On the performance of large Gaussian basis sets for the computation of total atomization energies

NASA Technical Reports Server (NTRS)

Martin, J. M. L.

1992-01-01

The total atomization energies of a number of molecules have been computed using an augmented coupled-cluster method and (5s4p3d2f1g) and 4s3p2d1f) atomic natural orbital (ANO) basis sets, as well as the correlation consistent valence triple zeta plus polarization (cc-pVTZ) correlation consistent valence quadrupole zeta plus polarization (cc-pVQZ) basis sets. The performance of ANO and correlation consistent basis sets is comparable throughout, although the latter can result in significant CPU time savings. Whereas the inclusion of g functions has significant effects on the computed Sigma D(e) values, chemical accuracy is still not reached for molecules involving multiple bonds. A Gaussian-1 (G) type correction lowers the error, but not much beyond the accuracy of the G1 model itself. Using separate corrections for sigma bonds, pi bonds, and valence pairs brings down the mean absolute error to less than 1 kcal/mol for the spdf basis sets, and about 0.5 kcal/mol for the spdfg basis sets. Some conclusions on the success of the Gaussian-1 and Gaussian-2 models are drawn.

The electronic structure of vanadium monochloride cation (VCl+): Tackling the complexities of transition metal species

NASA Astrophysics Data System (ADS)

DeYonker, Nathan J.; Halfen, DeWayne T.; Allen, Wesley D.; Ziurys, Lucy M.

2014-11-01

Six electronic states (X 4Σ-, A 4Π, B 4Δ, 2Φ, 2Δ, 2Σ+) of the vanadium monochloride cation (VCl+) are described using large basis set coupled cluster theory. For the two lowest quartet states (X 4Σ- and A 4Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T0) and spectroscopic constants (re, r0, Be, B0, bar De, He, ωe, v0, αe, ωexe) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X 4Σ-), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state (2Γ) has a Te of ˜11 200 cm-1. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.

Correlation consistent basis sets for actinides. I. The Th and U atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peterson, Kirk A., E-mail: kipeters@wsu.edu

New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc − pV nZ − PP and cc − pV nZ − DK3, as well as outer-core correlation (valence + 5s5p5d), cc − pwCV nZ − PP and cc − pwCV nZ − DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Bothmore » series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThF{sub n} (n = 2 − 4), ThO{sub 2}, and UF{sub n} (n = 4 − 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF{sub 4}, ThF{sub 3}, ThF{sub 2}, and ThO{sub 2} are all within their experimental uncertainties. Bond dissociation energies of ThF{sub 4} and ThF{sub 3}, as well as UF{sub 6} and UF{sub 5}, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF{sub 4} and ThO{sub 2}. The DKH3 atomization energy of ThO{sub 2} was calculated to be smaller than the DKH2 value by ∼1 kcal/mol.« less

Basis set construction for molecular electronic structure theory: natural orbital and Gauss-Slater basis for smooth pseudopotentials.

PubMed

Petruzielo, F R; Toulouse, Julien; Umrigar, C J

2011-02-14

A simple yet general method for constructing basis sets for molecular electronic structure calculations is presented. These basis sets consist of atomic natural orbitals from a multiconfigurational self-consistent field calculation supplemented with primitive functions, chosen such that the asymptotics are appropriate for the potential of the system. Primitives are optimized for the homonuclear diatomic molecule to produce a balanced basis set. Two general features that facilitate this basis construction are demonstrated. First, weak coupling exists between the optimal exponents of primitives with different angular momenta. Second, the optimal primitive exponents for a chosen system depend weakly on the particular level of theory employed for optimization. The explicit case considered here is a basis set appropriate for the Burkatzki-Filippi-Dolg pseudopotentials. Since these pseudopotentials are finite at nuclei and have a Coulomb tail, the recently proposed Gauss-Slater functions are the appropriate primitives. Double- and triple-zeta bases are developed for elements hydrogen through argon. These new bases offer significant gains over the corresponding Burkatzki-Filippi-Dolg bases at various levels of theory. Using a Gaussian expansion of the basis functions, these bases can be employed in any electronic structure method. Quantum Monte Carlo provides an added benefit: expansions are unnecessary since the integrals are evaluated numerically.

Novel analytical approach for strongly coupled waveguide arrays

NASA Astrophysics Data System (ADS)

Kohli, Niharika; Srivastava, Sangeeta; Sharma, Enakshi K.

2018-02-01

Coupled Mode theory and Variational methods are the most extensively used analytical methods for the study of coupled optical waveguides. In this paper we have discussed a variation of the Ritz Galerkin Variational method (RGVM) wherein the trial field is a superposition of an orthogonal basis set which in turn is generated from superposition of the individual waveguide modal fields using Gram Schmidt Orthogonalization Procedure (GSOP). The conventional coupled mode theory (CCMT), a modified coupled mode theory (MCMT) incorporating interaction terms that are neglected in CCMT, and an RGVM using orthogonal basis set (RG-GSOP) are compared for waveguide arrays of different materials. The exact effective indices values for these planar waveguide arrays are also studied. The different materials have their index-contrasts ranging between the GaAs/ AlGaAs system to Si/SiO2 system. It has been shown that the error in the effective indices values obtained from MCMT and CCMT is higher than RGVM-GSOP especially in the case of higher index-contrast. Therefore, for accurate calculations of the modal characteristics of planar waveguide arrays, even at higher index-contrasts, RGVM-GSOP is the best choice. Moreover, we obtain obviously orthogonal supermode fields and Hermitian matrix from RGVM-GSOP.

Auxiliary basis sets for density-fitting second-order Møller-Plesset perturbation theory: weighted core-valence correlation consistent basis sets for the 4d elements Y-Pd.

PubMed

Hill, J Grant

2013-09-30

Auxiliary basis sets (ABS) specifically matched to the cc-pwCVnZ-PP and aug-cc-pwCVnZ-PP orbital basis sets (OBS) have been developed and optimized for the 4d elements Y-Pd at the second-order Møller-Plesset perturbation theory level. Calculation of the core-valence electron correlation energies for small to medium sized transition metal complexes demonstrates that the error due to the use of these new sets in density fitting is three to four orders of magnitude smaller than that due to the OBS incompleteness, and hence is considered negligible. Utilizing the ABSs in the resolution-of-the-identity component of explicitly correlated calculations is also investigated, where it is shown that i-type functions are important to produce well-controlled errors in both integrals and correlation energy. Benchmarking at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations level indicates impressive convergence with respect to basis set size for the spectroscopic constants of 4d monofluorides; explicitly correlated double-ζ calculations produce results close to conventional quadruple-ζ, and triple-ζ is within chemical accuracy of the complete basis set limit. Copyright © 2013 Wiley Periodicals, Inc.

Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path.

PubMed

Varandas, A J C

2011-05-28

The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative stability to ΔE(ZPE) = (0.51 ± 0.08) kcal mol(-1). A scheme is also suggested to model the full-dimensional isomerization potential-energy surface using a quadratic expansion that is parametrically represented by a Fourier analysis in the torsion angle. The method illustrated at the raw and complete basis-set limit coupled-cluster levels can provide a valuable tool for a future analysis of the available (incomplete thus far) experimental rovibrational data. This journal is © the Owner Societies 2011

Computational study of the electronic spectra of the rare gas fluorohydrides HRgF (Rg = Ar, Kr, Xe, Rn)

NASA Astrophysics Data System (ADS)

van Hoeve, Miriam D.; Klobukowski, Mariusz

2018-03-01

Simulation of the electronic spectra of HRgF (Rg = Ar, Kr, Xe, Rn) was carried out using the time-dependent density functional method, with the CAMB3LYP functional and several basis sets augmented with even-tempered diffuse functions. A full spectral assignment for the HRgF systems was done. The effect of the rare gas matrix on the HRgF (Rg = Ar and Kr) spectra was investigated and it was found that the matrix blue-shifted the spectra. Scalar relativistic effects on the spectra were also studied and it was found that while the excitation energies of HArF and HKrF were insignificantly affected by relativistic effects, most of the excitation energies of HXeF and HRnF were red-shifted. Spin-orbit coupling was found to significantly affect excitation energies in HRnF. Analysis of performance of the model core potential basis set relative to all-electron (AE) basis sets showed that the former basis set increased computational efficiency and gave results similar to those obtained with the AE basis set.

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.

Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2.

PubMed

Solomonik, Victor G; Smirnov, Alexander N; Navarkin, Ilya S

2016-04-14

The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2

NASA Astrophysics Data System (ADS)

Solomonik, Victor G.; Smirnov, Alexander N.; Navarkin, Ilya S.

2016-04-01

The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

First example of a high-level correlated calculation of the indirect spin-spin coupling constants involving tellurium: tellurophene and divinyl telluride.

PubMed

Rusakov, Yury Yu; Krivdin, Leonid B; Østerstrøm, Freja F; Sauer, Stephan P A; Potapov, Vladimir A; Amosova, Svetlana V

2013-08-21

This paper documents the very first example of a high-level correlated calculation of spin-spin coupling constants involving tellurium taking into account relativistic effects, vibrational corrections and solvent effects for medium sized organotellurium molecules. The (125)Te-(1)H spin-spin coupling constants of tellurophene and divinyl telluride were calculated at the SOPPA and DFT levels, in good agreement with experimental data. A new full-electron basis set, av3z-J, for tellurium derived from the "relativistic" Dyall's basis set, dyall.av3z, and specifically optimized for the correlated calculations of spin-spin coupling constants involving tellurium was developed. The SOPPA method shows a much better performance compared to DFT, if relativistic effects calculated within the ZORA scheme are taken into account. Vibrational and solvent corrections are next to negligible, while conformational averaging is of prime importance in the calculation of (125)Te-(1)H spin-spin couplings. Based on the performed calculations at the SOPPA(CCSD) level, a marked stereospecificity of geminal and vicinal (125)Te-(1)H spin-spin coupling constants originating in the orientational lone pair effect of tellurium has been established, which opens a new guideline in organotellurium stereochemistry.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, J. Grant, E-mail: grant.hill@sheffield.ac.uk, E-mail: kipeters@wsu.edu; Peterson, Kirk A., E-mail: grant.hill@sheffield.ac.uk, E-mail: kipeters@wsu.edu

New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga–Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of themore » spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons.« less

Equation-of-motion coupled-cluster method for doubly ionized states with spin-orbit coupling.

PubMed

Wang, Zhifan; Hu, Shu; Wang, Fan; Guo, Jingwei

2015-04-14

In this work, we report implementation of the equation-of-motion coupled-cluster method for doubly ionized states (EOM-DIP-CC) with spin-orbit coupling (SOC) using a closed-shell reference. Double ionization potentials (DIPs) are calculated in the space spanned by 2h and 3h1p determinants with the EOM-DIP-CC approach at the CC singles and doubles level (CCSD). Time-reversal symmetry together with spatial symmetry is exploited to reduce computational effort. To circumvent the problem of unstable dianion references when diffuse basis functions are included, nuclear charges are scaled. Effect of this stabilization potential on DIPs is estimated based on results from calculations using a small basis set without diffuse basis functions. DIPs and excitation energies of some low-lying states for a series of open-shell atoms and molecules containing heavy elements with two unpaired electrons have been calculated with the EOM-DIP-CCSD approach. Results show that this approach is able to afford a reliable description on SOC splitting. Furthermore, the EOM-DIP-CCSD approach is shown to provide reasonable excitation energies for systems with a dianion reference when diffuse basis functions are not employed.

Exploring biorthonormal transformations of pair-correlation functions in atomic structure variational calculations

NASA Astrophysics Data System (ADS)

Verdebout, S.; Jönsson, P.; Gaigalas, G.; Godefroid, M.; Froese Fischer, C.

2010-04-01

Multiconfiguration expansions frequently target valence correlation and correlation between valence electrons and the outermost core electrons. Correlation within the core is often neglected. A large orbital basis is needed to saturate both the valence and core-valence correlation effects. This in turn leads to huge numbers of configuration state functions (CSFs), many of which are unimportant. To avoid the problems inherent to the use of a single common orthonormal orbital basis for all correlation effects in the multiconfiguration Hartree-Fock (MCHF) method, we propose to optimize independent MCHF pair-correlation functions (PCFs), bringing their own orthonormal one-electron basis. Each PCF is generated by allowing single- and double-excitations from a multireference (MR) function. This computational scheme has the advantage of using targeted and optimally localized orbital sets for each PCF. These pair-correlation functions are coupled together and with each component of the MR space through a low dimension generalized eigenvalue problem. Nonorthogonal orbital sets being involved, the interaction and overlap matrices are built using biorthonormal transformation of the coupled basis sets followed by a counter-transformation of the PCF expansions. Applied to the ground state of beryllium, the new method gives total energies that are lower than the ones from traditional complete active space (CAS)-MCHF calculations using large orbital active sets. It is fair to say that we now have the possibility to account for, in a balanced way, correlation deep down in the atomic core in variational calculations.

CCSD(T) potential energy and induced dipole surfaces for N2–H2(D2): retrieval of the collision-induced absorption integrated intensities in the regions of the fundamental and first overtone vibrational transitions.

PubMed

Buryak, Ilya; Lokshtanov, Sergei; Vigasin, Andrey

2012-09-21

The present work aims at ab initio characterization of the integrated intensity temperature variation of collision-induced absorption (CIA) in N(2)-H(2)(D(2)). Global fits of potential energy surface (PES) and induced dipole moment surface (IDS) were made on the basis of CCSD(T) (coupled cluster with single and double and perturbative triple excitations) calculations with aug-cc-pV(T,Q)Z basis sets. Basis set superposition error correction and extrapolation to complete basis set (CBS) limit techniques were applied to both energy and dipole moment. Classical second cross virial coefficient calculations accounting for the first quantum correction were employed to prove the quality of the obtained PES. The CIA temperature dependence was found in satisfactory agreement with available experimental data.

The HCO+-H2 van der Waals interaction: Potential energy and scattering

NASA Astrophysics Data System (ADS)

Massó, H.; Wiesenfeld, L.

2014-11-01

We compute the rigid-body, four-dimensional interaction potential between HCO+ and H2. The ab initio energies are obtained at the coupled-cluster single double triple level of theory, corrected for Basis Set Superposition Errors. The ab initio points are fit onto the spherical basis relevant for quantum scattering. We present elastic and rotationally inelastic coupled channels scattering between low lying rotational levels of HCO+ and para-/ortho-H2. Results are compared with similar earlier computations with He or isotropic para-H2 as the projectile. Computations agree with earlier pressure broadening measurements.

The HCO⁺-H₂ van der Waals interaction: potential energy and scattering.

PubMed

Massó, H; Wiesenfeld, L

2014-11-14

We compute the rigid-body, four-dimensional interaction potential between HCO(+) and H2. The ab initio energies are obtained at the coupled-cluster single double triple level of theory, corrected for Basis Set Superposition Errors. The ab initio points are fit onto the spherical basis relevant for quantum scattering. We present elastic and rotationally inelastic coupled channels scattering between low lying rotational levels of HCO(+) and para-/ortho-H2. Results are compared with similar earlier computations with He or isotropic para-H2 as the projectile. Computations agree with earlier pressure broadening measurements.

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Xantheas, Sotiris S.

2015-03-01

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.

Structure and energetics of Cr(CO)6 and Cr(CO)5

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Liu, Bowen; Lindh, Roland

1993-01-01

The geometric structures and energetics of Cr(CO)6 and Cr(CO)5 are determined at the modified coupled-pair functional, single and double excitation coupled-cluster (CCSD), and CCSD(T) levels of theory. For Cr(CO)6, the structure and force constants for the totally symmetric representation are in good agreement with experimental data once basis set constants are taken into account. In the largest basis set at the CCSD(T) level of theory, the total binding energy of CR(CO)6 is estimated at around 140 kcal/mol, or about 86 percent of the experimental value. In contrast, the first bond energy of Cr(CO)6 is very well described at the CCSD(T) level of theory, with the best estimated value of 38 kcal/mol being within the experimental uncertainty.

Straightening the Hierarchical Staircase for Basis Set Extrapolations: A Low-Cost Approach to High-Accuracy Computational Chemistry

NASA Astrophysics Data System (ADS)

Varandas, António J. C.

2018-04-01

Because the one-electron basis set limit is difficult to reach in correlated post-Hartree-Fock ab initio calculations, the low-cost route of using methods that extrapolate to the estimated basis set limit attracts immediate interest. The situation is somewhat more satisfactory at the Hartree-Fock level because numerical calculation of the energy is often affordable at nearly converged basis set levels. Still, extrapolation schemes for the Hartree-Fock energy are addressed here, although the focus is on the more slowly convergent and computationally demanding correlation energy. Because they are frequently based on the gold-standard coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)], correlated calculations are often affordable only with the smallest basis sets, and hence single-level extrapolations from one raw energy could attain maximum usefulness. This possibility is examined. Whenever possible, this review uses raw data from second-order Møller-Plesset perturbation theory, as well as CCSD, CCSD(T), and multireference configuration interaction methods. Inescapably, the emphasis is on work done by the author's research group. Certain issues in need of further research or review are pinpointed.

On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants

NASA Astrophysics Data System (ADS)

Zarycz, M. Natalia C.; Provasi, Patricio F.; Sauer, Stephan P. A.

2015-12-01

It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH4, NH3, H2O, SiH4, PH3, SH2, C2H2, C2H4, and C2H6. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

On the accuracy of explicitly correlated methods to generate potential energy surfaces for scattering calculations and clustering: application to the HCl-He complex.

PubMed

Ajili, Yosra; Hammami, Kamel; Jaidane, Nejm Eddine; Lanza, Mathieu; Kalugina, Yulia N; Lique, François; Hochlaf, Majdi

2013-07-07

We closely compare the accuracy of multidimensional potential energy surfaces (PESs) generated by the recently developed explicitly correlated coupled cluster (CCSD(T)-F12) methods in connection with the cc-pVXZ-F12 (X = D, T) and aug-cc-pVTZ basis sets and those deduced using the well-established orbital-based coupled cluster techniques employing correlation consistent atomic basis sets (aug-cc-pVXZ, X = T, Q, 5) and extrapolated to the complete basis set (CBS) limit. This work is performed on the benchmark rare gas-hydrogen halide interaction (HCl-He) system. These PESs are then incorporated into quantum close-coupling scattering dynamical calculations in order to check the impact of the accuracy of the PES on the scattering calculations. For this system, we deduced inelastic collisional data including (de-)excitation collisional and pressure broadening cross sections. Our work shows that the CCSD(T)-F12/aug-cc-pVTZ PES describes correctly the repulsive wall, the van der Waals minimum and long range internuclear distances whereas cc-pVXZ-F12 (X = D,T) basis sets are not diffuse enough for that purposes. Interestingly, the collision cross sections deduced from the CCSD(T)-F12/aug-cc-pVTZ PES are in excellent agreement with those obtained with CCSD(T)/CBS methodology. The position of the resonances and the general shape of these cross sections almost coincide. Since the cost of the electronic structure computations is reduced by several orders of magnitude when using CCSD(T)-F12/aug-cc-pVTZ compared to CCSD(T)/CBS methodology, this approach can be recommended as an alternative for generation of PESs of molecular clusters and for the interpretation of accurate scattering experiments as well as for a wide production of collisional data to be included in astrophysical and atmospherical models.

The electronic structure of vanadium monochloride cation (VCl{sup +}): Tackling the complexities of transition metal species

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeYonker, Nathan J., E-mail: ndyonker@memphis.edu; Halfen, DeWayne T.; Ziurys, Lucy M.

Six electronic states (X {sup 4}Σ{sup −}, A {sup 4}Π, B {sup 4}Δ, {sup 2}Φ, {sup 2}Δ, {sup 2}Σ{sup +}) of the vanadium monochloride cation (VCl{sup +}) are described using large basis set coupled cluster theory. For the two lowest quartet states (X {sup 4}Σ{sup −} and A {sup 4}Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T{sub 0}) and spectroscopic constants (r{sub e}, r{sub 0}, B{sub e}, B{sub 0}, D{sup ¯}{sub e}, H{sub e},more » ω{sub e}, v{sub 0}, α{sub e}, ω{sub e}x{sub e}) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X {sup 4}Σ{sup −}), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state ({sup 2}Γ) has a T{sub e} of ∼11 200 cm{sup −1}. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.« less

Photoinduced dynamics to photoluminescence in Ln3+ (Ln = Ce, Pr) doped β-NaYF4 nanocrystals computed in basis of non-collinear spin DFT with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Han, Yulun; Vogel, Dayton J.; Inerbaev, Talgat M.; May, P. Stanley; Berry, Mary T.; Kilin, Dmitri S.

2018-03-01

In this work, non-collinear spin DFT + U approaches with spin-orbit coupling (SOC) are applied to Ln3+ doped β-NaYF4 (Ln = Ce, Pr) nanocrystals in Vienna ab initio Simulation Package taking into account unpaired spin configurations using the Perdew-Burke-Ernzerhof functional in a plane wave basis set. The calculated absorption spectra from non-collinear spin DFT + U approaches are compared with that from spin-polarised DFT + U approaches. The spectral difference indicates the importance of spin-flip transitions of Ln3+ ions. Suite of codes for nonadiabatic dynamics has been developed for 2-component spinor orbitals. On-the-fly nonadiabatic coupling calculations provide transition probabilities facilitated by nuclear motion. Relaxation rates of electrons and holes are calculated using Redfield theory in the reduced density matrix formalism cast in the basis of non-collinear spin DFT + U with SOC. The emission spectra are calculated using the time-integrated method along the excited state trajectories based on nonadiabatic couplings.

The structure and energetics of Cr(CO)6 and Cr(CO)5

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Liu, Bowen; Lindh, Roland

1992-01-01

The geometric structure of Cr(CO)6 is optimized at the modified coupled pair functional (MCPF), single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD, and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD, and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used. Calculations using larger basis sets reduce the BSSE, but the total binding energy of Cr(CO)6 is still significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. In the largest basis set, the total CO binding energy of Cr(CO)6 is estimated to be 140 kcal/mol at the CCSD(T) level of theory, or about 86 percent of the experimental value. The remaining discrepancy between the experimental and theoretical value is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular an additional d function and an f function on each C and O are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive set (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

Explicitly correlated coupled-cluster theory using cusp conditions. II. Treatment of connected triple excitations.

PubMed

Köhn, Andreas

2010-11-07

The coupled-cluster singles and doubles method augmented with single Slater-type correlation factors (CCSD-F12) determined by the cusp conditions (also denoted as SP ansatz) yields results close to the basis set limit with only small overhead compared to conventional CCSD. Quantitative calculations on many-electron systems, however, require to include the effect of connected triple excitations at least. In this contribution, the recently proposed [A. Köhn, J. Chem. Phys. 130, 131101 (2009)] extended SP ansatz and its application to the noniterative triples correction CCSD(T) is reviewed. The approach allows to include explicit correlation into connected triple excitations without introducing additional unknown parameters. The explicit expressions are presented and analyzed, and possible simplifications to arrive at a computationally efficient scheme are suggested. Numerical tests based on an implementation obtained by an automated approach are presented. Using a partial wave expansion for the neon atom, we can show that the proposed ansatz indeed leads to the expected (L(max)+1)(-7) convergence of the noniterative triples correction, where L(max) is the maximum angular momentum in the orbital expansion. Further results are reported for a test set of 29 molecules, employing Peterson's F12-optimized basis sets. We find that the customary approach of using the conventional noniterative triples correction on top of a CCSD-F12 calculation leads to significant basis set errors. This, however, is not always directly visible for total CCSD(T) energies due to fortuitous error compensation. The new approach offers a thoroughly explicitly correlated CCSD(T)-F12 method with improved basis set convergence of the triples contributions to both total and relative energies.

Systematically convergent basis sets for transition metals. I. All-electron correlation consistent basis sets for the 3d elements Sc-Zn

NASA Astrophysics Data System (ADS)

Balabanov, Nikolai B.; Peterson, Kirk A.

2005-08-01

Sequences of basis sets that systematically converge towards the complete basis set (CBS) limit have been developed for the first-row transition metal elements Sc-Zn. Two families of basis sets, nonrelativistic and Douglas-Kroll-Hess (-DK) relativistic, are presented that range in quality from triple-ζ to quintuple-ζ. Separate sets are developed for the description of valence (3d4s) electron correlation (cc-pVnZ and cc-pVnZ-DK; n =T,Q, 5) and valence plus outer-core (3s3p3d4s) correlation (cc-pwCVnZ and cc-pwCVnZ-DK; n =T,Q, 5), as well as these sets augmented by additional diffuse functions for the description of negative ions and weak interactions (aug-cc-pVnZ and aug-cc-pVnZ-DK). Extensive benchmark calculations at the coupled cluster level of theory are presented for atomic excitation energies, ionization potentials, and electron affinities, as well as molecular calculations on selected hydrides (TiH, MnH, CuH) and other diatomics (TiF, Cu2). In addition to observing systematic convergence towards the CBS limits, both 3s3p electron correlation and scalar relativity are calculated to strongly impact many of the atomic and molecular properties investigated for these first-row transition metal species.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dutta, S.; Saha, J. K.; Chandra, R.

The Rayleigh-Ritz variational technique with a Hylleraas basis set is being tested for the first time to estimate the structural modifications of a lithium atom embedded in a weakly coupled plasma environment. The Debye-Huckel potential is used to mimic the weakly coupled plasma environment. The wave functions for both the helium-like lithium ion and the lithium atom are expanded in the explicitly correlated Hylleraas type basis set which fully takes care of the electron-electron correlation effect. Due to the continuum lowering under plasma environment, the ionization potential of the system gradually decreases leading to the destabilization of the atom. Themore » excited states destabilize at a lower value of the plasma density. The estimated ionization potential agrees fairly well with the few available theoretical estimates. The variation of one and two particle moments, dielectric susceptibility and magnetic shielding constant, with respect to plasma density is also been discussed in detail.« less

Carbon-Hydrogen Bond Activation in Hydridotris(pyrazolyl)borate Platinum(IV) Complexes:  Comparison of Density Functionals, Basis Sets, and Bonding Patterns.

PubMed

Vastine, Benjamin Alan; Webster, Charles Edwin; Hall, Michael B

2007-11-01

The reaction mechanism for the cycle beginning with the reductive elimination (RE) of methane from κ(3)-TpPt(IV)(CH3)2H (1) (Tp = hydridotris(pyrazolyl)borate) and subsequent oxidative addition (OA) of benzene to form finally κ(3)-TpPt(IV)(Ph)2H (19) was investigated by density functional theory (DFT). Two mechanistic steps are of particular interest, namely the barrier to C-H coupling (barrier 1 - Ba1) and the barrier to methane release (barrier 2 - Ba2). For 31 density functionals, the calculated values for Ba1 and Ba2 were benchmarked against the experimentally reported values of 26 (Ba1) and 35 (Ba2) kcal·mol(-1), respectively. Specifically, the values for Ba1 and Ba2, calculated at the B3LYP/double-ζ plus polarization level of theory, are 24.6 and 34.3 kcal·mol(-1), respectively. Overall, the best performing functional was BPW91 where the mae associated with the calculated values of the two barriers is 0.68 kcal·mol(-1). The calculated B3LYP values of Ba1 ranged between 20 and 26 kcal·mol(-1) for 12 effective core potential basis sets for platinum and 29 all-electron basis sets for the first row elements. Polarization functions for the first row elements were important for accurate values, but the addition of diffuse functions to non-hydrogen (+) and hydrogen atoms (++) had little effect on the calculated values. Basis set saturation was achieved with APNO basis sets utilized for first-row atoms. Bader's "Atoms in Molecules" was used to analyze the electron density of several complexes, and the electron density at the Pt-Nax bond critical point (trans to the active site for C-H coupling) varied over a wider range than any of the other Pt-N bonds.

Correlation consistent basis sets for lanthanides: The atoms La–Lu

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Qing; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples,more » CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd{sub 2}, GdF, and GdF{sub 3}. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd{sub 2}, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF{sub 3}.« less

Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

PubMed

Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

2016-02-05

Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

Narrowing the error in electron correlation calculations by basis set re-hierarchization and use of the unified singlet and triplet electron-pair extrapolation scheme: Application to a test set of 106 systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varandas, A. J. C., E-mail: varandas@uc.pt; Departamento de Física, Universidade Federal do Espírito Santo, 29075-910 Vitória; Pansini, F. N. N.

2014-12-14

A method previously suggested to calculate the correlation energy at the complete one-electron basis set limit by reassignment of the basis hierarchical numbers and use of the unified singlet- and triplet-pair extrapolation scheme is applied to a test set of 106 systems, some with up to 48 electrons. The approach is utilized to obtain extrapolated correlation energies from raw values calculated with second-order Møller-Plesset perturbation theory and the coupled-cluster singles and doubles excitations method, some of the latter also with the perturbative triples corrections. The calculated correlation energies have also been used to predict atomization energies within an additive scheme.more » Good agreement is obtained with the best available estimates even when the (d, t) pair of hierarchical numbers is utilized to perform the extrapolations. This conceivably justifies that there is no strong reason to exclude double-zeta energies in extrapolations, especially if the basis is calibrated to comply with the theoretical model.« less

Computational studies of metal-metal and metal-ligand interactions

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.

1992-01-01

The geometric structure of Cr(CO)6 is optimized at the modified coupled-pair functional (MCPF), single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. A detailed comparison of the properties of free CO is therefore given, at both the MCPF and CCSD/CCSD(T) levels of treatment, using a variety of basis sets. With very large one-particle basis sets, the SSCD(T) method gives excellent results for the bond distance, dipole moment and harmonic frequency of free CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used here and in a previous study. Calculations using larger basis sets reduced the BSSE, but the total binding energy of Cr(CO)6 is still significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. The remaining discrepancy between the experimental and theoretical total binding energy of Cr(CO)6 is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular an additional d function and an f function on each C and O are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive se (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

Gaussian basis sets for use in correlated molecular calculations. XI. Pseudopotential-based and all-electron relativistic basis sets for alkali metal (K-Fr) and alkaline earth (Ca-Ra) elements

NASA Astrophysics Data System (ADS)

Hill, J. Grant; Peterson, Kirk A.

2017-12-01

New correlation consistent basis sets based on pseudopotential (PP) Hamiltonians have been developed from double- to quintuple-zeta quality for the late alkali (K-Fr) and alkaline earth (Ca-Ra) metals. These are accompanied by new all-electron basis sets of double- to quadruple-zeta quality that have been contracted for use with both Douglas-Kroll-Hess (DKH) and eXact 2-Component (X2C) scalar relativistic Hamiltonians. Sets for valence correlation (ms), cc-pVnZ-PP and cc-pVnZ-(DK,DK3/X2C), in addition to outer-core correlation [valence + (m-1)sp], cc-p(w)CVnZ-PP and cc-pwCVnZ-(DK,DK3/X2C), are reported. The -PP sets have been developed for use with small-core PPs [I. S. Lim et al., J. Chem. Phys. 122, 104103 (2005) and I. S. Lim et al., J. Chem. Phys. 124, 034107 (2006)], while the all-electron sets utilized second-order DKH Hamiltonians for 4s and 5s elements and third-order DKH for 6s and 7s. The accuracy of the basis sets is assessed through benchmark calculations at the coupled-cluster level of theory for both atomic and molecular properties. Not surprisingly, it is found that outer-core correlation is vital for accurate calculation of the thermodynamic and spectroscopic properties of diatomic molecules containing these elements.

Parameter and Structure Inference for Nonlinear Dynamical Systems

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

2006-01-01

A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr

2013-11-07

Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality.more » By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.« less

Electronic and spectroscopic characterizations of SNP isomers

NASA Astrophysics Data System (ADS)

Trabelsi, Tarek; Al Mogren, Muneerah Mogren; Hochlaf, Majdi; Francisco, Joseph S.

2018-02-01

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ˜2.4 eV above the linear SNP isomer. The low-lying singlet and triplet electronic states of the linear SNP and SPN isomers were investigated using a multi-reference configuration interaction method and large basis set. Several bound electronic states were identified. However, their upper rovibrational levels were predicted to pre-dissociate, leading to S + PN, P + NS products, and multi-step pathways were discovered. For the ground states, a set of spectroscopic parameters were derived using standard and explicitly correlated coupled-cluster methods in conjunction with augmented correlation-consistent basis sets extrapolated to the complete basis set limit. We also considered scalar and core-valence effects. For linear isomers, the rovibrational spectra were deduced after generation of their 3D-potential energy surfaces along the stretching and bending coordinates and variational treatments of the nuclear motions.

Coupled-cluster based basis sets for valence correlation calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Claudino, Daniel; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu; Gargano, Ricardo

Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These newmore » sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via 〈r{sup n}〉 (−3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within “chemical accuracy” of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.« less

Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields.

PubMed

Zhu, Wuming; Trickey, S B

2017-12-28

In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li + , Be + , and B + , in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B field.

Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields

NASA Astrophysics Data System (ADS)

Zhu, Wuming; Trickey, S. B.

2017-12-01

In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li+, Be+, and B+, in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B field.

Third-order Douglas-Kroll Relativistic Coupled-Cluster Theory through Connected Single, Double, Triple, and Quadruple Substitutions: Applications to Diatomic and Triatomic Hydrides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirata, So; Yanai, Takeshi; De Jong, Wibe A.

Coupled-cluster methods including through and up to the connected single, double, triple, and quadruple substitutions (CCSD, CCSDT, and CCSDTQ) have been automatically derived and implemented for sequential and parallel executions for use in conjunction with a one-component third-order Douglas-Kroll (DK3) approximation for relativistic corrections. A combination of the converging electron-correlation methods, the accurate relativistic reference wave functions, and the use of systematic basis sets tailored to the relativistic approximation has been shown to predict the experimental singlet-triplet separations within 0.02 eV (0.5 kcal/mol) for five triatomic hydrides (CH2, NH2+, SiH2, PH2+, and AsH2+), the experimental bond lengths within 0.002 angstroms,more » rotational constants within 0.02 cm-1, vibration-rotation constants within 0.01 cm-1, centrifugal distortion constants within 2 %, harmonic vibration frequencies within 9 cm-1 (0.4 %), anharmonic vibrational constants within 2 cm-1, and dissociation energies within 0.03 eV (0.8 kcal/mol) for twenty diatomic hydrides (BH, CH, NH, OH, FH, AlH, SiH, PH, SH, ClH, GaH, GeH, AsH, SeH, BrH, InH, SnH, SbH, TeH, and IH) containing main-group elements across the second through fifth periods of the periodic table. In these calculations, spin-orbit effects on dissociation energies, which were assumed to be additive, were estimated from the measured spin-orbit coupling constants of atoms and diatomic molecules, and an electronic energy in the complete-basis-set, complete-electron-correlation limit has been extrapolated by the formula which was in turn based on the exponential-Gaussian extrapolation formula of the basis set dependence.« less

A density functional theory study of the magnetic exchange coupling in dinuclear manganese(II) inverse crown structures.

PubMed

Vélez, Ederley; Alberola, Antonio; Polo, Víctor

2009-12-17

The magnetic exchange coupling constants between two Mn(II) centers for a set of five inverse crown structures have been investigated by means of a methodology based on broken-symmetry unrestricted density functional theory. These novel and highly unstable compounds present superexchange interactions between two Mn centers, each one with S = 5/2 through anionic "guests" such as oxygen, benzene, or hydrides or through the cationic ring formed by amide ligands and alkali metals (Na, Li). Magnetic exchange couplings calculated at B3LYP/6-31G(d,p) level yield strong antiferromagnetic couplings for compounds linked via an oxygen atom or hydride and very small antiferromagnetic couplings for those linked via a benzene molecule, deprotonated in either 1,4- or 1,3- positions. Analysis of the magnetic orbitals and spin polarization maps provide an understanding of the exchange mechanism between the Mn centers. The dependence of J with respect to 10 different density functional theory potentials employed and the basis set has been analyzed.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Benchmark quality total atomization energies of small polyatomic molecules

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Taylor, Peter R.

1997-05-01

Successive coupled-cluster [CCSD(T)] calculations in basis sets of spdf, spdfg, and spdfgh quality, combined with separate Schwartz-type extrapolations A+B/(l+1/2)α of the self-consistent field (SCF) and correlation energies, permit the calculations of molecular total atomization energies (TAEs) with a mean absolute error of as low as 0.12 kcal/mol. For the largest molecule treated, C2H4, we find ∑D0=532.0 kcal/mol, in perfect agreement with experiment. The aug-cc-pV5Z basis set recovers on average about 99% of the valence correlation contribution to the TAE, and essentially the entire SCF contribution.

Efficient parallel architecture for highly coupled real-time linear system applications

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Homaifar, Abdollah; Barua, Soumavo

1988-01-01

A systematic procedure is developed for exploiting the parallel constructs of computation in a highly coupled, linear system application. An overall top-down design approach is adopted. Differential equations governing the application under consideration are partitioned into subtasks on the basis of a data flow analysis. The interconnected task units constitute a task graph which has to be computed in every update interval. Multiprocessing concepts utilizing parallel integration algorithms are then applied for efficient task graph execution. A simple scheduling routine is developed to handle task allocation while in the multiprocessor mode. Results of simulation and scheduling are compared on the basis of standard performance indices. Processor timing diagrams are developed on the basis of program output accruing to an optimal set of processors. Basic architectural attributes for implementing the system are discussed together with suggestions for processing element design. Emphasis is placed on flexible architectures capable of accommodating widely varying application specifics.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Simulation of the photodetachment spectrum of HHfO- using coupled-cluster calculations

NASA Astrophysics Data System (ADS)

Mok, Daniel K. W.; Dyke, John M.; Lee, Edmond P. F.

2016-12-01

The photodetachment spectrum of HHfO- was simulated using restricted-spin coupled-cluster single-double plus perturbative triple {RCCSD(T)} calculations performed on the ground electronic states of HHfO and HHfO-, employing basis sets of up to quintuple-zeta quality. The computed RCCSD(T) electron affinity of 1.67 ± 0.02 eV at the complete basis set limit, including Hf 5s25p6 core correlation and zero-point energy corrections, agrees well with the experimental value of 1.70 ± 0.05 eV from a recent photodetachment study [X. Li et al., J. Chem. Phys. 136, 154306 (2012)]. For the simulation, Franck-Condon factors were computed which included allowances for anharmonicity and Duschinsky rotation. Comparisons between simulated and experimental spectra confirm the assignments of the molecular carrier and electronic states involved but suggest that the experimental vibrational structure has suffered from poor signal-to-noise ratio. An alternative assignment of the vibrational structure to that suggested in the experimental work is presented.

Need for reaction coordinates to ensure a complete basis set in an adiabatic representation of ion-atom collisions

NASA Astrophysics Data System (ADS)

Rabli, Djamal; McCarroll, Ronald

2018-02-01

This review surveys the different theoretical approaches, used to describe inelastic and rearrangement processes in collisions involving atoms and ions. For a range of energies from a few meV up to about 1 keV, the adiabatic representation is expected to be valid and under these conditions, inelastic and rearrangement processes take place via a network of avoided crossings of the potential energy curves of the collision system. In general, such avoided crossings are finite in number. The non-adiabatic coupling, due to the breakdown of the Born-Oppenheimer separation of the electronic and nuclear variables, depends on the ratio of the electron mass to the nuclear mass terms in the total Hamiltonian. By limiting terms in the total Hamiltonian correct to first order in the electron to nuclear mass ratio, a system of reaction coordinates is found which allows for a correct description of both inelastic channels. The connection between the use of reaction coordinates in the quantum description and the electron translation factors of the impact parameter approach is established. A major result is that only when reaction coordinates are used, is it possible to introduce the notion of a minimal basis set. Such a set must include all avoided crossings including both radial coupling and long range Coriolis coupling. But, only when reactive coordinates are used, can such a basis set be considered as complete. In particular when the centre of nuclear mass is used as centre of coordinates, rather than the correct reaction coordinates, it is shown that erroneous results are obtained. A few results to illustrate this important point are presented: one concerning a simple two-state Landau-Zener type avoided crossing, the other concerning a network of multiple crossings in a typical electron capture process involving a highly charged ion with a neutral atom.

Analytical energy gradients for explicitly correlated wave functions. I. Explicitly correlated second-order Møller-Plesset perturbation theory

NASA Astrophysics Data System (ADS)

Győrffy, Werner; Knizia, Gerald; Werner, Hans-Joachim

2017-12-01

We present the theory and algorithms for computing analytical energy gradients for explicitly correlated second-order Møller-Plesset perturbation theory (MP2-F12). The main difficulty in F12 gradient theory arises from the large number of two-electron integrals for which effective two-body density matrices and integral derivatives need to be calculated. For efficiency, the density fitting approximation is used for evaluating all two-electron integrals and their derivatives. The accuracies of various previously proposed MP2-F12 approximations [3C, 3C(HY1), 3*C(HY1), and 3*A] are demonstrated by computing equilibrium geometries for a set of molecules containing first- and second-row elements, using double-ζ to quintuple-ζ basis sets. Generally, the convergence of the bond lengths and angles with respect to the basis set size is strongly improved by the F12 treatment, and augmented triple-ζ basis sets are sufficient to closely approach the basis set limit. The results obtained with the different approximations differ only very slightly. This paper is the first step towards analytical gradients for coupled-cluster singles and doubles with perturbative treatment of triple excitations, which will be presented in the second part of this series.

Structure and NMR spectra of some [2.2]paracyclophanes. The dilemma of [2.2]paracyclophane symmetry.

PubMed

Dodziuk, Helena; Szymański, Sławomir; Jaźwiński, Jarosław; Ostrowski, Maciej; Demissie, Taye Beyene; Ruud, Kenneth; Kuś, Piotr; Hopf, Henning; Lin, Shaw-Tao

2011-09-29

Density functional theory (DFT) quantum chemical calculations of the structure and NMR parameters for highly strained hydrocarbon [2.2]paracyclophane 1 and its three derivatives are presented. The calculated NMR parameters are compared with the experimental ones. By least-squares fitting of the (1)H spectra, almost all J(HH) coupling constants could be obtained with high accuracy. Theoretical vicinal J(HH) couplings in the aliphatic bridges, calculated using different basis sets (6-311G(d,p), and Huz-IV) reproduce the experimental values with essentially the same root-mean-square (rms) error of about 1.3 Hz, regardless of the basis set used. These discrepancies could be in part due to a considerable impact of rovibrational effects on the observed J(HH) couplings, since the latter show a measurable dependence on temperature. Because of the lasting literature controversies concerning the symmetry of parent compound 1, D(2h) versus D(2), a critical analysis of the relevant literature data is carried out. The symmetry issue is prone to confusion because, according to some literature claims, the two hypothetical enantiomeric D(2) structures of 1 could be separated by a very low energy barrier that would explain the occurrence of rovibrational effects on the observed vicinal J(HH) couplings. However, the D(2h) symmetry of 1 with a flat energy minimum could also account for these effects.

Relativistic theory of nuclear spin-rotation tensor with kinetically balanced rotational London orbitals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Yunlong; Zhang, Yong; Liu, Wenjian, E-mail: liuwjbdf@gmail.com

2014-10-28

Both kinetically balanced (KB) and kinetically unbalanced (KU) rotational London orbitals (RLO) are proposed to resolve the slow basis set convergence in relativistic calculations of nuclear spin-rotation (NSR) coupling tensors of molecules containing heavy elements [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]. While they perform rather similarly, the KB-RLO Ansatz is clearly preferred as it ensures the correct nonrelativistic limit even with a finite basis. Moreover, it gives rise to the same “direct relativistic mapping” between nuclear magnetic resonance shielding and NSR coupling tensors as that without using the London orbitals [Y. Xiao, Y. Zhang, andmore » W. Liu, J. Chem. Theory Comput. 10, 600 (2014)].« less

Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr

NASA Astrophysics Data System (ADS)

Feng, Rulin; Peterson, Kirk A.

2017-08-01

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP0 for PuO2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO2 is predicted to be the 0 g +5Σ state.

Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr.

PubMed

Feng, Rulin; Peterson, Kirk A

2017-08-28

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO 2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP 0 for PuO 2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO 2 is predicted to be the Σ0g+5 state.

Vibrational and rotational transitions in low-energy electron-diatomic-molecule collisions. I - Close-coupling theory in the moving body-fixed frame. II - Hybrid theory and close-coupling theory: An /l subscript z-prime/-conserving close-coupling approximation

NASA Technical Reports Server (NTRS)

Choi, B. H.; Poe, R. T.

1977-01-01

A detailed vibrational-rotational (V-R) close-coupling formulation of electron-diatomic-molecule scattering is developed in which the target molecular axis is chosen to be the z-axis and the resulting coupled differential equation is solved in the moving body-fixed frame throughout the entire interaction region. The coupled differential equation and asymptotic boundary conditions in the body-fixed frame are given for each parity, and procedures are outlined for evaluating V-R transition cross sections on the basis of the body-fixed transition and reactance matrix elements. Conditions are discussed for obtaining identical results from the space-fixed and body-fixed formulations in the case where a finite truncated basis set is used. The hybrid theory of Chandra and Temkin (1976) is then reformulated, relevant expressions and formulas for the simultaneous V-R transitions of the hybrid theory are obtained in the same forms as those of the V-R close-coupling theory, and distorted-wave Born-approximation expressions for the cross sections of the hybrid theory are presented. A close-coupling approximation that conserves the internuclear axis component of the incident electronic angular momentum (l subscript z-prime) is derived from the V-R close-coupling formulation in the moving body-fixed frame.

Spin-orbit splitted excited states using explicitly-correlated equation-of-motion coupled-cluster singles and doubles eigenvectors

NASA Astrophysics Data System (ADS)

Bokhan, Denis; Trubnikov, Dmitrii N.; Perera, Ajith; Bartlett, Rodney J.

2018-04-01

An explicitly-correlated method of calculation of excited states with spin-orbit couplings, has been formulated and implemented. Developed approach utilizes left and right eigenvectors of equation-of-motion coupled-cluster model, which is based on the linearly approximated explicitly correlated coupled-cluster singles and doubles [CCSD(F12)] method. The spin-orbit interactions are introduced by using the spin-orbit mean field (SOMF) approximation of the Breit-Pauli Hamiltonian. Numerical tests for several atoms and molecules show good agreement between explicitly-correlated results and the corresponding values, calculated in complete basis set limit (CBS); the highly-accurate excitation energies can be obtained already at triple- ζ level.

Accurate ab initio binding energies of the benzene dimer.

PubMed

Park, Young Choon; Lee, Jae Shin

2006-04-20

Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.

40 CFR 40.150 - Evaluation of applications.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... Relevancy, coupled with the results of technical review, will provide the basis for funding recommendations... will be reviewed for technical merit by at least one reviewer within EPA and at least two reviewers.... Recommendations for continuation of funding will be based on progress toward the accomplishment of the goals set...

Photoredox Catalysis Unlocks Single-Electron Elementary Steps in Transition Metal Catalyzed Cross-Coupling

PubMed Central

2016-01-01

Since initial reports, cross-coupling technologies employing photoredox catalysts to access novel reactivity have developed with increasing pace. In this Outlook, prominent examples from the recent literature are organized on the basis of the elementary transformation enabled by photoredox catalysis and are discussed in the context of relevant historical precedent in stoichiometric organometallic chemistry. This treatment allows mechanistic similarities inherent to odd-electron transition metal reactivity to be generalized to a set of lessons for future reaction development. PMID:27280163

Theoretical study of the hyperfine parameters of OH

NASA Technical Reports Server (NTRS)

Chong, Delano P.; Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.

1991-01-01

In the present study of the hyperfine parameters of O-17H as a function of the one- and n-particle spaces, all of the parameters except oxygen's spin density, b sub F(O), are sufficiently easily tractable to allow concentration on the computational requirements for accurate determination of b sub F(O). Full configuration-interaction (FCI) calculations in six Gaussian basis sets yield unambiguous results for (1) the effect of uncontracting the O s and p basis sets; (2) that of adding diffuse s and p functions; and (3) that of adding polarization functions to O. The size-extensive modified coupled-pair functional method yields b sub F values which are in fair agreement with FCI results.

A correlated ab initio study of linear carbon-chain radicals CnH (n = 2-7)

NASA Technical Reports Server (NTRS)

Woon, D. E.; Loew, G. H. (Principal Investigator)

1995-01-01

Linear carbon-chain radicals CnH for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2 sigma+ to 2 pi as the chain is extended. For C4H, the 2 sigma+ state was found to lie only 72 cm-1 below the 2 pi state in the estimated complete basis set limit for valence correlation. The C2H- and C3H- anions have also been characterized.

Magnetic exchange couplings from noncollinear perturbation theory: dinuclear CuII complexes.

PubMed

Phillips, Jordan J; Peralta, Juan E

2014-08-07

To benchmark the performance of a new method based on noncollinear coupled-perturbed density functional theory [J. Chem. Phys. 138, 174115 (2013)], we calculate the magnetic exchange couplings in a series of triply bridged ferromagnetic dinuclear Cu(II) complexes that have been recently synthesized [Phys. Chem. Chem. Phys. 15, 1966 (2013)]. We find that for any basis-set the couplings from our noncollinear coupled-perturbed methodology are practically identical to those of spin-projected energy-differences when a hybrid density functional approximation is employed. This demonstrates that our methodology properly recovers a Heisenberg description for these systems, and is robust in its predictive power of magnetic couplings. Furthermore, this indicates that the failure of density functional theory to capture the subtle variation of the exchange couplings in these complexes is not simply an artifact of broken-symmetry methods, but rather a fundamental weakness of current approximate density functionals for the description of magnetic couplings.

Interaction potentials and transport properties of Ba, Ba+, and Ba2+ in rare gases from He to Xe

NASA Astrophysics Data System (ADS)

Buchachenko, Alexei A.; Viehland, Larry A.

2018-04-01

A highly accurate, consistent set of ab initio interaction potentials is obtained for the title systems at the coupled cluster with singles, doubles, and non-iterative triples level of theory with extrapolation to the complete basis set limit. These potentials are shown to be more reliable than the previous potentials based on their long-range behavior, equilibrium properties, collision cross sections, and transport properties.

Magnetic exchange in {Gd(III)-radical} complexes: method assessment, mechanism of coupling and magneto-structural correlations.

PubMed

Gupta, Tulika; Rajeshkumar, Thayalan; Rajaraman, Gopalan

2014-07-28

Density functional studies have been performed on ten different {Gd(III)-radical} complexes exhibiting both ferro and antiferromagnetic exchange interaction with an aim to assess a suitable exchange-correlation functional within DFT formalism. This study has also been extended to probe the mechanism of magnetic coupling and to develop suitable magneto-structural correlations for this pair. Our method assessments reveal the following order of increasing accuracy for the evaluation of J values compared to experimental coupling constants: B(40HF)LYP < BHandHLYP < TPSSH < PW91 < PBE < BP86 < OLYP < BLYP < PBE0 < X3LYP < B3LYP < B2PLYP. Grimme's double-hybrid functional is found to be superior compared to other functionals tested and this is followed very closely by the conventional hybrid B3LYP functional. At the basis set front, our calculations reveal that the incorporation of relativistic effect is important in these calculations and the relativistically corrected effective core potential (ECP) basis set is found to yield better Js compared to other methods. The supposedly empty 5d/6s/6p orbitals of Gd(III) are found to play an important role in the mechanism of magnetic coupling and different contributions to the exchange terms are probed using Molecular Orbital (MO) and Natural Bond Orbital (NBO) analysis. Magneto-structural correlations for Gd-O distances, Gd-O-N angles and Gd-O-N-C dihedral angles are developed where the bond angles as well as dihedral angle parameters are found to dictate the sign and strength of the magnetic coupling in this series.

