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21 Nov 2011

Volume 135, Issue 19, Articles (19xxxx)

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J. Chem. Phys. 135, 194701 (2011); http://dx.doi.org/10.1063/1.3657857 (13 pages)

Max C. Watson, Yonggang Peng, Yujun Zheng, and Frank L. H. Brown
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Communication: Standard surface hopping predicts incorrect scaling for Marcus’ golden-rule rate: The decoherence problem cannot be ignored

Brian R. Landry and Joseph E. Subotnik

J. Chem. Phys. 135, 191101 (2011); http://dx.doi.org/10.1063/1.3663870 (4 pages)

Online Publication Date: 21 November 2011

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We evaluate the accuracy of Tully's surface hopping algorithm for the spin-boson model for the case of a small diabatic coupling parameter (V). We calculate the transition rates between diabatic surfaces, and we compare our results to the expected Marcus rates. We show that standard surface hopping yields an incorrect scaling with diabatic coupling (linear in V), which we demonstrate is due to an incorrect treatment of decoherence. By modifying standard surface hopping to include decoherence events, we recover the correct scaling (∼V2).
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05.30.Jp Boson systems
75.40.Gb Dynamic properties (dynamic susceptibility, spin waves, spin diffusion, dynamic scaling, etc.)
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Communication: A global hybrid generalized gradient approximation to the exchange-correlation functional that satisfies the second-order density-gradient constraint and has broad applicability in chemistry

Roberto Peverati and Donald G. Truhlar

J. Chem. Phys. 135, 191102 (2011); http://dx.doi.org/10.1063/1.3663871 (4 pages)

Online Publication Date: 21 November 2011

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We extend our recent SOGGA11 approximation to the exchange-correlation functional to include a percentage of Hartree-Fock exchange. The new functional, called SOGGA11-X, has better overall performance for a broad chemical database than any previously available global hybrid generalized gradient approximation, and in addition it satisfies an extra physical constraint in that it is correct to second order in the density-gradient.
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31.15.xr Self-consistent-field methods
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back to top Theoretical Methods and Algorithms

Phase diagram of hard tetrahedra

Amir Haji-Akbari, Michael Engel, and Sharon C. Glotzer

J. Chem. Phys. 135, 194101 (2011); http://dx.doi.org/10.1063/1.3651370 (10 pages)

Online Publication Date: 15 November 2011

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Advancements in the synthesis of faceted nanoparticles and colloids have spurred interest in the phase behavior of polyhedral shapes. Regular tetrahedra have attracted particular attention because they prefer local symmetries that are incompatible with periodicity. Two dense phases of regular tetrahedra have been reported recently. The densest known tetrahedron packing is achieved in a crystal of triangular bipyramids (dimers) with a packing density of 4000/4671 ≈ 85.63%. In simulation a dodecagonal quasicrystal is observed; its approximant, with periodic tiling (3.4.32.4), can be compressed to a packing fraction of 85.03%. Here, we show that the quasicrystal approximant is more stable than the dimer crystal for packing densities below 84% using Monte Carlo computer simulations and free energy calculations. To carry out the free energy calculations, we use a variation of the Frenkel-Ladd method for anisotropic shapes and thermodynamic integration. The enhanced stability of the approximant can be attributed to a network substructure, which maximizes the free volume (and hence the wiggle room) available to the particles and facilitates correlated motion of particles, which further contributes to entropy and leads to diffusion for packing densities below 65%. The existence of a solid-solid transition between structurally distinct phases not related by symmetry breaking – the approximant and the dimer crystal – is unusual for hard particle systems.
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61.44.Br Quasicrystals
65.40.gd Entropy
66.30.-h Diffusion in solids
64.70.K- Solid-solid transitions

Basis set convergence of the coupled-cluster correction, δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases

