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14 Oct 2011

Volume 135, Issue 14, Articles (14xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 144201 (2011); http://dx.doi.org/10.1063/1.3640418 (14 pages)

Andrew J. Pell, Guido Pintacuda, and Lyndon Emsley
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Communication: Multicanonical entropy-like solution of statistical temperature weighted histogram analysis method

Leandro G. Rizzi and Nelson A. Alves

J. Chem. Phys. 135, 141101 (2011); http://dx.doi.org/10.1063/1.3651627 (4 pages)

Online Publication Date: 10 October 2011

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A multicanonical update relation for calculation of the microcanonical entropy Smicro(E) by means of the estimates of the inverse statistical temperature βS, is proposed. This inverse temperature is obtained from the recently proposed statistical temperature weighted histogram analysis method (ST-WHAM). The performance of ST-WHAM concerning the computation of Smicro(E) from canonical measures, in a model with strong free-energy barriers, is also discussed on the basis of comparison with the multicanonical simulation estimates.
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05.70.Ce Thermodynamic functions and equations of state
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Communication: Enhancement of dopant dependent x-ray photoelectron spectroscopy peak shifts of Si by surface photovoltage

Hikmet Sezen and Sefik Suzer

J. Chem. Phys. 135, 141102 (2011); http://dx.doi.org/10.1063/1.3652964 (4 pages) | Cited 1 time

Online Publication Date: 10 October 2011

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Binding energies measured by x-ray photoelectron spectroscopy (XPS) are influenced by doping, since electrons are transferred to (p-type) and from (n-type) samples when they are introduced into the spectrometer, or brought into contact with each other (p-n junction). We show that the barely measurable Si2p binding energy difference between moderately doped n- and p-Si samples can be enhanced by photoillumination, due to reduction in surface band-bending, which otherwise screens this difference. Similar effects are also measured for samples containing oxide layers, since the band-bending at the buried oxide-Si interfaces is manifest as photovoltage shifts, although XPS does not probe the interface directly. The corresponding shift for the oxide layer of the p-Si is almost twice that of without the oxide, whereas no measurable shifts are observable for the oxide of the n-Si. These results are all related to band-bending effects and are vital in design and performance of photovoltaics and other related systems.
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73.40.Lq Other semiconductor-to-semiconductor contacts, p-n junctions, and heterojunctions
79.60.Bm Clean metal, semiconductor, and insulator surfaces
72.40.+w Photoconduction and photovoltaic effects
71.15.Nc Total energy and cohesive energy calculations
61.72.U- Doping and impurity implantation
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Communication: Quantitative Fourier-transform infrared data for competitive loading of small cages during all-vapor instantaneous formation of gas-hydrate aerosols

Nevin Uras-Aytemiz, I. Abrrey Monreal, and J. Paul Devlin

J. Chem. Phys. 135, 141103 (2011); http://dx.doi.org/10.1063/1.3652756 (3 pages)

Online Publication Date: 11 October 2011

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A simple method has been developed for the measurement of high quality FTIR spectra of aerosols of gas-hydrate nanoparticles. The application of this method enables quantitative observation of gas hydrates that form on subsecond timescales using our all-vapor approach that includes an ether catalyst rather than high pressures to promote hydrate formation. The sampling method is versatile allowing routine studies at temperatures ranging from 120 to 210 K of either a single gas or the competitive uptake of different gas molecules in small cages of the hydrates. The present study emphasizes hydrate aerosols formed by pulsing vapor mixtures into a cold chamber held at 160 or 180 K. We emphasize aerosol spectra from 6 scans recorded an average of 8 s after “instantaneous” hydrate formation as well as of the gas hydrates as they evolve with time. Quantitative aerosol data are reported and analyzed for single small-cage guests and for mixed hydrates of CO2, CH4, C2H2, N2O, N2, and air. The approach, combined with the instant formation of gas hydrates from vapors only, offers promise with respect to optimization of methods for the formation and control of gas hydrates.
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82.70.Rr Aerosols and foams
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
33.20.Ea Infrared spectra
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Communication: Folding of glycosylated proteins under confinement