Analytic energy gradients for the coupled-cluster singles and doubles method with the density-fitting approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozkaya, Uğur, E-mail: ugur.bozkaya@hacettepe.edu.tr; Department of Chemistry, Atatürk University, Erzurum 25240; Sherrill, C. David

2016-05-07

An efficient implementation is presented for analytic gradients of the coupled-cluster singles and doubles (CCSD) method with the density-fitting approximation, denoted DF-CCSD. Frozen core terms are also included. When applied to a set of alkanes, the DF-CCSD analytic gradients are significantly accelerated compared to conventional CCSD for larger molecules. The efficiency of our DF-CCSD algorithm arises from the acceleration of several different terms, which are designated as the “gradient terms”: computation of particle density matrices (PDMs), generalized Fock-matrix (GFM), solution of the Z-vector equation, formation of the relaxed PDMs and GFM, back-transformation of PDMs and GFM to the atomic orbitalmore » (AO) basis, and evaluation of gradients in the AO basis. For the largest member of the alkane set (C{sub 10}H{sub 22}), the computational times for the gradient terms (with the cc-pVTZ basis set) are 2582.6 (CCSD) and 310.7 (DF-CCSD) min, respectively, a speed up of more than 8-folds. For gradient related terms, the DF approach avoids the usage of four-index electron repulsion integrals. Based on our previous study [U. Bozkaya, J. Chem. Phys. 141, 124108 (2014)], our formalism completely avoids construction or storage of the 4-index two-particle density matrix (TPDM), using instead 2- and 3-index TPDMs. The DF approach introduces negligible errors for equilibrium bond lengths and harmonic vibrational frequencies.« less

Accurate energetics of small molecules containing third-row atoms Ga-Kr: A comparison of advanced ab initio and density functional theory

NASA Astrophysics Data System (ADS)

Yockel, Scott; Mintz, Benjamin; Wilson, Angela K.

2004-07-01

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

NASA Astrophysics Data System (ADS)

Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

Accurate potential energy, dipole moment curves, and lifetimes of vibrational states of heteronuclear alkali dimers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fedorov, Dmitry A.; Varganov, Sergey A., E-mail: svarganov@unr.edu; Derevianko, Andrei

2014-05-14

We calculate the potential energy curves, the permanent dipole moment curves, and the lifetimes of the ground and excited vibrational states of the heteronuclear alkali dimers XY (X, Y = Li, Na, K, Rb, Cs) in the X{sup 1}Σ{sup +} electronic state using the coupled cluster with singles doubles and triples method. All-electron quadruple-ζ basis sets with additional core functions are used for Li and Na, and small-core relativistic effective core potentials with quadruple-ζ quality basis sets are used for K, Rb, and Cs. The inclusion of the coupled cluster non-perturbative triple excitations is shown to be crucial for obtainingmore » the accurate potential energy curves. A large one-electron basis set with additional core functions is needed for the accurate prediction of permanent dipole moments. The dissociation energies are overestimated by only 14 cm{sup −1} for LiNa and by no more than 114 cm{sup −1} for the other molecules. The discrepancies between the experimental and calculated harmonic vibrational frequencies are less than 1.7 cm{sup −1}, and the discrepancies for the anharmonic correction are less than 0.1 cm{sup −1}. We show that correlation between atomic electronegativity differences and permanent dipole moment of heteronuclear alkali dimers is not perfect. To obtain the vibrational energies and wave functions the vibrational Schrödinger equation is solved with the B-spline basis set method. The transition dipole moments between all vibrational states, the Einstein coefficients, and the lifetimes of the vibrational states are calculated. We analyze the decay rates of the vibrational states in terms of spontaneous emission, and stimulated emission and absorption induced by black body radiation. In all studied heteronuclear alkali dimers the ground vibrational states have much longer lifetimes than any excited states.« less

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

PubMed

Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Weizhou, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn; Zhang, Yu; Sun, Tao

High-level coupled cluster singles, doubles, and perturbative triples [CCSD(T)] computations with up to the aug-cc-pVQZ basis set (1924 basis functions) and various extrapolations toward the complete basis set (CBS) limit are presented for the sandwich, T-shaped, and parallel-displaced benzene⋯naphthalene complex. Using the CCSD(T)/CBS interaction energies as a benchmark, the performance of some newly developed wave function and density functional theory methods has been evaluated. The best performing methods were found to be the dispersion-corrected PBE0 functional (PBE0-D3) and spin-component scaled zeroth-order symmetry-adapted perturbation theory (SCS-SAPT0). The success of SCS-SAPT0 is very encouraging because it provides one method for energy componentmore » analysis of π-stacked complexes with 200 atoms or more. Most newly developed methods do, however, overestimate the interaction energies. The results of energy component analysis show that interaction energies are overestimated mainly due to the overestimation of dispersion energy.« less

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miliordos, Evangelos; Aprà, Edoardo; Xantheas, Sotiris S.

We establish a new estimate for the binding energy between two benzene molecules in the parallel-displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum, (ii) the expansion of the orbital basis set, and (iii) the level of electron correlation. The calculations were performed at the second-order Møller–Plesset perturbation (MP2) and the coupled cluster including singles, doubles, and a perturbative estimate of triples replacement [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for basis set superposition error (BSSE), we have estimated the complete basis set (CBS) limit bymore » employing the family of Dunning’s correlation-consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2772 basis functions), whereas the largest CCSD(T) calculation was with the cc-pV5Z basis set (1752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-ζ quality, observing that both its intra- and intermolecular parts have practically converged with the triple-ζ quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [within <0.01 kcal/mol for MP2 and <0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSE-corrected binding energies was found to converge to the same CBS limit much faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for obtaining an accurate CBS limit. We considered extrapolations of the uncorrected (ΔE) and BSSE-corrected (ΔE cp) binding energies, their average value (ΔE ave), as well as the average of the latter over the plain and augmented sets (Δ~E ave) with the cardinal number of the basis set n. Our best estimate of the CCSD(T)/CBS limit for the π–π binding energy in the PD benzene dimer is D e = -2.65 ± 0.02 kcal/mol. The best CCSD(T)/cc-pV5Z calculated value is -2.62 kcal/mol, just 0.03 kcal/mol away from the CBS limit. For comparison, the MP2/CBS limit estimate is -5.00 ± 0.01 kcal/mol, demonstrating a 90% overbinding with respect to CCSD(T). Finally, the spin-component-scaled (SCS) MP2 variant was found to closely reproduce the CCSD(T) results for each basis set, while scaled opposite spin (SOS) MP2 yielded results that are too low when compared to CCSD(T).« less

A Correlated Ab Initio Study of Linear Carbon-Chain Radicals C(sub n)H (n=2-7)

NASA Technical Reports Server (NTRS)

Woon, David E.

1995-01-01

Linear carbon-chain radicals C(sub n) H for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2Sigma(+) to 2Pi as the chain is extended. For C4H, the 2Sigma(+) state was found to lie only 72 cm(exp -1) below the 2Pi state in the estimated complete basis set limit for valence correlation. The C2H(-) and C3H(-) anions have also been characterized.

How to compute isomerization energies of organic molecules with quantum chemical methods.

PubMed

Grimme, Stefan; Steinmetz, Marc; Korth, Martin

2007-03-16

The reaction energies for 34 typical organic isomerizations including oxygen and nitrogen heteroatoms are investigated with modern quantum chemical methods that have the perspective of also being applicable to large systems. The experimental reaction enthalpies are corrected for vibrational and thermal effects, and the thus derived "experimental" reaction energies are compared to corresponding theoretical data. A series of standard AO basis sets in combination with second-order perturbation theory (MP2, SCS-MP2), conventional density functionals (e.g., PBE, TPSS, B3-LYP, MPW1K, BMK), and new perturbative functionals (B2-PLYP, mPW2-PLYP) are tested. In three cases, obvious errors of the experimental values could be detected, and accurate coupled-cluster [CCSD(T)] reference values have been used instead. It is found that only triple-zeta quality AO basis sets provide results close enough to the basis set limit and that sets like the popular 6-31G(d) should be avoided in accurate work. Augmentation of small basis sets with diffuse functions has a notable effect in B3-LYP calculations that is attributed to intramolecular basis set superposition error and covers basic deficiencies of the functional. The new methods based on perturbation theory (SCS-MP2, X2-PLYP) are found to be clearly superior to many other approaches; that is, they provide mean absolute deviations of less than 1.2 kcal mol-1 and only a few (<10%) outliers. The best performance in the group of conventional functionals is found for the highly parametrized BMK hybrid meta-GGA. Contrary to accepted opinion, hybrid density functionals offer no real advantage over simple GGAs. For reasonably large AO basis sets, results of poor quality are obtained with the popular B3-LYP functional that cannot be recommended for thermochemical applications in organic chemistry. The results of this study are complementary to often used benchmarks based on atomization energies and should guide chemists in their search for accurate and efficient computational thermochemistry methods.

Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

PubMed

Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

2016-02-11

The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br.

Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

NASA Astrophysics Data System (ADS)

Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

2015-06-01

The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

An ab initio benchmark study of the H + CO --> HCO reaction

NASA Technical Reports Server (NTRS)

Woon, D. E.

1996-01-01

The H + CO --> HCO reaction has been characterized with correlation consistent basis sets at five levels of theory in order to benchmark the sensitivities of the barrier height and reaction ergicity to the one-electron and n-electron expansions of the electronic wave function. Single and multireference methods are compared and contrasted. The coupled cluster method RCCSD(T) was found to be in very good agreement with Davidson-corrected internally-contracted multireference configuration interaction (MRCI+Q). Second-order Moller-Plesset perturbation theory (MP2) was also employed. The estimated complete basis set (CBS) limits for the barrier height (in kcal/mol) for the five methods, including harmonic zero-point energy corrections, are MP2, 4.66; RCCSD, 4.78; RCCSD(T), 4.15; MRCI, 5.10; and MRCI+Q, 4.07. Similarly, the estimated CBS limits for the ergicity of the reaction are: MP2, -17.99; RCCSD, -13.34; RCCSD(T), -13.79; MRCI, -11.46; and MRCI+Q, -13.70. Additional basis set explorations for the RCCSD(T) method demonstrate that aug-cc-pVTZ sets, even with some functions removed, are sufficient to reproduce the CBS limits to within 0.1-0.3 kcal/mol.

Structure and energetics of InN and GaN dimers

NASA Astrophysics Data System (ADS)

Šimová, Lucia; Tzeli, Demeter; Urban, Miroslav; Černušák, Ivan; Theodorakopoulos, Giannoula; Petsalakis, Ioannis D.

2008-06-01

Large-scale mapping of various dimers of indium nitride and gallium nitride in singlet and triplet electronic states is reported. Second-order perturbation theory with Møller-Plesset partitioning of the Hamiltonian (MP2) and coupled-cluster with single and double excitations corrected for the triple excitations (CCSD(T)) are used for the geometry determinations and evaluation of excitation and dissociation energies. For gallium and nitrogen we have used the singly augmented correlation-consistent triple-zeta basis set (aug-cc-pVTZ), for indium we have used the aug-cc-pVTZ-pseudopotential basis set. The dissociation energies are corrected for basis set superposition error (BBSE) including geometrical relaxation of the monomers. We compare and discuss the similarities and dissimilarities in the structural patterns and energetics of both groups of isomers, including the effect of the BSSE. Our computations show that there are not only different ground states for In 2N 2 and Ga 2N 2 but also different numbers of stable stationary points on their potential energy surface. We compare our results with the molecular data published so far for these systems.

Ab Initio Calculations of Spin-Orbit Coupling for Heavy-Metal Containing Radicals

NASA Astrophysics Data System (ADS)

Cheng, Lan

2016-06-01

The perturbative treatment of spin-orbit coupling (SOC) on top of scalar-relativistic calculations is a cost-effective alternative to rigorous fully relativistic calculations. In this work the applicability of the perturbative scheme in the framework of spin-free exact two-component theory is demonstrated with calculations of SO splittings and SOC contributions to molecular properties in small heavy-metal containing radicals, including AuO, AuS, and ThO^+. The equation of motion coupled cluster techniques have been used to accurately account for the electron-correlation effects in these radicals, and basis-set effects are carefully analyzed. The computed results are compared with experimental measurements for SO splittings and dipole moments when available.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics

NASA Astrophysics Data System (ADS)

Ünal, Aslı; Bozkaya, Uǧur

2018-03-01

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol-1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol-1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol-1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics.

PubMed

Ünal, Aslı; Bozkaya, Uğur

2018-03-28

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol -1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol -1 . Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol -1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Three dimensional atom-diatom quantum reactive scattering calculations using absorbing potential: speed up of the propagation scheme.

PubMed

Stoecklin, T

2008-09-01

In this paper a new propagation scheme is proposed for atom-diatom reactive calculations using a negative imaginary potential (NIP) within a time independent approach. It is based on the calculation of a rotationally adiabatic basis set, the neglected coupling terms being re-added in the following step of the propagation. The results of this approach, which we call two steps rotationally adiabatic coupled states calculations (2-RACS), are compared to those obtained using the adiabatic DVR method (J. C. Light and Z. Bazic, J. Chem. Phys., 1987, 87, 4008; C. Leforestier, J. Chem. Phys., 1991, 94, 6388), to the NIP coupled states results of the team of Baer (D. M. Charutz, I. Last and M. Baer, J. Chem. Phys., 1997, 106, 7654) and to the exact results obtained by Zhang (J. Z. H. Zhang and W. H. Miller, J. Chem. Phys., 1989, 91, 1528) for the D + H(2) reaction. The example of implementation of our method of computation of the adiabatic basis will be given here in the coupled states approximation, as this method has proved to be very efficient in many cases and is quite fast.

Spectroscopic properties of Arx-Zn and Arx-Ag+ (x = 1,2) van der Waals complexes

NASA Astrophysics Data System (ADS)

Oyedepo, Gbenga A.; Peterson, Charles; Schoendorff, George; Wilson, Angela K.

2013-03-01

Potential energy curves have been constructed using coupled cluster with singles, doubles, and perturbative triple excitations (CCSD(T)) in combination with all-electron and pseudopotential-based multiply augmented correlation consistent basis sets [m-aug-cc-pV(n + d)Z; m = singly, doubly, triply, n = D,T,Q,5]. The effect of basis set superposition error on the spectroscopic properties of Ar-Zn, Ar2-Zn, Ar-Ag+, and Ar2-Ag+ van der Waals complexes was examined. The diffuse functions of the doubly and triply augmented basis sets have been constructed using the even-tempered expansion. The a posteriori counterpoise scheme of Boys and Bernardi and its generalized variant by Valiron and Mayer has been utilized to correct for basis set superposition error (BSSE) in the calculated spectroscopic properties for diatomic and triatomic species. It is found that even at the extrapolated complete basis set limit for the energetic properties, the pseudopotential-based calculations still suffer from significant BSSE effects unlike the all-electron basis sets. This indicates that the quality of the approximations used in the design of pseudopotentials could have major impact on a seemingly valence-exclusive effect like BSSE. We confirm the experimentally determined equilibrium internuclear distance (re), binding energy (De), harmonic vibrational frequency (ωe), and C1Π ← X1Σ transition energy for ArZn and also predict the spectroscopic properties for the low-lying excited states of linear Ar2-Zn (X1Σg, 3Πg, 1Πg), Ar-Ag+ (X1Σ, 3Σ, 3Π, 3Δ, 1Σ, 1Π, 1Δ), and Ar2-Ag+ (X1Σg, 3Σg, 3Πg, 3Δg, 1Σg, 1Πg, 1Δg) complexes, using the CCSD(T) and MR-CISD + Q methods, to aid in their experimental characterizations.

Investigation of Conjugate Heat Transfer in Turbine Blades and Vanes

NASA Technical Reports Server (NTRS)

Kassab, A. J.; Kapat, J. S.

2001-01-01

We report on work carried out to develop a 3-D coupled Finite Volume/BEM-based temperature forward/flux back (TFFB) coupling algorithm to solve the conjugate heat transfer (CHT) which arises naturally in analysis of systems exposed to a convective environment. Here, heat conduction within a structure is coupled to heat transfer to the external fluid which is convecting heat into or out of the solid structure. There are two basic approaches to solving coupled fluid structural systems. The first is a direct coupling where the solution of the different fields is solved simultaneously in one large set of equations. The second approach is a loose coupling strategy where each set of field equations is solved to provide boundary conditions for the other. The equations are solved in turn until an iterated convergence criterion is met at the fluid-solid interface. The loose coupling strategy is particularly attractive when coupling auxiliary field equations to computational fluid dynamics codes. We adopt the latter method in which the BEM is used to solve heat conduction inside a structure which is exposed to a convective field which in turn is resolved by solving the NASA Glenn compressible Navier-Stokes finite volume code Glenn-HT. The BEM code features constant and bi-linear discontinuous elements and an ILU-preconditioned GMRES iterative solver for the resulting non-symmetric algebraic set arising in the conduction solution. Interface of flux and temperature is enforced at the solid/fluid interface, and a radial-basis function scheme is used to interpolated information between the CFD and BEM surface grids. Additionally, relaxation is implemented in passing the fluxes from the conduction solution to the fluid solution. Results from a simple test example are reported.

Coupling Network Computing Applications in Air-cooled Turbine Blades Optimization

NASA Astrophysics Data System (ADS)

Shi, Liang; Yan, Peigang; Xie, Ming; Han, Wanjin

2018-05-01

Through establishing control parameters from blade outside to inside, the parametric design of air-cooled turbine blade based on airfoil has been implemented. On the basis of fast updating structure features and generating solid model, a complex cooling system has been created. Different flow units are modeled into a complex network topology with parallel and serial connection. Applying one-dimensional flow theory, programs have been composed to get pipeline network physical quantities along flow path, including flow rate, pressure, temperature and other parameters. These inner units parameters set as inner boundary conditions for external flow field calculation program HIT-3D by interpolation, thus to achieve full field thermal coupling simulation. Referring the studies in literatures to verify the effectiveness of pipeline network program and coupling algorithm. After that, on the basis of a modified design, and with the help of iSIGHT-FD, an optimization platform had been established. Through MIGA mechanism, the target of enhancing cooling efficiency has been reached, and the thermal stress has been effectively reduced. Research work in this paper has significance for rapid deploying the cooling structure design.

Coupled-cluster and explicitly correlated perturbation-theory calculations of the uracil anion.

PubMed

Bachorz, Rafał A; Klopper, Wim; Gutowski, Maciej

2007-02-28

A valence-type anion of the canonical tautomer of uracil has been characterized using explicitly correlated second-order Moller-Plesset perturbation theory (RI-MP2-R12) in conjunction with conventional coupled-cluster theory with single, double, and perturbative triple excitations. At this level of electron-correlation treatment and after inclusion of a zero-point vibrational energy correction, determined in the harmonic approximation at the RI-MP2 level of theory, the valence anion is adiabatically stable with respect to the neutral molecule by 40 meV. The anion is characterized by a vertical detachment energy of 0.60 eV. To obtain accurate estimates of the vertical and adiabatic electron binding energies, a scheme was applied in which electronic energy contributions from various levels of theory were added, each of them extrapolated to the corresponding basis-set limit. The MP2 basis-set limits were also evaluated using an explicitly correlated approach, and the results of these calculations are in agreement with the extrapolated values. A remarkable feature of the valence anionic state is that the adiabatic electron binding energy is positive but smaller than the adiabatic electron binding energy of the dipole-bound state.

A new ab initio potential energy surface for the NH-He complex

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Kłos, J.; Lique, F.

2018-02-01

We present a new three-dimensional potential energy surface (PES) for the NH(X3Σ-)-He van der Waals system, which explicitly takes into account the NH vibrational motion. The NH-He PES was obtained using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = Q, 5, 6) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. Using this new PES, we have studied the spectroscopy of the NH-He complex and we have determined a new rotational constant that agrees well with the available experimental data. Collisional excitation of NH(X3Σ-) by He was also studied at the close-coupling level. Calculations of the collisional excitation cross sections of the fine-structure levels of NH by He were performed for energies up to 3500 cm-1, which yield, after thermal average, rate coefficients up to 350 K. The calculated rate coefficients are compared with available experimental measurements at room temperature, and a reasonably good agreement is found between experimental and theoretical data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bazante, Alexandre P., E-mail: abazante@chem.ufl.edu; Bartlett, Rodney J.; Davidson, E. R.

The benzene radical anion is studied with ab initio coupled-cluster theory in large basis sets. Unlike the usual assumption, we find that, at the level of theory investigated, the minimum energy geometry is non-planar with tetrahedral distortion at two opposite carbon atoms. The anion is well known for its instability to auto-ionization which poses computational challenges to determine its properties. Despite the importance of the benzene radical anion, the considerable attention it has received in the literature so far has failed to address the details of its structure and shape-resonance character at a high level of theory. Here, we examinemore » the dynamic Jahn-Teller effect and its impact on the anion potential energy surface. We find that a minimum energy geometry of C{sub 2} symmetry is located below one D{sub 2h} stationary point on a C{sub 2h} pseudo-rotation surface. The applicability of standard wave function methods to an unbound anion is assessed with the stabilization method. The isotropic hyperfine splitting constants (A{sub iso}) are computed and compared to data obtained from experimental electron spin resonance experiments. Satisfactory agreement with experiment is obtained with coupled-cluster theory and large basis sets such as cc-pCVQZ.« less

Evolution in time of an N-atom system. I. A physical basis set for the projection of the master equation

NASA Astrophysics Data System (ADS)

Freedhoff, Helen

2004-01-01

We study an aggregate of N identical two-level atoms (TLA’s) coupled by the retarded interatomic interaction, using the Lehmberg-Agarwal master equation. First, we calculate the entangled eigenstates of the system; then, we use these eigenstates as a basis set for the projection of the master equation. We demonstrate that in this basis the equations of motion for the level populations, as well as the expressions for the emission and absorption spectra, assume a simple mathematical structure and allow for a transparent physical interpretation. To illustrate the use of the general theory in emission processes, we study an isosceles triangle of atoms, and present in the long wavelength limit the (cascade) emission spectrum for a hexagon of atoms fully excited at t=0. To illustrate its use for absorption processes, we tabulate (in the same limit) the biexciton absorption frequencies, linewidths, and relative intensities for polygons consisting of N=2,…,9 TLA’s.

Coupled-cluster treatment of molecular strong-field ionization

NASA Astrophysics Data System (ADS)

Jagau, Thomas-C.

2018-05-01

Ionization rates and Stark shifts of H2, CO, O2, H2O, and CH4 in static electric fields have been computed with coupled-cluster methods in a basis set of atom-centered Gaussian functions with a complex-scaled exponent. Consideration of electron correlation is found to be of great importance even for a qualitatively correct description of the dependence of ionization rates and Stark shifts on the strength and orientation of the external field. The analysis of the second moments of the molecular charge distribution suggests a simple criterion for distinguishing tunnel and barrier suppression ionization in polyatomic molecules.

Fully coupled six-dimensional calculations of the water dimer vibration-rotation-tunneling states with split Wigner pseudospectral approach. II. Improvements and tests of additional potentials

NASA Astrophysics Data System (ADS)

Fellers, R. S.; Braly, L. B.; Saykally, R. J.; Leforestier, C.

1999-04-01

The SWPS method is improved by the addition of H.E.G. contractions for generating a more compact basis. An error in the definition of the internal fragment axis system used in our previous calculation is described and corrected. Fully coupled 6D (rigid monomers) VRT states are computed for several new water dimer potential surfaces and compared with experiment and our earlier SWPS results. This work sets the stage for refinement of such potential surfaces via regression analysis of VRT spectroscopic data.

Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

PubMed

Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

2010-10-14

A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low excitation energies largely below the dissociation limit as well as a negligible IVR contribution.

Density functional studies on the exchange interaction of a dinuclear Gd(iii)-Cu(ii) complex: method assessment, magnetic coupling mechanism and magneto-structural correlations.

PubMed

Rajaraman, Gopalan; Totti, Federico; Bencini, Alessandro; Caneschi, Andrea; Sessoli, Roberta; Gatteschi, Dante

2009-05-07

Density functional calculations have been performed on a [Gd(iii)Cu(ii)] complex [L(1)CuGd(O(2)CCF(3))(3)(C(2)H(5)OH)(2)] () (where L(1) is N,N'-bis(3-ethoxy-salicylidene)-1,2-diamino-2-methylpropanato) with an aim of assessing a suitable functional within the DFT formalism to understand the mechanism of magnetic coupling and also to develop magneto-structural correlations. Encouraging results have been obtained in our studies where the application of B3LYP on the crystal structure of yields a ferromagnetic J value of -5.8 cm(-1) which is in excellent agreement with the experimental value of -4.42 cm(-1) (H = JS(Gd).S(Cu)). After testing varieties of functional for the method assessment we recommend the use of B3LYP with a combination of an effective core potential basis set. For all electron basis sets the relativistic effects should be incorporated either via the Douglas-Kroll-Hess (DKH) or zeroth-order regular approximation (ZORA) methods. A breakdown approach has been adopted where the calculations on several model complexes of have been performed. Their wave functions have been analysed thereafter (MO and NBO analysis) in order to gain some insight into the coupling mechanism. The results suggest, unambiguously, that the empty Gd(iii) 5d orbitals have a prominent role on the magnetic coupling. These 5d orbitals gain partial occupancy via Cu(ii) charge transfer as well as from the Gd(iii) 4f orbitals. A competing 4f-3d interaction associated with the symmetry of the complex has also been observed. The general mechanism hence incorporates both contributions and sets forth rather a prevailing mechanism for the 3d-4f coupling. The magneto-structural correlations reveal that there is no unique parameter which the J values are strongly correlated with, but an exponential relation to the J value found for the O-Cu-O-Gd dihedral angle parameter is the most credible correlation.

Calculation of binary magnetic properties and potential energy curve in xenon dimer: second virial coefficient of (129)Xe nuclear shielding.

PubMed

Hanni, Matti; Lantto, Perttu; Runeberg, Nino; Jokisaari, Jukka; Vaara, Juha

2004-09-22

Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.

Non-adiabatic dynamics of molecules in optical cavities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Bennett, Kochise; Mukamel, Shaul, E-mail: smukamel@uci.edu

2016-02-07

Strong coupling of molecules to the vacuum field of micro cavities can modify the potential energy surfaces thereby opening new photophysical and photochemical reaction pathways. While the influence of laser fields is usually described in terms of classical field, coupling to the vacuum state of a cavity has to be described in terms of dressed photon-matter states (polaritons) which require quantized fields. We present a derivation of the non-adiabatic couplings for single molecules in the strong coupling regime suitable for the calculation of the dressed state dynamics. The formalism allows to use quantities readily accessible from quantum chemistry codes likemore » the adiabatic potential energy surfaces and dipole moments to carry out wave packet simulations in the dressed basis. The implications for photochemistry are demonstrated for a set of model systems representing typical situations found in molecules.« less

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH.

PubMed

Kolmann, Stephen J; Jordan, Meredith J T

2010-02-07

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

NASA Astrophysics Data System (ADS)

Kolmann, Stephen J.; Jordan, Meredith J. T.

2010-02-01

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Many-body calculations of molecular electric polarizabilities in asymptotically complete basis sets

NASA Astrophysics Data System (ADS)

Monten, Ruben; Hajgató, Balázs; Deleuze, Michael S.

2011-10-01

The static dipole polarizabilities of Ne, CO, N2, F2, HF, H2O, HCN, and C2H2 (acetylene) have been determined close to the Full-CI limit along with an asymptotically complete basis set (CBS), according to the principles of a Focal Point Analysis. For this purpose the results of Finite Field calculations up to the level of Coupled Cluster theory including Single, Double, Triple, Quadruple and perturbative Pentuple excitations [CCSDTQ(P)] were used, in conjunction with suited extrapolations of energies obtained using augmented and doubly-augmented Dunning's correlation consistent polarized valence basis sets of improving quality. The polarizability characteristics of C2H4 (ethylene) and C2H6 (ethane) have been determined on the same grounds at the CCSDTQ level in the CBS limit. Comparison is made with results obtained using lower levels in electronic correlation, or taking into account the relaxation of the molecular structure due to an adiabatic polarization process. Vibrational corrections to electronic polarizabilities have been empirically estimated according to Born-Oppenheimer Molecular Dynamical simulations employing Density Functional Theory. Confrontation with experiment ultimately indicates relative accuracies of the order of 1 to 2%.

Towards development of enhanced fully-Lagrangian mesh-free computational methods for fluid-structure interaction

NASA Astrophysics Data System (ADS)

Khayyer, Abbas; Gotoh, Hitoshi; Falahaty, Hosein; Shimizu, Yuma

2018-02-01

Simulation of incompressible fluid flow-elastic structure interactions is targeted by using fully-Lagrangian mesh-free computational methods. A projection-based fluid model (moving particle semi-implicit (MPS)) is coupled with either a Newtonian or a Hamiltonian Lagrangian structure model (MPS or HMPS) in a mathematically-physically consistent manner. The fluid model is founded on the solution of Navier-Stokes and continuity equations. The structure models are configured either in the framework of Newtonian mechanics on the basis of conservation of linear and angular momenta, or Hamiltonian mechanics on the basis of variational principle for incompressible elastodynamics. A set of enhanced schemes are incorporated for projection-based fluid model (Enhanced MPS), thus, the developed coupled solvers for fluid structure interaction (FSI) are referred to as Enhanced MPS-MPS and Enhanced MPS-HMPS. Besides, two smoothed particle hydrodynamics (SPH)-based FSI solvers, being developed by the authors, are considered and their potential applicability and comparable performance are briefly discussed in comparison with MPS-based FSI solvers. The SPH-based FSI solvers are established through coupling of projection-based incompressible SPH (ISPH) fluid model and SPH-based Newtonian/Hamiltonian structure models, leading to Enhanced ISPH-SPH and Enhanced ISPH-HSPH. A comparative study is carried out on the performances of the FSI solvers through a set of benchmark tests, including hydrostatic water column on an elastic plate, high speed impact of an elastic aluminum beam, hydroelastic slamming of a marine panel and dam break with elastic gate.

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE PAGES

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; ...

2016-09-09

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

PubMed

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

2016-10-11

In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

Reduced-cost linear-response CC2 method based on natural orbitals and natural auxiliary functions

PubMed Central

Mester, Dávid

2017-01-01

A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller–Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices. After removing the NOs of low occupation number, natural auxiliary functions (NAFs) are constructed [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], and the NAF basis is also truncated. Our results show that, for a triple-zeta basis set, about 60% of the virtual MOs can be dropped, while the size of the fitting basis can be reduced by a factor of five. This results in a dramatic reduction of the computational costs of the solution of the CC2 equations, which are in our approach about as expensive as the evaluation of the MP2 and CIS(D) density matrices. All in all, an average speedup of more than an order of magnitude can be achieved at the expense of a mean absolute error of 0.02 eV in the calculated excitation energies compared to the canonical CC2 results. Our benchmark calculations demonstrate that the new approach enables the efficient computation of CC2 excitation energies for excited states of all types of medium-sized molecules composed of up to 100 atoms with triple-zeta quality basis sets. PMID:28527453

Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

NASA Astrophysics Data System (ADS)

Datta, Dipayan; Kossmann, Simone; Neese, Frank

2016-09-01

The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the threshold for the natural orbital occupation number cutoff by an order of magnitude compared to the DLPNO-CCSD energy calculations.

Two-component relativistic coupled-cluster methods using mean-field spin-orbit integrals

NASA Astrophysics Data System (ADS)

Liu, Junzi; Shen, Yue; Asthana, Ayush; Cheng, Lan

2018-01-01

A novel implementation of the two-component spin-orbit (SO) coupled-cluster singles and doubles (CCSD) method and the CCSD augmented with the perturbative inclusion of triple excitations [CCSD(T)] method using mean-field SO integrals is reported. The new formulation of SO-CCSD(T) features an atomic-orbital-based algorithm for the particle-particle ladder term in the CCSD equation, which not only removes the computational bottleneck associated with the large molecular-orbital integral file but also accelerates the evaluation of the particle-particle ladder term by around a factor of 4 by taking advantage of the spin-free nature of the instantaneous electron-electron Coulomb interaction. Benchmark calculations of the SO splittings for the thallium atom and a set of diatomic 2Π radicals as well as of the bond lengths and harmonic frequencies for a set of closed-shell diatomic molecules are presented. The basis-set and core-correlation effects in the calculations of these properties have been carefully analyzed.

Finite Nuclei in the Quark-Meson Coupling Model.

PubMed

Stone, J R; Guichon, P A M; Reinhard, P G; Thomas, A W

2016-03-04

We report the first use of the effective quark-meson coupling (QMC) energy density functional (EDF), derived from a quark model of hadron structure, to study a broad range of ground state properties of even-even nuclei across the periodic table in the nonrelativistic Hartree-Fock+BCS framework. The novelty of the QMC model is that the nuclear medium effects are treated through modification of the internal structure of the nucleon. The density dependence is microscopically derived and the spin-orbit term arises naturally. The QMC EDF depends on a single set of four adjustable parameters having a clear physics basis. When applied to diverse ground state data the QMC EDF already produces, in its present simple form, overall agreement with experiment of a quality comparable to a representative Skyrme EDF. There exist, however, multiple Skyrme parameter sets, frequently tailored to describe selected nuclear phenomena. The QMC EDF set of fewer parameters, derived in this work, is not open to such variation, chosen set being applied, without adjustment, to both the properties of finite nuclei and nuclear matter.

Imaging of the internal structure of comet 67P/Churyumov-Gerasimenko from radiotomography CONSERT Data (Rosetta Mission) through a full 3D regularized inversion of the Helmholtz equations on functional spaces

NASA Astrophysics Data System (ADS)

Barriot, Jean-Pierre; Serafini, Jonathan; Sichoix, Lydie; Benna, Mehdi; Kofman, Wlodek; Herique, Alain

We investigate the inverse problem of imaging the internal structure of comet 67P/ Churyumov-Gerasimenko from radiotomography CONSERT data by using a coupled regularized inversion of the Helmholtz equations. A first set of Helmholtz equations, written w.r.t a basis of 3D Hankel functions describes the wave propagation outside the comet at large distances, a second set of Helmholtz equations, written w.r.t. a basis of 3D Zernike functions describes the wave propagation throughout the comet with avariable permittivity. Both sets are connected by continuity equations over a sphere that surrounds the comet. This approach, derived from GPS water vapor tomography of the atmosphere,will permit a full 3D inversion of the internal structure of the comet, contrary to traditional approaches that use a discretization of space at a fraction of the radiowave wavelength.

Slater-type geminals in explicitly-correlated perturbation theory: application to n-alkanols and analysis of errors and basis-set requirements.

PubMed

Höfener, Sebastian; Bischoff, Florian A; Glöss, Andreas; Klopper, Wim

2008-06-21

In the recent years, Slater-type geminals (STGs) have been used with great success to expand the first-order wave function in an explicitly-correlated perturbation theory. The present work reports on this theory's implementation in the framework of the Turbomole suite of programs. A formalism is presented for evaluating all of the necessary molecular two-electron integrals by means of the Obara-Saika recurrence relations, which can be applied when the STG is expressed as a linear combination of a small number (n) of Gaussians (STG-nG geminal basis). In the Turbomole implementation of the theory, density fitting is employed and a complementary auxiliary basis set (CABS) is used for the resolution-of-the-identity (RI) approximation of explicitly-correlated theory. By virtue of this RI approximation, the calculation of molecular three- and four-electron integrals is avoided. An approximation is invoked to avoid the two-electron integrals over the commutator between the operators of kinetic energy and the STG. This approximation consists of computing commutators between matrices in place of operators. Integrals over commutators between operators would have occurred if the theory had been formulated and implemented as proposed originally. The new implementation in Turbomole was tested by performing a series of calculations on rotational conformers of the alkanols n-propanol through n-pentanol. Basis-set requirements concerning the orbital basis, the auxiliary basis set for density fitting and the CABS were investigated. Furthermore, various (constrained) optimizations of the amplitudes of the explicitly-correlated double excitations were studied. These amplitudes can be optimized in orbital-variant and orbital-invariant manners, or they can be kept fixed at the values governed by the rational generator approach, that is, by the electron cusp conditions. Electron-correlation effects beyond the level of second-order perturbation theory were accounted for by conventional coupled-cluster calculations with single, double and perturbative triple excitations [CCSD(T)]. The explicitly-correlated perturbation theory results were combined with CCSD(T) results and compared with literature data obtained by basis-set extrapolation.

Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sylvetsky, Nitai, E-mail: gershom@weizmann.ac.il; Martin, Jan M. L., E-mail: gershom@weizmann.ac.il; Peterson, Kirk A., E-mail: kipeters@wsu.edu

2016-06-07

In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H–He, B–Ne, and Al–Ar, is shown to be very close to the basis setmore » limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl{sub 4}) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than “valence limit + CV correction” approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from CCSD-F12b/cc-pV{Q,5}Z-F12 calculations, but the (T) component from conventional CCSD(T)/aug’-cc-pV{Q,5}Z + d calculations using Schwenke’s extrapolation; post-CCSD(T), core-valence, and relativistic corrections are to be obtained as in the original W4 theory. W4-F12 is found to agree slightly better than W4 with ATcT (active thermochemical tables) data, at a substantial saving in computation time and especially I/O overhead. A W4-F12 calculation on benzene is presented as a proof of concept.« less

Geminal-spanning orbitals make explicitly correlated reduced-scaling coupled-cluster methods robust, yet simple

NASA Astrophysics Data System (ADS)

Pavošević, Fabijan; Neese, Frank; Valeev, Edward F.

2014-08-01

We present a production implementation of reduced-scaling explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) method based on pair-natural orbitals (PNOs). A key feature is the reformulation of the explicitly correlated terms using geminal-spanning orbitals that greatly reduce the truncation errors of the F12 contribution. For the standard S66 benchmark of weak intermolecular interactions, the cc-pVDZ-F12 PNO CCSD F12 interaction energies reproduce the complete basis set CCSD limit with mean absolute error <0.1 kcal/mol, and at a greatly reduced cost compared to the conventional CCSD F12.

Fully coupled six-dimensional calculations of the water dimer vibration-rotation-tunneling states with split Wigner pseudospectral approach. II. Improvements and tests of additional potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fellers, R.S.; Braly, L.B.; Saykally, R.J.

The SWPS method is improved by the addition of H.E.G. contractions for generating a more compact basis. An error in the definition of the internal fragment axis system used in our previous calculation is described and corrected. Fully coupled 6D (rigid monomers) VRT states are computed for several new water dimer potential surfaces and compared with experiment and our earlier SWPS results. This work sets the stage for refinement of such potential surfaces via regression analysis of VRT spectroscopic data. {copyright} {ital 1999 American Institute of Physics.}

Spin Number Coherent States and the Problem of Two Coupled Oscillators

NASA Astrophysics Data System (ADS)

Ojeda-Guillén, D.; Mota, R. D.; Granados, V. D.

2015-07-01

From the definition of the standard Perelomov coherent states we introduce the Perelomov number coherent states for any su(2) Lie algebra. With the displacement operator we apply a similarity transformation to the su(2) generators and construct a new set of operators which also close the su(2) Lie algebra, being the Perelomov number coherent states the new basis for its unitary irreducible representation. We apply our results to obtain the energy spectrum, the eigenstates and the partition function of two coupled oscillators. We show that the eigenstates of two coupled oscillators are the SU(2) Perelomov number coherent states of the two-dimensional harmonic oscillator with an appropriate choice of the coherent state parameters. Supported by SNI-México, COFAA-IPN, EDD-IPN, EDI-IPN, SIP-IPN Project No. 20150935

Theoretical investigation of gas-surface interactions

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.

1990-01-01

A Dirac-Hartree-Fock code was developed for polyatomic molecules. The program uses integrals over symmetry-adapted real spherical harmonic Gaussian basis functions generated by a modification of the MOLECULE integrals program. A single Gaussian function is used for the nuclear charge distribution, to ensure proper boundary conditions at the nuclei. The Gaussian primitive functions are chosen to satisfy the kinetic balance condition. However, contracted functions which do not necessarily satisfy this condition may be used. The Fock matrix is constructed in the scalar basis and transformed to a jj-coupled 2-spinor basis before diagonalization. The program was tested against numerical results for atoms with a Gaussian nucleus and diatomic molecules with point nuclei. The energies converge on the numerical values as the basis set size is increased. Full use of molecular symmetry (restricted to D sub 2h and subgroups) is yet to be implemented.

Ordering of the O-O stretching vibrational frequencies in ozone

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.; Lee, Timothy J.; Scheiner, Andrew C.; Schaefer, Henry F., III

1989-01-01

The ordering of nu1 and nu3 for O3 is incorrectly predicted by most theoretical methods, including some very high level methods. The first systematic electron correlation method based on one-reference configuration to solve this problem is the coupled cluster single and double excitation method. However, a relatively large basis set, triple zeta plus double polarization is required. Comparison with other theoretical methods is made.

Inference of a Nonlinear Stochastic Model of the Cardiorespiratory Interaction

NASA Astrophysics Data System (ADS)

Smelyanskiy, V. N.; Luchinsky, D. G.; Stefanovska, A.; McClintock, P. V.

2005-03-01

We reconstruct a nonlinear stochastic model of the cardiorespiratory interaction in terms of a set of polynomial basis functions representing the nonlinear force governing system oscillations. The strength and direction of coupling and noise intensity are simultaneously inferred from a univariate blood pressure signal. Our new inference technique does not require extensive global optimization, and it is applicable to a wide range of complex dynamical systems subject to noise.

The quantum dynamics of electronically nonadiabatic chemical reactions

NASA Technical Reports Server (NTRS)

Truhlar, Donald G.

1993-01-01

Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally adiabatic functions in various quantum scattering algorithms.

H{sub 2} dissociation due to collisions with He

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohlinger, L.; Forrey, R. C.; Lee, Teck-Ghee

2007-10-15

Cross sections for dissociation of H{sub 2} due to collision with He are calculated for highly excited rovibrational states using the quantum-mechanical coupled-states approximation. An L{sup 2} Sturmian basis set with multiple length scales is used to provide a discrete representation of the H{sub 2} continuum which includes orbiting resonances and a nonresonant background. Cross sections are given over a range of translational energies for both resonant and nonresonant dissociation together with the most important bound-state transitions for many different initial states. The results demonstrate that it is possible to compute converged quantum-mechanical cross sections using basis sets of modestmore » size. It is found that collision-induced dissociation competes with inelastic scattering as a depopulation mechanism for the highly excited states. The relevance of the present calculations to astrophysical models is discussed.« less

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 1. Accurate thermochemistry and barrier heights.

PubMed

Alecu, I M; Truhlar, Donald G

2011-04-07

The reactions of CH(3)OH with the HO(2) and CH(3) radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)(Q)), core-valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol(-1) agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.

Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuev, Dmitry; Jagau, Thomas-C.; Krylov, Anna I.

2014-07-14

A production-level implementation of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) for electron attachment and excitation energies augmented by a complex absorbing potential (CAP) is presented. The new method enables the treatment of metastable states within the EOM-CC formalism in a similar manner as bound states. The numeric performance of the method and the sensitivity of resonance positions and lifetimes to the CAP parameters and the choice of one-electron basis set are investigated. A protocol for studying molecular shape resonances based on the use of standard basis sets and a universal criterion for choosing the CAP parameters are presented. Our resultsmore » for a variety of π{sup *} shape resonances of small to medium-size molecules demonstrate that CAP-augmented EOM-CCSD is competitive relative to other theoretical approaches for the treatment of resonances and is often able to reproduce experimental results.« less

A theoretical study of potentially observable chirality-sensitive NMR effects in molecules.

PubMed

Garbacz, Piotr; Cukras, Janusz; Jaszuński, Michał

2015-09-21

Two recently predicted nuclear magnetic resonance effects, the chirality-induced rotating electric polarization and the oscillating magnetization, are examined for several experimentally available chiral molecules. We discuss in detail the requirements for experimental detection of chirality-sensitive NMR effects of the studied molecules. These requirements are related to two parameters: the shielding polarizability and the antisymmetric part of the nuclear magnetic shielding tensor. The dominant second contribution has been computed for small molecules at the coupled cluster and density functional theory levels. It was found that DFT calculations using the KT2 functional and the aug-cc-pCVTZ basis set adequately reproduce the CCSD(T) values obtained with the same basis set. The largest values of parameters, thus most promising from the experimental point of view, were obtained for the fluorine nuclei in 1,3-difluorocyclopropene and 1,3-diphenyl-2-fluoro-3-trifluoromethylcyclopropene.

Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bross, David H.; Parmar, Payal; Peterson, Kirk A., E-mail: kipeters@wsu.edu

The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionizationmore » potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP{sub 3} through IP{sub 6}.« less

Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters.

PubMed

Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

2009-04-14

In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

Non-adiabatic dynamics around a conical intersection with surface-hopping coupled coherent states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humeniuk, Alexander; Mitrić, Roland, E-mail: roland.mitric@uni-wuerzburg.de

A surface-hopping extension of the coupled coherent states-method [D. Shalashilin and M. Child, Chem. Phys. 304, 103-120 (2004)] for simulating non-adiabatic dynamics with quantum effects of the nuclei is put forward. The time-dependent Schrödinger equation for the motion of the nuclei is solved in a moving basis set. The basis set is guided by classical trajectories, which can hop stochastically between different electronic potential energy surfaces. The non-adiabatic transitions are modelled by a modified version of Tully’s fewest switches algorithm. The trajectories consist of Gaussians in the phase space of the nuclei (coherent states) combined with amplitudes for an electronicmore » wave function. The time-dependent matrix elements between different coherent states determine the amplitude of each trajectory in the total multistate wave function; the diagonal matrix elements determine the hopping probabilities and gradients. In this way, both interference effects and non-adiabatic transitions can be described in a very compact fashion, leading to the exact solution if convergence with respect to the number of trajectories is achieved and the potential energy surfaces are known globally. The method is tested on a 2D model for a conical intersection [A. Ferretti, J. Chem. Phys. 104, 5517 (1996)], where a nuclear wavepacket encircles the point of degeneracy between two potential energy surfaces and interferes with itself. These interference effects are absent in classical trajectory-based molecular dynamics but can be fully incorpo rated if trajectories are replaced by surface hopping coupled coherent states.« less

Relativistic coupled-cluster calculations of the 173Yb nuclear quadrupole coupling constant for the YbF molecule

NASA Astrophysics Data System (ADS)

Pašteka, L. F.; Mawhorter, R. J.; Schwerdtfeger, P.

2016-04-01

We report calculations on the q(Yb) electric field gradient (EFG) for the X2Σ+ and A2Π1/2 electronic states of the ytterbium monofluoride (YbF) molecule at the molecular mean-field Dirac-Coulomb-Gaunt as well as scalar-relativistic coupled-cluster levels of theory using large uncontracted basis sets. Vibrational contributions are included in the final results. Our estimated nuclear quadrupole coupling constants of -3386(78) MHz and -2083(153) MHz for the X2Σ+ and A2Π1/2 states of 173YbF are in stark contrast to the only available experimental results (-2050(170) MHz and -1090(160) MHz) respectively, where the only similarity is the difference between the two values. Perturbative triple contributions in the coupled cluster treatment are significant and point towards the necessity to go to higher order in the coupled-cluster treatment in future calculations. We also present density functional calculations which show rather large variations for the Yb EFG with different functionals used; the best result was obtained using the CAM-B3LYP* functional.

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes

NASA Astrophysics Data System (ADS)

Maranzana, Andrea; Giordana, Anna; Indarto, Antonius; Tonachini, Glauco; Barone, Vincenzo; Causà, Mauro; Pavone, Michele

2013-12-01

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol-1. The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes.

PubMed

Maranzana, Andrea; Giordana, Anna; Indarto, Antonius; Tonachini, Glauco; Barone, Vincenzo; Causà, Mauro; Pavone, Michele

2013-12-28

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol(-1). The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

A novel simulation theory and model system for multi-field coupling pipe-flow system

NASA Astrophysics Data System (ADS)

Chen, Yang; Jiang, Fan; Cai, Guobiao; Xu, Xu

2017-09-01

Due to the lack of a theoretical basis for multi-field coupling in many system-level models, a novel set of system-level basic equations for flow/heat transfer/combustion coupling is put forward. Then a finite volume model of quasi-1D transient flow field for multi-species compressible variable-cross-section pipe flow is established by discretising the basic equations on spatially staggered grids. Combining with the 2D axisymmetric model for pipe-wall temperature field and specific chemical reaction mechanisms, a finite volume model system is established; a set of specific calculation methods suitable for multi-field coupling system-level research is structured for various parameters in this model; specific modularisation simulation models can be further derived in accordance with specific structures of various typical components in a liquid propulsion system. This novel system can also be used to derive two sub-systems: a flow/heat transfer two-field coupling pipe-flow model system without chemical reaction and species diffusion; and a chemical equilibrium thermodynamic calculation-based multi-field coupling system. The applicability and accuracy of two sub-systems have been verified through a series of dynamic modelling and simulations in earlier studies. The validity of this system is verified in an air-hydrogen combustion sample system. The basic equations and the model system provide a unified universal theory and numerical system for modelling and simulation and even virtual testing of various pipeline systems.

Nuclear spin-spin coupling in a van der Waals-bonded system: xenon dimer.

PubMed

Vaara, Juha; Hanni, Matti; Jokisaari, Jukka

2013-03-14

Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency shift of solute protons in a solution containing optically hyperpolarized (129)Xe nuclei. We carry out a first-principles computational study of the prototypic van der Waals-bonded xenon dimer, where the spin-spin coupling between two magnetically non-equivalent isotopes, J((129)Xe - (131)Xe), is observable. We use relativistic theory at the four-component Dirac-Hartree-Fock and Dirac-density-functional theory levels using novel completeness-optimized Gaussian basis sets and choosing the functional based on a comparison with correlated ab initio methods at the nonrelativistic level. J-coupling curves are provided at different levels of theory as functions of the internuclear distance in the xenon dimer, demonstrating cross-coupling effects between relativity and electron correlation for this property. Calculations on small Xe clusters are used to estimate the importance of many-atom effects on J((129)Xe - (131)Xe). Possibilities of observing J((129)Xe - (131)Xe) in liquid xenon are critically examined, based on molecular dynamics simulation. A simplistic spherical model is set up for the xenon dimer confined in a cavity, such as in microporous materials. It is shown that the on the average shorter internuclear distance enforced by the confinement increases the magnitude of the coupling as compared to the bulk liquid case, rendering J((129)Xe - (131)Xe) in a cavity a feasible target for experimental investigation.

Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, John H.; Cantrell, Sean A.

2010-01-01

The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.

Ab initio multireference study of the BN molecule

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.; Scuseria, Gustavo E.; Taylor, Peter R.

1992-01-01

The lowest 1Sigma(+) and 3Pi states of the BN molecule are studied using multireference configuration interaction (MRCI) and averaged coupled-pair functional (ACPF) methods and large atomic natural orbital (ANO) basis sets, as well as several coupled cluster methods. Our calculations strongly support a 3Pi ground state, but the a1Sigma(+) state lies only 381 +/- 100/cm higher. The a1Sigma(+) state wave function exhibits strong multireference character and, consequently, the predictions of the perturbationally-based single-reference CCSD(T) coupled cluster method are not as reliable in this case as the multireference results. The theoretical predictions for the spectroscopic constants of BN are in good agreement with experiment for the Chi3Pi state, but strongly suggest a misassignment of the fundamental vibrational frequency for the a1Sigma(+) state.

An efficient approach to CI: General matrix element formulas for spin-coupled particle-hole excitations

NASA Astrophysics Data System (ADS)

Tavan, Paul; Schulten, Klaus

1980-03-01

A new, efficient algorithm for the evaluation of the matrix elements of the CI Hamiltonian in the basis of spin-coupled ν-fold excitations (over orthonormal orbitals) is developed for even electron systems. For this purpose we construct an orthonormal, spin-adapted CI basis in the framework of second quantization. As a prerequisite, spin and space parts of the fermion operators have to be separated; this makes it possible to introduce the representation theory of the permutation group. The ν-fold excitation operators are Serber spin-coupled products of particle-hole excitations. This construction is also designed for CI calculations from multireference (open-shell) states. The 2N-electron Hamiltonian is expanded in terms of spin-coupled particle-hole operators which map any ν-fold excitation on ν-, and ν±1-, and ν±2-fold excitations. For the calculation of the CI matrix this leaves one with only the evaluation of overlap matrix elements between spin-coupled excitations. This leads to a set of ten general matrix element formulas which contain Serber representation matrices of the permutation group Sν×Sν as parameters. Because of the Serber structure of the CI basis these group-theoretical parameters are kept to a minimum such that they can be stored readily in the central memory of a computer for ν?4 and even for higher excitations. As the computational effort required to obtain the CI matrix elements from the general formulas is very small, the algorithm presented appears to constitute for even electron systems a promising alternative to existing CI methods for multiply excited configurations, e.g., the unitary group approach. Our method makes possible the adaptation of spatial symmetries and the selection of any subset of configurations. The algorithm has been implemented in a computer program and tested extensively for ν?4 and singlet ground and excited states.

Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

NASA Astrophysics Data System (ADS)

Huhn, William; Blum, Volker

2015-03-01

Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

Calculation of excitation energies from the CC2 linear response theory using Cholesky decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baudin, Pablo, E-mail: baudin.pablo@gmail.com; qLEAP – Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C; Marín, José Sánchez

2014-03-14

A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitioning form of the CC2 equations which reduces the dimension of the problem and avoids the storage of doubles amplitudes. We present calculation of excitation energies of benzene using a hierarchy of basis sets and compare the results with conventional CC2 calculations. The reduction of the scaling is evaluated as well asmore » the effect of the Cholesky decomposition parameter on the quality of the results. The new algorithm is used to perform an extrapolation to complete basis set investigation on the spectroscopically interesting benzylallene conformers. A set of calculations on medium-sized molecules is carried out to check the dependence of the accuracy of the results on the decomposition thresholds. Moreover, CC2 singlet excitation energies of the free base porphin are also presented.« less

Benchmark calculations with correlated molecular wavefunctions. XIII. Potential energy curves for He2, Ne2 and Ar2 using correlation consistent basis sets through augmented sextuple zeta

NASA Astrophysics Data System (ADS)

van Mourik, Tanja

1999-02-01

The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller-Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)]. For He2CCSD(T)/d-aug-cc-pV6Z calculations yield a well depth of 7.35cm-1 (10.58K), with an estimated complete basis set (CBS) limit of 7.40cm-1 (10.65K). The latter is smaller than the 'exact' well depth (Aziz, R. A., Janzen, A. R., and Moldover, M. R., 1995, Phys. Rev. Lett., 74, 1586) by about 0.2cm-1 (0.35K). The Ne well depth, computed with the CCSD(T)/d-aug-cc-pV6Z method, is 28.31cm-1 and the estimated CBS limit is 28.4cm-1, approximately 1cm-1 smaller than the empirical potential of Aziz, R. A., and Slaman, M., J., 1989, Chem. Phys., 130, 187. Inclusion of core and core-valence correlation effects has a negligible effect on the Ne well depth, decreasing it by only 0.04cm-1. For Ar2, CCSD(T)/ d-aug-cc-pV6Z calculations yield a well depth of 96.2cm-1. The corresponding HFDID potential of Aziz, R. A., 1993, J. chem. Phys., 99, 4518 predicts of D of 99.7cm-1. Inclusion of core and core-valence effects in Ar increases the well depth and decreases the discrepancy by approximately 1cm-1.

The Anharmonic Force Field of Ethylene, C2H4, by Means of Accurate Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Martin, Jan M. L.; Lee, Timothy J.; Taylor, Peter R.; Francois, Jean-Pierre; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The quartic force field of ethylene, C2H4, has been calculated ab initio using augmented coupled cluster, CCSD(T), methods and correlation consistent basis sets of spdf quality. For the C-12 isotopomers C2H4, C2H3D, H2CCD2, cis-C2H2D2, trans-C2H2D2, C2HD3, and C2D4, all fundamentals could be reproduced to better than 10 per centimeter, except for three cases of severe Fermi type 1 resonance. The problem with these three bands is identified as a systematic overestimate of the Kiij Fermi resonance constants by a factor of two or more; if this is corrected for, the predicted fundamentals come into excellent agreement with experiment. No such systematic overestimate is seen for Fermi type 2 resonances. Our computed harmonic frequencies suggest a thorough revision of the accepted experimentally derived values. Our computed and empirically corrected re geometry differs substantially from experimentally derived values: both the predicted rz geometry and the ground-state rotational constants are, however, in excellent agreement with experiment, suggesting revision of the older values. Anharmonicity constants agree well with experiment for stretches, but differ substantially for stretch-bend interaction constants, due to equality constraints in the experimental analysis that do not hold. Improved criteria for detecting Fermi and Coriolis resonances are proposed and found to work well, contrary to the established method based on harmonic frequency differences that fails to detect several important resonances for C2H4 and its isotopomers. Surprisingly good results are obtained with a small spd basis at the CCSD(T) level. The well-documented strong basis set effect on the v8 out-of-plane motion is present to a much lesser extent when correlation-optimized polarization functions are used. Complete sets of anharmonic, rovibrational coupling, and centrifugal distortion constants for the isotopomers are available as supplementary material to the paper.

Energy-consistent small-core pseudopotentials for 3d-transition metals adapted to quantum Monte Carlo calculations.

PubMed

Burkatzki, M; Filippi, Claudia; Dolg, M

2008-10-28

We extend our recently published set of energy-consistent scalar-relativistic Hartree-Fock pseudopotentials by the 3d-transition metal elements, scandium through zinc. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. The pseudopotentials and the accompanying basis sets (VnZ with n=T,Q) are given in standard Gaussian representation and their parameter sets are presented. Coupled cluster, configuration interaction, and QMC studies are carried out for the scandium and titanium atoms and their oxides, demonstrating the good performance of the pseudopotentials. Even though the choice of pseudopotential form is motivated by QMC, these pseudopotentials can also be employed in other quantum chemical approaches.

Predictive coupled-cluster isomer orderings for some Si{sub n}C{sub m} (m, n ≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Byrd, Jason N., E-mail: byrd.jason@ensco.com; ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940; Lutz, Jesse J., E-mail: jesse.lutz.ctr@afit.edu

The accurate determination of the preferred Si{sub 12}C{sub 12} isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for the opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies, and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC{sub 3} to Si{sub 12}C{sub 12}. It is found that post-MBPT(2) correlation energy plays a significant rolemore » in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and coupled-cluster theory with singles and doubles extrapolation with triple-ζ (T) correlation, the closo Si{sub 12}C{sub 12} isomer is identified to be the preferred isomer in the support of previous calculations [X. F. Duan and L. W. Burggraf, J. Chem. Phys. 142, 034303 (2015)]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post-MBPT(2) correlation energy are found to be an excellent balance between efficiency and accuracy.« less

Composite thermochemistry of gas phase U(VI)-containing molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bross, David H.; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Reaction energies have been calculated for a series of reactions involving UF{sub 6}, UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2} using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with themore » accurately known heat of formation of UF{sub 6} to determine the enthalpies of formation of UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2}. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO{sub 2}F{sub 2} was in excellent agreement with experiment, while the two results obtained for UO{sub 3} were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO{sub 2}(OH){sub 2} is predicted from this work to be −288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of −292.7 ± 6 kcal/mol.« less

Regional seismic wavefield computation on a 3-D heterogeneous Earth model by means of coupled traveling wave synthesis

USGS Publications Warehouse

Pollitz, F.F.

2002-01-01

I present a new algorithm for calculating seismic wave propagation through a three-dimensional heterogeneous medium using the framework of mode coupling theory originally developed to perform very low frequency (f < ???0.01-0.05 Hz) seismic wavefield computation. It is a Greens function approach for multiple scattering within a defined volume and employs a truncated traveling wave basis set using the locked mode approximation. Interactions between incident and scattered wavefields are prescribed by mode coupling theory and account for the coupling among surface waves, body waves, and evanescent waves. The described algorithm is, in principle, applicable to global and regional wave propagation problems, but I focus on higher frequency (typically f ??????0.25 Hz) applications at regional and local distances where the locked mode approximation is best utilized and which involve wavefields strongly shaped by propagation through a highly heterogeneous crust. Synthetic examples are shown for P-SV-wave propagation through a semi-ellipsoidal basin and SH-wave propagation through a fault zone.

Tunneling of coupled methyl quantum rotors in 4-methylpyridine: Single rotor potential versus coupling interaction

NASA Astrophysics Data System (ADS)

Khazaei, Somayeh; Sebastiani, Daniel

2017-11-01

We study the influence of rotational coupling between a pair of methyl rotators on the tunneling spectrum in condensed phase. Two interacting adjacent methyl groups are simulated within a coupled-pair model composed of static rotational potential created by the chemical environment and the interaction potential between two methyl groups. We solve the two-dimensional time-independent Schrödinger equation analytically by expanding the wave functions on the basis set of two independent free-rotor functions. We investigate three scenarios which differ with respect to the relative strength of single-rotor and coupling potential. For each scenario, we illustrate the dependence of the energy level scheme on the coupling strength. It is found that the main determinant of splitting energy levels tends to be a function of the ratio of strengths of coupling and single-rotor potential. The tunnel splitting caused by coupling is maximized for the coupled rotors in which their total hindering potential is relatively shallow. Such a weakly hindered methyl rotational potential is predicted for 4-methylpyridine at low temperature. The experimental observation of multiple tunneling peaks arising from a single type of methyl group in 4-methylpyridine in the inelastic neutron scattering spectrum is widely attributed to the rotor-rotor coupling. In this regard, using a set of first-principles calculations combined with the nudged elastic band method, we investigate the rotational potential energy surface (PES) of the coaxial pairs of rotors in 4-methylpyridine. A Numerov-type method is used to numerically solve the two-dimensional time-independent Schrödinger equation for the calculated 2D-density functional theory profile. Our computed energy levels reproduce the observed tunneling transitions well. Moreover, the calculated density distribution of the three methyl protons resembles the experimental nuclear densities obtained from the Fourier difference method. By mapping the calculated first-principles PES on the model, it is confirmed that the hindering potential in 4-methylpyridine consists of proportionally shallow single-rotor potential to coupling interaction.

Tunneling of coupled methyl quantum rotors in 4-methylpyridine: Single rotor potential versus coupling interaction.

PubMed

Khazaei, Somayeh; Sebastiani, Daniel

2017-11-21

We study the influence of rotational coupling between a pair of methyl rotators on the tunneling spectrum in condensed phase. Two interacting adjacent methyl groups are simulated within a coupled-pair model composed of static rotational potential created by the chemical environment and the interaction potential between two methyl groups. We solve the two-dimensional time-independent Schrödinger equation analytically by expanding the wave functions on the basis set of two independent free-rotor functions. We investigate three scenarios which differ with respect to the relative strength of single-rotor and coupling potential. For each scenario, we illustrate the dependence of the energy level scheme on the coupling strength. It is found that the main determinant of splitting energy levels tends to be a function of the ratio of strengths of coupling and single-rotor potential. The tunnel splitting caused by coupling is maximized for the coupled rotors in which their total hindering potential is relatively shallow. Such a weakly hindered methyl rotational potential is predicted for 4-methylpyridine at low temperature. The experimental observation of multiple tunneling peaks arising from a single type of methyl group in 4-methylpyridine in the inelastic neutron scattering spectrum is widely attributed to the rotor-rotor coupling. In this regard, using a set of first-principles calculations combined with the nudged elastic band method, we investigate the rotational potential energy surface (PES) of the coaxial pairs of rotors in 4-methylpyridine. A Numerov-type method is used to numerically solve the two-dimensional time-independent Schrödinger equation for the calculated 2D-density functional theory profile. Our computed energy levels reproduce the observed tunneling transitions well. Moreover, the calculated density distribution of the three methyl protons resembles the experimental nuclear densities obtained from the Fourier difference method. By mapping the calculated first-principles PES on the model, it is confirmed that the hindering potential in 4-methylpyridine consists of proportionally shallow single-rotor potential to coupling interaction.

Application of WRF/Chem over the Continental U.S. under the AQMEII Phase II: Part 2. Evaluation of 2010 Application and Responses of Air Quality and Meteorology-Chemistry Interactions to Changes in Emissions and Meteorology from 2006 to 2010

EPA Science Inventory

The Weather Research and Forecasting model with Chemistry (WRF/Chem) simulation with the 2005 Carbon Bond (CB05) gas-phase mechanism coupled to the Modal for Aerosol Dynamics for Europe (MADE) and the Volatility Basis Set (VBS) approach for secondary organic aerosol (SOA) (MADE/V...

An ab initio study of HCuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

HCuCO is studied using a large Gaussian basis set at the coupled cluster singles and doubles level of theory, including a perturbational estimate of the connected triples (CCSD(T)). In contrast with CuCO, HCuCO is linear. The Cu-CO bond in HCuCO is significantly stronger than in CuCO. These differences between HCuCO and CuCO are discussed in terms of theCu-H bond polarizing the Cu 4s electron away from the CO.

Thermodynamic properties of arsenic compounds and the heat of formation of the As atom from high level electronic structure calculations.

PubMed

Feller, David; Vasiliu, Monica; Grant, Daniel J; Dixon, David A

2011-12-29

Structures, vibrational frequencies, atomization energies at 0 K, and heats of formation at 0 and 298 K are predicted for the compounds As(2), AsH, AsH(2), AsH(3), AsF, AsF(2), and AsF(3) from frozen core coupled cluster theory calculations performed with large correlation consistent basis sets, up through augmented sextuple zeta quality. The coupled cluster calculations involved up through quadruple excitations. For As(2) and the hydrides, it was also possible to examine the impact of full configuration interaction on some of the properties. In addition, adjustments were incorporated to account for extrapolation to the frozen core complete basis set limit, core/valence correlation, scalar relativistic effects, the diagonal Born-Oppenheimer correction, and atomic spin orbit corrections. Based on our best theoretical D(0)(As(2)) and the experimental heat of formation of As(2), we propose a revised 0 K arsenic atomic heat of formation of 68.86 ± 0.8 kcal/mol. While generally good agreement was found between theory and experiment, the heat of formation of AsF(3) was an exception. Our best estimate is more than 7 kcal/mol more negative than the single available experimental value, which argues for a re-examination of that measurement. © 2011 American Chemical Society

The solitary wave solution of coupled Klein-Gordon-Zakharov equations via two different numerical methods

NASA Astrophysics Data System (ADS)

Dehghan, Mehdi; Nikpour, Ahmad

2013-09-01

In this research, we propose two different methods to solve the coupled Klein-Gordon-Zakharov (KGZ) equations: the Differential Quadrature (DQ) and Globally Radial Basis Functions (GRBFs) methods. In the DQ method, the derivative value of a function with respect to a point is directly approximated by a linear combination of all functional values in the global domain. The principal work in this method is the determination of weight coefficients. We use two ways for obtaining these coefficients: cosine expansion (CDQ) and radial basis functions (RBFs-DQ), the former is a mesh-based method and the latter categorizes in the set of meshless methods. Unlike the DQ method, the GRBF method directly substitutes the expression of the function approximation by RBFs into the partial differential equation. The main problem in the GRBFs method is ill-conditioning of the interpolation matrix. Avoiding this problem, we study the bases introduced in Pazouki and Schaback (2011) [44]. Some examples are presented to compare the accuracy and easy implementation of the proposed methods. In numerical examples, we concentrate on Inverse Multiquadric (IMQ) and second-order Thin Plate Spline (TPS) radial basis functions. The variable shape parameter (exponentially and random) strategies are applied in the IMQ function and the results are compared with the constant shape parameter.

The structural basis of arrestin-mediated regulation of G-protein-coupled receptors

PubMed Central

Gurevich, Vsevolod V.; Gurevich, Eugenia V.

2008-01-01

The 4 mammalian arrestins serve as almost universal regulators of the largest known family of signaling proteins, G-protein-coupled receptors (GPCRs). Arrestins terminate receptor interactions with G proteins, redirect the signaling to a variety of alternative pathways, and orchestrate receptor internalization and subsequent intracellular trafficking. The elucidation of the structural basis and fine molecular mechanisms of the arrestin–receptor interaction paved the way to the targeted manipulation of this interaction from both sides to produce very stable or extremely transient complexes that helped to understand the regulation of many biologically important processes initiated by active GPCRs. The elucidation of the structural basis of arrestin interactions with numerous non-receptor-binding partners is long overdue. It will allow the construction of fully functional arrestins in which the ability to interact with individual partners is specifically disrupted or enhanced by targeted mutagenesis. These “custom-designed” arrestin mutants will be valuable tools in defining the role of various interactions in the intricate interplay of multiple signaling pathways in the living cell. The identification of arrestin-binding sites for various signaling molecules will also set the stage for designing molecular tools for therapeutic intervention that may prove useful in numerous disorders associated with congenital or acquired disregulation of GPCR signaling. PMID:16460808

Charge transfer between O6+ and atomic hydrogen

NASA Astrophysics Data System (ADS)

Wu, Y.; Stancil, P. C.; Liebermann, H. P.; Buenker, R. J.; Schultz, D. R.; Hui, Y.

2011-05-01

The charge exchange process has been found to play a dominant role in the production of X-rays and/or EUV photons observed in cometary and planetary atmospheres and from the heliosphere. Charge transfer cross sections, especially state-selective cross sections, are necessary parameters in simulations of X-ray emission. In the present work, charge transfer due to collisions of ground state O6+(1s2 1 S) with atomic hydrogen has been investigated theoretically using the quantum-mechanical molecular-orbital close-coupling method (QMOCC). The multi-reference single- and double-excitation configuration interaction approach (MRDCI) has been applied to compute the adiabatic potential and nonadiabatic couplings, and the atomic basis sets used have been optimized with the method proposed previously to obtain precise potential data. Total and state-selective cross sections are calculated for energies between 10 meV/u and 10 keV/u. The QMOCC results are compared to available experimental and theoretical data as well as to new atomic-orbital close-coupling (AOCC) and classical trajectory Monte Carlo (CTMC) calculations. A recommended set of cross sections, based on the MOCC, AOCC, and CTMC calculations, is deduced which should aid in X-ray modeling studies.

Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nozirov, Farhod, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com; Stachów, Michał, E-mail: michal.stachow@gmail.com; Kupka, Teobald, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com

2014-04-14

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd)more » with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)« less

Application of the CC(P;Q) Hierarchy of Coupled-Cluster Methods to the Beryllium Dimer.

PubMed

Magoulas, Ilias; Bauman, Nicholas P; Shen, Jun; Piecuch, Piotr

2018-02-08

The performance of coupled-cluster approaches with higher-than-doubly excited clusters, including the CCSD(T), CCSD(2) T , CR-CC(2,3), CCSD(TQ), and CR-CC(2,4) corrections to CCSD, the active-space CCSDt, CCSDtq, and CCSDTq methods, and the CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) corrections to CCSDt, CCSDtq, and CCSDTq resulting from the CC(P;Q) formalism, in reproducing the CCSDT and CCSDTQ potential energy curves and vibrational term values characterizing Be 2 in its electronic ground state is assessed. The correlation-consistent aug-cc-pVnZ and aug-cc-pCVnZ (n = T and Q) basis sets are employed. Among the CCSD-based corrections, the completely renormalized CR-CC(2,3) and CR-CC(2,4) approaches perform the best. The CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) methods, especially CC(t;3) and CC(q;4), outperform other employed approaches in reproducing the CCSDT and CCSDTQ data. Composite schemes combining the all-electron CCSDT calculations extrapolated to the complete basis set limit with the frozen-core CC(q;4) and CCSDTQ computations using the aug-cc-pVTZ basis to account for connected quadruple excitations reproduce the latest experimental vibrational spectrum of Be 2 to within 4-5 cm -1 , when the vibrational spacings are examined, with typical errors being below 1-2 cm -1 . The resulting binding energies and equilibrium bond lengths agree with their experimentally derived counterparts to within ∼10 cm -1 and 0.01 Å.

An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

1995-01-01

A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

The X40×10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation.

PubMed

Kesharwani, Manoj K; Manna, Debashree; Sylvetsky, Nitai; Martin, Jan M L

2018-03-01

We have re-evaluated the X40×10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)-MP2 "high-level corrections" (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies and turns out to be more important for noncovalent interactions than is generally realized; (n-1)sp subvalence correlation is much less important. The (n-1)d subvalence term is dominated by core-valence correlation; with the smaller cc-pVDZ-F12-PP and cc-pVTZ-F12-PP basis sets, basis set convergence for the core-core contribution becomes sufficiently erratic that it may compromise results overall. The two factors conspire to generate discrepancies of up to 0.9 kcal/mol (0.16 kcal/mol RMS) between the original X40×10 data and the present revision.

High-level ab initio enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan.

PubMed

Feller, David; Simmie, John M

2012-11-29

A high-level ab initio thermochemical technique, known as the Feller-Petersen-Dixon method, is used to calculate the total atomization energies and hence the enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan itself as a means of rationalizing significant discrepancies in the literature. In order to avoid extremely large standard coupled cluster theory calculations, the explicitly correlated CCSD(T)-F12b variation was used with basis sets up to cc-pVQZ-F12. After extrapolating to the complete basis set limit and applying corrections for core/valence, scalar relativistic, and higher order effects, the final Δ(f)H° (298.15 K) values, with the available experimental values in parentheses are furan -34.8 ± 3 (-34.7 ± 0.8), 2-methylfuran -80.3 ± 5 (-76.4 ± 1.2), and 2,5-dimethylfuran -124.6 ± 6 (-128.1 ± 1.1) kJ mol(-1). The theoretical results exhibit a compelling internal consistency.

Computational Study of the Reactions of Methanol with the Hydroperoxyl and Methyl Radicals. Part I: Accurate Thermochemistry and Barrier Heights

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alecu, I. M.; Truhlar, D. G.

2011-04-07

The reactions of CH 3OH with the HO 2 and CH 3 radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2) Q), core–valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGAmore » density functionals can achieve sub-kcal mol -1 agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.« less

Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bross, David H.; Parmar, Payal; Peterson, Kirk A.

The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set (CBS) limit using new all-electron correlation consistent basis sets. The latter were carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons have been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. As amore » result, the final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV), and thus more reliable than the current experimental values of IP 3 through IP 6.« less

The protonation of N2O reexamined - A case study on the reliability of various electron correlation methods for minima and transition states

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1993-01-01

The protonation of N2O and the intramolecular proton transfer in N2OH(+) are studied using various basis sets and a variety of methods, including second-order many-body perturbation theory (MP2), singles and doubles coupled cluster (CCSD), the augmented coupled cluster (CCSD/T/), and complete active space self-consistent field (CASSCF) methods. For geometries, MP2 leads to serious errors even for HNNO(+); for the transition state, only CCSD/T/ produces a reliable geometry due to serious nondynamical correlation effects. The proton affinity at 298.15 K is estimated at 137.6 kcal/mol, in close agreement with recent experimental determinations of 137.3 +/- 1 kcal/mol.

Coupled cluster calculations for static and dynamic polarizabilities of C60

NASA Astrophysics Data System (ADS)

Kowalski, Karol; Hammond, Jeff R.; de Jong, Wibe A.; Sadlej, Andrzej J.

2008-12-01

New theoretical predictions for the static and frequency dependent polarizabilities of C60 are reported. Using the linear response coupled cluster approach with singles and doubles and a basis set especially designed to treat the molecular properties in external electric field, we obtained 82.20 and 83.62 Å3 for static and dynamic (λ =1064 nm) polarizabilities. These numbers are in a good agreement with experimentally inferred data of 76.5±8 and 79±4 Å3 [R. Antoine et al., J. Chem. Phys.110, 9771 (1999); A. Ballard et al., J. Chem. Phys.113, 5732 (2000)]. The reported results were obtained with the highest wave function-based level of theory ever applied to the C60 system.

Low-energy Scattering of Positronium by Atoms

NASA Technical Reports Server (NTRS)

Ray, Hasi

2007-01-01

The survey reports theoretical studies involving positronium (Ps) - atom scattering. Investigations carried out in last few decades have been briefly reviewed in this article. A brief description of close-coupling approximation (CCA), the first-Born approximation (FBA) and the Born-Oppenheimer approximation (BOA) for Ps-Atom systems are made. The CCA codes of Ray et a1 [1-6] are reinvestigated using very fine mesh-points to search for resonances. The article advocates the need for an extended basis set & a systematic study using CCAs.

The 3d Rydberg (3A2) electronic state observed by Herzberg and Shoosmith for methylene

NASA Astrophysics Data System (ADS)

Yamaguchi, Yukio; Schaefer, Henry F., III

1997-06-01

In 1959 and 1961 Herzberg and Shoosmith reported the vacuum ultraviolet spectrum of the triplet state of CH2. The present study focuses on a characterization of the upper state, the 3d Rydberg (3A2) state, observed at 1415 Å. The theoretical interpretation of these experiments is greatly complicated by the presence of a lower-lying 3A2 valence state with a very small equilibrium bond angle. Ab initio electronic structure methods involving self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), complete active space (CAS) SCF, state-averaged (SA) CASSCF, coupled cluster with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], CASSCF second-order (SO) CI, and SACASSCF-SOCI have been employed with six distinct basis sets. With the largest basis set, triple zeta plus triple polarization with two sets of higher angular momentum functions and three sets of diffuse functions TZ3P(2 f,2d)+3diff, the CISD level of theory predicts the equilibrium geometry of the 3d Rydberg (3A2) state to be re=1.093 Å and θe=141.3 deg. With the same basis set the energy (Te value) of the 3d Rydberg state relative to the ground (X˜ 3B1) state has been determined to be 201.6 kcal mol-1 (70 500 cm-1) at the CCSD (T) level, 200.92kcal mol-1 (70 270 cm-1) at the CASSCF-SOCI level, and 200.89kcal mol-1 (70 260 cm-1) at the SACASSCF-SOCI level of theory. These predictions are in excellent agreement with the experimental T0 value of 201.95 kcalmol-1 (70 634 cm-1) reported by Herzberg.

A momentum-space formulation without partial wave decomposition for scattering of two spin-half particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fachruddin, Imam, E-mail: imam.fachruddin@sci.ui.ac.id; Salam, Agus

2016-03-11

A new momentum-space formulation for scattering of two spin-half particles, both either identical or unidentical, is formulated. As basis states the free linear-momentum states are not expanded into the angular-momentum states, the system’s spin states are described by the product of the spin states of the two particles, and the system’s isospin states by the total isospin states of the two particles. We evaluate the Lippmann-Schwinger equations for the T-matrix elements in these basis states. The azimuthal behavior of the potential and of the T-matrix elements leads to a set of coupled integral equations for the T-matrix elements in twomore » variables only, which are the magnitude of the relative momentum and the scattering angle. Some symmetry relations for the potential and the T-matrix elements reduce the number of the integral equations to be solved. A set of six spin operators to express any interaction of two spin-half particles is introduced. We show the spin-averaged differential cross section as being calculated in terms of the solution of the set of the integral equations.« less

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

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

2018-05-01

Core-electron binding energies (CEBEs) computed within a Δ self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z + 1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy.

Shadow poles in coupled-channel problems calculated with the Berggren basis

NASA Astrophysics Data System (ADS)

Id Betan, R. M.; Kruppa, A. T.; Vertse, T.

2018-02-01

Background: In coupled-channels models the poles of the scattering S matrix are located on different Riemann sheets. Physical observables are affected mainly by poles closest to the physical region but sometimes shadow poles have considerable effect too. Purpose: The purpose of this paper is to show that in coupled-channels problems all poles of the S matrix can be located by an expansion in terms of a properly constructed complex-energy basis. Method: The Berggren basis is used for expanding the coupled-channels solutions. Results: The locations of the poles of the S matrix for the Cox potential, constructed for coupled-channels problems, were numerically calculated and compared with the exact ones. In a nuclear physics application the Jπ=3 /2+ resonant poles of 5He were calculated in a phenomenological two-channel model. The properties of both the normal and shadow resonances agree with previous findings. Conclusions: We have shown that, with an appropriately chosen Berggren basis, all poles of the S matrix including the shadow poles can be determined. We have found that the shadow pole of 5He migrates between Riemann sheets if the coupling strength is varied.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Papajak, Ewa; Truhlar, Donald G.

We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”,more » “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.« less

Calculation of Coupled Vibroacoustics Response Estimates from a Library of Available Uncoupled Transfer Function Sets

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Hunt, Ron; Fulcher, Clay; Towner, Robert; McDonald, Emmett

2012-01-01

The design and theoretical basis of a new database tool that quickly generates vibroacoustic response estimates using a library of transfer functions (TFs) is discussed. During the early stages of a launch vehicle development program, these response estimates can be used to provide vibration environment specification to hardware vendors. The tool accesses TFs from a database, combines the TFs, and multiplies these by input excitations to estimate vibration responses. The database is populated with two sets of uncoupled TFs; the first set representing vibration response of a bare panel, designated as H(sup s), and the second set representing the response of the free-free component equipment by itself, designated as H(sup c). For a particular configuration undergoing analysis, the appropriate H(sup s) and H(sup c) are selected and coupled to generate an integrated TF, designated as H(sup s +c). This integrated TF is then used with the appropriate input excitations to estimate vibration responses. This simple yet powerful tool enables a user to estimate vibration responses without directly using finite element models, so long as suitable H(sup s) and H(sup c) sets are defined in the database libraries. The paper discusses the preparation of the database tool and provides the assumptions and methodologies necessary to combine H(sup s) and H(sup c) sets into an integrated H(sup s + c). An experimental validation of the approach is also presented.

Prediction of the vibroacoustic behavior of a submerged shell with non-axisymmetric internal substructures by a condensed transfer function method

NASA Astrophysics Data System (ADS)

Meyer, V.; Maxit, L.; Guyader, J.-L.; Leissing, T.

2016-01-01

The vibroacoustic behavior of axisymmetric stiffened shells immersed in water has been intensively studied in the past. On the contrary, little attention has been paid to the modeling of these shells coupled to non-axisymmetric internal frames. Indeed, breaking the axisymmetry couples the circumferential orders of the Fourier series and considerably increases the computational costs. In order to tackle this issue, we propose a sub-structuring approach called the Condensed Transfer Function (CTF) method that will allow assembling a model of axisymmetric stiffened shell with models of non-axisymmetric internal frames. The CTF method is developed in the general case of mechanical subsystems coupled along curves. A set of orthonormal functions called condensation functions, which depend on the curvilinear abscissa along the coupling line, is considered. This set is then used as a basis for approximating and decomposing the displacements and the applied forces at the line junctions. Thanks to the definition and calculation of condensed transfer functions for each uncoupled subsystem and by using the superposition principle for passive linear systems, the behavior of the coupled subsystems can be deduced. A plane plate is considered as a test case to study the convergence of the method with respect to the type and the number of condensation functions taken into account. The CTF method is then applied to couple a submerged non-periodically stiffened shell described using the Circumferential Admittance Approach (CAA) with internal substructures described by Finite Element Method (FEM). The influence of non-axisymmetric internal substructures can finally be studied and it is shown that it tends to increase the radiation efficiency of the shell and can modify the vibrational and acoustic energy distribution.

Theoretical characterization of the F(2)O(3) molecule by coupled-cluster methods.

PubMed

Huang, Ming-Ju; Watts, John D

2010-09-23

Coupled-cluster calculations with extended basis sets that include noniterative connected triple excitations (CCSD(T)) have been used to study the FOOOF isomer of F(2)O(3). Second-order Moller-Plessett perturbation theory (MP2) and density-functional theory (B3LYP functional) calculations have also been performed for comparison. Two local minima of similar energy, namely, conformers of C(2) and C(s) symmetry have been located. Structures, harmonic vibrational frequencies, and standard enthalpies and free energies of formation have been calculated. The calculated bond lengths of F(2)O(3) are more characteristic of those in F(2)O and a "normal" peroxide than the unusual bond lengths in F(2)O(2). Both conformers have equal F-O and O-O bond lengths, contrary to a recent suggestion of an unsymmetrical structure. The harmonic vibrational frequencies can aid possible identification of gaseous F(2)O(3). The calculated Δ(f)H° and Δ(f)G° are 110 and 173 kJ mol(-1), respectively. These values are based on extrapolation of CCSD(T) results with augmented triple- and quadruple-ζ basis sets and are expected to be within chemical accuracy (i.e., 1 kcal mol(-1) or 4 kJ mol(-1)). F(2)O(3) is calculated to be stable to decomposition to either FO + FOO or F(2) + O(3), but unstable to decomposition to its elements, to F(2)O(2) + (1)/(2)O(2), and to F(2)O + O(2).

Nonadiabatic dynamics on the two coupled electronic PESs: the H+ + O2 system.

PubMed

Xavier, F George D

2010-09-30

Multistate adiabatic and diabatic PESs were computed for the H+ + O2 collision system in Jacobi coordinates, (R,r,γ) using the cc-pVTZ basis set and the ic-MRCI level of theory. In addition, all possible interaction potentials and nonadiabatic coupling matrix elements among those different electronic states were also computed. Comparisons with earlier computed interaction potentials were made wherever possible, and the differences between them is attributed to the multistate diabatization and the chosen level of theory and basis set. Focusing our attention on the ground-state (GS) and the first excited-state (ES) PES, quantum dynamics were performed using the 2 × 2 diabatic potential submatrix obtained from the multistate (four) diabatic potential matrix within the VCC-RIOSA scheme at two experimentally reported collision energies, E(cm) = 9.5 and 23 eV. The scattering quantities were computed for two experimentally observed collision processes, namely, the inelastic vibrational excitation (IVE), H+ + O2 (X3Σg(−),v = 0) → H+ + O2 (X3Σg(−),v′), and the vibrational charge transfer (VCT), H+ + O2 (X3Σg(−),v = 0) → H (2S) + O (X2Πg,v′′). Comparisons were made with experimental results and found an overall improvement relative to the earlier computed results, and the discrepancies, if any, could be brought down to minimum by further modification in employed ab initio PESs and the interaction potential.

Coupled-cluster and density functional theory studies of the electronic 0-0 transitions of the DNA bases.

PubMed

Ovchinnikov, Vasily A; Sundholm, Dage

2014-04-21

The 0-0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations. Excitation energies have also been calculated at the linear-response time-dependent density functional theory (TDDFT) level using the B3LYP functional. Large basis sets have been employed for ensuring that the obtained excitation energies are close to the basis-set limit. Zero-point vibrational energy corrections have been calculated at the B3LYP and CC2 levels for the ground and excited states rendering direct comparisons with high-precision spectroscopy measurements feasible. The obtained excitation energies for the 0-0 transitions of the first excited states of guanine tautomers are in good agreement with experimental values confirming the experimental assignment of the energetic order of the tautomers of the DNA bases. For the experimentally detected guanine tautomers, the first excited state corresponds to a π→π* transition, whereas for the tautomers of adenine, thymine, and the lowest tautomer of cytosine the transition to the first excited state has n →π* character. The calculations suggest that the 0-0 transitions of adenine, thymine, and cytosine are not observed in the absorption spectrum due to the weak oscillator strength of the formally symmetry-forbidden transitions, while 0-0 transitions of thymine have been detected in fluorescence excitation spectra.

DOE Office of Scientific and Technical Information (OSTI.GOV)

San Fabián, J.; Omar, S.; García de la Vega, J. M., E-mail: garcia.delavega@uam.es

The effect of a fraction of Hartree-Fock exchange on the calculated spin-spin coupling constants involving fluorine through a hydrogen bond is analyzed in detail. Coupling constants calculated using wavefunction methods are revisited in order to get high-level calculations using the same basis set. Accurate MCSCF results are obtained using an additive approach. These constants and their contributions are used as a reference for density functional calculations. Within the density functional theory, the Hartree-Fock exchange functional is split in short- and long-range using a modified version of the Coulomb-attenuating method with the SLYP functional as well as with the original B3LYP.more » Results support the difficulties for calculating hydrogen bond coupling constants using density functional methods when fluorine nuclei are involved. Coupling constants are very sensitive to the Hartree-Fock exchange and it seems that, contrary to other properties, it is important to include this exchange for short-range interactions. Best functionals are tested in two different groups of complexes: those related with anionic clusters of type [F(HF){sub n}]{sup −} and those formed by difluoroacetylene and either one or two hydrogen fluoride molecules.« less

Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication

PubMed Central

Mitternacht, Simon; Berezovsky, Igor N.

2011-01-01

Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited by the protein also in the absence of effector ligands. Previously, we developed the measure binding leverage to find sites where ligand binding can shift the conformational equilibrium of a protein. Binding leverage is calculated for a set of motion vectors representing independent conformational degrees of freedom. In this paper, to analyze allosteric communication between binding sites, we introduce the concept of leverage coupling, based on the assumption that only pairs of sites that couple to the same conformational degrees of freedom can be allosterically connected. We demonstrate how leverage coupling can be used to analyze allosteric communication in a range of enzymes (regulated by both ligand binding and post-translational modifications) and huge molecular machines such as chaperones. Leverage coupling can be calculated for any protein structure to analyze both biological and latent catalytic and regulatory sites. PMID:22174669

8D likelihood effective Higgs couplings extraction framework in h → 4ℓ

DOE PAGES

Chen, Yi; Di Marco, Emanuele; Lykken, Joe; ...

2015-01-23

We present an overview of a comprehensive analysis framework aimed at performing direct extraction of all possible effective Higgs couplings to neutral electroweak gauge bosons in the decay to electrons and muons, the so called ‘golden channel’. Our framework is based primarily on a maximum likelihood method constructed from analytic expressions of the fully differential cross sections for h → 4l and for the dominant irreduciblemore » $$ q\\overline{q} $$ → 4l background, where 4l = 2e2μ, 4e, 4μ. Detector effects are included by an explicit convolution of these analytic expressions with the appropriate transfer function over all center of mass variables. Utilizing the full set of observables, we construct an unbinned detector-level likelihood which is continuous in the effective couplings. We consider possible ZZ, Zγ, and γγ couplings simultaneously, allowing for general CP odd/even admixtures. A broad overview is given of how the convolution is performed and we discuss the principles and theoretical basis of the framework. This framework can be used in a variety of ways to study Higgs couplings in the golden channel using data obtained at the LHC and other future colliders.« less

Camera memory study for large space telescope. [charge coupled devices

NASA Technical Reports Server (NTRS)

Hoffman, C. P.; Brewer, J. E.; Brager, E. A.; Farnsworth, D. L.

1975-01-01

Specifications were developed for a memory system to be used as the storage media for camera detectors on the large space telescope (LST) satellite. Detectors with limited internal storage time such as intensities charge coupled devices and silicon intensified targets are implied. The general characteristics are reported of different approaches to the memory system with comparisons made within the guidelines set forth for the LST application. Priority ordering of comparisons is on the basis of cost, reliability, power, and physical characteristics. Specific rationales are provided for the rejection of unsuitable memory technologies. A recommended technology was selected and used to establish specifications for a breadboard memory. Procurement scheduling is provided for delivery of system breadboards in 1976, prototypes in 1978, and space qualified units in 1980.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

Accurate ab initio quartic force fields for the ions HCO(+) and HOC(+)

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Taylor, Peter R.; Lee, Timothy J.

1993-01-01

The quartic force fields of HCO(+) and HOC(+) have been computed using augmented coupled cluster methods and basis sets of spdf and spdfg quality. Calculations on HCN, CO, and N2 have been performed to assist in calibrating the computed results. Going from an spdf to an spdfg basis shortens triple bonds by about 0.004 A, and increases the corresponding harmonic frequency by 10-20/cm, leaving bond distances about 0.003 A too long and triple bond stretching frequencies about 5/cm too low. Accurate estimates for the bond distances, fundamental frequencies, and thermochemical quantities are given. HOC(+) lies 37.8 +/- 0.5 kcal/mol (0 K) above HCO(+); the classical barrier height for proton exchange is 76.7 +/- 1.0 kcal/mol.

NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid

NASA Astrophysics Data System (ADS)

Dikmen, Gökhan; Alver, Özgür

2015-11-01

Possible stable conformers and geometrical molecular structures of 6-Bromo-3-Pyridinyl Boronic acid (6B3PBA; C5H5BBrNO2) were studied experimentally and theoretically using FT-IR and Raman spectroscopic methods. FT-IR and Raman spectra were recorded in the region of 4000-400 cm-1 and 3700-400 cm-1, respectively. The structural properties were investigated further, using 1H, 13C, 1H coupled 13C, HETCOR, COSY and APT NMR techniques. The optimized geometric structures were searched by Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. Vibrational wavenumbers of 6B3PBA were calculated whereby B3LYP density functional methods including 6-311++G(d, p), 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. The comparison of the experimentally and theoretically obtained results using mean absolute error and experimental versus calculated correlation coefficients for the vibrational wavenumbers indicates that B3LYP method with 6-311++G(d, p) gives more satisfactory results for predicting vibrational wavenumbers when compared to the 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. However, this method and none of the mentioned methods here seem suitable for the calculations of OH stretching modes, most likely because increasing unharmonicity in the high wave number region and possible intra and inter molecular interactions at OH edges lead some deviations between experimental and theoretical results. Moreover, reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated using scaled quantum mechanical (SQM) method.

Benchmarking of density functionals for a soft but accurate prediction and assignment of (1) H and (13)C NMR chemical shifts in organic and biological molecules.

PubMed

Benassi, Enrico

2017-01-15

A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Estimating the intrinsic limit of the Feller-Peterson-Dixon composite approach when applied to adiabatic ionization potentials in atoms and small molecules

NASA Astrophysics Data System (ADS)

Feller, David

2017-07-01

Benchmark adiabatic ionization potentials were obtained with the Feller-Peterson-Dixon (FPD) theoretical method for a collection of 48 atoms and small molecules. In previous studies, the FPD method demonstrated an ability to predict atomization energies (heats of formation) and electron affinities well within a 95% confidence level of ±1 kcal/mol. Large 1-particle expansions involving correlation consistent basis sets (up to aug-cc-pV8Z in many cases and aug-cc-pV9Z for some atoms) were chosen for the valence CCSD(T) starting point calculations. Despite their cost, these large basis sets were chosen in order to help minimize the residual basis set truncation error and reduce dependence on approximate basis set limit extrapolation formulas. The complementary n-particle expansion included higher order CCSDT, CCSDTQ, or CCSDTQ5 (coupled cluster theory with iterative triple, quadruple, and quintuple excitations) corrections. For all of the chemical systems examined here, it was also possible to either perform explicit full configuration interaction (CI) calculations or to otherwise estimate the full CI limit. Additionally, corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, non-adiabatic effects, and other minor factors were considered. The root mean square deviation with respect to experiment for the ionization potentials was 0.21 kcal/mol (0.009 eV). The corresponding level of agreement for molecular enthalpies of formation was 0.37 kcal/mol and for electron affinities 0.20 kcal/mol. Similar good agreement with experiment was found in the case of molecular structures and harmonic frequencies. Overall, the combination of energetic, structural, and vibrational data (655 comparisons) reflects the consistent ability of the FPD method to achieve close agreement with experiment for small molecules using the level of theory applied in this study.

A full-dimensional potential energy surface and quantum dynamics of inelastic collision process for H2-HF

NASA Astrophysics Data System (ADS)

Yang, Dongzheng; Huang, Jing; Zuo, Junxiang; Hu, Xixi; Xie, Daiqian

2018-05-01

A full-dimensional ab initio potential energy surface for the H2-HF van der Waals complex was constructed by employing the coupled-cluster singles and doubles with noniterative inclusion of connected triples with augmented correlation-consistent polarised valence quadruple-zeta basis set plus bond functions. Using the improved coupled-states approximation including the nearest neighbor Coriolis couplings, we calculated the state-to-state scattering dynamics for pure rotational and ro-vibrational energy transfer processes. For pure rotational energy transfer, our results showed a different dynamical behavior for para-H2 and ortho-H2 in collision with hydrogen fluoride (HF), which is consistent with the previous study. Interestingly, some strong resonant peaks were presented in the cross sections for ro-vibrational energy transfer. In addition, the calculated vibrational-resolved rate constant is in agreement with the experimental results reported by Bott et al. These dynamics data can be further applied to the numerical simulation of HF chemical lasers.

Closed set of the uniqueness conditions and bifurcation criteria in generalized coupled thermoplasticity for small deformations

NASA Astrophysics Data System (ADS)

Śloderbach, Zdzisław

2016-05-01

This paper reports the results of a study into global and local conditions of uniqueness and the criteria excluding the possibility of bifurcation of the equilibrium state for small strains. The conditions and criteria are derived on the basis of an analysis of the problem of uniqueness of a solution involving the basic incremental boundary problem of coupled generalized thermo-elasto-plasticity. This work forms a follow-up of previous research (Śloderbach in Bifurcations criteria for equilibrium states in generalized thermoplasticity, IFTR Reports, 1980, Arch Mech 3(35):337-349, 351-367, 1983), but contains a new derivation of global and local criteria excluding a possibility of bifurcation of an equilibrium state regarding a comparison body dependent on the admissible fields of stress rate. The thermal elasto-plastic coupling effects, non-associated laws of plastic flow and influence of plastic strains on thermoplastic properties of a body were taken into account in this work. Thus, the mathematical problem considered here is not a self-conjugated problem.

Coupling of Large Amplitude Inversion with Other States

NASA Astrophysics Data System (ADS)

Pearson, John; Yu, Shanshan

2016-06-01

The coupling of a large amplitude motion with a small amplitude vibration remains one of the least well characterized problems in molecular physics. Molecular inversion poses a few unique and not intuitively obvious challenges to the large amplitude motion problem. In spite of several decades of theoretical work numerous challenges in calculation of transition frequencies and more importantly intensities persist. The most challenging aspect of this problem is that the inversion coordinate is a unique function of the overall vibrational state including both the large and small amplitude modes. As a result, the r-axis system and the meaning of the K-quantum number in the rotational basis set are unique to each vibrational state of large or small amplitude motion. This unfortunate reality has profound consequences to calculation of intensities and the coupling of nearly degenerate vibrational states. The case of NH3 inversion and inversion through a plane of symmetry in alcohols will be examined to find a general path forward.

Evolvable synthetic neural system

NASA Technical Reports Server (NTRS)

Curtis, Steven A. (Inventor)

2009-01-01

An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mardirossian, Narbe; Head-Gordon, Martin

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-11-09

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Potential energy surfaces of the ground and low-lying states of HCCS and NCS: CASSCF, MRCI and CCSD(T) studies

NASA Astrophysics Data System (ADS)

Li, Yumin; Iwata, Suehiro

1997-07-01

For astronomically interesting molecules, HCCS and NCS, the equilibrium geometries and potential energy curves of three states (X 2Π, A 2Π and B 2Σ+) as well as vertical excitation energies are studied using complete active space SCF (CASSCF), multi-reference configuration interaction (MRCI) and coupled cluster (CCSD(T)) methods with cc-pVTZ basis sets. The difference and similarity in the three states of HCCS and NCS are illustrated. The results obtained are in good agreement with available experimental data.

Multiconfigurational quantum propagation with trajectory-guided generalized coherent states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigolo, Adriano, E-mail: agrigolo@ifi.unicamp.br; Aguiar, Marcus A. M. de, E-mail: aguiar@ifi.unicamp.br; Viscondi, Thiago F., E-mail: viscondi@if.usp.br

2016-03-07

A generalized version of the coupled coherent states method for coherent states of arbitrary Lie groups is developed. In contrast to the original formulation, which is restricted to frozen-Gaussian basis sets, the extended method is suitable for propagating quantum states of systems featuring diversified physical properties, such as spin degrees of freedom or particle indistinguishability. The approach is illustrated with simple models for interacting bosons trapped in double- and triple-well potentials, most adequately described in terms of SU(2) and SU(3) bosonic coherent states, respectively.

Modulation of isochronous movements in a flexible environment: links between motion and auditory experience.

PubMed

Bravi, Riccardo; Del Tongo, Claudia; Cohen, Erez James; Dalle Mura, Gabriele; Tognetti, Alessandro; Minciacchi, Diego

2014-06-01

The ability to perform isochronous movements while listening to a rhythmic auditory stimulus requires a flexible process that integrates timing information with movement. Here, we explored how non-temporal and temporal characteristics of an auditory stimulus (presence, interval occupancy, and tempo) affect motor performance. These characteristics were chosen on the basis of their ability to modulate the precision and accuracy of synchronized movements. Subjects have participated in sessions in which they performed sets of repeated isochronous wrist's flexion-extensions under various conditions. The conditions were chosen on the basis of the defined characteristics. Kinematic parameters were evaluated during each session, and temporal parameters were analyzed. In order to study the effects of the auditory stimulus, we have minimized all other sensory information that could interfere with its perception or affect the performance of repeated isochronous movements. The present study shows that the distinct characteristics of an auditory stimulus significantly influence isochronous movements by altering their duration. Results provide evidence for an adaptable control of timing in the audio-motor coupling for isochronous movements. This flexibility would make plausible the use of different encoding strategies to adapt audio-motor coupling for specific tasks.

