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14 Feb 2013

Volume 138, Issue 6, Articles (06xxxx)

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J. Chem. Phys. 138, 064701 (2013); http://dx.doi.org/10.1063/1.4789807 (6 pages)

Shengfeng Cheng and Gary S. Grest
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Communication: Designed diamond ground state via optimized isotropic monotonic pair potentials

É. Marcotte, F. H. Stillinger, and Salvatore Torquato

J. Chem. Phys. 138, 061101 (2013); http://dx.doi.org/10.1063/1.4790634 (4 pages)

Online Publication Date: 8 February 2013

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We apply inverse statistical-mechanical methods to find a simple family of optimized isotropic, monotonic pair potentials (that may be experimentally realizable) whose classical ground state is the diamond crystal for the widest possible pressure range, subject to certain constraints (e.g., desirable phonon spectra). We also ascertain the ground-state phase diagram for a specific optimized potential to show that other crystal structures arise for pressures outside the diamond stability range. Cooling disordered configurations interacting with our optimized potential to absolute zero frequently leads to the desired diamond crystal ground state, revealing that the capture basin for the global energy minimum is large and broad relative to the local energy minima basins.
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81.30.Dz Phase diagrams of other materials
61.66.Fn Inorganic compounds
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Communication: Simulated tempering with fast on-the-fly weight determination

Phuong H. Nguyen, Yuko Okamoto, and Philippe Derreumaux

J. Chem. Phys. 138, 061102 (2013); http://dx.doi.org/10.1063/1.4792046 (4 pages)

Online Publication Date: 12 February 2013

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We propose an efficient method to enhance sampling in computer simulations by combining the simulated tempering algorithm with a fast on-the-fly weight determination scheme. The weights are self-updated via a trapezoid rule during the simulated tempering simulation. With our proposed scheme, simulated tempering requires neither prior trial simulations nor complicated update schemes. The advantage of our method over replica exchange molecular dynamics has been demonstrated with the study of the folding of the 20-residue alanine peptide and the aggregation of a trimer formed by the Alzheimer's peptide fragment Aβ16−22.
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31.15.xv Molecular dynamics and other numerical methods
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Communication: Van der Waals corrections for an improved structural description of telluride based materials

M. Micoulaut

J. Chem. Phys. 138, 061103 (2013); http://dx.doi.org/10.1063/1.4792195 (4 pages)

Online Publication Date: 12 February 2013

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Density functional theory (DFT), using the generalized gradient approximation, fails to reproduce the structure of liquid tellurides, which manifests by an overestimation of the interatomic bond distances. Here, we take into account dispersion forces in a semi-empirical way and apply such DFT simulations to liquid Ge15Te85. Substantial improvement of the simulated structure factor and pair distribution function is found, together with a change in the diffusion constant. A detailed analysis shows that such dispersion forces strongly affect the local geometry and first coordination shell of the atoms, whereas angular distributions remain unchanged.
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61.20.Gy Theory and models of liquid structure
61.25.-f Studies of specific liquid structures
66.10.C- Diffusion and thermal diffusion
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Communication: X-ray excited optical luminescence from TbCl3 at the giant resonance of terbium

F. Heigl, A. Jürgensen, X.-T. Zhou, Y.-F. Hu, L. Zuin, and T. K. Sham

J. Chem. Phys. 138, 061104 (2013); http://dx.doi.org/10.1063/1.4792043 (4 pages)

Online Publication Date: 13 February 2013

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We have studied the optical recombination channels of TbCl3 using x-ray excited optical luminescence at the N4,5 absorption edge of Tb (giant resonance) in both the energy and time domain. The luminescence exhibits a relatively fast 5D3, and a slow 5D4 decay channel in the blue and green, respectively. The rather short lifetime of the 5D3 state indicates that the decay is mainly driven by Tb-Tb ion interaction via non-radiative energy transfer (cross-relaxation). At the giant resonance the X-ray Absorption Near Edge Structure (XANES) recorded using partial photoluminescence yield is inverted. In the pre-edge region the contrast of the spectral feature is significantly better in optical XANES than in total electron yield. Changes in the intensity of 5D3–7F5 (544 nm) and 5D4–7F6 (382 nm) optical transitions as the excitation energy is tuned across the giant resonance are also noted. The results provide detailed insight into the dynamics of the optical recombination channels and an alternative method to obtain high sensitivity, high energy resolution XANES at the giant resonance of light emitting rare-earth materials.
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78.55.Hx Other solid inorganic materials
78.70.Dm X-ray absorption spectra
71.35.-y Excitons and related phenomena
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back to top Theoretical Methods and Algorithms