Dalit Shental-Bechor and Yaakov Levy

J. Chem. Phys. 135, 141104 (2011); http://dx.doi.org/10.1063/1.3650700 (4 pages)

Online Publication Date: 11 October 2011

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Conjugating flexible polymers (such as oligosaccharides) to proteins or confining a protein in a restricted volume often increases protein thermal stability. In this communication, we investigate the interplay between conjugation and confinement which is not trivial as the magnitude and the mechanism of stabilization are different in each instance. Using coarse-grained computational approach the folding biophysics is studied when the protein is placed in a sphere of variable radius and is conjugated to 0–6 mono- or penta-saccharides. We observe a synergistic effect on thermal stability when short oligosaccharides are attached and the modified protein is confined in a small cage. However, when large oligosaccharides are added, a conflict between confinement and glycosylation arises as the stabilizing effect of the cage is dramatically reduced and it is almost impossible to further stabilize the protein beyond the mild stabilization induced by the sugars.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.14.E- Proteins
36.20.Hb Configuration (bonds, dimensions)
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Communication: Consistent picture of lateral subdiffusion in lipid bilayers: Molecular dynamics simulation and exact results

Gerald R. Kneller, Krzysztof Baczynski, and Marta Pasenkiewicz-Gierula

J. Chem. Phys. 135, 141105 (2011); http://dx.doi.org/10.1063/1.3651800 (4 pages)

Online Publication Date: 12 October 2011

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This communication presents a molecular dynamics simulation study of a bilayer consisting of 128 dioleoyl-sn-glycero-3-phosphocholine molecules, which focusses on the center-of-mass diffusion of the lipid molecules parallel to the membrane plane. The analysis of the simulation results is performed within the framework of the generalized Langevin equation and leads to a consistent picture of subdiffusion. The mean square displacement of the lipid molecules evolves as ∝ tα, with α between 0.5 and 0.6, and the fractional diffusion coefficient is close to the experimental value for a similar system obtained by fluorescence correlation spectroscopy. We show that the long-time tails of the lateral velocity autocorrelation function and the associated memory function agree well with exact results which have been recently derived by asymptotic analysis [G. Kneller, J. Chem. Phys. 134, 224106 (2011)10.1063/1.3598483]. In this context, we define characteristic time scales for these two quantities.
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87.16.dj Dynamics and fluctuations
87.10.Tf Molecular dynamics simulation
87.15.ap Molecular dynamics simulation
87.15.Vv Diffusion
87.16.dp Transport, including channels, pores, and lateral diffusion
87.14.Cc Lipids
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Communication: Lateral phase separation of mixed polymer brushes physisorbed on planar substrates

Reid C. Van Lehn and Alfredo Alexander-Katz

J. Chem. Phys. 135, 141106 (2011); http://dx.doi.org/10.1063/1.3653937 (4 pages) | Cited 1 time

Online Publication Date: 13 October 2011

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Here, we present a new method to model lateral phase separation in mixed polymer brushes physisorbed to a planar surface with mobile grafting points. The model is based on a local mean field theory that combines a Flory-Huggins approximation for interaction enthalpies with an Alexander-de Gennes brush entropy contribution. Using Monte Carlo sampling, the application of these two interactions to a lattice model yields a range of phase behavior consistent with previous theoretical and experimental work. This model will be useful for predicting mixed polymer brush morphologies on planar surfaces and in principle can be extended to other geometries (e.g., spheres) and polymer systems.
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68.43.-h Chemisorption/physisorption: adsorbates on surfaces
64.75.Ef Mixing
64.75.Va Phase separation and segregation in polymer blends/polymeric solutions
61.41.+e Polymers, elastomers, and plastics
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Communication: Partial polarization transfer for single-scan spectroscopy and imaging