High-level ab initio studies of NO(X2Π)-O2(X3Σg -) van der Waals complexes in quartet states

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2018-05-01

Geometry optimisations were performed on nine different structures of NO(X2Π)-O2(X3Σg-) van der Waals complexes in their quartet states, using the explicitly correlated RCCSD(T)-F12b method with basis sets up to the cc-pVQZ-F12 level. For the most stable configurations, counterpoise-corrected optimisations as well as extrapolations to the complete basis set (CBS) were performed. The X structure in the 4A‧ state was found to be most stable, with a CBS binding energy of -157 cm-1. The slipped tilted structures with N closer to O2 (Slipt-N), as well as the slipped parallel structure with O of NO closer to O2 (Slipp-O) in 4A″ states have binding energies of about -130 cm-1. C2v and linear complexes are less stable. According to calculated harmonic frequencies, the X isomer is bound. Isotropic hyperfine coupling constants of the complex are compared with those of the monomers.

An ab initio study of the C3(+) cation using multireference methods

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Martin, J. M. L.; Francois, J. P.; Gijbels, R.

1991-01-01

The energy difference between the linear 2 sigma(sup +, sub u) and cyclic 2B(sub 2) structures of C3(+) has been investigated using large (5s3p2d1f) basis sets and multireference electron correlation treatments, including complete active space self consistent fields (CASSCF), multireference configuration interaction (MRCI), and averaged coupled-pair functional (ACPF) methods, as well as the single-reference quadratic configuration interaction (QCISD(T)) method. Our best estimate, including a correction for basis set incompleteness, is that the linear form lies above the cyclic from by 5.2(+1.5 to -1.0) kcal/mol. The 2 sigma(sup +, sub u) state is probably not a transition state, but a local minimum. Reliable computation of the cyclic/linear energy difference in C3(+) is extremely demanding of the electron correlation treatment used: of the single-reference methods previously considered, CCSD(T) and QCISD(T) perform best. The MRCI + Q(0.01)/(4s2p1d) energy separation of 1.68 kcal/mol should provide a comparison standard for other electron correlation methods applied to this system.

Ab initio intermolecular potential energy surface for the CO2—N2 system and related thermophysical properties

NASA Astrophysics Data System (ADS)

Crusius, Johann-Philipp; Hellmann, Robert; Castro-Palacio, Juan Carlos; Vesovic, Velisa

2018-06-01

A four-dimensional potential energy surface (PES) for the interaction between a rigid carbon dioxide molecule and a rigid nitrogen molecule was constructed based on quantum-chemical ab initio calculations up to the coupled-cluster level with single, double, and perturbative triple excitations. Interaction energies for a total of 1893 points on the PES were calculated using the counterpoise-corrected supermolecular approach and basis sets of up to quintuple-zeta quality with bond functions. The interaction energies were extrapolated to the complete basis set limit, and an analytical site-site potential function with seven sites for carbon dioxide and five sites for nitrogen was fitted to the interaction energies. The CO2—N2 cross second virial coefficient as well as the dilute gas shear viscosity, thermal conductivity, and binary diffusion coefficient of CO2—N2 mixtures were calculated for temperatures up to 2000 K to validate the PES and to provide reliable reference values for these important properties. The calculated values are in very good agreement with the best experimental data.

Interaction of monovalent cations with acetonitrile

NASA Astrophysics Data System (ADS)

Černušák, Ivan; Aranyosiová, Monika; Vollárová, Ol'ga; Velič, Dušan; Kirdajová, Ol'ga; Benko, Ján

Solvation of monovalent cations (Me+) of alkali metals=Na+, K+, Rb+, and Cs+, coinage metals=Cu+, Ag+, Au+, and p-block elements Ga+, In+, and Tl+ with acetonitrile was studied by means of ab initio calculations and time-of-flight secondary ion mass spectrometry (TOF-SIMS). The intermolecular interactions in the complexes Me+···CH3CN were investigated using the coupled clusters theory including single, double, and noniterative triple substitutions (CCSD(T)) in conjunction with the Pol and Pol-dk basis sets. The binding energies of these donor-acceptor complexes were estimated; taking into account the basis set superposition error, zero-point vibrations, correlation contribution, and scalar relativistic corrections. The theoretical ΔG0298 K values based on CCSD(T)/Pol and/or CCSD(T)/Pol-dk binding energies correlated well with experimental transfer Gibbs energies (from water to acetonitrile) for the series of cations. In the case of Au monocation, relativistic correction turned out to be extremely important. Composition of the complex of Ag+ and Na+ with acetonitrile was determined by using SIMS supporting both theoretical and experimental transfer Gibbs energies.

Correlation consistent basis sets for the atoms In–Xe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahler, Andrew; Wilson, Angela K., E-mail: akwilson@unt.edu

In this work, the correlation consistent family of Gaussian basis sets has been expanded to include all-electron basis sets for In–Xe. The methodology for developing these basis sets is described, and several examples of the performance and utility of the new sets have been provided. Dissociation energies and bond lengths for both homonuclear and heteronuclear diatomics demonstrate the systematic convergence behavior with respect to increasing basis set quality expected by the family of correlation consistent basis sets in describing molecular properties. Comparison with recently developed correlation consistent sets designed for use with the Douglas-Kroll Hamiltonian is provided.

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

NASA Astrophysics Data System (ADS)

Yu, Hua-Gen

2016-08-01

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using a multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH4 and H2CO are given, together with a comparison with previous results.

Discovering transnosological molecular basis of human brain diseases using biclustering analysis of integrated gene expression data.

PubMed

Cha, Kihoon; Hwang, Taeho; Oh, Kimin; Yi, Gwan-Su

2015-01-01

It has been reported that several brain diseases can be treated as transnosological manner implicating possible common molecular basis under those diseases. However, molecular level commonality among those brain diseases has been largely unexplored. Gene expression analyses of human brain have been used to find genes associated with brain diseases but most of those studies were restricted either to an individual disease or to a couple of diseases. In addition, identifying significant genes in such brain diseases mostly failed when it used typical methods depending on differentially expressed genes. In this study, we used a correlation-based biclustering approach to find coexpressed gene sets in five neurodegenerative diseases and three psychiatric disorders. By using biclustering analysis, we could efficiently and fairly identified various gene sets expressed specifically in both single and multiple brain diseases. We could find 4,307 gene sets correlatively expressed in multiple brain diseases and 3,409 gene sets exclusively specified in individual brain diseases. The function enrichment analysis of those gene sets showed many new possible functional bases as well as neurological processes that are common or specific for those eight diseases. This study introduces possible common molecular bases for several brain diseases, which open the opportunity to clarify the transnosological perspective assumed in brain diseases. It also showed the advantages of correlation-based biclustering analysis and accompanying function enrichment analysis for gene expression data in this type of investigation.

Discovering transnosological molecular basis of human brain diseases using biclustering analysis of integrated gene expression data

PubMed Central

2015-01-01

Background It has been reported that several brain diseases can be treated as transnosological manner implicating possible common molecular basis under those diseases. However, molecular level commonality among those brain diseases has been largely unexplored. Gene expression analyses of human brain have been used to find genes associated with brain diseases but most of those studies were restricted either to an individual disease or to a couple of diseases. In addition, identifying significant genes in such brain diseases mostly failed when it used typical methods depending on differentially expressed genes. Results In this study, we used a correlation-based biclustering approach to find coexpressed gene sets in five neurodegenerative diseases and three psychiatric disorders. By using biclustering analysis, we could efficiently and fairly identified various gene sets expressed specifically in both single and multiple brain diseases. We could find 4,307 gene sets correlatively expressed in multiple brain diseases and 3,409 gene sets exclusively specified in individual brain diseases. The function enrichment analysis of those gene sets showed many new possible functional bases as well as neurological processes that are common or specific for those eight diseases. Conclusions This study introduces possible common molecular bases for several brain diseases, which open the opportunity to clarify the transnosological perspective assumed in brain diseases. It also showed the advantages of correlation-based biclustering analysis and accompanying function enrichment analysis for gene expression data in this type of investigation. PMID:26043779

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hua-Gen, E-mail: hgy@bnl.gov

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using amore » multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH{sub 4} and H{sub 2}CO are given, together with a comparison with previous results.« less

The Linear Interaction Energy Method for the Prediction of Protein Stability Changes Upon Mutation

PubMed Central

Wickstrom, Lauren; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

The coupling of protein energetics and sequence changes is a critical aspect of computational protein design, as well as for the understanding of protein evolution, human disease, and drug resistance. In order to study the molecular basis for this coupling, computational tools must be sufficiently accurate and computationally inexpensive enough to handle large amounts of sequence data. We have developed a computational approach based on the linear interaction energy (LIE) approximation to predict the changes in the free energy of the native state induced by a single mutation. This approach was applied to a set of 822 mutations in 10 proteins which resulted in an average unsigned error of 0.82 kcal/mol and a correlation coefficient of 0.72 between the calculated and experimental ΔΔG values. The method is able to accurately identify destabilizing hot spot mutations however it has difficulty in distinguishing between stabilizing and destabilizing mutations due to the distribution of stability changes for the set of mutations used to parameterize the model. In addition, the model also performs quite well in initial tests on a small set of double mutations. Based on these promising results, we can begin to examine the relationship between protein stability and fitness, correlated mutations, and drug resistance. PMID:22038697

Range-Separated Brueckner Coupled Cluster Doubles Theory

NASA Astrophysics Data System (ADS)

Shepherd, James J.; Henderson, Thomas M.; Scuseria, Gustavo E.

2014-04-01

We introduce a range-separation approximation to coupled cluster doubles (CCD) theory that successfully overcomes limitations of regular CCD when applied to the uniform electron gas. We combine the short-range ladder channel with the long-range ring channel in the presence of a Bruckner renormalized one-body interaction and obtain ground-state energies with an accuracy of 0.001 a.u./electron across a wide range of density regimes. Our scheme is particularly useful in the low-density and strongly correlated regimes, where regular CCD has serious drawbacks. Moreover, we cure the infamous overcorrelation of approaches based on ring diagrams (i.e., the particle-hole random phase approximation). Our energies are further shown to have appropriate basis set and thermodynamic limit convergence, and overall this scheme promises energetic properties for realistic periodic and extended systems which existing methods do not possess.

XZP + 1d and XZP + 1d-DKH basis sets for second-row elements: application to CCSD(T) zero-point vibrational energy and atomization energy calculations.

PubMed

Campos, Cesar T; Jorge, Francisco E; Alves, Júlia M A

2012-09-01

Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5 %. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2 kcal mol(-1)) was found for SiH(4).

An efficient parallel algorithm for the calculation of canonical MP2 energies.

PubMed

Baker, Jon; Pulay, Peter

2002-09-01

We present the parallel version of a previous serial algorithm for the efficient calculation of canonical MP2 energies (Pulay, P.; Saebo, S.; Wolinski, K. Chem Phys Lett 2001, 344, 543). It is based on the Saebo-Almlöf direct-integral transformation, coupled with an efficient prescreening of the AO integrals. The parallel algorithm avoids synchronization delays by spawning a second set of slaves during the bin-sort prior to the second half-transformation. Results are presented for systems with up to 2000 basis functions. MP2 energies for molecules with 400-500 basis functions can be routinely calculated to microhartree accuracy on a small number of processors (6-8) in a matter of minutes with modern PC-based parallel computers. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1150-1156, 2002

Monomeric and dimeric structures, electronic properties and vibrational spectra of azelaic acid by HF and B3LYP methods

NASA Astrophysics Data System (ADS)

Kumar, Amarendra; Narayan, Vijay; Prasad, Onkar; Sinha, Leena

2012-08-01

Quantum chemical calculations of energies, dipole moment, polarizability, hyperpolarizability and vibrational wavenumbers of Azelaic acid (AZA) were carried out by using ab initio HF and B3LYP methods with 6-311++G(d,p) basis set. Hydrogen-bonded dimer of AZA, optimized by counterpoise correction, has also been studied by HF and B3LYP at the 6-311++G(d,p) level and the effects of molecular association through Osbnd H⋯O hydrogen bonding have been discussed. A complete vibrational analysis of AZA has been performed and assignments are made on the basis of potential energy distribution. The comparisons and assignments of the vibrational frequencies indicate that the experimental spectra also correspond acceptably with those of theoretically simulated spectra except the hydrogen-bonded coupled infrared vibrations.

Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality.

PubMed

Wang, Xiao-Gang; Carrington, Tucker

2017-03-14

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H 2 O-Cl - . When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H 2 O-Cl - , there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm.

Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2017-03-01

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H2O-Cl-. When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H2O-Cl-, there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm.

Potential energy curves of the Na2+ molecular ion from all-electron ab initio relativistic calculations

NASA Astrophysics Data System (ADS)

Bewicz, Anna; Musiał, Monika; Kucharski, Stanisław A.

2017-11-01

The equation-of-motion coupled-cluster method for electron affinity calculations has been used to study potential energy curves (PECs) for the Na+2 molecular ion. Although the studied molecule represents the open shell system the applied approach employs the closed shell Na+ 22 ion as the reference. In addition the Na+ 22 system dissociates into the closed shell fragments; hence, the restricted Hartree-Fock scheme can be used within the whole range of interatomic distances, from 2 to 45 Å. We used large basis set engaging 268 basis functions with all 21 electrons correlated. The relativistic effects are included via second-order Douglas-Kroll method. The computed PECs, spectroscopic molecular constants and vibrational energy levels agree well with experimental values if the latter are available or with other theoretical data.

Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2016-05-01

With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.

Rapid evaluation for dielectronic recombination rate coefficients of the H-like isoelectronic sequence.

NASA Astrophysics Data System (ADS)

Teng, H.; Xu, Z.

1996-09-01

The authors present a set of accurate formulae for the rapid calculation of dielectronic recombination rate coefficients of H-like ions from Ne (Z = 10) to Ni (Z = 29) with an electron temperature range from 0.6 to 10 keV. This set of formulae are obtained by fitting directly the dielectronic recombination rate coefficients calculated on the basis of the intermediate - coupling multi - configuration Hartree-Fock model made by Karim and Bhalla (1988). The dielectronic recombination rate coefficients from these formulae are in close agreement with the original results of Karim et al. The errors are generally less than 0.1%. The results are also compared with the ones obtained by a set of new rate formulae developed by Hahn. These formulae can be used for generating dielectronic recombination rate coefficients of some H-like ions where the explicit calculations are unavailable. The detailed results are tabulated and discussed.

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

PubMed Central

2017-01-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac–Coulomb and Dirac–Coulomb–Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved. PMID:28595411

Coupled-cluster, Möller Plesset (MP2), Density Fitted Local MP2, and Density Functional Theory Examination of the Energetic and Structural Features of Hydrophobic Solvation: Water and Pentane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghadar, Yasaman; Clark, Aurora E.

2012-02-02

The interaction potentials between immiscible polar and non-polar solvents are a major driving force behind the formation of liquid:liquid interfaces. In this work, the interaction energy of water–pentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [CCSD(T)], 2nd order Möller Plesset perturbation theory (MP2), density fitted local MP2 (DF-LMP2), as well as density functional theory using a wide variety of density functionals and several different basis sets. The M05-2X exchange correlation functionals exhibit excellent agreement with CCSD(T) and DF-LMP2 after taking into account basis set superposition error. The gas phase water–pentane interaction energy is found tomore » be quite sensitive to the specific pentane isomer (2,2- dimethylpropane vs. n-pentane) and relative orientation of the monomeric constituents. Subsequent solution phase cluster calculations of 2,2-dimethylpropane and n-pentane solvated by water indicate a positive free energy of solvation that is in good agreement with available experimental data. Structural parameters are quite sensitive to the density functional employed and reflect differences in the two-body interaction energy calculated by each method. In contrast, cluster calculations of pentane solvation of H2O solute are found to be inadequate for describing the organic solvent, likely due to limitations associated with the functionals employed (B3LYP, BHandH, and M05-2X).« less

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

NASA Astrophysics Data System (ADS)

Jäger, Benjamin; Bich, Eckard

2017-06-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

I + (H2O)2 → HI + (H2O)OH Forward and Reverse Reactions. CCSD(T) Studies Including Spin-Orbit Coupling.

PubMed

Wang, Hui; Li, Guoliang; Li, Qian-Shu; Xie, Yaoming; Schaefer, Henry F

2016-03-03

The potential energy profile for the atomic iodine plus water dimer reaction I + (H2O)2 → HI + (H2O)OH has been explored using the "Gold Standard" CCSD(T) method with quadruple-ζ correlation-consistent basis sets. The corresponding information for the reverse reaction HI + (H2O)OH → I + (H2O)2 is also derived. Both zero-point vibrational energies (ZPVEs) and spin-orbit (SO) coupling are considered, and these notably alter the classical energetics. On the basis of the CCSD(T)/cc-pVQZ-PP results, including ZPVE and SO coupling, the forward reaction is found to be endothermic by 47.4 kcal/mol, implying a significant exothermicity for the reverse reaction. The entrance complex I···(H2O)2 is bound by 1.8 kcal/mol, and this dissociation energy is significantly affected by SO coupling. The reaction barrier lies 45.1 kcal/mol higher than the reactants. The exit complex HI···(H2O)OH is bound by 3.0 kcal/mol relative to the asymptotic limit. At every level of theory, the reverse reaction HI + (H2O)OH → I + (H2O)2 proceeds without a barrier. Compared with the analogous water monomer reaction I + H2O → HI + OH, the additional water molecule reduces the relative energies of the entrance stationary point, transition state, and exit complex by 3-5 kcal/mol. The I + (H2O)2 reaction is related to the valence isoelectronic bromine and chlorine reactions but is distinctly different from the F + (H2O)2 system.

Costs of medically assisted reproduction treatment at specialized fertility clinics in the Danish public health care system: results from a 5-year follow-up cohort study.

PubMed

Christiansen, Terkel; Erb, Karin; Rizvanovic, Amra; Ziebe, Søren; Mikkelsen Englund, Anne L; Hald, Finn; Boivin, Jacky; Schmidt, Lone

2014-01-01

To examine the costs to the public health care system of couples in medically assisted reproduction. Longitudinal cohort study of infertile couples initiating medically assisted reproduction treatment. Specialized public fertility clinics in Denmark. Seven hundred and thirty-nine couples having no child at study entry and with data on kind of treatment and live birth (yes/no) for each treatment attempt at the specialized public fertility clinic. Treatment data for medically assisted reproduction attempts conducted at the public fertility clinics were abstracted from medical records. Flow diagrams were drawn for different standard treatment cycles and direct costs at each stage in the flow charts were measured and valued by a bottom-up procedure. Indirect costs were distributed to each treatment cycle on the basis of number of visits as basis. Costs were adjusted to 2012 prices using a constructed medical price index. Live birth, costs. Total costs per live birth in 2012 prices were estimated to 10,755€. Costs per treated couple - irrespective of whether the treatment was terminated by a live birth or not - were estimated at 6607€. Costs per live birth of women <35 years at treatment initiation were 9338€ and 15,040€ for women ≥35 years. The public costs for live births after conception with medically assisted reproduction treatment are relatively modest. The results can be generalized to public fertility treatment in Denmark and to other public treatment settings with similar limitations in numbers of public treatment cycles offered. © 2013 Nordic Federation of Societies of Obstetrics and Gynecology.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, Jonathon; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Neaton, Jeffrey B.

With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methodsmore » and systems examined, the most complete basis is Jensen’s pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.« less

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.

PubMed

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. Copyright 2008 Wiley Periodicals, Inc.

Accuracy of Lagrange-sinc functions as a basis set for electronic structure calculations of atoms and molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook

2015-03-07

We developed a self-consistent field program based on Kohn-Sham density functional theory using Lagrange-sinc functions as a basis set and examined its numerical accuracy for atoms and molecules through comparison with the results of Gaussian basis sets. The result of the Kohn-Sham inversion formula from the Lagrange-sinc basis set manifests that the pseudopotential method is essential for cost-effective calculations. The Lagrange-sinc basis set shows faster convergence of the kinetic and correlation energies of benzene as its size increases than the finite difference method does, though both share the same uniform grid. Using a scaling factor smaller than or equal tomore » 0.226 bohr and pseudopotentials with nonlinear core correction, its accuracy for the atomization energies of the G2-1 set is comparable to all-electron complete basis set limits (mean absolute deviation ≤1 kcal/mol). The same basis set also shows small mean absolute deviations in the ionization energies, electron affinities, and static polarizabilities of atoms in the G2-1 set. In particular, the Lagrange-sinc basis set shows high accuracy with rapid convergence in describing density or orbital changes by an external electric field. Moreover, the Lagrange-sinc basis set can readily improve its accuracy toward a complete basis set limit by simply decreasing the scaling factor regardless of systems.« less

Solvatochromic shifts from coupled-cluster theory embedded in density functional theory

NASA Astrophysics Data System (ADS)

Höfener, Sebastian; Gomes, André Severo Pereira; Visscher, Lucas

2013-09-01

Building on the framework recently reported for determining general response properties for frozen-density embedding [S. Höfener, A. S. P. Gomes, and L. Visscher, J. Chem. Phys. 136, 044104 (2012)], 10.1063/1.3675845, in this work we report a first implementation of an embedded coupled-cluster in density-functional theory (CC-in-DFT) scheme for electronic excitations, where only the response of the active subsystem is taken into account. The formalism is applied to the calculation of coupled-cluster excitation energies of water and uracil in aqueous solution. We find that the CC-in-DFT results are in good agreement with reference calculations and experimental results. The accuracy of calculations is mainly sensitive to factors influencing the correlation treatment (basis set quality, truncation of the cluster operator) and to the embedding treatment of the ground-state (choice of density functionals). This allows for efficient approximations at the excited state calculation step without compromising the accuracy. This approximate scheme makes it possible to use a first principles approach to investigate environment effects with specific interactions at coupled-cluster level of theory at a cost comparable to that of calculations of the individual subsystems in vacuum.

Broadband Noise of Fans - With Unsteady Coupling Theory to Account for Rotor and Stator Reflection/Transmission Effects

NASA Technical Reports Server (NTRS)

Hanson, Donald B.

2001-01-01

This report examines the effects on broadband noise generation of unsteady coupling between a rotor and stator in the fan stage of a turbofan engine. Whereas previous acoustic analyses treated the blade rows as isolated cascades, the present work accounts for reflection and transmission effects at both blade rows by tracking the mode and frequency scattering of pressure and vortical waves. The fan stage is modeled in rectilinear geometry to take advantage of a previously existing unsteady cascade theory for 3D perturbation waves and thereby use a realistic 3D turbulence spectrum. In the analysis, it was found that the set of participating modes divides itself naturally into "independent mode subsets" that couple only among themselves and not to the other such subsets. This principle is the basis for the analysis and considerably reduces computational effort. It also provides a simple, accurate scheme for modal averaging for further efficiency. Computed results for a coupled fan stage are compared with calculations for isolated blade rows. It is found that coupling increases downstream noise by 2 to 4 dB. Upstream noise is lower for isolated cascades and is further reduced by including coupling effects. In comparison with test data, the increase in the upstream/downstream differential indicates that broadband noise from turbulent inflow at the stator dominates downstream noise but is not a significant contributor to upstream noise.

Optimization of selected molecular orbitals in group basis sets.

PubMed

Ferenczy, György G; Adams, William H

2009-04-07

We derive a local basis equation which may be used to determine the orbitals of a group of electrons in a system when the orbitals of that group are represented by a group basis set, i.e., not the basis set one would normally use but a subset suited to a specific electronic group. The group orbitals determined by the local basis equation minimize the energy of a system when a group basis set is used and the orbitals of other groups are frozen. In contrast, under the constraint of a group basis set, the group orbitals satisfying the Huzinaga equation do not minimize the energy. In a test of the local basis equation on HCl, the group basis set included only 12 of the 21 functions in a basis set one might ordinarily use, but the calculated active orbital energies were within 0.001 hartree of the values obtained by solving the Hartree-Fock-Roothaan (HFR) equation using all 21 basis functions. The total energy found was just 0.003 hartree higher than the HFR value. The errors with the group basis set approximation to the Huzinaga equation were larger by over two orders of magnitude. Similar results were obtained for PCl(3) with the group basis approximation. Retaining more basis functions allows an even higher accuracy as shown by the perfect reproduction of the HFR energy of HCl with 16 out of 21 basis functions in the valence basis set. When the core basis set was also truncated then no additional error was introduced in the calculations performed for HCl with various basis sets. The same calculations with fixed core orbitals taken from isolated heavy atoms added a small error of about 10(-4) hartree. This offers a practical way to calculate wave functions with predetermined fixed core and reduced base valence orbitals at reduced computational costs. The local basis equation can also be used to combine the above approximations with the assignment of local basis sets to groups of localized valence molecular orbitals and to derive a priori localized orbitals. An appropriately chosen localization and basis set assignment allowed a reproduction of the energy of n-hexane with an error of 10(-5) hartree, while the energy difference between its two conformers was reproduced with a similar accuracy for several combinations of localizations and basis set assignments. These calculations include localized orbitals extending to 4-5 heavy atoms and thus they require to solve reduced dimension secular equations. The dimensions are not expected to increase with increasing system size and thus the local basis equation may find use in linear scaling electronic structure calculations.

Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Cho, Minhaeng

2013-05-01

The Hessian matrix reconstruction method initially developed to extract the basis mode frequencies, vibrational coupling constants, and transition dipoles of the delocalized amide I, II, and III vibrations of polypeptides and proteins from quantum chemistry calculation results is used to obtain those properties of delocalized O-H stretch modes in liquid water. Considering the water symmetric and asymmetric O-H stretch modes as basis modes, we here develop theoretical models relating vibrational frequencies, transition dipoles, and coupling constants of basis modes to local water configuration and solvent electric potential. Molecular dynamics simulation was performed to generate an ensemble of water configurations that was in turn used to construct vibrational Hamiltonian matrices. Obtaining the eigenvalues and eigenvectors of the matrices and using the time-averaging approximation method, which was developed by the Skinner group, to calculating the vibrational spectra of coupled oscillator systems, we could numerically simulate the O-H stretch IR spectrum of liquid water. The asymmetric line shape and weak shoulder bands were quantitatively reproduced by the present computational procedure based on vibrational exciton model, where the polarization effects on basis mode transition dipoles and inter-mode coupling constants were found to be crucial in quantitatively simulating the vibrational spectra of hydrogen-bond networking liquid water.

Accurate Methods for Large Molecular Systems (Preprint)

DTIC Science & Technology

2009-01-06

tensor, EFP calculations are basis set dependent. The smallest recommended basis set is 6- 31++G( d , p )52 The dependence of the computational cost of...and second order perturbation theory (MP2) levels with the 6-31G( d , p ) basis set. Additional SFM tests are presented for a small set of alpha...helices using the 6-31++G( d , p ) basis set. The larger 6-311++G(3df,2p) basis set is employed for creating all EFPs used for non- bonded interactions, since

Nuclear chirality, a model and the data

NASA Astrophysics Data System (ADS)

Starosta, K.; Koike, T.

2017-09-01

In the last decade, the manifestation of chirality in atomic nuclei has become the subject of numerous experimental and theoretical studies. The common feature of current model calculations is that the chiral geometry of angular momentum coupling is extracted from expectation values of orientation operators, rather than being a starting point in construction of a model. However, using the particle-hole coupling model for triaxial odd-odd nuclei it is possible to construct a basis which contains right-handed, left-handed and planar states of angular momentum coupling. If this basis is used, the chirality is an explicit rather than an extracted feature as in any other models with non-chiral bases. The time-reversal symmetry, which relates the basis states of opposite handedness, can be used to reduce the dimension of matrices for diagonalization of the model Hamiltonian, proving the effectiveness of this approach. Moreover, the final model eigenstate wave functions show a concentration of amplitudes among a relatively small number (˜1%) of components compared to the full model space. In that sense, the ‘chiral’ basis provides a useful tool to examine model predictions providing direct insight into the structure of doublet states. In this work, similarities and differences between the rotational behaviour of an axial and triaxial body provide a starting point for derivation of the basis optimal for valence nucleon coupling to an axial and a triaxial core. The derived ‘chiral’ basis is optimal for coupling of a valence particle and hole to the triaxial core. Model predictions are presented and discussed. A comprehensive review of current experimental data on observed chiral band candidates is also provided.

Approaching the theoretical limit in periodic local MP2 calculations with atomic-orbital basis sets: the case of LiH.

PubMed

Usvyat, Denis; Civalleri, Bartolomeo; Maschio, Lorenzo; Dovesi, Roberto; Pisani, Cesare; Schütz, Martin

2011-06-07

The atomic orbital basis set limit is approached in periodic correlated calculations for solid LiH. The valence correlation energy is evaluated at the level of the local periodic second order Møller-Plesset perturbation theory (MP2), using basis sets of progressively increasing size, and also employing "bond"-centered basis functions in addition to the standard atom-centered ones. Extended basis sets, which contain linear dependencies, are processed only at the MP2 stage via a dual basis set scheme. The local approximation (domain) error has been consistently eliminated by expanding the orbital excitation domains. As a final result, it is demonstrated that the complete basis set limit can be reached for both HF and local MP2 periodic calculations, and a general scheme is outlined for the definition of high-quality atomic-orbital basis sets for solids. © 2011 American Institute of Physics

Time-dependent density functional theory description of total photoabsorption cross sections

NASA Astrophysics Data System (ADS)

Tenorio, Bruno Nunes Cabral; Nascimento, Marco Antonio Chaer; Rocha, Alexandre Braga

2018-02-01

The time-dependent version of the density functional theory (TDDFT) has been used to calculate the total photoabsorption cross section of a number of molecules, namely, benzene, pyridine, furan, pyrrole, thiophene, phenol, naphthalene, and anthracene. The discrete electronic pseudo-spectra, obtained in a L2 basis set calculation were used in an analytic continuation procedure to obtain the photoabsorption cross sections. The ammonia molecule was chosen as a model system to compare the results obtained with TDDFT to those obtained with the linear response coupled cluster approach in order to make a link with our previous work and establish benchmarks.

Magnetic anisotropy in nickel complexes as determined by combined magnetic susceptibility/magnetization/theoretical studies

NASA Astrophysics Data System (ADS)

Mašlejová, Anna; Boča, Roman; Dlháň, L.'ubor; Herchel, Radovan

2004-05-01

The zero-field splitting in nickel(II) complexes was modeled by considering all relevant operators (electron repulsion, crystal-field, spin-orbit coupling, orbital-Zeeman, and spin-Zeeman) in the complete basis set spanned by d n-atomic terms. D-values between weak and strong crystal field limits were evaluated from the crystal-field multiplets as well as using the spin Hamiltonian formalism. Importance of the anisotropic orbital reduction factors is discussed and exemplified by D/hc=-22 cm-1 as subtracted from magnetic data for [Ni(imidazole) 4(acetate) 2] complex.

Pathogenesis of Ovarian Serous Carcinoma as the Basis for Immunologic Directed Diagnosis and Treatment

DTIC Science & Technology

2006-08-01

0.49 (0.50) Vector 0.40 (0.49) 0.41 (0.50) HOXA7 0.42 (0.49) 0.43 (0.49) Hsp27 0.42 (0.49) 0.37 (0.48) CA125 0.99 (0.07...2/ neu and HOXB7; ref. 11). Autoantibody to heat shock proteins (Hsp), notably Hsp27 and Hsp90 (23–25), has also been associated with ovarian cancer...tagged recombinant TAA. Similarly, a further six distinct sets of LabMAP carboxylated microspheres were directly coupled to 25 Ag purified Hsp27 , Hsp70

General analysis of group velocity effects in collinear optical parametric amplifiers and generators.

PubMed

Arisholm, Gunnar

2007-05-14

Group velocity mismatch (GVM) is a major concern in the design of optical parametric amplifiers (OPAs) and generators (OPGs) for pulses shorter than a few picoseconds. By simplifying the coupled propagation equations and exploiting their scaling properties, the number of free parameters for a collinear OPA is reduced to a level where the parameter space can be studied systematically by simulations. The resulting set of figures show the combinations of material parameters and pulse lengths for which high performance can be achieved, and they can serve as a basis for a design.

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Three-body approach to the K-d scattering length in particle basis

NASA Astrophysics Data System (ADS)

Bahaoui, A.; Fayard, C.; Mizutani, T.; Saghai, B.

2002-11-01

We report on the first calculation of the scattering length AK-d based on a relativistic three-body approach where the K¯N coupled channel two-body input amplitudes have been obtained with the chiral SU(3) constraint, but with isospin symmetry breaking effects taken into account. Results are compared with a recent calculation applying a similar set of two-body amplitudes, based on the fixed center approximation, and for which we find significant deviations from the three-body results. Effects of the deuteron D-wave component, pion-nucleon, and hyperon-nucleon interactions are also evaluated.

Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xuefei; Zhang, Wenjing; Tang, Mingsheng

2015-05-12

Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn–Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules againstmore » the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal–ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core–valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.« less

The energy separation between the classical and nonclassical isomers of protonated acetylene - An extensive study in one- and n-particle space saturation

NASA Technical Reports Server (NTRS)

Lindh, Roland; Rice, Julia E.; Lee, Timothy J.

1991-01-01

The energy separation between the classical and nonclassical forms of protonated acetylene has been reinvestigated in light of the recent experimentally deduced lower bound to this value of 6.0 kcal/mol. The objective of the present study is to use state-of-the-art ab initio quantum mechanical methods to establish this energy difference to within chemical accuracy (i.e., about 1 kcal/mol). The one-particle basis sets include up to g-type functions and the electron correlation methods include single and double excitation coupled-cluster (CCSD), the CCSD(T) extension, multireference configuration interaction, and the averaged coupled-pair functional methods. A correction for zero-point vibrational energies has also been included, yielding a best estimate for the energy difference between the classical and nonclassical forms of 3.7 + or - 1.3 kcal/mol.

A relativistic coupled-cluster interaction potential and rovibrational constants for the xenon dimer

NASA Astrophysics Data System (ADS)

Jerabek, Paul; Smits, Odile; Pahl, Elke; Schwerdtfeger, Peter

2018-01-01

An accurate potential energy curve has been derived for the xenon dimer using state-of-the-art relativistic coupled-cluster theory up to quadruple excitations accounting for both basis set superposition and incompleteness errors. The data obtained is fitted to a computationally efficient extended Lennard-Jones potential form and to a modified Tang-Toennies potential function treating the short- and long-range part separately. The vibrational spectrum of Xe2 obtained from a numerical solution of the rovibrational Schrödinger equation and subsequently derived spectroscopic constants are in excellent agreement with experimental values. We further present solid-state calculations for xenon using a static many-body expansion up to fourth-order in the xenon interaction potential including dynamic effects within the Einstein approximation. Again we find very good agreement with the experimental (face-centred cubic) lattice constant and cohesive energy.

Theoretical study of the alkaline-earth metal superoxides BeO2 through SrO2

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Sodupe, Mariona; Langhoff, Stephen R.

1992-01-01

Three competing bonding mechanisms have been identified for the alkaline-earth metal superoxides: these result in a change in the optimal structure and ground state as the alkaline-earth metal becomes heavier. For example, BeO2 has a linear 3Sigma(-)g ground-state structure, whereas both CaO2 and SrO2 have C(2v)1A1 structures. For MgO2, the theoretical calculations are less definitive, as the 3A2 C(2v) structure is computed to lie only about 3 kcal/mol above the 3Sigma(-)g linear structure. The bond dissociation energies for the alkaline-earth metal superoxides have been computed using extensive Gaussian basis sets and treating electron correlation at the modified coupled-pair functional or coupled-cluster singles and doubles level with a perturbational estimate of the triple excitations.

Low rank factorization of the Coulomb integrals for periodic coupled cluster theory.

PubMed

Hummel, Felix; Tsatsoulis, Theodoros; Grüneis, Andreas

2017-03-28

We study a tensor hypercontraction decomposition of the Coulomb integrals of periodic systems where the integrals are factorized into a contraction of six matrices of which only two are distinct. We find that the Coulomb integrals can be well approximated in this form already with small matrices compared to the number of real space grid points. The cost of computing the matrices scales as O(N 4 ) using a regularized form of the alternating least squares algorithm. The studied factorization of the Coulomb integrals can be exploited to reduce the scaling of the computational cost of expensive tensor contractions appearing in the amplitude equations of coupled cluster methods with respect to system size. We apply the developed methodologies to calculate the adsorption energy of a single water molecule on a hexagonal boron nitride monolayer in a plane wave basis set and periodic boundary conditions.

Meta genome-wide network from functional linkages of genes in human gut microbial ecosystems.

PubMed

Ji, Yan; Shi, Yixiang; Wang, Chuan; Dai, Jianliang; Li, Yixue

2013-03-01

The human gut microbial ecosystem (HGME) exerts an important influence on the human health. In recent researches, meta-genomics provided deep insights into the HGME in terms of gene contents, metabolic processes and genome constitutions of meta-genome. Here we present a novel methodology to investigate the HGME on the basis of a set of functionally coupled genes regardless of their genome origins when considering the co-evolution properties of genes. By analyzing these coupled genes, we showed some basic properties of HGME significantly associated with each other, and further constructed a protein interaction map of human gut meta-genome to discover some functional modules that may relate with essential metabolic processes. Compared with other studies, our method provides a new idea to extract basic function elements from meta-genome systems and investigate complex microbial environment by associating its biological traits with co-evolutionary fingerprints encoded in it.

Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions.

PubMed

Boström, Jonas; Aquilante, Francesco; Pedersen, Thomas Bondo; Lindh, Roland

2009-06-09

The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Møller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.

On the Angular Dependence of the Vicinal Fluorine-Fluorine Coupling Constant in 1,2-Difluoroethane:  Deviation from a Karplus-like Shape.

PubMed

Provasi, Patricio F; Sauer, Stephan P A

2006-07-01

The angular dependence of the vicinal fluorine-fluorine coupling constant, (3)JFF, for 1,2-difluoroethane has been investigated with several polarization propagator methods. (3)JFF and its four Ramsey contributions were calculated using the random phase approximation (RPA), its multiconfigurational generalization, and both second-order polarization propagator approximations (SOPPA and SOPPA(CCSD)), using locally dense basis sets. The geometries were optimized for each dihedral angle at the level of density functional theory using the B3LYP functional and fourth-order Møller-Plesset perturbation theory. The resulting coupling constant curves were fitted to a cosine series with 8 coefficients. Our results are compared with those obtained previously and values estimated from experiment. It is found that the inclusion of electron correlation in the calculation of (3)JFF reduces the absolute values. This is mainly due to changes in the FC contribution, which for dihedral angles around the trans conformation even changes its sign. This sign change is responsible for the breakdown of the Karplus-like curve.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Electric dipole (hyper)polarizabilities of selected X2Y2 and X3Y3 (X = Al, Ga, In and Y = P, As): III-V semiconductor clusters. An ab initio comparative study.

PubMed

Karamanis, Panaghiotis; Pouchan, Claude; Leszczynski, Jerzy

2008-12-25

A systematic ab initio comparative study of the (hyper)polarizabilities of selected III-V stoichiometric semiconductor clusters has been carried out. Our investigation focuses on the ground state structures of the dimers and on two dissimilar trimer configurations of aluminum, gallium, indium phosphide and arsenide. The basis set effect on both the polarizabilities and hyperpolarizabilities of the studied systems has been explicitly taken into account relying on the augmented correlation consistent aug-cc-pVnZ (n = D, T, Q, and 5) basis sets series. In addition, a rough estimation of the effects of the relativistic effects on the investigated properties is provided by extension of the study to include calculations performed with relativistic electron core potentials (or pseudopotentials). Electron correlation effects have been estimated utilizing methods of increasing predictive reliability, e.g., the Møller-Plesset many body perturbation theory and the couple cluster approach. Our results reveal that in the considered semiconductor species the Group III elements (Al, Ga, In) play a vital role on the values of their relative (hyper)polarizability. At all levels of theory employed the most hyperpolarizable clusters are the indium derivatives while the aluminum arsenide clusters also exhibit high, comparable hyperpolarizabilities. The less hyperpolarizable species are those composed of gallium and this is associated with the strong influence of the nuclear charge on the valence electrons of Ga due to the poor shielding that is provided by the semicore d electrons. In addition, the analysis of the electronic structure and the hyperpolarizability magnitudes reveals that clusters, in which their bonding is characterized by strong electron transfer from the electropositive to the electronegative atoms, are less hyperpolarizable than species in which the corresponding electron transfer is weaker. Lastly, from the methodological point of view our results point out that the hyperpolarizabilities of those species converge when an augmented triple-zeta quality basis set is used and, also, that the second order Møller-Plesset approximation (MP2) overestimates considerably their second hyperpolarizabilities with respect to the highest level of coupled cluster theory applied in this study (CCSD(T)).

Refined energetic ordering for sulphate-water (n = 3-6) clusters using high-level electronic structure calculations

NASA Astrophysics Data System (ADS)

Lambrecht, Daniel S.; McCaslin, Laura; Xantheas, Sotiris S.; Epifanovsky, Evgeny; Head-Gordon, Martin

2012-10-01

This work reports refinements of the energetic ordering of the known low-energy structures of sulphate-water clusters ? (n = 3-6) using high-level electronic structure methods. Coupled cluster singles and doubles with perturbative triples (CCSD(T)) is used in combination with an estimate of basis set effects up to the complete basis set limit using second-order Møller-Plesset theory. Harmonic zero-point energy (ZPE), included at the B3LYP/6-311 + + G(3df,3pd) level, was found to have a significant effect on the energetic ordering. In fact, we show that the energetic ordering is a result of a delicate balance between the electronic and vibrational energies. Limitations of the ZPE calculations, both due to electronic structure errors, and use of the harmonic approximation, probably constitute the largest remaining errors. Due to the often small energy differences between cluster isomers, and the significant role of ZPE, deuteration can alter the relative energies of low-lying structures, and, when it is applied in conjunction with calculated harmonic ZPEs, even alters the global minimum for n = 5. Experiments on deuterated clusters, as well as more sophisticated vibrational calculations, may therefore be quite interesting.

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

The leap-frog effect of ring currents in benzene.

PubMed

Ligabue, Andrea; Soncini, Alessandro; Lazzeretti, Paolo

2002-03-06

Symmetry arguments show that the ring-current model proposed by Pauling, Lonsdale, and London to explain the enhanced diamagnetism of benzene is flawed by an intrinsic drawback. The minimal basis set of six atomic 2p orbitals taken into account to develop such a model is inherently insufficient to predict a paramagnetic contribution to the perpendicular component of magnetic susceptibility in planar ring systems such as benzene. Analogous considerations can be made for the hypothetical H(6) cyclic molecule. A model allowing for extended basis sets is necessary to rationalize the magnetism of aromatics. According to high-quality coupled Hartree-Fock calculations, the trajectories of the current density vector field induced by a magnetic field perpendicular to the skeletal plane of benzene in the pi electrons are noticeably different from those typical of a Larmor diamagnetic circulation, in that (i) significant deformation of the orbits from circular to hexagonal symmetry occurs, which is responsible for a paramagnetic contribution of pi electrons to the out-of-plane component of susceptibility, and (ii) a sizable component of the pi current density vector parallel to the inducing field is predicted. This causes a waving motion of pi electrons; streamlines are characterized by a "leap-frog effect".

Coupled Segmentation of Nuclear and Membrane-bound Macromolecules through Voting and Multiphase Level Set

PubMed Central

Wen, Quan

2014-01-01

Membrane-bound macromolecules play an important role in tissue architecture and cell-cell communication, and is regulated by almost one-third of the genome. At the optical scale, one group of membrane proteins expresses themselves as linear structures along the cell surface boundaries, while others are sequestered; and this paper targets the former group. Segmentation of these membrane proteins on a cell-by-cell basis enables the quantitative assessment of localization for comparative analysis. However, such membrane proteins typically lack continuity, and their intensity distributions are often very heterogeneous; moreover, nuclei can form large clump, which further impedes the quantification of membrane signals on a cell-by-cell basis. To tackle these problems, we introduce a three-step process to (i) regularize the membrane signal through iterative tangential voting, (ii) constrain the location of surface proteins by nuclear features, where clumps of nuclei are segmented through a delaunay triangulation approach, and (iii) assign membrane-bound macromolecules to individual cells through an application of multi-phase geodesic level-set. We have validated our method using both synthetic data and a dataset of 200 images, and are able to demonstrate the efficacy of our approach with superior performance. PMID:25530633

Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.; Walch, Stephen P.

2002-01-01

As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

DOE PAGES

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.; ...

2017-07-21

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route.

PubMed

Penocchio, Emanuele; Piccardo, Matteo; Barone, Vincenzo

2015-10-13

The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.

A Computational Study on the Ground and Excited States of Nickel Silicide.

PubMed

Schoendorff, George; Morris, Alexis R; Hu, Emily D; Wilson, Angela K

2015-09-17

Nickel silicide has been studied with a range of computational methods to determine the nature of the Ni-Si bond. Additionally, the physical effects that need to be addressed within calculations to predict the equilibrium bond length and bond dissociation energy within experimental error have been determined. The ground state is predicted to be a (1)Σ(+) state with a bond order of 2.41 corresponding to a triple bond with weak π bonds. It is shown that calculation of the ground state equilibrium geometry requires a polarized basis set and treatment of dynamic correlation including up to triple excitations with CR-CCSD(T)L resulting in an equilibrium bond length of only 0.012 Å shorter than the experimental bond length. Previous calculations of the bond dissociation energy resulted in energies that were only 34.8% to 76.5% of the experimental bond dissociation energy. It is shown here that use of polarized basis sets, treatment of triple excitations, correlation of the valence and subvalence electrons, and a Λ coupled cluster approach is required to obtain a bond dissociation energy that deviates as little as 1% from experiment.

A full-dimensional ab initio potential energy surface and rovibrational energies of the Ar–HF complex

NASA Astrophysics Data System (ADS)

Huang, Jing; Zhou, Yanzi; Xie, Daiqian

2018-04-01

We report a new full-dimensional ab initio potential energy surface for the Ar-HF van der Waals complex at the level of coupled-cluster singles and doubles with noniterative inclusion of connected triples levels [CCSD(T)] using augmented correlation-consistent quintuple-zeta basis set (aV5Z) plus bond functions. Full counterpoise correction was employed to correct the basis-set superposition error. The hypersurface was fitted using artificial neural network method with a root mean square error of 0.1085 cm-1 for more than 8000 ab initio points. The complex was found to prefer a linear Ar-H-F equilibrium structure. The three-dimensional discrete variable representation method and the Lanczos propagation algorithm were then employed to calculate the rovibrational states without separating inter- and intra- molecular nuclear motions. The calculated vibrational energies of Ar-HF differ from the experiment values within about 1 cm-1 on the first four HF vibrational states, and the predicted pure rotational energies on (0000) and (1000) vibrational states are deviated from the observed value by about 1%, which shows the accuracy of our new PES.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossi, Tuomas P., E-mail: tuomas.rossi@alumni.aalto.fi; Sakko, Arto; Puska, Martti J.

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate thatmore » the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.« less

Equation-of-motion coupled-cluster method for doubly ionized states with spin-orbit coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhifan; Hu, Shu; Guo, Jingwei

2015-04-14

In this work, we report implementation of the equation-of-motion coupled-cluster method for doubly ionized states (EOM-DIP-CC) with spin-orbit coupling (SOC) using a closed-shell reference. Double ionization potentials (DIPs) are calculated in the space spanned by 2h and 3h1p determinants with the EOM-DIP-CC approach at the CC singles and doubles level (CCSD). Time-reversal symmetry together with spatial symmetry is exploited to reduce computational effort. To circumvent the problem of unstable dianion references when diffuse basis functions are included, nuclear charges are scaled. Effect of this stabilization potential on DIPs is estimated based on results from calculations using a small basis setmore » without diffuse basis functions. DIPs and excitation energies of some low-lying states for a series of open-shell atoms and molecules containing heavy elements with two unpaired electrons have been calculated with the EOM-DIP-CCSD approach. Results show that this approach is able to afford a reliable description on SOC splitting. Furthermore, the EOM-DIP-CCSD approach is shown to provide reasonable excitation energies for systems with a dianion reference when diffuse basis functions are not employed.« less

An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3

NASA Astrophysics Data System (ADS)

Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

2008-12-01

A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born-Oppenheimer correction was added. Our best purely ab initio PES, denoted "mixed," is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10300cm-1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J =0-2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J =0-6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J =0-2 is 0.023cm-1 and that for each band is always ⩽0.06cm-1. For J =3-5 the rms error is always ⩽0.15cm-1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Bo; Kowalski, Karol

The representation and storage of two-electron integral tensors are vital in large- scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this paper, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition ofmore » the two-electron integral tensor in our implementation. For the size of atomic basis set N_b ranging from ~ 100 up to ~ 2, 000, the observed numerical scaling of our implementation shows O(N_b^{2.5~3}) versus O(N_b^{3~4}) of single CD in most of other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic-orbital (AO) two-electron integral tensor from O(N_b^4) to O(N_b^2 log_{10}(N_b)) with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled- cluster formalism employing single and double excitations (CCSD) on several bench- mark systems including the C_{60} molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10^{-4} to 10^{-3} to give acceptable compromise between efficiency and accuracy.« less

Ab initio anharmonic vibrational frequency predictions for linear proton-bound complexes OC-H(+)-CO and N(2)-H(+)-N(2).

PubMed

Terrill, Kasia; Nesbitt, David J

2010-08-01

Ab initio anharmonic transition frequencies are calculated for strongly coupled (i) asymmetric and (ii) symmetric proton stretching modes in the X-H(+)-X linear ionic hydrogen bonded complexes for OCHCO(+) and N(2)HN(2)(+). The optimized potential surface is calculated in these two coordinates for each molecular ion at CCSD(T)/aug-cc-pVnZ (n = 2-4) levels and extrapolated to the complete-basis-set limit (CBS). Slices through both 2D surfaces reveal a relatively soft potential in the asymmetric proton stretching coordinate at near equilibrium geometries, which rapidly becomes a double minimum potential with increasing symmetric proton acceptor center of mass separation. Eigenvalues are obtained by solution of the 2D Schrödinger equation with potential/kinetic energy coupling explicity taken into account, converged in a distributed Gaussian basis set as a function of grid density. The asymmetric proton stretch fundamental frequency for N(2)HN(2)(+) is predicted at 848 cm(-1), with strong negative anharmonicity in the progression characteristic of a shallow "particle in a box" potential. The corresponding proton stretch fundamental for OCHCO(+) is anomalously low at 386 cm(-1), but with a strong alternation in the vibrational spacing due to the presence of a shallow D(infinityh) transition state barrier (Delta = 398 cm(-1)) between the two equivalent minimum geometries. Calculation of a 2D dipole moment surface and transition matrix elements reveals surprisingly strong combination and difference bands with appreciable intensity throughout the 300-1500 cm(-1) region. Corrected for zero point (DeltaZPE) and thermal vibrational excitation (DeltaE(vib)) at 300 K, the single and double dissociation energies in these complexes are in excellent agreement with thermochemical gas phase ion data.

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations.

