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21 Feb 2013

Volume 138, Issue 7, Articles (07xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 138, 071101 (2013); http://dx.doi.org/10.1063/1.4790571 (4 pages)

Selena M. Russell, Yousoo Kim, Da-Jiang Liu, J. W. Evans, and P. A. Thiel
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Communication: Structure, formation, and equilibration of ensembles of Ag-S complexes on an Ag surface

Selena M. Russell, Yousoo Kim, Da-Jiang Liu, J. W. Evans, and P. A. Thiel

J. Chem. Phys. 138, 071101 (2013); http://dx.doi.org/10.1063/1.4790571 (4 pages)

Online Publication Date: 15 February 2013

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We have utilized conditions of very low temperature (4.7 K) and very low sulfur coverage to isolate and identify Ag-S complexes that exist on the Ag(111) surface. The experimental conditions are such that the complexes form at temperatures above the temperature of observation. These complexes can be regarded as polymeric chains of varying length, with an Ag4S pyramid at the core of each monomeric unit. Steps may catalyze the formation of the chains and this mechanism may be reflected in the chain length distribution.
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82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
68.35.B- Structure of clean surfaces (and surface reconstruction)
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Communication: Spectroscopic evidence for a planar cyclic CO trimer

Mojtaba Rezaei, S. Sheybani-Deloui, N. Moazzen-Ahmadi, K. H. Michaelian, and A. R. W. McKellar

J. Chem. Phys. 138, 071102 (2013); http://dx.doi.org/10.1063/1.4793220 (3 pages)

Online Publication Date: 15 February 2013

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A high-resolution spectrum in the region of 2144 cm−1 is assigned to the previously elusive CO trimer. In spite of interference from the CO dimer and some remaining unexplained details, there is strong evidence for a planar, cyclic, C-bonded trimer structure, with C3h symmetry and 4.42 Å intermolecular separation, in agreement with theoretical calculations. A modest vibrational blueshift of +0.85 cm−1 is observed for the CO trimer, as compared to +0.71 cm−1 for the C-bonded form of the dimer.
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33.20.Ea Infrared spectra
33.70.Jg Line and band widths, shapes, and shifts
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Fm Bond strengths, dissociation energies
33.15.Mt Rotation, vibration, and vibration-rotation constants
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Communication: Origin of the contributions to DNA structure in phages

Christopher G. Myers and B. Montgomery Pettitt

J. Chem. Phys. 138, 071103 (2013); http://dx.doi.org/10.1063/1.4791708 (4 pages) | Cited 1 time

Online Publication Date: 19 February 2013

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Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.14.gk DNA
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Communication: One-photon phase control of cis-trans isomerization in retinal

Carlos A. Arango and Paul Brumer

J. Chem. Phys. 138, 071104 (2013); http://dx.doi.org/10.1063/1.4792834 (4 pages)

Online Publication Date: 21 February 2013

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We computationally demonstrate the one-photon phase control of retinal isomerization under conditions of low laser intensity. The calculations, utilizing the multiconfigurational time dependent Hartree method, include coupling between the two modes that are active in isomerization and the background molecular vibrational environment. Noting previously unsuccessful computations highlights the significance of this result.
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82.30.Qt Isomerization and rearrangement
82.50.-m Photochemistry
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Communication: Ab initio Joule–Thomson inversion data for argon

Jonas Wiebke, Florian Senn, Elke Pahl, and Peter Schwerdtfeger

J. Chem. Phys. 138, 071105 (2013); http://dx.doi.org/10.1063/1.4792371 (3 pages)

Online Publication Date: 21 February 2013

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The Joule–Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule–Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
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51.30.+i Thermodynamic properties, equations of state
05.70.Jk Critical point phenomena
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back to top Theoretical Methods and Algorithms

Direct ΔMBPT(2) method for ionization potentials, electron affinities, and excitation energies using fractional occupation numbers

