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Sample records for accurate theoretical calculations

  1. Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides.

    PubMed

    Sastre, S; Casasnovas, R; Muñoz, F; Frau, J

    2016-04-28

    Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods. PMID:27052591

  2. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  3. How Accurately can we Calculate Thermal Systems?

    SciTech Connect

    Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A

    2004-04-20

    I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.

  4. Accurate theoretical chemistry with coupled pair models.

    PubMed

    Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan

    2009-05-19

    Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now

  5. Accurate free energy calculation along optimized paths.

    PubMed

    Chen, Changjun; Xiao, Yi

    2010-05-01

    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  6. Accurate calculation of diffraction-limited encircled and ensquared energy.

    PubMed

    Andersen, Torben B

    2015-09-01

    Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873

  7. Strategy Guideline. Accurate Heating and Cooling Load Calculations

    SciTech Connect

    Burdick, Arlan

    2011-06-01

    This guide presents the key criteria required to create accurate heating and cooling load calculations and offers examples of the implications when inaccurate adjustments are applied to the HVAC design process. The guide shows, through realistic examples, how various defaults and arbitrary safety factors can lead to significant increases in the load estimate. Emphasis is placed on the risks incurred from inaccurate adjustments or ignoring critical inputs of the load calculation.

  8. Strategy Guideline: Accurate Heating and Cooling Load Calculations

    SciTech Connect

    Burdick, A.

    2011-06-01

    This guide presents the key criteria required to create accurate heating and cooling load calculations and offers examples of the implications when inaccurate adjustments are applied to the HVAC design process. The guide shows, through realistic examples, how various defaults and arbitrary safety factors can lead to significant increases in the load estimate. Emphasis is placed on the risks incurred from inaccurate adjustments or ignoring critical inputs of the load calculation.

  9. Theoretical Calculations of Atomic Data for Spectroscopy

    NASA Technical Reports Server (NTRS)

    Bautista, Manuel A.

    2000-01-01

    Several different approximations and techniques have been developed for the calculation of atomic structure, ionization, and excitation of atoms and ions. These techniques have been used to compute large amounts of spectroscopic data of various levels of accuracy. This paper presents a review of these theoretical methods to help non-experts in atomic physics to better understand the qualities and limitations of various data sources and assess how reliable are spectral models based on those data.

  10. Calculation of Accurate Hexagonal Discontinuity Factors for PARCS

    SciTech Connect

    Pounders. J., Bandini, B. R. , Xu, Y, and Downar, T. J.

    2007-11-01

    In this study we derive a methodology for calculating discontinuity factors consistent with the Triangle-based Polynomial Expansion Nodal (TPEN) method implemented in PARCS for hexagonal reactor geometries. The accuracy of coarse-mesh nodal methods is greatly enhanced by permitting flux discontinuities at node boundaries, but the practice of calculating discontinuity factors from infinite-medium (zero-current) single bundle calculations may not be sufficiently accurate for more challenging problems in which there is a large amount of internodal neutron streaming. The authors therefore derive a TPEN-based method for calculating discontinuity factors that are exact with respect to generalized equivalence theory. The method is validated by reproducing the reference solution for a small hexagonal core.

  11. Accurate pressure gradient calculations in hydrostatic atmospheric models

    NASA Technical Reports Server (NTRS)

    Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet

    1987-01-01

    A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.

  12. Accurate calculations of bound rovibrational states for argon trimer

    SciTech Connect

    Brandon, Drew; Poirier, Bill

    2014-07-21

    This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar{sub 3}), using the ScalIT suite of parallel codes. The Ar{sub 3} rovibrational energy levels are computed to a very high level of accuracy (10{sup −3} cm{sup −1} or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar{sub 3} are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar{sub 3} is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar{sub 3} may be found in the current literature—and only for the lowest-lying rotational excitations.

  13. Highly Accurate Calculations of the Phase Diagram of Cold Lithium

    NASA Astrophysics Data System (ADS)

    Shulenburger, Luke; Baczewski, Andrew

    The phase diagram of lithium is particularly complicated, exhibiting many different solid phases under the modest application of pressure. Experimental efforts to identify these phases using diamond anvil cells have been complemented by ab initio theory, primarily using density functional theory (DFT). Due to the multiplicity of crystal structures whose enthalpy is nearly degenerate and the uncertainty introduced by density functional approximations, we apply the highly accurate many-body diffusion Monte Carlo (DMC) method to the study of the solid phases at low temperature. These calculations span many different phases, including several with low symmetry, demonstrating the viability of DMC as a method for calculating phase diagrams for complex solids. Our results can be used as a benchmark to test the accuracy of various density functionals. This can strengthen confidence in DFT based predictions of more complex phenomena such as the anomalous melting behavior predicted for lithium at high pressures. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  14. Accurate calculation of field and carrier distributions in doped semiconductors

    NASA Astrophysics Data System (ADS)

    Yang, Wenji; Tang, Jianping; Yu, Hongchun; Wang, Yanguo

    2012-06-01

    We use the numerical squeezing algorithm(NSA) combined with the shooting method to accurately calculate the built-in fields and carrier distributions in doped silicon films (SFs) in the micron and sub-micron thickness range and results are presented in graphical form for variety of doping profiles under different boundary conditions. As a complementary approach, we also present the methods and the results of the inverse problem (IVP) - finding out the doping profile in the SFs for given field distribution. The solution of the IVP provides us the approach to arbitrarily design field distribution in SFs - which is very important for low dimensional (LD) systems and device designing. Further more, the solution of the IVP is both direct and much easy for all the one-, two-, and three-dimensional semiconductor systems. With current efforts focused on the LD physics, knowing of the field and carrier distribution details in the LD systems will facilitate further researches on other aspects and hence the current work provides a platform for those researches.

  15. Accurate ionization potential of semiconductors from efficient density functional calculations

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2016-07-01

    Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.

  16. Accurate theoretical and experimental characterization of optical grating coupler.

    PubMed

    Fesharaki, Faezeh; Hossain, Nadir; Vigne, Sebastien; Chaker, Mohamed; Wu, Ke

    2016-09-01

    Periodic structures, acting as reflectors, filters, and couplers, are a fundamental building block section in many optical devices. In this paper, a three-dimensional simulation of a grating coupler, a well-known periodic structure, is conducted. Guided waves and leakage characteristics of an out-of-plane grating coupler are studied in detail, and its coupling efficiency is examined. Furthermore, a numerical calibration analysis is applied through a commercial software package on the basis of a full-wave finite-element method to calculate the complex propagation constant of the structure and to evaluate the radiation pattern. For experimental evaluation, an optimized grating coupler is fabricated using electron-beam lithography technique and plasma etching. An excellent agreement between simulations and measurements is observed, thereby validating the demonstrated method. PMID:27607706

  17. Accurate calculation of the K photoionization around the minimum near threshold

    NASA Astrophysics Data System (ADS)

    Theodosiou, Constantine

    2003-05-01

    The accurate prediction of the location of Cooper minima in the photoionization cross sections of alkali metal atoms have been used in the past as a refined test for theoretical calculations. The older measuerements of Hudson and Carter(JOSA 57, 1471 (1967)) for potassium were drastically improved near the minimum by Sandner et al. (Phys. Rev. A 23, 2732 (1981)). The latter work found good overall agreement with the most accurate calculations, but the observed minimum had an overall shift and is clearly narrower than the calculated one. We have revisited the theoretical treatment within the Coulomb approximation with a central potential core approach (CACP)(Phys. Rev. A 30, 2881 (1984)), treating carefully the relativistic effects. We find excellent agreement with the measurements of Sandner et al.. Our study indicates that the improvement stems from the separate treatment of the ɛ p_3/2 and ɛ p_1/2 partial photoionization cross sections, in addition to the inclusion of a realistic central potential to describe the ion core.

  18. Spectroscopically Accurate Calculations of the Rovibrational Energies of Diatomic Hydrogen

    NASA Astrophysics Data System (ADS)

    Perry, Jason

    2005-05-01

    The Born-Oppenheimer approximation has been used to calculate the rotational and vibrational states of diatomic hydrogen. Because it is an approximation, our group now wants to use a Born-Oppenheimer potential to calculate the electronic energy that has been corrected to match closely with spectroscopic results. We are using a code that has corrections for adiabatic, relativistic, radiative, and non-adiabatic effects. The rovibrational energies have now been calculated for both bound and quasi-bound states. We also want to compute quadrupole transition probabilities for diatomic hydrogen. These calculations aspire to investigate diatomic hydrogen in astrophysical environments.

  19. Theoretical Calculations of Equations of State

    NASA Astrophysics Data System (ADS)

    Prakash, Madappa

    2016-07-01

    The modeling of core-collapse supernovae, neutron stars from their birth to old age, and binary mergers of compact stars requires a detailed knowledge of the equation of state (EOS) of matter at finite temperature. Thermodynamic state variables such as the free energy, energy per baryon, pressure, entropy per baryon, specific heats, chemical potentials of the various species and their derivatives with respect to number densities, thermal and adiabatic indices, etc., all play distinct roles in large-scale computer simulations involving compact objects. In this talk, recent developments in the calculation of the thermal properties of dense matter will be reviewed. Recent results from beyond relativistic mean field theory will be discussed. Highlights will include the role of non-nucleonic degrees of freedom at finite temperature, and possible avenues for future investigations.

  20. General formula for accurate calculation of halofullerenes polarizability

    NASA Astrophysics Data System (ADS)

    Sabirov, D. Sh.; Garipova, R. R.; Bulgakov, R. G.

    2012-01-01

    At the first time mean polarizabilities of fluoro-, chloro-, bromo[60]fullerenes have been calculated. The dependences of halofullerenes polarizabilities on the structure and the number of halogen atoms in a molecule have been analyzed. The phenomenon of polarizability depression is typical for all compounds under study. General formula for calculation of all classes of halofullerenes mean polarizabilities has been derived based on polarizability depression. Its applicability to related compounds (C70 fullerene choro-derivatives and hypothetical iodo[60]fullerenes) has been shown.

  1. Time-accurate Navier-Stokes calculations with multigrid acceleration

    NASA Technical Reports Server (NTRS)

    Melson, N. D.; Sanetrik, Mark D.; Atkins, Harold L.

    1993-01-01

    An efficient method for calculating unsteady flows is presented, with emphasis on a modified version of the thin-layer Navier-Stokes equations. Fourier stability analysis is used to illustrate the effect of treating the source term implicitly instead of explicity, as well as to illustrate other algorithmic choices. A 2D circular cylinder (with a Reynolds number of 1200 and a Mach number of 0.3) is calculated. The present scheme requires only about 10 percent of the computer time required by global minimum time stepping.

  2. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    SciTech Connect

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.

  3. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  4. Accurate characterization of Monte Carlo calculated electron beams for radiotherapy.

    PubMed

    Ma, C M; Faddegon, B A; Rogers, D W; Mackie, T R

    1997-03-01

    Monte Carlo studies of dose distributions in patients treated with radiotherapy electron beams would benefit from generalized models of clinical beams if such models introduce little error into the dose calculations. Methodology is presented for the design of beam models, including their evaluation in terms of how well they preserve the character of the clinical beam, and the effect of the beam models on the accuracy of dose distributions calculated with Monte Carlo. This methodology has been used to design beam models for electron beams from two linear accelerators, with either a scanned beam or a scattered beam. Monte Carlo simulations of the accelerator heads are done in which a record is kept of the particle phase-space, including the charge, energy, direction, and position of every particle that emerges from the treatment head, along with a tag regarding the details of the particle history. The character of the simulated beams are studied in detail and used to design various beam models from a simple point source to a sophisticated multiple-source model which treats particles from different parts of a linear accelerator as from different sub-sources. Dose distributions calculated using both the phase-space data and the multiple-source model agree within 2%, demonstrating that the model is adequate for the purpose of Monte Carlo treatment planning for the beams studied. Benefits of the beam models over phase-space data for dose calculation are shown to include shorter computation time in the treatment head simulation and a smaller disk space requirement, both of which impact on the clinical utility of Monte Carlo treatment planning.

  5. Perspective: Accurate ro-vibrational calculations on small molecules

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan

    2016-09-01

    In what has been described as the fourth age of quantum chemistry, variational nuclear motion programs are now routinely being used to obtain the vibration-rotation levels and corresponding wavefunctions of small molecules to the sort of high accuracy demanded by comparison with spectroscopy. In this perspective, I will discuss the current state-of-the-art which, for example, shows that these calculations are increasingly competitive with measurements or, indeed, replacing them and thus becoming the primary source of data on key processes. To achieve this accuracy ab initio requires consideration of small effects, routinely ignored in standard calculations, such as those due to quantum electrodynamics. Variational calculations are being used to generate huge lists of transitions which provide the input for models of radiative transport through hot atmospheres and to fill in or even replace measured transition intensities. Future prospects such as the study of molecular states near dissociation, which can provide a link with low-energy chemical reactions, are discussed.

  6. The Calculation of Accurate Metal-Ligand Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)

    1997-01-01

    The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.

  7. How Accurately Can We Calculate Neutrons Slowing Down In Water ?

    SciTech Connect

    Cullen, D E; Blomquist, R; Greene, M; Lent, E; MacFarlane, R; McKinley, S; Plechaty, E; Sublet, J C

    2006-03-30

    We have compared the results produced by a variety of currently available Monte Carlo neutron transport codes for the relatively simple problem of a fast source of neutrons slowing down and thermalizing in water. Initial comparisons showed rather large differences in the calculated flux; up to 80% differences. By working together we iterated to improve the results by: (1) insuring that all codes were using the same data, (2) improving the models used by the codes, and (3) correcting errors in the codes; no code is perfect. Even after a number of iterations we still found differences, demonstrating that our Monte Carlo and supporting codes are far from perfect; in particularly we found that the often overlooked nuclear data processing codes can be the weakest link in our systems of codes. The results presented here represent the today's state-of-the-art, in the sense that all of the Monte Carlo codes are modern, widely available and used codes. They all use the most up-to-date nuclear data, and the results are very recent, weeks or at most a few months old; these are the results that current users of these codes should expect to obtain from them. As such, the accuracy and limitations of the codes presented here should serve as guidelines to code users in interpreting their results for similar problems. We avoid crystal ball gazing, in the sense that we limit the scope of this report to what is available to code users today, and we avoid predicting future improvements that may or may not actual come to pass. An exception that we make is in presenting results for an improved thermal scattering model currently being testing using advanced versions of NJOY and MCNP that are not currently available to users, but are planned for release in the not too distant future. The other exception is to show comparisons between experimentally measured water cross sections and preliminary ENDF/B-VII thermal scattering law, S({alpha},{beta}) data; although these data are strictly

  8. Equilibrium gas flow computations. I - Accurate and efficient calculation of equilibrium gas properties

    NASA Technical Reports Server (NTRS)

    Liu, Yen; Vinokur, Marcel

    1989-01-01

    This paper treats the accurate and efficient calculation of thermodynamic properties of arbitrary gas mixtures for equilibrium flow computations. New improvements in the Stupochenko-Jaffe model for the calculation of thermodynamic properties of diatomic molecules are presented. A unified formulation of equilibrium calculations for gas mixtures in terms of irreversible entropy is given. Using a highly accurate thermo-chemical data base, a new, efficient and vectorizable search algorithm is used to construct piecewise interpolation procedures with generate accurate thermodynamic variable and their derivatives required by modern computational algorithms. Results are presented for equilibrium air, and compared with those given by the Srinivasan program.

  9. An accurate potential energy curve for helium based on ab initio calculations

    NASA Astrophysics Data System (ADS)

    Janzen, A. R.; Aziz, R. A.

    1997-07-01

    Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.

  10. SMARTIES: User-friendly codes for fast and accurate calculations of light scattering by spheroids

    NASA Astrophysics Data System (ADS)

    Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.

    2016-05-01

    We provide a detailed user guide for SMARTIES, a suite of MATLAB codes for the calculation of the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. SMARTIES is a MATLAB implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. The theory behind the improvements in numerical accuracy and convergence is briefly summarized, with reference to the original publications. Instructions of use, and a detailed description of the code structure, its range of applicability, as well as guidelines for further developments by advanced users are discussed in separate sections of this user guide. The code may be useful to researchers seeking a fast, accurate and reliable tool to simulate the near-field and far-field optical properties of elongated particles, but will also appeal to other developers of light-scattering software seeking a reliable benchmark for non-spherical particles with a challenging aspect ratio and/or refractive index contrast.

  11. An Effective Method to Accurately Calculate the Phase Space Factors for β - β - Decay

    DOE PAGES

    Neacsu, Andrei; Horoi, Mihai

    2016-01-01

    Accurate calculations of the electron phase space factors are necessary for reliable predictions of double-beta decay rates and for the analysis of the associated electron angular and energy distributions. We present an effective method to calculate these phase space factors that takes into account the distorted Coulomb field of the daughter nucleus, yet it allows one to easily calculate the phase space factors with good accuracy relative to the most exact methods available in the recent literature.

  12. Nitroborazines as potential high energy materials: density functional theoretical calculations.

    PubMed

    Janning, Jay D; Ball, David W

    2010-05-01

    As part of a search for new high energy density materials, we used density functional theoretical calculations to determine the thermochemical properties of various nitro-substituted borazine molecules. Optimized geometries, vibrational frequencies and spectra, and enthalpies of formation and combustion were determined for nitroborazine, dinitroborazine, trinitroborazine, and methyltrinitroborazine with substituents on either the boron atoms or the nitrogen atoms of the parent borazine ring. Our results indicate that the specific enthalpy of combustion ranged from 4 to 11 kJ g(-1), with increasing substitution of nitro groups lowering the energy of combustion per unit mass.

  13. Potential theoretic methods for far field sound radiation calculations

    NASA Technical Reports Server (NTRS)

    Hariharan, S. I.; Stenger, Edward J.; Scott, J. R.

    1995-01-01

    In the area of computational acoustics, procedures which accurately predict the far-field sound radiation are much sought after. A systematic development of such procedures are found in a sequence of papers by Atassi. The method presented here is an alternate approach to predicting far field sound based on simple layer potential theoretic methods. The main advantages of this method are: it requires only a simple free space Green's function, it can accommodate arbitrary shapes of Kirchoff surfaces, and is readily extendable to three-dimensional problems. Moreover, the procedure presented here, though tested for unsteady lifting airfoil problems, can easily be adapted to other areas of interest, such as jet noise radiation problems. Results are presented for lifting airfoil problems and comparisons are made with the results reported by Atassi. Direct comparisons are also made for the flat plate case.

  14. The theoretical shape of sucrose crystals from energy calculations

    NASA Astrophysics Data System (ADS)

    Saska, Michael; Myerson, Allan S.

    1983-05-01

    The surface energies of individual crystallographic faces of crystalline sucrose were calculated using two forms of the 6-exp (Buckingham) potential. Hydrogen bond energies were calculated as a sum of O-H, O…H and O…O interactions where the Lippincott-Schroeder short-range potential was used for O-H and O…H pairs and the 6-exp potential for the non-bonded O…O interactions. Assuming that the surface energy equals half of the cohesive energy of the crystal, the attachment and surface energies of most of the faces found on as sucrose crystal were calculated. A computer program was written to draw the theoretical shape of crystals given the positions (central distances) of its faces. The resulting sucrose shapes are elongated along the c-axis. It is argued that the c-axis elongated habit is an intrinsic shape for vapor grown sucrose crystals (if realizable) and it is suggested that the usual shapes of solution grown sucrose crystals can be explained in terms of solvent (water) adsorption.

  15. Preliminary theoretical acoustic and rf sounding calculations for MILL RACE

    SciTech Connect

    Warshaw, S.I.; Dubois, P.F.

    1981-11-02

    As participant in DOE/ISA's Ionospheric Monitoring Program, LLNL has the responsibility of providing theoretical understanding and calculational support for experimental activities carried out by Los Alamos National Laboratory in using ionospheric sounders to remotely detect violent atmospheric phenomena. We have developed a system of interconnected computer codes which simulate the entire range of atmospheric and ionospheric processes involved in this remote detection procedure. We are able to model the acoustic pulse shape from an atmospheric explosion, the subsequent nonlinear transport of this energy to all parts of the immediate atmosphere including the ionosphere, and the propagation of high-frequency ratio waves through the acoustically perturbed ionosphere. Los Alamos' coverage of DNA's MILL RACE event provided an excellent opportunity to assess the credibility of the calculational system to correctly predict how ionospheric sounders would respond to a surface-based chemical explosion. In this experiment, 600 tons of high explosive were detonated at White Sands Missile Range at 12:35:40 local time on 16 September 1981. Vertical incidence rf phase sounders and bistatic oblique incidence rf sounders fielded by Los Alamos and SRI International throughout New Mexico and southern Colorado detected the ionospheric perturbation that ensued. A brief account of preliminary calculations of the acoustic disturbance and the predicted ionospheric sounder signatures for MILL RACE is presented. (WHK)

  16. Accurate calculation of conductive conductances in complex geometries for spacecrafts thermal models

    NASA Astrophysics Data System (ADS)

    Garmendia, Iñaki; Anglada, Eva; Vallejo, Haritz; Seco, Miguel

    2016-02-01

    The thermal subsystem of spacecrafts and payloads is always designed with the help of Thermal Mathematical Models. In the case of the Thermal Lumped Parameter (TLP) method, the non-linear system of equations that is created is solved to calculate the temperature distribution and the heat power that goes between nodes. The accuracy of the results depends largely on the appropriate calculation of the conductive and radiative conductances. Several established methods for the determination of conductive conductances exist but they present some limitations for complex geometries. Two new methods are proposed in this paper to calculate accurately these conductive conductances: The Extended Far Field method and the Mid-Section method. Both are based on a finite element calculation but while the Extended Far Field method uses the calculation of node mean temperatures, the Mid-Section method is based on assuming specific temperature values. They are compared with traditionally used methods showing the advantages of these two new methods.