PubMed

Peng, Bo; Kowalski, Karol

2017-09-12

The representation and storage of two-electron integral tensors are vital in large-scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this work, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of the atomic basis set, N b , ranging from ∼100 up to ∼2,000, the observed numerical scaling of our implementation shows [Formula: see text] versus [Formula: see text] cost of performing single CD on the two-electron integral tensor in most of the other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic orbital (AO) two-electron integral tensor from [Formula: see text] to [Formula: see text] with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled cluster formalism employing single and double excitations (CCSD) on several benchmark systems including the C 60 molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10 -4 to 10 -3 to give acceptable compromise between efficiency and accuracy.

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2017-06-01

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

Explicit hydration of ammonium ion by correlated methods employing molecular tailoring approach

NASA Astrophysics Data System (ADS)

Singh, Gurmeet; Verma, Rahul; Wagle, Swapnil; Gadre, Shridhar R.

2017-11-01

Explicit hydration studies of ions require accurate estimation of interaction energies. This work explores the explicit hydration of the ammonium ion (NH4+) employing Møller-Plesset second order (MP2) perturbation theory, an accurate yet relatively less expensive correlated method. Several initial geometries of NH4+(H2O)n (n = 4 to 13) clusters are subjected to MP2 level geometry optimisation with correlation consistent aug-cc-pVDZ (aVDZ) basis set. For large clusters (viz. n > 8), molecular tailoring approach (MTA) is used for single point energy evaluation at MP2/aVTZ level for the estimation of MP2 level binding energies (BEs) at complete basis set (CBS) limit. The minimal nature of the clusters upto n ≤ 8 is confirmed by performing vibrational frequency calculations at MP2/aVDZ level of theory, whereas for larger clusters (9 ≤ n ≤ 13) such calculations are effected via grafted MTA (GMTA) method. The zero point energy (ZPE) corrections are done for all the isomers lying within 1 kcal/mol of the lowest energy one. The resulting frequencies in N-H region (2900-3500 cm-1) and in O-H stretching region (3300-3900 cm-1) are in found to be in excellent agreement with the available experimental findings for 4 ≤ n ≤ 13. Furthermore, GMTA is also applied for calculating the BEs of these clusters at coupled cluster singles and doubles with perturbative triples (CCSD(T)) level of theory with aVDZ basis set. This work thus represents an art of the possible on contemporary multi-core computers for studying explicit molecular hydration at correlated level theories.

Ab initio studies of the Rg–NO{sup +}(X{sup 1}Σ{sup +}) van der Waals complexes (Rg = He, Ne, Ar, Kr, and Xe)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orek, Cahit; Bulut, Niyazi, E-mail: jklos@umd.edu, E-mail: francois.lique@univ-lehavre.fr, E-mail: bulut-niyazi@yahoo.com; Kłos, Jacek, E-mail: jklos@umd.edu, E-mail: francois.lique@univ-lehavre.fr, E-mail: bulut-niyazi@yahoo.com

2016-05-28

We used the explicitly correlated variant of the coupled clusters method with single, double, and noniterative triple excitations [CCSD(T)-F12] to compute two-dimensional potential energy surfaces of van der Waals complexes formed by rare gas atoms (Rg) and NO{sup +}(X{sup 1}Σ{sup +}) cations. We used the correlation-consistent, triple-zeta (cc-pVTZ-F12) atomic basis sets, and for Kr and Xe rare gases, we employed corresponding pseudopotential cc-pVTZ-PP-F12 atomic basis sets. These basis sets were additionally augmented with mid-bond functions. The complexes are all of skewed T-shape type with Rg atom being closer to the N-side. Using analytical representation of the potentials, we have estimatedmore » zero-point energy corrected dissociation energies from anharmonic calculations with BOUND program and also from the harmonic approximation. The binding energies increase with the polarization of the Rg atom in series from He to Xe and are 196 cm{sup −1}, 360 cm{sup −1}, 1024 cm{sup −1}, 1434 cm{sup −1}, and 2141 cm{sup −1}, respectively. Their corresponding dissociation energies are 132 cm{sup −1}, 300 cm{sup −1}, 927 cm{sup −1}, 1320 cm{sup −1}, and 1994 cm{sup −1} for the complexes with He to Xe, respectively. We find good agreement with previous theoretical and experimental results. The harmonic vibrational frequencies were calculated for the bending and stretching modes of the Rg–NO{sup +} complexes.« less

Shear Resistance between Concrete-Concrete Surfaces

NASA Astrophysics Data System (ADS)

Kovačovic, Marek

2013-12-01

The application of precast beams and cast-in-situ structural members cast at different times has been typical of bridges and buildings for many years. A load-bearing frame consists of a set of prestressed precast beams supported by columns and diaphragms joined with an additionally cast slab deck. This article is focused on the theoretical and experimental analyses of the shear resistance at an interface. The first part of the paper deals with the state-of-art knowledge of the composite behaviour of concrete-concrete structures and a comparison of the numerical methods introduced in the relevant standards. In the experimental part, a set of specimens with different interface treatments was tested until failure in order to predict the composite behaviour of coupled beams. The experimental part was compared to the numerical analysis performed by means of FEM basis nonlinear software.

Quantum Dynamics with Short-Time Trajectories and Minimal Adaptive Basis Sets.

PubMed

Saller, Maximilian A C; Habershon, Scott

2017-07-11

Methods for solving the time-dependent Schrödinger equation via basis set expansion of the wave function can generally be categorized as having either static (time-independent) or dynamic (time-dependent) basis functions. We have recently introduced an alternative simulation approach which represents a middle road between these two extremes, employing dynamic (classical-like) trajectories to create a static basis set of Gaussian wavepackets in regions of phase-space relevant to future propagation of the wave function [J. Chem. Theory Comput., 11, 8 (2015)]. Here, we propose and test a modification of our methodology which aims to reduce the size of basis sets generated in our original scheme. In particular, we employ short-time classical trajectories to continuously generate new basis functions for short-time quantum propagation of the wave function; to avoid the continued growth of the basis set describing the time-dependent wave function, we employ Matching Pursuit to periodically minimize the number of basis functions required to accurately describe the wave function. Overall, this approach generates a basis set which is adapted to evolution of the wave function while also being as small as possible. In applications to challenging benchmark problems, namely a 4-dimensional model of photoexcited pyrazine and three different double-well tunnelling problems, we find that our new scheme enables accurate wave function propagation with basis sets which are around an order-of-magnitude smaller than our original trajectory-guided basis set methodology, highlighting the benefits of adaptive strategies for wave function propagation.

Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr.

PubMed

Mitin, Alexander V

2013-09-05

The 2df polarization functions for the modified m6-31G basis sets of the third-row atoms Ga through Kr (Int J Quantum Chem, 2007, 107, 3028; Int J. Quantum Chem, 2009, 109, 1158) are proposed. The performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets were examined in molecular calculations carried out by the density functional theory (DFT) method with B3LYP hybrid functional, Møller-Plesset perturbation theory of the second order (MP2), quadratic configuration interaction method with single and double substitutions and were compared with those for the known 6-31G basis sets as well as with the other similar 641 and 6-311G basis sets with and without polarization functions. Obtained results have shown that the performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets are better in comparison with the performances of the known 6-31G, 6-31G(d,p) and 6-31G(2df,p) basis sets. These improvements are mainly reached due to better approximations of different electrons belonging to the different atomic shells in the modified basis sets. Applicability of the modified basis sets in thermochemical calculations is also discussed. © 2013 Wiley Periodicals, Inc.

Using monomer vibrational wavefunctions to compute numerically exact (12D) rovibrational levels of water dimer

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2018-02-01

We compute numerically exact rovibrational levels of water dimer, with 12 vibrational coordinates, on the accurate CCpol-8sf ab initio flexible monomer potential energy surface [C. Leforestier et al., J. Chem. Phys. 137, 014305 (2012)]. It does not have a sum-of-products or multimode form and therefore quadrature in some form must be used. To do the calculation, it is necessary to use an efficient basis set and to develop computational tools, for evaluating the matrix-vector products required to calculate the spectrum, that obviate the need to store the potential on a 12D quadrature grid. The basis functions we use are products of monomer vibrational wavefunctions and standard rigid-monomer basis functions (which involve products of three Wigner functions). Potential matrix-vector products are evaluated using the F matrix idea previously used to compute rovibrational levels of 5-atom and 6-atom molecules. When the coupling between inter- and intra-monomer coordinates is weak, this crude adiabatic type basis is efficient (only a few monomer vibrational wavefunctions are necessary), although the calculation of matrix elements is straightforward. It is much easier to use than an adiabatic basis. The product structure of the basis is compatible with the product structure of the kinetic energy operator and this facilitates computation of matrix-vector products. Compared with the results obtained using a [6 + 6]D adiabatic approach, we find good agreement for the inter-molecular levels and larger differences for the intra-molecular water bend levels.

Using monomer vibrational wavefunctions to compute numerically exact (12D) rovibrational levels of water dimer.

PubMed

Wang, Xiao-Gang; Carrington, Tucker

2018-02-21

We compute numerically exact rovibrational levels of water dimer, with 12 vibrational coordinates, on the accurate CCpol-8sf ab initio flexible monomer potential energy surface [C. Leforestier et al., J. Chem. Phys. 137, 014305 (2012)]. It does not have a sum-of-products or multimode form and therefore quadrature in some form must be used. To do the calculation, it is necessary to use an efficient basis set and to develop computational tools, for evaluating the matrix-vector products required to calculate the spectrum, that obviate the need to store the potential on a 12D quadrature grid. The basis functions we use are products of monomer vibrational wavefunctions and standard rigid-monomer basis functions (which involve products of three Wigner functions). Potential matrix-vector products are evaluated using the F matrix idea previously used to compute rovibrational levels of 5-atom and 6-atom molecules. When the coupling between inter- and intra-monomer coordinates is weak, this crude adiabatic type basis is efficient (only a few monomer vibrational wavefunctions are necessary), although the calculation of matrix elements is straightforward. It is much easier to use than an adiabatic basis. The product structure of the basis is compatible with the product structure of the kinetic energy operator and this facilitates computation of matrix-vector products. Compared with the results obtained using a [6 + 6]D adiabatic approach, we find good agreement for the inter-molecular levels and larger differences for the intra-molecular water bend levels.

Coupled Dictionary Learning for the Detail-Enhanced Synthesis of 3-D Facial Expressions.

PubMed

Liang, Haoran; Liang, Ronghua; Song, Mingli; He, Xiaofei

2016-04-01

The desire to reconstruct 3-D face models with expressions from 2-D face images fosters increasing interest in addressing the problem of face modeling. This task is important and challenging in the field of computer animation. Facial contours and wrinkles are essential to generate a face with a certain expression; however, these details are generally ignored or are not seriously considered in previous studies on face model reconstruction. Thus, we employ coupled radius basis function networks to derive an intermediate 3-D face model from a single 2-D face image. To optimize the 3-D face model further through landmarks, a coupled dictionary that is related to 3-D face models and their corresponding 3-D landmarks is learned from the given training set through local coordinate coding. Another coupled dictionary is then constructed to bridge the 2-D and 3-D landmarks for the transfer of vertices on the face model. As a result, the final 3-D face can be generated with the appropriate expression. In the testing phase, the 2-D input faces are converted into 3-D models that display different expressions. Experimental results indicate that the proposed approach to facial expression synthesis can obtain model details more effectively than previous methods can.

Electron-transfer boat-vibration mechanism for superconductivity in organic molecules based on BEDT-TTF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demiralp, E.; Dasgupta, S.; Goddard, W.A. III

1995-08-09

The highest T{sub c} organic superconductors all involve the organic molecule bis(ethylenedithio)tetrathiafulvalene (denoted as BEDT-TTF or ET) coupled with an appropriate acceptor. This leads to ET, ET{sup +}, or (ET){sub 2}{sup +} species in the crystal. Using ab initio Hartree-Fock calculations (6-31G** basis set), we show that ET deforms to a boat structure with an energy 28 meV (0.65 kcal/mol) lower than that of planar ET (D{sub 2} symmetry). On the other hand, ET{sup +} is planar. Thus, conduction in this system leads to a coupling between charge transfer and the boat deformation vibrational modes at 20 cm{sup -1} (ET)more » and 28 cm{sup -1} (ET{sup +}). We suggest that this electron-phonon coupling is responsible for the superconductivity and predict the isotope shifts ({delta}T{sub c}) for experimental tests of the electron-transfer boat-vibration (ET-BV) mechanism. The low frequency of this boat mode and its coupling to various lattice modes could explain the sensitivity of T{sub c} to defects, impurities, and pressure. We suggest that new higher temperature organic donors can be sought by finding modifications that change the frequency and stability of this boat distortion mode. 25 refs., 5 figs., 4 tabs.« less

Towards topological quantum computer

NASA Astrophysics Data System (ADS)

Melnikov, D.; Mironov, A.; Mironov, S.; Morozov, A.; Morozov, An.

2018-01-01

Quantum R-matrices, the entangling deformations of non-entangling (classical) permutations, provide a distinguished basis in the space of unitary evolutions and, consequently, a natural choice for a minimal set of basic operations (universal gates) for quantum computation. Yet they play a special role in group theory, integrable systems and modern theory of non-perturbative calculations in quantum field and string theory. Despite recent developments in those fields the idea of topological quantum computing and use of R-matrices, in particular, practically reduce to reinterpretation of standard sets of quantum gates, and subsequently algorithms, in terms of available topological ones. In this paper we summarize a modern view on quantum R-matrix calculus and propose to look at the R-matrices acting in the space of irreducible representations, which are unitary for the real-valued couplings in Chern-Simons theory, as the fundamental set of universal gates for topological quantum computer. Such an approach calls for a more thorough investigation of the relation between topological invariants of knots and quantum algorithms.

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

2016-07-28

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures.

PubMed

Papior, Nick R; Calogero, Gaetano; Brandbyge, Mads

2018-06-27

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C 60 ). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures

NASA Astrophysics Data System (ADS)

Papior, Nick R.; Calogero, Gaetano; Brandbyge, Mads

2018-06-01

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C60). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Demonstration of Weight-Four Parity Measurements in the Surface Code Architecture.

PubMed

Takita, Maika; Córcoles, A D; Magesan, Easwar; Abdo, Baleegh; Brink, Markus; Cross, Andrew; Chow, Jerry M; Gambetta, Jay M

2016-11-18

We present parity measurements on a five-qubit lattice with connectivity amenable to the surface code quantum error correction architecture. Using all-microwave controls of superconducting qubits coupled via resonators, we encode the parities of four data qubit states in either the X or the Z basis. Given the connectivity of the lattice, we perform a full characterization of the static Z interactions within the set of five qubits, as well as dynamical Z interactions brought along by single- and two-qubit microwave drives. The parity measurements are significantly improved by modifying the microwave two-qubit gates to dynamically remove nonideal Z errors.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

IVF with planned single-embryo transfer versus IUI with ovarian stimulation in couples with unexplained subfertility: an economic analysis.

PubMed

van Rumste, Minouche M E; Custers, Inge M; van Wely, Madelon; Koks, Carolien A; van Weering, Hans G I; Beckers, Nicole G M; Scheffer, Gabrielle J; Broekmans, Frank J M; Hompes, Peter G A; Mochtar, Monique H; van der Veen, Fulco; Mol, Ben W J

2014-03-01

Couples with unexplained subfertility are often treated with intrauterine insemination (IUI) with ovarian stimulation, which carries the risk of multiple pregnancies. An explorative randomized controlled trial was performed comparing one cycle of IVF with elective single-embryo transfer (eSET) versus three cycles of IUI-ovarian stimulation in couples with unexplained subfertility and a poor prognosis for natural conception, to assess the economic burden of the treatment modalities. The main outcome measures were ongoing pregnancy rates and costs. This study randomly assigned 58 couples to IVF-eSET and 58 couples to IUI-ovarian stimulation. The ongoing pregnancy rates were 24% in with IVF-eSET versus 21% with IUI-ovarian stimulation, with two and three multiple pregnancies, respectively. The mean cost per included couple was significantly different: €2781 with IVF-eSET and €1876 with IUI-ovarian stimulation (P<0.01). The additional costs per ongoing pregnancy were €2456 for IVF-eSET. In couples with unexplained subfertility, one cycle of IVF-eSET cost an additional €900 per couple compared with three cycles of IUI-ovarian stimulation, for no increase in ongoing pregnancy rates or decrease in multiple pregnancies. When IVF-eSET results in higher ongoing pregnancy rates, IVF would be the preferred treatment. Couples that have been trying to conceive unsuccessfully are often treated with intrauterine insemination (IUI) and medication to improve egg production (ovarian stimulation). This treatment carries the risk of multiple pregnancies like twins. We performed an explorative study among those couples that had a poor prognosis for natural conception. One cycle of IVF with transfer of one selected embryo (elective single-embryo transfer, eSET) was compared with three cycles of IUI-ovarian stimulation. The aim of this study was to assess the economic burden of both treatments. The Main outcome measures were number of good pregnancies above 12weeks and costs. We randomly assigned 58 couples to IVF-eSET and 58 couples to IUI-ovarian stimulation. The ongoing pregnancy rates were comparable: 24% with IVF-eSET versus 21% with IUI-ovarian stimulation. There were two multiple pregnancies with IVF-eSET and three multiple pregnancies with IUI-ovarian stimulation. The mean cost per included couple was significantly different, €2781 with IVF-eSET and €1876 with IUI-ovarian stimulation. The additional costs per ongoing pregnancy were €2456 for IVF-eSET. In couples with unexplained subfertility, one cycle of IVF-eSET costed an additional €900 per couple compared to three cycles of IUI-ovarian stimulation, for no increase in ongoing pregnancy rates or decrease in multiple pregnancies. We conclude that IUI-ovarian stimulation is the preferred treatment to start with. When IVF-eSET results in a higher ongoing pregnancy rate (>38%), IVF would be the preferred treatment. Copyright © 2013 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

PubMed Central

Mochida, Keiichi; Uehara-Yamaguchi, Yukiko; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo

2011-01-01

Accumulated transcriptome data can be used to investigate regulatory networks of genes involved in various biological systems. Co-expression analysis data sets generated from comprehensively collected transcriptome data sets now represent efficient resources that are capable of facilitating the discovery of genes with closely correlated expression patterns. In order to construct a co-expression network for barley, we analyzed 45 publicly available experimental series, which are composed of 1,347 sets of GeneChip data for barley. On the basis of a gene-to-gene weighted correlation coefficient, we constructed a global barley co-expression network and classified it into clusters of subnetwork modules. The resulting clusters are candidates for functional regulatory modules in the barley transcriptome. To annotate each of the modules, we performed comparative annotation using genes in Arabidopsis and Brachypodium distachyon. On the basis of a comparative analysis between barley and two model species, we investigated functional properties from the representative distributions of the gene ontology (GO) terms. Modules putatively involved in drought stress response and cellulose biogenesis have been identified. These modules are discussed to demonstrate the effectiveness of the co-expression analysis. Furthermore, we applied the data set of co-expressed genes coupled with comparative analysis in attempts to discover potentially Triticeae-specific network modules. These results demonstrate that analysis of the co-expression network of the barley transcriptome together with comparative analysis should promote the process of gene discovery in barley. Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/. PMID:21441235

Derivation of a formula for the resonance integral for a nonorthogonal basis set

PubMed Central

Yim, Yung-Chang; Eyring, Henry

1981-01-01

In a self-consistent field calculation, a formula for the off-diagonal matrix elements of the core Hamiltonian is derived for a nonorthogonal basis set by a polyatomic approach. A set of parameters is then introduced for the repulsion integral formula of Mataga-Nishimoto to fit the experimental data. The matrix elements computed for the nonorthogonal basis set in the π-electron approximation are transformed to those for an orthogonal basis set by the Löwdin symmetrical orthogonalization. PMID:16593009

A physiology-based model describing heterogeneity in glucose metabolism: the core of the Eindhoven Diabetes Education Simulator (E-DES).

PubMed

Maas, Anne H; Rozendaal, Yvonne J W; van Pul, Carola; Hilbers, Peter A J; Cottaar, Ward J; Haak, Harm R; van Riel, Natal A W

2015-03-01

Current diabetes education methods are costly, time-consuming, and do not actively engage the patient. Here, we describe the development and verification of the physiological model for healthy subjects that forms the basis of the Eindhoven Diabetes Education Simulator (E-DES). E-DES shall provide diabetes patients with an individualized virtual practice environment incorporating the main factors that influence glycemic control: food, exercise, and medication. The physiological model consists of 4 compartments for which the inflow and outflow of glucose and insulin are calculated using 6 nonlinear coupled differential equations and 14 parameters. These parameters are estimated on 12 sets of oral glucose tolerance test (OGTT) data (226 healthy subjects) obtained from literature. The resulting parameter set is verified on 8 separate literature OGTT data sets (229 subjects). The model is considered verified if 95% of the glucose data points lie within an acceptance range of ±20% of the corresponding model value. All glucose data points of the verification data sets lie within the predefined acceptance range. Physiological processes represented in the model include insulin resistance and β-cell function. Adjusting the corresponding parameters allows to describe heterogeneity in the data and shows the capabilities of this model for individualization. We have verified the physiological model of the E-DES for healthy subjects. Heterogeneity of the data has successfully been modeled by adjusting the 4 parameters describing insulin resistance and β-cell function. Our model will form the basis of a simulator providing individualized education on glucose control. © 2014 Diabetes Technology Society.

Theoretical investigations on the mechanism of benzoin condensation catalyzed by pyrido[1,2-a]-2-ethyl[1,2,4]triazol-3-ylidene.

PubMed

He, Yunqing; Xue, Ying

2011-03-03

A new annulated N-heterocyclic carbene (NHC), pyrido[1,2-a]-2-ethyl[1,2,4]triazol-3-ylidene, has been synthesized and its good catalytic activity for benzoin condensation has been experimentally determined by You and co-workers recently [ Ma , Y. J. , Wei , S. P. , Lan , J. B. , Wang , J. Z. , Xie , R. G. , and You , J. S. J. Org. Chem. 2008 , 73 , 8256 ]. In this work, the mechanism of the title reaction has been intensively studied computationally by employing the density functional theory (B3LYP) method in conjunction with 6-31+G(d) and 6-311+G(2d,p) basis sets. Our results indicate that path A (in which a sequence of intermolecular proton transfers between two carbene/benzaldehyde coupling intermediates affords enamine) and path B (in which a t-BuOH assisted hydrogen transfer generates enamine) proposed on the basis of the Breslow mechanism are competitive for their similar barriers. In path A, the first intermolecular proton transfer between two N-heterocyclic carbene/benzaldehyde coupled intermediates to form tertiary alcohol and enolate anion is theoretically the rate-determining step with corresponding barrier (30.93 kcal/mol), while the t-BuOH assisted hydrogen transfer generating Breslow enamine is the rate-determining step with corresponding barrier (28.84 kcal/mol) in path B. The coupling of carbene and benzaldehyde, and the coupling of enamine and another benzaldehyde to form a C-C bond are partially rate-determining for their relatively significant barriers (24.06 and 26.95 kcal/mol, respectively), being the same in both paths A and B. Our results are in nice agreement with the experimental result in a kinetic investigation of thiazolium ion-catalyzed benzoin condensation performed by White and Leeper in 2001.

Sensitivity of mechanical and metabolic functions to changes in coronary perfusion: A metabolic basis of perfusion-contraction coupling.

PubMed

Askenasy, N

2000-05-01

Experimental evidence indicates a metabolic basis of contraction-perfusion coupling during an increase in cardiac work load. This study aims to characterize adjustment of myocardial energy metabolism in response to acute low flow ischemia (LFI), and to determine its involvement in perfusion-contraction coupling. Intracellular parameters were measured in isolated rat hearts by NMR spectroscopy and biochemical methods during 30 min of graded LFI and reperfusion as compared to continuous perfusion (control). Oxygen pressure was set to reach maximal oxygen extraction at 70% coronary flow rate (CFR), therefore oxygen limitation was proportional to coronary underperfusion. At 69, 38 and 10% CFR left ventricular pressures decreased to 71, 43 and 25% of pre-ischemic values respectively (P<0.005 v 97% in control) without an increase in diastolic tone, and recovered to 92+/-3% after 30 min of reperfusion. Despite hydrolysis of high energy phosphates and cellular acidification, ADP concentrations were stable in underperfused hearts. At 69, 38 and 10% CFR, cytosolic phosphorylation potentials (PP) decreased from 74+/-10 m M(-1)during pre-ischemia to 40+/-6, 25+/-4 and 14+/-4 m M(-1)respectively (P<0.05 v 63+/-9 m M(-1)in control), and lactate efflux increased to 256+/-18, 386+/-22 and 490+/-43 micromol /gdw respectively (P<0.005 v 186+/-22 micromol/gdw in control). Glycogen contents decreased (P<0.005 v control) and accounted for 27-30% of lactate efflux. These results indicate: (a) proportionate depression of contraction force and glycogen contents, and increased glucose uptake and anaerobic energy production in the underperfused myocardium. Coordinated modulation of these parameters attributes cytosolic PP a regulatory function; (b) resetting of cytosolic PP to lower levels mediates perfusion-contraction coupling during graded LFI. The data are consistent with the concept that glycolytic energy production improves myocardial tolerance to ischemia. Copyright 2000 Academic Press.

An efficient and near linear scaling pair natural orbital based local coupled cluster method.

PubMed

Riplinger, Christoph; Neese, Frank

2013-01-21

In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009)]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 10(5)-10(6) relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD ("domain based LPNO-CCSD"). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy estimate based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calculations reported here featured >8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.

Communication: A novel implementation to compute MP2 correlation energies without basis set superposition errors and complete basis set extrapolation.

PubMed

Dixit, Anant; Claudot, Julien; Lebègue, Sébastien; Rocca, Dario

2017-06-07

By using a formulation based on the dynamical polarizability, we propose a novel implementation of second-order Møller-Plesset perturbation (MP2) theory within a plane wave (PW) basis set. Because of the intrinsic properties of PWs, this method is not affected by basis set superposition errors. Additionally, results are converged without relying on complete basis set extrapolation techniques; this is achieved by using the eigenvectors of the static polarizability as an auxiliary basis set to compactly and accurately represent the response functions involved in the MP2 equations. Summations over the large number of virtual states are avoided by using a formalism inspired by density functional perturbation theory, and the Lanczos algorithm is used to include dynamical effects. To demonstrate this method, applications to three weakly interacting dimers are presented.

An implementation of the QMR method based on coupled two-term recurrences

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Nachtigal, Noeel M.

1992-01-01

The authors have proposed a new Krylov subspace iteration, the quasi-minimal residual algorithm (QMR), for solving non-Hermitian linear systems. In the original implementation of the QMR method, the Lanczos process with look-ahead is used to generate basis vectors for the underlying Krylov subspaces. In the Lanczos algorithm, these basis vectors are computed by means of three-term recurrences. It has been observed that, in finite precision arithmetic, vector iterations based on three-term recursions are usually less robust than mathematically equivalent coupled two-term vector recurrences. This paper presents a look-ahead algorithm that constructs the Lanczos basis vectors by means of coupled two-term recursions. Implementation details are given, and the look-ahead strategy is described. A new implementation of the QMR method, based on this coupled two-term algorithm, is described. A simplified version of the QMR algorithm without look-ahead is also presented, and the special case of QMR for complex symmetric linear systems is considered. Results of numerical experiments comparing the original and the new implementations of the QMR method are reported.

Comparative pulsation calculations with OP and OPAL opacities

NASA Technical Reports Server (NTRS)

Kanbur, Shashi M.; Simon, Norman R.

1994-01-01

Comparative linear nonadiabatic pulsation calculations are presented using the OPAL and Opacity Project opacities. The two sets of opacities include effects due to intermediate coupling and fine structure as well as new abundances. We used two mass luminosity (M-L) relations, one standard (BIT), and one employing substantial convective core overshoot (COV). The two sets of opacities cannot be differentiated on the basis of the stellar pulsation calculations presented here. The BIT relation can model the beat and bump Cepheids with masses between 4 and 7 solar mass, while if the overshoot relation is used, masses between 2 and 6 solar mass are required. In the RR Lyrae regime, we find the inferred masses of globular cluster RRd stars to be little influenced by the choice of OPAL or OP. Finally, the limited modeling we have done is not able to constrain the Cepheid M-L relation based upon period ratios observed in the beat and bump stars.

Correlation consistent valence basis sets for use with the Stuttgart-Dresden-Bonn relativistic effective core potentials: The atoms Ga-Kr and In-Xe

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Sundermann, Andreas

2001-02-01

We propose large-core correlation-consistent (cc) pseudopotential basis sets for the heavy p-block elements Ga-Kr and In-Xe. The basis sets are of cc-pVTZ and cc-pVQZ quality, and have been optimized for use with the large-core (valence-electrons only) Stuttgart-Dresden-Bonn (SDB) relativistic pseudopotentials. Validation calculations on a variety of third-row and fourth-row diatomics suggest them to be comparable in quality to the all-electron cc-pVTZ and cc-pVQZ basis sets for lighter elements. Especially the SDB-cc-pVQZ basis set in conjunction with a core polarization potential (CPP) yields excellent agreement with experiment for compounds of the later heavy p-block elements. For accurate calculations on Ga (and, to a lesser extent, Ge) compounds, explicit treatment of 13 valence electrons appears to be desirable, while it seems inevitable for In compounds. For Ga and Ge, we propose correlation consistent basis sets extended for (3d) correlation. For accurate calculations on organometallic complexes of interest to homogenous catalysis, we recommend a combination of the standard cc-pVTZ basis set for first- and second-row elements, the presently derived SDB-cc-pVTZ basis set for heavier p-block elements, and for transition metals, the small-core [6s5p3d] Stuttgart-Dresden basis set-relativistic effective core potential combination supplemented by (2f1g) functions with exponents given in the Appendix to the present paper.

An Efficient Method Coupling Kernel Principal Component Analysis with Adjoint-Based Optimal Control and Its Goal-Oriented Extensions

NASA Astrophysics Data System (ADS)

Thimmisetty, C.; Talbot, C.; Tong, C. H.; Chen, X.

2016-12-01

The representativeness of available data poses a significant fundamental challenge to the quantification of uncertainty in geophysical systems. Furthermore, the successful application of machine learning methods to geophysical problems involving data assimilation is inherently constrained by the extent to which obtainable data represent the problem considered. We show how the adjoint method, coupled with optimization based on methods of machine learning, can facilitate the minimization of an objective function defined on a space of significantly reduced dimension. By considering uncertain parameters as constituting a stochastic process, the Karhunen-Loeve expansion and its nonlinear extensions furnish an optimal basis with respect to which optimization using L-BFGS can be carried out. In particular, we demonstrate that kernel PCA can be coupled with adjoint-based optimal control methods to successfully determine the distribution of material parameter values for problems in the context of channelized deformable media governed by the equations of linear elasticity. Since certain subsets of the original data are characterized by different features, the convergence rate of the method in part depends on, and may be limited by, the observations used to furnish the kernel principal component basis. By determining appropriate weights for realizations of the stochastic random field, then, one may accelerate the convergence of the method. To this end, we present a formulation of Weighted PCA combined with a gradient-based means using automatic differentiation to iteratively re-weight observations concurrent with the determination of an optimal reduced set control variables in the feature space. We demonstrate how improvements in the accuracy and computational efficiency of the weighted linear method can be achieved over existing unweighted kernel methods, and discuss nonlinear extensions of the algorithm.

Decoherence in adiabatic quantum computation

NASA Astrophysics Data System (ADS)

Albash, Tameem; Lidar, Daniel A.

2015-06-01

Recent experiments with increasingly larger numbers of qubits have sparked renewed interest in adiabatic quantum computation, and in particular quantum annealing. A central question that is repeatedly asked is whether quantum features of the evolution can survive over the long time scales used for quantum annealing relative to standard measures of the decoherence time. We reconsider the role of decoherence in adiabatic quantum computation and quantum annealing using the adiabatic quantum master-equation formalism. We restrict ourselves to the weak-coupling and singular-coupling limits, which correspond to decoherence in the energy eigenbasis and in the computational basis, respectively. We demonstrate that decoherence in the instantaneous energy eigenbasis does not necessarily detrimentally affect adiabatic quantum computation, and in particular that a short single-qubit T2 time need not imply adverse consequences for the success of the quantum adiabatic algorithm. We further demonstrate that boundary cancellation methods, designed to improve the fidelity of adiabatic quantum computing in the closed-system setting, remain beneficial in the open-system setting. To address the high computational cost of master-equation simulations, we also demonstrate that a quantum Monte Carlo algorithm that explicitly accounts for a thermal bosonic bath can be used to interpolate between classical and quantum annealing. Our study highlights and clarifies the significantly different role played by decoherence in the adiabatic and circuit models of quantum computing.

Hybrid Grid and Basis Set Approach to Quantum Chemistry DMRG

NASA Astrophysics Data System (ADS)

Stoudenmire, Edwin Miles; White, Steven

We present a new approach for using DMRG for quantum chemistry that combines the advantages of a basis set with that of a grid approximation. Because DMRG scales linearly for quasi-one-dimensional systems, it is feasible to approximate the continuum with a fine grid in one direction while using a standard basis set approach for the transverse directions. Compared to standard basis set methods, we reach larger systems and achieve better scaling when approaching the basis set limit. The flexibility and reduced costs of our approach even make it feasible to incoporate advanced DMRG techniques such as simulating real-time dynamics. Supported by the Simons Collaboration on the Many-Electron Problem.

Universal modal radiation laws for all thermal emitters

PubMed Central

Zhu, Linxiao; Fan, Shanhui

2017-01-01

We derive four laws relating the absorptivity and emissivity of thermal emitters. Unlike the original Kirchhoff radiation law derivations, these derivations include diffraction, and so are valid also for small objects, and can also cover nonreciprocal objects. The proofs exploit two recent approaches. First, we express all fields in terms of the mode-converter basis sets of beams; these sets, which can be uniquely established for any linear optical object, give orthogonal input beams that are coupled one-by-one to orthogonal output beams. Second, we consider thought experiments using universal linear optical machines, which allow us to couple appropriate beams and black bodies. Two of these laws can be regarded as rigorous extensions of previously known laws: One gives a modal version of a radiation law for reciprocal objects—the absorptivity of any input beam equals the emissivity into the “backward” (i.e., phase-conjugated) version of that beam; another gives the overall equality of the sums of the emissivities and the absorptivities for any object, including nonreciprocal ones. The other two laws, valid for reciprocal and nonreciprocal objects, are quite different from previous relations. One shows universal equivalence of the absorptivity of each mode-converter input beam and the emissivity into its corresponding scattered output beam. The other gives unexpected equivalences of absorptivity and emissivity for broad classes of beams. Additionally, we prove these orthogonal mode-converter sets of input and output beams are the ones that maximize absorptivities and emissivities, respectively, giving these beams surprising additional physical meaning. PMID:28396436

Self-compression of spatially limited laser pulses in a system of coupled light-guides

NASA Astrophysics Data System (ADS)

Balakin, A. A.; Litvak, A. G.; Mironov, V. A.; Skobelev, S. A.

2018-04-01

The self-action features of wave packets propagating in a 2D system of equidistantly arranged fibers are studied analytically and numerically on the basis of the discrete nonlinear Schrödinger equation. Self-consistent equations for the characteristic scales of a Gaussian wave packet are derived on the basis of the variational approach, which are proved numerically for powers P < 10 P_cr , slightly exceeding the critical one for self-focusing. At higher powers, the wave beams become filamented, and their amplitude is limited due to the nonlinear breaking of the interaction between neighboring light-guides. This makes it impossible to collect a powerful wave beam in a single light-guide. Variational analysis shows the possibility of the adiabatic self-compression of soliton-like laser pulses in the process of 3D self-focusing on the central light-guide. However, further increase of the field amplitude during self-compression leads to the development of longitudinal modulation instability and the formation of a set of light bullets in the central fiber. In the regime of hollow wave beams, filamentation instability becomes predominant. As a result, it becomes possible to form a set of light bullets in optical fibers located on the ring.

Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conover, David R.; Crawford, Alasdair J.; Fuller, Jason

This Protocol provides a set of “best practices” for characterizing energy storage systems (ESSs) and measuring and reporting their performance. It serves as a basis for assessing how an ESS will perform with respect to key performance attributes relevant to different applications. It is intended to provide a valid and accurate basis for the comparison of different ESSs. By achieving the stated purpose, the Protocol will enable more informed decision-making in the selection of ESSs for various stationary applications. The Protocol identifies general information and technical specifications relevant in describing an ESS and also defines a set of test, measurement,more » and evaluation criteria with which to express the performance of ESSs that are intended for energy-intensive and/or power-intensive stationary applications. An ESS includes a storage device, battery management system, and any power conversion systems installed with the storage device. The Protocol is agnostic with respect to the storage technology and the size and rating of the ESS. The Protocol does not apply to single-use storage devices and storage devices that are not coupled with power conversion systems, nor does it address safety, security, or operations and maintenance of ESSs, or provide any pass/fail criteria.« less

Conversations between anthropology and psychiatry: drawing out the best from interdisciplinarity in global mental health.

PubMed

Rosso Buckton, Amanda

2015-12-01

Conversations between anthropologists and psychiatrists have led to new theoretical trajectories, research agendas and clinical practices as social scientists and medical practitioners forged new understandings about the interaction of culture, personhood and illness. However, the demands of global mental health, coupled with health service provision requirements, mean that mental health interventions set up with the best intentions can fail to take into account the knowledge and expertise that social sciences can contribute to a programme's success. In this paper, I reflect on conversations between an anthropologist and mental health professionals in direct reference to data analysis of an AusAID mental health capacity-building programme undertaken in the Pacific region. Social and cultural perspectives embedded within programmes can provide richer, more contextualised interventions. In drawing on the combined expertise of anthropology and psychiatry, new taken-for-granted reference points embedding cultural approaches form the basis for delivery of global mental health programmes. These perspectives include: Locating mental health programmes within development critiques. Situating the subjects of development within contextualised settings, acknowledging and respecting local knowledge, understandings and practices. A focus on interdisciplinarity as the basis for future practice in global mental health projects. © The Royal Australian and New Zealand College of Psychiatrists 2015.

Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde.

PubMed

Morgan, W James; Matthews, Devin A; Ringholm, Magnus; Agarwal, Jay; Gong, Justin Z; Ruud, Kenneth; Allen, Wesley D; Stanton, John F; Schaefer, Henry F

2018-03-13

Geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the CCSDTQ/CBS and CCSDT(Q)/CBS equilibrium structure of the S 0 ground state of H 2 CO where excellent agreement is observed with previous work and experimentally derived results. A fourth-order expansion about this CCSDT(Q)/CBS reference geometry using the same level of theory produces an exceptional level of agreement to spectroscopically observed vibrational band origins with a MAE of 0.57 cm -1 . Second-order vibrational perturbation theory (VPT2) and variational discrete variable representation (DVR) results are contrasted and discussed. Vibration-rotation, anharmonicity, and centrifugal distortion constants from the VPT2 analysis are reported and compared to previous work. Additionally, an initial application of a sum-over-states fourth-order vibrational perturbation theory (VPT4) formalism is employed herein, utilizing quintic and sextic derivatives obtained with a recursive algorithmic approach for response theory.

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Density functional theory calculations of the lowest energy quintet and triplet states of model hemes: role of functional, basis set, and zero-point energy corrections.

PubMed

Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

2008-04-24

We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results insignificantly for iron(II) porphyrin coordinated with imidazole. Poor performance of a "locally dense" basis set with a large number of basis functions on the Fe center was observed in calculation of quintet-triplet gaps. Our results lead to a series of suggestions for density functional theory calculations of quintet-triplet energy gaps in ferrohemes with a single axial imidazole; these suggestions are potentially applicable for other transition-metal complexes.

Equation of motion coupled cluster methods for electron attachment and ionization potential in polyacenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaskaran-Nair, Kiran; Kowalski, Karol; Jarrell, Mark

2015-11-05

Polyacenes have attracted considerable attention due to their use in organic based optoelectronic materials. Polyacenes are polycyclic aromatic hydrocarbons composed of fused benzene rings. Key to understanding and design of new functional materials is an understanding of their excited state properties starting with their electron affinity (EA) and ionization potential (IP). We have developed a highly accurate and com- putationally e*fficient EA/IP equation of motion coupled cluster singles and doubles (EA/IP-EOMCCSD) method that is capable of treating large systems and large basis set. In this study we employ the EA/IP-EOMCCSD method to calculate the electron affinity and ionization potential ofmore » naphthalene, anthracene, tetracene, pentacene, hex- acene and heptacene. We have compared our results with other previous theoretical studies and experimental data. Our EA/IP results are in very good agreement with experiment and when compared with the other theoretical investigations our results represent the most accurate calculations as compared to experiment.« less

Aeroelastic effects in multi-rotor vehicles with application to a hybrid heavy lift system. Part 1: Formulation of equations of motion

NASA Technical Reports Server (NTRS)

Venkatesan, C.; Friedman, P.

1984-01-01

This report presents a set of governing coupled differential equations for a model of a hybrid aircraft. The model consists of multiple rotor systems connected by an elastic interconnecting structure, with options to add any combination of or all of the following components; i.e., thrusters, a buoyant hull, and an underslung weight. The dynamic equations are written for the individual blade with hub motions, for the rigid body motions of the whole model, and also for the flexible modes of the interconnecting structure. One of the purposes of this study is to serve as the basis of a numerical study aimed at determining the aeroelastic stability and structural response characteristics of a Hybrid Heavy Lift Airship (HHLA). It is also expected that the formulation may be applicable to analyzing stability and responses of dual rotor helicopters such as a Heavy Lift Helicopter (HLH). Futhermore, the model is capable of representing coupled rotor/body aeromechanical problems of single rotor helicopters.

The relative entropy is fundamental to adaptive resolution simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kreis, Karsten; Graduate School Materials Science in Mainz, Staudingerweg 9, 55128 Mainz; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy withmore » respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.« less

A highly accurate ab initio potential energy surface for methane.

PubMed

Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

2016-09-14

A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

The relative entropy is fundamental to adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Potestio, Raffaello

2016-07-01

Adaptive resolution techniques are powerful methods for the efficient simulation of soft matter systems in which they simultaneously employ atomistic and coarse-grained (CG) force fields. In such simulations, two regions with different resolutions are coupled with each other via a hybrid transition region, and particles change their description on the fly when crossing this boundary. Here we show that the relative entropy, which provides a fundamental basis for many approaches in systematic coarse-graining, is also an effective instrument for the understanding of adaptive resolution simulation methodologies. We demonstrate that the use of coarse-grained potentials which minimize the relative entropy with respect to the atomistic system can help achieve a smoother transition between the different regions within the adaptive setup. Furthermore, we derive a quantitative relation between the width of the hybrid region and the seamlessness of the coupling. Our results do not only shed light on the what and how of adaptive resolution techniques but will also help setting up such simulations in an optimal manner.

The structure and energetics of the HCN → HNC transition state

NASA Astrophysics Data System (ADS)

Lee, Timothy J.; Rendell, Alistair P.

1991-03-01

The optimum geometries and quadratic force constants of HCN, HNC and the transition state connecting them have been determined at the single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory. Energy differences were evaluated using the CCSD and CCSD(T) methods in conjunction with large atomic natural orbital basis sets containing g-type basis functions on the heavy atoms and f-type functions on hydrogen. The most reliable structure obtained for the transition state has bond distances of 1.194, 1.188 and 1.389 Å for rCN, rCH and rNH, respectively. Including a correction for zero-point vibrational energies, the transition state is predicted to be 44.6 ± 1.0 kcal/mol above the HCN isomer, while HNC is predicted to be 14.4 ± 1.0 kcal/mol above HCN. The latter value is in excellent agreement with the most recent experimental determination (14.8 ± 2.0 kcal/mol).

Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. II. Validation and comparison with experiments

NASA Astrophysics Data System (ADS)

Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

2013-10-01

In this work, we validate a new, fully analytical method for calculating Raman intensities of periodic systems, developed and presented in Paper I [L. Maschio, B. Kirtman, M. Rérat, R. Orlando, and R. Dovesi, J. Chem. Phys. 139, 164101 (2013)]. Our validation of this method and its implementation in the CRYSTAL code is done through several internal checks as well as comparison with experiment. The internal checks include consistency of results when increasing the number of periodic directions (from 0D to 1D, 2D, 3D), comparison with numerical differentiation, and a test of the sum rule for derivatives of the polarizability tensor. The choice of basis set as well as the Hamiltonian is also studied. Simulated Raman spectra of α-quartz and of the UiO-66 Metal-Organic Framework are compared with the experimental data.

Estimates of electronic coupling for excess electron transfer in DNA

NASA Astrophysics Data System (ADS)

Voityuk, Alexander A.

2005-07-01

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31G* and extended 6-31++G** basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack.

Localized basis sets for unbound electrons in nanoelectronics.

PubMed

Soriano, D; Jacob, D; Palacios, J J

2008-02-21

It is shown how unbound electron wave functions can be expanded in a suitably chosen localized basis sets for any desired range of energies. In particular, we focus on the use of Gaussian basis sets, commonly used in first-principles codes. The possible usefulness of these basis sets in a first-principles description of field emission or scanning tunneling microscopy at large bias is illustrated by studying a simpler related phenomenon: The lifetime of an electron in a H atom subjected to a strong electric field.

Numerically Exact Calculation of Rovibrational Levels of Cl^-H_2O

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2014-06-01

Large amplitude vibrations of Van der Waals clusters are important because they reveal large regions of a potential energy surface (PES). To calculate spectra of Van der Waals clusters it is common to use an adiabatic approximation. When coupling between intra- and inter-molecular coordinates is important non-adiabatic coupling cannot be neglected and it is therefore critical to develop and test theoretical methods that couple both types of coordinates. We have developed new product basis and contracted basis Lanczos methods for Van der Waals complexes and tested them by computing rovibrational energy levels of Cl^-H_2O. The new product basis is made of functions of the inter-monomer distance, Wigner functions that depend on Euler angles specifying the orientation of H_2O with respect to a frame attached to the inter-monomer Jacobi vector, basis functions for H_2O vibration, and Wigner functions that depend on Euler angles specifying the orientation of the inter-monomer Jacobi vector with respect to a space-fixed frame. An advantage of this product basis is that it can be used to make an efficient contracted basis by replacing the vibrational basis functions for the monomer with monomer vibrational wavefunctions. Due to weak coupling between intra- and inter-molecular coordinates, only a few tens of monomer vibrational wavefunctions are necessary. The validity of the two new methods is established by comparing energy levels with benchmark rovibrational levels obtained with polyspherical coordinates and spherical harmonic type basis functions. For all bases, product structure is exploited to calculate eigenvalues with the Lanczos algorithm. For Cl^-H_2O, we are able, for the first time, to compute accurate splittings due to tunnelling between the two equivalent C_s minima. We use the PES of Rheinecker and Bowman (RB). Our results are in good agreement with experiment for the five fundamental bands observed. J. Rheinecker and J. M. Bowman, J. Chem. Phys. 124 131102 (2006) J. Rheinecker and J. M. Bowman, J. Chem. Phys. 125 133206 (2006)} S. Horvath, A. B. McCoy, B. M. Elliott, G. H. Weddle, J. R. Roscioli, and M. A. Johnson J. Phys. Chem. A 114 1556 (2010)

Enhanced Soundings for Local Coupling Studies Field Campaign Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferguson, Craig R; Santanello, Joseph A; Gentine, Pierre

This document presents initial analyses of the enhanced radiosonde observations obtained during the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility Enhanced Soundings for Local Coupling Studies Field Campaign (ESLCS), which took place at the ARM Southern Great Plains (SGP) Central Facility (CF) from June 15 to August 31, 2015. During ESLCS, routine 4-times-daily radiosonde measurements at the ARM-SGP CF were augmented on 12 days (June 18 and 29; July 11, 14, 19, and 26; August 15, 16, 21, 25, 26, and 27) with daytime 1-hourly radiosondes and 10-minute ‘trailer’ radiosondes every 3 hours. These 12more » intensive operational period (IOP) days were selected on the basis of prior-day qualitative forecasts of potential land-atmosphere coupling strength. The campaign captured 2 dry soil convection advantage days (June 29 and July 14) and 10 atmospherically controlled days. Other noteworthy IOP events include: 2 soil dry-down sequences (July 11-14-19 and August 21-25-26), a 2-day clear-sky case (August 15-16), and the passing of Tropical Storm Bill (June 18). To date, the ESLCS data set constitutes the highest-temporal-resolution sampling of the evolution of the daytime planetary boundary layer (PBL) using radiosondes at the ARM-SGP. The data set is expected to contribute to: 1) improved understanding and modeling of the diurnal evolution of the PBL, particularly with regard to the role of local soil wetness, and (2) new insights into the appropriateness of current ARM-SGP CF thermodynamic sampling strategies.« less

Near Hartree-Fock quality GTO basis sets for the second-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry

1987-01-01

Energy optimized, near Hartree-Fock quality Gaussian basis sets ranging in size from (17s12p) to (20s15p) are presented for the ground states of the second-row atoms for Na(2P), Na(+), Na(-), Mg(3P), P(-), S(-), and Cl(-). In addition, optimized supplementary functions are given for the ground state basis sets to describe the negative ions, and the excited Na(2P) and Mg(3P) atomic states. The ratios of successive orbital exponents describing the inner part of the 1s and 2p orbitals are found to be nearly independent of both nuclear charge and basis set size. This provides a method of obtaining good starting estimates for other basis set optimizations.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit.

PubMed

Lemke, Kono H

2017-06-21

This study presents results for the binding energy and geometry of the H 2 S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of D e , E ZPE , D o , and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of D e are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance r SS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H 2 S dimer geometry and binding energy. As regards the structure of (H 2 S) 2 , MPn, CCSD, and CCSD(T) level values of r SS , obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy D e are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies D e with E ZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields D o = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

This study presents results for the binding energy and geometry of the H2S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of De, EZPE, Do, and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of De are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance rSS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H2S dimer geometry and binding energy. As regards the structure of (H2S)2, MPn, CCSD, and CCSD(T) level values of rSS, obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy De are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies De with EZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields Do = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

Relativistic Prolapse-Free Gaussian Basis Sets of Quadruple-ζ Quality: (aug-)RPF-4Z. III. The f-Block Elements.

PubMed

Teodoro, Tiago Quevedo; Visscher, Lucas; da Silva, Albérico Borges Ferreira; Haiduke, Roberto Luiz Andrade

2017-03-14

The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-ζ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression. Moreover, through the choice of C/P characteristic exponents from functions of lower angular momentum spaces, a reduction in the computational demand is attained in relativistic calculations based on the kinetic balance condition. The present study thus complements the RPF-4Z sets for the whole periodic table (Z ≤ 118). The sets are available as Supporting Information and can also be found at http://basis-sets.iqsc.usp.br .

Combination of large and small basis sets in electronic structure calculations on large systems

NASA Astrophysics Data System (ADS)

Røeggen, Inge; Gao, Bin

2018-04-01

Two basis sets—a large and a small one—are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method

NASA Astrophysics Data System (ADS)

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-01

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method.