Valerie A. Norton and Daniel P. Weitekamp

J. Chem. Phys. 135, 141107 (2011); http://dx.doi.org/10.1063/1.3652965 (4 pages)

Online Publication Date: 13 October 2011

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A method is presented to partially transfer nuclear spin polarization from one isotope S to another isotope I by the way of heteronuclear spin couplings, while minimizing the loss of spin order to other degrees of freedom. The desired I spin polarization to be detected is a design parameter, while the sequence of pulses at the two Larmor frequencies is optimized to store the greatest unused S spin longitudinal polarization for subsequent use. The unitary evolution for the case of INS spin systems illustrates the potentially ideal efficiency of this strategy, which is of particular interest when the spin-lattice relaxation time of S greatly exceeds that of I. Explicit timing and pulses are tabulated for the cases for which M ⩽ 10 partial transfers each result in equal final polarization of 1/M or more compared to the final I polarization expected in a single transfer for N = 1, 2, or 3 I spins. Advantages for the ratiometric study of reacting molecules and hyperpolarized initial conditions are outlined.
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33.25.+k Nuclear resonance and relaxation
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Communication: State-to-state quantum dynamics study of the OH + CO → H + CO2 reaction in full dimensions (J = 0)

Shu Liu, Xin Xu, and Dong H. Zhang

J. Chem. Phys. 135, 141108 (2011); http://dx.doi.org/10.1063/1.3653787 (4 pages) | Cited 4 times

Online Publication Date: 14 October 2011

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A full dimensional state-to-state quantum dynamics study is carried out for the prototypical complex-formation OH + CO → H + CO2 reaction in the ground rovibrational initial state on the Lakin-Troya-Schatz-Harding potential energy surface by using the reactant-product decoupling method. With three heavy atoms and deep wells on the reaction path, the reaction represents a huge challenge for accurate quantum dynamics study. This state-to-state calculation is the first such a study on a four-atom reaction other than the H2 + OH ↔ H2O + H and its isotope analogies. The product CO2 vibrational and rotational state distributions, and product energy partitioning information are presented for ground initial rovibrational state with the total angular momentum J = 0.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Bc State selected dynamics and product distribution
82.20.Hf Product distribution
82.20.Kh Potential energy surfaces for chemical reactions
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The hierarchical expansion of the kinetic energy operator in curvilinear coordinates extended to the vibrational configuration interaction method

D. Strobusch and Ch. Scheurer

J. Chem. Phys. 135, 144101 (2011); http://dx.doi.org/10.1063/1.3646514 (6 pages)

Online Publication Date: 10 October 2011

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The hierarchical expansion of the kinetic energy operator in curvilinear coordinates presented earlier for the vibrational self-consistent field technique is extended to the vibrational configuration interaction (VCI) method. The high accuracy of the modified VCI method is demonstrated by computing first excitation energies of the H2O2 molecule using an analytic potential (PCPSDE) and showing convergence to accurate results from full dimensional discrete variable representation calculations.
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31.15.vq Electron correlation calculations for polyatomic molecules
33.20.Tp Vibrational analysis
31.15.xr Self-consistent-field methods

Surface hopping with Ehrenfest excited potential

Sean A. Fischer, Craig T. Chapman, and Xiaosong Li

J. Chem. Phys. 135, 144102 (2011); http://dx.doi.org/10.1063/1.3646920 (8 pages)

Online Publication Date: 10 October 2011

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Given the exponentially scaling cost of full quantum calculations, approximations need to be employed for the simulation of the time evolution of chemical systems. We present a modified version of surface hopping that has the potential to treat larger systems. This is accomplished through an Ehrenfest-like treatment of the excited states, thereby reducing the dynamics to transitions between the ground state and a mean-field excited state. A simplified description of the excited states is achieved, while still allowing for an accurate description of disparate reaction channels. We test our mean-field approximation for the excited states on a series of model problems. Results are compared to the standard surface hopping procedure, with its explicit treatment of all excited states, and the traditional Ehrenfest approach, with its averaging together of all states.
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31.50.Df Potential energy surfaces for excited electronic states
31.50.Bc Potential energy surfaces for ground electronic states

Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: Study of the optical and magnetic properties of diazines in water