  17. Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  18. Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  19. Possible calcium centers for hydrogen storage applications: An accurate many-body study by AFQMC calculations with large basis sets

    NASA Astrophysics Data System (ADS)

    Purwanto, Wirawan; Krakauer, Henry; Zhang, Shiwei; Virgus, Yudistira

    2011-03-01

    Weak H2 physisorption energies present a significant challenge to first-principle theoretical modeling and prediction of materials for H storage. There has been controversy regarding the accuracy of DFT on systems involving Ca cations. We use the auxiliary-field quantum Monte Carlo (AFQMC) method to accurately predict the binding energy of Ca + , - 4{H}2 . AFQMC scales as Nbasis3and has demonstrated accuracy similar to or better than the gold-standard coupled cluster CCSD(T) method. We apply a modified Cholesky decomposition to achieve efficient Hubbard-Stratonovich transformation in AFQMC at large basis sizes. We employ the largest correlation consistent basis sets available, up to Ca/cc-pCV5Z, to extrapolate to the complete basis limit. The calculated potential energy curve exhibits binding with a double-well structure. Supported by DOE and NSF. Calculations were performed at OLCF Jaguar and CPD.

  20. The calculation of theoretical chromospheric models and the interpretation of solar spectra from rockets and spacecraft

    NASA Technical Reports Server (NTRS)

    Avrett, E. H.

    1984-01-01

    Models and spectra of sunspots were studied, because they are important to energy balance and variability discussions. Sunspot observations in the ultraviolet region 140 to 168 nn was obtained by the NRL High Resolution Telescope and Spectrograph. Extensive photometric observations of sunspot umbrae and prenumbrae in 10 chanels covering the wavelength region 387 to 3800 nm were made. Cool star opacities and model atmospheres were computed. The Sun is the first testcase, both to check the opacity calculations against the observed solar spectrum, and to check the purely theoretical model calculation against the observed solar energy distribution. Line lists were finally completed for all the molecules that are important in computing statistical opacities for energy balance and for radiative rate calculations in the Sun (except perhaps for sunspots). Because many of these bands are incompletely analyzed in the laboratory, the energy levels are not well enough known to predict wavelengths accurately for spectrum synthesis and for detailed comparison with the observations.

  1. Time-accurate unsteady aerodynamic and aeroelastic calculations for wings using Euler equations

    NASA Technical Reports Server (NTRS)

    Guruswamy, Guru P.

    1988-01-01

    A time-accurate approach to simultaneously solve the Euler flow equations and modal structural equations of motion is presented for computing aeroelastic responses of wings. The Euler flow eauations are solved by a time-accurate finite difference scheme with dynamic grids. The coupled aeroelastic equations of motion are solved using the linear acceleration method. The aeroelastic configuration adaptive dynamic grids are time accurately generated using the aeroelastically deformed shape of the wing. The unsteady flow calculations are validated wih experiment, both for a semi-infinite wing and a wall-mounted cantilever rectangular wings. Aeroelastic responses are computed for a rectangular wing using the modal data generated by the finite-element method. The robustness of the present approach in computing unsteady flows and aeroelastic responses that are beyond the capability of earlier approaches using the potential equations are demonstrated.

  2. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  3. Accurate near-field calculation in the rigorous coupled-wave analysis method

    NASA Astrophysics Data System (ADS)

    Weismann, Martin; Gallagher, Dominic F. G.; Panoiu, Nicolae C.

    2015-12-01

    The rigorous coupled-wave analysis (RCWA) is one of the most successful and widely used methods for modeling periodic optical structures. It yields fast convergence of the electromagnetic far-field and has been adapted to model various optical devices and wave configurations. In this article, we investigate the accuracy with which the electromagnetic near-field can be calculated by using RCWA and explain the observed slow convergence and numerical artifacts from which it suffers, namely unphysical oscillations at material boundaries due to the Gibbs phenomenon. In order to alleviate these shortcomings, we also introduce a mathematical formulation for accurate near-field calculation in RCWA, for one- and two-dimensional straight and slanted diffraction gratings. This accurate near-field computational approach is tested and evaluated for several representative test-structures and configurations in order to illustrate the advantages provided by the proposed modified formulation of the RCWA.

  4. A localized basis that allows fast and accurate second order Moller-Plesset calculations

    SciTech Connect

    Subotnik, Joseph E.; Head-Gordon, Martin

    2004-10-27

    We present a method for computing a basis of localized orthonormal orbitals (both occupied and virtual), in whose representation the Fock matrix is extremely diagonal-dominant. The existence of these orbitals is shown empirically to be sufficient for achieving highly accurate MP@ energies, calculated according to Kapuy's method. This method (which we abbreviate KMP2), which involves a different partitioning of the n-electron Hamiltonian, scales at most quadratically with potential for linearity in the number of electrons. As such, we believe the KMP2 algorithm presented here could be the basis of a viable approach to local correlation calculations.

  5. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.; Dixon, David A.

    2008-11-01

    High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

  6. Accurate calculation of computer-generated holograms using angular-spectrum layer-oriented method.

    PubMed

    Zhao, Yan; Cao, Liangcai; Zhang, Hao; Kong, Dezhao; Jin, Guofan

    2015-10-01

    Fast calculation and correct depth cue are crucial issues in the calculation of computer-generated hologram (CGH) for high quality three-dimensional (3-D) display. An angular-spectrum based algorithm for layer-oriented CGH is proposed. Angular spectra from each layer are synthesized as a layer-corresponded sub-hologram based on the fast Fourier transform without paraxial approximation. The proposed method can avoid the huge computational cost of the point-oriented method and yield accurate predictions of the whole diffracted field compared with other layer-oriented methods. CGHs of versatile formats of 3-D digital scenes, including computed tomography and 3-D digital models, are demonstrated with precise depth performance and advanced image quality. PMID:26480062

  7. Accurate calculation of control-augmented structural eigenvalue sensitivities using reduced-order models

    NASA Technical Reports Server (NTRS)

    Livne, Eli

    1989-01-01

    A method is presented for generating mode shapes for model order reduction in a way that leads to accurate calculation of eigenvalue derivatives and eigenvalues for a class of control augmented structures. The method is based on treating degrees of freedom where control forces act or masses are changed in a manner analogous to that used for boundary degrees of freedom in component mode synthesis. It is especially suited for structures controlled by a small number of actuators and/or tuned by a small number of concentrated masses whose positions are predetermined. A control augmented multispan beam with closely spaced natural frequencies is used for numerical experimentation. A comparison with reduced-order eigenvalue sensitivity calculations based on the normal modes of the structure shows that the method presented produces significant improvements in accuracy.

  8. Thermochemistry and Charge Delocalization in Cyclization Reactions Using Accurate Quantum Monte Carlo Calculations

    NASA Astrophysics Data System (ADS)

    Saritas, Kayahan; Grossman, Jeffrey C.

    2015-03-01

    Molecules that undergo pericyclic isomerization reactions find interesting optical and energy storage applications, because of their usually high quantum yields, large spectral shifts and small structural changes upon light absorption. These reactions induce a drastic change in the conjugated structure such that substituents that become a part of the conjugated system upon isomerization can play an important role in determining properties such as enthalpy of isomerization and HOMO-LUMO gap. Therefore, theoretical investigations dealing with such systems should be capable of accurately capturing the interplay between electron correlation and exchange effects. In this work, we examine the dihydroazulene isomerization as an example conjugated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict thermochemical properties and to benchmark results from density functional theory (DFT) methods. Although DFT provides sufficient accuracy for similar systems, in this particular system, DFT predictions of ground state and reaction paths are inconsistent and non-systematic errors arise. We present a comparison between QMC and DFT results for enthalpy of isomerization, HOMO-LUMO gap and charge densities with a range of DFT functionals.

  9. Accurate and approximate calculations of Raman scattering in the atmosphere of Neptune

    NASA Astrophysics Data System (ADS)

    Sromovsky, L. A.

    2005-01-01

    Raman scattering by H 2 in Neptune's atmosphere has significant effects on its reflectivity for λ<0.5 μm, producing baseline decreases of ˜20% in a clear atmosphere and ˜10% in a hazy atmosphere. However, few accurate Raman calculations are carried out because of their complexity and computational costs. Here we present the first radiation transfer algorithm that includes both polarization and Raman scattering and facilitates computation of spatially resolved spectra. New calculations show that Cochran and Trafton's (1978, Astrophys. J. 219, 756-762) suggestion that light reflected in the deep CH 4 bands is mainly Raman scattered is not valid for current estimates of the CH 4 vertical distribution, which implies only a 4% Raman contribution. Comparisons with IUE, HST, and groundbased observations confirm that high altitude haze absorption is reducing Neptune's geometric albedo by ˜6% in the 0.22-0.26 μm range and by ˜13% in the 0.35-0.45 μm range. A sample haze model with 0.2 optical depths of 0.2-μm radius particles between 0.1 and 0.8 bars fits reasonably well, but is not a unique solution. We used accurate calculations to evaluate several approximations of Raman scattering. The Karkoschka (1994, Icarus 111, 174-192) method of applying Raman corrections to calculated spectra and removing Raman effects from observed spectra is shown to have limited applicability and to undercorrect the depths of weak CH 4 absorption bands. The relatively large Q-branch contribution observed by Karkoschka is shown to be consistent with current estimates of Raman cross-sections. The Wallace (1972, Astrophys. J. 176, 249-257) approximation, produces geometric albedo ˜5% low as originally proposed, but can be made much more accurate by including a scattering contribution from the vibrational transition. The original Pollack et al. (1986, Icarus 65, 442-466) approximation is inaccurate and unstable, but can be greatly improved by several simple modifications. A new

  10. Highly Accurate Quantum-Chemical Calculations for the Interstellar Molecules C_3 and l-C_3H^+

    NASA Astrophysics Data System (ADS)

    Botschwina, Peter; Schröder, Benjamin; Stein, Christopher; Sebald, Peter; Oswald, Rainer

    2014-06-01

    Composite potential energy surfaces with coupled-cluster contributions up to CCSDTQP were constructed for C_3 and l-C_3H^+ and used in the calculation of spectroscopic properties. The use of very large AO basis sets and the consideration of higher-order correlation beyond CCSD(T) is of utmost importance for C_3 in order to arrive at quantitative spectroscopic data. The first detection of l-C_3H^+ in the interstellar medium was reported by Pety et al., who attributed 9 radio lines observed in the horsehead photodissociation region to that species. That assignment was questioned by the recent theoretical work of Huang et al. However, our more accurate calculations are well in support of the original assignment. The calculated ground-state rotational constant is B_0 = 11248 MHz, only 0.03% off from the radio astronomical value of 11244.9512±0.0015 MHz. The ratio of centrifugal distortion constants D_0(exp.)/D_e(theor.) of 1.8 is quite large, but reasonable in comparison with C_3O and C_3. J. Pety, P. Gratier, V. Guzmán, E. Roueff, M. Gerin et al., Astron. Astrophys. 2012, A68, 1-8. X. Huang, R. C. Fortenberry, T. J. Lee, Astrophys. J. Lett. 2013, 768:L25, 1-5. P. Botschwina, R. Oswald, J. Chem. Phys. 2008, 129, 044305

  11. Accurate first-principles calculations for 12CH3D infrared spectra from isotopic and symmetry transformations.

    PubMed

    Rey, Michaël; Nikitin, Andrei V; Tyuterev, Vladimir G

    2014-07-28

    Accurate variational high-resolution spectra calculations in the range 0-8000 cm(-1) are reported for the first time for the monodeutered methane ((12)CH3D). Global calculations were performed by using recent ab initio surfaces for line positions and line intensities derived from the main isotopologue (12)CH4. Calculation of excited vibrational levels and high-J rovibrational states is described by using the normal mode Eckart-Watson Hamiltonian combined with irreducible tensor formalism and appropriate numerical procedures for solving the quantum nuclear motion problem. The isotopic H→D substitution is studied in details by means of symmetry and nonlinear normal mode coordinate transformations. Theoretical spectra predictions are given up to J = 25 and compared with the HITRAN 2012 database representing a compilation of line lists derived from analyses of experimental spectra. The results are in very good agreement with available empirical data suggesting that a large number of yet unassigned lines in observed spectra could be identified and modeled using the present approach. PMID:25084919

  12. Theoretical foundation of patient v. population preferences in calculating QALYs.

    PubMed

    Gandjour, Afschin

    2010-01-01

    The cost-effectiveness of health care interventions is often evaluated using quality-adjusted life years (QALYs) as a measure of outcome. There is a debate on whether QALYs should use patient preferences as opposed to community preferences. This article shows that patient preferences have a theoretical foundation in preference-utilitarian theory and welfare economics. In contrast, this study found no compelling theoretical basis for community preferences. There is a need for further development of a normative framework to inform the choice of preference source. PMID:20511562

  13. Fast and accurate inductance and coupling calculation for a multi-layer Nb process

    NASA Astrophysics Data System (ADS)

    Fourie, Coenrad J.; Takahashi, Akitomo; Yoshikawa, Nobuyuki

    2015-03-01

    Currently, fabrication processes for superconductive integrated circuits are moving to multiple wiring and shielding layers, some of which are placed below the main ground plane (GP) and device layers. The Advanced Industrial Science and Technology advanced process (ADP2) was the first such multi-layer Nb process with planarized passive transmission line and GP layers below the junction layer, and is at the time of writing still the most developed. This process allows complex circuit designs, and accurate inductance extraction helps to push the boundaries of the layouts possible. We show that the position of ground connections between ground layers influences the inductance of structures for which these GPs act as return path, and that this needs to be accounted for in modelling. However, due to the number of wiring layers and GPs, full layout modelling of large cells causes long calculation times. In this paper we discuss methods with which to reduce model size, and calibrate InductEx calculations using these methods against measured results. We show that model reduction followed by calibration results in fast calculation times while good accuracy is maintained. We also show that InductEx correctly handles coupling between conductors in a multi-layer layout, and how to model layouts to gauge unwanted coupling between power lines and single flux quantum electronics.

  14. Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry.

    PubMed

    Umer, Muhammad; Kopp, Wassja A; Leonhard, Kai

    2015-12-01

    We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 - both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably. PMID:26646881

  15. Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry

    NASA Astrophysics Data System (ADS)

    Umer, Muhammad; Kopp, Wassja A.; Leonhard, Kai

    2015-12-01

    We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 — both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably.

  16. Highly accurate video coordinate generation for automatic 3-D trajectory calculation

    NASA Astrophysics Data System (ADS)

    Macleod, A.; Morris, Julian R. W.; Lyster, M.

    1990-08-01

    Most TV-based motion analysis systems, including the original version of 1/ICON, produce 3D coordinates by combining pre-tracked 2D trajectories from each camera. The latest version of the system, VICON-VX, uses totally automatic 3D trajectory calculation using the Geometric Self Identification (GSI) technique. This is achieved by matching unsorted 2D image coordinates from all cameras, looking for intersecting marker 'rays', and matching intersections into 3D trajectories. Effective GSI, with low false-positive intersection rates is only possible with highly accurate 2D data, produced by stable, high-resolution coordinate generators, and incorporating appropriate compensation for lens distortions. Data capture software and hardware have been completely redesigned to achieve this accuracy, together with higher throughput rates and better resistance to errors. In addition, a new ADC facility has been incorporated to allow very high speed analog data acquisition, synchronised with video measurements.

  17. Temperature dependent effective potential method for accurate free energy calculations of solids

    NASA Astrophysics Data System (ADS)

    Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

    2013-03-01

    We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

  18. Accurate Calculations of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory.

    PubMed

    Semenov, Alexander; Babikov, Dmitri

    2014-01-16

    For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N2 collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections at higher temperatures and/or for polyatomic molecules and heavier quenchers, which is computationally close to impossible within the full-quantum framework.

  19. Retention Projection Enables Accurate Calculation of Liquid Chromatographic Retention Times Across Labs and Methods

    PubMed Central

    Abate-Pella, Daniel; Freund, Dana M.; Ma, Yan; Simón-Manso, Yamil; Hollender, Juliane; Broeckling, Corey D.; Huhman, David V.; Krokhin, Oleg V.; Stoll, Dwight R.; Hegeman, Adrian D.; Kind, Tobias; Fiehn, Oliver; Schymanski, Emma L.; Prenni, Jessica E.; Sumner, Lloyd W.; Boswell, Paul G.

    2015-01-01

    Identification of small molecules by liquid chromatography-mass spectrometry (LC-MS) can be greatly improved if the chromatographic retention information is used along with mass spectral information to narrow down the lists of candidates. Linear retention indexing remains the standard for sharing retention data across labs, but it is unreliable because it cannot properly account for differences in the experimental conditions used by various labs, even when the differences are relatively small and unintentional. On the other hand, an approach called “retention projection” properly accounts for many intentional differences in experimental conditions, and when combined with a “back-calculation” methodology described recently, it also accounts for unintentional differences. In this study, the accuracy of this methodology is compared with linear retention indexing across eight different labs. When each lab ran a test mixture under a range of multi-segment gradients and flow rates they selected independently, retention projections averaged 22-fold more accurate for uncharged compounds because they properly accounted for these intentional differences, which were more pronounced in steep gradients. When each lab ran the test mixture under nominally the same conditions, which is the ideal situation to reproduce linear retention indices, retention projections still averaged 2-fold more accurate because they properly accounted for many unintentional differences between the LC systems. To the best of our knowledge, this is the most successful study to date aiming to calculate (or even just to reproduce) LC gradient retention across labs, and it is the only study in which retention was reliably calculated under various multi-segment gradients and flow rates chosen independently by labs. PMID:26292625

  20. Theoretical calculations of hyperfine coupling constants for muoniated butyl radicals.

    PubMed

    Chen, Ya Kun; Fleming, Donald G; Wang, Yan Alexander

    2011-04-01

    The hyperfine coupling constants (HFCCs) of all the butyl radicals that can be produced by muonium (Mu) addition to butene isomers (1- and 2-butene and isobutene) have been calculated, to compare with the experimental results for the muon and proton HFFCs for these radicals reported in paper II (Fleming, D. G.; et al. J. Phys. Chem. A 2011, 10.1021/jp109676b) that follows. The equilibrium geometries and HFCCs of these muoniated butyl radicals as well as their unsubstituted isotopomers were treated at both the spin-unrestricted MP2/EPR-III and B3LYP/EPR-III levels of theory. Comparisons with calculations carried out for the EPR-II basis set have also been made. All calculations were carried out in vacuo at 0 K only. A C-Mu bond elongation scheme that lengthens the equilibrium C-H bond by a factor of 1.076, on the basis of recent quantum calculations of the muon HFCCs of the ethyl radical, has been exploited to determine the vibrationally corrected muon HFCCs. The sensitivity of the results to small variations around this scale factor was also investigated. The computational methodology employed was "benchmarked" in comparisons with the ethyl radical, both with higher level calculations and with experiment. For the β-HFCCs of interest, compared to B3LYP, the MP2 calculations agree better with higher level theories and with experiment in the case of the eclipsed C-Mu bond and are generally deemed to be more reliable in predicting the equilibrium conformations and muon HFCCs near 0 K, in the absence of environmental effects. In some cases though, the experimental results in paper II demonstrate that environmental effects enhance the muon HFCC in the solid phase, where much better agreement with the experimental muon HFCCs near 0 K is found from B3LYP than from MP2. This seemingly better level of agreement is probably fortuitous, due to error cancellations in the DFT calculations, which appear to mimic these environmental effects. For the staggered proton HFCCs of the

  1. Theoretical Calculation of the N_2 Broadened Half-Widths of H_2O

    NASA Astrophysics Data System (ADS)

    Tipping, R. H.; Ma, Q.