Ariana Beste, Álvaro Vázquez-Mayagoitia, and J. V. Ortiz

J. Chem. Phys. 138, 074101 (2013); http://dx.doi.org/10.1063/1.4790626 (13 pages)

Online Publication Date: 15 February 2013

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A direct method (D-ΔMBPT(2)) to calculate second-order ionization potentials (IPs), electron affinities (EAs), and excitation energies is developed. The ΔMBPT(2) method is defined as the correlated extension of the ΔHF method. Energy differences are obtained by integrating the energy derivative with respect to occupation numbers over the appropriate parameter range. This is made possible by writing the second-order energy as a function of the occupation numbers. Relaxation effects are fully included at the SCF level. This is in contrast to linear response theory, which makes the D-ΔMBPT(2) applicable not only to single excited but also higher excited states. We show the relationship of the D-ΔMBPT(2) method for IPs and EAs to a second-order approximation of the effective Fock-space coupled-cluster Hamiltonian and a second-order electron propagator method. We also discuss the connection between the D-ΔMBPT(2) method for excitation energies and the CIS-MP2 method. Finally, as a proof of principle, we apply our method to calculate ionization potentials and excitation energies of some small molecules. For IPs, the ΔMBPT(2) results compare well to the second-order solution of the Dyson equation. For excitation energies, the deviation from equation of motion coupled cluster singles and doubles increases when correlation becomes more important. When using the numerical integration technique, we encounter difficulties that prevented us from reaching the ΔMBPT(2) values. Most importantly, relaxation beyond the Hartree-Fock level is significant and needs to be included in future research.
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31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Radial correlation effects on interconfigurational excitations at the end of the lanthanide series: A restricted active space second order perturbation study of Yb2+ and SrCl2:Yb2+

Zoila Barandiarán and Luis Seijo

J. Chem. Phys. 138, 074102 (2013); http://dx.doi.org/10.1063/1.4790166 (11 pages)

Online Publication Date: 15 February 2013

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At the end of the lanthanide series, 4f → 5d and other interconfigurational transitions, in which one electron is excited from a tight 4f orbital to a much more diffuse one, occur with a break of many f-f pairs, which make the electron correlation effects dominant. For instance, the large energy gap of 25 000 cm−1 (∼29 500 cm−1 without spin-orbit coupling) above the 4f14 ground state of the SrCl2:Yb2+ material is mostly due to electron correlation. In effect, a minimal multiconfigurational restricted active space (RASSCF) calculation that includes only the 4f14 ground and 4f135d and 4f136s open-shell excited configurations gives a very small gap (5400 cm−1), whereas the correlation corrections to the 4f14 → 4f135d(eg) transition energies at the second order perturbation theory (RASPT2) level are very large: 35 599 ± 439 cm−1, in average, for all excited states. These corrections are too large to be accurate at second order perturbation level. When a second f-shell is also included in the active space and single and double excitations to the 5d, 6s, and 5f shells are treated variationally, the (extended) RASSCF energy gap above the ground state and the electronic transitions increase by 22 038 ± 120 cm−1 and the RASPT2 correlation energy corrections become small (−721 ± 571 cm−1), as it is desirable for a second order perturbation. A comparative analysis of both RASPT2 results reveals that the lack of the second f-shell accounts for 12 700 cm−1 of the 14 223 ± 80 cm−1 overestimation of interconfigurational transitions energies by the minimal RASPT2 calculation, which indicates an inaccurate calculation of the differential radial correlation between the 4f14 and 4f135d configurations by second order perturbation theory. In order to establish practical and accurate procedures for the calculation of 4f → 5d and other interconfigurational transitions at the end of the lanthanide series, the above and other RASSCF/RASPT2 calculations on the ionization potential of Yb2+ in gas phase and in SrCl2 have been benchmarked in this paper against coupled cluster (coupled cluster singles and doubles and triples ) calculations, and RASSCF/RASPT2 calculations on the absorption spectrum of SrCl2:Yb2+ have been compared with experiment. The results support that variational calculation of SD 4f → 5f excitations prior to RASPT2 calculations can be a realistic, accurate, and feasible choice to model radial correlation effects at the end of the lanthanide series.
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31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.ep Variational particle-number approach
31.15.vj Electron correlation calculations for atoms and ions: excited states

Benchmarks of improved complete basis set extrapolation schemes designed for standard CCSD(T) atomization energies