Michael S. Marshall, Lori A. Burns, and C. David Sherrill

J. Chem. Phys. 135, 194102 (2011); http://dx.doi.org/10.1063/1.3659142 (10 pages) | Cited 3 times

Online Publication Date: 15 November 2011

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In benchmark-quality studies of non-covalent interactions, it is common to estimate interaction energies at the complete basis set (CBS) coupled-cluster through perturbative triples [CCSD(T)] level of theory by adding to CBS second-order perturbation theory (MP2) a “coupled-cluster correction,” δMP2CCSD(T), evaluated in a modest basis set. This work illustrates that commonly used basis sets such as 6-31G*(0.25) can yield large, even wrongly signed, errors for δMP2CCSD(T) that vary significantly by binding motif. Double-ζ basis sets show more reliable results when used with explicitly correlated methods to form a δMP2−F12CCSD(T*)−F12 correction, yielding a mean absolute deviation of 0.11 kcal mol−1 for the S22 test set. Examining the coupled-cluster correction for basis sets up to sextuple-ζ in quality reveals that δMP2CCSD(T) converges monotonically only beyond a turning point at triple-ζ or quadruple-ζ quality. In consequence, CBS extrapolation of δMP2CCSD(T) corrections before the turning point, generally CBS (aug-cc-pVDZ,aug-cc-pVTZ), are found to be unreliable and often inferior to aug-cc-pVTZ alone, especially for hydrogen-bonding systems. Using the findings of this paper, we revise some recent benchmarks for non-covalent interactions, namely the S22, NBC10, HBC6, and HSG test sets. The maximum differences in the revised benchmarks are 0.080, 0.060, 0.257, and 0.102 kcal mol−1, respectively.
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31.15.bw Coupled-cluster theory
33.15.Fm Bond strengths, dissociation energies
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

A distance-dependent parameterization of the extended Hubbard model for conjugated and aromatic hydrocarbons derived from stretched ethene

Thomas G. Schmalz, Luis Serrano-Andrés, Vicenta Sauri, Manuela Merchán, and Josep M. Oliva

J. Chem. Phys. 135, 194103 (2011); http://dx.doi.org/10.1063/1.3659294 (10 pages)

Online Publication Date: 16 November 2011

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The Hubbard model, which is widely used in physics but is mostly unfamiliar to chemists, provides an attractive yet simple model for chemistry beyond the self consistent field molecular orbital approximation. The Hubbard model adds an effective electron-electron repulsion when two electrons occupy the same atomic orbital to the familiar Hückel Hamiltonian. Thus it breaks the degeneracy between excited singlet and triplet states and allows an explicit treatment of electron correlation. We show how to evaluate the parameters of the model from high-level ab initio calculations on two-atom fragments and then to transfer the parameters to large molecules and polymers where accurate ab initio calculations are difficult or impossible. The recently developed MS-RASPT2 method is used to generate accurate potential energy curves for ethene as a function of carbon-carbon bond length, which are used to parameterize the model for conjugated hydrocarbons. Test applications to several conjugated/aromatic molecules show that even though the model is very simple, it is capable of reasonably accurate predictions for bond lengths, and predicts molecular excitation energies in reasonable agreement with those from the MS-RASPT2 method.
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31.50.Df Potential energy surfaces for excited electronic states
31.15.ae Electronic structure and bonding characteristics
31.15.xp Perturbation theory
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Potential-functional embedding theory for molecules and materials

Chen Huang and Emily A. Carter

J. Chem. Phys. 135, 194104 (2011); http://dx.doi.org/10.1063/1.3659293 (17 pages) | Cited 2 times

Online Publication Date: 17 November 2011

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We introduce a potential-functional embedding theory by reformulating a recently proposed density-based embedding theory in terms of functionals of the embedding potential. This potential-functional based theory completes the dual problem in the context of embedding theory for which density-functional embedding theory has existed for two decades. With this potential-functional formalism, it is straightforward to solve for the unique embedding potential shared by all subsystems. We consider charge transfer between subsystems and discuss how to treat fractional numbers of electrons in subsystems. We show that one is able to employ different energy functionals for different subsystems in order to treat different regions with theories of different levels of accuracy, if desired. The embedding potential is solved for by directly minimizing the total energy functional, and we discuss how to efficiently calculate the gradient of the total energy functional with respect to the embedding potential. Forces are also derived, thereby making it possible to optimize structures and account for nuclear dynamics. We also extend the theory to spin-polarized cases. Numerical examples of the theory are given for some homo- and hetero-nuclear diatomic molecules and a more complicated test of a six-hydrogen-atom chain. We also test our theory in a periodic bulk environment with calculations of basic properties of bulk NaCl, by treating each atom as a subsystem. Finally, we demonstrate the theory for water adsorption on the MgO(001)surface.
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34.70.+e Charge transfer
31.15.E- Density-functional theory