    2010-06-01

    For many applications, in addition to accurate spectral line frequencies and intensities one needs accurate Lorentzian parameters (half-widths, pressure shifts, and their temperature dependencies). Because of the importance of H_2O in the Earth's atmosphere, extensive compilations of these data are available in the HITRAN database. Recently, ab initio calculations have been carried out and databases containing tens of millions of line frequencies and intensities are available. Obviously, it is not possible to measure their Lorentzian parameters, and one must rely on theoretical calculations. For many years researchers have used the Robert-Bonamy (RB) formalism; however, we recently discovered a subtle error was made in their original derivation, and this modification is not negligible for certain systems. In this theory the internal motions are treated quantum mechanically, while the translational motion is treated classically. In order to achieve the desired accuracy, one needs to use a realistic interaction potential, and a realistic trajectory model for the translational motion. Because of the large number of potential matrix elements appearing in the standard application of the RB theory, one is forced to introduce cut-offs that may limit the accuracy attainable. To obviate the necessity of low-order cut-offs and achieve results for half-widths to the accuracy of the interaction potential, we recently reformulated the theory using the coordinate representation. In the present paper, we present results to study the effects of using different experimental half-width data to obtain the parameters in several models for the interaction potential, and the effects of different trajectory models for treating the relative motion. From our detailed analysis, we are able to draw several conclusions that should help theorists to make choices in order to achieve realistic theoretical half-widths and to assess their accuracy. Q. Ma, R. H. Tipping, and C. Boulet, J. Chem

  2. Accurate band gaps of semiconductors and insulators from Quantum Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Nazarov, Roman; Hood, Randolph; Morales, Miguel

    2015-03-01

    Ab initio calculations are useful tools in developing materials with targeted band gaps for semiconductor industry. Unfortunately, the main workhorse of ab initio calculations - density functional theory (DFT) in local density approximation (LDA) or generalized gradient approximation (GGA) underestimates band gaps. Several approaches have been proposed starting from empirical corrections to more elaborate exchange-correlation functionals to deal with this problem. But none of these work well for the entire range of semiconductors and insulators. Deficiencies of DFT as a mean field method can be overcome using many-body techniques. Quantum Monte Carlo (QMC) methods can obtain a nearly exact numerical solutions of both total energies and spectral properties. Diffusion Monte Carlo (DMC), the most widely used QMC method, has been shown to provide gold standard results for different material properties, including spectroscopic constants of dimers and clusters, equation of state for solids, accurate descriptions of defects in metals and insulators. To test DMC's accuracy in a wider range of semiconductors and insulators we have computed band gaps of several semiconductors and insulators. We show that DMC can provide superior agreement with experiment compared with more traditional DFT approaches including high level exchange-correlation functionals (e.g. HSE).

  3. Universal model for accurate calculation of tracer diffusion coefficients in gas, liquid and supercritical systems.

    PubMed

    Lito, Patrícia F; Magalhães, Ana L; Gomes, José R B; Silva, Carlos M

    2013-05-17

    In this work it is presented a new model for accurate calculation of binary diffusivities (D12) of solutes infinitely diluted in gas, liquid and supercritical solvents. It is based on a Lennard-Jones (LJ) model, and contains two parameters: the molecular diameter of the solvent and a diffusion activation energy. The model is universal since it is applicable to polar, weakly polar, and non-polar solutes and/or solvents, over wide ranges of temperature and density. Its validation was accomplished with the largest database ever compiled, namely 487 systems with 8293 points totally, covering polar (180 systems/2335 points) and non-polar or weakly polar (307 systems/5958 points) mixtures, for which the average errors were 2.65% and 2.97%, respectively. With regard to the physical states of the systems, the average deviations achieved were 1.56% for gaseous (73 systems/1036 points), 2.90% for supercritical (173 systems/4398 points), and 2.92% for liquid (241 systems/2859 points). Furthermore, the model exhibited excellent prediction ability. Ten expressions from the literature were adopted for comparison, but provided worse results or were not applicable to polar systems. A spreadsheet for D12 calculation is provided online for users in Supplementary Data.

  4. Thermochemical properties and contribution groups for ketene dimers and related structures from theoretical calculations.

    PubMed

    Morales, Giovanni; Martínez, Ramiro

    2009-07-30

    This research's main goals were to analyze ketene dimers' relative stability and expand group additivity value (GAV) methodology for estimating the thermochemical properties of high-weight ketene polymers (up to tetramers). The CBS-Q multilevel procedure and statistical thermodynamics were used for calculating the thermochemical properties of 20 cyclic structures, such as diketenes, cyclobutane-1,3-diones, cyclobut-2-enones and pyran-4-ones, as well as 57 acyclic base compounds organized into five groups. According to theoretical heat of formation predictions, diketene was found to be thermodynamically favored over cyclobutane-1,3-dione and its enol-tautomeric form (3-hydroxycyclobut-2-enone). This result did not agree with old combustion experiments. 3-Hydroxycyclobut-2-enone was found to be the least stable dimer and its reported experimental detection in solution may have been due to solvent effects. Substituted diketenes had lower stability than substituted cyclobutane-1,3-diones with an increased number of methyl substituents, suggesting that cyclobutane-1,3-dione type dimers are the major products because of thermodynamic control of alkylketene dimerization. Missing GAVs for the ketene dimers and related structures were calculated through linear regression on the 57 acyclic base compounds. Corrections for non next neighbor interactions (such as gauche, eclipses, and internal hydrogen bond) were needed for obtaining a highly accurate and precise regression model. To the best of our knowledge, the hydrogen bond correction for GAV methodology is the first reported in the literature; this correction was correlated to MP2/6-31Gdagger and HF/6-31Gdagger derived geometries to facilitate its application. GAVs assessed by the linear regression model were able to reproduce acyclic compounds' theoretical thermochemical properties and experimental heat of formation for acetylacetone. Ring formation and substituent position corrections were calculated by consecutively

  5. Thermochemical properties and contribution groups for ketene dimers and related structures from theoretical calculations.

    PubMed

    Morales, Giovanni; Martínez, Ramiro

    2009-07-30

    This research's main goals were to analyze ketene dimers' relative stability and expand group additivity value (GAV) methodology for estimating the thermochemical properties of high-weight ketene polymers (up to tetramers). The CBS-Q multilevel procedure and statistical thermodynamics were used for calculating the thermochemical properties of 20 cyclic structures, such as diketenes, cyclobutane-1,3-diones, cyclobut-2-enones and pyran-4-ones, as well as 57 acyclic base compounds organized into five groups. According to theoretical heat of formation predictions, diketene was found to be thermodynamically favored over cyclobutane-1,3-dione and its enol-tautomeric form (3-hydroxycyclobut-2-enone). This result did not agree with old combustion experiments. 3-Hydroxycyclobut-2-enone was found to be the least stable dimer and its reported experimental detection in solution may have been due to solvent effects. Substituted diketenes had lower stability than substituted cyclobutane-1,3-diones with an increased number of methyl substituents, suggesting that cyclobutane-1,3-dione type dimers are the major products because of thermodynamic control of alkylketene dimerization. Missing GAVs for the ketene dimers and related structures were calculated through linear regression on the 57 acyclic base compounds. Corrections for non next neighbor interactions (such as gauche, eclipses, and internal hydrogen bond) were needed for obtaining a highly accurate and precise regression model. To the best of our knowledge, the hydrogen bond correction for GAV methodology is the first reported in the literature; this correction was correlated to MP2/6-31Gdagger and HF/6-31Gdagger derived geometries to facilitate its application. GAVs assessed by the linear regression model were able to reproduce acyclic compounds' theoretical thermochemical properties and experimental heat of formation for acetylacetone. Ring formation and substituent position corrections were calculated by consecutively

  6. Calorimetric determinations and theoretical calculations of polymorphs of thalidomide

    NASA Astrophysics Data System (ADS)

    Lara-Ochoa, F.; Pérez, G. Espinosa; Mijangos-Santiago, F.

    2007-09-01

    The analysis of the thermograms of thalidomide obtained for the two reported polymorphs α and β by differential scanning calorimetry (DSC) shows some inconsistencies that are discussed in the present work. The conception of a new polymorph form, named β ∗, allowed us to explain the observed thermal behavior more satisfactorily. This new polymorph shows enantiotropy with both α and β polymorphs, reflected in the unique endotherm obtained in the DSC-thermograms, when a heating rate of 10 °C/min is applied. Several additional experiments, such as re-melting of both polymorph forms, showed that there is indeed a new polymorph with an endotherm located between the endotherms of α and β. IR, Raman, and powder X-ray permit us to characterize the isolated compound, resulting from the re-melting of both polymorph forms. Mechanical calculations were performed to elucidate the conformations of each polymorph, and ab initio quantum chemical calculations were performed to determine the energy of the more stable conformers and the spatial cell energy for both polymorphs α and β. These results suggested a possible conformation for the newly discovered polymorph β ∗.

  7. Hydrogen in Ag-doped ZnO: theoretical calculations.

    PubMed

    He, H Y; Hu, J; Pan, B C

    2009-05-28

    Based on density functional theory calculations, we systematically investigate the behaviors of a H atom in Ag-doped ZnO involving the preference sites, diffusion behaviors, the electronic structures, and vibrational properties. We find that a H atom can migrate to the doped Ag to form a Ag-H complex by overcoming energy barriers of 0.3-1.0 eV. The lowest-energy site for H location is the bond center of a Ag-O in the basal plane. Moreover, H can migrate between this site and its equivalent sites with energy cost of less than 0.5 eV. In contrast, dissociation of such a Ag-H complex needs energy of about 1.1-1.3 eV. This implies that the Ag-H complexes can commonly exist in the Ag-doped ZnO, which have a negative effect on the desirable p-type carrier concentrations of Ag-doped ZnO. In addition, based on the frozen phonon calculation, the vibrational properties of ZnO with a Ag-H complex are predicted. Some new vibrational modes associated with the Ag-H complex present in the vibrational spectrum of the system.

  8. Fast and Accurate Radiative Transfer Calculations Using Principal Component Analysis for (Exo-)Planetary Retrieval Models

    NASA Astrophysics Data System (ADS)

    Kopparla, P.; Natraj, V.; Shia, R. L.; Spurr, R. J. D.; Crisp, D.; Yung, Y. L.

    2015-12-01

    Radiative transfer (RT) computations form the engine of atmospheric retrieval codes. However, full treatment of RT processes is computationally expensive, prompting usage of two-stream approximations in current exoplanetary atmospheric retrieval codes [Line et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT computations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those few optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Kopparla et al. [2015, in preparation] extended the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Here, we apply the PCA method to a some typical (exo-)planetary retrieval problems. Comparisons between the new model, called Universal Principal Component Analysis Radiative Transfer (UPCART) model, two-stream models and line-by-line RT models are performed, for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the top of the atmosphere for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and stellar and viewing geometries. We demonstrate that very accurate radiance and flux estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases, as compared to a numerically exact line-by-line RT model. The accuracy is enhanced when the results are convolved to typical instrument resolutions. The operational speed and accuracy of UPCART can be further improved by optimizing binning schemes and parallelizing the codes, work

  9. Theoretical calculations on the electron absorption spectra of selected Polycyclic Aromatic Hydrocarbons (PAH) and derivatives

    NASA Technical Reports Server (NTRS)

    Du, Ping

    1993-01-01

    As a theoretical component of the joint effort with the laboratory of Dr. Lou Allamandola to search for potential candidates for interstellar organic carbon compound that are responsible for the visible diffuse interstellar absorption bands (DIB's), quantum mechanical calculations were performed on the electron absorption spectra of selected polycyclic aromatic hydrocarbons (PAH) and derivatives. In the completed project, 15 different species of naphthalene, its hydrogen abstraction and addition derivatives, and corresponding cations and anions were studied. Using semiempirical quantum mechanical method INDO/S, the ground electronic state of each species was evaluated with restricted Hartree-Fock scheme and limited configuration interaction. The lowest energy spin state for each species was used for electron absorption calculations. Results indicate that these calculations are accurate enough to reproduce the spectra of naphthalene cation and anion observed in neon matrix. The spectral pattern of the hydrogen abstraction and addition derivatives predicted based on these results indicate that the electron configuration of the pi orbitals of these species is the dominant determinant. A combined list of 19 absorptions calculated from 4500 A to 10,400 A were compiled and suggested as potential candidates that are relevant for the DIB's absorptions. Continued studies on pyrene and derivatives revealed the ground state symmetries and multiplicities of its neutral, anionic, and cationic species. Spectral calculations show that the cation (B(sub 3g)-2) and the anion (A(sub u)-2) are more likely to have low energy absorptions in the regions between 10 kK and 20 kK, similar to naphthalene. These absorptions, together with those to be determined from the hydrogen abstraction and addition derivatives of pyrene, can be used to provide additional candidates and suggest experimental work in the search for interstellar compounds that are responsible for DIB's.

  10. Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

    PubMed

    Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav

    2013-10-28

    We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

  11. Properties of Solar Thermal Fuels by Accurate Quantum Monte Carlo Calculations

    NASA Astrophysics Data System (ADS)

    Saritas, Kayahan; Ataca, Can; Grossman, Jeffrey C.

    2014-03-01

    Efficient utilization of the sun as a renewable and clean energy source is one of the major goals of this century due to increasing energy demand and environmental impact. Solar thermal fuels are materials that capture and store the sun's energy in the form of chemical bonds, which can then be released as heat on demand and charged again. Previous work on solar thermal fuels faced challenges related to the cyclability of the fuel over time, as well as the need for higher energy densities. Recently, it was shown that by templating photoswitches onto carbon nanostructures, both high energy density as well as high stability can be achieved. In this work, we explore alternative molecules to azobenzene in such a nano-templated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict the energy storage potential for each molecule. Our calculations show that in many cases the level of accuracy provided by density functional theory (DFT) is sufficient. However, in some cases, such as dihydroazulene, the drastic change in conjugation upon light absorption causes the DFT predictions to be inconsistent and incorrect. For this case, we compare our QMC results for the geometric structure, band gap and reaction enthalpy with different DFT functionals.

  12. Is the Separable Propagator Perturbation Approach Accurate in Calculating Angle Resolved Photoelectron Diffraction Spectra?

    NASA Astrophysics Data System (ADS)

    Ng, C. N.; Chu, T. P.; Wu, Huasheng; Tong, S. Y.; Huang, Hong

    1997-03-01

    We compare multiple scattering results of angle-resolved photoelectron diffraction spectra between the exact slab method and the separable propagator perturbation method. In the slab method,footnote C.H. Li, A.R. Lubinsky and S.Y. Tong, Phys. Rev. B17, 3128 (1978). the source wave and multiple scattering within the strong scattering atomic layers are expanded in spherical waves while interlayer scattering is expressed in plane waves. The transformation between spherical waves and plane waves is done exactly. The plane waves are then matched across the solid-vacuum interface to a single outgoing plane wave in the detector's direction. The separable propagator perturbation approach uses two approximations: (i) A separable representation of the Green's function propagator and (ii) A perturbation expansion of multiple scattering terms. Results of c(2x2) S-Ni(001) show that this approximate method fails to converge due to the very slow convergence of the separable representation for scattering angles less than 90^circ. However, this method is accurate in the backscattering regime and may be applied to XAFS calculations.(J.J. Rehr and R.C. Albers, Phys. Rev. B41, 8139 (1990).) The use of this method for angle-resolved photoelectron diffraction spectra is substantially less reliable.

  13. A hybrid approach for rapid, accurate, and direct kilovoltage radiation dose calculations in CT voxel space

    SciTech Connect

    Kouznetsov, Alexei; Tambasco, Mauro

    2011-03-15

    Purpose: To develop and validate a fast and accurate method that uses computed tomography (CT) voxel data to estimate absorbed radiation dose at a point of interest (POI) or series of POIs from a kilovoltage (kV) imaging procedure. Methods: The authors developed an approach that computes absorbed radiation dose at a POI by numerically evaluating the linear Boltzmann transport equation (LBTE) using a combination of deterministic and Monte Carlo (MC) techniques. This hybrid approach accounts for material heterogeneity with a level of accuracy comparable to the general MC algorithms. Also, the dose at a POI is computed within seconds using the Intel Core i7 CPU 920 2.67 GHz quad core architecture, and the calculations are performed using CT voxel data, making it flexible and feasible for clinical applications. To validate the method, the authors constructed and acquired a CT scan of a heterogeneous block phantom consisting of a succession of slab densities: Tissue (1.29 cm), bone (2.42 cm), lung (4.84 cm), bone (1.37 cm), and tissue (4.84 cm). Using the hybrid transport method, the authors computed the absorbed doses at a set of points along the central axis and x direction of the phantom for an isotropic 125 kVp photon spectral point source located along the central axis 92.7 cm above the phantom surface. The accuracy of the results was compared to those computed with MCNP, which was cross-validated with EGSnrc, and served as the benchmark for validation. Results: The error in the depth dose ranged from -1.45% to +1.39% with a mean and standard deviation of -0.12% and 0.66%, respectively. The error in the x profile ranged from -1.3% to +0.9%, with standard deviations of -0.3% and 0.5%, respectively. The number of photons required to achieve these results was 1x10{sup 6}. Conclusions: The voxel-based hybrid method evaluates the LBTE rapidly and accurately to estimate the absorbed x-ray dose at any POI or series of POIs from a kV imaging procedure.

  14. Accurate collision-induced line-coupling parameters for the fundamental band of CO in He - Close coupling and coupled states scattering calculations

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Boissoles, J.; Boulet, C.

    1988-01-01

    The first accurate theoretical values for off-diagonal (i.e., line-coupling) pressure-broadening cross sections are presented. Calculations were done for CO perturbed by He at thermal collision energies using an accurate ab initio potential energy surface. Converged close coupling, i.e., numerically exact values, were obtained for coupling to the R(0) and R(2) lines. These were used to test the coupled states (CS) and infinite order sudden (IOS) approximate scattering methods. CS was found to be of quantitative accuracy (a few percent) and has been used to obtain coupling values for lines to R(10). IOS values are less accurate, but, owing to their simplicity, may nonetheless prove useful as has been recently demonstrated.

  15. Accurate and efficient calculation of discrete correlation functions and power spectra

    NASA Astrophysics Data System (ADS)

    Xu, Y. F.; Liu, J. M.; Zhu, W. D.

    2015-07-01

    Operational modal analysis (OMA), or output-only modal analysis, has been widely conducted especially when excitation applied on a structure is unknown or difficult to measure. Discrete cross-correlation functions and cross-power spectra between a reference data series and measured response data series are bases for OMA to identify modal properties of a structure. Such functions and spectra can be efficiently transformed from each other using the discrete Fourier transform (DFT) and inverse DFT (IDFT) based on the cross-correlation theorem. However, a direct application of the theorem and transforms, including the DFT and IDFT, can yield physically erroneous results due to periodic extension of the DFT on a function of a finite length to be transformed, which is false most of the time. Padding zero series to ends of data series before applying the theorem and transforms can reduce the errors, but the results are still physically erroneous. A new methodology is developed in this work to calculate discrete cross-correlation functions of non-negative time delays and associated cross-power spectra, referred to as half spectra, for OMA. The methodology can be extended to cross-correlation functions of any time delays and associated cross-power spectra, referred to as full spectra. The new methodology is computationally efficient due to use of the transforms. Data series are properly processed to avoid the errors caused by the periodic extension, and the resulting cross-correlation functions and associated cross-power spectra perfectly comply with their definitions. A coherence function, a convergence function, and a convergence index are introduced to evaluate qualities of measured cross-correlation functions and associated cross-power spectra. The new methodology was numerically and experimentally applied to an ideal two-degree-of-freedom (2-DOF) mass-spring-damper system and a damaged aluminum beam, respectively, and OMA was conducted using half spectra to estimate

  16. Accurate potential energy curve of the LiH{sup +} molecule calculated with explicitly correlated Gaussian functions

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  17. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    PubMed

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  18. A Concise Theoretical Method for Profile-Drag Calculation; Advance Report

    NASA Technical Reports Server (NTRS)

    Nitzberg, Gerald E.

    1944-01-01

    In this report a method is presented for the calculation of the profile drag of airfoil sections. The method requlres only a knowledge of the theoretical velocity distribution and can be applied readily once this dlstribution is ascertained. Comparison of calculated and experimental drag characteristics for several airfoils shows a satisfactory agreement. Sample calculatlons are included.

  19. Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

    NASA Astrophysics Data System (ADS)

    Moreira, Rafael Y. O.; Brasil, Davi S. B.; Alves, Cláudio N.; Guilhon, Giselle M. S. P.; Santos, Lourivaldo S.; Arruda, Mara S. P.; Müller, Adolfo H.; Barbosa, Patrícia S.; Abreu, Alcicley S.; Silva, Edilene O.; Rumjanek, Victor M.; Souza, Jaime, Jr.; da Silva, Albérico B. F.; Santos, Regina H. De A.

    Julocrotine, N-(2,6-dioxo-1-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data.0

  20. DICOM organ dose does not accurately represent calculated dose in mammography

    NASA Astrophysics Data System (ADS)

    Suleiman, Moayyad E.; Brennan, Patrick C.; McEntee, Mark F.

    2016-03-01

    This study aims to analyze the agreement between the mean glandular dose estimated by the mammography unit (organ dose) and mean glandular dose calculated using Dance et al published method (calculated dose). Anonymised digital mammograms from 50 BreastScreen NSW centers were downloaded and exposure information required for the calculation of dose was extracted from the DICOM header along with the organ dose estimated by the system. Data from quality assurance annual tests for the included centers were collected and used to calculate the mean glandular dose for each mammogram. Bland-Altman analysis and a two-tailed paired t-test were used to study the agreement between calculated and organ dose and the significance of any differences. A total of 27,869 dose points from 40 centers were included in the study, mean calculated dose and mean organ dose (+/- standard deviation) were 1.47 (+/-0.66) and 1.38 (+/-0.56) mGy respectively. A statistically significant 0.09 mGy bias (t = 69.25; p<0.0001) with 95% limits of agreement between calculated and organ doses ranging from -0.34 and 0.52 were shown by Bland-Altman analysis, which indicates a small yet highly significant difference between the two means. The use of organ dose for dose audits is done at the risk of over or underestimating the calculated dose, hence, further work is needed to identify the causal agents for differences between organ and calculated doses and to generate a correction factor for organ dose.

  1. JCZS: An Intermolecular Potential Database for Performing Accurate Detonation and Expansion Calculations

    SciTech Connect

    Baer, M.R.; Hobbs, M.L.; McGee, B.C.

    1998-11-03

    Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.