Vinícius Manzoni, Marcelo L. Lyra, Kaline Coutinho, and Sylvio Canuto

J. Chem. Phys. 135, 144103 (2011); http://dx.doi.org/10.1063/1.3644894 (10 pages)

Online Publication Date: 10 October 2011

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A combination of the polarizable continuum model (PCM) and the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology, PCM-MM/QM, is used to include the solute electronic polarization and then study the solvent effects on the low-lying n→π* excitation energy and the 15N nuclear magnetic shielding of pyrazine and pyridazine in aqueous environment. The results obtained with PCM-MM/QM are compared with two other procedures, i.e., the conventional PCM and the iterative and sequential QM/MM (I-QM/MM). The QM calculations are made using density functional theory in the three procedures. For the excitation energies, the time-dependent B3LYP/6-311+G(d) model is used. For the magnetic shielding, the B3LYP/aug-pcS2(N)/pcS2(C,O,H) is used with the gauge-including atomic orbitals. In both cases, i.e., PCM-MM/QM and I-QM/MM, that use a discrete model of the solvent, the solute is surrounded by a first shell of explicit water molecules embedded by an electrostatic field of point charges for the outer shells. The best results are obtained including 28 explicit water molecules for the spectral calculations and 9 explicit water molecules for the magnetic shielding. Using the PCM-MM/QM methodology the results for the n→π* excitation energies of pyridazine and pyrazine are 32 070 ± 80 cm−1 and 32 675 ± 60 cm−1, respectively, in good agreement with the corresponding I-MM/QM results of 32 540 ± 80 cm−1 and 32 710 ± 60 cm−1 and the experimental results of 33 450–33 580 cm−1 and 32 700–33 300 cm−1. For the 15N magnetic shielding, the corresponding numbers for the gas-water shifts obtained with PCM-MM/QM are 47.4 ± 1.3 ppm for pyridazine and 19.7 ± 1.1 ppm for pyrazine, compared with the I-QM/MM values of 53.4 ± 1.3 ppm and 19.5 ± 1.2 ppm and the experimental results of 42–54 ppm and 17–22 ppm, respectively. The agreement between the two procedures is found to be very good and both are in agreement with the experimental values. PCM-MM/QM approach gives a good solute polarization and could be considered in obtaining reliable results within the expected QM/MM accuracy. With this electronic polarization, the solvent effects on the electronic absorption spectra and the 15N magnetic shielding of the diazines in water are well described by using only an electrostatic approximation. Finally, it is remarked that the experimental and theoretical results suggest that the 15N nuclear magnetic shielding of any diazine has a clear dependence with the solvent polarity but not directly with the solute-solvent hydrogen bonds.
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31.70.Dk Environmental and solvent effects
31.15.E- Density-functional theory
31.30.-i Corrections to electronic structure
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Robust conductance of dumbbell molecular junctions with fullerene anchoring groups

Troels Markussen, Mikkel Settnes, and Kristian S. Thygesen

J. Chem. Phys. 135, 144104 (2011); http://dx.doi.org/10.1063/1.3646510 (6 pages)

Online Publication Date: 11 October 2011

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The conductance of a molecular wire connected to metallic electrodes is known to be sensitive to the atomic structure of the molecule-metal contact. This contact is to a large extent determined by the anchoring group linking the molecular wire to the metal. It has been found experimentally that a dumbbell construction with C60 molecules acting as anchors yields more well-defined conductances as compared to the widely used thiol anchoring groups. Here, we use density functional theory to investigate the electronic properties of this dumbbell construction. The conductance is found to be stable against variations in the detailed bonding geometry and in good agreement with the experimental value of G = 3×10−4 G0. Electron tunneling across the molecular bridge occurs via the lowest unoccupied orbitals of C60 which are pinned close to the Fermi energy due to partial charge transfer. Our findings support the original motivation to achieve conductance values more stable towards changes in the structure of the molecule-metal contact leading to larger reproducibility in experiments.
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73.40.Ns Metal-nonmetal contacts
73.40.Gk Tunneling