Accurate potential energy surfaces with a DFT+U(R) approach

Heather J. Kulik and Nicola Marzari

J. Chem. Phys. 135, 194105 (2011); http://dx.doi.org/10.1063/1.3660353 (10 pages)

Online Publication Date: 18 November 2011

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We introduce an improvement to the Hubbard U augmented density functional approach known as DFT+U that incorporates variations in the value of self-consistently calculated, linear-response U with changes in geometry. This approach overcomes the one major shortcoming of previous DFT+U studies, i.e., the use of an averaged Hubbard U when comparing energies for different points along a potential energy surface is no longer required. While DFT+U is quite successful at providing accurate descriptions of localized electrons (e.g., d or f) by correcting self-interaction errors of standard exchange correlation functionals, we show several diatomic molecule examples where this position-dependent DFT+U(R) provides a significant two- to four-fold improvement over DFT+U predictions, when compared to accurate correlated quantum chemistry and experimental references. DFT+U(R) reduces errors in binding energies, frequencies, and equilibrium bond lengths by applying the linear-response, position-dependent U(R) at each configuration considered. This extension is most relevant where variations in U are large across the points being compared, as is the case with covalent diatomic molecules such as transition-metal oxides. We thus provide a tool for deciding whether a standard DFT+U approach is sufficient by determining the strength of the dependence of U on changes in coordinates. We also apply this approach to larger systems with greater degrees of freedom and demonstrate how DFT+U(R) may be applied automatically in relaxations, transition-state finding methods, and dynamics.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.50.-x Potential energy surfaces
31.15.xr Self-consistent-field methods
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Dj Interatomic distances and angles
33.15.Bh General molecular conformation and symmetry; stereochemistry

Spin-adapted open-shell time-dependent density functional theory. III. An even better and simpler formulation

Zhendong Li and Wenjian Liu

J. Chem. Phys. 135, 194106 (2011); http://dx.doi.org/10.1063/1.3660688 (14 pages) | Cited 1 time

Online Publication Date: 18 November 2011

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The recently proposed spin-adapted time-dependent density functional theory (S-TD-DFT) [Z. Li and W. Liu, J. Chem. Phys. 133, 064106 (2010)]10.1063/1.3463799 resolves the spin-contamination problem in describing singly excited states of high spin open-shell systems. It is an extension of the standard restricted open-shell Kohn-Sham-based TD-DFT which can only access those excited states due to singlet-coupled single excitations. It is also far superior over the unrestricted Kohn-Sham-based TD-DFT (U-TD-DFT) which suffers from severe spin contamination for those excited states due to triplet-coupled single excitations. Nonetheless, the accuracy of S-TD-DFT for high spin open-shell systems is still inferior to TD-DFT for well-behaved closed-shell systems. The reason can be traced back to the violation of the spin degeneracy conditions (SDC) by approximate exchange-correlation (XC) functionals. Noticing that spin-adapted random phase approximation (S-RPA) can indeed maintain the SDC by virtue of the Wigner-Eckart theorem, a hybrid ansatz combining the good of S-TD-DFT and S-RPA can immediately be envisaged. The resulting formalism, dubbed as X-TD-DFT, is free of spin contamination and can also be viewed as a S-RPA correction to the XC kernel of U-TD-DFT. Compared with S-TD-DFT, X-TD-DFT leads to much improved results for the low-lying excited states of, e.g., N2+, yet with much reduced computational cost. Therefore, X-TD-DFT can be recommended for routine calculations of excited states of high spin open-shell systems.
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31.15.ee Time-dependent density functional theory
31.50.Df Potential energy surfaces for excited electronic states
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On the entropy of relaxing deterministic systems

Denis J. Evans, Stephen R. Williams, and Debra J. Searles

J. Chem. Phys. 135, 194107 (2011); http://dx.doi.org/10.1063/1.3660203 (6 pages)

Online Publication Date: 18 November 2011

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In this paper, we re-visit Gibbs’ second (unresolved) paradox, namely the constancy of the fine-grained Gibbs entropy for autonomous Hamiltonian systems. We compare and contrast the different roles played by dissipation and entropy both at equilibrium where dissipation is identically zero and away from equilibrium where entropy cannot be defined and seems unnecessary in any case. Away from equilibrium dissipation is a powerful quantity that can always be defined and that appears as the central argument of numerous exact theorems: the fluctuation, relaxation, and dissipation theorems and the newly derived Clausius inequality.
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05.70.Ce Thermodynamic functions and equations of state
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Differential geometry based solvation model. III. Quantum formulation