David Feller

J. Chem. Phys. 138, 074103 (2013); http://dx.doi.org/10.1063/1.4791560 (9 pages) | Cited 1 time

Online Publication Date: 15 February 2013

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Simple modifications of complete basis set extrapolation formulas chosen from the literature are examined with respect to their abilities to reproduce a diverse set of 183 reference atomization energies derived primarily from very large basis set standard, frozen core coupled-cluster singles, doubles plus perturbative triples (CCSD(T)) with the aug-cc-pVnZ basis sets. This reference set was augmented with a few larger chemical systems treated with explicitly correlated CCSD(T)-F12b using a quadruple zeta quality basis set followed by extrapolation to complete basis set limit. Tuning the extrapolation formula parameters for the present reference set resulted in substantial reductions in the error metrics. In the case of the best performing approach, the aVnZ extrapolated results are equivalent to or better than results obtained from raw aV(n + 3)Z basis set calculations. To the extent this behavior holds for molecules outside the reference set, it represents an improvement of at least one basis set level over the original formulations and a further significant reduction in the amount of computer time needed to accurately approximate the basis set limit.
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31.15.bw Coupled-cluster theory

Rigorously extensive orbital-invariant renormalized perturbative triples corrections from quasi-variational coupled cluster theory

James B. Robinson and Peter J. Knowles

J. Chem. Phys. 138, 074104 (2013); http://dx.doi.org/10.1063/1.4791636 (14 pages)

Online Publication Date: 19 February 2013

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We show that, by making use of the linked tensor objects inherent to the approach, Orbital-optimised Quasi-Variational Coupled Cluster Theory (OQVCCD) leads naturally to a computationally-trivial, rigorously extensive, and orbital-invariant renormalization of the standard (T) correction for the perturbative inclusion of the effects of connected triple excitations. The resulting prototype method, renormalized perturbative triple OQVCCD (R-OQVCCD(T)), is demonstrated to predict potential energy curves for single bond-breaking processes of significantly higher accuracy than OQVCCD with the standard perturbative triple-excitation correction (OQVCCD(T)) itself, and to be in good numerical correspondence with the existing renormalized (R-CCSD(T)) and completely renormalized (CR-CCSD(T)) coupled-cluster singles doubles triples methods, while continuing to provide descriptions of multiple bond-breaking processes of OQVCCD(T) quality.
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31.15.bw Coupled-cluster theory
31.15.vj Electron correlation calculations for atoms and ions: excited states
31.15.xt Variational techniques
31.50.Df Potential energy surfaces for excited electronic states

Magnetohydrodynamic motion of a colloidal sphere with self-electrochemical surface reactions in a spherical cavity

Tzu H. Hsieh and Huan J. Keh

J. Chem. Phys. 138, 074105 (2013); http://dx.doi.org/10.1063/1.4791637 (8 pages)

Online Publication Date: 19 February 2013

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An analytical study is presented for the magnetic-field-induced motion of a colloidal sphere with spontaneous electrochemical reactions on its surface situated at the center of a spherical cavity filled with an electrolyte solution at the quasi-steady state. The zeta potential associated with the particle surface may have an arbitrary distribution, whereas the electric double layers adjoining the particle and cavity surfaces are taken to be thin relative to the particle size and the spacing between the solid surfaces. The electric current and magnetic flux density distributions are solved for the particle and fluid phases of arbitrary electric conductivities and magnetic permeabilities. Applying a generalized reciprocal theorem to the Stokes equations with a Lorentz force term resulting from these density distributions for the fluid motion, we obtain explicit formulas for the translational and angular velocities of the colloidal sphere valid for all values of the particle-to-cavity size ratio. The particle velocities decrease monotonically with an increase in this size ratio. For the limiting case of an infinitely large cavity, our result reduces to the relevant solution for an unconfined spherical particle. The boundary effect on the movement of the particle with interfacial self-electrochemical reactions induced by the magnetohydrodynamic force is equivalent to that in sedimentation and much stronger than that in general phoretic motions.
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82.45.-h Electrochemistry and electrophoresis
82.45.Jn Surface structure, reactivity and catalysis
82.70.Dd Colloids
47.57.jd Electrokinetic effects
47.65.-d Magnetohydrodynamics and electrohydrodynamics

Interatomic methods for the dispersion energy derived from the adiabatic connection fluctuation-dissipation theorem

Alexandre Tkatchenko, Alberto Ambrosetti, and Robert A. DiStasio, Jr.