An overlap fitted chain of spheres exchange method

Róbert Izsák and Frank Neese

J. Chem. Phys. 135, 144105 (2011); http://dx.doi.org/10.1063/1.3646921 (11 pages)

Online Publication Date: 11 October 2011

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The “chain of spheres” (COS) algorithm, as part of the RIJCOSX SCF procedure, approximates the exchange term by performing analytic integration with respect to the coordinates of only one of the two electrons, whereas for the remaining coordinates, integration is carried out numerically. In the present work, we attempt to enhance the efficiency of the method by minimizing numerical errors in the COS procedure. The main idea is based on the work of Friesner and consists of finding a fitting matrix, Q, which leads the numerical and analytically evaluated overlap matrices to coincide. Using Q, the evaluation of exchange integrals can indeed be improved. Improved results and timings are obtained with the present default grid setup for both single point calculations and geometry optimizations. The fitting procedure results in a reduction of grid sizes necessary for achieving chemical accuracy. We demonstrate this by testing a number of grids and comparing results to the fully analytic and the earlier COS approximations. This turns out to be favourable for total and reaction energies, for which chemical accuracy can now be reached with a corresponding ∼30% speedup over the original RIJCOSX procedure for single point energies. Results are slightly less favourable for the accuracy of geometry optimizations, but the procedure is still shown to yield geometries with errors well below the method inherent errors of the employed theoretical framework.
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31.15.xr Self-consistent-field methods
33.15.Bh General molecular conformation and symmetry; stereochemistry

The effects of shape and flexibility on bio-engineered fd-virus suspensions

M. Dennison, M. Dijkstra, and R. van Roij

J. Chem. Phys. 135, 144106 (2011); http://dx.doi.org/10.1063/1.3646951 (13 pages)

Online Publication Date: 11 October 2011

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We present a theoretical model to describe binary mixtures of semi-flexible rods, applied here to fd-virus suspensions. We investigate the effects of rod stiffness on both monodisperse and binary systems, studying thick-thin and long-short mixtures. For monodisperse systems, we find that fd-virus particles have to be made extremely stiff to even approach the behavior of rigid rods. For thick-thin mixtures, we find increasingly rich phase behavior as the rods are either made more flexible or if their diameter ratio is increased. For long-short rod mixtures we find that the phase behavior is controlled by the relative stiffness of the rods, with increasing the stiffness of the long rods or decreasing that of the short rods resulting in richer phase behavior. We also calculate the state point dependent effective shape of the rods. The flexible rods studied here always behave as shorter, thicker rigid rods, but with an effective shape that varies widely throughout the phase diagrams, and plays a key role in determining phase behavior.
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87.17.Rt Cell adhesion and cell mechanics
82.70.Kj Emulsions and suspensions

Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation

Dejun Si and Hui Li

J. Chem. Phys. 135, 144107 (2011); http://dx.doi.org/10.1063/1.3649947 (7 pages)

Online Publication Date: 12 October 2011

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The analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculations are derived and implemented for spin-restricted closed shell (RMP2), Z-averaged spin-restricted open shell (ZAPT2), and spin-unrestricted open shell (UMP2) cases. Using these methods, the geometries of the S0 ground state and the T1 state of three nucleobase pairs (guanine-cytosine, adenine-thymine, and adenine-uracil) in the gas phase and aqueous solution phase are optimized. It is found that in both the gas phase and the aqueous solution phase the hydrogen bonds in the T1 state pairs are weakened by ∼1 kcal/mol as compared to those in the S0 state pairs.
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31.15.xp Perturbation theory
31.50.Bc Potential energy surfaces for ground electronic states
31.50.Df Potential energy surfaces for excited electronic states
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Fm Bond strengths, dissociation energies

Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution

Xuehui Chen, Yunxiang Sun, Xiongbo An, and Dengming Ming

J. Chem. Phys. 135, 144108 (2011); http://dx.doi.org/10.1063/1.3647314 (10 pages)

Online Publication Date: 12 October 2011

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Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78 300 atoms) and to F-actin filament structures of up to 39-mer, 228 813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another.
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87.15.hp Conformational changes
87.14.E- Proteins
87.15.B- Structure of biomolecules

A new Monte Carlo method for getting the density of states of atomic cluster systems