PubMed

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-21

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Moller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol(-1). Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

ARTSY-J: Convenient and precise measurement of 3JHNHα couplings in medium-size proteins from TROSY-HSQC spectra

NASA Astrophysics Data System (ADS)

Roche, Julien; Ying, Jinfa; Shen, Yang; Torchia, Dennis A.; Bax, Ad

2016-07-01

A new and convenient method, named ARTSY-J, is introduced that permits extraction of the 3JHNHα couplings in proteins from the relative intensities in a pair of 15N-1H TROSY-HSQC spectra. The pulse scheme includes 3JHNHα dephasing of the narrower TROSY 1HN-{15N} doublet component during a delay, integrated into the regular two-dimensional TROSY-HSQC pulse scheme, and compares the obtained intensity with a reference spectrum where 3JHNHα dephasing is suppressed. The effect of passive 1Hα spin flips downscales the apparent 3JHNHα coupling by a uniform factor that depends approximately linearly on both the duration of the 3JHNHα dephasing delay and the 1H-1H cross relaxation rate. Using such a correction factor, which accounts for the effects of both inhomogeneity of the radiofrequency field and 1Hα spin flips, agreement between prior and newly measured values for the small model protein GB3 is better than 0.3 Hz. Measurement for the HIV-1 protease homodimer (22 kDa) yields 3JHNHα values that agree to better than 0.7 Hz with predictions made on the basis of a previously parameterized Karplus equation. Although for Gly residues the two individual 3JHNHα couplings cannot be extracted from a single set of ARTSY-J spectra, the measurement provides valuable ϕ angle information.

Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.

PubMed

Koukounas, Constantine; Mavridis, Aristides

2008-11-06

The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.

LQR Control of Thin Shell Dynamics: Formulation and Numerical Implementation

NASA Technical Reports Server (NTRS)

delRosario, R. C. H.; Smith, R. C.

1997-01-01

A PDE-based feedback control method for thin cylindrical shells with surface-mounted piezoceramic actuators is presented. Donnell-Mushtari equations modified to incorporate both passive and active piezoceramic patch contributions are used to model the system dynamics. The well-posedness of this model and the associated LQR problem with an unbounded input operator are established through analytic semigroup theory. The model is discretized using a Galerkin expansion with basis functions constructed from Fourier polynomials tensored with cubic splines, and convergence criteria for the associated approximate LQR problem are established. The effectiveness of the method for attenuating the coupled longitudinal, circumferential and transverse shell displacements is illustrated through a set of numerical examples.

Benchmarking a quantum teleportation protocol in superconducting circuits using tomography and an entanglement witness.

PubMed

Baur, M; Fedorov, A; Steffen, L; Filipp, S; da Silva, M P; Wallraff, A

2012-01-27

Teleportation of a quantum state may be used for distributing entanglement between distant qubits in quantum communication and for quantum computation. Here we demonstrate the implementation of a teleportation protocol, up to the single-shot measurement step, with superconducting qubits coupled to a microwave resonator. Using full quantum state tomography and evaluating an entanglement witness, we show that the protocol generates a genuine tripartite entangled state of all three qubits. Calculating the projection of the measured density matrix onto the basis states of two qubits allows us to reconstruct the teleported state. Repeating this procedure for a complete set of input states we find an average output state fidelity of 86%.

LETTER TO THE EDITOR: Two-centre exchange integrals for complex exponent Slater orbitals

NASA Astrophysics Data System (ADS)

Kuang, Jiyun; Lin, C. D.

1996-12-01

The one-dimensional integral representation for the Fourier transform of a two-centre product of B functions (finite linear combinations of Slater orbitals) with real parameters is generalized to include B functions with complex parameters. This one-dimensional integral representation allows for an efficient method of calculating two-centre exchange integrals with plane-wave electronic translational factors (ETF) over Slater orbitals of real/complex exponents. This method is a significant improvement on the previous two-dimensional quadrature method of the integrals. A new basis set of the form 0953-4075/29/24/005/img1 is proposed to improve the description of pseudo-continuum states in the close-coupling treatment of ion - atom collisions.

Antihydrogen-hydrogen elastic scattering at thermal energies using an atomic-orbital technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinha, Prabal K.; Chaudhuri, Puspitapallab; Ghosh, A.S.

2003-05-01

In view of the recent interest in the trapping of antihydrogen atom H(bar sign), at very low temperatures, H-bar-H scattering has been investigated at low incident energies using a close-coupling model with the basis set H-bar(1s,2s,2p-bar)+H(1s,2s,2p-bar). The predicted s-wave elastic phase shifts, scattering length, and effective range are in a good agreement with the other recent predictions of Jonsell et al. and of Armour and Chamberlain. The results indicate that the atomic orbital expansion model is suitable to study the H-bar-H scattering at ultracold temperatures.

Average dynamics of a finite set of coupled phase oscillators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dima, Germán C., E-mail: gdima@df.uba.ar; Mindlin, Gabriel B.

2014-06-15

We study the solutions of a dynamical system describing the average activity of an infinitely large set of driven coupled excitable units. We compared their topological organization with that reconstructed from the numerical integration of finite sets. In this way, we present a strategy to establish the pertinence of approximating the dynamics of finite sets of coupled nonlinear units by the dynamics of its infinitely large surrogate.

Average dynamics of a finite set of coupled phase oscillators

PubMed Central

Dima, Germán C.; Mindlin, Gabriel B.

2014-01-01

We study the solutions of a dynamical system describing the average activity of an infinitely large set of driven coupled excitable units. We compared their topological organization with that reconstructed from the numerical integration of finite sets. In this way, we present a strategy to establish the pertinence of approximating the dynamics of finite sets of coupled nonlinear units by the dynamics of its infinitely large surrogate. PMID:24985426

Average dynamics of a finite set of coupled phase oscillators.

PubMed

Dima, Germán C; Mindlin, Gabriel B

2014-06-01

We study the solutions of a dynamical system describing the average activity of an infinitely large set of driven coupled excitable units. We compared their topological organization with that reconstructed from the numerical integration of finite sets. In this way, we present a strategy to establish the pertinence of approximating the dynamics of finite sets of coupled nonlinear units by the dynamics of its infinitely large surrogate.

Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

NASA Technical Reports Server (NTRS)

Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

1990-01-01

New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

On basis set superposition error corrected stabilization energies for large n-body clusters.

PubMed

Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

2011-10-07

In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections. © 2011 American Institute of Physics

Mechanical design of walking machines.

PubMed

Arikawa, Keisuke; Hirose, Shigeo

2007-01-15

The performance of existing actuators, such as electric motors, is very limited, be it power-weight ratio or energy efficiency. In this paper, we discuss the method to design a practical walking machine under this severe constraint with focus on two concepts, the gravitationally decoupled actuation (GDA) and the coupled drive. The GDA decouples the driving system against the gravitational field to suppress generation of negative power and improve energy efficiency. On the other hand, the coupled drive couples the driving system to distribute the output power equally among actuators and maximize the utilization of installed actuator power. First, we depict the GDA and coupled drive in detail. Then, we present actual machines, TITAN-III and VIII, quadruped walking machines designed on the basis of the GDA, and NINJA-I and II, quadruped wall walking machines designed on the basis of the coupled drive. Finally, we discuss walking machines that travel on three-dimensional terrain (3D terrain), which includes the ground, walls and ceiling. Then, we demonstrate with computer simulation that we can selectively leverage GDA and coupled drive by walking posture control.

High quality Gaussian basis sets for fourth-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry; Faegri, Knut, Jr.

1992-01-01

Energy optimized Gaussian basis sets of triple-zeta quality for the atoms Rb-Xe have been derived. Two series of basis sets are developed: (24s 16p 10d) and (26s 16p 10d) sets which were expanded to 13d and 19p functions as the 4d and 5p shells become occupied. For the atoms lighter than Cd, the (24s 16p 10d) sets with triple-zeta valence distributions are higher in energy than the corresponding double-zeta distribution. To ensure a triple-zeta distribution and a global energy minimum, the (26s 16p 10d) sets were derived. Total atomic energies from the largest basis sets are between 198 and 284 (mu)E(sub H) above the numerical Hartree-Fock energies.

Couples' Reports of Relationship Problems in a Naturalistic Therapy Setting

ERIC Educational Resources Information Center

Boisvert, Marie-Michele; Wright, John; Tremblay, Nadine; McDuff, Pierre

2011-01-01

Understanding couples' relationship problems is fundamental to couple therapy. Although research has documented common relationship problems, no study has used open-ended questions to explore problems in couples seeking therapy in naturalistic settings. The present study used a reliable coding system to explore the relationship problems reported…

Coupling model of aerobic waste degradation considering temperature, initial moisture content and air injection volume.

PubMed

Ma, Jun; Liu, Lei; Ge, Sai; Xue, Qiang; Li, Jiangshan; Wan, Yong; Hui, Xinminnan

2018-03-01

A quantitative description of aerobic waste degradation is important in evaluating landfill waste stability and economic management. This research aimed to develop a coupling model to predict the degree of aerobic waste degradation. On the basis of the first-order kinetic equation and the law of conservation of mass, we first developed the coupling model of aerobic waste degradation that considered temperature, initial moisture content and air injection volume to simulate and predict the chemical oxygen demand in the leachate. Three different laboratory experiments on aerobic waste degradation were simulated to test the model applicability. Parameter sensitivity analyses were conducted to evaluate the reliability of parameters. The coupling model can simulate aerobic waste degradation, and the obtained simulation agreed with the corresponding results of the experiment. Comparison of the experiment and simulation demonstrated that the coupling model is a new approach to predict aerobic waste degradation and can be considered as the basis for selecting the economic air injection volume and appropriate management in the future.

Comparison of eigenvectors for coupled seismo-electromagnetic layered-Earth modelling

NASA Astrophysics Data System (ADS)

Grobbe, N.; Slob, E. C.; Thorbecke, J. W.

2016-07-01

We study the accuracy and numerical stability of three eigenvector sets for modelling the coupled poroelastic and electromagnetic layered-Earth response. We use a known eigenvector set, its flux-normalized version and a newly derived flux-normalized set. The new set is chosen such that the system is properly uncoupled when the coupling between the poroelastic and electromagnetic fields vanishes. We carry out two different numerical stability tests: the first test focuses on the internal system, eigenvector and eigenvalue consistency; the second test investigates the stability and preciseness of the flux-normalized systems by looking at identity relations. We find that the known set shows the largest deviation for both tests, whereas the new set performs best. In two additional numerical modelling experiments, these numerical inaccuracies are shown to generate numerical noise levels comparable to small signals, such as signals coming from the important interface conversion responses, especially when the coupling coefficient is small. When coupling vanishes completely, the known set does not produce proper results. The new set produces numerically stable and accurate results in all situations. We therefore strongly recommend to use this newly derived set for future layered-Earth seismo-electromagnetic modelling experiments.

Relativistic well-tempered Gaussian basis sets for helium through mercury

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, S.; Matsuoka, O.

1989-10-01

Exponent parameters of the nonrelativistically optimized well-tempered Gaussian basis sets of Huzinaga and Klobukowski have been employed for Dirac--Fock--Roothaan calculations without their reoptimization. For light atoms He (atomic number {ital Z}=2)--Rh ({ital Z}=45), the number of exponent parameters used has been the same as the nonrelativistic basis sets and for heavier atoms Pd ({ital Z}=46)--Hg({ital Z}=80), two 2{ital p} (and three 3{ital d}) Gaussian basis functions have been augmented. The scheme of kinetic energy balance and the uniformly charged sphere model of atomic nuclei have been adopted. The qualities of the calculated basis sets are close to the Dirac--Fock limit.

Performance assessment of density functional methods with Gaussian and Slater basis sets using 7σ orbital momentum distributions of N2O

NASA Astrophysics Data System (ADS)

Wang, Feng; Pang, Wenning; Duffy, Patrick

2012-12-01

Performance of a number of commonly used density functional methods in chemistry (B3LYP, Bhandh, BP86, PW91, VWN, LB94, PBe0, SAOP and X3LYP and the Hartree-Fock (HF) method) has been assessed using orbital momentum distributions of the 7σ orbital of nitrous oxide (NNO), which models electron behaviour in a chemically significant region. The density functional methods are combined with a number of Gaussian basis sets (Pople's 6-31G*, 6-311G**, DGauss TZVP and Dunning's aug-cc-pVTZ as well as even-tempered Slater basis sets, namely, et-DZPp, et-QZ3P, et-QZ+5P and et-pVQZ). Orbital momentum distributions of the 7σ orbital in the ground electronic state of NNO, which are obtained from a Fourier transform into momentum space from single point electronic calculations employing the above models, are compared with experimental measurement of the same orbital from electron momentum spectroscopy (EMS). The present study reveals information on performance of (a) the density functional methods, (b) Gaussian and Slater basis sets, (c) combinations of the density functional methods and basis sets, that is, the models, (d) orbital momentum distributions, rather than a group of specific molecular properties and (e) the entire region of chemical significance of the orbital. It is found that discrepancies of this orbital between the measured and the calculated occur in the small momentum region (i.e. large r region). In general, Slater basis sets achieve better overall performance than the Gaussian basis sets. Performance of the Gaussian basis sets varies noticeably when combining with different Vxc functionals, but Dunning's augcc-pVTZ basis set achieves the best performance for the momentum distributions of this orbital. The overall performance of the B3LYP and BP86 models is similar to newer models such as X3LYP and SAOP. The present study also demonstrates that the combinations of the density functional methods and the basis sets indeed make a difference in the quality of the calculated orbitals.

A Comparison of the Behavior of Functional/Basis Set Combinations for Hydrogen-Bonding in the Water Dimer with Emphasis on Basis Set Superposition Error

PubMed Central

Plumley, Joshua A.; Dannenberg, J. J.

2011-01-01

We evaluate the performance of nine functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-DFT molecular orbital calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise corrected PES. The calculated ΔE's with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, due to error compensation, the smaller basis sets gave the best results (in comparison to experimental and high level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. Since many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: 1) D95(d,p) with B3LYP, B97D, M06 or MPWB1k; 2) 6-311G(d,p) with B3LYP; 3) D95++(d,p) with B3LYP, B97D or MPWB1K; 4)6-311++G(d,p) with B3LYP or B97D; and 5) aug-cc-pVDZ with M05-2X, M06-2X or X3LYP. PMID:21328398

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error.

PubMed

Plumley, Joshua A; Dannenberg, J J

2011-06-01

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP. Copyright © 2011 Wiley Periodicals, Inc.

Improved resistivity imaging of groundwater solute plumes using POD-based inversion

NASA Astrophysics Data System (ADS)

Oware, E. K.; Moysey, S. M.; Khan, T.

2012-12-01

We propose a new approach for enforcing physics-based regularization in electrical resistivity imaging (ERI) problems. The approach utilizes a basis-constrained inversion where an optimal set of basis vectors is extracted from training data by Proper Orthogonal Decomposition (POD). The key aspect of the approach is that Monte Carlo simulation of flow and transport is used to generate a training dataset, thereby intrinsically capturing the physics of the underlying flow and transport models in a non-parametric form. POD allows for these training data to be projected onto a subspace of the original domain, resulting in the extraction of a basis for the inversion that captures characteristics of the groundwater flow and transport system, while simultaneously allowing for dimensionality reduction of the original problem in the projected space We use two different synthetic transport scenarios in heterogeneous media to illustrate how the POD-based inversion compares with standard Tikhonov and coupled inversion. The first scenario had a single source zone leading to a unimodal solute plume (synthetic #1), whereas, the second scenario had two source zones that produced a bimodal plume (synthetic #2). For both coupled inversion and the POD approach, the conceptual flow and transport model used considered only a single source zone for both scenarios. Results were compared based on multiple metrics (concentration root-mean square error (RMSE), peak concentration, and total solute mass). In addition, results for POD inversion based on 3 different data densities (120, 300, and 560 data points) and varying number of selected basis images (100, 300, and 500) were compared. For synthetic #1, we found that all three methods provided qualitatively reasonable reproduction of the true plume. Quantitatively, the POD inversion performed best overall for each metric considered. Moreover, since synthetic #1 was consistent with the conceptual transport model, a small number of basis vectors (100) contained enough a priori information to constrain the inversion. Increasing the amount of data or number of selected basis images did not translate into significant improvement in imaging results. For synthetic #2, the RMSE and error in total mass were lowest for the POD inversion. However, the peak concentration was significantly overestimated by the POD approach. Regardless, the POD-based inversion was the only technique that could capture the bimodality of the plume in the reconstructed image, thus providing critical information that could be used to reconceptualize the transport problem. We also found that, in the case of synthetic #2, increasing the number of resistivity measurements and the number of selected basis vectors allowed for significant improvements in the reconstructed images.

Characterizing and Understanding the Remarkably Slow Basis Set Convergence of Several Minnesota Density Functionals for Intermolecular Interaction Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

For a set of eight equilibrium intermolecular complexes, it is discovered in this paper that the basis set limit (BSL) cannot be reached by aug-cc-pV5Z for three of the Minnesota density functionals: M06-L, M06-HF, and M11-L. In addition, the M06 and M11 functionals exhibit substantial, but less severe, difficulties in reaching the BSL. By using successively finer grids, it is demonstrated that this issue is not related to the numerical integration of the exchange-correlation functional. In addition, it is shown that the difficulty in reaching the BSL is not a direct consequence of the structure of the augmented functions inmore » Dunning’s basis sets, since modified augmentation yields similar results. By using a very large custom basis set, the BSL appears to be reached for the HF dimer for all of the functionals. As a result, it is concluded that the difficulties faced by several of the Minnesota density functionals are related to an interplay between the form of these functionals and the structure of standard basis sets. It is speculated that the difficulty in reaching the basis set limit is related to the magnitude of the inhomogeneity correction factor (ICF) of the exchange functional. A simple modification of the M06-L exchange functional that systematically reduces the basis set superposition error (BSSE) for the HF dimer in the aug-cc-pVQZ basis set is presented, further supporting the speculation that the difficulty in reaching the BSL is caused by the magnitude of the exchange functional ICF. In conclusion, the BSSE is plotted with respect to the internuclear distance of the neon dimer for two of the examined functionals.« less

Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Arnold, James (Technical Monitor)

1998-01-01

The addition of tight functions to sulphur and extrapolation to the complete basis set limit are required to obtain accurate atomization energies. Six different extrapolation procedures are tried. The best atomization energies come from the series of basis sets that yield the most consistent results for all extrapolation techniques. In the variable alpha approach, alpha values larger than 4.5 or smaller than 3, appear to suggest that the extrapolation may not be reliable. It does not appear possible to determine a reliable basis set series using only the triple and quadruple zeta based sets. The scalar relativistic effects reduce the atomization of SO and SO2 by 0.34 and 0.81 kcal/mol, respectively, and clearly must be accounted for if a highly accurate atomization energy is to be computed. The magnitude of the core-valence (CV) contribution to the atomization is affected by missing diffuse valence functions. The CV contribution is much more stable if basis set superposition errors are accounted for. A similar study of SF, SF(+), and SF6 shows that the best family of basis sets varies with the nature of the S bonding.

Calculating Interaction Energies Using First Principle Theories: Consideration of Basis Set Superposition Error and Fragment Relaxation

ERIC Educational Resources Information Center

Bowen, J. Philip; Sorensen, Jennifer B.; Kirschner, Karl N.

2007-01-01

The analysis explains the basis set superposition error (BSSE) and fragment relaxation involved in calculating the interaction energies using various first principle theories. Interacting the correlated fragment and increasing the size of the basis set can help in decreasing the BSSE to a great extent.

Complete basis set extrapolations for low-lying triplet electronic states of acetylene and vinylidene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherrill, C. David; Byrd, Edward F. C.; Head-Gordon, Martin

2000-07-22

A recent study by Ahmed, Peterka, and Suits [J. Chem. Phys. 110, 4248 (1999)] has presented the first experimentally derived estimate of the singlet-triplet gap in the simplest alkyne, acetylene. Their value, T{sub 0}(a(tilde sign) {sup 3}B{sub 2})=28 900 cm{sup -1}, does not agree with previous theoretical predictions using the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] method and a triple-{zeta} plus double polarization plus f-function basis set (TZ2P f ), which yields 30 500{+-}1000 cm{sup -1}. This discrepancy has prompted us to investigate possible deficiencies in this usually-accurate theoretical approach. Employing extrapolations to the complete basis set limit alongmore » with corrections for full connected triple excitations, core correlation, and even relativistic effects, we obtain a value of 30 900 cm-1 (estimated uncertainty {+-}230 cm-1), demonstrating that the experimental value is underestimated. To assist in the interpretation of anticipated future experiments, we also present highly accurate excitation energies for the other three low-lying triplet states of acetylene, a(tilde sign) {sup 3}B{sub u}(33 570{+-}230 cm{sup -1}), b(tilde sign) {sup 3}A{sub u}(36 040{+-}260 cm{sup -1}), and b(tilde sign) {sup 3}A{sub 2}(38 380{+-}260 cm{sup -1}), and the three lowest-lying states of vinylidene, X(tilde sign) {sup 1}A{sub 1}(15 150{+-}230 cm{sup -1}), a(tilde sign) {sup 3}B{sub 2}(31 870{+-}230 cm{sup -1}), and b(tilde sign) {sup 3}A{sub 2}(36 840{+-}350 cm{sup -1}). Finally, we assess the ability of density functional theory (DFT) and the Gaussian-3 method to match our benchmark results for adiabatic excitation energies of C{sub 2}H{sub 2}. (c) 2000 American Institute of Physics.« less

Complexes and saddle point structures, vibrational frequencies and relative energies of intermediates for CH2Br + HBr «-» CH3Br + Br

NASA Astrophysics Data System (ADS)

Espinosa-Garcia, J.

Ab initio molecular orbital theory was used to study parts of the reaction between the CH2Br radical and the HBr molecule, and two possibilities were analysed: attack on the hydrogen and attack on the bromine of the HBr molecule. Optimized geometries and harmonic vibrational frequencies were calculated at the second-order Moller-Plesset perturbation theory levels, and comparison with available experimental data was favourable. Then single-point calculations were performed at several higher levels of calculation. In the attack on the hydrogen of HBr, two stationary points were located on the direct hydrogen abstraction reaction path: a very weak hydrogen bonded complex of reactants, C···HBr, close to the reactants, followed by the saddle point (SP). The effects of level of calculation (method + basis set), spin projection, zeropoint energy, thermal corrections (298K), spin-orbit coupling and basis set superposition error (BSSE) on the energy changes were analysed. Taking the reaction enthalpy (298K) as reference, agreement with experiment was obtained only when high correlation energy and large basis sets were used. It was concluded that at room temperature (i.e., with zero-point energy and thermal corrections), when the BSSE was included, the complex disappears and the activation enthalpy (298K) ranges from 0.8kcal mol-1 to 1.4kcal mol-1 above the reactants, depending on the level of calculation. It was concluded also that this result is the balance of a complicated interplay of many factors, which are affected by uncertainties in the theoretical calculations. Finally, another possible complex (X complex), which involves the alkyl radical being attracted to the halogen end of HBr (C···BrH), was explored also. It was concluded that this X complex does not exist at room temperature.

Mechanistic and kinetic study of the CH3CO + O2 reaction.

PubMed

Hou, Hua; Li, Aixiao; Hu, Hongyi; Li, Yuzhen; Li, Hui; Wang, Baoshan

2005-06-08

Potential-energy surface of the CH3CO + O2 reaction has been calculated by ab initio quantum chemistry methods. The geometries were optimized using the second-order Moller-Plesset theory (MP2) with the 6-311G(d,p) basis set and the coupled-cluster theory with single and double excitations (CCSD) with the correlation consistent polarized valence double zeta (cc-pVDZ) basis set. The relative energies were calculated using the Gaussian-3 second-order Moller-Plesset theory with the CCSD/cc-pVDZ geometries. Multireference self-consistent-field and MP2 methods were also employed using the 6-311G(d,p) and 6-311++G(3df,2p) basis sets. Both addition/elimination and direct abstraction mechanisms have been investigated. It was revealed that acetylperoxy radical [CH3C(O)OO] is the initial adduct and the formation of OH and alpha-lactone [CH2CO2(1A')] is the only energetically accessible decomposition channel. The other channels, e.g., abstraction, HO2 + CH2CO, O + CH3CO2, CO + CH3O2, and CO2 + CH3O, are negligible. Multichannel Rice-Ramsperger-Kassel-Marcus theory and transition state theory (E-resolved) were employed to calculate the overall and individual rate coefficients and the temperature and pressure dependences. Fairly good agreement between theory and experiments has been obtained without any adjustable parameters. It was concluded that at pressures below 3 Torr, OH and CH2CO2(1A') are the major nascent products of the oxidation of acetyl radicals, although CH2CO2(1A') might either undergo unimolecular decomposition to form the final products of CH2O + CO or react with OH and Cl to generate H2O and HCl. The acetylperoxy radicals formed by collisional stabilization are the major products at the elevated pressures. In atmosphere, the yield of acetylperoxy is nearly unity and the contribution of OH is only marginal.

Hyperpolarizability of H 2O revisited: accurate estimate of the basis set limit and the size of electron correlation effects

NASA Astrophysics Data System (ADS)

Maroulis, George

1998-06-01

A large (18s 13p 8d 5f / 12s 7p 3d 2f) basis set consisting of 256 uncontracted gaussian-type functions is expected to yield values near the Hartree-Fock limit for the static hyperpolarizability of H 2O: βzxx=-9.40, βzyy=-1.35, βzzz=-7.71 and β¯=-11.07 for βαβγ ( e3a03Eh-2) and γxxxx=569, γyyyy=1422, γzzzz=907, γxxyy=338, γyyzz=389, γzzxx=287 and γ¯=985 for γαβγδ ( e4a04Eh-3) at the experimental equilibrium geometry (with z as the C 2 axis, molecule on the xz plane). The respective electron correlation corrections obtained with the single, double and perturbatively linked triple excitations coupled-cluster method and a [9s 6p 6d 3f / 6s 4p 2d 1f] basis set are βzxx=-0.45, βzyy=-4.19, βzzz=-6.09, β¯=-6.44 and γxxxx=267, γyyyy=1228, γzzzz=574, γxxyy=295, γyyzz=322, γzzxx=152, γ¯=721 . For the static limit we propose β¯=-17.5±0.3 e3a03Eh-2 and γ¯=(171±6)×10 1e4a04Eh-3, in near agreement with the experimental findings of β¯=-19.2±0.9 e3a03Eh-2 and γ¯=1800±150 e4a04Eh-3 deduced from EFISH measurements at 1064 nm by Kaatz et al. [P. Kaatz, E.A. Donley, D.P. Shelton, J. Chem. Phys. 108 (1998) 849].

51V solid-state NMR and density functional theory studies of vanadium environments in V(V)O2 dipicolinic acid complexes

NASA Astrophysics Data System (ADS)

Bolte, Stephanie E.; Ooms, Kristopher J.; Polenova, Tatyana; Baruah, Bharat; Crans, Debbie C.; Smee, Jason J.

2008-02-01

V51 solid-state NMR and density functional theory (DFT) investigations are reported for a series of pentacoordinate dioxovanadium(V)-dipicolinate [V(V )O2-dipicolinate] and heptacoordinate aquahydroxylamidooxovanadium(V)-dipicolinate [V(V)O-dipicolinate] complexes. These compounds are of interest because of their potency as phosphatase inhibitors as well as their insulin enhancing properties and potential for the treatment of diabetes. Experimental solid-state NMR results show that the electric field gradient tensors in the V(V )O2-dipicolinate derivatives are affected significantly by substitution on the dipicolinate ring and range from 5.8to8.3MHz. The chemical shift anisotropies show less dramatic variations with respect to the ligand changes and range between -550 and -600ppm. To gain insights on the origins of the NMR parameters, DFT calculations were conducted for an extensive series of the V(V )O2- and V(V)O-dipicolinate complexes. To assess the level of theory required for the accurate calculation of the V51 NMR parameters, different functionals, basis sets, and structural models were explored in the DFT study. It is shown that the original x-ray crystallographic geometries, including all counterions and solvation water molecules within 5Å of the vanadium, lead to the most accurate results. The choice of the functional and the basis set at a high level of theory has a relatively minor impact on the outcome of the chemical shift anisotropy calculations; however, the use of large basis sets is necessary for accurate calculations of the quadrupole coupling constants for several compounds of the V(V )O2 series. These studies demonstrate that even though the vanadium compounds under investigations exhibit distorted trigonal bipyramidal coordination geometry, they have a "perfect" trigonal bipyramidal electronic environment. This observation could potentially explain why vanadate and vanadium(V) adducts are often recognized as potent transition state analogs.

Theoretical study of hyperfine coupling constants and electron spin g factors for X2Σ diatomics from Groups 1 and 2

NASA Astrophysics Data System (ADS)

Bruna, Pablo J.; Grein, Friedrich

The ESR parameters of the cations Be 2 + , Mg 2 + , Ca 2 + , BeMg + , BeCa + , MgCa + and the mixed radicals ZBe, ZMg, ZCa (Z = Li, Na, K), all having a X 2 Σu + (1 σg 2 1 σu )/X 2 Sigma + (1 σ2 2 σ) ground state, have been studied theoretically. The A iso and A dip constants have been calculated with UHF, CISD, MP2, B3LYP, PW91PW91 wavefunctions, and 6-311+G(2df) basis sets. The electron spin g factors (magnetic moment μs) have been evaluated from correlated (MRDCI) wavefunctions, using a Hamiltonian based on Breit-Pauli theory with perturbation expansions up to second order, and 6-311+ G(2d) basis sets. As expected for s-rich radicals, the hyperfine spectra are governed by the A iso terms. Both Δg|| and Δg Υ̂values are negative, but Δg|| lies close to zero. For Δg Υ̂, the coupling with 1 2 Π(u) dominates the sum-over-states expansions. Although the singly occupied MOs (SOMO) are mostly of s character, the | Δg Υ̂| are relatively large, up to 5200 ppm for cationic, and up to 7850 ppm for neutral radicals. These large values are caused by low excitation energies and high magnetic transition moments, the latter due to the fact that the σ*( s - s ) SOMO has the same nodal properties as a p σorbital. Of the radicals considered here, an ESR spectrum is available only for Mg2+. Our theoretical A iso of-287 MHz reproduces well the matrix result (-291 MHz). Calculated values of-10 ppm for Deltag|| and of-1280 ppm for Deltag Υ̂give an average < Δg> =-860 ppm that lies within the experimental range of-600( ±300) ppm in Ne, and of-1300( ±500) ppm in Ar matrices.

Ab initio coupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone

DOE PAGES

Hansen, Jared A.; Bauman, Nicholas P.; Shen, Jun; ...

2015-12-09

In this paper, the four, closely spaced, lowest energy electronic states of the challenging, D 4h-symmetric, 1,2,3,4-cyclobutanetetraone (C 4O 4) molecule have been investigated using high-level ab initio methods. The calculated states include the closed-shell singlet 8π( 1A 1g) state, the singlet 10π( 1A 1g) state, in which the π-type lowest unoccupied molecular orbital (LUMO) of the 8π( 1A 1g) reference is doubly occupied and the σ-type highest occupied molecular orbital (HOMO) is empty, and the open-shell singlet and triplet states, designated as 9π( 1B 2u) and 9π( 3B 2u), respectively, originating from single occupancy of the HOMO and LUMO.more » Our focus is on single-reference coupled-cluster (CC) approaches capable of handling electronic near-degeneracies in diradicals, especially the completely renormalised CR-CC(2,3) and active-space CCSDt methods, along with their CCSD and EOMCCSD counterparts. The internally contracted multi-reference configuration interaction calculations with a quasi-degenerate Davidson correction are performed as well. Our computations demonstrate that the state ordering is 9π( 3B 2u) < 8π( 1A 1g) < 9π( 1B 2u) < 10π( 1A 1g) and that the 8π( 1A 1g) - 9π( 3B 2u) gap is in the 7–11 kJ/mol range, in reasonable agreement with the negative ion photoelectron spectroscopy measurements, which give 6.27 ± 0.5 kJ/mol. Finally, in addition to the theory level used, geometry relaxation and basis set play a significant role in determining the state ordering and energy spacings. In particular, it is unsafe to use lower level, non-CC geometries and smaller basis sets.« less

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

Galbraith, John Morrison; James, Andrew M.; Nemes, Coleen T.

2014-03-01

Structural weights and bond dissociation energies have been determined for H-F, H-X, and F-X molecules (-X = -OH, -NH2, and -CH3) at the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) levels of theory with the aug-cc-pVDZ and 6-31++G(d,p) basis sets. At the BOVB level, the aug-cc-pVDZ basis set yields a counterintuitive ordering of ionic structural weights when the initial heavy atom s-type basis functions are included. For H-F, H-OH, and F-X, the ordering follows chemical intuition when these basis functions are not included. These counterintuitive weights are shown to be a result of the diffuse polarisation function on one VB fragment being spatially located, in part, on the other VB fragment. Except in the case of F-CH3, this problem is corrected with the 6-31++G(d,p) basis set. The initial heavy atom s-type functions are shown to make an important contribution to the VB orbitals and bond dissociation energies and, therefore, should not be excluded. It is recommended to not use diffuse basis sets in valence bond calculations unless absolutely necessary. If diffuse basis sets are needed, the 6-31++G(d,p) basis set should be used with caution and the structural weights checked against VBSCF values which have been shown to follow the expected ordering in all cases.

Nonadiabatic Coupling

NASA Astrophysics Data System (ADS)

Kryachko, Eugene S.

The general features of the nonadiabatic coupling and its relation to molecular properties are surveyed. Some consequences of the [`]equation of motion', formally expressing a [`]smoothness' of a given molecular property within the diabatic basis, are demonstrated. A particular emphasis is made on the relation between a [`]smoothness' of the electronic dipole moment and the generalized Mulliken-Hush formula for the diabatic electronic coupling.

42 CFR 435.733 - Post-eligibility treatment of income of institutionalized individuals in States using more...

Code of Federal Regulations, 2010 CFR

2010-10-01

... Medicaid on the basis of blindness or disability; (ii) $60 a month for an institutionalized couple if both... home maintenance. For single individuals and couples, an amount (in addition to the personal needs allowance) for maintenance of the individual's or couple's home if— (1) The amount is deducted for not more...

42 CFR 436.832 - Post-eligibility treatment of income of institutionalized individuals: Application of patient...

Code of Federal Regulations, 2010 CFR

2010-10-01

... Medicaid on the basis of blindness or disability; (ii) $60 a month for an institutionalized couple if both... deduction: Allowance for home maintenance. For single individuals and couples, an amount (in addition to the personal needs allowance) for maintenance of the individual's or couple's home if— (1) The amount is...

The Nonlinear Steepest Descent Method to Long-Time Asymptotics of the Coupled Nonlinear Schrödinger Equation

NASA Astrophysics Data System (ADS)

Geng, Xianguo; Liu, Huan

2018-04-01

The Riemann-Hilbert problem for the coupled nonlinear Schrödinger equation is formulated on the basis of the corresponding 3× 3 matrix spectral problem. Using the nonlinear steepest descent method, we obtain leading-order asymptotics for the Cauchy problem of the coupled nonlinear Schrödinger equation.

On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

NASA Astrophysics Data System (ADS)

Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

Towards an integrated forecasting system for fisheries on habitat-bound stocks

NASA Astrophysics Data System (ADS)

Christensen, A.; Butenschön, M.; Gürkan, Z.; Allen, I. J.

2013-03-01

First results of a coupled modelling and forecasting system for fisheries on habitat-bound stocks are being presented. The system consists currently of three mathematically, fundamentally different model subsystems coupled offline: POLCOMS providing the physical environment implemented in the domain of the north-west European shelf, the SPAM model which describes sandeel stocks in the North Sea, and the third component, the SLAM model, which connects POLCOMS and SPAM by computing the physical-biological interaction. Our major experience by the coupling model subsystems is that well-defined and generic model interfaces are very important for a successful and extendable coupled model framework. The integrated approach, simulating ecosystem dynamics from physics to fish, allows for analysis of the pathways in the ecosystem to investigate the propagation of changes in the ocean climate and to quantify the impacts on the higher trophic level, in this case the sandeel population, demonstrated here on the basis of hindcast data. The coupled forecasting system is tested for some typical scientific questions appearing in spatial fish stock management and marine spatial planning, including determination of local and basin-scale maximum sustainable yield, stock connectivity and source/sink structure. Our presented simulations indicate that sandeel stocks are currently exploited close to the maximum sustainable yield, even though periodic overfishing seems to have occurred, but large uncertainty is associated with determining stock maximum sustainable yield due to stock inherent dynamics and climatic variability. Our statistical ensemble simulations indicates that the predictive horizon set by climate interannual variability is 2-6 yr, after which only an asymptotic probability distribution of stock properties, like biomass, are predictable.

Relativistic effects on the NMR parameters of Si, Ge, Sn, and Pb alkynyl compounds: Scalar versus spin-orbit effects

NASA Astrophysics Data System (ADS)

Demissie, Taye B.

2017-11-01

The NMR chemical shifts and indirect spin-spin coupling constants of 12 molecules containing 29Si, 73Ge, 119Sn, and 207Pb [X(CCMe)4, Me2X(CCMe)2, and Me3XCCH] are presented. The results are obtained from non-relativistic as well as two- and four-component relativistic density functional theory (DFT) calculations. The scalar and spin-orbit relativistic contributions as well as the total relativistic corrections are determined. The main relativistic effect in these molecules is not due to spin-orbit coupling but rather to the scalar relativistic contraction of the s-shells. The correlation between the calculated and experimental indirect spin-spin coupling constants showed that the four-component relativistic density functional theory (DFT) approach using the Perdew's hybrid scheme exchange-correlation functional (PBE0; using the Perdew-Burke-Ernzerhof exchange and correlation functionals) gives results in good agreement with experimental values. The indirect spin-spin coupling constants calculated using the spin-orbit zeroth order regular approximation together with the hybrid PBE0 functional and the specially designed J-coupling (JCPL) basis sets are in good agreement with the results obtained from the four-component relativistic calculations. For the coupling constants involving the heavy atoms, the relativistic corrections are of the same order of magnitude compared to the non-relativistically calculated results. Based on the comparisons of the calculated results with available experimental values, the best results for all the chemical shifts and non-existing indirect spin-spin coupling constants for all the molecules are reported, hoping that these accurate results will be used to benchmark future DFT calculations. The present study also demonstrates that the four-component relativistic DFT method has reached a level of maturity that makes it a convenient and accurate tool to calculate indirect spin-spin coupling constants of "large" molecular systems involving heavy atoms.

Vibrational spectra of halide-water dimers: Insights on ion hydration from full-dimensional quantum calculations on many-body potential energy surfaces

NASA Astrophysics Data System (ADS)

Bajaj, Pushp; Wang, Xiao-Gang; Carrington, Tucker; Paesani, Francesco

2018-03-01

Full-dimensional vibrational spectra are calculated for both X-(H2O) and X-(D2O) dimers (X = F, Cl, Br, I) at the quantum-mechanical level. The calculations are carried out on two sets of recently developed potential energy functions (PEFs), namely, Thole-type model energy (TTM-nrg) and many-body energy (MB-nrg), using the symmetry-adapted Lanczos algorithm with a product basis set including all six vibrational coordinates. Although both TTM-nrg and MB-nrg PEFs are derived from coupled-cluster single double triple-F12 data obtained in the complete basis set limit, they differ in how many-body effects are represented at short range. Specifically, while both models describe long-range interactions through the combination of two-body dispersion and many-body classical electrostatics, the relatively simple Born-Mayer functions employed in the TTM-nrg PEFs to represent short-range interactions are replaced in the MB-nrg PEFs by permutationally invariant polynomials to achieve chemical accuracy. For all dimers, the MB-nrg vibrational spectra are in close agreement with the available experimental data, correctly reproducing anharmonic and nuclear quantum effects. In contrast, the vibrational frequencies calculated with the TTM-nrg PEFs exhibit significant deviations from the experimental values. The comparison between the TTM-nrg and MB-nrg results thus reinforces the notion that an accurate representation of both short-range interactions associated with electron density overlap and long-range many-body electrostatic interactions is necessary for a correct description of hydration phenomena at the molecular level.

COMPARATIVE ASSESSMENT OF THE COMPOSITION AND CHARGE STATE OF NITROGENASE FeMo-COFACTOR

PubMed Central

Harris, Travis V.; Szilagyi, Robert K.

2011-01-01

A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed the exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional and basis set. Overall, we found that a more oxidized [MoIV-2FeII-5FeIII-9S2−-C4−] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria, and is thus favored over the currently preferred composition of [MoIV-4FeII-3FeIII-9S2−-N3−] from the literature. PMID:21545160

Interactions of C+(2PJ) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

NASA Astrophysics Data System (ADS)

Tuttle, William D.; Thorington, Rebecca L.; Viehland, Larry A.; Breckenridge, W. H.; Wright, Timothy G.

2018-03-01

Accurate interatomic potentials were calculated for the interaction of a singly charged carbon cation, C+, with a single rare gas atom, RG (RG = Ne-Xe). The RCCSD(T) method and basis sets of quadruple-ζ and quintuple-ζ quality were employed; each interaction energy was counterpoise corrected and extrapolated to the basis set limit. The lowest C+(2P) electronic term of the carbon cation was considered, and the interatomic potentials calculated for the diatomic terms that arise from these: 2Π and 2Σ+. Additionally, the interatomic potentials for the respective spin-orbit levels were calculated, and the effect on the spectroscopic parameters was examined. In doing this, anomalously large spin-orbit splittings for RG = Ar-Xe were found, and this was investigated using multi-reference configuration interaction calculations. The latter indicated a small amount of RG → C+ electron transfer and this was used to rationalize the observations. This is taken as evidence of an incipient chemical interaction, which was also examined via contour plots, Birge-Sponer plots and various population analyses across the C+-RG series (RG = He-Xe), with the latter showing unexpected results. Trends in several spectroscopic parameters were examined as a function of the increasing atomic number of the RG atom. Finally, each set of RCCSD(T) potentials was employed, including spin-orbit coupling to calculate the transport coefficients for C+ in RG, and the results were compared with the limited available data. This article is part of the theme issue `Modern theoretical chemistry'.

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability.

PubMed

Parrish, Robert M; Burns, Lori A; Smith, Daniel G A; Simmonett, Andrew C; DePrince, A Eugene; Hohenstein, Edward G; Bozkaya, Uğur; Sokolov, Alexander Yu; Di Remigio, Roberto; Richard, Ryan M; Gonthier, Jérôme F; James, Andrew M; McAlexander, Harley R; Kumar, Ashutosh; Saitow, Masaaki; Wang, Xiao; Pritchard, Benjamin P; Verma, Prakash; Schaefer, Henry F; Patkowski, Konrad; King, Rollin A; Valeev, Edward F; Evangelista, Francesco A; Turney, Justin M; Crawford, T Daniel; Sherrill, C David

2017-07-11

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.

Application of the finite-field coupled-cluster method to calculate molecular properties relevant to electron electric-dipole-moment searches

NASA Astrophysics Data System (ADS)

Abe, M.; Prasannaa, V. S.; Das, B. P.

2018-03-01

Heavy polar diatomic molecules are currently among the most promising probes of fundamental physics. Constraining the electric dipole moment of the electron (e EDM ), in order to explore physics beyond the standard model, requires a synergy of molecular experiment and theory. Recent advances in experiment in this field have motivated us to implement a finite-field coupled-cluster (FFCC) approach. This work has distinct advantages over the theoretical methods that we had used earlier in the analysis of e EDM searches. We used relativistic FFCC to calculate molecular properties of interest to e EDM experiments, that is, the effective electric field (Eeff) and the permanent electric dipole moment (PDM). We theoretically determine these quantities for the alkaline-earth monofluorides (AEMs), the mercury monohalides (Hg X ), and PbF. The latter two systems, as well as BaF from the AEMs, are of interest to e EDM searches. We also report the calculation of the properties using a relativistic finite-field coupled-cluster approach with single, double, and partial triples' excitations, which is considered to be the gold standard of electronic structure calculations. We also present a detailed error estimate, including errors that stem from our choice of basis sets, and higher-order correlation effects.

Numerical solution of the exact cavity equations of motion for an unstable optical resonator.

PubMed

Bowers, M S; Moody, S E

1990-09-20

We solve numerically, we believe for the first time, the exact cavity equations of motion for a realistic unstable resonator with a simple gain saturation model. The cavity equations of motion, first formulated by Siegman ["Exact Cavity Equations for Lasers with Large Output Coupling," Appl. Phys. Lett. 36, 412-414 (1980)], and which we term the dynamic coupled modes (DCM) method of solution, solve for the full 3-D time dependent electric field inside the optical cavity by expanding the field in terms of the actual diffractive transverse eigenmodes of the bare (gain free) cavity with time varying coefficients. The spatially varying gain serves to couple the bare cavity transverse modes and to scatter power from mode to mode. We show that the DCM method numerically converges with respect to the number of eigenmodes in the basis set. The intracavity intensity in the numerical example shown reaches a steady state, and this steady state distribution is compared with that computed from the traditional Fox and Li approach using a fast Fourier transform propagation algorithm. The output wavefronts from both methods are quite similar, and the computed output powers agree to within 10%. The usefulness and advantages of using this method for predicting the output of a laser, especially pulsed lasers used for coherent detection, are discussed.

Sharing the trousers: gender roles and relationships in an HIV-prevention trial in Zimbabwe.

PubMed

Montgomery, Elizabeth T; Chidanyika, Agnes; Chipato, Tsungai; van der Straten, Ariane

2012-01-01

Male and female gender roles and inequalities are important in contributing to the disproportionate burden of HIV experienced by women in sub-Saharan Africa. Within the context of an HIV prevention trial, we aimed to describe and understand male partner influence on women's use of HIV-prevention methods. Our presumption was not that regressive gender norms prevailed - rather, that a wide range of gendered attitudes and dynamics would be expressed among couples. Data from 16 focus groups with Zimbabwean female trial participants and their male partners and 4 in-depth couples interviews were collected, and form the basis of the analysis. Findings offer descriptions of how couples have adapted techniques for negotiating modern household economies and sexual decision-making in a manner that both preserves traditional gender roles, while accommodating women's entrance into new domains such as the workforce or an HIV-prevention trial. Women's agency to introduce novel female-initiated-method use into her intimate relationships is described. Men and women's accounts of method introduction and use suggest different perceptions about the locus of sexual decision making. The study provides unique insight into a gendered context that is dynamic yet sensitive to change, which in turn can provide useful information to more appropriately guide HIV-prevention activities in this setting.

Modeling Photoelectron Spectra of CuO, Cu2O, and CuO2 Anions with Equation-of-Motion Coupled-Cluster Methods: An Adventure in Fock Space.

PubMed

Orms, Natalie; Krylov, Anna I

2018-04-12

The experimental photoelectron spectra of di- and triatomic copper oxide anions have been reported previously. We present an analysis of the experimental spectra of the CuO - , Cu 2 O - , and CuO 2 - anions using equation-of-motion coupled-cluster (EOM-CC) methods. The open-shell electronic structure of each molecule demands a unique combination of EOM-CC methods to achieve an accurate and balanced representation of the multiconfigurational anionic- and neutral-state manifolds. Analysis of the Dyson orbitals associated with photodetachment from CuO - reveals the strong non-Koopmans character of the CuO states. For the lowest detachment energy, a good agreement between theoretical and experimental values is obtained with CCSD(T) (coupled-cluster with single and double excitations and perturbative account of triple excitations). The (T) correction is particularly important for Cu 2 O - . Use of a relativistic pseudopotential and matching basis set improves the quality of results in most cases. EOM-DIP-CCSD analysis of the low-lying states of CuO 2 - reveals multiple singlet and triplet anionic states near the triplet ground state, adding an extra layer of complexity to the interpretation of the experimental CuO 2 - photoelectron spectrum.

Unraveling torsional bath interactions with the CO stretching state in methanol

NASA Astrophysics Data System (ADS)

Pearson, John C.; Daly, Adam M.; Lees, Ronald M.

2015-12-01

Quantum mechanical models describing the effects of a C3 internal rotor have been successful in modeling all the torsional manifolds of isolated vibrational states. However, modeling the coupling between nearly degenerate small amplitude vibrations in the C3 internal rotation case remains far from satisfactory and a variety of practical and fundamental questions persist on basis sets, the relative importance of effects and how the problem should be approached. The ν8 C-O stretching state of methanol has been well studied with infrared techniques and has the potential to serve as an experimental reference data set for the development of models for the coupled large and small amplitude motion case. A combined infrared-microwave study of the lowest K A-states of vt = 3, vt = 4 and ν8 has been performed to understand the nature of the interactions between ν8 the excited torsional states. The interaction between vt = 4 and ν8 at K = 0+ has been confirmed to be Fermi type with magnitude of 2.5 cm-1. Additionally, the fundamental a-symmetry and b-symmetry Coriolis interactions between vt = 3 and ν8 have been estimated to be 8900 MHz and -360 MHz, respectively. The magnitude of these interactions suggests that modeling the ν8 state, the vt = 3 state, and the vt = 4 states will have to carefully account for these interactions.

Coherent States for the Two-Dimensional Dirac-Moshinsky Oscillator Coupled to an External Magnetic Field

NASA Astrophysics Data System (ADS)

Ojeda-Guillén, D.; Mota, R. D.; Granados, V. D.

2015-03-01

We show that the (2+1)-dimensional Dirac-Moshinsky oscillator coupled to an external magnetic field can be treated algebraically with the SU(1,1) group theory and its group basis. We use the su(1,1) irreducible representation theory to find the energy spectrum and the eigenfunctions. Also, with the su(1,1) group basis we construct the relativistic coherent states in a closed form for this problem. Supported by SNI-México, COFAA-IPN, EDI-IPN, EDD-IPN, SIP-IPN project number 20140598

Electrical system for pulse-width modulated control of a power inverter using phase-shifted carrier signals and related operating methods

DOEpatents

Welchko, Brian A [Torrance, CA

2012-02-14

Systems and methods are provided for pulse-width modulated control of power inverter using phase-shifted carrier signals. An electrical system comprises an energy source and a motor. The motor has a first set of windings and a second set of windings, which are electrically isolated from each other. An inverter module is coupled between the energy source and the motor and comprises a first set of phase legs coupled to the first set of windings and a second set of phase legs coupled to the second set of windings. A controller is coupled to the inverter module and is configured to achieve a desired power flow between the energy source and the motor by modulating the first set of phase legs using a first carrier signal and modulating the second set of phase legs using a second carrier signal. The second carrier signal is phase-shifted relative to the first carrier signal.

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

PubMed

Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

2015-12-03

The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.

An ab initio study of the low-lying doublet states of AgO and AgS

NASA Astrophysics Data System (ADS)

Bauschlicher, Charles W.; Partridge, Harry; Langhoff, Stephen R.