J. Chem. Phys. 138, 074106 (2013); http://dx.doi.org/10.1063/1.4789814 (9 pages) | Cited 2 times

Online Publication Date: 19 February 2013

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Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory calculations. However, when applied to more than two atoms, these methods are still frequently perceived to be based on ad hoc assumptions, rather than a rigorous derivation from quantum mechanics. Starting from the adiabatic connection fluctuation-dissipation (ACFD) theorem, an exact expression for the electronic exchange-correlation energy, we demonstrate that the pairwise interatomic dispersion energy for an arbitrary collection of isotropic polarizable dipoles emerges from the second-order expansion of the ACFD formula upon invoking the random-phase approximation (RPA) or the full-potential approximation. Moreover, for a system of quantum harmonic oscillators coupled through a dipole-dipole potential, we prove the equivalence between the full interaction energy obtained from the Hamiltonian diagonalization and the ACFD-RPA correlation energy. This property makes the Hamiltonian diagonalization an efficient method for the calculation of the many-body dispersion energy. In addition, we show that the switching function used to damp the dispersion interaction at short distances arises from a short-range screened Coulomb potential, whose role is to account for the spatial spread of the individual atomic dipole moments. By using the ACFD formula, we gain a deeper understanding of the approximations made in the interatomic pairwise approaches, providing a powerful formalism for further development of accurate and efficient methods for the calculation of the dispersion energy.
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34.20.Cf Interatomic potentials and forces
31.15.eg Exchange-correlation functionals (in current density functional theory)
32.30.-r Atomic spectra

Molecular electrostatic potential at the atomic sites in the effective core potential approximation

Michał Lesiuk and Janusz Zachara

J. Chem. Phys. 138, 074107 (2013); http://dx.doi.org/10.1063/1.4792198 (9 pages)

Online Publication Date: 19 February 2013

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Considering calculations of the molecular electrostatic potential at the atomic sites (MEP@AS) in the presence of effective core potentials (ECP), we found that the consequent use of the definition of MEP@AS based on the energy derivative with respect to nuclear charge leads to a formula that differs by one term from the result of simple application of Coulomb's law. We have developed a general method to analytically treat derivatives of ECP with respect to nuclear charge. Benchmarking calculations performed on a set of simple molecules show that our formula leads to a systematic decrease in the error connected with the introduction of ECP when compared to all-electron results. Because of a straightforward implementation and relatively low costs of the developed procedure we suggest to use it by default.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.A- Ab initio calculations

ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

T. Verstraelen, P. W. Ayers, V. Van Speybroeck, and M. Waroquier

J. Chem. Phys. 138, 074108 (2013); http://dx.doi.org/10.1063/1.4791569 (20 pages)

Online Publication Date: 19 February 2013

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A new polarizable force field (PFF), namely atom-condensed Kohn-Sham density functional theory approximated to second order (ACKS2), is proposed for the efficient computation of atomic charges and linear response properties of extended molecular systems. It is derived from Kohn-Sham density functional theory (KS-DFT), making use of two novel ingredients in the context of PFFs: (i) constrained atomic populations and (ii) the Legendre transform of the Kohn-Sham kinetic energy. ACKS2 is essentially an extension of the Electronegativity Equalization Method (EEM) [W. J. Mortier, S. K. Ghosh, and S. Shankar, J. Am. Chem. Soc. 108, 4315 (1986)]10.1021/ja00275a013 in which two major EEM shortcomings are fixed: ACKS2 predicts a linear size-dependence of the dipole polarizability in the macroscopic limit and correctly describes the charge distribution when a molecule dissociates. All ACKS2 parameters are defined as atoms-in-molecules expectation values. The implementation of ACKS2 is very similar to that of EEM, with only a small increase in computational cost.
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31.15.ec Hohenberg-Kohn theorem and formal mathematical properties, completeness theorems
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
34.70.+e Charge transfer
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)

Density functionals for static, dynamical, and strong correlation

Axel D. Becke

J. Chem. Phys. 138, 074109 (2013); http://dx.doi.org/10.1063/1.4790598 (10 pages) | Cited 1 time

Online Publication Date: 20 February 2013

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In this work, our exact-exchange-based static + dynamical correlation density functional [A. D. Becke, J. Chem. Phys. 122, 064101 (2005)]10.1063/1.1844493 is generalized to include “strong” correlation, i.e., accurate computations on dissociating chemical systems without breaking space or spin symmetries and without using multi-determinantal reference states. Also, we introduce a strong-correlation benchmark set composed of space- and spin-symmetrized open-shell atoms on which the generalized functional is tested. Initial results are very promising.
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31.15.E- Density-functional theory
31.15.eg Exchange-correlation functionals (in current density functional theory)