Calculating excited state properties using Kohn-Sham density functional theory

Magnus W. D. Hanson-Heine, Michael W. George, and Nicholas A. Besley

J. Chem. Phys. 138, 064101 (2013); http://dx.doi.org/10.1063/1.4789813 (8 pages)

Online Publication Date: 8 February 2013

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The accuracy of excited states calculated with Kohn-Sham density functional theory using the maximum overlap method has been assessed for the calculation of adiabatic excitation energies, excited state structures, and excited state harmonic and anharmonic vibrational frequencies for open-shell singlet excited states. The computed Kohn-Sham adiabatic excitation energies are improved significantly by post self-consistent field spin-purification, but remain too low compared with experiment with a larger error than time-dependent density functional theory. Excited state structures and vibrational frequencies are also improved by spin-purification. The structures show a comparable accuracy to time-dependent density functional theory, while the harmonic vibrational frequencies are found to be more accurate for the majority of vibrational modes. The computed harmonic vibrational frequencies are also further improved by perturbative anharmonic corrections, suggesting a good description of the potential energy surface. Overall, excited state Kohn-Sham density functional theory is shown to provide an efficient method for the calculation of excited state structures and vibrational frequencies in open-shell singlet systems and provides a promising technique that can be applied to study large systems.
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33.20.Tp Vibrational analysis
31.15.E- Density-functional theory
31.50.Df Potential energy surfaces for excited electronic states

Reduced atomic pair-interaction design (RAPID) model for simulations of proteins

Boris Ni and Andrij Baumketner

J. Chem. Phys. 138, 064102 (2013); http://dx.doi.org/10.1063/1.4790160 (12 pages)

Online Publication Date: 8 February 2013

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Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.
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87.15.A- Theory, modeling, and computer simulation
87.15.B- Structure of biomolecules
87.15.hm Folding dynamics
36.20.Ey Conformation (statistics and dynamics)
36.20.Fz Constitution (chains and sequences)
87.14.E- Proteins

Amino-acid-dependent main-chain torsion-energy terms for protein systems

Yoshitake Sakae and Yuko Okamoto

J. Chem. Phys. 138, 064103 (2013); http://dx.doi.org/10.1063/1.4774159 (8 pages)

Online Publication Date: 11 February 2013

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Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters for main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for ψ (N-Cα-C-N) and ζ (Cβ-Cα-C-N) angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of α-helical and β-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field.
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87.14.E- Proteins
33.20.Tp Vibrational analysis
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An efficient method for calculating dynamical hyperpolarizabilities using real-time time-dependent density functional theory

Feizhi Ding, Benjamin E. Van Kuiken, Bruce E. Eichinger, and Xiaosong Li

J. Chem. Phys. 138, 064104 (2013); http://dx.doi.org/10.1063/1.4790583 (9 pages) | Cited 1 time

Online Publication Date: 13 February 2013

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In this paper we present a time-domain time-dependent density functional theory (TDDFT) approach to calculate frequency-dependent polarizability and hyperpolarizabilities. In this approach, the electronic degrees of freedom are propagated within the density matrix based TDDFT framework using the efficient modified midpoint and unitary transformation algorithm. We use monochromatic waves as external perturbations and apply the finite field method to extract various orders of the time-dependent dipole moment. By fitting each order of time-dependent dipole to sinusoidal waves with harmonic frequencies, one can obtain the corresponding (hyper)polarizability tensors. This approach avoids explicit Fourier transform and therefore does not require long simulation time. The method is illustrated with application to the optically active organic molecule para-nitroaniline, of which the frequency-dependent polarizability α(−ω; ω), second-harmonic generation β(−2ω; ω, ω), optical rectification β(0; −ω, ω), third-harmonic generation γ(−3ω; ω, ω, ω), and degenerate four-wave mixing γ(−ω; ω, ω, −ω) are calculated.
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31.15.ee Time-dependent density functional theory
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
43.25.-x Nonlinear acoustics
31.15.ap Polarizabilities and other atomic and molecular properties

Trapping of diffusing particles by clusters of absorbing disks on a reflecting wall with disk centers on sites of a square lattice

Alexander M. Berezhkovskii, Leonardo Dagdug, Marco-Vinicio Vazquez, Vladimir A. Lizunov, Joshua Zimmerberg, and Sergey M. Bezrukov