  2. An accurate, efficient algorithm for calculation of quantum transport in extended structures

    SciTech Connect

    Godin, T.J.; Haydock, R.

    1994-05-01

    In device structures with dimensions comparable to carrier inelastic scattering lengths, the quantum nature of carriers will cause interference effects that cannot be modeled by conventional techniques. The basic equations that govern these ``quantum`` circuit elements present significant numerical challenges. The authors describe the block recursion method, an accurate, efficient method for solving the quantum circuit problem. They demonstrate this method by modeling dirty inversion layers.

  3. The CPA Equation of State and an Activity Coefficient Model for Accurate Molar Enthalpy Calculations of Mixtures with Carbon Dioxide and Water/Brine

    SciTech Connect

    Myint, P. C.; Hao, Y.; Firoozabadi, A.

    2015-03-27

    Thermodynamic property calculations of mixtures containing carbon dioxide (CO2) and water, including brines, are essential in theoretical models of many natural and industrial processes. The properties of greatest practical interest are density, solubility, and enthalpy. Many models for density and solubility calculations have been presented in the literature, but there exists only one study, by Spycher and Pruess, that has compared theoretical molar enthalpy predictions with experimental data [1]. In this report, we recommend two different models for enthalpy calculations: the CPA equation of state by Li and Firoozabadi [2], and the CO2 activity coefficient model by Duan and Sun [3]. We show that the CPA equation of state, which has been demonstrated to provide good agreement with density and solubility data, also accurately calculates molar enthalpies of pure CO2, pure water, and both CO2-rich and aqueous (H2O-rich) mixtures of the two species. It is applicable to a wider range of conditions than the Spycher and Pruess model. In aqueous sodium chloride (NaCl) mixtures, we show that Duan and Sun’s model yields accurate results for the partial molar enthalpy of CO2. It can be combined with another model for the brine enthalpy to calculate the molar enthalpy of H2O-CO2-NaCl mixtures. We conclude by explaining how the CPA equation of state may be modified to further improve agreement with experiments. This generalized CPA is the basis of our future work on this topic.

  4. The Dirac equation in electronic structure calculations: Accurate evaluation of DFT predictions for actinides

    SciTech Connect

    Wills, John M; Mattsson, Ann E

    2012-06-06

    Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.

  5. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    NASA Astrophysics Data System (ADS)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  6. The Calculation of Accurate Harmonic Frequencies of Large Molecules: The Polycyclic Aromatic Hydrocarbons, a Case Study

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Arnold, James O. (Technical Monitor)

    1996-01-01

    The vibrational frequencies and infrared intensities of naphthalene neutral and cation are studied at the self-consistent-field (SCF), second-order Moller-Plesset (MP2), and density functional theory (DFT) levels using a variety of one-particle basis sets. Very accurate frequencies can be obtained at the DFT level in conjunction with large basis sets if they are scaled with two factors, one for the C-H stretches and a second for all other modes. We also find remarkably good agreement at the B3LYP/4-31G level using only one scale factor. Unlike the neutral PAHs where all methods do reasonably well for the intensities, only the DFT results are accurate for the PAH cations. The failure of the SCF and MP2 methods is caused by symmetry breaking and an inability to describe charge delocalization. We present several interesting cases of symmetry breaking in this study. An assessment is made as to whether an ensemble of PAH neutrals or cations could account for the unidentified infrared bands observed in many astronomical sources.

  7. Do Bond Functions Help for the Calculation of Accurate Bond Energies?

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

    1998-01-01

    The bond energies of 8 chemically bound diatomics are computed using several basis sets with and without bond functions (BF). The bond energies obtained using the aug-pVnZ+BF basis sets (with a correction for basis set superposition error, BSSE) tend to be slightly smaller that the results obtained using the aug-pV(n+I)Z basis sets, but slightly larger than the BSSE corrected aug-pV(n+I)Z results. The aug-cc-pVDZ+BF and aug-cc-pVTZ+BF basis sets yield reasonable estimates of bond energies, but, in most cases, these results cannot be considered highly accurate. Extrapolation of the results obtained with basis sets including bond functions appears to be inferior to the results obtained by extrapolation using atom-centered basis sets. Therefore bond functions do not appear to offer a path for obtaining highly accurate results for chemically bound systems at a lower computational cost than atom centered basis sets.

  8. Validation of the new code package APOLLO2.8 for accurate PWR neutronics calculations

    SciTech Connect

    Santamarina, A.; Bernard, D.; Blaise, P.; Leconte, P.; Palau, J. M.; Roque, B.; Vaglio, C.; Vidal, J. F.

    2013-07-01

    This paper summarizes the Qualification work performed to demonstrate the accuracy of the new APOLLO2.S/SHEM-MOC package based on JEFF3.1.1 nuclear data file for the prediction of PWR neutronics parameters. This experimental validation is based on PWR mock-up critical experiments performed in the EOLE/MINERVE zero-power reactors and on P.I. Es on spent fuel assemblies from the French PWRs. The Calculation-Experiment comparison for the main design parameters is presented: reactivity of UOX and MOX lattices, depletion calculation and fuel inventory, reactivity loss with burnup, pin-by-pin power maps, Doppler coefficient, Moderator Temperature Coefficient, Void coefficient, UO{sub 2}-Gd{sub 2}O{sub 3} poisoning worth, Efficiency of Ag-In-Cd and B4C control rods, Reflector Saving for both standard 2-cm baffle and GEN3 advanced thick SS reflector. From this qualification process, calculation biases and associated uncertainties are derived. This code package APOLLO2.8 is already implemented in the ARCADIA new AREVA calculation chain for core physics and is currently under implementation in the future neutronics package of the French utility Electricite de France. (authors)

  9. Theoretical calculation of light-induced forces and torques on complex microrotors

    NASA Astrophysics Data System (ADS)

    Liu, Yuxiang; Zhu, Anding; Huang, Wenhao

    2004-12-01

    In this letter, we propose the new theoretical investigation on the optical forces and torques on complex microrotors. On the basis of R. C. Gauthier"s hybrid ray-wave model, the optical forces and toques on two complex asymmetric micro-objects, the conical microrotor and the helical microrotor, are analyzed. The viscous drag torque is estimated by Stokes flow to obtain the rotational speed. The results of our computation agree well with the previously published experimental results, which indicates that our approach of the optical torque calculation is suitable for other complex microrotors and that the theoretical calculation is very helpful to optimum design of light-driven microrotors.

  10. The absolute configuration of (+)-oxopropaline D by theoretical calculation of specific rotation and asymmetric synthesis.

    PubMed

    Kuwada, Takeshi; Fukui, Miyako; Hata, Toshiyuki; Choshi, Tominari; Nobuhiro, Junko; Ono, Yukio; Hibino, Satoshi

    2003-01-01

    The specific optical rotations of (R)-oxopropaline D calculated by two ab initio MO methods were +52+/-31 degrees and +61+/-29 degrees, respectively, and (+)-oxopropaline D (3) was presumed to have an R-configuration. On the basis of this theoretical result, the reaction of 1-litio-beta-carboline with (R)-glyceraldehyde acetonide followed by oxidation with MnO(2) gave (R)-oxopropaline D acetonide (4a), which was consistent with the previously synthesized (+)-oxopropaline D acetonide (4) in all respects. From the results of theoretical calculations and the experimental synthesis, we determined that natural (+)-oxopropaline D (3) has an R-configuration.

  11. Accurate Calculation of Oscillator Strengths for CI II Lines Using Non-orthogonal Wavefunctions

    NASA Technical Reports Server (NTRS)

    Tayal, S. S.

    2004-01-01

    Non-orthogonal orbitals technique in the multiconfiguration Hartree-Fock approach is used to calculate oscillator strengths and transition probabilities for allowed and intercombination lines in Cl II. The relativistic corrections are included through the Breit-Pauli Hamiltonian. The Cl II wave functions show strong term dependence. The non-orthogonal orbitals are used to describe the term dependence of radial functions. Large sets of spectroscopic and correlation functions are chosen to describe adequately strong interactions in the 3s(sup 2)3p(sup 3)nl (sup 3)Po, (sup 1)Po and (sup 3)Do Rydberg series and to properly account for the important correlation and relaxation effects. The length and velocity forms of oscillator strength show good agreement for most transitions. The calculated radiative lifetime for the 3s3p(sup 5) (sup 3)Po state is in good agreement with experiment.

  12. New density functional parameterizations to accurate calculations of electric field gradient variations among compounds.

    PubMed

    Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade

    2015-10-30

    This research provides a performance investigation of density functional theory and also proposes new functional parameterizations to deal with electric field gradient (EFG) calculations at nuclear positions. The entire procedure is conducted within the four-component formalism. First, we noticed that traditional hybrid and long-range corrected functionals are more efficient in the description of EFG variations for a set of elements (indium, antimony, iodine, lutetium, and hafnium) among linear molecules. Thus, we selected the PBE0, B3LYP, and CAM-B3LYP functionals and promoted a reoptimization of their parameters for a better description of these EFG changes. The PBE0q variant developed here showed an overall promising performance in a validation test conducted with potassium, iodine, copper, and gold. In general, the correlation coefficients found in linear regressions between experimental nuclear quadrupole coupling constants and calculated EFGs are improved while the systematic EFG errors also decrease as a result of this reparameterization. PMID:26284820

  13. A rapid and accurate method for calculation of stratospheric photolysis rates with molecular scattering

    NASA Technical Reports Server (NTRS)

    Boughner, Robert E.

    1986-01-01

    A method for calculating the photodissociation rates needed for photochemical modeling of the stratosphere, which includes the effects of molecular scattering, is described. The procedure is based on Sokolov's method of averaging functional correction. The radiation model and approximations used to calculate the radiation field are examined. The approximated diffuse fields and photolysis rates are compared with exact data. It is observed that the approximate solutions differ from the exact result by 10 percent or less at altitudes above 15 km; the photolysis rates differ from the exact rates by less than 5 percent for altitudes above 10 km and all zenith angles, and by less than 1 percent for altitudes above 15 km.

  14. Accurate calculation of Stokes drag for point-particle tracking in two-way coupled flows

    NASA Astrophysics Data System (ADS)

    Horwitz, J. A. K.; Mani, A.

    2016-08-01

    In this work, we propose and test a method for calculating Stokes drag applicable to particle-laden fluid flows where two-way momentum coupling is important. In the point-particle formulation, particle dynamics are coupled to fluid dynamics via a source term that appears in the respective momentum equations. When the particle Reynolds number is small and the particle diameter is smaller than the fluid scales, it is common to approximate the momentum coupling source term as the Stokes drag. The Stokes drag force depends on the difference between the undisturbed fluid velocity evaluated at the particle location, and the particle velocity. However, owing to two-way coupling, the fluid velocity is modified in the neighborhood of a particle, relative to its undisturbed value. This causes the computed Stokes drag force to be underestimated in two-way coupled point-particle simulations. We develop estimates for the drag force error as function of the particle size relative to the grid size. Because the disturbance field created by the particle contaminates the surrounding fluid, correctly calculating the drag force cannot be done solely by direct interpolation of the fluid velocity. Instead, we develop a correction method that calculates the undisturbed fluid velocity from the computed disturbed velocity field by adding an estimate of the velocity disturbance created by the particle. The correction scheme is tested for a particle settling in an otherwise quiescent fluid and is found to reduce the error in computed settling velocity by an order of magnitude compared with common interpolation schemes.

  15. Efficient Use of an Adapting Database of Ab Initio Calculations To Generate Accurate Newtonian Dynamics.

    PubMed

    Shaughnessy, M C; Jones, R E

    2016-02-01

    We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm.

  16. Efficient Use of an Adapting Database of Ab Initio Calculations To Generate Accurate Newtonian Dynamics.

    PubMed

    Shaughnessy, M C; Jones, R E

    2016-02-01

    We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825

  17. Easy and accurate calculation of programmed temperature gas chromatographic retention times by back-calculation of temperature and hold-up time profiles.

    PubMed

    Boswell, Paul G; Carr, Peter W; Cohen, Jerry D; Hegeman, Adrian D

    2012-11-01

    Linear retention indices are commonly used to identify compounds in programmed-temperature gas chromatography (GC), but they are unreliable unless the original experimental conditions used to measure them are stringently reproduced. However, differences in many experimental conditions may be properly taken into account by calculating programmed-temperature retention times of compounds from their measured isothermal retention vs. temperature relationships. We call this approach "retention projection". Until now, retention projection has been impractical because it required very precise, meticulous measurement of the temperature vs. time and hold-up time vs. temperature profiles actually produced by a specific GC instrument to be accurate. Here we present a new, easy-to-use methodology to precisely measure those profiles: we spike a sample with 25 n-alkanes and use their measured, programmed-temperature retention times to precisely back-calculate what the instrument profiles must have been. Then, when we use those back-calculated profiles to project retention times of 63 chemically diverse compounds, we found that the projections are extremely accurate (e.g. to ±0.9 s in a 40 min ramp). They remained accurate with different temperature programs, GC instruments, inlet pressures, flow rates, and with columns taken from different batches of stationary phase while the accuracy of retention indices became worse the more the experimental conditions were changed from the original ones used to measure them. We also developed new, open-source software (http://www.retentionprediction.org/gc) to demonstrate the system.

  18. Accurate calculation of binding energies for molecular clusters - Assessment of different models

    NASA Astrophysics Data System (ADS)

    Friedrich, Joachim; Fiedler, Benjamin

    2016-06-01

    In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.

  19. Effective approach for accurately calculating individual energy of polar heterojunction interfaces

    NASA Astrophysics Data System (ADS)

    Akiyama, Toru; Nakane, Harunobu; Nakamura, Kohji; Ito, Tomonori

    2016-09-01

    We propose a direct approach for calculating individual energy of polar semiconductor interfaces using density functional theory calculations. This approach is applied to polar interfaces between group-III nitrides (AlN and GaN) and SiC and clarifies the interplay of chemical bonding and charge neutrality at the interface, which is crucial for the stability and polarity of group-III nitrides on SiC substrates. The ideal interface is stabilized among various atomic arrangements over the wide range of the chemical potential on Si-face SiC, whereas those with intermixing are favorable on C-face SiC. The stabilization of the ideal interfaces resulting in Ga-polar GaN and Al-polar AlN films on Si-face SiC is consistent with experiments, suggesting that our approach is versatile to evaluate various polar heterojunction interfaces as well as group-III nitrides on semiconductor substrates.

  20. Accurate and fast stray radiation calculation based on improved backward ray tracing.

    PubMed

    Yang, Liu; XiaoQiang, An; Qian, Wang

    2013-02-01

    An improved method of backward ray tracing is proposed according to the theory of geometrical optics and thermal radiation heat transfer. The accuracy is essentially raised comparing to the traditional backward ray tracing because ray orders and weight factors are taken into account and the process is designed as sequential and recurring steps to trace and calculate different order stray lights. Meanwhile, it needs very small computation comparing to forward ray tracing because irrelevant surfaces and rays are excluded from the tracing. The effectiveness was verified in the stray radiation analysis for a cryogenic infrared (IR) imaging system, as the results coincided with the actual stray radiation irradiance distributions in the real images. The computation amount was compared with that of forward ray tracing in the narcissus calculation for another cryogenic IR imaging system, it was found that to produce the same accuracy result, the computation of the improved backward ray tracing is far smaller than that of forward ray tracing by at least 2 orders of magnitude.

  1. Accurate quantum dynamics calculations using symmetrized Gaussians on a doubly dense Von Neumann lattice

    SciTech Connect

    Halverson, Thomas; Poirier, Bill

    2012-12-14

    In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a 'weylet' basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality-the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).

  2. Accurate spectroscopic calculations of 21 electronic states of ClO radical including transition properties

    NASA Astrophysics Data System (ADS)

    Wang, Xinxin; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-08-01

    The potential energy curves were calculated for the 21 states (X2Π, A2Π, 32Π, 42Π, 52Π, 12Σ+, 22Σ+, 32Σ+, 12Σ-, 22Σ-, 32Σ-, 12Δ, 22Δ, 32Δ, 12Φ, 14Σ+, a4Σ-, 24Σ-, 14Π, 24Π and 14Δ), which originated from the two lowest dissociation channels of ClO radical. The calculations were done for internuclear separations approximately from 0.08 to 1.10 nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV5Z basis set. Of these 21 states, the 14Π, 24Π, 32Δ, 42Π, 52Π, 12Φ, 32Σ+, 14Δ and 24Σ- states are repulsive. The 12Δ, 12Σ-, 14Σ+, 22Σ-, 12Σ+, 22Σ+, 22Δ and 32Σ- states are very weakly bound. Only the A2Π state has one barrier. The avoided crossing exists between the A2Π and the 32Π state. However, the avoided crossing does not generate any double wells. Core- valence correlation correction was accounted for at the level of an aug-cc-pCVQZ basis set. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pVQZ basis set. All the potential energy curves were extrapolated to the complete basis set limit. The spectroscopic parameters were determined. The 12Σ-, 22Σ-, 32Σ- and 14Σ+ states may be very difficult to be detected in an experiment, since each of these Λ-S states has only one or two vibrational states. The Franck-Condon factors and radiative lifetimes were calculated for several low vibrational levels of the A2Π - X2Π, 32Π - a4Σ-, 22Δ - a4Σ- and 32Σ- - 12Σ- transitions. The spin-orbit coupling effect on the spectroscopic parameters of the X2Π, A2Π, 32Π, a4Σ- and 22Σ+ states were discussed. The spectroscopic properties reported here can be expected to be reliably predicted ones.

  3. Accurate bond energies of biodiesel methyl esters from multireference averaged coupled-pair functional calculations.

    PubMed

    Oyeyemi, Victor B; Keith, John A; Carter, Emily A

    2014-09-01

    Accurate bond dissociation energies (BDEs) are important for characterizing combustion chemistry, particularly the initial stages of pyrolysis. Here we contribute to evaluating the thermochemistry of biodiesel methyl ester molecules using ab initio BDEs derived from a multireference averaged coupled-pair functional (MRACPF2)-based scheme. Having previously validated this approach for hydrocarbons and a variety of oxygenates, herein we provide further validation for bonds within carboxylic acids and methyl esters, finding our scheme predicts BDEs within chemical accuracy (i.e., within 1 kcal/mol) for these molecules. Insights into BDE trends with ester size are then analyzed for methyl formate through methyl crotonate. We find that the carbonyl group in the ester moiety has only a local effect on BDEs. C═C double bonds in ester alkyl chains are found to increase the strengths of bonds adjacent to the double bond. An important exception are bonds beta to C═C or C═O bonds, which produce allylic-like radicals upon dissociation. The observed trends arise from different degrees of geometric relaxation and resonance stabilization in the radicals produced. We also compute BDEs in various small alkanes and alkenes as models for the long hydrocarbon chain of actual biodiesel methyl esters. We again show that allylic bonds in the alkenes are much weaker than those in the small methyl esters, indicating that hydrogen abstractions are more likely at the allylic site and even more likely at bis-allylic sites of alkyl chains due to more electrons involved in π-resonance in the latter. Lastly, we use the BDEs in small surrogates to estimate heretofore unknown BDEs in large methyl esters of biodiesel fuels.

  4. Accurate bond energies of biodiesel methyl esters from multireference averaged coupled-pair functional calculations.

    PubMed

    Oyeyemi, Victor B; Keith, John A; Carter, Emily A

    2014-09-01

    Accurate bond dissociation energies (BDEs) are important for characterizing combustion chemistry, particularly the initial stages of pyrolysis. Here we contribute to evaluating the thermochemistry of biodiesel methyl ester molecules using ab initio BDEs derived from a multireference averaged coupled-pair functional (MRACPF2)-based scheme. Having previously validated this approach for hydrocarbons and a variety of oxygenates, herein we provide further validation for bonds within carboxylic acids and methyl esters, finding our scheme predicts BDEs within chemical accuracy (i.e., within 1 kcal/mol) for these molecules. Insights into BDE trends with ester size are then analyzed for methyl formate through methyl crotonate. We find that the carbonyl group in the ester moiety has only a local effect on BDEs. C═C double bonds in ester alkyl chains are found to increase the strengths of bonds adjacent to the double bond. An important exception are bonds beta to C═C or C═O bonds, which produce allylic-like radicals upon dissociation. The observed trends arise from different degrees of geometric relaxation and resonance stabilization in the radicals produced. We also compute BDEs in various small alkanes and alkenes as models for the long hydrocarbon chain of actual biodiesel methyl esters. We again show that allylic bonds in the alkenes are much weaker than those in the small methyl esters, indicating that hydrogen abstractions are more likely at the allylic site and even more likely at bis-allylic sites of alkyl chains due to more electrons involved in π-resonance in the latter. Lastly, we use the BDEs in small surrogates to estimate heretofore unknown BDEs in large methyl esters of biodiesel fuels. PMID:24621192

  5. Economical and accurate protocol for calculating hydrogen-bond-acceptor strengths.

    PubMed

    El Kerdawy, Ahmed; Tautermann, Christofer S; Clark, Timothy; Fox, Thomas

    2013-12-23

    A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques. PMID:24289323

  6. Properties of metastable alkaline-earth-metal atoms calculated using an accurate effective core potential

    SciTech Connect

    Santra, Robin; Christ, Kevin V.; Greene, Chris H.