Comparison of finite difference based methods to obtain sensitivities of stochastic chemical kinetic models

Rishi Srivastava, David F. Anderson, and James B. Rawlings

J. Chem. Phys. 138, 074110 (2013); http://dx.doi.org/10.1063/1.4790650 (10 pages) | Cited 1 time

Online Publication Date: 20 February 2013

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Sensitivity analysis is a powerful tool in determining parameters to which the system output is most responsive, in assessing robustness of the system to extreme circumstances or unusual environmental conditions, in identifying rate limiting pathways as a candidate for drug delivery, and in parameter estimation for calculating the Hessian of the objective function. Anderson [SIAM J. Numer. Anal. 50, 2237 (2012)]10.1137/110849079 shows the advantages of the newly developed coupled finite difference (CFD) estimator over the common reaction path (CRP) [M. Rathinam, P. W. Sheppard, and M. Khammash, J. Chem. Phys. 132, 034103 (2010)]10.1063/1.3280166 estimator. In this paper, we demonstrate the superiority of the CFD estimator over the common random number (CRN) estimator in a number of scenarios not considered previously in the literature, including the sensitivity of a negative log likelihood function for parameter estimation, the sensitivity of being in a rare state, and a sensitivity with fast fluctuating species. In all examples considered, the superiority of CFD over CRN is demonstrated. We also provide an example in which the CRN method is superior to the CRP method, something not previously observed in the literature. These examples, along with Anderson's results, lead to the conclusion that CFD is currently the best estimator in the class of finite difference estimators of stochastic chemical kinetic models.
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82.20.Fd Collision theories; trajectory models
02.70.Bf Finite-difference methods

Open-shell pair interaction energy decomposition analysis (PIEDA): Formulation and application to the hydrogen abstraction in tripeptides

Mandy C. Green, Dmitri G. Fedorov, Kazuo Kitaura, Joseph S. Francisco, and Lyudmila V. Slipchenko

J. Chem. Phys. 138, 074111 (2013); http://dx.doi.org/10.1063/1.4790616 (10 pages)

Online Publication Date: 21 February 2013

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An open-shell extension of the pair interaction energy decomposition analysis (PIEDA) within the framework of the fragment molecular orbital (FMO) method is developed. The open-shell PIEDA method allows the analysis of inter- and intramolecular interactions in terms of electrostatic, exchange-repulsion, charge-transfer, dispersion, and optional polarization energies for molecular systems with a radical or high-spin fragment. Taking into account the low computational cost and scalability of the FMO and PIEDA methods, the new scheme provides a means to characterize the stabilization of radical and open-shell sites in biologically relevant species. The open-shell PIEDA is applied to the characterization of intramolecular interactions in capped trialanine upon hydrogen abstraction (HA) at various sites on the peptide. Hydrogen abstraction reaction is the first step in the oxidative pathway initiated by reactive oxygen or nitrogen species, associated with oxidative stress. It is found that HA results in significant geometrical reorganization of the trialanine peptide. Depending on the HA site, terminal interactions in the radical fold conformers may become weaker or stronger compared to the parent molecule, and often change the character of the non-covalent bonding from amide stacking to hydrogen bonding.
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99.10.Cd Errata
87.14.ef Peptides
87.15.Fh Bonding; mechanisms of bond breakage
87.15.ht Ultrafast dynamics; charge transfer
87.15.R- Reactions and kinetics
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways

Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

Ryan R. Cheng, Alexander T. Hawk, and Dmitrii E. Makarov

J. Chem. Phys. 138, 074112 (2013); http://dx.doi.org/10.1063/1.4792206 (11 pages)

Online Publication Date: 21 February 2013

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Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often adequately described by simple polymer models. In particular, the Rouse model with internal friction (RIF) captures internal friction effects as observed in single-molecule fluorescence correlation spectroscopy (FCS) studies of a number of proteins. Here we use RIF, and its non-free draining analog, Zimm model with internal friction, to explore the effect of internal friction on the rate with which intramolecular contacts can be formed within the unfolded chain. Unlike the reconfiguration times inferred from FCS experiments, which depend linearly on the solvent viscosity, the first passage times to form intramolecular contacts are shown to display a more complex viscosity dependence. We further describe scaling relationships obeyed by contact formation times in the limits of high and low internal friction. Our findings provide experimentally testable predictions that can serve as a framework for the analysis of future studies of contact formation in proteins.
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87.15.La Mechanical properties
87.14.E- Proteins
87.15.hm Folding dynamics
87.15.mq Luminescence
36.20.Ey Conformation (statistics and dynamics)
36.20.Kd Electronic structure and spectra
back to top Atoms, Molecules, and Clusters