1990-11-01

Spectroscopic constants ( Do, re, μ e, Te) are determined for the doublet states of AgO and AgS below ≈ 30000 cm -1. valence basis sets are employed in conjunction with relativistic effective core potentials (RECPs). Electron correlation is included using the modified coupled-pair functional (MCPF) and multireferenceconfiguration interaction (MRCI) methods. The A 2Σ +-X 2Π band system is found to occur in the near infrared ( ≈ 9000 cm -1) and to be relatively weak with a radiative lifetime of 900 μs for A 2Σ + (ν = 0). The weakly bound C 2Π state (our notation), the upper state of the blue system, is found to require high levels of theoretical treatment to determine a quantitatively accurate potential. The red system is assigned as a transition from the C 2Π state to the previously unobserved A 2Σ + state. Several additional transitions are identified that should be detectable experiment A more limited study is performed for the vertical excitation spectrum of AgS. In addition, a detailed all-electron study of the X 2Π and A 2Σ + states of AgO is carried out using large atomic natural orbital (ANO) basis sets. Our best calculated Do value for AgO is significantly less than the experimental value, which suggests that there may be some systematic error in the experimental determination.

Large-Scale Computation of Nuclear Magnetic Resonance Shifts for Paramagnetic Solids Using CP2K.

PubMed

Mondal, Arobendo; Gaultois, Michael W; Pell, Andrew J; Iannuzzi, Marcella; Grey, Clare P; Hutter, Jürg; Kaupp, Martin

2018-01-09

Large-scale computations of nuclear magnetic resonance (NMR) shifts for extended paramagnetic solids (pNMR) are reported using the highly efficient Gaussian-augmented plane-wave implementation of the CP2K code. Combining hyperfine couplings obtained with hybrid functionals with g-tensors and orbital shieldings computed using gradient-corrected functionals, contact, pseudocontact, and orbital-shift contributions to pNMR shifts are accessible. Due to the efficient and highly parallel performance of CP2K, a wide variety of materials with large unit cells can be studied with extended Gaussian basis sets. Validation of various approaches for the different contributions to pNMR shifts is done first for molecules in a large supercell in comparison with typical quantum-chemical codes. This is then extended to a detailed study of g-tensors for extended solid transition-metal fluorides and for a series of complex lithium vanadium phosphates. Finally, lithium pNMR shifts are computed for Li 3 V 2 (PO 4 ) 3 , for which detailed experimental data are available. This has allowed an in-depth study of different approaches (e.g., full periodic versus incremental cluster computations of g-tensors and different functionals and basis sets for hyperfine computations) as well as a thorough analysis of the different contributions to the pNMR shifts. This study paves the way for a more-widespread computational treatment of NMR shifts for paramagnetic materials.

HM{sup +}–RG complexes (M = group 2 metal; RG = rare gas): Physical vs. chemical interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, Joe P.; Dodson, Hannah; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk

2015-04-21

Previous work on the HM{sup +}–He complexes (M = Be–Ra) has been extended to the cases of the heavier rare gas atoms, HM{sup +}–RG (RG = Ne–Rn). Optimized geometries and harmonic vibrational frequencies have been calculated using MP2 theory and quadruple-ζ quality basis sets. Dissociation energies for the loss of the rare gas atom have been calculated at these optimized geometries using coupled cluster with single and double excitations and perturbative triples, CCSD(T)theory, extrapolating interaction energies to the basis set limit. Comparisons are made between the present data and the previously obtained helium results, as well as to those ofmore » the bare HM{sup +} molecules; furthermore, comparisons are made to the related M{sup +}–RG and M{sup 2+}–RG complexes. Partial atomic charge analyses have also been undertaken, and these used to test a simple charge-induced dipole model. Molecular orbital diagrams are presented together with contour plots of the natural orbitals from the quadratic configuration with single and double excitations (QCISD) density. The conclusion is that the majority of these complexes are physically bound, with very little sharing of electron density; however, for M = Be, and to a lesser extent M = Mg, some evidence for chemical effects is seen in HM{sup +}–RG complexes involving RG atoms with the higher atomic numbers.« less

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

Jacobian projection reduced-order models for dynamic systems with contact nonlinearities

NASA Astrophysics Data System (ADS)

Gastaldi, Chiara; Zucca, Stefano; Epureanu, Bogdan I.

2018-02-01

In structural dynamics, the prediction of the response of systems with localized nonlinearities, such as friction dampers, is of particular interest. This task becomes especially cumbersome when high-resolution finite element models are used. While state-of-the-art techniques such as Craig-Bampton component mode synthesis are employed to generate reduced order models, the interface (nonlinear) degrees of freedom must still be solved in-full. For this reason, a new generation of specialized techniques capable of reducing linear and nonlinear degrees of freedom alike is emerging. This paper proposes a new technique that exploits spatial correlations in the dynamics to compute a reduction basis. The basis is composed of a set of vectors obtained using the Jacobian of partial derivatives of the contact forces with respect to nodal displacements. These basis vectors correspond to specifically chosen boundary conditions at the contacts over one cycle of vibration. The technique is shown to be effective in the reduction of several models studied using multiple harmonics with a coupled static solution. In addition, this paper addresses another challenge common to all reduction techniques: it presents and validates a novel a posteriori error estimate capable of evaluating the quality of the reduced-order solution without involving a comparison with the full-order solution.

Basis set limit and systematic errors in local-orbital based all-electron DFT

NASA Astrophysics Data System (ADS)

Blum, Volker; Behler, Jörg; Gehrke, Ralf; Reuter, Karsten; Scheffler, Matthias

2006-03-01

With the advent of efficient integration schemes,^1,2 numeric atom-centered orbitals (NAO's) are an attractive basis choice in practical density functional theory (DFT) calculations of nanostructured systems (surfaces, clusters, molecules). Though all-electron, the efficiency of practical implementations promises to be on par with the best plane-wave pseudopotential codes, while having a noticeably higher accuracy if required: Minimal-sized effective tight-binding like calculations and chemically accurate all-electron calculations are both possible within the same framework; non-periodic and periodic systems can be treated on equal footing; and the localized nature of the basis allows in principle for O(N)-like scaling. However, converging an observable with respect to the basis set is less straightforward than with competing systematic basis choices (e.g., plane waves). We here investigate the basis set limit of optimized NAO basis sets in all-electron calculations, using as examples small molecules and clusters (N2, Cu2, Cu4, Cu10). meV-level total energy convergence is possible using <=50 basis functions per atom in all cases. We also find a clear correlation between the errors which arise from underconverged basis sets, and the system geometry (interatomic distance). ^1 B. Delley, J. Chem. Phys. 92, 508 (1990), ^2 J.M. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002).

pyGIMLi: An open-source library for modelling and inversion in geophysics

NASA Astrophysics Data System (ADS)

Rücker, Carsten; Günther, Thomas; Wagner, Florian M.

2017-12-01

Many tasks in applied geosciences cannot be solved by single measurements, but require the integration of geophysical, geotechnical and hydrological methods. Numerical simulation techniques are essential both for planning and interpretation, as well as for the process understanding of modern geophysical methods. These trends encourage open, simple, and modern software architectures aiming at a uniform interface for interdisciplinary and flexible modelling and inversion approaches. We present pyGIMLi (Python Library for Inversion and Modelling in Geophysics), an open-source framework that provides tools for modelling and inversion of various geophysical but also hydrological methods. The modelling component supplies discretization management and the numerical basis for finite-element and finite-volume solvers in 1D, 2D and 3D on arbitrarily structured meshes. The generalized inversion framework solves the minimization problem with a Gauss-Newton algorithm for any physical forward operator and provides opportunities for uncertainty and resolution analyses. More general requirements, such as flexible regularization strategies, time-lapse processing and different sorts of coupling individual methods are provided independently of the actual methods used. The usage of pyGIMLi is first demonstrated by solving the steady-state heat equation, followed by a demonstration of more complex capabilities for the combination of different geophysical data sets. A fully coupled hydrogeophysical inversion of electrical resistivity tomography (ERT) data of a simulated tracer experiment is presented that allows to directly reconstruct the underlying hydraulic conductivity distribution of the aquifer. Another example demonstrates the improvement of jointly inverting ERT and ultrasonic data with respect to saturation by a new approach that incorporates petrophysical relations in the inversion. Potential applications of the presented framework are manifold and include time-lapse, constrained, joint, and coupled inversions of various geophysical and hydrological data sets.

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

PubMed Central

Send, Robert; Kaila, Ville R. I.; Sundholm, Dage

2011-01-01

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV . By using a RVS energy threshold of 50 eV , the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2∕TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics∕molecular mechanics separation schemes. PMID:21663351

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems.

PubMed

Send, Robert; Kaila, Ville R I; Sundholm, Dage

2011-06-07

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes. © 2011 American Institute of Physics

Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

2017-05-01

This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Benchmark of Ab Initio Bethe-Salpeter Equation Approach with Numeric Atom-Centered Orbitals

NASA Astrophysics Data System (ADS)

Liu, Chi; Kloppenburg, Jan; Kanai, Yosuke; Blum, Volker

The Bethe-Salpeter equation (BSE) approach based on the GW approximation has been shown to be successful for optical spectra prediction of solids and recently also for small molecules. We here present an all-electron implementation of the BSE using numeric atom-centered orbital (NAO) basis sets. In this work, we present benchmark of BSE implemented in FHI-aims for low-lying excitation energies for a set of small organic molecules, the well-known Thiel's set. The difference between our implementation (using an analytic continuation of the GW self-energy on the real axis) and the results generated by a fully frequency dependent GW treatment on the real axis is on the order of 0.07 eV for the benchmark molecular set. We study the convergence behavior to the complete basis set limit for excitation spectra, using a group of valence correlation consistent NAO basis sets (NAO-VCC-nZ), as well as for standard NAO basis sets for ground state DFT with extended augmentation functions (NAO+aug). The BSE results and convergence behavior are compared to linear-response time-dependent DFT, where excellent numerical convergence is shown for NAO+aug basis sets.

Kinetic balance and variational bounds failure in the solution of the Dirac equation in a finite Gaussian basis set

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Faegri, Knut, Jr.

1990-01-01

The paper investigates bounds failure in calculations using Gaussian basis sets for the solution of the one-electron Dirac equation for the 2p1/2 state of Hg(79+). It is shown that bounds failure indicates inadequacies in the basis set, both in terms of the exponent range and the number of functions. It is also shown that overrepresentation of the small component space may lead to unphysical results. It is concluded that it is important to use matched large and small component basis sets with an adequate size and exponent range.

Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

2006-03-09

Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar + CF ₄ intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF₄potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF₄ potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation ofmore » the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar + CF₄by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.« less

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Static electric polarizabilities and first hyperpolarizabilities of molecular ions RgH + (Rg = He, Ne, Ar, Kr, Xe): ab initio study

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Antušek, Andrej; Holka, Filip; Sadlej, Joanna

2009-06-01

Extensive ab initio calculations of static electric properties of molecular ions of general formula RgH + (Rg = He, Ne, Ar, Kr, Xe) involving the finite field method and coupled cluster CCSD(T) approach have been done. The relativistic effects were taken into account by Douglas-Kroll-Hess approximation. The numerical stability and reliability of calculated values have been tested using the systematic sequence of Dunning's cc-pVXZ-DK and ANO-RCC-VQZP basis sets. The influence of ZPE and pure vibrational contribution has been discussed. The component αzz has increasing trend in RgH + while the relativistic effect on αzz leads to a small increase of this molecular parameter.

Using Density Functional Theory (DFT) for the Calculation of Atomization Energies

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.

Collisional excitation of interstellar PO(X2Π) by He: new ab initio potential energy surfaces and scattering calculations

NASA Astrophysics Data System (ADS)

Lique, François; Jiménez-Serra, Izaskun; Viti, Serena; Marinakis, Sarantos

2018-01-01

We present the first ab initio potential energy surfaces (PESs) for the PO(X2Π)-He van der Waals system. The PESs were obtained using the open-shell partially spin-restricted coupled cluster approach with single, double and perturbative triple excitations [UCCSD(T)]. The augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) basis set was employed supplemented by mid-bond functions. Integral and differential cross sections for the rotational excitation in PO-He collisions were calculated using the new PES and compared with results in similar systems. Finally, our work presents the first hyperfine-resolved cross sections for this system that are needed for accurate modelling in astrophysical environments.

VizieR Online Data Catalog: Protonated oxirane characterization (Puzzarini+, 2014)

NASA Astrophysics Data System (ADS)

Puzzarini, C.; Ali, A.; Biczysko, M.; Barone, V.

2017-04-01

The coupled-cluster (CC) singles and doubles approximation augmented by a perturbative treatment of triple excitations (CCSD(T); Raghavachari et al., 1989, ChPhL, 157, 479) was employed in molecular structure and anharmonic force-field calculations. Harmonic force fields were also computed using the less expensive and less accurate second-order Moller-Plesset perturbation theory (MP2; Moller & Plesset, 1934, PhRv, 46, 618). CCSD(T) and MP2 calculations were carried out in conjunction with the correlation-consistent basis sets, (aug)-cc-p(C)VnZ (n = T, Q) (Dunning, 1989, JChPh, 90, 1007; Kendall et al., 1992, JChPh, 96, 6796; Woon & Dunning, 1995, JChPh, 103, 4572), with the quantum-chemical CFour program package employed throughout. (4 data files).

The Molecular Structure of cis-FONO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Rice, Julia E.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

The 129Xe nuclear shielding surfaces for Xe interacting with linear molecules CO2, N2, and CO

NASA Astrophysics Data System (ADS)

de Dios, Angel C.; Jameson, Cynthia J.

1997-09-01

We have calculated the intermolecular nuclear magnetic shielding surfaces for 129Xe in the systems Xe-CO2, Xe-N2, and Xe-CO using a gauge-invariant ab initio method at the coupled Hartree-Fock level with gauge-including atomic orbitals (GIAO). Implementation of a large basis set (240 basis functions) on the Xe gives very small counterpoise corrections which indicates that the basis set superposition errors in the calculated shielding values are negligible. These are the first intermolecular shielding surfaces for Xe-molecule systems. The surfaces are highly anisotropic and can be described adequately by a sum of inverse even powers of the distance with explicit angle dependence in the coefficients expressed by Legendre polynomials P2n(cos θ), n=0-3, for Xe-CO2 and Xe-N2. The Xe-CO shielding surface is well described by a similar functional form, except that Pn(cos θ), n=0-4 were used. When averaged over the anisotropic potential function these shielding surfaces provide the second virial coefficient of the nuclear magnetic resonance (NMR) chemical shift observed in gas mixtures. The energies from the self-consistent field (SCF) calculations were used to construct potential surfaces, using a damped dispersion form. These potential functions are compared with existing potentials in their predictions of the second virial coefficients of NMR shielding, the pressure virial coefficients, the density coefficient of the mean-square torque from infrared absorption, and the rotational constants and other average properties of the van der Waals complexes. Average properties of the van der Waals complexes were obtained by quantum diffusion Monte Carlo solutions of the vibrational motion using the various potentials and compared with experiment.

A coupled-mode theory for multiwaveguide systems satisfying the reciprocity theorem and power conservation

NASA Technical Reports Server (NTRS)

Chuang, Shun-Lien

1987-01-01

Two sets of coupled-mode equations for multiwaveguide systems are derived using a generalized reciprocity relation; one set for a lossless system, and the other for a general lossy or lossless system. The second set of equations also reduces to those of the first set in the lossless case under the condition that the transverse field components are chosen to be real. Analytical relations between the coupling coefficients are shown and applied to the coupling of mode equations. It is shown analytically that these results satisfy exactly both the reciprocity theorem and power conservation. New orthogonal relations between the supermodes are derived in matrix form, with the overlap integrals taken into account.

Convergence of the Light-Front Coupled-Cluster Method in Scalar Yukawa Theory

NASA Astrophysics Data System (ADS)

Usselman, Austin

We use Fock-state expansions and the Light-Front Coupled-Cluster (LFCC) method to study mass eigenvalue problems in quantum field theory. Specifically, we study convergence of the method in scalar Yukawa theory. In this theory, a single charged particle is surrounded by a cloud of neutral particles. The charged particle can create or annihilate neutral particles, causing the n-particle state to depend on the n + 1 and n - 1-particle state. Fock state expansion leads to an infinite set of coupled equations where truncation is required. The wave functions for the particle states are expanded in a basis of symmetric polynomials and a generalized eigenvalue problem is solved for the mass eigenvalue. The mass eigenvalue problem is solved for multiple values for the coupling strength while the number of particle states and polynomial basis order are increased. Convergence of the mass eigenvalue solutions is then obtained. Three mass ratios between the charged particle and neutral particles were studied. This includes a massive charged particle, equal masses and massive neutral particles. Relative probability between states can also be explored for more detailed understanding of the process of convergence with respect to the number of Fock sectors. The reliance on higher order particle states depended on how large the mass of the charge particle was. The higher the mass of the charged particle, the more the system depended on higher order particle states. The LFCC method solves this same mass eigenvalue problem using an exponential operator. This exponential operator can then be truncated instead to form a finite system of equations that can be solved using a built in system solver provided in most computational environments, such as MatLab and Mathematica. First approximation in the LFCC method allows for only one particle to be created by the new operator and proved to be not powerful enough to match the Fock state expansion. The second order approximation allowed one and two particles to be created by the new operator and converged to the Fock state expansion results. This showed the LFCC method to be a reliable replacement method for solving quantum field theory problems.

An integral-factorized implementation of the driven similarity renormalization group second-order multireference perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hannon, Kevin P.; Li, Chenyang; Evangelista, Francesco A., E-mail: francesco.evangelista@emory.edu

2016-05-28

We report an efficient implementation of a second-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT2) [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)]. Our implementation employs factorized two-electron integrals to avoid storage of large four-index intermediates. It also exploits the block structure of the reference density matrices to reduce the computational cost to that of second-order Møller–Plesset perturbation theory. Our new DSRG-MRPT2 implementation is benchmarked on ten naphthyne isomers using basis sets up to quintuple-ζ quality. We find that the singlet-triplet splittings (Δ{sub ST}) of the naphthyne isomers strongly depend onmore » the equilibrium structures. For a consistent set of geometries, the Δ{sub ST} values predicted by the DSRG-MRPT2 are in good agreements with those computed by the reduced multireference coupled cluster theory with singles, doubles, and perturbative triples.« less

New potential energy surface for the HCS{sup +}–He system and inelastic rate coefficients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubernet, Marie-Lise; Quintas-Sánchez, Ernesto; Tuckey, Philip

2015-07-28

A new high quality potential energy surface is calculated at a coupled-cluster single double triple level with an aug-cc-pV5Z basis set for the HCS{sup +}–He system. This potential energy surface is used in low energy quantum scattering calculations to provide a set of (de)-excitation cross sections and rate coefficients among the first 20 rotational levels of HCS{sup +} by He in the range of temperature from 5 K to 100 K. The paper discusses the impact of the new ab initio potential energy surface on the cross sections at low energy and provides a comparison with the HCO{sup +}–He system.more » The HCS{sup +}–He rate coefficients for the strongest transitions differ by factors of up to 2.5 from previous rate coefficients; thus, analysis of astrophysical spectra should be reconsidered with the new rate coefficients.« less

Development of an electronic seepage chamber for extended use in a river.

PubMed

Fritz, Brad G; Mendoza, Donaldo P; Gilmore, Tyler J

2009-01-01

Seepage chambers have been used to characterize the flux of water across the water-sediment interface in a variety of settings. In this work, an electronic seepage chamber was developed specifically for long-term use in a large river where hydraulic gradient reversals occur frequently with river-stage variations. A bidirectional electronic flowmeter coupled with a seepage chamber was used to measure temporal changes in the magnitude and direction of water flux across the water-sediment interface over an 8-week period. The specific discharge measured from the seepage chamber compared favorably with measurements of vertical hydraulic gradient and previous specific discharge calculations. This, as well as other supporting data, demonstrates the effectiveness of the electronic seepage chamber to accurately quantify water flux in two directions over a multimonth period in this setting. The ability to conduct multimonth measurements of water flux at a subhourly frequency in a river system is a critical capability for a seepage chamber in a system where hydraulic gradients change on a daily and seasonal basis.

Polarized atomic orbitals for self-consistent field electronic structure calculations

NASA Astrophysics Data System (ADS)

Lee, Michael S.; Head-Gordon, Martin

1997-12-01

We present a new self-consistent field approach which, given a large "secondary" basis set of atomic orbitals, variationally optimizes molecular orbitals in terms of a small "primary" basis set of distorted atomic orbitals, which are simultaneously optimized. If the primary basis is taken as a minimal basis, the resulting functions are termed polarized atomic orbitals (PAO's) because they are valence (or core) atomic orbitals which have distorted or polarized in an optimal way for their molecular environment. The PAO's derive their flexibility from the fact that they are formed from atom-centered linear-combinations of the larger set of secondary atomic orbitals. The variational conditions satisfied by PAO's are defined, and an iterative method for performing a PAO-SCF calculation is introduced. We compare the PAO-SCF approach against full SCF calculations for the energies, dipoles, and molecular geometries of various molecules. The PAO's are potentially useful for studying large systems that are currently intractable with larger than minimal basis sets, as well as offering potential interpretative benefits relative to calculations in extended basis sets.

Study of the charge dependence of the pion–nucleon coupling constant on the basis of data on low-energy nucleon–nucleon interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babenko, V. A.; Petrov, N. M., E-mail: pet2@ukr.net

2016-01-15

The relation between quantities that characterize the pion–nucleon and nucleon–nucleon interactions is studied with allowance for the fact that, at low energies, nuclear forces in nucleon–nucleon systems are mediated predominantly by one-pion exchange. On the basis of the values currently recommended for the low-energy parameters of the proton–proton interaction, the charged pion–nucleon coupling constant is evaluated at g{sub π}{sup 2}±/4π = 14.55(13). This value is in perfect agreement with the experimental value of g{sub π}{sup 2}±/4π = 14.52(26) found by the Uppsala Neutron Research Group. At the same time, the value obtained for the charged pion–nucleon coupling constant differs sizablymore » from the value of the pion–nucleon coupling constant for neutral pions, which is g{sub π}{sup 2} 0/4π = 13.55(13). This is indicative of a substantial charge dependence of the coupling constant.« less

Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

PubMed Central

Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

2015-01-01

The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

Tungsten Hydride Phosphorus- and Arsenic-Bearing Molecules with Double and Triple W-P and W-As Bonds.

PubMed

Andrews, Lester; Cho, Han-Gook; Fang, Zongtang; Vasiliu, Monica; Dixon, David A

2018-05-07

Laser ablation of tungsten metal provides W atoms which react with phosphine and arsine during condensation in excess argon and neon, leading to major new infrared (IR) absorptions. Annealing, UV irradiation, and deuterium substitution experiments coupled with electronic structure calculations at the density functional theory level led to the assignment of the observed IR absorptions to the E≡WH 3 and HE═WH 2 molecules for E = P and As. The potential energy surfaces for hydrogen transfer from PH 3 to the W were calculated at the coupled-cluster CCSD(T)/complete basis set level. Additional weak bands in the phosphide and arsenide W-H stretching region are assigned to the molecules with loss of H from W, E≡WH 2 . The electronic structure calculations show that the E≡WH 3 molecules have a W-E triple bond, the HE═WH 2 molecules have a W-E double bond, and the H 2 E-WH molecules have a W-E single bond. The formation of multiple E-W bonds leads to increasing stability for the isomers.

A pair natural orbital based implementation of CCSD excitation energies within the framework of linear response theory

NASA Astrophysics Data System (ADS)

Frank, Marius S.; Hättig, Christof

2018-04-01

We present a pair natural orbital (PNO)-based implementation of coupled cluster singles and doubles (CCSD) excitation energies that builds upon the previously proposed state-specific PNO approach to the excited state eigenvalue problem. We construct the excited state PNOs for each state separately in a truncated orbital specific virtual basis and use a local density-fitting approximation to achieve an at most quadratic scaling of the computational costs for the PNO construction. The earlier reported excited state PNO construction is generalized such that a smooth convergence of the results for charge transfer states is ensured for general coupled cluster methods. We investigate the accuracy of our implementation by applying it to a large and diverse test set comprising 153 singlet excitations in organic molecules. Already moderate PNO thresholds yield mean absolute errors below 0.01 eV. The performance of the implementation is investigated through the calculations on alkene chains and reveals an at most cubic cost-scaling for the CCSD iterations with the system size.

Ice Sheet Model Intercomparison Project (ISMIP6) contribution to CMIP6

PubMed Central

Nowicki, Sophie M.J.; Payne, Tony; Larour, Eric; Seroussi, Helene; Goelzer, Heiko; Lipscomb, William; Gregory, Jonathan; Abe-Ouchi, Ayako; Shepherd, Andrew

2018-01-01

Reducing the uncertainty in the past, present and future contribution of ice sheets to sea-level change requires a coordinated effort between the climate and glaciology communities. The Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6) is the primary activity within the Coupled Model Intercomparison Project – phase 6 (CMIP6) focusing on the Greenland and Antarctic Ice Sheets. In this paper, we describe the framework for ISMIP6 and its relationship to other activities within CMIP6. The ISMIP6 experimental design relies on CMIP6 climate models and includes, for the first time within CMIP, coupled ice sheet – climate models as well as standalone ice sheet models. To facilitate analysis of the multi-model ensemble and to generate a set of standard climate inputs for standalone ice sheet models, ISMIP6 defines a protocol for all variables related to ice sheets. ISMIP6 will provide a basis for investigating the feedbacks, impacts, and sea-level changes associated with dynamic ice sheets and for quantifying the uncertainty in ice-sheet-sourced global sea-level change. PMID:29697697

Coupling Between Metabolism and Compartmentalization: Vesicle Growth in the Presence of Dipeptides

NASA Technical Reports Server (NTRS)

Wei, C.; Pohorille, A.

2017-01-01

A fundamental unresolved question in studies on the origin of life is: how different, ubiquitous protocellular functions begun to work in concert setting the stage for Darwinian evolution of nascent life? From this perspective, of particular significance is coupling between growth of protocellular compartments and the encapsulated, primordial metabolism, which is one of the focal topics of the current ISSOL meeting. Specifically, growth and division of cells facilitated by the products of a metabolic reaction would confer an evolutionary advantage on protocells encapsulating this reaction, as their population would increase at the expense of other protocells. Along these lines, Adamala and Szostak have recently demonstrated that a dipeptide captured inside fatty acid vesicles catalyzes the formation of other dipeptides from activated monomers. Some of the newly synthesized dipeptides, in turn, are capable to promote competitive growth of vesicles in the presence of fatty acid micelles. As vesicles become larger, they adapt filamentous shape, which has been shown to promote their division. On the basis of computer simulations, we provide a molecularly detailed explanation of this process and draw conclusions about its generality.

Fault zone structure determined through the analysis of earthquake arrival times

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michelini, A.

1991-10-01

This thesis develops and applies a technique for the simultaneous determination of P and S wave velocity models and hypocenters from a set of arrival times. The velocity models are parameterized in terms of cubic B-splines basis functions which permit the retrieval of smooth models that can be used directly for generation of synthetic seismograms using the ray method. In addition, this type of smoothing limits the rise of instabilities related to the poor resolving power of the data. V{sub P}/V{sub S} ratios calculated from P and S models display generally instabilities related to the different ray-coverages of compressional andmore » shear waves. However, V{sub P}/V{sub S} ratios are important for correct identification of rock types and this study introduces a new methodology based on adding some coupling (i.e., proportionality) between P and S models which stabilizes the V{sub P}/V{sub S} models around some average preset value determined from the data. Tests of the technique with synthetic data show that this additional coupling regularizes effectively the resulting models.« less

Fault zone structure determined through the analysis of earthquake arrival times

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michelini, Alberto

1991-10-01

This thesis develops and applies a technique for the simultaneous determination of P and S wave velocity models and hypocenters from a set of arrival times. The velocity models are parameterized in terms of cubic B-splines basis functions which permit the retrieval of smooth models that can be used directly for generation of synthetic seismograms using the ray method. In addition, this type of smoothing limits the rise of instabilities related to the poor resolving power of the data. V P/V S ratios calculated from P and S models display generally instabilities related to the different ray-coverages of compressional andmore » shear waves. However, V P/V S ratios are important for correct identification of rock types and this study introduces a new methodology based on adding some coupling (i.e., proportionality) between P and S models which stabilizes the V P/V S models around some average preset value determined from the data. Tests of the technique with synthetic data show that this additional coupling regularizes effectively the resulting models.« less

Theoretical studies of the electronic spectrum of tellurium monosulfide.

PubMed

Chattopadhyaya, Surya; Nath, Abhijit; Das, Kalyan Kumar

2013-08-01

Ab initio based multireference singles and doubles configuration interaction (MRDCI) study including spin-orbit coupling is carried out to explore the electronic structure and spectroscopic properties of tellurium monosulfide (TeS) molecule by employing relativistic effective core potentials (RECP) and suitable Gaussian basis sets of the constituent atoms. Potential energy curves correlating with the lowest and second dissociation limit are constructed and spectroscopic constants (T(e), r(e), and ω(e)) of several low-lying bound Λ-S electronic states up to 3.68 eV of energy are computed. The binding energies and electric dipole moments (μ(e)) of the ground and the low-lying excited Λ-S states are also computed. The effects of the spin-orbit coupling on the electronic spectrum of the species are studied in details and compared with the available data. The transition probabilities of some dipole-allowed and spin-forbidden transitions are computed and radiative lifetimes of some excited states at lowest vibrational level are estimated from the transition probability data. Copyright © 2013 Elsevier B.V. All rights reserved.

Rotationally inelastic scattering of PN by para-H2(j = 0) at low/moderate temperature

NASA Astrophysics Data System (ADS)

Najar, F.; Naouai, M.; Hanini, H. El; Jaidane, N.

2017-12-01

Calculation of the collisional rate coefficients with the most abundant species has been motivated by the desire to interpret observations of molecules in the interstellar medium. This paper will be concerned with rotational excitation of the phosphorus nitride (PN) molecule in its ground vibrational state by collisions with para-H2(j = 0). Ab intio potential energy surface for the PN-H2 van der Waals system, considering both molecules as rigid rotors, was computed via CCSD(T) method using the aug-cc-pVTZ basis sets, augmented by a bond functions placed at midway between the PN and H2 centres of mass. Cross-sections among the 40 first rotational levels of PN in collisions with para-H2(j = 0) were obtained using close coupling and coupled states calculations, for total energies up to 3000 cm- 1. Rate coefficients are presented for temperatures ranging from 5 to 300 K. A strong propensity favouring even Δj transitions is found. The comparison of the new PN-H2 rate coefficients with previously calculated PN-He rate coefficients shows that significant differences exist.

Ice Sheet Model Intercomparison Project (ISMIP6) Contribution to CMIP6

NASA Technical Reports Server (NTRS)

Nowicki, Sophie M. J.; Payne, Tony; Larour, Eric; Seroussi, Helene; Goelzer, Heiko; Lipscomb, William; Gregory, Jonathan; Abe-Ouchi, Ayako; Shepherd, Andrew

2016-01-01

Reducing the uncertainty in the past, present, and future contribution of ice sheets to sea-level change requires a coordinated effort between the climate and glaciology communities. The Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6) is the primary activity within the Coupled Model Intercomparison Project phase 6 (CMIP6) focusing on the Greenland and Antarctic ice sheets. In this paper, we describe the framework for ISMIP6 and its relationship with other activities within CMIP6. The ISMIP6 experimental design relies on CMIP6 climate models and includes, for the first time within CMIP, coupled ice-sheetclimate models as well as standalone ice-sheet models. To facilitate analysis of the multi-model ensemble and to generate a set of standard climate inputs for standalone ice-sheet models, ISMIP6 defines a protocol for all variables related to ice sheets. ISMIP6 will provide a basis for investigating the feedbacks, impacts, and sea-level changes associated with dynamic ice sheets and for quantifying the uncertainty in ice-sheet-sourced global sea-level change.

Modeling L2,3-Edge X-ray Absorption Spectroscopy with Real-Time Exact Two-Component Relativistic Time-Dependent Density Functional Theory.

PubMed

Kasper, Joseph M; Lestrange, Patrick J; Stetina, Torin F; Li, Xiaosong

2018-04-10

X-ray absorption spectroscopy is a powerful technique to probe local electronic and nuclear structure. There has been extensive theoretical work modeling K-edge spectra from first principles. However, modeling L-edge spectra directly with density functional theory poses a unique challenge requiring further study. Spin-orbit coupling must be included in the model, and a noncollinear density functional theory is required. Using the real-time exact two-component method, we are able to variationally include one-electron spin-orbit coupling terms when calculating the absorption spectrum. The abilities of different basis sets and density functionals to model spectra for both closed- and open-shell systems are investigated using SiCl 4 and three transition metal complexes, TiCl 4 , CrO 2 Cl 2 , and [FeCl 6 ] 3- . Although we are working in the real-time framework, individual molecular orbital transitions can still be recovered by projecting the density onto the ground state molecular orbital space and separating contributions to the time evolving dipole moment.

String Scale Gauge Coupling Unification with Vector-Like Exotics and Noncanonical U(1)Y Normalization

NASA Astrophysics Data System (ADS)

Barger, V.; Jiang, Jing; Langacker, Paul; Li, Tianjun

We use a new approach to study string scale gauge coupling unification systematically, allowing both the possibility of noncanonical U(1)Y normalization and the existence of vector-like particles whose quantum numbers are the same as those of the Standard Model (SM) fermions and their Hermitian conjugates and the SM adjoint particles. We first give all the independent sets (Yi) of particles that can be employed to achieve SU(3)C and SU(2)L string scale gauge coupling unification and calculate their masses. Second, for a noncanonical U(1)Y normalization, we obtain string scale SU(3)C ×SU(2)L ×U(1)Y gauge coupling unification by choosing suitable U(1)Y normalizations for each of the Yi sets. Alternatively, for the canonical U(1)Y normalization, we achieve string scale gauge coupling unification by considering suitable combinations of the Yi sets or by introducing additional independent sets (Zi), that do not affect the SU(3)C ×SU(2)L unification at tree level, and then choosing suitable combinations, one from the Yi sets and one from the Zi sets. We also briefly discuss string scale gauge coupling unification in models with higher Kac-Moody levels for SU(2)L or SU(3)C.

Renormalization of Collective Modes in Large-Scale Neural Dynamics

NASA Astrophysics Data System (ADS)

Moirogiannis, Dimitrios; Piro, Oreste; Magnasco, Marcelo O.

2017-05-01

The bulk of studies of coupled oscillators use, as is appropriate in Physics, a global coupling constant controlling all individual interactions. However, because as the coupling is increased, the number of relevant degrees of freedom also increases, this setting conflates the strength of the coupling with the effective dimensionality of the resulting dynamics. We propose a coupling more appropriate to neural circuitry, where synaptic strengths are under biological, activity-dependent control and where the coupling strength and the dimensionality can be controlled separately. Here we study a set of N→ ∞ strongly- and nonsymmetrically-coupled, dissipative, powered, rotational dynamical systems, and derive the equations of motion of the reduced system for dimensions 2 and 4. Our setting highlights the statistical structure of the eigenvectors of the connectivity matrix as the fundamental determinant of collective behavior, inheriting from this structure symmetries and singularities absent from the original microscopic dynamics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicholson, J. C.

Performance metrics for evaluating commercial fixatives are often not readily available for important parameters that must be considered per the facility safety basis and the facility Basis for Interim Operations (BIO). One such parameter is the behavior of such materials in varied, “non-ideal” conditions where ideal is defined as 75 °F, 40% RH. Coupled with the inherent flammable nature of the fixative materials that can act to propagate flame along surfaces that are otherwise fireproof (concrete, sheet metal), much is left unknown when considering the safety basis implications for introducing these materials into nuclear facilities. Through SRNL’s efforts, three (3)more » fixatives, one (1) decontamination gel, and six (6) intumescent coatings were examined for their responses to environmental conditions to determine whether these materials were impervious to non-nominal temperatures and humidities that may be found in nuclear facilities. Characteristics that were examined included set-to-touch time, dust free time, and adhesion testing of the fully cured compounds. Of these ten materials, three were two-part epoxy materials while the other seven consisted of only one constituent. The results show that the epoxies tested are unable to cure in sub-freezing temperatures, with the low temperatures inhibiting crosslinking to a very significant degree. These efforts show significant inhibiting of performance for non-nominal environmental conditions, something that must be addressed both in the decision process for a fixative material to apply and per the safety basis to ensure the accurate flammability and material at risk is calculated.« less

Automated large-scale purification of a G protein-coupled receptor for neurotensin.

PubMed

White, Jim F; Trinh, Loc B; Shiloach, Joseph; Grisshammer, Reinhard

2004-04-30

Structure determination of integral membrane proteins requires milligram amounts of purified, functional protein on a regular basis. Here, we describe a protocol for the purification of a G protein-coupled neurotensin receptor fusion protein at the 3-mg or 10-mg level using immobilized metal affinity chromatography and a neurotensin column in a fully automated mode. Fermentation at a 200-l scale of Escherichia coli expressing functional receptors provides the material needed to feed into the purification routine. Constructs with tobacco etch virus protease recognition sites at either end of the receptor allow the isolation of neurotensin receptor devoid of its fusion partners. The presented expression and purification procedures are simple and robust, and provide the basis for crystallization experiments of receptors on a routine basis.

Zombie states for description of structure and dynamics of multi-electron systems

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.

2018-05-01

Canonical Coherent States (CSs) of Harmonic Oscillator have been extensively used as a basis in a number of computational methods of quantum dynamics. However, generalising such techniques for fermionic systems is difficult because Fermionic Coherent States (FCSs) require complicated algebra of Grassmann numbers not well suited for numerical calculations. This paper introduces a coherent antisymmetrised superposition of "dead" and "alive" electronic states called here Zombie State (ZS), which can be used in a manner of FCSs but without Grassmann algebra. Instead, for Zombie States, a very simple sign-changing rule is used in the definition of creation and annihilation operators. Then, calculation of electronic structure Hamiltonian matrix elements between two ZSs becomes very simple and a straightforward technique for time propagation of fermionic wave functions can be developed. By analogy with the existing methods based on Canonical Coherent States of Harmonic Oscillator, fermionic wave functions can be propagated using a set of randomly selected Zombie States as a basis. As a proof of principles, the proposed Coupled Zombie States approach is tested on a simple example showing that the technique is exact.

Mode synthesizing atomic force microscopy and mode-synthesizing sensing

DOEpatents

Passian, Ali; Thundat, Thomas George; Tetard, Laurene

2013-05-17

A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

Mode-synthesizing atomic force microscopy and mode-synthesizing sensing

DOEpatents

Passain, Ali; Thundat, Thomas George; Tetard, Laurene

2014-07-22

A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

Code of Federal Regulations, 2010 CFR

2010-10-01

... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE... BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a fee schedule basis...

The Ising model coupled to 2d orders

NASA Astrophysics Data System (ADS)

Glaser, Lisa

2018-04-01

In this article we make first steps in coupling matter to causal set theory in the path integral. We explore the case of the Ising model coupled to the 2d discrete Einstein Hilbert action, restricted to the 2d orders. We probe the phase diagram in terms of the Wick rotation parameter β and the Ising coupling j and find that the matter and the causal sets together give rise to an interesting phase structure. The couplings give rise to five different phases. The causal sets take on random or crystalline characteristics as described in Surya (2012 Class. Quantum Grav. 29 132001) and the Ising model can be correlated or uncorrelated on the random orders and correlated, uncorrelated or anti-correlated on the crystalline orders. We find that at least one new phase transition arises, in which the Ising spins push the causal set into the crystalline phase.

Evaluation of an effective multifaceted implementation strategy for elective single-embryo transfer after in vitro fertilization.

PubMed

Kreuwel, I A M; van Peperstraten, A M; Hulscher, M E J L; Kremer, J A M; Grol, R P T M; Nelen, W L D M; Hermens, R P M G

2013-02-01

What is the relationship between the rate of elective single-embryo transfer (eSET) and couples' exposure to different elements of a multifaceted implementation strategy? Additional elements in a multifaceted implementation strategy do not result in an increased eSET rate. A multifaceted eSET implementation strategy with four different elements is effective in increasing the eSET rate by 11%. It is unclear whether every strategy element contributes equally to the strategy's effectiveness. An observational study was performed among 222 subfertile couples included in a previously performed randomized controlled trial. Of the 222 subfertile couples included, 109 couples received the implementation strategy and 113 couples received standard IVF care. A multivariate regression analysis assessed the effectiveness of four different strategy elements on the decision about the number embryos to be transferred. Questionnaires evaluated the experiences of couples with the different elements. Of the couples who received the implementation strategy, almost 50% (52/109) were exposed to all the four elements of the strategy. The remaining 57 couples who received two or three elements of the strategy could be divided into two further classes of exposure. Our analysis demonstrated that additional elements do not result in an increased eSET rate. In addition to the physician's advice, couples rated a decision aid and a counselling session as more important for their decision to transfer one or two embryos, compared with a phone call and a reimbursement offer (P < 0.001). The differences in eSET rate between exposure groups failed to reach significance, probably because of the small numbers of couples in each exposure group. Adding more elements to an implementation strategy does not always result in an increased effectiveness, which is in concordance with recent literature. This in-depth evaluation of a multifaceted intervention strategy could therefore help to modify strategies, by making them more effective and less expensive.

A Bistable Microelectronic Circuit for Sensing Extremely Low Electric Field

DTIC Science & Technology

2010-01-01

potential system describing the ferromagnetic ma- terials employed in the fluxgate magnetometers .1 To give a clearer picture of the separations between...this behavior in a specific prototype system comprised of three unidirectionally coupled ferromagnetic cores, the basis of a coupled core fluxgate ... magnetometer . Another prototypical quartic poten- tial based system of coupled overdamped Duffing elements has been applied to describe the dynamics

Projected Hybrid Orbitals: A General QM/MM Method

PubMed Central

2015-01-01

A projected hybrid orbital (PHO) method was described to model the covalent boundary in a hybrid quantum mechanical and molecular mechanical (QM/MM) system. The PHO approach can be used in ab initio wave function theory and in density functional theory with any basis set without introducing system-dependent parameters. In this method, a secondary basis set on the boundary atom is introduced to formulate a set of hybrid atomic orbtials. The primary basis set on the boundary atom used for the QM subsystem is projected onto the secondary basis to yield a representation that provides a good approximation to the electron-withdrawing power of the primary basis set to balance electronic interactions between QM and MM subsystems. The PHO method has been tested on a range of molecules and properties. Comparison with results obtained from QM calculations on the entire system shows that the present PHO method is a robust and balanced QM/MM scheme that preserves the structural and electronic properties of the QM region. PMID:25317748

Electromagnetic versus electrical coupling of personal frequency modulation (FM) receivers to cochlear implant sound processors.

PubMed

Schafer, Erin C; Romine, Denise; Musgrave, Elizabeth; Momin, Sadaf; Huynh, Christy

2013-01-01

Previous research has suggested that electrically coupled frequency modulation (FM) systems substantially improved speech-recognition performance in noise in individuals with cochlear implants (CIs). However, there is limited evidence to support the use of electromagnetically coupled (neck loop) FM receivers with contemporary CI sound processors containing telecoils. The primary goal of this study was to compare speech-recognition performance in noise and subjective ratings of adolescents and adults using one of three contemporary CI sound processors coupled to electromagnetically and electrically coupled FM receivers from Oticon. A repeated-measures design was used to compare speech-recognition performance in noise and subjective ratings without and with the FM systems across three test sessions (Experiment 1) and to compare performance at different FM-gain settings (Experiment 2). Descriptive statistics were used in Experiment 3 to describe output differences measured through a CI sound processor. Experiment 1 included nine adolescents or adults with unilateral or bilateral Advanced Bionics Harmony (n = 3), Cochlear Nucleus 5 (n = 3), and MED-EL OPUS 2 (n = 3) CI sound processors. In Experiment 2, seven of the original nine participants were tested. In Experiment 3, electroacoustic output was measured from a Nucleus 5 sound processor when coupled to the electromagnetically coupled Oticon Arc neck loop and electrically coupled Oticon R2. In Experiment 1, participants completed a field trial with each FM receiver and three test sessions that included speech-recognition performance in noise and a subjective rating scale. In Experiment 2, participants were tested in three receiver-gain conditions. Results in both experiments were analyzed using repeated-measures analysis of variance. Experiment 3 involved electroacoustic-test measures to determine the monitor-earphone output of the CI alone and CI coupled to the two FM receivers. The results in Experiment 1 suggested that both FM receivers provided significantly better speech-recognition performance in noise than the CI alone; however, the electromagnetically coupled receiver provided significantly better speech-recognition performance in noise and better ratings in some situations than the electrically coupled receiver when set to the same gain. In Experiment 2, the primary analysis suggested significantly better speech-recognition performance in noise for the neck-loop versus electrically coupled receiver, but a second analysis, using the best performance across gain settings for each device, revealed no significant differences between the two FM receivers. Experiment 3 revealed monitor-earphone output differences in the Nucleus 5 sound processor for the two FM receivers when set to the +8 setting used in Experiment 1 but equal output when the electrically coupled device was set to a +16 gain setting and the electromagnetically coupled device was set to the +8 gain setting. Individuals with contemporary sound processors may show more favorable speech-recognition performance in noise electromagnetically coupled FM systems (i.e., Oticon Arc), which is most likely related to the input processing and signal processing pathway within the CI sound processor for direct input versus telecoil input. Further research is warranted to replicate these findings with a larger sample size and to develop and validate a more objective approach to fitting FM systems to CI sound processors. American Academy of Audiology.

Theoretical study of the magnetic exchange coupling behavior substituting Cr(III) with Mo(III) in cyano-bridged transition metal complexes

NASA Astrophysics Data System (ADS)

Zhang, Yi-Quan; Luo, Cheng-Lin

Molecular magnetism in a series of cyano-bridged first and second transition metal complexes has been investigated using density functional theory (DFT) combined with the broken-symmetry (BS) approach. Several exchange-correlation (XC) functionals in the ADF package were used to investigate complexes I [-(Me3tacn)2(cyclam)NiMo2(CN)6]2+, II [-(Me3tacn)2(cyclam)Ni-Cr2(CN)6]2+, III [(Me3tacn)6MnMo6(CN)18]2+, and IV [(Me3tacn)6MnCr6(CN)18]2+ (Me3tacn = N,N?,N‴-trimethyl-1,4,7-triazacyclononane). For models A (the molded structure of complex I) and B (the modeled structure of complex II), all the XCs given qualitatively reasonable results and predict ferromagnetic coupling character between M (M = MoIII for A or CrIII for B) and NiII in coincidence with the experimental results (see Tables and ). The calculated using Operdew, OPBE, O3LYP, and B3LYP functionals and experimental J values show that substituting CrIII with MoIII will enhance the ferromagnetic exchange coupling interactions. But VWN, PW91, PBE, VSXC, and tau-HCTH functionals have no way to differentiate the relative strength of the intramolecular magnetic exchange coupling interactions of A and B correctly. For models C (the modeled structure of complex III) and D (the modeled structure of complex IV), all the XCs in ADF and B3LYP in Gaussian 03 with several basis sets show that substituting CrIII with MoIII will enhance the antiferromagnetic exchange coupling interactions. From the above calculations, the substitution of CrIII by MoIII will enhance the magnetic coupling interactions, whether the magnetic coupling interactions are ferro- or antiferromagnetic. Moreover, Kahn's model was applied to investigate the above facts.

A novel Gaussian-Sinc mixed basis set for electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.

2015-08-14

A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definablemore » and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.« less

Computation of indirect nuclear spin-spin couplings with reduced complexity in pure and hybrid density functional approximations.

PubMed

Luenser, Arne; Kussmann, Jörg; Ochsenfeld, Christian

2016-09-28

We present a (sub)linear-scaling algorithm to determine indirect nuclear spin-spin coupling constants at the Hartree-Fock and Kohn-Sham density functional levels of theory. Employing efficient integral algorithms and sparse algebra routines, an overall (sub)linear scaling behavior can be obtained for systems with a non-vanishing HOMO-LUMO gap. Calculations on systems with over 1000 atoms and 20 000 basis functions illustrate the performance and accuracy of our reference implementation. Specifically, we demonstrate that linear algebra dominates the runtime of conventional algorithms for 10 000 basis functions and above. Attainable speedups of our method exceed 6 × in total runtime and 10 × in the linear algebra steps for the tested systems. Furthermore, a convergence study of spin-spin couplings of an aminopyrazole peptide upon inclusion of the water environment is presented: using the new method it is shown that large solvent spheres are necessary to converge spin-spin coupling values.

Visualization of arrestin recruitment by a G Protein-Coupled Receptor

PubMed Central

Reis, Rosana I.; Huang, Li-Yin; Tripathi-Shukla, Prachi; Qian, Jiang; Li, Sheng; Blanc, Adi; Oleskie, Austin N.; Dosey, Anne M.; Su, Min; Liang, Cui-Rong; Gu, Ling-Ling; Shan, Jin-Ming; Chen, Xin; Hanna, Rachel; Choi, Minjung; Yao, Xiao Jie; Klink, Bjoern U.; Kahsai, Alem W.; Sidhu, Sachdev S.; Koide, Shohei; Penczek, Pawel A.; Kossiakoff, Anthony A.; Jr, Virgil L. Woods; Kobilka, Brian K.; Skiniotis, Georgios; Lefkowitz, Robert J.

2014-01-01

G Protein Coupled Receptors (GPCRs) are critically regulated by β-arrestins (βarrs), which not only desensitize G protein signaling but also initiate a G protein independent wave of signaling1-5. A recent surge of structural data on a number of GPCRs, including the β2 adrenergic receptor (β2AR)-G protein complex, has provided novel insights into the structural basis of receptor activation6-11. Lacking however has been complementary information on recruitment of βarrs to activated GPCRs primarily due to challenges in obtaining stable receptor-βarr complexes for structural studies. Here, we devised a strategy for forming and purifying a functional β2AR-βarr1 complex that allowed us to visualize its architecture by single particle negative stain electron microscopy (EM) and to characterize the interactions between β2AR and βarr1 using hydrogen-deuterium exchange mass spectrometry (HDXMS) and chemical cross-linking. EM 2D averages and 3D reconstructions reveal bimodal binding of βarr1 to the β2AR, involving two separate sets of interactions, one with the phosphorylated carboxy-terminus of the receptor and the other with its seven-transmembrane core. Areas of reduced HDX together with identification of cross-linked residues suggest engagement of the finger loop of βarr1 with the seven-transmembrane core of the receptor. In contrast, focal areas of increased HDX indicate regions of increased dynamics in both N and C domains of βarr1 when coupled to the β2AR. A molecular model of the β2AR-βarr signaling complex was made by docking activated βarr1 and β2AR crystal structures into the EM map densities with constraints provided by HDXMS and cross-linking, allowing us to obtain valuable insights into the overall architecture of a receptor-arrestin complex. The dynamic and structural information presented herein provides a framework for better understanding the basis of GPCR regulation by arrestins. PMID:25043026

Implementation details of the coupled QMR algorithm

NASA Technical Reports Server (NTRS)

Freund, Roland W.; Nachtigal, Noel M.

