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At least 1,153 records · Page 64

Electronic Energies Are Not Enough: An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H + GPGG Conformers

Peptides and proteins exist not as single, lowest energy structures but as ensembles of states separated by small barriers. In order to study these species we must be able to correctly identify their gas phase conformational distributions, and ion mobility spectrometry (IMS) has arisen as an experimental method for assessing the gas phase energetics of flexible peptides. Here, we present a thorough exploration and benchmarking of the low energy conformers of the small, hairpin peptide H+ GPGG with the aid of ion mobility spectrometry against a wide swath of density functionals (35 dispersion-corrected and uncorrected functionals represented by 21 unique exchange–correlation functionals) and wave function theory methods (15 total levels of theory). The three experimentally resolved IMS peaks were found to correspond to three distinct pairs of conformers, each pair composed of species differing only by the chair or boat configuration of the proline. Two of the H+ GPGG conformer pairs possess a cis configuration about the Pro–Gly1 peptide bond while the other adopts a trans configuration. While the experimental spectrum reports a higher intensity for the cis-1 conformer than the trans conformer, 13 WFT levels of theory, including a complete basis set CCSD(T) extrapolation, obtain trans to be favored in terms of the electronic energy. This same effect is seen in 14 of the 18 dispersion-corrected density functionals studied, whereas the remaining 17 functionals show more variety. Only when Gibbs free energies are considered do the WFT methods and dispersion-corrected functionals reflect the experimental distribution. CAM-B3LYP-D3BJ emerges as the best-performing density functional, matching the experimental distribution and the CCSD(T)/CBS relative energies within 6%. Further analysis reveals the trans conformer to be favored electronically, but entropically disfavored, leading to the experimental preference of the cis-1 conformer. Furthermore, these results highlight the danger in considering only the electronic energies, which is common practice in electronic structure theory predictions of conformational energy distributions. Additionally, the effects of temperature and scaling of the frequencies used in obtaining the Gibbs free energies are explored.

Energy↗

Effects of Selenium Doping in Zinc Telluride from First Principles

We report point defects and compensation in zinc telluride have been subjects of study for several decades due to the compound’s scientific/technological applications. Despite this, there remains some disagreement in the literature as to the fine details of its defect chemistry. Recently, it has also come under renewed interest due to the emerging Cd( 1–x )Zn x Te( 1–y )Se y material family, used in nuclear radiation detector applications. In this article, we use state-of-the-art computational tools to re-examine the native defect chemistry of ZnTe and explore how it changes upon addition of selenium using density functional theory with screened hybrid exchange–correlation functionals, thermochemical models of the equilibration environment, and statistical mechanics models of the point defect ensemble.

II-VI semiconductors↗

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

74 ATOMIC AND MOLECULAR PHYSICS↗

Quantum diffusion with drift and the Einstein relation. II

This paper is a companion to Paper I [W. De Roeck, J. Fröhlich, and K. Schnelli, “Quantum diffusion with drift and the Einstein relation. I,” J. Math. Phys. 55, 075206 (2014)]. The purpose of this paper is to describe and prove a certain number of technical results used in Paper I, but not proven there. Both papers concern long-time properties (diffusion, drift) of the motion of a driven quantum particle coupled to an array of thermal reservoirs. The main technical results derived in the present paper are: (1) an asymptotic perturbation theory applicable for small driving force, and (2) the construction of time-dependent correlation functions of particle observables.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Toward tailorable surfaces: A combined theoretical and experimental study of lanthanum niobate layered perovskites

A comprehensive theoretical investigation of the MLaNb{sub 2}O{sub 7} (M = H, Li, Na, K, Rb, and Cs) series of ion-exchangeable layered perovskite is presented. These perovskites are in particular interesting in view of their potential applications as inorganic supports for the design of new hybrid inorganic-organic proton conductors. In particular, their structural and electronic properties have been investigated by periodic calculations in the framework of Density Functional Theory, using different exchange-correlation functionals. A general very good agreement with the available experimental (XRD, NPD, and EXAFS) data has been found. The structure of the protonated HLaNb{sub 2}O{sub 7} form has also been further clarified and a new tetragonal space group is proposed for this compound, better reproducing the experimental cell parameters and yielding to a more realistic picture of the system. The electronic investigation highlighted that all the compounds considered are very similar to each other and that the interaction between interlayer cations and perovskite slabs is purely ionic, except for the proton that is, instead, covalently bound.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High angular momentum states of lithium atom, studied with symmetry-projected explicitly correlated Gaussian lobe functions