Total, elastic, and inelastic cross sections for positron and electron collisions with tetrahydrofuran

Luca Chiari, Emma Anderson, Wade Tattersall, J. R. Machacek, Prasanga Palihawadana, Casten Makochekanwa, James P. Sullivan, Gustavo García, Francisco Blanco, R. P. McEachran, M. J. Brunger, and Stephen J. Buckman

J. Chem. Phys. 138, 074301 (2013); http://dx.doi.org/10.1063/1.4789584 (15 pages) | Cited 1 time

Online Publication Date: 15 February 2013

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We present total, elastic, and inelastic cross sections for positron and electron scattering from tetrahydrofuran (THF) in the energy range between 1 and 5000 eV. Total cross sections (TCS), positronium formation cross sections, the summed inelastic integral cross sections (ICS) for electronic excitations and direct ionization, as well as elastic differential cross sections (DCS) at selected incident energies, have been measured for positron collisions with THF. The positron beam used to carry out these experiments had an energy resolution in the range 40–100 meV (full-width at half-maximum). We also present TCS results for positron and electron scattering from THF computed within the independent atom model using the screening corrected additivity rule approach. In addition, we calculated positron-impact elastic DCS and the sum over all inelastic ICS (except rotations and vibrations). While our integral and differential positron cross sections are the first of their kind, we compare our TCS with previous literature values for this species. We also provide a comparison between positron and electron-impact cross sections, in order to uncover any differences or similarities in the scattering dynamics with these two different projectiles.
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34.80.Bm Elastic scattering
34.80.Uv Positron scattering
34.80.Gs Molecular excitation and ionization
31.15.X- Alternative approaches
36.10.Dr Positronium

Experimental and theoretical cross sections for positron collisions with 3-hydroxy-tetrahydrofuran

Luca Chiari, Prasanga Palihawadana, J. R. Machacek, Casten Makochekanwa, Gustavo García, Francisco Blanco, R. P. McEachran, M. J. Brunger, Stephen J. Buckman, and James P. Sullivan

J. Chem. Phys. 138, 074302 (2013); http://dx.doi.org/10.1063/1.4790620 (11 pages) | Cited 1 time

Online Publication Date: 15 February 2013

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Cross section results from a joint experimental and theoretical investigation into positron scattering from 3-hydroxy-tetrahydrofuran (3H-THF) are presented. Total and positronium (Ps) formation cross sections have been measured from 1 to 190 eV using the positron beamline at the Australian National University, which has an energy resolution between 60 and 100 meV. The total cross section (TCS) and the elastic and total inelastic integral cross sections in the energy range between 1 and 1000 eV have been computed within the Independent Atom Model using the Screening Corrected Additivity Rule approach. In addition, we have calculated elastic differential cross sections at selected incident energies. Our computations represent the first theoretical results reported for this target species, while our measured Ps formation cross sections are also novel. Comparison of the present TCS with the previous results from the University of Trento shows a good level of agreement at the lowest energies. We also provide a comparison between the present cross sections for 3H-THF and those from our earlier study on the parent molecule tetrahydrofuran.
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36.10.Dr Positronium
34.80.Gs Molecular excitation and ionization