1992-01-01

The original quasi-minimal residual method (QMR) relies on the three-term look-ahead Lanczos process, to generate basis vectors for the underlying Krylov subspaces. However, empirical observations indicate that, in finite precision arithmetic, three-term vector recurrences are less robust than mathematically equivalent coupled two-term recurrences. Therefore, we recently proposed a new implementation of the QMR method based on a coupled two-term look-ahead Lanczos procedure. In this paper, we describe implementation details of this coupled QMR algorithm, and we present results of numerical experiments.

Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies

PubMed Central

Bernal-Casas, David; Fang, Zhongnan; Lee, Jin Hyung

2017-01-01

A large number of fMRI studies have shown that the temporal dynamics of evoked BOLD responses can be highly heterogeneous. Failing to model heterogeneous responses in statistical analysis can lead to significant errors in signal detection and characterization and alter the neurobiological interpretation. However, to date it is not clear that, out of a large number of options, which methods are robust against variability in the temporal dynamics of BOLD responses in block-design studies. Here, we used rodent optogenetic fMRI data with heterogeneous BOLD responses and simulations guided by experimental data as a means to investigate different analysis methods’ performance against heterogeneous BOLD responses. Evaluations are carried out within the general linear model (GLM) framework and consist of standard basis sets as well as independent component analysis (ICA). Analyses show that, in the presence of heterogeneous BOLD responses, conventionally used GLM with a canonical basis set leads to considerable errors in the detection and characterization of BOLD responses. Our results suggest that the 3rd and 4th order gamma basis sets, the 7th to 9th order finite impulse response (FIR) basis sets, the 5th to 9th order B-spline basis sets, and the 2nd to 5th order Fourier basis sets are optimal for good balance between detection and characterization, while the 1st order Fourier basis set (coherence analysis) used in our earlier studies show good detection capability. ICA has mostly good detection and characterization capabilities, but detects a large volume of spurious activation with the control fMRI data. PMID:27993672

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

The rotation-vibration structure of the SO 2 C 1B 2 state explained by a new internal coordinate force field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Jun; Park, G. Barratt; Field, Robert W.

A new quartic force field for the SO 2 C ~ 1B 2 state has been derived, based on high resolution data from S 16O 2 and S 18O 2. Included are eight b 2 symmetry vibrational levels of S 16O 2 reported in the first paper of this series [G. B. Park, et al., J. Chem. Phys. 144, 144311 (2016)]. Many of the experimental observables not included in the fit, such as the Franck-Condon intensities and the Coriolis-perturbed effective C rotational constants of highly anharmonic C ~ state vibrational levels, are well reproduced using our force field. Because themore » two stretching modes of the C ~ state are strongly coupled via Fermi-133 interaction, the vibrational structure of the C state is analyzed in a Fermi-system basis set, constructed explicitly in this work via partial diagonalization of the vibrational Hamiltonian. The physical significance of the Fermi-system basis is discussed in terms of semiclassical dynamics, based on study of Fermi-resonance systems by Kellman and coworkers [M. E. Kellman and L. Xiao, J. Chem. Phys. 93, 5821 (1990)]. By diagonalizing the vibrational Hamiltonian in the Fermi-system basis, the vibrational characters of all vibrational levels can be determined unambiguously. It is shown that the bending mode cannot be treated separately from the coupled stretching modes, particularly at vibrational energies of more than 2000 cm –1. Based on our force field, the structure of the Coriolis interactions in the C ~ state of SO 2 is also discussed. As a result, we identify the origin of the alternating patterns in the effective C rotational constants of levels in the vibrational progressions of the symmetry-breaking mode, ν β (which correlates with the antisymmetric stretching mode in our assignment scheme).« less

The rotation-vibration structure of the SO 2 C 1B 2 state explained by a new internal coordinate force field

DOE PAGES

Jiang, Jun; Park, G. Barratt; Field, Robert W.

2016-04-14

A new quartic force field for the SO 2 C ~ 1B 2 state has been derived, based on high resolution data from S 16O 2 and S 18O 2. Included are eight b 2 symmetry vibrational levels of S 16O 2 reported in the first paper of this series [G. B. Park, et al., J. Chem. Phys. 144, 144311 (2016)]. Many of the experimental observables not included in the fit, such as the Franck-Condon intensities and the Coriolis-perturbed effective C rotational constants of highly anharmonic C ~ state vibrational levels, are well reproduced using our force field. Because themore » two stretching modes of the C ~ state are strongly coupled via Fermi-133 interaction, the vibrational structure of the C state is analyzed in a Fermi-system basis set, constructed explicitly in this work via partial diagonalization of the vibrational Hamiltonian. The physical significance of the Fermi-system basis is discussed in terms of semiclassical dynamics, based on study of Fermi-resonance systems by Kellman and coworkers [M. E. Kellman and L. Xiao, J. Chem. Phys. 93, 5821 (1990)]. By diagonalizing the vibrational Hamiltonian in the Fermi-system basis, the vibrational characters of all vibrational levels can be determined unambiguously. It is shown that the bending mode cannot be treated separately from the coupled stretching modes, particularly at vibrational energies of more than 2000 cm –1. Based on our force field, the structure of the Coriolis interactions in the C ~ state of SO 2 is also discussed. As a result, we identify the origin of the alternating patterns in the effective C rotational constants of levels in the vibrational progressions of the symmetry-breaking mode, ν β (which correlates with the antisymmetric stretching mode in our assignment scheme).« less

Prediction of dioxin/furan incinerator emissions using low-molecular-weight volatile products of incomplete combustion.

PubMed

Lemieux, P M; Lee, C W; Ryan, J V

2000-12-01

Emissions of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDDs/Fs) from incinerators and other stationary combustion sources are of environmental concern because of the toxicity of certain PCDD/F congeners. Measurement of trace levels of PCDDs/Fs in combustor emissions is not a trivial matter. Development of one or more simple, easy-to-measure, reliable indicators of stack PCDD/F concentrations not only would enable incinerator operators to economically optimize system performance with respect to PCDD/F emissions, but could also provide a potential technique for demonstrating compliance status on a more frequent basis. This paper focuses on one approach to empirically estimate PCDD/F emissions using easy-to-measure volatile organic C2 chlorinated alkene precursors coupled with flue gas cleaning parameters. Three data sets from pilot-scale incineration experiments were examined for correlations between C2 chlorinated alkenes and PCDDs/Fs. Each data set contained one or more C2 chloroalkenes that were able to account for a statistically significant fraction of the variance in PCDD/F emissions. Variations in the vinyl chloride concentrations were able to account for the variations in the PCDD/F concentrations strongly in two of the three data sets and weakly in one of the data sets.

Prediction of Dioxin/Furan Incinerator Emissions Using Low-Molecular-Weight Volatile Products of Incomplete Combustion.

PubMed

Lemieux, P M; Lee, C W; Ryan, J V

2000-12-01

Emissions of polychlorinated dibenzo-p-dioxins and poly-chlorinated dibenzofurans (PCDDs/Fs) from incinerators and other stationary combustion sources are of environmental concern because of the toxicity of certain PCDD/F congeners. Measurement of trace levels of PCDDs/Fs in combustor emissions is not a trivial matter. Development of one or more simple, easy-to-measure, reliable indicators of stack PCDD/F concentrations not only would enable incinerator operators to economically optimize system performance with respect to PCDD/F emissions, but could also provide a potential technique for demonstrating compliance status on a more frequent basis. This paper focuses on one approach to empirically estimate PCDD/F emissions using easy-to-measure volatile organic C 2 chlorinated alk-ene precursors coupled with flue gas cleaning parameters. Three data sets from pilot-scale incineration experiments were examined for correlations between C 2 chlorinated alk-enes and PCDDs/Fs. Each data set contained one or more C 2 chloroalkenes that were able to account for a statistically significant fraction of the variance in PCDD/F emissions. Variations in the vinyl chloride concentrations were able to account for the variations in the PCDD/F concentrations strongly in two of the three data sets and weakly in one of the data sets.

Conventional and Explicitly Correlated ab Initio Benchmark Study on Water Clusters: Revision of the BEGDB and WATER27 Data Sets.

PubMed

Manna, Debashree; Kesharwani, Manoj K; Sylvetsky, Nitai; Martin, Jan M L

2017-07-11

Benchmark ab initio energies for BEGDB and WATER27 data sets have been re-examined at the MP2 and CCSD(T) levels with both conventional and explicitly correlated (F12) approaches. The basis set convergence of both conventional and explicitly correlated methods has been investigated in detail, both with and without counterpoise corrections. For the MP2 and CCSD-MP2 contributions, rapid basis set convergence observed with explicitly correlated methods is compared to conventional methods. However, conventional, orbital-based calculations are preferred for the calculation of the (T) term, since it does not benefit from F12. CCSD(F12*) converges somewhat faster with the basis set than CCSD-F12b for the CCSD-MP2 term. The performance of various DFT methods is also evaluated for the BEGDB data set, and results show that Head-Gordon's ωB97X-V and ωB97M-V functionals outperform all other DFT functionals. Counterpoise-corrected DSD-PBEP86 and raw DSD-PBEPBE-NL also perform well and are close to MP2 results. In the WATER27 data set, the anionic (deprotonated) water clusters exhibit unacceptably slow basis set convergence with the regular cc-pVnZ-F12 basis sets, which have only diffuse s and p functions. To overcome this, we have constructed modified basis sets, denoted aug-cc-pVnZ-F12 or aVnZ-F12, which have been augmented with diffuse functions on the higher angular momenta. The calculated final dissociation energies of BEGDB and WATER27 data sets are available in the Supporting Information. Our best calculated dissociation energies can be reproduced through n-body expansion, provided one pushes to the basis set and electron correlation limit for the two-body term; for the three-body term, post-MP2 contributions (particularly CCSD-MP2) are important for capturing the three-body dispersion effects. Terms beyond four-body can be adequately captured at the MP2-F12 level.

On the Use of a Mixed Gaussian/Finite-Element Basis Set for the Calculation of Rydberg States

NASA Technical Reports Server (NTRS)

Thuemmel, Helmar T.; Langhoff, Stephen (Technical Monitor)

1996-01-01

Configuration-interaction studies are reported for the Rydberg states of the helium atom using mixed Gaussian/finite-element (GTO/FE) one particle basis sets. Standard Gaussian valence basis sets are employed, like those, used extensively in quantum chemistry calculations. It is shown that the term values for high-lying Rydberg states of the helium atom can be obtained accurately (within 1 cm -1), even for a small GTO set, by augmenting the n-particle space with configurations, where orthonormalized interpolation polynomials are singly occupied.

Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roemelt, Michael, E-mail: michael.roemelt@theochem.rub.de

Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctionsmore » are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.« less

Full four-component relativistic calculations of the one-bond 77Se-13C spin-spin coupling constants in the series of selenium heterocycles and their parent open-chain selenides.

PubMed

Rusakov, Yury Yu; Rusakova, Irina L; Krivdin, Leonid B

2014-05-01

Four-component relativistic calculations of (77)Se-(13)C spin-spin coupling constants have been performed in the series of selenium heterocycles and their parent open-chain selenides. It has been found that relativistic effects play an essential role in the selenium-carbon coupling mechanism and could result in a contribution of as much as 15-25% of the total values of the one-bond selenium-carbon spin-spin coupling constants. In the overall contribution of the relativistic effects to the total values of (1)J(Se,C), the scalar relativistic corrections (negative in sign) by far dominate over the spin-orbit ones (positive in sign), the latter being of less than 5%, as compared to the former (ca 20%). A combination of nonrelativistic second-order polarization propagator approach (CC2) with the four-component relativistic density functional theory scheme is recommended as a versatile tool for the calculation of (1)J(Se,C). Solvent effects in the values of (1)J(Se,C) calculated within the polarizable continuum model for the solvents with different dielectric constants (ε 2.2-78.4) are next to negligible decreasing negative (1)J(Se,C) in absolute value by only about 1 Hz. The use of the locally dense basis set approach applied herewith for the calculation of (77)Se-(13)C spin-spin coupling constants is fully justified resulting in a dramatic decrease in computational cost with only 0.1-0.2-Hz loss of accuracy. Copyright © 2014 John Wiley & Sons, Ltd.

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

PubMed

Jiang, Wei; Roux, Benoît

2010-07-01

Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

Perturbation corrections to Koopmans' theorem. V - A study with large basis sets

NASA Technical Reports Server (NTRS)

Chong, D. P.; Langhoff, S. R.

1982-01-01

The vertical ionization potentials of N2, F2 and H2O were calculated by perturbation corrections to Koopmans' theorem using six different basis sets. The largest set used includes several sets of polarization functions. Comparison is made with measured values and with results of computations using Green's functions.

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

We present a new basis set as an alternative to Legendre polynomials for the variational treatment of bending vibrational degrees of freedom in order to highly reduce the number of basis functions. This basis set is inspired from the harmonic oscillator eigenfunctions but is defined for a bending angle in the range theta in [0:pi]. The aim is to bring the basis functions closer to the final (ro)vibronic wave functions nature. Our methodology is extended to complicated potential energy surfaces, such as quasilinearity or multiequilibrium geometries, by using several free parameters in the basis functions. These parameters allow several density maxima, linear or not, around which the basis functions will be mainly located. Divergences at linearity in integral computations are resolved as generalized Legendre polynomials. All integral computations required for the evaluation of molecular Hamiltonian matrix elements are given for both discrete variable representation and finite basis representation. Convergence tests for the low energy vibronic states of HCCH(++), HCCH(+), and HCCS are presented.

Density-Functional Theory description of transport in the single-electron transistor

NASA Astrophysics Data System (ADS)

Zawadzki, Krissia; Oliveira, Luiz N.

The Kondo effect governs the low-temperature transport properties of the single electron transistor (SET), a quantum dot bridging two electron gases. In the weak coupling limit, for odd dot occupation, the gate-potential profile of the conductance approaches a step, known as the Kondo plateau. The plateau and other SET properties being well understood on the basis of the Anderson model, more realistic (i. e., DFT) descriptions of the device are now desired. This poses a challenge, since the SET is strongly correlated. DFT computations that reproduce the conductance plateau have been reported, e. g., by, which rely on the exact functional provided by the Bethe-Ansatz solution for the Anderson model. Here, sticking to DFT tradition, we employ a functional derived from a homogeneous system: the parametrization of the Lieb-Wu solution for the Hubbard model due to. Our computations reproduce the plateau and yield other results in accurate agreement with the exact diagonalization of the Anderson Hamiltonian. The prospects for extensions to realistic descriptions of two-dimensional nanostructured devices will be discussed. Luiz N. Oliveira thanks CNPq (312658/2013-3) and Krissia Zawadzki thanks CNPq (140703/2014-4) for financial support.

IVF twins: buy one get one free?

PubMed

Ismail, Laura; Mittal, Monica; Kalu, Emmanuel

2012-10-01

There has been an overall increase in the incidence of multiple pregnancies and assisted reproduction technology is largely responsible for this rise. Although twins may appeal to couples undergoing in vitro fertilisation (IVF), they have been associated with serious health consequences to the babies, their mothers and the family unit, as well as having massive financial implications for the National Health Service. Transfer of more than one embryo during IVF is mainly responsible for IVF twins, and elective transfer of a single embryo at a time with cryopreservation of surplus embryos for later transfer has been shown to be an effective strategy to minimise the risk of twins without compromising IVF success rates. Factors that will impact on the success of the policy of elective single embryo transfer (eSET) include improvement in embryo selection for transfer, better cryopreservation techniques and adequate state funding for IVF. However, in implementing the policy of eSET it is important that each case is assessed on an individual basis since in some situations (e.g. in older women) the transfer of two embryos may be more cost effective. Adequate and continuous education of all stakeholders is essential if the policy of eSET is to be successful in the UK.

Radial Basis Function Based Quadrature over Smooth Surfaces

DTIC Science & Technology

2016-03-24

Radial Basis Functions φ(r) Piecewise Smooth (Conditionally Positive Definite) MN Monomial |r|2m+1 TPS thin plate spline |r|2mln|r| Infinitely Smooth...smooth surfaces using polynomial interpolants, while [27] couples Thin - Plate Spline interpolation (see table 1) with Green’s integral formula [29

Aging Couples in Dual-Career/Earner Families.

PubMed

Reeves, Joy B; Darville, Ray L

1992-01-01

The authors present results of an empirical study of 611 mature couples in a dual-career or dual-earner famil where at least one spouse is a member of The National Retired Teacher's Association and is retired. We hypothesize that degree of role-sharing will va among mature couples in this special population on the basis of sexcted personal and social characteristics. Through discriminant analysis we identify which personal and social variables best predict whether or not couples currently share roles. We also determine the change in role-sharing over time for these couples. Our hypothesis is confirmed.

Light-propagation management in coupled waveguide arrays: Quantitative experimental and theoretical assessment from band structures to functional patterns

NASA Astrophysics Data System (ADS)

Moison, Jean-Marie; Belabas, Nadia; Levenson, Juan Ariel; Minot, Christophe

2012-09-01

We assess the band structure of arrays of coupled optical waveguides both by ab initio calculations and by experiments, with an excellent quantitative agreement without any adjustable physical parameter. The band structures we obtain can deviate strongly from the expectations of the standard coupled mode theory approximation, but we describe them efficiently by a few parameters within an extended coupled mode theory. We also demonstrate that this description is in turn a firm and simple basis for accurate beam management in functional patterns of coupled waveguides, in full accordance with their design.

Extrapolating MP2 and CCSD explicitly correlated correlation energies to the complete basis set limit with first and second row correlation consistent basis sets

NASA Astrophysics Data System (ADS)

Hill, J. Grant; Peterson, Kirk A.; Knizia, Gerald; Werner, Hans-Joachim

2009-11-01

Accurate extrapolation to the complete basis set (CBS) limit of valence correlation energies calculated with explicitly correlated MP2-F12 and CCSD(T)-F12b methods have been investigated using a Schwenke-style approach for molecules containing both first and second row atoms. Extrapolation coefficients that are optimal for molecular systems containing first row elements differ from those optimized for second row analogs, hence values optimized for a combined set of first and second row systems are also presented. The new coefficients are shown to produce excellent results in both Schwenke-style and equivalent power-law-based two-point CBS extrapolations, with the MP2-F12/cc-pV(D,T)Z-F12 extrapolations producing an average error of just 0.17 mEh with a maximum error of 0.49 for a collection of 23 small molecules. The use of larger basis sets, i.e., cc-pV(T,Q)Z-F12 and aug-cc-pV(Q,5)Z, in extrapolations of the MP2-F12 correlation energy leads to average errors that are smaller than the degree of confidence in the reference data (˜0.1 mEh). The latter were obtained through use of very large basis sets in MP2-F12 calculations on small molecules containing both first and second row elements. CBS limits obtained from optimized coefficients for conventional MP2 are only comparable to the accuracy of the MP2-F12/cc-pV(D,T)Z-F12 extrapolation when the aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z basis sets are used. The CCSD(T)-F12b correlation energy is extrapolated as two distinct parts: CCSD-F12b and (T). While the CCSD-F12b extrapolations with smaller basis sets are statistically less accurate than those of the MP2-F12 correlation energies, this is presumably due to the slower basis set convergence of the CCSD-F12b method compared to MP2-F12. The use of larger basis sets in the CCSD-F12b extrapolations produces correlation energies with accuracies exceeding the confidence in the reference data (also obtained in large basis set F12 calculations). It is demonstrated that the use of the 3C(D) Ansatz is preferred for MP2-F12 CBS extrapolations. Optimal values of the geminal Slater exponent are presented for the diagonal, fixed amplitude Ansatz in MP2-F12 calculations, and these are also recommended for CCSD-F12b calculations.

An Alternate Set of Basis Functions for the Electromagnetic Solution of Arbitrarily-Shaped, Three-Dimensional, Closed, Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present an alternate set of basis functions, each defined over a pair of planar triangular patches, for the method of moments solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped, closed, conducting surfaces. The present basis functions are point-wise orthogonal to the pulse basis functions previously defined. The prime motivation to develop the present set of basis functions is to utilize them for the electromagnetic solution of dielectric bodies using a surface integral equation formulation which involves both electric and magnetic cur- rents. However, in the present work, only the conducting body solution is presented and compared with other data.

Correction of energy-dependent systematic errors in dual-energy X-ray CT using a basis material coefficients transformation method

NASA Astrophysics Data System (ADS)

Goh, K. L.; Liew, S. C.; Hasegawa, B. H.

1997-12-01

Computer simulation results from our previous studies showed that energy dependent systematic errors exist in the values of attenuation coefficient synthesized using the basis material decomposition technique with acrylic and aluminum as the basis materials, especially when a high atomic number element (e.g., iodine from radiographic contrast media) was present in the body. The errors were reduced when a basis set was chosen from materials mimicking those found in the phantom. In the present study, we employed a basis material coefficients transformation method to correct for the energy-dependent systematic errors. In this method, the basis material coefficients were first reconstructed using the conventional basis materials (acrylic and aluminum) as the calibration basis set. The coefficients were then numerically transformed to those for a more desirable set materials. The transformation was done at the energies of the low and high energy windows of the X-ray spectrum. With this correction method using acrylic and an iodine-water mixture as our desired basis set, computer simulation results showed that accuracy of better than 2% could be achieved even when iodine was present in the body at a concentration as high as 10% by mass. Simulation work had also been carried out on a more inhomogeneous 2D thorax phantom of the 3D MCAT phantom. The results of the accuracy of quantitation were presented here.

Stabilizing coherence with nested environments: a numerical study using kicked Ising models

NASA Astrophysics Data System (ADS)

González-Gutiérrez, C.; Villaseñor, E.; Pineda, C.; Seligman, T. H.

2016-08-01

We study a tripartite system of coupled spins, where a first set of one or two spins is our central system which is coupled to another set considered, the near environment, in turn coupled to the third set, the far environment. The dynamics considered are those of a generalized kicked spin chain in the regime of quantum chaotic dynamics. This allows us to test recent results that suggest that the presence of a far environment, coupled to the near environment, slows decoherence of the central system. After an extensive numerical study, we confirm previous results for extreme values and special cases. In particular, under a wide variety of circumstances an increasing coupling between near and far environment, slows decoherence, as measured by purity, and protects internal entanglement.

Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies.

PubMed

Liu, Jia; Duffy, Ben A; Bernal-Casas, David; Fang, Zhongnan; Lee, Jin Hyung

2017-02-15

A large number of fMRI studies have shown that the temporal dynamics of evoked BOLD responses can be highly heterogeneous. Failing to model heterogeneous responses in statistical analysis can lead to significant errors in signal detection and characterization and alter the neurobiological interpretation. However, to date it is not clear that, out of a large number of options, which methods are robust against variability in the temporal dynamics of BOLD responses in block-design studies. Here, we used rodent optogenetic fMRI data with heterogeneous BOLD responses and simulations guided by experimental data as a means to investigate different analysis methods' performance against heterogeneous BOLD responses. Evaluations are carried out within the general linear model (GLM) framework and consist of standard basis sets as well as independent component analysis (ICA). Analyses show that, in the presence of heterogeneous BOLD responses, conventionally used GLM with a canonical basis set leads to considerable errors in the detection and characterization of BOLD responses. Our results suggest that the 3rd and 4th order gamma basis sets, the 7th to 9th order finite impulse response (FIR) basis sets, the 5th to 9th order B-spline basis sets, and the 2nd to 5th order Fourier basis sets are optimal for good balance between detection and characterization, while the 1st order Fourier basis set (coherence analysis) used in our earlier studies show good detection capability. ICA has mostly good detection and characterization capabilities, but detects a large volume of spurious activation with the control fMRI data. Copyright © 2016 Elsevier Inc. All rights reserved.

Wideband analytical equivalent circuit for one-dimensional periodic stacked arrays.

PubMed

Molero, Carlos; Rodríguez-Berral, Raúl; Mesa, Francisco; Medina, Francisco; Yakovlev, Alexander B

2016-01-01

A wideband equivalent circuit is proposed for the accurate analysis of scattering from a set of stacked slit gratings illuminated by a plane wave with transverse magnetic or electric polarization that impinges normally or obliquely along one of the principal planes of the structure. The slit gratings are printed on dielectric slabs of arbitrary thickness, including the case of closely spaced gratings that interact by higher-order modes. A Π-circuit topology is obtained for a pair of coupled arrays, with fully analytical expressions for all the circuit elements. This equivalent Π circuit is employed as the basis to derive the equivalent circuit of finite stacks with any given number of gratings. Analytical expressions for the Brillouin diagram and the Bloch impedance are also obtained for infinite periodic stacks.

A note on the electric quadrupole and higher electric moments of ozone (O3)

NASA Astrophysics Data System (ADS)

Maroulis, George

2012-02-01

We have obtained accurate ab initio and density functional theory values for the quadrupole, octopole and hexadecapole electric moments of the cyclic and open forms of ozone. Our best values have been calculated at the coupled cluster level of theory with molecule-specific basis sets. For the quadrupole moment (Θαβ/ea02) they are Θyy = -1.366 (cyclic), Θxx = -1.202, Θyy = 1.426 and Θxx = -0.223 (open). For the octopole (Ωαβγ/ea03) and hexadecapole (Φαβγδ/ea04) moments our best results are Ωzzz = 2.25, Φyyyy = 19.53 (cyclic), Ωxxz = 3.28, Ωzzz = -2.97, Φxxxx = -6.00, Φyyyy = -3.90 and Φzzzz = -3.54 (open).

Smad3 allostery links TGF-β receptor kinase activation to transcriptional control

PubMed Central

Qin, Bin Y.; Lam, Suvana S.; Correia, John J.; Lin, Kai

2002-01-01

Smad3 transduces the signals of TGF-βs, coupling transmembrane receptor kinase activation to transcriptional control. The membrane-associated molecule SARA (Smad Anchor for Receptor Activation) recruits Smad3 for phosphorylation by the receptor kinase. Upon phosphorylation, Smad3 dissociates from SARA and enters the nucleus, in which its transcriptional activity can be repressed by Ski. Here, we show that SARA and Ski recognize specifically the monomeric and trimeric forms of Smad3, respectively. Thus, trimerization of Smad3, induced by phosphorylation, simultaneously activates the TGF-β signal by driving Smad3 dissociation from SARA and sets up the negative feedback mechanism by Ski. Structural models of the Smad3/SARA/receptor kinase complex and Smad3/Ski complex provide insights into the molecular basis of regulation. PMID:12154125

Is autism partly a consolidation disorder?

PubMed

Femia, Lisa A; Hasselmo, Michael E

2002-12-01

Computational modeling has been useful for understanding processes of encoding and consolidation in cortical structures. In particular, this work suggests a role of neuromodulators in setting dynamics for consolidation processes during different stages of waking and sleep. Because autistic individuals show symptoms of a cognitive nature coupled with a high prevalence of comorbid conditions such as epileptiform discharge during sleep and sleep disorders, it is possible that autism could involve a breakdown in consolidation processes, which are essential to build effective cognitive representations of the environment on the basis of individual experiences. In this article, theories of consolidation during different stages of waking and sleep and the role of different neuromodulators in these consolidation processes are reviewed in conjunction with different features of autism, which may be understood in the context of these theories.

Point Set Denoising Using Bootstrap-Based Radial Basis Function.

PubMed

Liew, Khang Jie; Ramli, Ahmad; Abd Majid, Ahmad

2016-01-01

This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study.

Solid-state EPR strategies for the structural characterization of paramagnetic NO adducts of frustrated Lewis pairs (FLPs)

NASA Astrophysics Data System (ADS)

de Oliveira, Marcos; Wiegand, Thomas; Elmer, Lisa-Maria; Sajid, Muhammad; Kehr, Gerald; Erker, Gerhard; Magon, Claudio José; Eckert, Hellmut

2015-03-01

Anisotropic interactions present in three new nitroxide radicals prepared by N,N addition of NO to various borane-phosphane frustrated Lewis pairs (FLPs) have been characterized by continuous-wave (cw) and pulsed X-band EPR spectroscopies in solid FLP-hydroxylamine matrices at 100 K. Anisotropic g-tensor values and 11B, 14N, and 31P hyperfine coupling tensor components have been extracted from continuous-wave lineshape analyses, electron spin echo envelope modulation (ESEEM), and hyperfine sublevel correlation spectroscopy (HYSCORE) experiments with the help of computer simulation techniques. Suitable fitting constraints are developed on the basis of density functional theory (DFT) calculations. These calculations reveal that different from the situation in standard nitroxide radicals (TEMPO), the g-tensors are non-coincident with any of the nuclear hyperfine interaction tensors. The determination of these interaction parameters turns out to be successful, as the cw- and pulse EPR experiments are highly complementary in informational content. While the continuous-wave lineshape is largely influenced by the anisotropic hyperfine coupling to 14N and 31P, the ESEEM and HYSCORE spectra contain important information about the 11B hyperfine coupling and nuclear electric quadrupolar interaction. The set of cw- and pulsed EPR experiments, with fitting constraints developed by DFT calculations, defines an efficient strategy for the structural analysis of paramagnetic FLP adducts.

Solid-state EPR strategies for the structural characterization of paramagnetic NO adducts of frustrated Lewis pairs (FLPs)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliveira, Marcos de; Magon, Claudio José; Wiegand, Thomas

2015-03-28

Anisotropic interactions present in three new nitroxide radicals prepared by N,N addition of NO to various borane-phosphane frustrated Lewis pairs (FLPs) have been characterized by continuous-wave (cw) and pulsed X-band EPR spectroscopies in solid FLP-hydroxylamine matrices at 100 K. Anisotropic g-tensor values and {sup 11}B, {sup 14}N, and {sup 31}P hyperfine coupling tensor components have been extracted from continuous-wave lineshape analyses, electron spin echo envelope modulation (ESEEM), and hyperfine sublevel correlation spectroscopy (HYSCORE) experiments with the help of computer simulation techniques. Suitable fitting constraints are developed on the basis of density functional theory (DFT) calculations. These calculations reveal that differentmore » from the situation in standard nitroxide radicals (TEMPO), the g-tensors are non-coincident with any of the nuclear hyperfine interaction tensors. The determination of these interaction parameters turns out to be successful, as the cw- and pulse EPR experiments are highly complementary in informational content. While the continuous-wave lineshape is largely influenced by the anisotropic hyperfine coupling to {sup 14}N and {sup 31}P, the ESEEM and HYSCORE spectra contain important information about the {sup 11}B hyperfine coupling and nuclear electric quadrupolar interaction. The set of cw- and pulsed EPR experiments, with fitting constraints developed by DFT calculations, defines an efficient strategy for the structural analysis of paramagnetic FLP adducts.« less

Aeroelastic System Development Using Proper Orthogonal Decomposition and Volterra Theory

NASA Technical Reports Server (NTRS)

Lucia, David J.; Beran, Philip S.; Silva, Walter A.

2003-01-01

This research combines Volterra theory and proper orthogonal decomposition (POD) into a hybrid methodology for reduced-order modeling of aeroelastic systems. The out-come of the method is a set of linear ordinary differential equations (ODEs) describing the modal amplitudes associated with both the structural modes and the POD basis functions for the uid. For this research, the structural modes are sine waves of varying frequency, and the Volterra-POD approach is applied to the fluid dynamics equations. The structural modes are treated as forcing terms which are impulsed as part of the uid model realization. Using this approach, structural and uid operators are coupled into a single aeroelastic operator. This coupling converts a free boundary uid problem into an initial value problem, while preserving the parameter (or parameters) of interest for sensitivity analysis. The approach is applied to an elastic panel in supersonic cross ow. The hybrid Volterra-POD approach provides a low-order uid model in state-space form. The linear uid model is tightly coupled with a nonlinear panel model using an implicit integration scheme. The resulting aeroelastic model provides correct limit-cycle oscillation prediction over a wide range of panel dynamic pressure values. Time integration of the reduced-order aeroelastic model is four orders of magnitude faster than the high-order solution procedure developed for this research using traditional uid and structural solvers.

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

An Alternative Mechanism for the Dimerization of Formic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brinkman, Nicole R.; Tschumper, Gregory; Yan, Ge

Gas-phase formic acid exists primarily as a cyclic dimer. The mechanism of dimerization has been traditionally considered to be a synchronous process; however, recent experimental findings suggest a possible alternative mechanism by which two formic acid monomers proceed through an acyclic dimer to the cyclic dimer in a stepwise process. To investigate this newly proposed process of dimerization in formic acid, density functional theory and second-order Moeller-Plesset perturbation theory (MP2) have been used to optimize cis and trans monomers of formic acid, the acyclic and cyclic dimers, and the acyclic and cyclic transition states between minima. Single-point energies of themore » trans monomer, dimer minima, and transition states at the MP2/TZ2P+diff optimized geometries were computed at the coupled-cluster level of theory including singles and doubles with perturbatively applied triple excitations [CCSD(T)] with an aug-cc-pVTZ basis set to obtain an accurate determination of energy barriers and dissociation energies. A counterpoise correction was performed to determine an estimate of the basis set superposition error in computing relative energies. The explicitly correlated MP2 method of Kutzelnigg and Klopper (MP2-R12) was used to provide an independent means for obtaining the MP2 one-particle limit. The cyclic minimum is predicted to be 6.3 kcal/mol more stable than the acyclic minimum, and the barrier to double proton transfer is 7.1 kcal/mol.« less

Møller-Plesset perturbation energies and distances for HeC(20) extrapolated to the complete basis set limit.

PubMed

Varandas, A J C

2009-02-01

The potential energy surface for the C(20)-He interaction is extrapolated for three representative cuts to the complete basis set limit using second-order Møller-Plesset perturbation calculations with correlation consistent basis sets up to the doubly augmented variety. The results both with and without counterpoise correction show consistency with each other, supporting that extrapolation without such a correction provides a reliable scheme to elude the basis-set-superposition error. Converged attributes are obtained for the C(20)-He interaction, which are used to predict the fullerene dimer ones. Time requirements show that the method can be drastically more economical than the counterpoise procedure and even competitive with Kohn-Sham density functional theory for the title system.

Exact exchange-correlation potentials of singlet two-electron systems

NASA Astrophysics Data System (ADS)

Ryabinkin, Ilya G.; Ospadov, Egor; Staroverov, Viktor N.

2017-10-01

We suggest a non-iterative analytic method for constructing the exchange-correlation potential, v XC ( r ) , of any singlet ground-state two-electron system. The method is based on a convenient formula for v XC ( r ) in terms of quantities determined only by the system's electronic wave function, exact or approximate, and is essentially different from the Kohn-Sham inversion technique. When applied to Gaussian-basis-set wave functions, the method yields finite-basis-set approximations to the corresponding basis-set-limit v XC ( r ) , whereas the Kohn-Sham inversion produces physically inappropriate (oscillatory and divergent) potentials. The effectiveness of the procedure is demonstrated by computing accurate exchange-correlation potentials of several two-electron systems (helium isoelectronic series, H2, H3 + ) using common ab initio methods and Gaussian basis sets.

Activated protein C: biased for translation.

PubMed

Griffin, John H; Zlokovic, Berislav V; Mosnier, Laurent O

2015-05-07

The homeostatic blood protease, activated protein C (APC), can function as (1) an antithrombotic on the basis of inactivation of clotting factors Va and VIIIa; (2) a cytoprotective on the basis of endothelial barrier stabilization and anti-inflammatory and antiapoptotic actions; and (3) a regenerative on the basis of stimulation of neurogenesis, angiogenesis, and wound healing. Pharmacologic therapies using recombinant human and murine APCs indicate that APC provides effective acute or chronic therapies for a strikingly diverse range of preclinical injury models. APC reduces the damage caused by the following: ischemia/reperfusion in brain, heart, and kidney; pulmonary, kidney, and gastrointestinal inflammation; sepsis; Ebola virus; diabetes; and total lethal body radiation. For these beneficial effects, APC alters cell signaling networks and gene expression profiles by activating protease-activated receptors 1 and 3. APC's activation of these G protein-coupled receptors differs completely from thrombin's activation mechanism due to biased signaling via either G proteins or β-arrestin-2. To reduce APC-associated bleeding risk, APC variants were engineered to lack >90% anticoagulant activity but retain normal cell signaling. Such a neuroprotective variant, 3K3A-APC (Lys191-193Ala), has advanced to clinical trials for ischemic stroke. A rich data set of preclinical knowledge provides a solid foundation for potential translation of APC variants to future novel therapies. © 2015 by The American Society of Hematology.

Gravitational Wave Oscillations in Bigravity.

PubMed

Max, Kevin; Platscher, Moritz; Smirnov, Juri

2017-09-15

We derive consistent equations for gravitational wave oscillations in bigravity. In this framework a second dynamical tensor field is introduced in addition to general relativity and coupled such that one massless and one massive linear combination arise. Only one of the two tensors is the physical metric coupling to matter, and thus the basis in which gravitational waves propagate is different from the basis where the wave is produced and detected. Therefore, one should expect-in analogy to neutrino oscillations-to observe an oscillatory behavior. We show for the first time how this behavior arises explicitly, discuss phenomenological implications, and present new limits on the graviton parameter space in bigravity.

Coupled-channel approach to strangeness S = -2 baryon-bayron interactions in lattice QCD

NASA Astrophysics Data System (ADS)

Sasaki, Kenji; Aoki, Sinya; Doi, Takumi; Hatsuda, Tetsuo; Ikeda, Yoichi; Inoue, Takashi; Ishii, Noriyoshi; Murano, Keiko

2015-11-01

Baryon-baryon interactions with strangeness S=-2 with flavor SU(3) breaking are calculated for the first time by using the HAL QCD method extended to the coupled-channel system in lattice QCD. The potential matrices are extracted from the Nambu-Bethe-Salpeter wave functions obtained by the 2+1-flavor gauge configurations of the CP-PACS/JLQCD Collaborations with a physical volume of (1.93 fm)^3 and with m_{π }/m_K=0.96, 0.90, 0.86. The spatial structure and the quark mass dependence of the potential matrix in the baryon basis and in the SU(3) basis are investigated.

Self-diffusion and conductivity in an ultracold strongly coupled plasma: Calculation by the method of molecular dynamics

NASA Astrophysics Data System (ADS)

Zelener, B. B.; Zelener, B. V.; Manykin, E. A.; Bronin, S. Ya; Bobrov, A. A.; Khikhlukha, D. R.

2018-01-01

We present results of calculations by the method of molecular dynamics of self-diffusion and conductivity of electron and ion components of ultracold plasma in a comparison with available theoretical and experimental data. For the ion self-diffusion coefficient, good agreement was obtained with experiments on ultracold plasma. The results of the calculation of self-diffusion also agree well with other calculations performed for the same values of the coupling parameter, but at high temperatures. The difference in the results of the conductivity calculations on the basis of the current autocorrelation function and on the basis of the diffusion coefficient is discussed.

Probing the mutational interplay between primary and promiscuous protein functions: a computational-experimental approach.

PubMed

Garcia-Seisdedos, Hector; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

2012-01-01

Protein promiscuity is of considerable interest due its role in adaptive metabolic plasticity, its fundamental connection with molecular evolution and also because of its biotechnological applications. Current views on the relation between primary and promiscuous protein activities stem largely from laboratory evolution experiments aimed at increasing promiscuous activity levels. Here, on the other hand, we attempt to assess the main features of the simultaneous modulation of the primary and promiscuous functions during the course of natural evolution. The computational/experimental approach we propose for this task involves the following steps: a function-targeted, statistical coupling analysis of evolutionary data is used to determine a set of positions likely linked to the recruitment of a promiscuous activity for a new function; a combinatorial library of mutations on this set of positions is prepared and screened for both, the primary and the promiscuous activities; a partial-least-squares reconstruction of the full combinatorial space is carried out; finally, an approximation to the Pareto set of variants with optimal primary/promiscuous activities is derived. Application of the approach to the emergence of folding catalysis in thioredoxin scaffolds reveals an unanticipated scenario: diverse patterns of primary/promiscuous activity modulation are possible, including a moderate (but likely significant in a biological context) simultaneous enhancement of both activities. We show that this scenario can be most simply explained on the basis of the conformational diversity hypothesis, although alternative interpretations cannot be ruled out. Overall, the results reported may help clarify the mechanisms of the evolution of new functions. From a different viewpoint, the partial-least-squares-reconstruction/Pareto-set-prediction approach we have introduced provides the computational basis for an efficient directed-evolution protocol aimed at the simultaneous enhancement of several protein features and should therefore open new possibilities in the engineering of multi-functional enzymes.

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach

PubMed Central

Garcia-Seisdedos, Hector; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

2012-01-01

Protein promiscuity is of considerable interest due its role in adaptive metabolic plasticity, its fundamental connection with molecular evolution and also because of its biotechnological applications. Current views on the relation between primary and promiscuous protein activities stem largely from laboratory evolution experiments aimed at increasing promiscuous activity levels. Here, on the other hand, we attempt to assess the main features of the simultaneous modulation of the primary and promiscuous functions during the course of natural evolution. The computational/experimental approach we propose for this task involves the following steps: a function-targeted, statistical coupling analysis of evolutionary data is used to determine a set of positions likely linked to the recruitment of a promiscuous activity for a new function; a combinatorial library of mutations on this set of positions is prepared and screened for both, the primary and the promiscuous activities; a partial-least-squares reconstruction of the full combinatorial space is carried out; finally, an approximation to the Pareto set of variants with optimal primary/promiscuous activities is derived. Application of the approach to the emergence of folding catalysis in thioredoxin scaffolds reveals an unanticipated scenario: diverse patterns of primary/promiscuous activity modulation are possible, including a moderate (but likely significant in a biological context) simultaneous enhancement of both activities. We show that this scenario can be most simply explained on the basis of the conformational diversity hypothesis, although alternative interpretations cannot be ruled out. Overall, the results reported may help clarify the mechanisms of the evolution of new functions. From a different viewpoint, the partial-least-squares-reconstruction/Pareto-set-prediction approach we have introduced provides the computational basis for an efficient directed-evolution protocol aimed at the simultaneous enhancement of several protein features and should therefore open new possibilities in the engineering of multi-functional enzymes. PMID:22719242

The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison phase results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Rühaak, Wolfram

2016-04-01

Climate change impacts in permafrost regions have received considerable attention recently due to the pronounced warming trends experienced in recent decades and which have been projected into the future. Large portions of these permafrost regions are characterized by surface water bodies (lakes, rivers) that interact with the surrounding permafrost often generating taliks (unfrozen zones) within the permafrost that allow for hydrologic interactions between the surface water bodies and underlying aquifers and thus influence the hydrologic response of a landscape to climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model past and future evolution such units (Kurylyk et al. 2014). However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, which can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. A benchmark exercise was initialized at the end of 2014. Participants convened from USA, Canada, Europe, representing 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones (Kurylyk et al. 2014; Grenier et al. in prep.; Rühaak et al. 2015). They range from simpler, purely thermal 1D cases to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in a cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test case databases at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases TH2 & TH3. Both cases are essentially theoretical but include the full complexity of the coupled non-linear set of equations (heat transfer with conduction, advection, phase change and Darcian flow). The complete set of inter-comparison results shows that the participating codes all produce simulations which are quantitatively similar and correspond to physical intuition. From a quantitative perspective, they agree well over the whole set of performance measures. The differences among the simulation results will be discussed in more depth throughout the test cases especially for the identification of the threshold times for each system as these exhibited the least agreement. However, the results suggest that in spite of the difficulties associated with the resolution of the set of TH equations (coupled and non-linear structure with phase change providing steep slopes), the developed codes provide robust results with a qualitatively reasonable representation of the processes and offer a quantitatively realistic basis. Further perspectives of the exercise will also be presented.

Parity breaking signatures from a Chern-Simons coupling during inflation: the case of non-Gaussian gravitational waves

NASA Astrophysics Data System (ADS)

Bartolo, Nicola; Orlando, Giorgio

2017-07-01

Considering high-energy modifications of Einstein gravity during inflation is an interesting issue. We can constrain the strength of the new gravitational terms through observations of inflationary imprints in the actual universe. In this paper we analyze the effects on slow-roll models due to a Chern-Simons term coupled to the inflaton field through a generic coupling function f(phi). A well known result is the polarization of primordial gravitational waves (PGW) into left and right eigenstates, as a consequence of parity breaking. In such a scenario the modifications to the power spectrum of PGW are suppressed under the conditions that allow to avoid the production of ghost gravitons at a certain energy scale, the so-called Chern-Simons mass MCS. In general it has been recently pointed out that there is very little hope to efficiently constrain chirality of PGW on the basis solely of two-point statistics from future CMB data, even in the most optimistic cases. Thus we search if significant parity breaking signatures can arise at least in the bispectrum statistics. We find that the tensor-tensor-scalar bispectra langle γ γ ζ rangle for each polarization state are the only ones that are not suppressed. Their amplitude, setting the level of parity breaking during inflation, is proportional to the second derivative of the coupling function f(phi) and they turn out to be maximum in the squeezed limit. We comment on the squeezed-limit consistency relation arising in the case of chiral gravitational waves, and on possible observables to constrain these signatures.

Chromophore-Dependent Intramolecular Exciton-Vibrational Coupling in the FMO Complex: Quantification and Importance for Exciton Dynamics.

PubMed

Padula, Daniele; Lee, Myeong H; Claridge, Kirsten; Troisi, Alessandro

2017-11-02

In this paper, we adopt an approach suitable for monitoring the time evolution of the intramolecular contribution to the spectral density of a set of identical chromophores embedded in their respective environments. We apply the proposed method to the Fenna-Matthews-Olson (FMO) complex, with the objective to quantify the differences among site-dependent spectral densities and the impact of such differences on the exciton dynamics of the system. Our approach takes advantage of the vertical gradient approximation to reduce the computational demands of the normal modes analysis. We show that the region of the spectral density that is believed to strongly influence the exciton dynamics changes significantly in the timescale of tens of nanoseconds. We then studied the impact of the intramolecular vibrations on the exciton dynamics by considering a model of FMO in a vibronic basis and neglecting the interaction with the environment to isolate the role of the intramolecular exciton-vibration coupling. In agreement with the assumptions in the literature, we demonstrate that high frequency modes at energy much larger than the excitonic energy splitting have negligible influence on exciton dynamics despite the large exciton-vibration coupling. We also find that the impact of including the site-dependent spectral densities on exciton dynamics is not very significant, indicating that it may be acceptable to apply the same spectral density on all sites. However, care needs to be taken for the description of the exciton-vibrational coupling in the low frequency part of intramolecular modes because exciton dynamics is more susceptible to low frequency modes despite their small Huang-Rhys factors.

On the basis set convergence of electron–electron entanglement measures: helium-like systems

PubMed Central

Hofer, Thomas S.

2013-01-01

A systematic investigation of three different electron–electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li+ and Be2+ using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one–electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li+ and Be2+. In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used. PMID:24790952

On the basis set convergence of electron-electron entanglement measures: helium-like systems.

PubMed

Hofer, Thomas S

2013-01-01

A systematic investigation of three different electron-electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li(+) and Be(2+) using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one-electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li(+) and Be(2+). In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used.

Orbital-Dependent Density Functionals for Chemical Catalysis

DTIC Science & Technology

2014-10-17

noncollinear density functional theory to show that the low-spin state of Mn3 in a model of the oxygen -evolving complex of photosystem II avoids...DK, which denotes the cc-pV5Z-DK basis set for 3d metals and hydrogen and the ma-cc- pV5Z-DK basis set for oxygen ) and to nonrelativistic all...cc-pV5Z basis set for oxygen ). As compared to NCBS-DK results, all ECP calculations perform worse than def2-TZVP all-electron relativistic

Electric dipole moment of diatomic molecules by configuration interaction. IV.

NASA Technical Reports Server (NTRS)

Green, S.

1972-01-01

The theory of basis set dependence in configuration interaction calculations is discussed, taking into account a perturbation model which is valid for small changes in the self-consistent field orbitals. It is found that basis set corrections are essentially additive through first order. It is shown that an error found in a previously published dipole moment calculation by Green (1972) for the metastable first excited state of CO was indeed due to an inadequate basis set as claimed.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2007-01-01

In this work, we present a new set of basis functions, de ned over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also de ned over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present a new set of basis functions, defined over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also defined over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

Evaluation of Environmental Conditions on the Curing Of Commercial Fixative and Intumescent Coatings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicholson, J. C.

2016-09-26

Performance metrics for evaluating commercial fixatives are often not readily available for important parameters that must be considered per the facility safety basis and the facility Basis for Interim Operations (BIO). One such parameter is the behavior of such materials in varied, “non-ideal” conditions where ideal is defined as 75 °F, 40% RH. Coupled with the inherent flammable nature of the fixative materials that can act to propagate flame along surfaces that are otherwise fireproof (concrete, sheet metal), much is left unknown when considering the safety basis implications for introducing these materials into nuclear facilities. Through SRNL’s efforts, three (3)more » fixatives, one (1) decontamination gel, and six (6) intumescent coatings were examined for their responses to environmental conditions to determine whether these materials were impervious to non-nominal temperatures and humidities that may be found in nuclear facilities. Characteristics that were examined included set-to-touch time, dust free time, and adhesion testing of the fully cured compounds. Of these ten materials, three were two-part epoxy materials while the other seven consisted of only one constituent. The results show that the epoxies tested are unable to cure in sub-freezing temperatures, with the low temperatures inhibiting crosslinking to a very significant degree. These efforts show significant inhibiting of performance for non-nominal environmental conditions, something that must be addressed both in the decision process for a fixative material to apply and per the safety basis to ensure the accurate flammability and material at risk is calculated.« less

Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency.

PubMed

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-21

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency

NASA Astrophysics Data System (ADS)

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-01

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Computational Chemistry Modeling of the Atmospheric Fate of Toxic Industrial Compounds (TICs)

DTIC Science & Technology

2007-06-01

1+G(3df,2p) number of atoms and number of basis functions) of the (LRG) compounds under study precludes the use of coupled 0 Zero Point Energy ( ZPE ...overlap (NDDO) The extrapolated energy = E(QCI) + E(LRG) - Hamiltonian that is reparameterized to accurately E(SML) + ZPE reproduce coupled cluster

Nonlinear coupled equations for electrochemical cells as developed by the general equation for nonequilibrium reversible-irreversible coupling.

PubMed

Bedeaux, Dick; Kjelstrup, Signe; Öttinger, Hans Christian

2014-09-28

We show how the Butler-Volmer and Nernst equations, as well as Peltier effects, are contained in the general equation for nonequilibrium reversible and irreversible coupling, GENERIC, with a unique definition of the overpotential. Linear flux-force relations are used to describe the transport in the homogeneous parts of the electrochemical system. For the electrode interface, we choose nonlinear flux-force relationships. We give the general thermodynamic basis for an example cell with oxygen electrodes and electrolyte from the solid oxide fuel cell. In the example cell, there are two activated chemical steps coupled also to thermal driving forces at the surface. The equilibrium exchange current density obtains contributions from both rate-limiting steps. The measured overpotential is identified at constant temperature and stationary states, in terms of the difference in electrochemical potential of products and reactants. Away from these conditions, new terms appear. The accompanying energy flux out of the surface, as well as the heat generation at the surface are formulated, adding to the general thermodynamic basis.