Method of construction of wave functions approximating eigenfunctions of the L{sup ^2} operator is proposed for high angular momentum states of few-electron atoms. Basis functions are explicitly correlated Gaussian lobes, projected onto irreducible representations of finite point groups. Variational calculations have been carried out for the lowest states of lithium atom, with quantum number L in the range from 1 to 8. Nonrelativistic energies accurate to several dozens of nanohartree have been obtained. For 2{sup 2}P, 3{sup 2}D, and 4{sup 2}F states they agree well with the reference results. Transition frequencies have been computed and compared with available experimental data.

97 MATHEMATICS AND COMPUTING↗

Photoelectron spectroscopy of B{sub 4}O{sub 4}{sup −}: Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B{sub 4}O{sub 4}{sup 0/−} clusters. The measured PES spectra of B{sub 4}O{sub 4}{sup −} exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDE of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of C{sub s} B{sub 4}O{sub 4}{sup −} ({sup 2}A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D{sub 2h} B{sub 4}O{sub 4}{sup −} ({sup 2}B{sub 2g}) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B{sub 2}O{sub 2} core bonded with terminal BO and/or BO{sub 2} groups. The same Y-shaped and rhombic structures are also located for the B{sub 4}O{sub 4} neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B{sub 4}O{sub 4}{sup 0/−} clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B{sub 4}O{sub 4}{sup 0/−} clusters. This work is the first experimental study on a molecular system with an o-bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulation of circularly polarized luminescence spectra using coupled cluster theory

We report the first computations of circularly polarized luminescence (CPL) rotatory strengths at the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) level of theory. Using a test set of eight chiral ketones, we compare both dipole and rotatory strengths for absorption (electronic circular dichroism) and emission to the results from time-dependent density-functional theory (TD-DFT) and available experimental data for both valence and Rydberg transitions. For two of the compounds, we obtained optimized geometries of the lowest several excited states using both EOM-CCSD and TD-DFT and determined that structures and EOM-CCSD transition properties obtained with each structure were sufficiently similar that TD-DFT optimizations were acceptable for the remaining test cases. Agreement between EOM-CCSD and the Becke three-parameter exchange function and Lee-Yang-Parr correlation functional (B3LYP) corrected using the Coulomb attenuating method (CAM-B3LYP) is typically good for most of the transitions, though agreement with the uncorrected B3LYP functional is significantly worse for all reported properties. The choice of length vs. velocity representation of the electric dipole operator has little impact on the EOM-CCSD transition strengths for nearly all of the states we examined. For a pair of closely related β, γ-enones, (1R)-7-methylenebicyclo[2.2.1]heptan-2-one and (1S)-2-methylenebicyclo[2.2.1]heptan-7-one, we find that EOM-CCSD and CAM-B3LYP agree with the energetic ordering of the two possible excited-state conformations, resulting in good agreement with experimental rotatory strengths in both absorption and emission, whereas B3LYP yields a qualitatively incorrect result for the CPL signal of (1S)-2-methylenebicyclo[2.2.1]heptan-7-one. Finally, we predict that one of the compounds considered here, trans-bicyclo[3.3.0]octane-3,7-dione, is unique in that it exhibits an achiral ground state and a chiral first excited state, leading to a strong CPL signal but a weak circular dichroism signal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-linear non-local molecular electrodynamics with nano-optical fields

The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields may vary appreciably across the molecular length scale. Rather than incrementally adding higher multipoles, it is advantageous and more physically transparent to describe the optical process using non-local response functions that intrinsically include all multi-poles. In this work, we present a semi-classical approach for calculating non-local response functions based on the minimal coupling Hamiltonian. The first, second, and third order response functions are expressed in terms of correlation functions of the charge and the current densities. Finally, this approach is based on the gauge invariant current rather than the polarization, and on the vector potential rather than the electric and magnetic fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Generalized quasiharmonic approximation via space group irreducible derivatives