Classical dynamics of state-resolved hyperthermal O(3P) + H2O(1A1) collisions

Matthew Braunstein and Patrick F. Conforti

J. Chem. Phys. 138, 074303 (2013); http://dx.doi.org/10.1063/1.4790589 (16 pages) | Cited 1 time

Online Publication Date: 15 February 2013

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Classical dynamics calculations are performed for O(3P) + H2O(1A1) collisions from 2 to 10 km s‑1 (4.1–101.3 kcal mol−1), focusing on product internal energies. Several methods are used to produce ro-vibrationally state-resolved product cross sections and to enforce zero-point maintenance from analysis of the classical trajectories. Two potential energy surfaces are used: (1) a recently developed set of global reactive surfaces for the three lowest triplet states which model OH formation, H elimination to make H + OOH, O-atom exchange, and collisional excitation and (2) a non-reactive surface used in past classical and quantum collision studies. Comparisons to these previous studies suggest that for H2O vibrational excitation, classical dynamics which include Gaussian binning procedures and/or selected zero-point maintenance algorithms can produce results which approximate quantum scattering cross sections fairly well. Without these procedures, the classical cross sections can be many orders of magnitude greater than the quantum cross sections for exciting the bending vibration of H2O, especially near threshold. The classical cross section over-estimate is due to energy borrowing from stretching modes which dip below zero-point values. For results on the reactive surfaces, the present calculations show that at higher velocities there is an unusually large amount of product internal excitation. For OOH, where 40% of available collision energy goes into internal motion, the excited product vibrational and rotational energy distributions are relatively flat and values of the OOH rotational angular momentum exceed J = 100. Other product channel distributions show an exponential fall-off with energy consistent with an energy gap law. The present detailed distributions and cross sections can serve as a guide for future hyperthermal measurements of this system.
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34.50.Lf Chemical reactions
31.50.Df Potential energy surfaces for excited electronic states
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Vq Vibration-rotation analysis
34.20.Gj Intermolecular and atom-molecule potentials and forces
34.50.Gb Electronic excitation and ionization of molecules

Coherent π-electron dynamics of (P)-2,2′-biphenol induced by ultrashort linearly polarized UV pulses: Angular momentum and ring current

H. Mineo, S. H. Lin, and Y. Fujimura

J. Chem. Phys. 138, 074304 (2013); http://dx.doi.org/10.1063/1.4790595 (16 pages)

Online Publication Date: 15 February 2013

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The results of a theoretical investigation of coherent π-electron dynamics for nonplanar (P)-2,2′-biphenol induced by ultrashort linearly polarized UV pulses are presented. Expressions for the time-dependent coherent angular momentum and ring current are derived by using the density matrix method. The time dependence of these coherences is determined by the off-diagonal density matrix element, which can be obtained by solving the coupled equations of motion of the electronic-state density matrix. Dephasing effects on coherent angular momentum and ring current are taken into account within the Markov approximation. The magnitudes of the electronic angular momentum and current are expressed as the sum of expectation values of the corresponding operators in the two phenol rings (L and R rings). Here, L (R) denotes the phenol ring in the left (right)-hand side of (P)-2,2′-biphenol. We define the bond current between the nearest neighbor carbon atoms Ci and Cj as an electric current through a half plane perpendicular to the Ci–Cj bond. The bond current can be expressed in terms of the inter-atomic bond current. The inter-atomic bond current (bond current) depends on the position of the half plane on the bond and has the maximum value at the center. The coherent ring current in each ring is defined by averaging over the bond currents. Since (P)-2,2′-biphenol is nonplanar, the resultant angular momentum is not one-dimensional. Simulations of the time-dependent coherent angular momentum and ring current of (P)-2,2′-biphenol excited by ultrashort linearly polarized UV pulses are carried out using the molecular parameters obtained by the time-dependent density functional theory (TD-DFT) method. Oscillatory behaviors in the time-dependent angular momentum (ring current), which can be called angular momentum (ring current) quantum beats, are classified by the symmetry of the coherent state, symmetric or antisymmetric. The bond current of the bridge bond linking the L and R rings is zero for the symmetric coherent state, while it is nonzero for the antisymmetric coherent state. The magnitudes of ring current and ring current-induced magnetic field are also evaluated, and their possibility as a control parameter in ultrafast switching devices is discussed. The present results give a detailed description of the theoretical treatment reported in our previous paper [H. Mineo, M. Yamaki, Y. Teranish, M. Hayashi, S. H. Lin, and Y. Fujimura, J. Am. Chem. Soc. 134, 14279 (2012)10.1021/ja3047848].
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33.80.Wz Other multiphoton processes
31.15.ee Time-dependent density functional theory
33.15.Fm Bond strengths, dissociation energies

Characteristic oxygen K-edge circular dichroism spectra of amino acid films by improved measurement technique

Yudai Izumi, Maiko Tanabe, Akiko Imazu, Aki Mimoto, Masahito Tanaka, Akane Agui, Takayuki Muro, and Kazumichi Nakagawa