J.-M. Soudan, M. Basire, J.-M. Mestdagh, and C. Angelié

J. Chem. Phys. 135, 144109 (2011); http://dx.doi.org/10.1063/1.3647333 (15 pages) | Cited 1 time

Online Publication Date: 12 October 2011

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A novel Monte Carlo flat histogram algorithm is proposed to get the classical density of states in terms of the potential energy, g(Ep), for systems with continuous variables such as atomic clusters. It aims at avoiding the long iterative process of the Wang-Landau method and controlling carefully the convergence, but keeping the ability to overcome energy barriers. Our algorithm is based on a preliminary mapping in a series of points (called a σ-mapping), obtained by a two-parameter local probing of g(Ep), and it converges in only two subsequent reweighting iterations on large intervals. The method is illustrated on the model system of a 432 atom cluster bound by a Rydberg type potential. Convergence properties are first examined in detail, particularly in the phase transition zone. We get g(Ep) varying by a factor 103700 over the energy range [0.01 < Ep < 6000 eV], covered by only eight overlapping intervals. Canonical quantities are derived, such as the internal energy U(T) and the heat capacity CV(T). This reveals the solid to liquid phase transition, lying in our conditions at the triple point. This phase transition is further studied by computing a Lindemann-Berry index, the atomic cluster density n(r), and the pressure, demonstrating the progressive surface melting at this triple point. Some limited results are also given for 1224 and 4044 atom clusters.
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71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations
71.20.-b Electron density of states and band structure of crystalline solids
73.21.-b Electron states and collective excitations in multilayers, quantum wells, mesoscopic, and nanoscale systems
71.70.Di Landau levels
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Model for the fast estimation of basis set superposition error in biomolecular systems

John C. Faver, Zheng Zheng, and Kenneth M. Merz, Jr.

J. Chem. Phys. 135, 144110 (2011); http://dx.doi.org/10.1063/1.3641894 (8 pages) | Cited 2 times

Online Publication Date: 12 October 2011

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Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds.
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87.15.R- Reactions and kinetics
87.14.E- Proteins

Ab initio investigation of titanium hydroxide isomers and their cations, TiOH0, + and HTiO0, +

Evangelos Miliordos, James F. Harrison, and Katharine L. C. Hunt

J. Chem. Phys. 135, 144111 (2011); http://dx.doi.org/10.1063/1.3644963 (13 pages)

Online Publication Date: 13 October 2011

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We studied the electronic and geometrical structure of the [Ti, O, H]0, + species, using large basis sets and both single-reference coupled cluster and multireference configuration interaction methodologies. The electronic structure of HTiO0, + is interpreted qualitatively in terms of a hydrogen atom bonding to TiO0, +, while the structure of TiOH0, + is interpreted in terms of Ti+, 2 + bonding to OH−. Potential energy profiles are reported as functions of the Ti–OH and H–TiO bond lengths, and of the H–Ti–O angle. For a total of 33 stationary points on the potential energy surfaces, we report absolute energies, geometries, and harmonic frequencies. For the neutral species, dipole moments are also given.
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31.15.ae Electronic structure and bonding characteristics
31.15.bw Coupled-cluster theory
31.15.V- Electron correlation calculations for atoms, ions and molecules
33.15.Fm Bond strengths, dissociation energies
31.50.-x Potential energy surfaces
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

Dynamics of interatomic Coulombic decay in quantum dots

Annika Bande, Kirill Gokhberg, and Lorenz S. Cederbaum

J. Chem. Phys. 135, 144112 (2011); http://dx.doi.org/10.1063/1.3646205 (13 pages)

Online Publication Date: 13 October 2011

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In this work we demonstrate that the interatomic Coulombic decay (ICD), an ultrafast electron relaxation process known for atoms and molecules, is possible in general binding potentials. We used the multiconfiguration time-dependent Hartree method for fermions to study ICD in real time in a two-electron model system of two potential wells. Two decay channels were identified and analyzed by using the box stabilization analysis as well as by evaluating the autocorrelation function and measuring the outgoing electron flux during time-propagations. The total and partial ICD widths of an excited state localized in one potential well as a function of the distance between the two potentials was obtained. Finally, we discuss the results with a view to a possible application of ICD in quantum dot technology.
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68.65.Hb Quantum dots (patterned in quantum wells)
73.21.La Quantum dots