Zhan Chen and Guo-Wei Wei

J. Chem. Phys. 135, 194108 (2011); http://dx.doi.org/10.1063/1.3660212 (19 pages)

Online Publication Date: 18 November 2011

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Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models which allow the solvent-solute interface to be determined by the variation of a total free energy functional. Atomic fixed partial charges (point charges) are used in our earlier models, which depends on existing molecular mechanical force field software packages for partial charge assignments. As most force field models are parameterized for a certain class of molecules or materials, the use of partial charges limits the accuracy and applicability of our earlier models. Moreover, fixed partial charges do not account for the charge rearrangement during the solvation process. The present work proposes a differential geometry based multiscale solvation model which makes use of the electron density computed directly from the quantum mechanical principle. To this end, we construct a new multiscale total energy functional which consists of not only polar and nonpolar solvation contributions, but also the electronic kinetic and potential energies. By using the Euler-Lagrange variation, we derive a system of three coupled governing equations, i.e., the generalized Poisson-Boltzmann equation for the electrostatic potential, the generalized Laplace-Beltrami equation for the solvent-solute boundary, and the Kohn-Sham equations for the electronic structure. We develop an iterative procedure to solve three coupled equations and to minimize the solvation free energy. The present multiscale model is numerically validated for its stability, consistency and accuracy, and is applied to a few sets of molecules, including a case which is difficult for existing solvation models. Comparison is made to many other classic and quantum models. By using experimental data, we show that the present quantum formulation of our differential geometry based multiscale solvation model improves the prediction of our earlier models, and outperforms some explicit solvation model.
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87.15.H- Dynamics of biomolecules
02.40.Hw Classical differential geometry
31.15.E- Density-functional theory
87.14.-g Biomolecules: types

Dispersion interactions in density-functional theory: An adiabatic-connection analysis

Marie D. Strømsheim, Naveen Kumar, Sonia Coriani, Espen Sagvolden, Andrew M. Teale, and Trygve Helgaker

J. Chem. Phys. 135, 194109 (2011); http://dx.doi.org/10.1063/1.3660357 (16 pages)

Online Publication Date: 21 November 2011

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We present an analysis of the dispersion interaction energy and forces in density-functional theory from the point of view of the adiabatic connection between the Kohn–Sham non-interacting and fully interacting systems. Accurate coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] densities are computed for the helium dimer and used to construct the exchange-correlation potential of Kohn–Sham theory, showing agreement with earlier results presented for the Hartree–Fock–Kohn–Sham method [M. Allen and D. J. Tozer, J. Chem. Phys. 117, 11113 (2002)10.1063/1.1522715]. The accuracy of the methodology utilized to determine these solutions is checked by calculation of the Hellmann–Feynman forces based on the Kohn–Sham densities, which are compared with analytic CCSD(T) forces. To ensure that this comparison is valid in a finite atomic-orbital basis set, we employ floating Gaussian basis functions throughout and all results are counterpoise corrected. The subtle charge-rearrangement effects associated with the dispersion interaction are highlighted as the origin of a large part of the dispersion force. To recover the exchange-correlation components of the interaction energy, adiabatic connections are constructed for the supermolecular system and for its constituent atoms; subtraction of the resulting adiabatic-connection curves followed by integration over the interaction strength recovers the exchange-correlation contribution relevant to the density-functional description of the dispersion interaction. The results emphasize the long-ranged, dynamically correlated nature of the dispersion interaction between closed-shell species. An alternative adiabatic-connection path is also explored, where the electronic interactions are introduced in a manner that emphasizes the range of the electronic interactions, highlighting their purely long-ranged nature, consistent with the success of range-separated hybrid approaches in this context.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.bw Coupled-cluster theory

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

John D. Chodera and Michael R. Shirts

J. Chem. Phys. 135, 194110 (2011); http://dx.doi.org/10.1063/1.3660669 (15 pages)

Online Publication Date: 21 November 2011

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The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in discovering new ways to enhance the phase space mixing of these protocols in order to improve sampling of uncorrelated configurations. Here, we demonstrate how both of these classes of algorithms can be considered as special cases of Gibbs sampling within a Markov chain Monte Carlo framework. Gibbs sampling is a well-studied scheme in the field of statistical inference in which different random variables are alternately updated from conditional distributions. While the update of the conformational degrees of freedom by Metropolis Monte Carlo or molecular dynamics unavoidably generates correlated samples, we show how judicious updating of the thermodynamic state indices—corresponding to thermodynamic parameters such as temperature or alchemical coupling variables—can substantially increase mixing while still sampling from the desired distributions. We show how state update methods in common use can lead to suboptimal mixing, and present some simple, inexpensive alternatives that can increase mixing of the overall Markov chain, reducing simulation times necessary to obtain estimates of the desired precision. These improved schemes are demonstrated for several common applications, including an alchemical expanded ensemble simulation, parallel tempering, and multidimensional replica exchange umbrella sampling.
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05.70.Ce Thermodynamic functions and equations of state
02.50.Ga Markov processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Asymmetric stochastic localization in geometry controlled kinetics