J. Chem. Phys. 138, 074305 (2013); http://dx.doi.org/10.1063/1.4790599 (10 pages)

Online Publication Date: 15 February 2013

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Circular dichroism (CD) spectroscopy in the soft x-ray energy region is a new tool to study the local structure of chiral materials. In this paper, we introduce a method to measure high-quality CD spectra in the oxygen K-edge energy region. Characteristic CD spectra of thin films of the amino acids L-tyrosine and L-aspartic acid are reported and compared with those of films of L-alanine and L-serine. The signals from the oxygen 1s → π* transitions of COO−, which is a common moiety in these amino acids, reflect the local geometry of each amino acid.
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87.15.M- Spectra of biomolecules
36.20.Hb Configuration (bonds, dimensions)
36.20.Kd Electronic structure and spectra
87.14.E- Proteins
87.15.B- Structure of biomolecules

Effect of geometrical orientation on the charge-transfer energetics of supramolecular (tetraphenyl)-porphyrin/C60 dyads

Marco Olguin, Rajendra R. Zope, and Tunna Baruah

J. Chem. Phys. 138, 074306 (2013); http://dx.doi.org/10.1063/1.4790623 (8 pages)

Online Publication Date: 15 February 2013

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The charge transfer (CT) excited state energies of donor-acceptor (D/A) pairs determine the achievable open-circuit voltage of D/A-based organic solar cell devices. Changes in the relative orientation of donor-acceptor pairs at the interface influence the frontier orbital energy levels, which impacts the dissociation of bound excitons at the D/A-interface. We examine the effect of relative orientation on CT excited state energies of porphyrin-fullerene dyads. The donors studied are base- and Zn-tetraphenyl porphyrin coupled to C60 as the acceptor molecule in an end-on configuration. We compare the energetics of a few low-lying CT states for the end-on geometry to our previously calculated CT energetics of a co-facial orientation. The calculated CT excitation energies are larger for the end-on orientation in comparison to the co-facial structure by about 0.7 eV, which primarily occurs due to a decrease in exciton binding energy in going from the co-facial to the end-on orientation. Furthermore, changes in relative donor-acceptor orientation have a larger impact on the CT energies than changes in donor-acceptor distance.
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71.35.-y Excitons and related phenomena
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
88.40.hj Efficiency and performance of solar cells
88.40.jr Organic photovoltaics

Effect of length on the position of negative differential resistance and realization of multifunction in fused oligothiophenes based molecular device

Jiaping Fan, Nahashon Ndegwa Gathitu, Yingfei Chang, and Jingping Zhang

J. Chem. Phys. 138, 074307 (2013); http://dx.doi.org/10.1063/1.4790805 (5 pages) | Cited 1 time

Online Publication Date: 15 February 2013

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The length modulation of electron transport properties for molecular devices based on fused oligothiophenes has been investigated theoretically using a combination of non-equilibrium Green's functions and first-principles density functional theory. The results show that the lengths of the molecules have a distinct influence on the position of negative differential resistance (NDR) of the molecular devices. By exploring the effect on transmission properties of substituent groups, hexathieno[3,2-b:2′,3′-d]thiophene with –NH2 and –NO2 substituents (model L) can be regard as a good candidate of multifunctional molecular device, which shows excellent rectifying performance (the largest rectification ration is 14.3 at 1.2 V) and clear NDR behavior (at 1.4 V).
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85.65.+h Molecular electronic devices
02.30.-f Function theory, analysis

Classical calculations of radiative association in absence of electronic transitions

Magnus Gustafsson

J. Chem. Phys. 138, 074308 (2013); http://dx.doi.org/10.1063/1.4790862 (7 pages)

Online Publication Date: 15 February 2013

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A formula for the cross section of radiative association where no electronic transitions take place is derived and tested for diatomic molecules. The approach is based on classical mechanics and therefore it is valid for direct, i.e., non-resonant, radiative association. For the formation of carbon monoxide (CO) and the cyano radical (CN), in the X1Σ+ and A1Π states, respectively, the treatment reproduces the baselines of the cross sections obtained using quantum mechanical perturbation theory. The method overestimates the formation cross section of potassium sodide (NaK) by about 8%. For the lower mass diatoms hydrogen fluoride (HF) and deuterium hydride (HD), the formula overestimates the cross sections by 12% and 60%, respectively. The formula can be used alone for estimates of radiative association rate constants, or in combination with Breit-Wigner theory to include resonance contributions.
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82.30.Nr Association, addition, insertion, cluster formation
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