 4 times

Online Publication Date: 6 October 2008

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We have investigated the electronic structure of anionic and neutral Bi2Si5 by means of anion photoelectron spectroscopy and density functional calculations. Both the experiments and calculations reveal that the Bi2Si5− anion prefers to adopt a distorted trigonal-bipyramidal structure with Bi2 bridges. Following the isolobal analogy between divalent Si and B–H group, we show that both neutral Bi2Si5 and neutral Bi2B5H5 adopt similar pentagonal-bipyrmidal geometries and have analogous orbital energy patterns.
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71.20.Gj Other metals and alloys
61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
79.60.-i Photoemission and photoelectron spectra

On the electron correlation effects on electronic and vibrational hyperpolarizability of merocyanine dyes

Robert Zaleśny, Manthos G. Papadopoulos, Wojciech Bartkowiak, and Anna Kaczmarek

J. Chem. Phys. 129, 134310 (2008); http://dx.doi.org/10.1063/1.2985736 (4 pages) | Cited 5 times

Online Publication Date: 6 October 2008

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Using various ab initio methods (including many-body perturbation theory and coupled cluster method), the full tensor of electronic and vibrational contributions to the first-order hyperpolarizability (β) for three molecules belonging to the group of merocyanine dyes was computed. Unexpectedly large correlation effects were observed in the electronic counterpart of nonlinear optical response. The analysis of the electronic structure, performed for one of the investigated molecules, reveals that it is the polarity of the low-lying excited state that is affected most upon inclusion of the electron correlation. The vibrational contributions to β are not significantly influenced by the applied level of theory.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.ap Polarizabilities and other atomic and molecular properties
31.15.bw Coupled-cluster theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
33.15.Mt Rotation, vibration, and vibration-rotation constants

The influence of C2 dimers on the stability of TimCn metcar clusters

Jan-Ole Joswig and Michael Springborg

J. Chem. Phys. 129, 134311 (2008); http://dx.doi.org/10.1063/1.2989958 (7 pages) | Cited 1 time

Online Publication Date: 7 October 2008

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We present results of an investigation of small TimCn clusters with different stoichiometries in order to throw light on the occurrence of carbon dimers in these structures. Previous studies of transition metal (M) metallocarbohedrene (metcar) clusters MmCn have proposed that C2 dimers play a special role. In the special case of TimCn metcars these dimers have been observed in several studies. We shall show that clusters containing C2 dimers are energetically favored with respect to those containing only single carbon atoms or trimers, especially when the dimers occupy the corner positions of cubic clusters. Moreover, we find that cubic structures are more stable than corresponding double-cage metcars. Finally, a highly symmetric Ti6C10 metcar cluster is presented and proposed to be the global-minimum structure of this stoichiometry.
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36.40.Mr Spectroscopy and geometrical structure of clusters

Rotational molecular dynamics of laser-manipulated bromotrifluoromethane studied by x-ray absorption

Christian Buth and Robin Santra

J. Chem. Phys. 129, 134312 (2008); http://dx.doi.org/10.1063/1.2987365 (12 pages) | Cited 6 times

Online Publication Date: 7 October 2008

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We present a computational study of the rotational molecular dynamics of bromotrifluoromethane (CF3Br) molecules in gas phase. The rotation is manipulated with an off-resonant 800 nm laser. The molecules are treated as rigid rotors. Frequently, we use a computationally efficient linear rotor model for CF3Br, which we compare with selected results for full symmetric-rotor computations. The expectation value 〈cos2 ϑ〉(t) is discussed. Especially, the transition from impulsive to adiabatic alignment, the temperature dependence of the maximally achievable alignment, and its intensity dependence are investigated. In a next step, we examine resonant x-ray absorption as an accurate tool to study laser manipulation of molecular rotation. Specifically, we investigate the impact of the x-ray pulse duration on the signal (particularly its temporal resolution) and study the temperature dependence of the achievable absorption. Most importantly, we demonstrated that using picosecond x-ray pulses, one can accurately measure the expectation value 〈cos2 ϑ〉(t) for impulsively aligned CF3Br molecules. We point out that a control of the rotational dynamics opens up a novel way to imprint shapes onto long x-ray pulses on a picosecond time scale. For our computations, we determine the dynamic polarizability tensor of CF3Br using ab initio molecular linear-response theory in conjunction with wave function models of increasing sophistication: Coupled-cluster singles (CCS), second-order approximate coupled-cluster singles and doubles (CC2), and coupled-cluster singles and doubles (CCSD).
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33.20.Rm X-ray spectra
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.ap Polarizabilities and other atomic and molecular properties
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis
33.80.-b Photon interactions with molecules
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