The quasiharmonic approximation (QHA) is the simplest nontrivial approximation for interacting phonons under constant pressure, bringing the effects of anharmonicity into temperature-dependent observables. Nonetheless, the QHA is often implemented with additional approximations due to the complexity of computing phonons under arbitrary strains, and the generalized QHA, which employs constant stress boundary conditions, has not been completely developed. In this work we formulate the generalized QHA, providing a practical algorithm for computing the strain state and other observables as a function of temperature and true stress. We circumvent the complexity of computing phonons under arbitrary strains by employing irreducible second-order displacement derivatives of the Born-Oppenheimer potential and their strain dependence, which are efficiently and precisely computed using the lone irreducible derivative approach. We formulate two complementary strain parametrizations: a discretized strain grid interpolation and a Taylor series expansion in symmetrized strain. We illustrate our approach by evaluating the temperature and pressure dependence of select elastic constants and the thermal expansion in thoria (ThO 2 ) using density functional theory with three exchange-correlation functionals. The QHA results are compared to our measurements of the elastic constant tensor using time-domain Brillouin scattering and inelastic neutron scattering. Our irreducible derivative approach simplifies the implementation of the generalized QHA, which will facilitate reproducible, data-driven applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Many-Body Signatures of Collective Decay in Atomic Chains

Fully inverted atoms placed at exactly the same location synchronize as they deexcite, and light is emitted in a burst (known as “Dicke’s superradiance”). We investigate the role of finite interatomic separation on correlated decay in mesoscopic chains and provide an understanding in terms of collective jump operators. We show that the superradiant burst survives at small distances, despite Hamiltonian dipole-dipole interactions. However, for larger separations, competition between different jump operators leads to dephasing, suppressing superradiance. Collective effects are still significant for arrays with lattice constants of the order of a wavelength, and lead to a photon emission rate that decays nonexponentially in time. We calculate the two-photon correlation function and demonstrate that emission is correlated and directional, as well as sensitive to small changes in the interatomic distance. Furthermore, these features can be measured in current experimental setups, and are robust to realistic imperfections.

74 ATOMIC AND MOLECULAR PHYSICS↗

Monte Carlo simulation of the classical two-dimensional one component plasma

Monte Carlo simulation, lattice dynamics in the harmonic approximation, and solution of the hypernetted chain equation were used to study the classical two-dimensional one component plasma. The system consists of a single species of charged particles immersed in a uniform neutralizing background. The particles interact via a l/r potential, where r is the two dimensional separation. Equations of state were calculated for both the liquid and solid phases. Results of calculation of the thermodynamic functions and one and two particle correlation functions are presented.

Gann, R. C.↗

Optical and radio variability in blazars

An analysis is presented of the optical (0.44 micron) and radio flux density variations (4.8, 8.0, and 14.5 GHz) of the five best observed variable AGN, of which three are BL Lac objects and two are optically violent variable (OVV) quasars. For each object the nature of the variability at individual wavelengths is determined by using a structure function analysis and the autocorrelation function as calculated from the discrete correlation technique. Both techniques yield similar results, showing that the optical variations are similar for all objects and are a combination of flicker and shot noise. The radio variability is distinct, being described by shot noise (less variation at short times), with the two OVVs exhibiting the most extreme behavior. The time lag between the variations at the three radio frequencies and the optical flux is studied with the discrete cross-correlation function and the mean variance methods. It is concluded that the optical and radio emitting regions are physically related, exist on distinct time scales, and excite their synchrotron emitting plasmas differently.

Hufnagel, Beth R.↗

The FMOS-COSMOS Survey of Star-forming Galaxies at Z ∼ 1.6. V: Properties of Dark Matter Halos Containing Hα Emitting Galaxies