Debasish Mondal and Deb Shankar Ray

J. Chem. Phys. 135, 194111 (2011); http://dx.doi.org/10.1063/1.3658486 (9 pages) | Cited 1 time

Online Publication Date: 21 November 2011

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We consider the motion of Brownian particles confined in a two-dimensional symmetric bilobal enclosure with uneven cross section. Varying cross section of the confinement results in an effective entropic potential in reduced dimension. By employing two external noise forces, one additive and another multiplicative along x direction, we demonstrate that a correlation between them causes a symmetry breaking of entropic stability, i.e., a difference in relative stability of two lobes. This leads to an asymmetric localization of population in the stationary state. A two-state model is proposed to explain the asymmetric localization of population due to entropic diffusion.
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05.40.Jc Brownian motion
05.60.-k Transport processes
05.70.Ce Thermodynamic functions and equations of state
02.50.Ey Stochastic processes
05.10.Gg Stochastic analysis methods (Fokker-Planck, Langevin, etc.)

The effect of a mechanical force on quantum reaction rate: Quantum Bell formula

Dmitrii E. Makarov

J. Chem. Phys. 135, 194112 (2011); http://dx.doi.org/10.1063/1.3661157 (5 pages)

Online Publication Date: 21 November 2011

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The purpose of this note is to derive a quantum-mechanical analog of Bell's formula, which describes the sensitivity of a chemical reaction to a mechanical pulling force. According to this formula, the reaction rate depends exponentially on the force f, i.e., k( f ) ∼ exp( f / fc), where the force scale fc is estimated as the thermal energy kBT divided by a distance a between the reactant and transition states along the pulling coordinate. Here I use instanton theory to show that, at low temperatures where quantum tunneling is dominant, this force scale becomes fc ∼ ℏω/a (in the limit where frictional damping is absent) or fc ∼ ℏτ−1/a (in the strong damping limit). Here ω is a characteristic vibration frequency along the pulling coordinate and τ is a characteristic relaxation time in the reactant state. That is, unlike the classical case where fc is unaffected by dissipation, this force scale becomes friction dependent in the quantum limit. I further derive higher-order corrections in the force dependence of the rate, describe generalizations to many degrees of freedom, and discuss connection to other quantum rate theories.
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82.20.Wt Computational modeling; simulation
33.20.Tp Vibrational analysis
82.20.Pm Rate constants, reaction cross sections, and activation energies

Binary systems from quantum cluster equilibrium theory

Marc Brüssel, Eva Perlt, Sebastian B. C. Lehmann, Michael von Domaros, and Barbara Kirchner

J. Chem. Phys. 135, 194113 (2011); http://dx.doi.org/10.1063/1.3662071 (10 pages)

Online Publication Date: 21 November 2011

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An extension of the quantum cluster equilibrium theory to treat binary mixtures is introduced in this work. The necessary equations are derived and a possible implementation is presented. In addition an alternative sampling procedure using widely available experimental data for the quantum cluster equilibrium approach is suggested and tested. An illustrative example, namely, the binary mixture of water and dimethyl sulfoxide, is given to demonstrate the new approach. A basic cluster set is introduced containing the relevant cluster motifs. The populations computed by the quantum cluster equilibrium approach are compared to the experimental data. Furthermore, the excess Gibbs free energy is computed and compared to experiments as well.
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64.75.Ef Mixing
65.20.-w Thermal properties of liquids
67.10.Fj Quantum statistical theory
05.30.-d Quantum statistical mechanics
64.75.Cd Phase equilibria of fluid mixtures, including gases, hydrates, etc.

Direct perturbation theory in terms of energy derivatives: Scalar-relativistic treatment up to sixth order

Werner Schwalbach, Stella Stopkowicz, Lan Cheng, and Jürgen Gauss

J. Chem. Phys. 135, 194114 (2011); http://dx.doi.org/10.1063/1.3659316 (14 pages) | Cited 1 time

Online Publication Date: 21 November 2011

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A formulation of sixth-order direct perturbation theory (DPT) to treat relativistic effects in quantum-chemical calculations is presented in the framework of derivative theory. Detailed expressions for DPT6 are given at the Hartree–Fock level in terms of the third derivative of the energy with respect to the relativistic perturbation parameter defined as λrel = c−2. They were implemented for the computation of scalar-relativistic energy corrections. The convergence of the scalar-relativistic DPT expansion is studied for energies and first-order properties such as dipole moment and electric-field gradient within the series of the hydrogen halides (HX, X = F, Cl, Br, I, and At). Comparison with spin-free Dirac–Coulomb calculations indicates that the DPT series exhibits a smooth and monotonic convergence. The rate of convergence, however, depends on the charge of the involved nuclei and significantly slows down for heavy-element compounds.
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31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
back to top Advanced Experimental Techniques