    2004-04-01

    The first three electronically excited states in the alkaline-earth-metal atoms magnesium, calcium, and strontium comprise the (nsnp){sup 3}P{sub J}{sup o}(J=0,1,2) fine-structure manifold. All three states are metastable and are of interest for optical atomic clocks as well as for cold-collision physics. An efficient technique--based on a physically motivated potential that models the presence of the ionic core--is employed to solve the Schroedinger equation for the two-electron valence shell. In this way, radiative lifetimes, laser-induced clock shifts, and long-range interaction parameters are calculated for metastable Mg, Ca, and Sr.

  7. Economical and accurate protocol for calculating hydrogen-bond-acceptor strengths.

    PubMed

    El Kerdawy, Ahmed; Tautermann, Christofer S; Clark, Timothy; Fox, Thomas

    2013-12-23

    A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.

  8. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model.

    PubMed

    Palmer, David S; Sergiievskyi, Volodymyr P; Jensen, Frank; Fedorov, Maxim V

    2010-07-28

    We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force-field methods of structure optimization and atomic partial charge calculation. The final model gave a systematic error with a standard deviation of 2.6 kcal/mol for a test set of 31 molecules selected from the SAMPL1 blind challenge set [J. P. Guthrie, J. Phys. Chem. B 113, 4501 (2009)]. After parametrization of this model to include terms for the excluded volume and the number of atoms of different types in the molecule, the root mean squared error for a test set of 19 molecules was less than 1.2 kcal/mol.

  9. Accurate calculation and assignment of highly excited vibrational levels of floppy triatomic molecules in a basis of adiabatic vibrational eigenstates

    NASA Astrophysics Data System (ADS)

    Bačić, Z.

    1991-09-01

    We show that the triatomic adiabatic vibrational eigenstates (AVES) provide a convenient basis for accurate discrete variable representation (DVR) calculation and automatic assignment of highly excited, large amplitude motion vibrational states of floppy triatomic molecules. The DVR-AVES states are eigenvectors of the diagonal (in the stretch states) blocks of the adiabatically rearranged triatomic DVR-ray eigenvector (DVR-REV) Hamiltonian [J. C. Light and Z. Bačić, J. Chem. Phys. 87, 4008 (1987)]. The transformation of the full triatomic vibrational Hamiltonian from the DVR-REV basis to the new DVR-AVES basis is simple, and does not involve calculation of any new matrix elements. No dynamical approximation is made in the energy level calculation by the DVR-AVES approach; its accuracy and efficiency are identical to those of the DVR-REV method. The DVR-AVES states, as the adiabatic approximation to the vibrational states of a triatomic molecule, are labeled by three vibrational quantum numbers. Consequently, accurate large amplitude motion vibrational levels obtained by diagonalizing the full vibrational Hamiltonian transformed to the DVR-AVES basis, can be assigned automatically by the code, with the three quantum numbers of the dominant DVR-AVES state associated with the largest (by modulus) eigenvector element in the DVR-AVES basis. The DVR-AVES approach is used to calculate accurate highly excited localized and delocalized vibrational levels of HCN/HNC and LiCN/LiNC. A significant fraction of localized states of both systems, below and above the isomerization barrier, is assigned automatically, without inspection of wave function plots or separate approximate calculations.

  10. Accurate ab initio calculations which demonstrate a 3 Pi u ground state for Al2

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.; Taylor, Peter R.; Walch, Stephen P.

    1986-01-01

    The spectroscopic parameters and separations between the three low-lying X 3 Pi u, A 3 Sigma g -, and a 1 Sigma g + states of Al2 are studied as a function of both the one-particle and n-particle basis set. Approximate correlation treatments are calibrated against full Cl calculations correlating the six valence electrons in a double-zeta plus two d-function basis set. Since the CASSCF/MRCI 3 Pi u to 3 Sigma g - separation is in excellent agreement wtih the FCI value, the MRCI calculations were carried out in an extended (20s13p6d4f)/(6s5p3d2f) gaussian basis. Including a small correction for relativistic effects, the best estimate is that 3 Sigma g - state lies 174/cm above the 3 Pi u ground state. The 1 Sigma g + state lies at least 2000/cm higher in energy. At the CPF level, inclusion of 2s and 2p correlation has little effect on D sub e, reduces T sub e by only 26/cm, and shortens the bond lengths by about 0.02 a sub o. Further strong support for a 3 Pi u ground state comes from the experimental absorption spectra, since both observed transitions can be convincingly assigned as 3 Pi u yields 3 Pi g. The (2) 3 Pi g state is observed to be sensitive to the level of correlation treatment, and to have its minimum shifted to shorter rho values, such that the strongest experimental absorption peak probably corresponds to the 0 yields 2 transition.

  11. Structure and properties of electronic and hole centers in CsBr from theoretical calculations

    SciTech Connect

    Halliday, Matthew T.; Hess, Wayne P.; Shluger, Alexander L.

    2015-06-24

    The electronic structure, geometry, diffusion barriers and optical properties of fundamental defects of CsBr are calculated using hybrid functional DFT and TD- DFT methods. The B3LYP functional with a modified exchange contribution has been used in an embedded cluster scheme to model the structure and spectroscopic properties of self-trapped triplet exciton, interstitial Br atoms and ions, self-trapped holes and Br vacancies. The calculated migration barriers and positions of maxima of optical absorption bands are in good agreement with experiment, justifying the obtained defect geometries. The o*-center triplet exciton luminescence energy is also accurately calculated.

  12. Efficiency and power loss in d. c. chopper circuits. [Theoretical calculation

    SciTech Connect

    Beck, M.O.

    1981-01-01

    The object of this paper was to investigate the efficiency and source of power losses of various classes of dc chopper circuits. The study involved a theoretical calculation of the power losses, supported by a considerable amount of practical work on full power-rated traction motor test bed. 3 refs.

  13. Quantitative analysis of nanometer anatase-rutile mixtures via experimentation and theoretical calculation.

    PubMed

    Guo, Li; Zhou, Zhiqiang; Jia, Peiyun; Ye, Feng

    2012-12-01

    In this paper, we developed a method based on X-ray diffractometry for determining the weight ratio of nanometer anatase to rutile or their relative amounts in TiO2 polymorphs, and corresponding formulas for such determination were put forward. The very key constant K in these formulas has been specially evaluated by experimentalizing nanometer polymorphs of titanium dioxide. Furthermore, a theoretical value of K was obtained through detailed theoretical calculation based on X-ray powder diffraction theory. The K value concluded from experimentation coincides well with that yielded from theoretical calculation, thus the validity and reliability of the experimental K value has been further confirmed. This coincidence may also suggest the applicability of X-ray powder diffraction theory to nanometer crystals. With this method, the relative amounts of nanometer anatase and rutile in their mixtures or the weight ratio of nanometer anatase to rutile in any a mixture can be easily determined only upon a XRD test.

  14. Accurate Gaussian basis sets for atomic and molecular calculations obtained from the generator coordinate method with polynomial discretization.

    PubMed

    Celeste, Ricardo; Maringolo, Milena P; Comar, Moacyr; Viana, Rommel B; Guimarães, Amanda R; Haiduke, Roberto L A; da Silva, Albérico B F

    2015-10-01

    Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.

  15. Accurate Diels-Alder reaction energies from efficient density functional calculations.

    PubMed

    Mezei, Pál D; Csonka, Gábor I; Kállay, Mihály

    2015-06-01

    We assess the performance of the semilocal PBE functional; its global hybrid variants; the highly parametrized empirical M06-2X and M08-SO; the range separated rCAM-B3LYP and MCY3; the atom-pairwise or nonlocal dispersion corrected semilocal PBE and TPSS; the dispersion corrected range-separated ωB97X-D; the dispersion corrected double hybrids such as PWPB95-D3; the direct random phase approximation, dRPA, with Hartree-Fock, Perdew-Burke-Ernzerhof, and Perdew-Burke-Ernzerhof hybrid reference orbitals and the RPAX2 method based on a Perdew-Burke-Ernzerhof exchange reference orbitals for the Diels-Alder, DARC; and self-interaction error sensitive, SIE11, reaction energy test sets with large, augmented correlation consistent valence basis sets. The dRPA energies for the DARC test set are extrapolated to the complete basis set limit. CCSD(T)/CBS energies were used as a reference. The standard global hybrid functionals show general improvements over the typical endothermic energy error of semilocal functionals, but despite the increased accuracy the precision of the methods increases only slightly, and thus all reaction energies are simply shifted into the exothermic direction. Dispersion corrections give mixed results for the DARC test set. Vydrov-Van Voorhis 10 correction to the reaction energies gives superior quality results compared to the too-small D3 correction. Functionals parametrized for energies of noncovalent interactions like M08-SO give reasonable results without any dispersion correction. The dRPA method that seamlessly and theoretically correctly includes noncovalent interaction energies gives excellent results with properly chosen reference orbitals. As the results for the SIE11 test set and H2(+) dissociation show that the dRPA methods suffer from delocalization error, good reaction energies for the DARC test set from a given method do not prove that the method is free from delocalization error. The RPAX2 method shows good performance for the DARC

  16. Line Shape Parameters for CO_2 Transitions: Accurate Predictions from Complex Robert-Bonamy Calculations

    NASA Astrophysics Data System (ADS)

    Lamouroux, Julien; Gamache, Robert R.

    2013-06-01

    A model for the prediction of the vibrational dependence of CO_2 half-widths and line shifts for several broadeners, based on a modification of the model proposed by Gamache and Hartmann, is presented. This model allows the half-widths and line shifts for a ro-vibrational transition to be expressed in terms of the number of vibrational quanta exchanged in the transition raised to a power p and a reference ro-vibrational transition. Complex Robert-Bonamy calculations were made for 24 bands for lower rotational quantum numbers J'' from 0 to 160 for N_2-, O_2-, air-, and self-collisions with CO_2. In the model a Quantum Coordinate is defined by (c_1 Δν_1 + c_2 Δν_2 + c_3 Δν_3)^p where a linear least-squares fit to the data by the model expression is made. The model allows the determination of the slope and intercept as a function of rotational transition, broadening gas, and temperature. From these fit data, the half-width, line shift, and the temperature dependence of the half-width can be estimated for any ro-vibrational transition, allowing spectroscopic CO_2 databases to have complete information for the line shape parameters. R. R. Gamache, J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transfer. {{83}} (2004), 119. R. R. Gamache, J. Lamouroux, J. Quant. Spectrosc. Radiat. Transfer. {{117}} (2013), 93.

  17. Dark matter scattering on electrons: Accurate calculations of atomic excitations and implications for the DAMA signal

    NASA Astrophysics Data System (ADS)

    Roberts, B. M.; Dzuba, V. A.; Flambaum, V. V.; Pospelov, M.; Stadnik, Y. V.

    2016-06-01

    We revisit the WIMP-type dark matter scattering on electrons that results in atomic ionization and can manifest itself in a variety of existing direct-detection experiments. Unlike the WIMP-nucleon scattering, where current experiments probe typical interaction strengths much smaller than the Fermi constant, the scattering on electrons requires a much stronger interaction to be detectable, which in turn requires new light force carriers. We account for such new forces explicitly, by introducing a mediator particle with scalar or vector couplings to dark matter and to electrons. We then perform state-of-the-art numerical calculations of atomic ionization relevant to the existing experiments. Our goals are to consistently take into account the atomic physics aspect of the problem (e.g., the relativistic effects, which can be quite significant) and to scan the parameter space—the dark matter mass, the mediator mass, and the effective coupling strength—to see if there is any part of the parameter space that could potentially explain the DAMA modulation signal. While we find that the modulation fraction of all events with energy deposition above 2 keV in NaI can be quite significant, reaching ˜50 %, the relevant parts of the parameter space are excluded by the XENON10 and XENON100 experiments.

  18. Geometric constraints in semiclassical initial value representation calculations in Cartesian coordinates: accurate reduction in zero-point energy.

    PubMed

    Issack, Bilkiss B; Roy, Pierre-Nicholas

    2005-08-22

    An approach for the inclusion of geometric constraints in semiclassical initial value representation calculations is introduced. An important aspect of the approach is that Cartesian coordinates are used throughout. We devised an algorithm for the constrained sampling of initial conditions through the use of multivariate Gaussian distribution based on a projected Hessian. We also propose an approach for the constrained evaluation of the so-called Herman-Kluk prefactor in its exact log-derivative form. Sample calculations are performed for free and constrained rare-gas trimers. The results show that the proposed approach provides an accurate evaluation of the reduction in zero-point energy. Exact basis set calculations are used to assess the accuracy of the semiclassical results. Since Cartesian coordinates are used, the approach is general and applicable to a variety of molecular and atomic systems.

  19. Full Dimensional Vibrational Calculations for Methane Using AN Accurate New AB Initio Based Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei

    2014-06-01

    New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).

  20. Progress Towards the Accurate Calculation of Anharmonic Vibrational States of Fluxional Molecules and Clusters Without a Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Petit, Andrew S.; McCoy, Anne B.

    2011-06-01

    The accurate calculation of anharmonic vibrational states of highly fluxional systems is complicated by the need to first obtain the full-dimensional potential energy surface(PES). Although commonly exploited as a way around this problem, grid-based methodologies scale exponentially with system size while reduced dimensional approaches are highly system dependent, both in terms of the details of their application and in terms of their suitability. Moreover, the achievement of converged variational calculations of highly anharmonic systems is complicated by the necessity of using a very large basis and hence the construction and diagonalization of enormous Hamiltonian matrices. We report here our recent efforts to develop an algorithm capable of accurately calculating anharmonic vibrational energies, even for very floppy systems, without first obtaining a PES and using only a handful of basis functions per degree of freedom. More specifically, the potential energy and G-matrix elements are calculated on a set of points obtained from a Monte Carlo sampling of the most important regions of configuration space, allowing for a significant reduction in the number of required sampling points. The Hamiltonian matrix is then constructed using an evolving basis which, with each iteration, captures the effect of building H from an ever-expanding basis despite the fact that the actual dimensionality of H is fixed throughout the calculation. This latter property of the algorithm also greatly reduces the size of basis needed for the calculation relative to more traditional variational approaches. The results obtained from the application of our method to several test systems, including ion water complexes, will be reported along with its observed convergence properties.

  1. Modifying scoping codes to accurately calculate TMI-cores with lifetimes greater than 500 effective full-power days

    SciTech Connect

    Bai, D.; Levine, S.L. ); Luoma, J.; Mahgerefteh, M. )

    1992-01-01

    The Three Mile Island unit 1 core reloads have been designed using fast but accurate scoping codes, PSUI-LEOPARD and ADMARC. PSUI-LEOPARD has been normalized to EPRI-CPM2 results and used to calculate the two-group constants, whereas ADMARC is a modern two-dimensional, two-group diffusion theory nodal code. Problems in accuracy were encountered for cycles 8 and higher as the core lifetime was increased beyond 500 effective full-power days. This is because the heavier loaded cores in both {sup 235}U and {sup 10}B have harder neutron spectra, which produces a change in the transport effect in the baffle reflector region, and the burnable poison (BP) simulations were not accurate enough for the cores containing the increased amount of {sup 10}B required in the BP rods. In the authors study, a technique has been developed to take into account the change in the transport effect in the baffle region by modifying the fast neutron diffusion coefficient as a function of cycle length and core exposure or burnup. A more accurate BP simulation method is also developed, using integral transport theory and CPM2 data, to calculate the BP contribution to the equivalent fuel assembly (supercell) two-group constants. The net result is that the accuracy of the scoping codes is as good as that produced by CASMO/SIMULATE or CPM2/SIMULATE when comparing with measured data.

  2. The calculation of theoretical chromospheric models and predicted OSO 1 spectra

    NASA Technical Reports Server (NTRS)

    Avrett, E. H.

    1975-01-01

    Theoretical solar chromospheric and photospheric models are computed for use in analyzing OSO 8 spectra. The Vernazza, Avrett, and Loeser (1976) solar model is updated and self-consistent non-LTE number densities for H I, He I, He II, C I, Mg I, Al I, Si I, and H(-) are produced. These number densities are used in the calculation of a theoretical solar spectrum from 90 to 250 nm, including approximately 7000 lines in non-LTE. More than 60,000 lines of other elements are treated with approximate source functions.

  3. Rotational isomerism of some chloroacetamides: Theoretical and experimental studies through calculations, infrared and NMR

    NASA Astrophysics Data System (ADS)

    Santos, Marcela F.; Braga, Carolyne B.; Rozada, Thiago C.; Basso, Ernani A.; Fiorin, Barbara C.

    2014-08-01

    The geometries involved in the conformational equilibria of 2,2-dichloro-N-cyclohexyl-N-methyl-acetamide (DCCMA) and 2-chloro-N,N-dicyclohexylacetamide (CDCA) were investigated. Theoretical calculations at the B3LYP/cc-pVDZ level of theory showed that gauche forms (Clsbnd Csbnd Cdbnd O) are the most stable and the predominant conformers in isolated phase. Both compounds had the conformational behavior in solvents of different polarities estimated from theoretical calculations with the PCM (Polarizable Continuum Model), at the same level of theory, using infrared data from deconvolution of the carbonyl absorption bands and 13C NMR spectra. Their IR spectra showed two carbonyl absorptions and that the conformer with the highest dipole moment had its population increased when the most polar solvents were used, in accordance with the theoretical calculation in solution. 1JCH coupling constants were obtained from their NMR spectra, and revealed that there was population variation of conformers with solvent exchange. Experimental data (NMR and IR) as well as calculations including the solvent effects followed the same trend.

  4. Theoretical calculations of pressure broadening coefficients for H2O perturbed by hydrogen or helium gas

    NASA Technical Reports Server (NTRS)

    Gamache, Robert R.; Pollack, James B.

    1995-01-01

    Halfwidths were calculated for H2O with H2 as a broadening gas and were estimated for He as the broadening species. The calculations used the model of Robert and Bonamy with parabolic trajectories and all relevant terms in the interaction potential. The calculations investigated the dependence of the halfwidth on the order of the atom-atom expansion, the rotational states, and the temperature in the range 200 to 400K. Finally, calculations were performed for many transitions of interest in the 5 micrometer window region of the spectrum. The resulting data will be supplied to Dr. R. Freedman for extracting accurate water mixing ratios from the analysis of the thermal channels for the Net Flux experiment on the Galileo probe.

  5. New explicit equations for the accurate calculation of the growth and evaporation of hydrometeors by the diffusion of water vapor

    NASA Technical Reports Server (NTRS)

    Srivastava, R. C.; Coen, J. L.

    1992-01-01

    The traditional explicit growth equation has been widely used to calculate the growth and evaporation of hydrometeors by the diffusion of water vapor. This paper reexamines the assumptions underlying the traditional equation and shows that large errors (10-30 percent in some cases) result if it is used carelessly. More accurate explicit equations are derived by approximating the saturation vapor-density difference as a quadratic rather than a linear function of the temperature difference between the particle and ambient air. These new equations, which reduce the error to less than a few percent, merit inclusion in a broad range of atmospheric models.

  6. On the controversial fitting of susceptibility curves of ferromagnetic Cu(II) cubanes: insights from theoretical calculations.

    PubMed

    Calzado, Carmen J

    2013-01-21

    This paper reports a theoretical analysis of the electronic structure and magnetic properties of a tetranuclear Cu(II) complex, [Cu(4) (HL)(4)], which has a 4+2 cubane-like structure (H(3) L=N,N'-(2-hydroxypropane-1,3-diyl)bis(acetylacetoneimine)). These theoretical calculations indicate a quintet (S=2) ground state; the energy-level distribution of the magnetic states confirm Heisenberg behaviour and correspond to an S(4) spin-spin interaction model. The dominant interaction is the ferromagnetic coupling between the pseudo-dimeric units (J(1) =22.2 cm(-1)), whilst a weak and ferromagnetic interaction is found within the pseudo-dimeric units (J(2) =1.4 cm(-1)). The amplitude and sign of these interactions are consistent with the structure and arrangement of the magnetic Cu 3d orbitals; they accurately simulate the thermal dependence of magnetic susceptibility, but do not agree with the reported J values (J(1) =38.4 cm(-1), J(2) =-18.0 cm(-1)) that result from the experimental fitting. This result is not an isolated case; many other polynuclear systems, in particular 4+2 Cu(II) cubanes, have been reported in which the fitted magnetic terms are not consistent with the geometrical features of the system. In this context, theoretical evaluation can be considered as a valuable tool in the interpretation of the macroscopic behaviour, thus providing clues for a rational and directed design of new materials with specific properties.

  7. Mass spectrometry and theoretical calculations about the loss of methyl radical from methoxilated coumarins

    NASA Astrophysics Data System (ADS)

    Borkowski, Eduardo J.; Cecati, Francisco M.; Suvire, Fernando D.; Ruiz, Diego M.; Ardanaz, Carlos E.; Romanelli, Gustavo P.; Enriz, Ricardo D.

    2015-08-01

    In this study we have performed CID mass spectrometry measurements and theoretical calculations in a selected series of coumarins. Our theoretical and experimental results indicate that there is room for reasonable doubts about the fragmentation way previously proposed by Shapiro and Djerassi (1965). A complementary explanation about the fragmentation way of the methyl loss from methoxy coumarins has been reported in this work. Our results demonstrated that different theoretical models are very useful to explain the fragmentation occurred in MS, supporting the usual rules of fragmentation. Although the QTAIM analysis gives a good correlation in order to explain the formation of p-quinoid resonance forms; however, the best correlation has been obtained using the NBO approximation as well as from the Wiberg indexes.