Effective Hamiltonian for femtosecond vibrational dynamics

George L. Barnes and Michael E. Kellman

J. Chem. Phys. 135, 144113 (2011); http://dx.doi.org/10.1063/1.3650481 (5 pages) | Cited 1 time

Online Publication Date: 13 October 2011

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Time propagation of zero-order states of an effective spectroscopic Hamiltonian is tested against femtosecond time dependent dynamics of adiabatic wavepackets evolving on a model potential energy surface for two coupled modes of the radical HO2 with multiple potential wells and above barrier motion. A generalized Hamiltonian which breaks the usual conserved polyad action by including extra resonance couplings (V2:1 and V3:1) successfully describes the time evolution after the further addition of two “ultrafast” couplings. These new couplings are a nonresonant coupling a1a2+a1†a2† and a resonant coupling V1:1 that functions as an ultrafast term because the system is far from 1:1 frequency resonance.
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33.20.Tp Vibrational analysis
31.50.Bc Potential energy surfaces for ground electronic states
33.15.Mt Rotation, vibration, and vibration-rotation constants

All-atom modeling of anisotropic atomic fluctuations in protein crystal structures

Jeffrey Hafner and Wenjun Zheng

J. Chem. Phys. 135, 144114 (2011); http://dx.doi.org/10.1063/1.3646312 (10 pages)

Online Publication Date: 13 October 2011

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The accurate modeling of protein dynamics in crystalline states is essential for the development of computational techniques for simulating protein dynamics under physiological conditions. Following a previous coarse-grained modeling study of atomic fluctuations in protein crystal structures, we have refined our modeling with all-atom representation and force field. We have calculated the anisotropic atomic fluctuations of a protein structure interacting with its crystalline environment either explicitly (by including neighboring proteins into modeling) or implicitly (by adding harmonic restraints to surface atoms involved in crystal contacts). The modeling results are assessed in comparison with the experimental anisotropic displacement parameters (ADP) determined by X-ray crystallography. For a list of 40 high-resolution protein crystal structures, we have found that the optimal modeling of ADPs is achieved when the protein-environment interactions are much weaker than the internal interactions within a protein structure. Therefore, the intrinsic dynamics of a protein structure is only weakly perturbed by crystal packing. We have also found no noticeable improvement in the accuracy of ADP modeling by using all-atom over coarse-grained representation and force field, which justifies the use of coarse-grained modeling to investigate protein dynamics with both efficiency and accuracy.
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87.14.E- Proteins
87.15.B- Structure of biomolecules
87.15.H- Dynamics of biomolecules

Multidimensional treatment of stochastic solvent dynamics in photoinduced proton-coupled electron transfer processes: Sequential, concerted, and complex branching mechanisms

Alexander V. Soudackov, Anirban Hazra, and Sharon Hammes-Schiffer

J. Chem. Phys. 135, 144115 (2011); http://dx.doi.org/10.1063/1.3651083 (14 pages)

Online Publication Date: 13 October 2011

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A theoretical approach for the multidimensional treatment of photoinduced proton-coupled electron transfer (PCET) processes in solution is presented. This methodology is based on the multistate continuum theory with an arbitrary number of diabatic electronic states representing the relevant charge distributions in a general PCET system. The active electrons and transferring proton(s) are treated quantum mechanically, and the electron-proton vibronic free energy surfaces are represented as functions of multiple scalar solvent coordinates corresponding to the single electron and proton transfer reactions involved in the PCET process. A dynamical formulation of the dielectric continuum theory is used to derive a set of coupled generalized Langevin equations of motion describing the time evolution of these collective solvent coordinates. The parameters in the Langevin equations depend on the solvent properties, such as the dielectric constants, relaxation time, and molecular moment of inertia, as well as the solute properties. The dynamics of selected intramolecular nuclear coordinates, such as the proton donor-acceptor distance or a torsional angle within the PCET complex, may also be included in this formulation. A surface hopping method in conjunction with the Langevin equations of motion is used to simulate the nonadiabatic dynamics on the multidimensional electron-proton vibronic free energy surfaces following photoexcitation. This theoretical treatment enables the description of both sequential and concerted mechanisms, as well as more complex processes involving a combination of these mechanisms. The application of this methodology to a series of model systems corresponding to collinear and orthogonal PCET illustrates fundamental aspects of these different mechanisms and elucidates the significance of proton vibrational relaxation and nonequilibrium solvent dynamics.
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34.70.+e Charge transfer
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.70.Dk Environmental and solvent effects