J. Chem. Phys. 138, 064105 (2013); http://dx.doi.org/10.1063/1.4790370 (6 pages)

Online Publication Date: 13 February 2013

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A simple approximate formula is derived for the rate constant that describes steady-state flux of diffusing particles through a cluster of perfectly absorbing disks on the otherwise reflecting flat wall, assuming that the disk centers occupy neighboring sites of a square lattice. A distinctive feature of trapping by a disk cluster is that disks located at the cluster periphery shield the disks in the center of the cluster. This competition of the disks for diffusing particles makes it impossible to find an exact analytical solution for the rate constant in the general case. To derive the approximate formula, we use a recently suggested approach [A. M. Berezhkovskii, L. Dagdug, V. A. Lizunov, J. Zimmerberg, and S. M. Bezrukov, J. Chem. Phys. 136, 211102 (2012)]10.1063/1.4726015, which is based on the replacement of the disk cluster by an effective uniform partially absorbing spot. The formula shows how the rate constant depends on the size and shape of the cluster. To check the accuracy of the formula, we compare its predictions with the values of the rate constant obtained from Brownian dynamics simulations. The comparison made for 18 clusters of various shapes and sizes shows good agreement between the theoretical predictions and numerical results.
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05.40.Jc Brownian motion
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
05.60.-k Transport processes
02.60.-x Numerical approximation and analysis

Gaussian-based multiconfiguration time-dependent Hartree: A two-layer approach. I. Theory

S. Römer, M. Ruckenbauer, and I. Burghardt

J. Chem. Phys. 138, 064106 (2013); http://dx.doi.org/10.1063/1.4788830 (13 pages)

Online Publication Date: 13 February 2013

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We describe a novel two-layer variant of the Gaussian-based multiconfiguration time-dependent Hartree (G-MCTDH) approach which improves on the performance and convergence properties of quantum propagation based on variationally evolving frozen Gaussians (FGs). While the standard scheme uses factorizable multi-dimensional FGs, the present approach combines these into flexible, MCTDH-like single-particle functions. At the same time, the expensive variational evolution of the Gaussian parameters is reduced to low-dimensional subspaces. As a result, the novel scheme significantly alleviates the current bottleneck to accurate propagation in G-MCTDH and its variational multiconfigurational Gaussian (vMCG) variant. Since the first-layer single-particle functions are chosen to be orthogonal, the present approach can be straightforwardly combined with existing multi-layer MCTDH schemes.
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31.15.xr Self-consistent-field methods
31.15.xt Variational techniques
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Explicitly correlated atomic orbital basis second order Møller–Plesset theory

David S. Hollman, Jeremiah J. Wilke, and Henry F. Schaefer

J. Chem. Phys. 138, 064107 (2013); http://dx.doi.org/10.1063/1.4790582 (11 pages)

Online Publication Date: 14 February 2013

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The scope of problems treatable by ab initio wavefunction methods has expanded greatly through the application of local approximations. In particular, atomic orbital (AO) based wavefunction methods have emerged as powerful techniques for exploiting sparsity and have been applied to biomolecules as large as 1707 atoms [S. A. Maurer, D. S. Lambrecht, D. Flaig, and C. Ochsenfeld, J. Chem. Phys. 136, 144107 (2012)]10.1063/1.3693908. Correlated wavefunction methods, however, converge notoriously slowly to the basis set limit and, excepting the use of large basis sets, will suffer from a severe basis set incompleteness error (BSIE). The use of larger basis sets is prohibitively expensive for AO basis methods since, for example, second-order Møller-Plesset perturbation theory (MP2) scales linearly with the number of atoms, but still scales as O(N5) in the number of functions per atom. Explicitly correlated F12 methods have been shown to drastically reduce BSIE for even modestly sized basis sets. In this work, we therefore explore an atomic orbital based formulation of explicitly correlated MP2-F12 theory. We present working equations for the new method, which produce results identical to the widely used molecular orbital (MO) version of MP2-F12 without resorting to a delocalized MO basis. We conclude with a discussion of several possible approaches to a priori screening of contraction terms in our method and the prospects for a linear scaling implementation of AO-MP2-F12. The discussion includes concrete examples involving noble gas dimers and linear alkane chains.
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31.15.xp Perturbation theory
31.15.A- Ab initio calculations

High-density correlation energy expansion of the one-dimensional uniform electron gas