  8. Energy from CO2 using capacitive electrodes--theoretical outline and calculation of open circuit voltage.

    PubMed

    Paz-Garcia, J M; Schaetzle, O; Biesheuvel, P M; Hamelers, H V M

    2014-03-15

    Recently, a new technology has been proposed for the utilization of energy from CO2 emissions (Hamelers et al., 2014). The principle consists of controlling the dilution process of CO2-concentrated gas (e.g., exhaust gas) into CO2-dilute gas (e.g., air) thereby extracting a fraction of the released mixing energy. In this paper, we describe the theoretical fundamentals of this technology when using a pair of charge-selective capacitive electrodes. We focus on the behavior of the chemical system consisting of CO2 gas dissolved in water or monoethanolamine solution. The maximum voltage given for the capacitive cell is theoretically calculated, based on the membrane potential. The different aspects that affect this theoretical maximum value are discussed.

  9. Theoretical calculation of the interannual variability of the Earth's insolation with daily resolution

    NASA Astrophysics Data System (ADS)

    Fedorov, V. M.

    2016-05-01

    Based on the astronomical ephemerides DE-406, theoretical calculations have been performed of the interannual variability of the Earth's insolation related to celestial-mechanical processes for 365 points of a tropical year in the time period from 1900 to 2050. It has been determined that the average amplitude of variations of the interannual insolation is 0.310 W/m2 (0.023% of the solar constant). The calculated variations are characterized by strict periodicity that corresponds with the length of a synodic month. Connection between the extreme values of the calculated insolation variability and syzygies has been defined. The average amplitude of the calculated variability exceeds by 1.7 times (0.01% of the solar constant) the amplitude of the interannual variability in the 11-year variation of the total Earth's insolation.

  10. Nuclear radii calculations in various theoretical approaches for nucleus-nucleus interactions

    SciTech Connect

    Merino, C.; Novikov, I. S.; Shabelski, Yu.

    2009-12-15

    The information about sizes and nuclear density distributions in unstable (radioactive) nuclei is usually extracted from the data on interaction of radioactive nuclear beams with a nuclear target. We show that in the case of nucleus-nucleus collisions the values of the parameters depend somewhat strongly on the considered theoretical approach and on the assumption about the parametrization of the nuclear density distribution. The obtained values of root-mean-square radii (R{sub rms}) for stable nuclei with atomic weights A=12-40 vary by approximately 0.1 fm when calculated in the optical approximation, in the rigid target approximation, and using the exact expression of the Glauber theory. We present several examples of R{sub rms} radii calculations using these three theoretical approaches and compare these results with the data obtained from electron-nucleus scattering.

  11. Efficient and accurate linear algebraic methods for large-scale electronic structure calculations with nonorthogonal atomic orbitals

    NASA Astrophysics Data System (ADS)

    Teng, H.; Fujiwara, T.; Hoshi, T.; Sogabe, T.; Zhang, S.-L.; Yamamoto, S.

    2011-04-01

    The need for large-scale electronic structure calculations arises recently in the field of material physics, and efficient and accurate algebraic methods for large simultaneous linear equations become greatly important. We investigate the generalized shifted conjugate orthogonal conjugate gradient method, the generalized Lanczos method, and the generalized Arnoldi method. They are the solver methods of large simultaneous linear equations of the one-electron Schrödinger equation and map the whole Hilbert space to a small subspace called the Krylov subspace. These methods are applied to systems of fcc Au with the NRL tight-binding Hamiltonian [F. Kirchhoff , Phys. Rev. BJCOMEL1098-012110.1103/PhysRevB.63.195101 63, 195101 (2001)]. We compare results by these methods and the exact calculation and show them to be equally accurate. The system size dependence of the CPU time is also discussed. The generalized Lanczos method and the generalized Arnoldi method are the most suitable for the large-scale molecular dynamics simulations from the viewpoint of CPU time and memory size.

  12. Stretch calculated from grip distance accurately approximates mid-specimen stretch in large elastic arteries in uniaxial tensile tests.

    PubMed

    Tian, Lian; Henningsen, Joseph; Salick, Max R; Crone, Wendy C; Gunderson, McLean; Dailey, Seth H; Chesler, Naomi C

    2015-07-01

    The mechanical properties of vascular tissues affect hemodynamics and can alter disease progression. The uniaxial tensile test is a simple and effective method for determining the stress-strain relationship in arterial tissue ex vivo. To enable calculation of strain, stretch can be measured directly with image tracking of markers on the tissue or indirectly from the distance between the grips used to hold the specimen. While the imaging technique is generally considered more accurate, it also requires more analysis, and the grip distance method is more widely used. The purpose of this study is to compare the stretch of the testing specimen calculated from the grip distance method to that obtained from the imaging method for canine descending aortas and large proximal pulmonary arteries. Our results showed a significant difference in stretch between the two methods; however, this difference was consistently less than 2%. Therefore, the grip distance method is an accurate approximation of the stretch in large elastic arteries in the uniaxial tensile test. PMID:25881308

  13. Band-Filling Correction Method for Accurate Adsorption Energy Calculations: A Cu/ZnO Case Study.

    PubMed

    Hellström, Matti; Spångberg, Daniel; Hermansson, Kersti; Broqvist, Peter

    2013-11-12

    We present a simple method, the "band-filling correction", to calculate accurate adsorption energies (Eads) in the low coverage limit from finite-size supercell slab calculations using DFT. We show that it is necessary to use such a correction if charge transfer takes place between the adsorbate and the substrate, resulting in the substrate bands either filling up or becoming depleted. With this correction scheme, we calculate Eads of an isolated Cu atom adsorbed on the ZnO(101̅0) surface. Without the correction, the calculated Eads is highly coverage-dependent, even for surface supercells that would typically be considered very large (in the range from 1 nm × 1 nm to 2.5 nm × 2.5 nm). The correction scheme works very well for semilocal functionals, where the corrected Eads is converged within 0.01 eV for all coverages. The correction scheme also works well for hybrid functionals if a large supercell is used and the exact exchange interaction is screened. PMID:26583386

  14. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH2(+).

    PubMed

    Li, Y Q; Zhang, P Y; Han, K L

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.

  15. Evaluation of steam sterilization processes: comparing calculations using temperature data and biointegrator reduction data and calculation of theoretical temperature difference.

    PubMed

    Lundahl, Gunnel

    2007-01-01

    When calculating of the physical F121.1 degrees c-value by the equation F121.1 degrees C = t x 10(T-121.1/z the temperature (T), in combination with the z-value, influences the F121.1 degrees c-value exponentially. Because the z-value for spores of Geobacillus stearothermophilus often varies between 6 and 9, the biological F-value (F(Bio) will not always correspond to the F0-value based on temperature records from the sterilization process calculated with a z-value of 10, even if the calibration of both of them are correct. Consequently an error in calibration of thermocouples and difference in z-values influences the F121.1 degrees c-values logarithmically. The paper describes how results from measurements with different z-values can be compared. The first part describes the mathematics of a calculation program, which makes it easily possible to compare F0-values based on temperature records with the F(BIO)-value based on analysis of bioindicators such as glycerin-water-suspension sensors. For biological measurements, a suitable bioindicator with a high D121-value can be used (such a bioindicator can be manufactured as described in the article "A Method of Increasing Test Range and Accuracy of Bioindicators-Geobacillus stearothermophilus Spores"). By the mathematics and calculations described in this macro program it is possible to calculate for every position the theoretical temperature difference (deltaT(th)) needed to explain the difference in results between the thermocouple and the biointegrator. Since the temperature difference is a linear function and constant all over the process this value is an indication of the magnitude of an error. A graph and table from these calculations gives a picture of the run. The second part deals with product characteristics, the sterilization processes, loading patterns. Appropriate safety margins have to be chosen in the development phase of a sterilization process to achieve acceptable safety limits. Case studies are

  16. Reevaluation of experiments and new theoretical calculations for electron-impact excitation of C3+

    NASA Astrophysics Data System (ADS)

    Janzen, P. H.; Gardner, L. D.; Reisenfeld, D. B.; Savin, D. W.; Kohl, J. L.; Bartschat, K.

    1999-06-01

    Experimental absolute-rate coefficients for electron-impact excitation of C3+ (2s 2S1/2-->2p 2P1/2,3/2) near threshold [D. W. Savin, L. D. Gardner, D. B. Reisenfeld, A. R. Young, and J. L. Kohl, Phys. Rev. A 51, 2162 (1995)] have been reanalyzed to include a more accurate determination of optical efficiency and revised radiometric uncertainties which reduce the total systematic uncertainty of the results. Also, new R matrix with pseudostates (RMPS) calculations for this transition near threshold are presented. Comparison of the RMPS results to those of simpler close-coupling calculations indicates the importance of accounting for target continuum effects. The reanalyzed results of Savin et al. are in excellent agreement with the RMPS calculations; comparisons are also made to other measurements of this excitation. Agreement with the RMPS results is better for fluorescence technique measurements than for electron-energy-loss measurements.

  17. A formula for calculating theoretical photoelectron fluxes resulting from the He/+/ 304 A solar spectral line

    NASA Technical Reports Server (NTRS)

    Richards, P. G.; Torr, D. G.

    1981-01-01

    A simplified method for the evaluation of theoretical photoelectron fluxes in the upper atmosphere resulting from the solar radiation at 304 A is presented. The calculation is based on considerations of primary and cascade (secondary) photoelectron production in the two-stream model, where photoelectron transport is described by two electron streams, one moving up and one moving down, and of loss rates due to collisions with neutral gases and thermal electrons. The calculation is illustrated for the case of photoelectrons at an energy of 24.5 eV, and it is noted that the 24.5-eV photoelectron flux may be used to monitor variations in the solar 304 A flux. Theoretical calculations based on various ionization and excitation cross sections of Banks et al. (1974) are shown to be in generally good agreement with AE-E measurements taken between 200 and 235 km, however the use of more recent, larger cross sections leads to photoelectron values a factor of two smaller than observations but in agreement with previous calculations. It is concluded that a final resolution of the photoelectron problem may depend on a reevaluation of the inelastic electron collision cross sections.

  18. Towards a spectroscopically accurate set of potentials for heavy hydride laser cooling candidates: Effective core potential calculations of BaH

    NASA Astrophysics Data System (ADS)

    Moore, Keith; McLaughlin, Brendan M.; Lane, Ian C.

    2016-04-01

    BaH (and its isotopomers) is an attractive molecular candidate for laser cooling to ultracold temperatures and a potential precursor for the production of ultracold gases of hydrogen and deuterium. The theoretical challenge is to simulate the laser cooling cycle as reliably as possible and this paper addresses the generation of a highly accurate ab initio 2Σ+ potential for such studies. The performance of various basis sets within the multi-reference configuration-interaction (MRCI) approximation with the Davidson correction is tested and taken to the Complete Basis Set (CBS) limit. It is shown that the calculated molecular constants using a 46 electron effective core-potential and even-tempered augmented polarized core-valence basis sets (aug-pCVnZ-PP, n = 4 and 5) but only including three active electrons in the MRCI calculation are in excellent agreement with the available experimental values. The predicted dissociation energy De for the X2Σ+ state (extrapolated to the CBS limit) is 16 895.12 cm-1 (2.094 eV), which agrees within 0.1% of a revised experimental value of <16 910.6 cm-1, while the calculated re is within 0.03 pm of the experimental result.

  19. Raman and infrared spectra and theoretical calculations of dipicolinic acid, dinicotinic acid, and their dianions

    NASA Astrophysics Data System (ADS)

    McCann, Kathleen; Laane, Jaan

    2008-11-01

    The Raman and infrared spectra of dipicolinic acid (DPA) and dinicotinic acid (DNic) and their salts (CaDPA, Na 2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Because of extensive intermolecular hydrogen bonding in the crystals of these molecules, the calculated structures and spectra for the individual molecules agree only moderately well with the experimental values. Theoretical calculations were also carried out for DPA dimers and DPA·2H 2O to better understand the intermolecular interactions. The spectra do show that DPA and its calcium salt, which are present in anthrax spores, can be distinguished from the very similar DNic and CaDNic.

  20. Theoretical calculation of product contents: battery and cathode ray tube examples.

    PubMed

    Thomas, Valerie M

    2003-05-01

    Most product environmental assessments are based on manufacturer-supplied data on the material content of the product. This paper explores the potential for the material content of key components to be estimated with theoretical calculations. Two examples, the amount of cadmium in a nickel-cadmium battery and the amount of lead in a TV or computer CRT monitor, are developed. Both an upper and a lower limit on the amount of cadmium in a nickel-cadmium battery are calculated on the basis of the battery's chemical reaction. The amount of lead shielding needed in a TV or CRT computer monitor is estimated on the basis of the potential difference through which electrons are accelerated and the absorption length of photons in lead. Such calculations can be used as benchmarks in product environmental assessments, providing validation of manufacturer-supplied data and providing insight into the composition and design of products.

  1. Theoretical prediction of high pressure phase transition in ScC and YC: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.

    2013-08-01

    The structural stability of ScC and YC has been analyzed under hydrostatic compression employing the first-principles calculations using the plane-wave pseudopotential method. The comparison of theoretically calculated enthalpies of rocksalt type (B1), primitive orthorhombic (Pmmn), and CsCl type (B2) structures as a function of pressure suggests that the B1 structure transforms to Pmmn phase instead of transforming to B2 phase that predicted by Soni et al. [J. Phys. Chem. Solids 72, 810 (2011)]. The pressure for B1 to Pmmn transition predicted for ScC and YC are ˜80 GPa and ˜30 GPa, respectively. To further substantiate the outcomes of our static lattice calculations, we have performed lattice dynamic calculations also. Our lattice dynamic calculations correctly demonstrate that the B1 phase is dynamically stable structure at ambient condition. Further, for both the carbides, we find that the Pmmn structure becomes dynamically stable around the transition pressure whereas the B2 structure remains unstable, supporting the B1 to Pmmn phase transition predicted by our static lattice calculations.

  2. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    PubMed

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  3. Accurate and Efficient Calculation of van der Waals Interactions Within Density Functional Theory by Local Atomic Potential Approach

    SciTech Connect

    Sun, Y. Y.; Kim, Y. H.; Lee, K.; Zhang, S. B.

    2008-01-01

    Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.

  4. Calculation of stress intensity factors in an isotropic multicracked plate. Part 1: Theoretical development

    NASA Technical Reports Server (NTRS)

    Binienda, W. K.; Arnold, S. M.; Tan, H. Q.

    1992-01-01

    An essential part of describing the damage state and predicting the damage growth in a multicracked plate is the accurate calculation of stress intensity factors (SIF's). Here, a methodology and rigorous solution formulation for SIF's of a multicracked plate, with fully interacting cracks, subjected to a far-field arbitrary stress state is presented. The fundamental perturbation problem is derived, and the steps needed to formulate the system of singular integral equations whose solution gives rise to the evaluation of the SIF's are identified. This analytical derivation and numerical solution are obtained by using intelligent application of symbolic computations and automatic FORTRAN generation capabilities (described in the second part of this paper). As a result, a symbolic/FORTRAN package, named SYMFRAC, that is capable of providing accurate SIF's at each crack tip was developed and validated.

  5. Voronoi-cell finite difference method for accurate electronic structure calculation of polyatomic molecules on unstructured grids

    SciTech Connect

    Son, Sang-Kil

    2011-03-01

    We introduce a new numerical grid-based method on unstructured grids in the three-dimensional real-space to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a discrete Laplacian operator based on Voronoi cells and their natural neighbors, featuring high adaptivity and simplicity. To resolve multicenter Coulomb singularity in all-electron calculations of polyatomic molecules, this method utilizes highly adaptive molecular grids which consist of spherical atomic grids. It provides accurate and efficient solutions for the Schroedinger equation and the Poisson equation with the all-electron Coulomb potentials regardless of the coordinate system and the molecular symmetry. For numerical examples, we assess accuracy of the VFD method for electronic structures of one-electron polyatomic systems, and apply the method to the density-functional theory for many-electron polyatomic molecules.

  6. Rapid and accurate determination of total lung capacity (TLC) from routine chest radiograms using a programmable hand-held calculator.

    PubMed

    Rodgers, R P; Tannen, R

    1983-01-01

    Since its appearance in 1960, the method of Barnhard and associates for the determination of total lung capacity (TLC) from routine chest radiograms has been widely studied in normal and diseased subjects. The method appears to be as accurate as the current definitive procedure, total body plethysmography. The method is in routine use in major medical institutions where the procedure has been automated, but the method does not seem to have gained the wide use it deserves. This is likely due to the tedium of the technique when performed manually--a single determination can require 30 min. We present here an implementation of the Barnhard method for the HP41-C hand-held programmable calculator. In conjunction with the use of a transparent reticle used for obtaining the required measurements, the program allows a single measurement to be made in under 12 minutes. We hope this technique will make radiographic TLC measurements more broadly accessible to the medical profession. PMID:6872526

  7. Theoretical calculation of the melting curve of Cu-Zr binary alloys

    DOE PAGES

    Gunawardana, K. G.S.H.; Wilson, S. R.; Mendelev, M. I.; Song, Xueyu

    2014-11-14

    Helmholtz free energies of the dominant binary crystalline solids found in the Cu-Zr system at high temperatures close to the melting curve are calculated. This theoretical approach combines fundamental measure density functional theory (applied to the hard-sphere reference system) and a perturbative approach to include the attractive interactions. The studied crystalline solids are Cu(fcc), Cu51Zr14(β), CuZr(B2), CuZr2(C11b), Zr(hcp), and Zr(bcc). The calculated Helmholtz free energies of crystalline solids are in good agreement with results from molecular-dynamics (MD) simulations. Using the same perturbation approach, the liquid phase free energies are calculated as a function of composition and temperature, from which themore » melting curve of the entire composition range of this system can be obtained. Phase diagrams are determined in this way for two leading embedded atom method potentials, and the results are compared with experimental data. Furthermore, theoretical melting temperatures are compared both with experimental values and with values obtained directly from MD simulations at several compositions.« less

  8. Theoretical calculation of the melting curve of Cu-Zr binary alloys

    SciTech Connect

    Gunawardana, K. G.S.H.; Wilson, S. R.; Mendelev, M. I.; Song, Xueyu

    2014-11-14

    Helmholtz free energies of the dominant binary crystalline solids found in the Cu-Zr system at high temperatures close to the melting curve are calculated. This theoretical approach combines fundamental measure density functional theory (applied to the hard-sphere reference system) and a perturbative approach to include the attractive interactions. The studied crystalline solids are Cu(fcc), Cu51Zr14(β), CuZr(B2), CuZr2(C11b), Zr(hcp), and Zr(bcc). The calculated Helmholtz free energies of crystalline solids are in good agreement with results from molecular-dynamics (MD) simulations. Using the same perturbation approach, the liquid phase free energies are calculated as a function of composition and temperature, from which the melting curve of the entire composition range of this system can be obtained. Phase diagrams are determined in this way for two leading embedded atom method potentials, and the results are compared with experimental data. Furthermore, theoretical melting temperatures are compared both with experimental values and with values obtained directly from MD simulations at several compositions.

  9. Theoretical study of the electronic structure with dipole moment calculations of barium monofluoride

    NASA Astrophysics Data System (ADS)

    Tohme, Samir N.; Korek, Mahmoud

    2015-12-01

    The potential energy curves have been investigated for the 41 lowest doublet and quartet electronic states in the 2s+1Λ± representation below 55,000 cm-1 of the molecule BaF via CASSCF and MRCI (single and double excitations with Davidson correction) calculations. Twenty-five electronic states have been studied here theoretically for the first time. The crossing and avoided crossing of 20 doublet electronic states have been studied in the region 30,000-50,000 cm-1. The harmonic frequency ωe, the internuclear distance Re, the rotational constant Be, the electronic energy with respect to the ground state Te, and the permanent and transition dipole moments have been calculated in addition to static dipole polarizability of the ground state. By using the canonical functions approach, the eigenvalue Ev, the rotational constant Bv, and the abscissas of the turning points Rmin and Rmax have been calculated for the electronic states up to the vibrational level v=98. The comparison of these values with the theoretical results available in the literature shows a very good agreement.

  10. A simple theoretical approach to calculate the electrical conductivity of nonideal copper plasma

    SciTech Connect

    Zaghloul, Mofreh R.

    2008-04-15

    A simple theoretical approach to calculate the electrical conductivity of partially ionized nonideal copper plasma is introduced. The densities of plasma species are calculated, to machine accuracy, including electronic excitation and allowing for high ionization states up to the atomic number of the element. Depression of ionization energies is taken into account using an interpolation formula that is valid over a wide range of densities. The formula yields the results of the Debye-Hueckel and the ion-sphere models at the limiting boundaries of low and high densities, respectively. The nonideal Coulomb logarithm is represented by an analytic wide-range formula supplemented by a specially tailored cutoff parameter. Effects of excluding excited and high ionization states on the calculation of ionization equilibrium and electrical conductivity of copper are investigated and assessed. Computational results of the electrical conductivity are compared with results from other theoretical models and available experimental measurements and showed reasonable agreement. A discussion about the choice of the ion-sphere radius is included and concerns about thermodynamic inconsistency when using the modified nonideal Saha equations are discussed and cleared.

  11. Regioselective enzymatic acylations of polyhydroxylated eudesmanes: semisynthesis, theoretical calculations, and biotransformation of cyclic sulfites.