We study the properties of dark matter halos that contain star-forming galaxies at 1.43 ≤ z ≤ 1.74, using the FMOS-COSMOS survey. The sample consists of 516 objects with a detection of the Hα emission line, which represent the star forming population at this epoch, having a stellar mass range of 10{sup 9.57} ≤ M {sub *}/M {sub ⊙} ≲ 10{sup 11.4} and a star-formation rate range of 15 ≲ SFR/(M {sub ⊙} yr{sup −1}) ≲ 600. We measure the projected two-point correlation function while carefully taking into account observational biases, and find a significant clustering amplitude at scales of 0.04–10 h {sup −1} cMpc, with a correlation length r{sub 0}=5.26{sub −0.62}{sup +0.75} h{sup −1} cMpc and a bias b=2.44{sub −0.32}{sup +0.38}. We interpret our clustering measurement using a halo occupation distribution model. The sample galaxies appear to reside in halos with mass M{sub h}=4.71{sub −1.62}{sup +1.19}×10{sup 12} h{sup −1} M{sub ⊙} on average, which will likely become present-day halos of mass M {sub h} (z = 0) ∼ 2 × 10{sup 13} h {sup −1} M {sub ⊙}, equivalent to the typical halo mass scale of galaxy groups. We then confirm the decline of the stellar-to-halo mass ratio at M {sub h} < 10{sup 12} M {sub ⊙}, finding M {sub *}/M {sub h} ≈ 5 × 10{sup −3} at M {sub h} = 7. 5 × 10{sup 11} M {sub ⊙}, which is lower by a factor of 2–4 than those measured at higher masses (M {sub h} ∼ 10{sup 12–13} M {sub ⊙}). Finally, we use our results to illustrate the future capabilities of Subaru’s Prime-Focus Spectrograph, a next-generation instrument that will provide strong constraints on the galaxy-formation scenario by obtaining precise measurements of galaxy clustering at z > 1.

79 ASTRONOMY AND ASTROPHYSICS↗

Freezing lines of colloidal Yukawa spheres. II. Local structure and characteristic lengths

Using the Rogers-Young (RY) integral equation scheme for the static pair correlation functions combined with the liquid-phase Hansen-Verlet freezing rule, we study the generic behavior of the radial distribution function and static structure factor of monodisperse charge-stabilized suspensions with Yukawa-type repulsive particle interactions at freezing. In a related article, labeled Paper I [J. Gapinski, G. Nägele, and A. Patkowski, J. Chem. Phys. 136, 024507 (2012)], this hybrid method was used to determine two-parameter freezing lines for experimentally controllable parameters, characteristic of suspensions of charged silica spheres in dimethylformamide. A universal scaling of the RY radial distribution function maximum is shown to apply to the liquid-bcc and liquid-fcc segments of the universal freezing line. A thorough analysis is made of the behavior of characteristic distances and wavenumbers, next-neighbor particle coordination numbers, osmotic compressibility factor, and the Ravaché-Mountain-Streett minimum-maximum radial distribution function ratio.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ising model observables and non-backtracking walks

This paper presents an alternative proof of the connection between the partition function of the Ising model on a finite graph G and the set of non-backtracking walks on G. The techniques used also give formulas for spin-spin correlation functions in terms of non-backtracking walks. The main tools used are Viennot's theory of heaps of pieces and turning numbers on surfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

THE NEXT GENERATION VIRGO CLUSTER SURVEY. XV. THE PHOTOMETRIC REDSHIFT ESTIMATION FOR BACKGROUND SOURCES

The Next Generation Virgo Cluster Survey (NGVS) is an optical imaging survey covering 104 deg{sup 2} centered on the Virgo cluster. Currently, the complete survey area has been observed in the u*giz bands and one third in the r band. We present the photometric redshift estimation for the NGVS background sources. After a dedicated data reduction, we perform accurate photometry, with special attention to precise color measurements through point-spread function homogenization. We then estimate the photometric redshifts with the Le Phare and BPZ codes. We add a new prior that extends to i {sub AB} = 12.5 mag. When using the u* griz bands, our photometric redshifts for 15.5 mag ≤ i ≲ 23 mag or z {sub phot} ≲ 1 galaxies have a bias |Δz| < 0.02, less than 5% outliers, a scatter σ{sub outl.rej.}, and an individual error on z {sub phot} that increases with magnitude (from 0.02 to 0.05 and from 0.03 to 0.10, respectively). When using the u*giz bands over the same magnitude and redshift range, the lack of the r band increases the uncertainties in the 0.3 ≲ z {sub phot} ≲ 0.8 range (–0.05 < Δz < –0.02, σ{sub outl.rej} ∼ 0.06, 10%-15% outliers, and z {sub phot.err.} ∼ 0.15). We also present a joint analysis of the photometric redshift accuracy as a function of redshift and magnitude. We assess the quality of our photometric redshifts by comparison to spectroscopic samples and by verifying that the angular auto- and cross-correlation function w(θ) of the entire NGVS photometric redshift sample across redshift bins is in agreement with the expectations.

79 ASTRONOMY AND ASTROPHYSICS↗