Pierre-François Loos

J. Chem. Phys. 138, 064108 (2013); http://dx.doi.org/10.1063/1.4790613 (5 pages) | Cited 1 time

Online Publication Date: 14 February 2013

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We show that the expression of the high-density (i.e., small-rs) correlation energy per electron for the one-dimensional uniform electron gas can be obtained by conventional perturbation theory and is of the form εc(rs) = −π2/360 + 0.00845 rs + …, where rs is the average radius of an electron. Combining these new results with the low-density correlation energy expansion, we propose a local-density approximation correlation functional, which deviates by a maximum of 0.1 mhartree compared to the benchmark diffusion Monte Carlo calculations.
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71.10.Ca Electron gas, Fermi gas
back to top Advanced Experimental Techniques

14N overtone NMR spectra under magic angle spinning: Experiments and numerically exact simulations

Luke A. O’Dell and Andreas Brinkmann

J. Chem. Phys. 138, 064201 (2013); http://dx.doi.org/10.1063/1.4775592 (10 pages) | Cited 3 times

Online Publication Date: 11 February 2013

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It was recently shown that high resolution 14N overtone NMR spectra can be obtained directly under magic angle spinning (MAS) conditions [L. A. O’Dell and C. I. Ratcliffe, Chem. Phys. Lett. 514, 168 (2011)]10.1016/j.cplett.2011.08.030. Preliminary experimental results showed narrowed powder pattern widths, a frequency shift that is dependent on the MAS rate, and an apparent absence of spinning sidebands, observations which appeared to be inconsistent with previous theoretical treatments. Herein, we reproduce these effects using numerically exact simulations that take into account the full nuclear spin Hamiltonian. Under sample spinning, the 14N overtone signal is split into five (0, ±1, ±2) overtone sidebands separated by the spinning frequency. For a powder sample spinning at the magic angle, the +2ωr sideband is dominant while the others show significantly lower signal intensities. The resultant MAS powder patterns show characteristic quadrupolar lineshapes from which the 14N quadrupolar parameters and isotropic chemical shift can be determined. Spinning the sample at other angles is shown to alter both the shapes and relative intensities of the five overtone sidebands, with MAS providing the benefit of averaging dipolar couplings and shielding anisotropy. To demonstrate the advantages of this experimental approach, we present the 14N overtone MAS spectrum obtained from L-histidine, in which powder patterns from all three nitrogen sites are clearly resolved.
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76.60.Cq Chemical and Knight shifts
71.70.Jp Nuclear states and interactions
75.10.Dg Crystal-field theory and spin Hamiltonians

Short range order in bimetallic nanoalloys: An extended X-ray absorption fine structure study

Anatoly I. Frenkel, Qi Wang, Sergio I. Sanchez, Matthew W. Small, and Ralph G. Nuzzo

J. Chem. Phys. 138, 064202 (2013); http://dx.doi.org/10.1063/1.4790509 (7 pages)

Online Publication Date: 12 February 2013

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Partial coordination numbers measured by extended X-ray absorption fine structure (EXAFS) spectroscopy have been used for decades to resolve between different compositional motifs in bulk and nanoscale bimetallic alloys. Due to the ensemble-averaging nature of EXAFS, the values of the coordination numbers in nanoparticles cannot be simply interpreted in terms of the degree of alloying or segregation if the compositional distribution is broad. We demonstrate that a Cowley short range order parameter is an objective measure of either the segregation tendency (e.g., a core-shell type) or the degree of randomness (in homogeneous nanoalloys). This criterion can be used even in the case when the clusters are random but have broad compositional distributions. All cases are illustrated using the analyses of EXAFS data obtained in three different nanoscale bimetallic systems: Pt(core)-Pd(shell), Pd(core)-Pt(shell), and Pt-Pd random alloy.
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78.70.Dm X-ray absorption spectra
64.75.Jk Phase separation and segregation in nanoscale systems
61.46.Df Structure of nanocrystals and nanoparticles ("colloidal" quantum dots but not gate-isolated embedded quantum dots)
back to top Atoms, Molecules, and Clusters

Photo-induced electron detachment of protein polyanions in the VUV range

Claire Brunet, Rodolphe Antoine, Philippe Dugourd, Francis Canon, Alexandre Giuliani, and Laurent Nahon