    PubMed

    García-Granados, A; Melguizo, E; Parra, A; Simeó, Y; Viseras, B; Dobado, J A; Molina, J; Arias, J M

    2000-12-01

    Different lipase enzymes have been tested in order to perform regioselective acetylations on the eudesmane tetrol from vulgarin. High yields (95%) of 1,12-diacetoxy derivative (4) were achieved in 1 h with Candida antarctica lipase (CAL). However, only the 12-acetyl derivative (6) was obtained in similar yield with Mucor miehei (MML) or Candida cylindracea (CCL) lipases. The enzymatic protection at C-1 and C-12 has been used to form eudesmane cyclic-sulfites between C-6 and C-4 atoms. The R/S-sulfur configuration has been assigned by means of the experimental and theoretical (13)C and (1)H NMR chemical shifts. The theoretical shifts were calculated using the GIAO method, with a MM+ geometry optimization followed by a single-point calculation at the B3LYP/6-31G(*) level (B3LYP/6-31G(*)//MM+). Moreover, B3LYP/6-31G(*) geometry optimizations were carried out to test the B3LYP/6-31G(*)//MM+ results, for the deacetylated sulfites (12 and 15). In addition to the delta(C) and delta(H) shifts, the (3)J(HH) coupling constants were also calculated and compared with the experimental values when available. Finally, different reactivities have been checked in both sulfites by biotransformation with Rhizopus nigricans. While the R-sulfite gave 2 alpha- and 11 beta-hydroxylated metabolites, the S-sulfite yielded only regioselective deacetylations. Furthermore, both sulfites showed different reactivities in redox processes.

  12. Towards more accurate molecular dynamics calculation of thermal conductivity: Case study of GaN bulk crystals

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Aubry, S.; Jones, R. E.; Greenstein, A.; Schelling, P. K.

    2009-03-01

    Significant differences exist among literature for thermal conductivity of various systems computed using molecular dynamics simulation. In some cases, unphysical results, for example, negative thermal conductivity, have been found. Using GaN as an example case and the direct nonequilibrium method, extensive molecular dynamics simulations and Monte Carlo analysis of the results have been carried out to quantify the uncertainty level of the molecular dynamics methods and to identify the conditions that can yield sufficiently accurate calculations of thermal conductivity. We found that the errors of the calculations are mainly due to the statistical thermal fluctuations. Extrapolating results to the limit of an infinite-size system tend to magnify the errors and occasionally lead to unphysical results. The error in bulk estimates can be reduced by performing longer time averages using properly selected systems over a range of sample lengths. If the errors in the conductivity estimates associated with each of the sample lengths are kept below a certain threshold, the likelihood of obtaining unphysical bulk values becomes insignificant. Using a Monte Carlo approach developed here, we have determined the probability distributions for the bulk thermal conductivities obtained using the direct method. We also have observed a nonlinear effect that can become a source of significant errors. For the extremely accurate results presented here, we predict a [0001] GaN thermal conductivity of 185W/Km at 300 K, 102W/Km at 500 K, and 74W/Km at 800 K. Using the insights obtained in the work, we have achieved a corresponding error level (standard deviation) for the bulk (infinite sample length) GaN thermal conductivity of less than 10W/Km , 5W/Km , and 15W/Km at 300 K, 500 K, and 800 K, respectively.

  13. Accurate reporting of adherence to inhaled therapies in adults with cystic fibrosis: methods to calculate “normative adherence”

    PubMed Central

    Hoo, Zhe Hui; Curley, Rachael; Campbell, Michael J; Walters, Stephen J; Hind, Daniel; Wildman, Martin J

    2016-01-01

    Background Preventative inhaled treatments in cystic fibrosis will only be effective in maintaining lung health if used appropriately. An accurate adherence index should therefore reflect treatment effectiveness, but the standard method of reporting adherence, that is, as a percentage of the agreed regimen between clinicians and people with cystic fibrosis, does not account for the appropriateness of the treatment regimen. We describe two different indices of inhaled therapy adherence for adults with cystic fibrosis which take into account effectiveness, that is, “simple” and “sophisticated” normative adherence. Methods to calculate normative adherence Denominator adjustment involves fixing a minimum appropriate value based on the recommended therapy given a person’s characteristics. For simple normative adherence, the denominator is determined by the person’s Pseudomonas status. For sophisticated normative adherence, the denominator is determined by the person’s Pseudomonas status and history of pulmonary exacerbations over the previous year. Numerator adjustment involves capping the daily maximum inhaled therapy use at 100% so that medication overuse does not artificially inflate the adherence level. Three illustrative cases Case A is an example of inhaled therapy under prescription based on Pseudomonas status resulting in lower simple normative adherence compared to unadjusted adherence. Case B is an example of inhaled therapy under-prescription based on previous exacerbation history resulting in lower sophisticated normative adherence compared to unadjusted adherence and simple normative adherence. Case C is an example of nebulizer overuse exaggerating the magnitude of unadjusted adherence. Conclusion Different methods of reporting adherence can result in different magnitudes of adherence. We have proposed two methods of standardizing the calculation of adherence which should better reflect treatment effectiveness. The value of these indices can

  14. Accurate Time-Dependent Wave Packet Calculations for the O(+) + H2 → OH(+) + H Ion-Molecule Reaction.

    PubMed

    Bulut, N; Castillo, J F; Jambrina, P G; Kłos, J; Roncero, O; Aoiz, F J; Bañares, L

    2015-12-17

    Accurate quantum reactive scattering time-dependent wave packet close-coupling calculations have been carried out to determine total reaction probabilities and integral cross sections for the O(+) + H2 → OH(+) + H reaction in a range of collision energies from 10(-3) eV up to 1.0 eV for the H2 rovibrational states (v = 0; j = 0, 1, 2) and (v = 1; j = 0) using the potential energy surface (PES) by Martı́nez et al. As expected for a barrierless reaction, the reaction cross section decays rapidly with collision energy, Ec, following a behavior that nearly corresponds to that predicted by the Langevin model. Rotational excitation of H2 into j = 1, 2 has a very moderate effect on reactivity, similarly to what happens with vibrational excitation below Ec ≈ 0.3 eV. However, at higher collision energies the cross section increases notably when H2 is promoted to v = 1. This effect is explained by resorting to the effective potentials in the entrance channel. The integral cross sections have been used to calculate rate constants in the temperature range 200-1000 K. A good overall agreement has been found with the available experimental data on integral cross sections and rate constants. In addition, time-independent quantum mechanical and quasi-classical trajectory (QCT) calculations have been performed on the same PES aimed to compare the various methodologies and to discern the detailed mechanism of the title reaction. In particular, the analysis of individual trajectories has made it possible to explain, in terms of the coupling between reagent relative velocity and the topography of the PES, the presence of a series of alternating maxima and minima in the collision energy dependence of the QCT reaction probabilities for the reactions with H2(v=0,1,j=0), which are absent in the quantum mechanical calculations.

  15. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  16. Theoretical Calculations of Photoabsorption of Several Alicyclic Molecules in the Vacuum Ultraviolet Region

    SciTech Connect

    Matsuzawa, Nobuyuki; Ishitani, Akihiko; Dixon, David A.; Uda, Tsuyoshi

    2001-06-13

    In order to aid in the design of transparent materials for use as photoresists for F2 lithography (157 nm), we have performed time-dependent density functional theory (TD-DFT) calculations of the photoabsorption of molecules in the vacuum ultraviolet region. The application of this TD-DFT method to the prediction of photoabsorption was benchmarked using model molecules such as formaldehyde, and an empirical equation for correcting the calculated transition energy was obtained. The TD-DFT method with the empirical correction equation provides dramatically more accurate results than those obtained with the CIS (single-excitation configuration interaction) method, which we employed in previous studies. We used it to predict the photoabsorption of various molecules such as methanol, t-butylalcohol, acetic acid, methyl acetate, cycloalkane, norbonane, tricyclodecane, tetrahydropyrane, adamantane, maleic anhydride and their fluorinated derivatives.

  17. Infrared, Raman and ultraviolet with circular dichroism analysis and theoretical calculations of tedizolid

    NASA Astrophysics Data System (ADS)

    Michalska, Katarzyna; Mizera, Mikołaj; Lewandowska, Kornelia; Cielecka-Piontek, Judyta

    2016-07-01

    Tedizolid is the newest antibacterial agent from the oxazolidinone class. For its identification, FT-IR (2000-400 cm-1) and Raman (2000-400 cm-1) analyses were proposed. Studies of the enantiomeric purity of tedizolid were conducted based on ultraviolet-circular dichroism (UV-CD) analysis. Density functional theory (DFT) with the B3LYP hybrid functional and 6-311G(2df,2pd) basis set was used for support of the analysis of the FT-IR and Raman spectra. Theoretical methods made it possible to conduct HOMO and LUMO analysis, which was used to determine the charge transfer for two tedizolid enantiomers. Molecular electrostatic potential maps were calculated with the DFT method for both tedizolid enantiomers. The relationship between the results of ab initio calculations and knowledge about the chemical-biological properties of R- and S-tedizolid enantiomers is also discussed.

  18. MRI-aided tissues interface characterization: An accurate signal propagation time calculation method for UWB breast tumor imaging

    NASA Astrophysics Data System (ADS)

    Wang, Liang; Xiao, Xia; Kikkawa, Takamaro

    2016-12-01

    Radar-based ultrawideband (UWB) microwave imaging is expected to be a safe, low-cost tool for breast cancer detection. However, since radar wave travels at different speeds in different tissues, propagation time is hard to be estimated in heterogeneous breast. Wrongly estimated propagation time leads to error of tumor location in resulting image, aka imaging error. In this paper, we develop a magnetic resonance imaging-aided (MRI-aided) propagation time calculation technique which is independent from radar imaging system but can help decrease the imaging error. The technique can eliminate the influence of the rough interface between fat layer and gland layer in breast and get relative accurate thicknesses of two layers. The propagation time in each layer is calculated and summed. The summed propagation time is used in Confocal imaging algorithm to increase the accuracy of resulting image. 25 patients' breast models with glands of varying size are classified into four categories for imaging simulation tests. Imaging accuracy in terms of tumor location along x-direction has been improved for 21 among 25 cases, as a result, overall around 50% improvement compared to conventional UWB imaging.

  19. Accurate multireference configuration interaction calculations of the 24 Λ-S states and 60 Ω states of the BO+ cation

    NASA Astrophysics Data System (ADS)

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-11-01

    The potential energy curves were calculated for the 24 Λ-S states correlating with the lowest four dissociation channels of the BO+ cation. The potential energy curves were also computed for the 60 Ω states generated from the 24 Λ-S states. Calculations were made for internuclear separations from 0.08 to 1.05 nm using the CASSCF method, which was followed by the icMRCI approach with the correlation-consistent basis sets. Core-valence correlation, scalar relativistic and basis extrapolation were accounted for. Of the 24 Λ-S states, only three states (25Π, 15Σ-, and 25Σ-) were found to be repulsive; only the 15Δ state was found to be a very weakly-bound state; and the E1Π, 23Π, and 15Π states were found to be very strong bound. In addition, the B1Σ+ and 31Σ+ states have double wells by the avoided crossing between the two states. The a3Π, 13Σ-, and 23Σ- states are inverted with the spin-orbit coupling effect included. The spectroscopic parameters were determined and the vibrational properties of several Λ-S states were predicted. Comparison with available experimental data shows that the methodology employed is highly accurate for this system.

  20. Accurate multireference configuration interaction calculations of the 24 Λ-S states and 60 Ω states of the BO(+) cation.

    PubMed

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-11-01

    The potential energy curves were calculated for the 24 Λ-S states correlating with the lowest four dissociation channels of the BO(+) cation. The potential energy curves were also computed for the 60 Ω states generated from the 24 Λ-S states. Calculations were made for internuclear separations from 0.08 to 1.05nm using the CASSCF method, which was followed by the icMRCI approach with the correlation-consistent basis sets. Core-valence correlation, scalar relativistic and basis extrapolation were accounted for. Of the 24 Λ-S states, only three states (2(5)Π, 1(5)Σ(-), and 2(5)Σ(-)) were found to be repulsive; only the 1(5)Δ state was found to be a very weakly-bound state; and the E(1)Π, 2(3)Π, and 1(5)Π states were found to be very strong bound. In addition, the B(1)Σ(+) and 3(1)Σ(+) states have double wells by the avoided crossing between the two states. The a(3)Π, 1(3)Σ(-), and 2(3)Σ(-) states are inverted with the spin-orbit coupling effect included. The spectroscopic parameters were determined and the vibrational properties of several Λ-S states were predicted. Comparison with available experimental data shows that the methodology employed is highly accurate for this system. PMID:27289351

  1. An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings

    SciTech Connect

    Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas; Neugebauer, Johannes

    2013-02-07

    Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlap matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Angstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.

  2. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    NASA Astrophysics Data System (ADS)

    Zhang, Du; Yang, Weitao

    2016-10-01

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and double excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K4), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.

  3. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    DOE PAGES

    Zhang, Du; Yang, Weitao

    2016-10-13

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and doublemore » excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K^{4}), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.« less

  4. Theoretical calculation (DFT), Raman and surface-enhanced Raman scattering (SERS) study of ponceau 4R

    NASA Astrophysics Data System (ADS)

    Xie, Yunfei; Li, Yan; Sun, Yingying; Wang, Heya; Qian, He; Yao, Weirong

    2012-10-01

    Ponceau 4R is used as a coloring agent in many different products, such as food, drinks, medicines, cosmetics and tobacco. However, ponceau 4R also shows carcinogenic, teratogenic and mutagenic behavior in high doses. In this work, standard Raman, theoretical Raman and surface-enhanced Raman scattering (SERS) spectra have been used to investigate ponceau 4R. More specifically, density functional theory (DFT) calculations have been used to calculate the optimized Raman spectrum of ponceau 4R at the B3LYP/6-31G(d) level. This has provided a better understanding of the optimized geometry and vibrational frequencies of this dye. In addition, the experimental spectrum of ponceau 4R has been compared with the theoretical spectrum; good agreement was obtained. Finally, it has shown that using SERS the detection limit of the ponceau 4R solution can be as low as 5 μg/mL. This has been achieved by SERS measurements of ponceau 4R on a substrate of gold nanoparticles. The SERS peaks at 1030, 1236, 1356 and 1502 cm-1 were chosen as index for semi-quantitative analysis, showing that the SERS technique provided a useful ultrasensitive method for the detection of ponceau 4R.

  5. Investigation on the Gas-Phase Decomposition of Trichlorfon by GC-MS and Theoretical Calculation

    PubMed Central

    Jiang, Kezhi; Zhang, Ningwen; Zhang, Hu; Wang, Jianmei; Qian, Mingrong

    2015-01-01

    The gas phase pyrolysis of trichlorfon was investigated by the on-line gas chromatography – mass spectrometry (GC-MS) pyrolysis and theoretical calculations. Two reaction channels were proposed in the pyrolytic reaction, by analyzing the detected pyrolytic products in the total ion chromatography, including 2,2,2-trichloroacetaldehyde, dimethyl phosphite, and dichlorvos. Theoretical calculations showed that there is an intramolecular hydrogen bond between the hydroxyl group and the phosphate O atom in trichlorfon, through which the hydroxyl H atom can be easily transferred to phosphate O atom to trigger two pyrolytic channels. In path-a, migration of H atom results in direct decomposition of trichlorfon to give 2,2,2-trichloroacetaldehyde and dimethyl phosphite in one step. In path-b, migration of H atom in trichlorfon is combined with formation of the O-P bond to give an intermediate, followed by HCl elimination to afford dichlorvos. Path-a is kinetically more favorable than path-b, which is consistent with the GC-MS results. PMID:25856549

  6. A Mathematical Solution to the Theoretical Band Gap Underestimation: Predictive Calculations of Properties of Semiconductors

    NASA Astrophysics Data System (ADS)

    Bagayoko, Diola

    2008-03-01

    Most density functional theory (DFT) calculations find band gaps that are 30-50 percent smaller than the experimental ones, as illustrated in this presentation that recalls some popular explanations of this band gap problem, i.e., self-interaction effects and derivative discontinuities of the exchange correlation energy. A survey of the increasingly numerous approaches aimed at resolving the theoretical underestimation follows these explanations. These approaches include the Green function and screened Coulomb approximation (GWA), time dependent density functional theory (TDDFT), the exact exchange and screened exchange methods, and the use of local density approximation (LDA) potentials plus additional potentials located at atomic sites. Using the Rayleigh theorem, we describe a basis set and variational effect inherently associated with calculations that employ a linear combination of atomic orbitals (LCAO) in a variational approach of the Rayleigh-Ritz type. This description concomitantly shows a source of large underestimation errors in calculated band gaps, i.e., an often dramatic lowering of some unoccupied energies on account of the Rayleigh theorem as opposed to the Hamiltonian. We present the Bagayoko, Zhao, and Williams (BZW) method [Phys. Rev. B 60, 1563 (1999); PRB 74, 245214 (2006); and PRB 76, 037101 (2007)] that follows from the description of the aforementioned effect and that leads (a) to DFT and LDA calculated band gaps of semiconductors in agreement with experiment and (b) theoretical predictions of band gaps that are confirmed by experiment. Unlike most calculations, BZW computations solve, self-consistently, a system of two coupled equations. DFT-BZW calculated effective masses and optical properties (dielectric functions) also agree with measurements. We illustrate ten years of success of the BZW method with its results for GaN, C, Si, 3C-SIC, 4H-SiC, ZnO, AlAs, Ge, ZnSe, w-InN, InAs, and AlN. We conclude with a request to revisit beliefs

  7. Theoretical calculation of nitrogen isotope equilibrium exchange fractionation factors for various NOy molecules

    NASA Astrophysics Data System (ADS)

    Walters, Wendell W.; Michalski, Greg

    2015-09-01

    The nitrogen stable isotope ratio (15N/14N) of nitrogen oxides (NOx = NO + NO2) and its oxidation products (NOy = NOx + PAN (peroxyacetyl nitrate = C2H3NO5) + HNO3 + NO3 + HONO + N2O5 + ⋯ + particulate nitrates) has been suggested as a tool for partitioning NOx sources; however, the impact of nitrogen (N) equilibrium isotopic fractionation on 15N/14N ratios during the conversion of NOx to NOy must also be considered, but few fractionation factors for these processes have been determined. To address this limitation, computational quantum chemistry calculations of harmonic frequencies, reduced partition function ratios (15β), and N equilibrium isotope exchange fractionation factors (αA/B) were performed for various gaseous and aqueous NOy molecules in the rigid rotor and harmonic oscillator approximations using the B3LYP and EDF2 density functional methods for the mono-substitution of 15N. The calculated harmonic frequencies, 15β, and αA/B are in good agreement with available experimental measurements, suggesting the potential to use computational methods to calculate αA/B values for N isotope exchange processes that are difficult to measure experimentally. Additionally, the effects of solvation (water) on 15β and αA/B were evaluated using the IEF-PCM model, and resulted in lower 15β and αA/B values likely due to the stabilization of the NOy molecules from dispersion interactions with water. Overall, our calculated 15β and αA/B values are accurate in the rigid rotor and harmonic oscillator approximations and will allow for the estimation of αA/B involving various NOy molecules. These calculated αA/B values may help to explain the trends observed in the N stable isotope ratio of NOy molecules in the atmosphere.

  8. Experimentation and theoretic calculation of a BODIPY sensor based on photoinduced electron transfer for ions detection.

    PubMed

    Lu, Hua; Zhang, ShuShu; Liu, HanZhuang; Wang, YanWei; Shen, Zhen; Liu, ChunGen; You, XiaoZeng

    2009-12-24

    A boron-dipyrromethene (BODIPY)-based fluorescence probe with a N,N'-(pyridine-2, 6-diylbis(methylene))-dianiline substituent (1) has been prepared by condensation of 2,6-pyridinedicarboxaldehyde with 8-(4-amino)-4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene and reduction by NaBH(4). The sensing properties of compound 1 toward various metal ions are investigated via fluorometric titration in methanol, which show highly selective fluorescent turn-on response in the presence of Hg(2+) over the other metal ions, such as Li(+), Na(+), K(+), Ca(2+), Mg(2+), Pb(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Ag(+), and Mn(2+). Computational approach has been carried out to investigate the mechanism why compound 1 provides different fluorescent signal for Hg(2+) and other ions. Theoretic calculations of the energy levels show that the quenching of the bright green fluorescence of boradiazaindacene fluorophore is due to the reductive photoinduced electron transfer (PET) from the aniline subunit to the excited state of BODIPY fluorophore. In metal complexes, the frontier molecular orbital energy levels changes greatly. Binding Zn(2+) or Cd(2+) ion leads to significant decreasing of both the HOMO and LUMO energy levels of the receptor, thus inhibit the reductive PET process, whereas an oxidative PET from the excited state fluorophore to the receptor occurs, vice versa, which also quenches the fluorescence. However, for 1-Hg(2+) complex, both the reductive and oxidative PETs are prohibited; therefore, strong fluorescence emission from the fluorophore can be observed experimentally. The agreement of the experimental results and theoretic calculations suggests that our calculation method can be applicable as guidance for the design of new chemosensors for other metal ions. PMID:19950967

  9. Experimentation and Theoretic Calculation of a BODIPY Sensor Based on Photoinduced Electron Transfer for Ions Detection

    NASA Astrophysics Data System (ADS)

    Lu, Hua; Zhang, Shushu; Liu, Hanzhuang; Wang, Yanwei; Shen, Zhen; Liu, Chungen; You, Xiaozeng

    2009-12-01

    A boron-dipyrromethene (BODIPY)-based fluorescence probe with a N,N'-(pyridine-2, 6-diylbis(methylene))-dianiline substituent (1) has been prepared by condensation of 2,6-pyridinedicarboxaldehyde with 8-(4-amino)-4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene and reduction by NaBH4. The sensing properties of compound 1 toward various metal ions are investigated via fluorometric titration in methanol, which show highly selective fluorescent turn-on response in the presence of Hg2+ over the other metal ions, such as Li+, Na+, K+, Ca2+, Mg2+, Pb2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Ag+, and Mn2+. Computational approach has been carried out to investigate the mechanism why compound 1 provides different fluorescent signal for Hg2+ and other ions. Theoretic calculations of the energy levels show that the quenching of the bright green fluorescence of boradiazaindacene fluorophore is due to the reductive photoinduced electron transfer (PET) from the aniline subunit to the excited state of BODIPY fluorophore. In metal complexes, the frontier molecular orbital energy levels changes greatly. Binding Zn2+ or Cd2+ ion leads to significant decreasing of both the HOMO and LUMO energy levels of the receptor, thus inhibit the reductive PET process, whereas an oxidative PET from the excited state fluorophore to the receptor occurs, vice versa, which also quenches the fluorescence. However, for 1-Hg2+ complex, both the reductive and oxidative PETs are prohibited; therefore, strong fluorescence emission from the fluorophore can be observed experimentally. The agreement of the experimental results and theoretic calculations suggests that our calculation method can be applicable as guidance for the design of new chemosensors for other metal ions.