Novel coherent two-dimensional optical spectroscopy probes of chirality exchange and fluctuations in molecules

František Šanda and Shaul Mukamel

J. Chem. Phys. 135, 194201 (2011); http://dx.doi.org/10.1063/1.3658277 (15 pages)

Online Publication Date: 16 November 2011

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We demonstrate how stochastic transitions between molecular configurations with opposite senses of chirality may be probed by 2D optical signals with specific pulse polarization configurations. The third-order optical response of molecular dimers (such as biphenyls) with dynamical axial chirality is calculated to order of k2 in the wavevector of light. Spectroscopic signatures of equilibrium chirality fluctuations are predicted for three dynamical models (Ornstein-Uhlenbeck, two-state jump, and diffusion in double well) of the dihedral angle that controls the chirality.
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33.55.+b Optical activity and dichroism
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
33.15.Bh General molecular conformation and symmetry; stereochemistry
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Sum frequency generation-compressive sensing microscope

Xiaojun Cai, Bian Hu, Ting Sun, Kevin F. Kelly, and Steven Baldelli

J. Chem. Phys. 135, 194202 (2011); http://dx.doi.org/10.1063/1.3660202 (11 pages)

Online Publication Date: 17 November 2011

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A new sum frequency generation imaging microscope using a novel sampling theory, compressive sensing (CS), has been developed for surface studies. CS differentiates itself from the conventional sampling methods by collecting fewer measurements than the traditional methods to reconstruct a high quality image. Pseudorandom patterns were applied to a light modulator and reflected the sum frequency (SF) signal generated from the sample into a photomultiplier tube detector. The image of the sample was reconstructed using sparsity preserving algorithms from the SF signal. The influences of the number of CS testing patterns applied and the number of SF pulses acquired for each pattern on the quality of the images was investigated and a comparison of the image quality with the traditional raster scan was made at varying resolutions for a gold patterned Si surface. Our results demonstrate the CS technique achieved 16 times the pixel density beyond the resolution where the raster scan strategy lost its ability to image the sample due to the dilution of the SF signal below the detection limit of the detector.
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07.60.Pb Conventional optical microscopes
42.65.Ky Frequency conversion; harmonic generation, including higher-order harmonic generation
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Molecular-beam study of the ammonia–noble gas systems: Characterization of the isotropic interaction and insights into the nature of the intermolecular potential

Fernando Pirani, Luiz F. Roncaratti, Leonardo Belpassi, Francesco Tarantelli, and D. Cappelletti

J. Chem. Phys. 135, 194301 (2011); http://dx.doi.org/10.1063/1.3660199 (7 pages)

Online Publication Date: 15 November 2011

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We report new high resolution molecular beam experiments aimed at characterizing the intermolecular interaction in the NH3–Ng (Ng = He, Ne, Ar, Kr, Xe) weakly bound complexes. Integral cross section data are obtained over a sufficiently wide velocity range and with rotationally hot NH3 molecules to produce (except for the NH3–He case) a well resolved “glory” quantum interference pattern. Data analysis, carried out by employing a recently proposed potential model, allows unique information on the absolute scale of the intermolecular interaction to be obtained both at long range and at the equilibrium distance. An extensive and internally consistent comparison with the behavior of the corresponding Kr–Ng systems is exploited in order to identify those cases where an interaction component due to charge transfer effects provides an appreciable intermolecular bond stabilization that is clearly distinct from and must be added to the standard van der Waals plus induction picture. The results of the present investigation extend the phenomenology of perturbative charge transfer effects in gas phase complexes involving hydrogenated molecules.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
37.20.+j Atomic and molecular beam sources and techniques
33.15.Fm Bond strengths, dissociation energies
33.15.Mt Rotation, vibration, and vibration-rotation constants
34.70.+e Charge transfer

Cross sections and rate constants for OH + H2 reaction on three different potential energy surfaces for ro-vibrationally excited reagents