J. Chem. Phys. 138, 064301 (2013); http://dx.doi.org/10.1063/1.4790165 (4 pages)

Online Publication Date: 8 February 2013

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Biomolecular polyanions mainly relax by electron emission after UV excitation. Here, we study photodetachment of protein polyanions in the 6–16 eV VUV range by coupling a linear quadrupole ion trap with a synchrotron beamline. Gas-phase VUV action spectra of electrospray-produced multiply deprotonated insulin (5.6 kDa) and myoglobin (16.7 kDa) proteins are reported, which significantly increases the amount of data available on the optical response of proteins in the VUV. The influence of the protein charge and oxidation state upon the electron detachment efficiency is discussed. For small protein such as insulin, it appears that higher charge states produce higher detachment yields. Investigations on oxidized species show that the nature of the groups bearing the negative charges has an influence on the yields. For larger proteins, comparison of two forms of myoglobin clearly indicate that the three-dimensional structure does not impact much on the shape and the magnitude of the photodetachment spectra, in spite of a slight shift for the first electronic excited states.
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87.15.mn Photoionization
33.80.Eh Autoionization, photoionization, and photodetachment
34.50.Gb Electronic excitation and ionization of molecules
87.53.-j Effects of ionizing radiation on biological systems

Development of a molecular-dynamics-based cluster-heat-capacity model for study of homogeneous condensation in supersonic water-vapor expansions

Arnaud Borner, Zheng Li, and Deborah A. Levin

J. Chem. Phys. 138, 064302 (2013); http://dx.doi.org/10.1063/1.4790476 (17 pages)

Online Publication Date: 11 February 2013

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Supersonic expansions to vacuum produce clusters of sufficiently small size that properties such as heat capacities and latent heat of evaporation cannot be described by bulk vapor thermodynamic values. In this work the Monte-Carlo Canonical-Ensemble (MCCE) method was used to provide potential energies and constant-volume heat capacities for small water clusters. The cluster structures obtained using the well-known simple point charge model were found to agree well with earlier simulations using more rigorous potentials. The MCCE results were used as the starting point for molecular dynamics simulations of the evaporation rate as a function of cluster temperature and size which were found to agree with unimolecular dissociation theory and classical nucleation theory. The heat capacities and latent heat obtained from the MCCE simulations were used in direct-simulation Monte-Carlo of two experiments that measured Rayleigh scattering and terminal dimer mole fraction of supersonic water-jet expansions. Water-cluster temperature and size were found to be influenced by the use of kinetic rather than thermodynamic heat-capacity and latent-heat values as well as the nucleation model.
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65.20.-w Thermal properties of liquids
02.50.-r Probability theory, stochastic processes, and statistics
02.60.-x Numerical approximation and analysis
78.35.+c Brillouin and Rayleigh scattering; other light scattering
64.70.fm Thermodynamics studies of evaporation and condensation

Lowest triplet (n, π*) electronic state of acrolein: Determination of structural parameters by cavity ringdown spectroscopy and quantum-chemical methods

Nikolaus C. Hlavacek, Michael O. McAnally, and Stephen Drucker

J. Chem. Phys. 138, 064303 (2013); http://dx.doi.org/10.1063/1.4789793 (13 pages)

Online Publication Date: 11 February 2013

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The cavity ringdown absorption spectrum of acrolein (propenal, CH2=CH—CH=O) was recorded near 412 nm, under bulk-gas conditions at room temperature and in a free-jet expansion. The measured spectral region includes the 000 band of the T1(n, π*) ← S0 system. We analyzed the 000 rotational contour by using the STROTA computer program [R. H. Judge et al., J. Chem. Phys. 103, 5343 (1995)]10.1063/1.470569 , which incorporates an asymmetric rotor Hamiltonian for simulating and fitting singlet-triplet spectra. We used the program to fit T1(n, π*) inertial constants to the room-temperature contour. The determined values (cm−1), with 2σ confidence intervals, are A = 1.662 ± 0.003, B = 0.1485 ± 0.0006, C = 0.1363 ± 0.0004. Linewidth analysis of the jet-cooled spectrum yielded a value of 14 ± 2 ps for the lifetime of isolated acrolein molecules in the T1(n, π*), v = 0 state. We discuss the observed lifetime in the context of previous computational work on acrolein photochemistry. The spectroscopically derived inertial constants for the T1(n, π*) state were used to benchmark a variety of computational methods. One focus was on complete active space methods, such as complete active space self-consistent field (CASSCF) and second-order perturbation theory with a CASSCF reference function (CASPT2), which are applicable to excited states. We also examined the equation-of-motion coupled-cluster and time-dependent density function theory excited-state methods, and finally unrestricted ground-state techniques, including unrestricted density functional theory and unrestricted coupled-cluster theory with single and double and perturbative triple excitations. For each of the above methods, we or others [O. S. Bokareva et al., Int. J. Quantum Chem. 108, 2719 (2008)]10.1002/qua.21803 used a triple zeta-quality basis set to optimize the T1(n, π*) geometry of acrolein. We find that the multiconfigurational methods provide the best agreement with fitted inertial constants, while the economical unrestricted Perdew-Burke-Ernzerhof exchange-correlation hybrid functional (UPBE0) technique performs nearly as well.
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33.20.Kf Visible spectra
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.70.Jg Line and band widths, shapes, and shifts
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
31.50.Df Potential energy surfaces for excited electronic states
33.15.Bh General molecular conformation and symmetry; stereochemistry
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Zero-field splitting in nickel(II) complexes: A comparison of DFT and multi-configurational wavefunction calculations