An efficient local coupled cluster method for accurate thermochemistry of large systems

Hans-Joachim Werner and Martin Schütz

J. Chem. Phys. 135, 144116 (2011); http://dx.doi.org/10.1063/1.3641642 (15 pages)

Online Publication Date: 13 October 2011

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An efficient local coupled cluster method with single and double excitation operators and perturbative treatment of triple excitations [DF-LCCSD(T)] is described. All required two-electron integrals are evaluated using density fitting approximations. These have a negligible effect on the accuracy but reduce the computational effort by 1–2 orders of magnitude, as compared to standard integral-direct methods. Excitations are restricted to local subsets of non-orthogonal virtual orbitals (domain approximation). Depending on distance criteria, the correlated electron pairs are classified into strong, close, weak, and very distant pairs. Only strong pairs, which typically account for more than 90% of the correlation energy, are optimized in the LCCSD treatment. The remaining close and weak pairs are approximated by LMP2 (local second-order Møller-Plesset perturbation theory); very distant pairs are neglected. It is demonstrated that the accuracy of this scheme can be significantly improved by including the close pair LMP2 amplitudes in the LCCSD equations, as well as in the perturbative treatment of the triples excitations. Using this ansatz for the wavefunction, the evaluation and transformation of the two-electron integrals scale cubically with molecular size. If local density fitting approximations are activated, this is reduced to linear scaling. The LCCSD iterations scale quadratically, but linear scaling can be achieved by neglecting some terms involving contractions of single excitations. The accuracy and efficiency of the method is systematically tested using various approximations, and calculations for molecules with up to 90 atoms and 2636 basis functions are presented.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry

An explicitly correlated local coupled cluster method for calculations of large molecules close to the basis set limit

Thomas B. Adler and Hans-Joachim Werner

J. Chem. Phys. 135, 144117 (2011); http://dx.doi.org/10.1063/1.3647565 (16 pages)

Online Publication Date: 13 October 2011

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A new explicitly correlated local coupled-cluster method with single and double excitations and a perturbative treatment of triple excitations [DF-LCCSD(T0)-F12x (x = a,b)] is presented. By means of truncating the virtual orbital space to pair-specific local domains (domain approximation) and a simplified treatment of close, weak and distant pairs using LMP2-F12 (pair approximation) the scaling of the computational cost with molecular size is strongly reduced. The basis set incompleteness errors as well as the errors due to the domain approximation are largely eliminated by the explicitly correlated terms. All integrals are computed using efficient density fitting (DF) approximations. The accuracy of the method is investigated for 52 reactions involving medium size molecules. A comparison of DF-LCCSD(T0)-F12x reaction energies with canonical CCSD(T)-F12x calculations shows that the errors introduced by the domain approximation are indeed very small. Care must be taken to keep the errors due to the additional pair approximation equally small, and appropriate distance criteria are recommended. Using these parameters, the root mean square (RMS) deviations of DF-LCCSD(T0)-F12a calculations with triple-ζ basis sets from estimated CCSD(T) complete basis set (CBS) limits and experimental data amount to only 1.5 kJ mol−1 and 2.9 kJ mol−1, respectively. For comparison, the RMS deviation of the CCSD(T)/CBS values from the experimental values amounts to 3.0 kJ mol−1. The potential of the method is demonstrated for five reactions of biochemical or pharmacological interest which include molecules with up to 61 atoms. These calculations show that molecules of this size can now be treated routinely and yield results that are close to the CCSD(T) complete basis set limits.
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36.20.Kd Electronic structure and spectra
31.15.xp Perturbation theory
31.15.bw Coupled-cluster theory
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