Sayak Bhattacharya, Aditya N. Panda, and Hans-Dieter Meyer

J. Chem. Phys. 135, 194302 (2011); http://dx.doi.org/10.1063/1.3660222 (7 pages)

Online Publication Date: 15 November 2011

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A systematic study of the reagent ro-vibrational excitations in H2 + OH reaction is presented on three different potential energy surfaces using the multiconfiguration time-dependent Hartree method. An exact form of the kinetic energy operator including Coriolis coupling has been used. Coupled channel results on WDSE surface for vibrational excitation of H2 produce very large cross sections in accordance with the previous approximate results. The rate constant obtained for H2(v = 1) at 300 K on the YZCL2 surface shows an excellent agreement with the most recent experimental result. Quantum dynamical results for ro-vibrational excitation of reagents obtained on the WSLFH surface show similar behavior to previous quasiclassical trajectory studies. The integral cross sections obtained for excited reagent rotations exhibit contrasting trends on the three surfaces. The effects are explained considering the different orientations of the transition state structure and the individual surface characteristics.
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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.Kh Potential energy surfaces for chemical reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
33.20.Vq Vibration-rotation analysis

Photodissociation of N2O: Triplet states and triplet channel

R. Schinke, J. A. Schmidt, and M. S. Johnson

J. Chem. Phys. 135, 194303 (2011); http://dx.doi.org/10.1063/1.3660349 (9 pages) | Cited 2 times

Online Publication Date: 17 November 2011

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The role of triplet states in the UV photodissociation of N2O is investigated by means of quantum mechanical wave packet calculations. Global potential energy surfaces are calculated for the lowest two 3A′ and the lowest two 3A′′ states at the multi-reference configuration interaction level of electronic structure theory using the augmented valence quadruple zeta atomic basis set. Because of extremely small transition dipole moments with the ground electronic state, excitation of the triplet states has only a marginal effect on the far red tail of the absorption cross section. The calculations do not show any hint of an increased absorption around 280 nm as claimed by early experimental studies. The peak observed in several electron energy loss spectra at 5.4 eV is unambiguously attributed to the lowest triplet state 13A′. Excitation of the 21A′ state and subsequent transition to the repulsive branch of the 23A′′ state at intermediate NN–O separations, promoted by spin-orbit coupling, is identified as the main pathway to the N2(1Σg+)+O(3P) triplet channel. The yield, determined in two-state wave packet calculations employing calculated spin-orbit matrix elements, is 0.002 as compared to 0.005 ± 0.002 measured by Nishida et al. [J. Phys. Chem. A 108, 2451 (2004)]10.1021/jp037034o.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
31.50.Df Potential energy surfaces for excited electronic states
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.20.Lg Ultraviolet spectra
31.15.vj Electron correlation calculations for atoms and ions: excited states
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
34.80.Gs Molecular excitation and ionization

Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins

Dmitry Zuev, Ksenia B. Bravaya, Maria V. Makarova, and Anna I. Krylov

J. Chem. Phys. 135, 194304 (2011); http://dx.doi.org/10.1063/1.3660350 (8 pages)

Online Publication Date: 17 November 2011

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Electronic structure calculations of microhydrated model chromophores (in their deprotonated anionic forms) of the photoactive yellow and green fluorescent proteins (PYP and GFP) are reported. Electron-detachment and excitation energies as well as binding energies of mono- and dihydrated isomers are computed and analyzed. Microhydration has different effects on the excited and ionized states. In lower-energy planar isomers, the interaction with one water molecule blueshifts the excitation energies by 0.1–0.2 eV, whereas the detachment energies increase by 0.4–0.8 eV. The important consequence is that microhydration by just one water molecule converts the resonance (autoionizing) excited states of the bare chromophores into bound states. In the lower-energy microhydrated clusters, interactions with water have negligible effect on the chromophore geometry; however, we also identified higher-energy dihydrated clusters of PYP in which two water molecules form hydrogen-bonding network connecting the carboxylate and phenolate moieties and the chromophore is strongly distorted resulting in a significant shift of excitation energies (up to 0.6 eV).
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87.15.R- Reactions and kinetics
87.15.B- Structure of biomolecules
87.15.Fh Bonding; mechanisms of bond breakage
87.14.E- Proteins

Insights into mechanistic photodissociation of chloroacetone from a combination of electronic structure calculation and molecular dynamics simulation