A. Kubica, J. Kowalewski, D. Kruk, and M. Odelius

J. Chem. Phys. 138, 064304 (2013); http://dx.doi.org/10.1063/1.4790167 (9 pages)

Online Publication Date: 11 February 2013

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The zero-field splitting (ZFS) is an important quantity in the electron spin Hamiltonian for S = 1 or higher. We report calculations of the ZFS in some six- and five-coordinated nickel(II) complexes (S = 1), using different levels of theory within the framework of the ORCA program package [F. Neese, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2, 73 (2012)]10.1002/wcms.81 . We compare the high-end ab initio calculations (complete active space self-consistent field and n-electron valence state perturbation theory), making use of both the second-order perturbation theory and the quasi-degenerate perturbation approach, with density functional theory (DFT) methods using different functionals. The pattern of results obtained at the ab initio levels is quite consistent and in reasonable agreement with experimental data. The DFT methods used to calculate the ZFS give very strongly functional-dependent results and do not seem to function well for our systems.
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31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.15.E- Density-functional theory
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.30.Gs Hyperfine interactions and isotope effects
33.15.Pw Fine and hyperfine structure

A multireference perturbation study of the NN stretching frequency of trans-azobenzene in nπ* excitation and an implication for the photoisomerization mechanism

Yu Harabuchi, Moe Ishii, Akira Nakayama, Takeshi Noro, and Tetsuya Taketsugu

J. Chem. Phys. 138, 064305 (2013); http://dx.doi.org/10.1063/1.4790611 (7 pages) | Cited 1 time

Online Publication Date: 13 February 2013

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A multireference second-order perturbation theory is applied to calculate equilibrium structures and vibrational frequencies of trans-azobenzene in the ground and nπ* excited states, as well as the reaction pathways for rotation and inversion mechanism in the nπ* excited state. It is found that the NN stretching frequency exhibits a slight increase at the minimum energy structure in the nπ* state, which is explained by the mixing of the NN stretching mode with the CN symmetric stretching mode. We also calculate the NN stretching frequency at several selected structures along the rotation and inversion pathways in the nπ* state, and show that the frequency decreases gradually along the rotation pathway while it increases by ca. 300 cm−1 along the inversion pathway. The frequencies and energy variations along the respective pathways indicate that the rotation pathway is more consistent with the experimental observation of the NN stretching frequency in nπ* excitation.
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33.20.Tp Vibrational analysis
82.20.Bc State selected dynamics and product distribution
82.50.-m Photochemistry
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Mt Rotation, vibration, and vibration-rotation constants

Density functional theory and global optimization study of SnmPbn clusters (7 ⩽ m + n ⩽ 12, 0 ⩽ m/(m + n) ⩽ 1)

Slava Orel and René Fournier

J. Chem. Phys. 138, 064306 (2013); http://dx.doi.org/10.1063/1.4790607 (7 pages)

Online Publication Date: 14 February 2013

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The global minima of the neutral binary SnmPbn atomic clusters, 7 ⩽ m + n ⩽ 12, of all the possible stoichiometric ratios have been found using tabu search in descriptor space and density functional theory. The effects of spin-orbit coupling on optimized geometries and energies are important. All of the binary clusters form substitution alloys. Apart from the 11-atom case, the pure clusters of the same size have the same ground state geometry. The relative energies of the isomers of a cluster depend on, in order of decreasing importance: the overall geometry; the specific sites occupied by the two atom types; and the degree of segregation. The total cohesive energy difference between the lowest energy homotops is typically on the order of 0.02 eV. The mixing/segregation trends are found to be very different depending on the size of the basis set. Calculations generally overestimate the dipole moments. The trends in calculated dipole moments agree with experiment for the lead-rich clusters, and to a lesser degree, the tin-rich clusters.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Effects of 3He impurities on the superfluid response of the 4He monolayer on a C20 molecule

Hyeondeok Shin and Yongkyung Kwon

J. Chem. Phys. 138, 064307 (2013); http://dx.doi.org/10.1063/1.4792204 (6 pages)

Online Publication Date: 14 February 2013

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The path-integral Monte Carlo calculations have been performed to investigate the effects of 3He impurities on structural and superfluid properties of the 4He monolayer on a single C20 molecule. According to our previous study, the helium monolayer exhibits different quantum states for different numbers of 4He adatoms and is completed to form a commensurate solid where nanoscale supersolidity can be realized through the activation of mobile vacancy states. We first observe that different structures for different numbers of helium atoms are mostly preserved with the replacement of a few 4He atoms with the same number of 3He atoms, whether the helium layer is a fluid or a solid. However, the substitution of 3He impurities is found to have different effects on the superfluid response of the helium layer, depending on its quantum state. For a partially-filled fluid layer the superfluid fraction decreases monotonically with the increasing 3He concentration, which can be understood in terms of the suppression of exchange couplings among 4He atoms due to the presence of 3He impurities. On the other hand, the substitution of a few 3He impurity atoms may increase the superfluid fraction of a near-complete monolayer that is in a crystalline solid state. The enhancement of superfluidity in a solid layer is interpreted to be due to interstitial and vacancy defects promoted by larger quantum fluctuations of lighter 3He atoms. This provides strong evidence that the 4He monolayer on C20 shows the vacancy-based supersolidity near its completion.
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67.25.D- Superfluid phase
67.30.H- Superfluid phase of 3He
02.50.-r Probability theory, stochastic processes, and statistics
71.70.Gm Exchange interactions
67.30.hm Impurities

Towards a first-principles model of Fermi resonance in the alkyl CH stretch region: Application to 1,2-diphenylethane and 2,2,2-paracyclophane

Evan G. Buchanan, Jacob C. Dean, Timothy S. Zwier, and Edwin L. Sibert, III

J. Chem. Phys. 138, 064308 (2013); http://dx.doi.org/10.1063/1.4790163 (11 pages) | Cited 2 times

Online Publication Date: 14 February 2013

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The spectroscopy of two flexible hydrocarbons, 1,2-diphenylethane (DPE) and 2,2,2-paracyclophane (TCP) is presented, and a predictive theoretical model for describing the alkyl CH stretch region of these hydrocarbons is developed. Ultraviolet hole-burning spectroscopy identified two isomers of DPE and a single conformation of TCP present in the supersonic jet expansion. Through the analysis of the ground state low-frequency vibronic spectroscopy obtained by dispersed fluorescence, conformational assignments were made for both DPE and TCP. The two isomers of DPE were found to retain the low energy structures of butane, being present in both the gauche and anti structures. TCP forms a C2 symmetric structure, differing from the predicted lower energy C3 conformation by the symmetry of the ethano bridges (−CH2CH2−) linking the phenyl substituents. Resonant ion-dip infrared spectroscopy is used to record single-conformation IR spectra of the two conformers of DPE and the single conformer of TCP in the alkyl CH stretch region and in the mid-IR that covers the CH bend fundamentals. A local mode Hamiltonian that incorporates cubic stretch-bend coupling is developed. Its parameters are obtained from density functional theory methods. Full dimensional calculations are compared to those that use reduced dimensional Hamiltonians in which anharmonic CH stretches and scissor modes are Fermi coupled. Excellent agreement is found. Scale factors of select terms in the reduced dimensional Hamiltonian are determined by fitting the theoretical Hamiltonian to the anti-DPE spectrum. The scaled Hamiltonian is then used to predict successfully structures for the remaining lower symmetry experimentally determined spectra in the alkyl CH stretch region.
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31.15.A- Ab initio calculations
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.20.Ea Infrared spectra
33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.50.Dq Fluorescence and phosphorescence spectra
back to top Liquids, Glasses, and Crystals