Lin Shen, Lihong Liu, Jun Cao, and Wei-Hai Fang

J. Chem. Phys. 135, 194305 (2011); http://dx.doi.org/10.1063/1.3660356 (10 pages)

Online Publication Date: 17 November 2011

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The stationary and intersection structures on the S0 and S1 potential energy surfaces of CH3COCH2Cl have been determined by the CAS(10,8)/cc-pVDZ optimizations and their relative energies are refined by the CASPT2//CAS(10,8)/cc-pVDZ single-point calculations. Non-adiabatic molecular dynamics simulations were performed on the basis of the state-averaged CAS(10,8)/cc-pVDZ calculated energies, energy gradients, and Hessian matrix for the S0 and S1 states. It is found that the features of the S1 potential energy surface and non-adiabatic effect control the selectivity of the two α-C–C bond fissions, which provides a reasonable explanation why one α-C–C bond was observed as a primary channel and the other is ruled out even if CH3COCH2Cl is excited at 193 nm. The β-C–Cl fission is determined to be a dominant channel once the CH3COCH2Cl molecule is excited to the S1 state and the β-C–Cl:α-C–C branching ratio is estimated by the RRKM rate theory to be 15:1 at 193 nm, which is overestimated in comparison with the value of ∼11:1 inferred experimentally. The present calculation reveals that the α-C–C fission might take place in the ground electronic state as a result of the S1 → S0 internal conversion upon photolysis at 308 nm. However, the measured kinetic energy distributions of the α-C–C fission products suggest that the fission does not involve internal conversion to the ground state. To solve this issue, we need to perform non-adiabatic quantum dynamics simulation on accurate S0, S1, and S2 potential energy surfaces, which is still a challenging task currently.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.xv Molecular dynamics and other numerical methods
31.15.xr Self-consistent-field methods
31.50.Bc Potential energy surfaces for ground electronic states
33.15.Bh General molecular conformation and symmetry; stereochemistry

On the nature of electron correlation in C60

David Stück, Thomas A. Baker, Paul Zimmerman, Westin Kurlancheek, and Martin Head-Gordon

J. Chem. Phys. 135, 194306 (2011); http://dx.doi.org/10.1063/1.3661158 (5 pages) | Cited 1 time

Online Publication Date: 17 November 2011

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The ground state restricted Hartree Fock (RHF) wave function of C60 is found to be unstable with respect to spin symmetry breaking, and further minimization leads to a significantly spin contaminated unrestricted Hartree Fock (UHF) solution (〈S2〉 = 7.5, 9.6 for singlet and triplet, respectively). The nature of the symmetry breaking in C60 relative to the radicaloid fullerene, C36, is assessed by energy lowering of the UHF solution, 〈S2〉, and the unpaired electron number. We conclude that the high value of each of these measures in C60 is not attributable to strong correlation behavior as is the case for C36. Instead, their origin is from the collective effect of relatively weak, global correlations present in the π space of both fullerenes. Second order perturbation (MP2) calculations of the singlet triplet gap are significantly more accurate with RHF orbitals than UHF orbitals, while orbital optimized opposite spin second order correlation (O2) performs even better.
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31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.vj Electron correlation calculations for atoms and ions: excited states
31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods

Following the excited state relaxation dynamics of indole and 5-hydroxyindole using time-resolved photoelectron spectroscopy

Ruth Livingstone, Oliver Schalk, Andrey E. Boguslavskiy, Guorong Wu, L. Therese Bergendahl, Albert Stolow, Martin J. Paterson, and Dave Townsend

J. Chem. Phys. 135, 194307 (2011); http://dx.doi.org/10.1063/1.3659231 (12 pages)

Online Publication Date: 17 November 2011

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Time-resolved photoelectron spectroscopy was used to obtain new information about the dynamics of electronic relaxation in gas-phase indole and 5-hydroxyindole following UV excitation with femtosecond laser pulses centred at 249 nm and 273 nm. Our analysis of the data was supported by ab initio calculations at the coupled cluster and complete-active-space self-consistent-field levels. The optically bright 1La and 1Lb electronic states of 1ππ* character and spectroscopically dark and dissociative 1πσ* states were all found to play a role in the overall relaxation process. In both molecules we conclude that the initially excited 1La state decays non-adiabatically on a sub 100 fs timescale via two competing pathways, populating either the subsequently long-lived 1Lb state or the 1πσ* state localised along the N-H coordinate, which exhibits a lifetime on the order of 1 ps. In the case of 5-hydroxyindole, we conclude that the 1πσ* state localised along the O-H coordinate plays little or no role in the relaxation dynamics at the two excitation wavelengths studied.
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33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
31.15.ae Electronic structure and bonding characteristics
31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods
33.60.+q Photoelectron spectra
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