Further details on the phase diagram of hard ellipsoids of revolution

Gustavo Bautista-Carbajal, Arturo Moncho-Jordá, and Gerardo Odriozola

J. Chem. Phys. 138, 064501 (2013); http://dx.doi.org/10.1063/1.4789957 (9 pages)

Online Publication Date: 8 February 2013

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In recent work we revisited the phase diagram of hard ellipsoids of revolution (spheroids) by means of replica exchange Monte Carlo simulations. This was done by setting random initial configurations, and allows to confirm the formation of sm2 crystal structures at high densities [P. Pfleiderer and T. Schilling, Phys. Rev. E 75, 020402 (2007)10.1103/PhysRevE.75.020402] for large anisotropies and stretched-fcc for small anisotropies. In this work we employed the same technique but setting the starting cells as sm2 crystal structures having the maximum known packing density [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004)10.1103/PhysRevLett.92.255506]. This procedure yields a very rich behavior for quasi-spherical oblates and prolates. These systems, from low to high pressures, show the following phases: isotropic fluid, plastic solid, stretched-fcc solid, and sm2 solid. The first three transitions are first order, whereas the last one is a subtle, probably high order transition. This picture is consistent with the fact of having the sm2 structure capable of producing the maximally achievable density.
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81.30.Dz Phase diagrams of other materials
64.30.Jk Equations of state of nonmetals
61.30.Cz Molecular and microscopic models and theories of liquid crystal structure

NMR relaxation study of water dynamics in superparamagnetic iron-oxide-loaded vesicles

Yu-Wen Chen (陳育文), Chu-Jung Hsieh (謝渠蓉), Chao-Min Lin (林昭閔), and Dennis W. Hwang (黃聖言)

J. Chem. Phys. 138, 064502 (2013); http://dx.doi.org/10.1063/1.4789958 (8 pages)

Online Publication Date: 8 February 2013

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Superparamagnetic iron oxide (SPIO) nanoparticles have been introduced as contrast agents for clinical applications in magnetic resonance imaging. Recently, SPIO has been also used for tracking cells. However, NMR relaxation of water molecules behaves differently in a SPIO solution and SPIO-loaded cells. In this study, we used water-in-oil-in-water double emulsions to mimic cellular environments. The MR relaxation induced by the SPIO-loaded vesicles and SPIO solution indicates that T2* is sensitive to the iron concentration alone, and the behavior was very similar in both SPIO-loaded vesicles and SPIO solution. However, T2 relaxation of water in SPIO-loaded vesicles was faster than that in a SPIO solution. In addition, the contribution of water inside and outside the vesicles was clarified by replacing H2O with D2O, and water inside the vesicles was found to cause a nonlinear iron concentration dependency. The studied dilution revealed that vesicle aggregation undergoes a structural transition upon dilution by a certain amount of water. R2* relaxation is sensitive to this structural change and shows an obvious nonlinear iron concentration dependency when the SPIO loading is sufficiently high. Random walk simulations demonstrated that in the assumed model, the vesicles aggregate structures causing the differences between R2* and R2 relaxation of water in vesicles in the presence of SPIO particles.
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87.16.dt Structure, static correlations, domains, and rafts
87.64.kj NMR
82.70.Kj Emulsions and suspensions
87.18.Ed Cell aggregation
87.16.A- Theory, modeling, and simulations

Different structures give similar vibrational spectra: The case of OH− in aqueous solution

Pavlin D. Mitev, Philippe A. Bopp, Jasmina Petreska, Kaline Coutinho, Hans Ågren, Ljupco Pejov, and Kersti Hermansson

J. Chem. Phys. 138, 064503 (2013); http://dx.doi.org/10.1063/1.4775589 (10 pages)

Online Publication Date: 11 February 2013

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We have calculated the anharmonic OH−(aq) vibrational spectrum in aqueous solution with a “classical Monte Carlo simulation + QM/MM + vibrational” sequential approach. A new interaction model was used in the Monte Carlo simulations: a modified version of the charged-ring hydroxide-water model from the literature. This spectrum is compared with experiment and with a spectrum based on CPMD-generated structures, and the hydration structures and H-bonding for the two models are compared. We find that: (i) the solvent-induced frequency shift as well as the absolute OH− frequency are in good agreement with experiment using the two models; (ii) the Raman and IR bands are very similar, in agreement with experiment; (iii) the hydration structure and H-bonding around the ion are very different with the two ion-water interaction models (charged-ring and CPMD); (iv) a cancellation effect between different regions of the hydration shell makes the total spectra similar for the two interaction models, although their hydration structures are different; (v) the net OH− frequency shift is a blueshift of about +80 cm−1 with respect to frequency of the gas-phase ion.
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33.20.Tp Vibrational analysis
33.70.Jg Line and band widths, shapes, and shifts
02.50.Ng Distribution theory and Monte Carlo studies
33.15.Fm Bond strengths, dissociation energies
33.20.Ea Infrared spectra
33.20.Fb Raman and Rayleigh spectra (including optical scattering)
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