  10. Accurate Monte Carlo modeling of cyclotrons for optimization of shielding and activation calculations in the biomedical field

    NASA Astrophysics Data System (ADS)

    Infantino, Angelo; Marengo, Mario; Baschetti, Serafina; Cicoria, Gianfranco; Longo Vaschetto, Vittorio; Lucconi, Giulia; Massucci, Piera; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano

    2015-11-01

    Biomedical cyclotrons for production of Positron Emission Tomography (PET) radionuclides and radiotherapy with hadrons or ions are widely diffused and established in hospitals as well as in industrial facilities and research sites. Guidelines for site planning and installation, as well as for radiation protection assessment, are given in a number of international documents; however, these well-established guides typically offer analytic methods of calculation of both shielding and materials activation, in approximate or idealized geometry set up. The availability of Monte Carlo codes with accurate and up-to-date libraries for transport and interactions of neutrons and charged particles at energies below 250 MeV, together with the continuously increasing power of nowadays computers, makes systematic use of simulations with realistic geometries possible, yielding equipment and site specific evaluation of the source terms, shielding requirements and all quantities relevant to radiation protection. In this work, the well-known Monte Carlo code FLUKA was used to simulate two representative models of cyclotron for PET radionuclides production, including their targetry; and one type of proton therapy cyclotron including the energy selection system. Simulations yield estimates of various quantities of radiological interest, including the effective dose distribution around the equipment, the effective number of neutron produced per incident proton and the activation of target materials, the structure of the cyclotron, the energy degrader, the vault walls and the soil. The model was validated against experimental measurements and comparison with well-established reference data. Neutron ambient dose equivalent H*(10) was measured around a GE PETtrace cyclotron: an average ratio between experimental measurement and simulations of 0.99±0.07 was found. Saturation yield of 18F, produced by the well-known 18O(p,n)18F reaction, was calculated and compared with the IAEA recommended

  11. Theoretical Calculations of Elastic and Inelastic Scattering of Electrons from Ar^+

    NASA Astrophysics Data System (ADS)

    Griffin, D. C.; Pindzola, M. S.; Shaw, J. A.; Badnell, N. R.

    1996-05-01

    We report on theoretical calculations of differential and partial cross sections for elastic scattering of electrons from Ar^+ and total cross sections for electron-impact excitation and ionization of Ar^+. The elastic scattering calculations are performed using the R-matrix method and are compared to measurements. The excitation cross sections are calculated using both the distorted-wave and the R-matrix close-coupling approximations, while the ionization cross sections are determined from the distorted-wave approximation, and include the effects of final-state correlation. The effects of core polarization and resonance contributions on the excitation cross sections are examined carefully. Rate coefficients for ionization and excitation to the levels of 3p^44p ^4D, together with radiative rates from the levels of 3p^44p ^4D to all possible lower levels, will be entered into the ADAS collisional-radiative modeling codes(H. P. Summers \\underlineADAS User's Manual), JET-IR(94)06. Work supported by the Department of Energy to generate density-dependent parameters for use in the interpretation of on-going emissivity measurements from tokamak plasmas.

  12. Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane

    SciTech Connect

    Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas

    2014-04-28

    Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.

  13. The theoretical tensile strength of fcc crystals predicted from shear strength calculations

    NASA Astrophysics Data System (ADS)

    Černý, M.; Pokluda, J.

    2009-04-01

    This work presents a simple way of estimating uniaxial tensile strength on the basis of theoretical shear strength calculations, taking into account its dependence on a superimposed normal stress. The presented procedure enables us to avoid complicated and time-consuming analyses of elastic stability of crystals under tensile loading. The atomistic simulations of coupled shear and tensile deformations in cubic crystals are performed using first principles computational code based on pseudo-potentials and the plane wave basis set. Six fcc crystals are subjected to shear deformations in convenient slip systems and a special relaxation procedure controls the stress tensor. The obtained dependence of the ideal shear strength on the normal tensile stress seems to be almost linearly decreasing for all investigated crystals. Taking these results into account, the uniaxial tensile strength values in three crystallographic directions were evaluated by assuming a collapse of the weakest shear system. Calculated strengths for \\langle 001\\rangle and \\langle 111\\rangle loading were found to be mostly lower than previously calculated stresses related to tensile instability but rather close to those obtained by means of the shear instability analysis. On the other hand, the strengths for \\langle 110\\rangle loading almost match the stresses related to tensile instability.

  14. A convenient method for calculation of ionic diffusion coefficients for accurate selected ion flow tube mass spectrometry, SIFT-MS

    NASA Astrophysics Data System (ADS)

    Dryahina, K.; Spanel, P.

    2005-07-01

    A method to calculate diffusion coefficients of ions important for the selected ion flow tube mass spectrometry, SIFT-MS, is presented. The ions, on which this method is demonstrated, include the SIFT-MS precursors H3O+(H2O)0,1,2,3, NO.+(H2O)0,1,2 and O2+ and the product ions relevant to analysis of breath trace metabolites ammonia (NH3+(H2O)0,1,2, NH4+(H2O)0,1,2), acetaldehyde (C2H4OH+(H2O)0,1,2), acetone (CH3CO+, (CH3)2CO+, (CH3)2COH+(H2O)0,1, (CH3)2CO.NO+), ethanol (C2H5OHH+(H2O)0,1,2) and isoprene (C5H7+, C5H8+, C5H9+). Theoretical model of the (12, 4) potential for interaction between the ions and the helium atoms is used, with the repulsive part approximated by the mean hard-sphere cross section and the attractive part describing ion-induced dipole interactions. The reduced zero-field mobilities at 300 K are calculated using the Viehland and Mason theory [L.A. Viehland, S.L. Lin, E.A. Mason, At. Data Nucl. Data Tables, 60 (1995) 37-95], parameterised by a simple formula as a function of the mean hard-sphere cross section, and converted to diffusion coefficients using the Einstein relation. The method is tested on a set of experimental data for simple ions and cluster ions.

  15. Accurate energy bands calculated by the hybrid quasiparticle self-consistent GW method implemented in the ecalj package

    NASA Astrophysics Data System (ADS)

    Deguchi, Daiki; Sato, Kazunori; Kino, Hiori; Kotani, Takao

    2016-05-01

    We have recently implemented a new version of the quasiparticle self-consistent GW (QSGW) method in the ecalj package released at http://github.com/tkotani/ecalj. Since the new version of the ecalj package is numerically stable and more accurate than the previous versions, we can perform calculations easily without being bothered with tuning input parameters. Here we examine its ability to describe energy band properties, e.g., band-gap energy, eigenvalues at special points, and effective mass, for a variety of semiconductors and insulators. We treat C, Si, Ge, Sn, SiC (in 2H, 3C, and 4H structures), (Al, Ga, In) × (N, P, As, Sb), (Zn, Cd, Mg) × (O, S, Se, Te), SiO2, HfO2, ZrO2, SrTiO3, PbS, PbTe, MnO, NiO, and HgO. We propose that a hybrid QSGW method, where we mix 80% of QSGW and 20% of LDA, gives universally good agreement with experiments for these materials.

  16. Efficient calculation of molecular configurational entropies using an information theoretic approximation

    PubMed Central

    King, Bracken M.; Silver, Nathaniel W.; Tidor, Bruce

    2012-01-01

    Accurate computation of free energy changes upon molecular binding remains a challenging problem, and changes in configurational entropy are especially difficult due both to the potentially large numbers of local minima, anharmonicity, and high-order coupling among degrees of freedom. Here we propose a new method to compute molecular entropies based on the maximum information spanning tree (MIST) approximation that we have previously developed. Estimates of high-order couplings using only low-order terms provide excellent convergence properties, and the theory is also guaranteed to bound the entropy. The theory is presented together with applications to the calculation of the entropies of a variety of small molecules and the binding entropy change for a series of HIV protease inhibitors. The MIST framework developed here is demonstrated to compare favorably with results computed using the related mutual information expansion (MIE) approach, and an analysis of similarities between the methods is presented. PMID:22229789

  17. Accurate rotational constant and bond lengths of hexafluorobenzene by femtosecond rotational Raman coherence spectroscopy and ab initio calculations

    SciTech Connect

    Den, Takuya S.; Frey, Hans-Martin; Leutwyler, Samuel

    2014-11-21

    The gas-phase rotational motion of hexafluorobenzene has been measured in real time using femtosecond (fs) time-resolved rotational Raman coherence spectroscopy (RR-RCS) at T = 100 and 295 K. This four-wave mixing method allows to probe the rotation of non-polar gas-phase molecules with fs time resolution over times up to ∼5 ns. The ground state rotational constant of hexafluorobenzene is determined as B{sub 0} = 1029.740(28) MHz (2σ uncertainty) from RR-RCS transients measured in a pulsed seeded supersonic jet, where essentially only the v = 0 state is populated. Using this B{sub 0} value, RR-RCS measurements in a room temperature gas cell give the rotational constants B{sub v} of the five lowest-lying thermally populated vibrationally excited states ν{sub 7/8}, ν{sub 9}, ν{sub 11/12}, ν{sub 13}, and ν{sub 14/15}. Their B{sub v} constants differ from B{sub 0} by between −1.02 MHz and +2.23 MHz. Combining the B{sub 0} with the results of all-electron coupled-cluster CCSD(T) calculations of Demaison et al. [Mol. Phys. 111, 1539 (2013)] and of our own allow to determine the C-C and C-F semi-experimental equilibrium bond lengths r{sub e}(C-C) = 1.3866(3) Å and r{sub e}(C-F) = 1.3244(4) Å. These agree with the CCSD(T)/wCVQZ r{sub e} bond lengths calculated by Demaison et al. within ±0.0005 Å. We also calculate the semi-experimental thermally averaged bond lengths r{sub g}(C-C)=1.3907(3) Å and r{sub g}(C-F)=1.3250(4) Å. These are at least ten times more accurate than two sets of experimental gas-phase electron diffraction r{sub g} bond lengths measured in the 1960s.

  18. Theoretical gas to liquid shift of (15)N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations.

    PubMed

    Gerber, Iann C; Jolibois, Franck

    2015-05-14

    Chemical shift requires the knowledge of both the sample and a reference magnetic shielding. In few cases as nitrogen (15N), the standard experimental reference corresponds to its liquid phase. Theoretical estimate of NMR magnetic shielding parameters of compounds in their liquid phase is then mandatory but usually replaced by an easily-get gas phase value, forbidding direct comparisons with experiments. We propose here to combine ab initio molecular dynamic simulations with the calculations of magnetic shielding using GIAO approach on extracted cluster's structures from MD. Using several computational strategies, we manage to accurately calculate 15N magnetic shielding of nitromethane in its liquid phase. Theoretical comparison between liquid and gas phase allows us to extrapolate an experimental value for the 15N magnetic shielding of nitromethane in gas phase between -121.8 and -120.8 ppm.

  19. Conformational and stereoeletronic investigations of muscarinic agonists of acetylcholine by NMR and theoretical calculations

    NASA Astrophysics Data System (ADS)

    da Silva, Julio Cesar A.; Ducati, Lucas C.; Rittner, Roberto

    2012-05-01

    NMR solvent effects and theoretical calculations showed muscarinic agonists present a large stability for their near synclinal conformations, indicating the presence of significant stabilization factors. Analysis of the results clearly indicated that this stability is not determined by the dihedral around the substituted C-C ethane bond, as stated by some authors, but a consequence of the geometry adopted in order to maximize N+/O interactions in this type of molecules. It can be assumed that acetylcholine and its muscarinic agonists exhibit their biologic activity when the positively charged nitrogen and the oxygen atoms are in the same side of the molecule within an interatomic distance ranging from 3.0 to 6.0 Å.

  20. Theoretical Characterization of Visual Signatures and Calculation of Approximate Global Harmonic Frequency Scaling Factors

    NASA Astrophysics Data System (ADS)

    Kashinski, D. O.; Nelson, R. G.; Chase, G. M.; di Nallo, O. E.; Byrd, E. F. C.

    2016-05-01

    We are investigating the accuracy of theoretical models used to predict the visible, ultraviolet, and infrared spectra, as well as other properties, of product materials ejected from the muzzle of currently fielded systems. Recent advances in solid propellants has made the management of muzzle signature (flash) a principle issue in weapons development across the calibers. A priori prediction of the electromagnetic spectra of formulations will allow researchers to tailor blends that yield desired signatures and determine spectrographic detection ranges. Quantum chemistry methods at various levels of sophistication have been employed to optimize molecular geometries, compute unscaled harmonic frequencies, and determine the optical spectra of specific gas-phase species. Electronic excitations are being computed using Time Dependent Density Functional Theory (TD-DFT). Calculation of approximate global harmonic frequency scaling factors for specific DFT functionals is also in progress. A full statistical analysis and reliability assessment of computational results is currently underway. Work supported by the ARL, DoD-HPCMP, and USMA.

  1. A theoretical prediction of hydrogen molecule dissociation-recombination rates including an accurate treatment of internal state nonequilibrium effects

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.

    1990-01-01

    The dissociation and recombination of H2 over the temperature range 1000-5000 K are calculated in a nonempirical manner. The computation procedure involves the calculation of the state-to-state energy transfer rate coefficients, the solution of the 349 coupled equations which form the master equation, and the determination of the phenomenological rate coefficients. The nonempirical results presented here are in good agreement with experimental data at 1000 and 3000 K.

  2. Vibrationally resolved photoelectron imaging of Cu2H- and AgCuH- and theoretical calculations.

    PubMed

    Xie, Hua; Li, Xiaoyi; Zhao, Lijuan; Liu, Zhiling; Qin, Zhengbo; Wu, Xia; Tang, Zichao; Xing, Xiaopeng

    2013-02-28

    Vibrationally resolved photoelectron spectra have been obtained for Cu(2)H(-) and AgCuH(-) using photoelectron imaging at 355 nm. Two transition bands X and A are observed for each spectrum. The X bands in both spectra show the vibration progressions of the Cu-H stretching mode and the broad peaks of these progressions indicate significant structural changes from Cu(2)H(-) and AgCuH(-) to their neutral ground states. The A bands in the spectra of Cu(2)H(-) and CuAgH(-) show stretching progressions of Cu-Cu and Ag-Cu, respectively. The contours of these two progressions are pretty narrow, indicating relatively small structural changes from Cu(2)H(-) and AgCuH(-) to their neutral excited states. Calculations based on density functional theory indicate that the ground states of Cu(2)H(-) and AgCuH(-) and the first excited states of their neutrals are linear, whereas their neutral ground states are bent. The photoelectron detachment energies and vibrational frequencies from these calculations are in good agreement with the experimental observations. Especially, the theoretical predication of linear structures for the anions and the neutral excited states are supported by the spectral features of A bands, in which the bending modes are inactive. Comparisons among the vertical detachment energies of Cu(2)H(-), AgCuH(-), and their analogs help to elucidate electronic characteristics of coinage metal elements and hydrogen in small clusters.

  3. Conformational equilibrium and hydrogen bonding in liquid 2-phenylethylamine explored by Raman spectroscopy and theoretical calculations.

    PubMed

    Xie, Min; Qi, Yajing; Hu, Yongjun

    2011-04-14

    2-Phenylethylamine (PEA) is the simplest aromatic amine neurotransmitter, as well as one of the most important. In this work, the conformational equilibrium and hydrogen bonding in liquid PEA were studied by means of Raman spectroscopy and theoretical calculations (DFT/MP2). By changing the orientation of the ethyl and the NH(2) group, nine possible conformers of PEA were found, including four degenerate conformers. Comparison of the experimental Raman spectra of liquid PEA and the calculated Raman spectra of the five typical conformers in selected regions (550-800 and 1250-1500 cm(-1)) revealed that the five conformers can coexist in conformational equilibrium in the liquid. The NH(2) stretching mode of the liquid is red-shifted by ca. 30 cm(-1) relative to that of an isolated PEA molecule (measured previously), implying that intermolecular N-H···N hydrogen bonds play an important role in liquid PEA. The relative intensity of the Raman band at 762 cm(-1) was found to increase with increasing temperature, indicating that the anti conformer might be favorable in liquid PEA at room temperature. The blue shift of the band for the bonded N-H stretch with increasing temperature also provides evidence of the existence of intermolecular N-H···N hydrogen bonds.

  4. Conformational preferences for some 5-substituted 2-acetylthiophenes through infrared spectroscopy and theoretical calculations.

    PubMed

    Rittner, Roberto; Ducati, Lucas C; Tormena, Cláudio F; Fiorin, Barbara C; Braga, Carolyne B

    2011-09-01

    The s-cis-trans isomerisms of some derivatives of thiophene (2-acetyl, AT; 2-acetyl-5-bromo, ABT and 2-acetyl-5-chloro, ACT) were analyzed, using data from deconvolution of their carbonyl absorption bands in two solvents (CCl4 and CHCl3). These infrared data showed that the O,S-cis conformer largely predominates in the studied solvents and that the same occurs in the gas phase, as observed from theoretical calculations. The latter results were obtained using B3LYP/6-311++G(3df,3p) and MP2/6-311++G(3df,3p) levels of theory, with zero-point energy correction. Moreover, the use of the IEFPCM (Integral Equation Formalism Polarizable Continuum Model) to take into account the solvent effects, using the same levels of theory, confirmed the results observed from infrared data. Low temperature 13C NMR spectra in CS2/CD2Cl2 (-90 °C) and in acetone-d6 (-80°C) did not show pairs of signals for each carbon, due to the known low energy barrier (∼8 kcal mol(-1)) for the cis-trans interconversion. Data from NBO calculations show that the nO(2)→σS-C5* and nO(2)→σC2-C3* interactions occur only in the O,S-cis isomer and can explain its conformational preference.

  5. Theoretical calculating the thermodynamic properties of solid sorbents for CO{sub 2} capture applications

    SciTech Connect

    Duan, Yuhua

    2012-11-02

    Since current technologies for capturing CO{sub 2} to fight global climate change are still too energy intensive, there is a critical need for development of new materials that can capture CO{sub 2} reversibly with acceptable energy costs. Accordingly, solid sorbents have been proposed to be used for CO{sub 2} capture applications through a reversible chemical transformation. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO{sub 2} sorbent candidates from the vast array of possible solid materials has been proposed and validated. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO{sub 2} adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO{sub 2} capture reactions by the solids of interest, we were able to screen only those solid materials for which lower capture energy costs are expected at the desired pressure and temperature conditions. Only those selected CO{sub 2} sorbent candidates were further considered for experimental validations. The ab initio thermodynamic technique has the advantage of identifying thermodynamic properties of CO{sub 2} capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. Such methodology not only can be used to search for good candidates from existing database of solid materials, but also can provide some guidelines for synthesis new materials. In this presentation, we first introduce our screening methodology and the results on a testing set of solids with known thermodynamic properties to validate our methodology. Then, by applying our computational method

  6. Nitrogen-broadened lineshapes in the oxygen A-band: Experimental results and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Predoi-Cross, Adriana; Holladay, Christopher; Heung, Henry; Bouanich, Jean-Pierre; Mellau, Georg Ch.; Keller, Reimund; Hurtmans, Daniel R.

    2008-09-01

    We report measurements for N 2-broadening, pressure-shift and line mixing coefficients for 55 oxygen transitions in the A-band retrieved using a multispectrum fitting technique. Nineteen laboratory absorption spectra were recorded at 0.02 cm -1 resolution using a multi-pass absorption cell with path length of 1636.9 cm and the IFS 120 Fourier transform spectrometer located at Justus-Liebig-University in Giessen, Germany. The total sample pressures ranged from 8.8 to 3004.5 Torr with oxygen volume mixing ratios in nitrogen ranging between 0.057 and 0.62. An Exponential Power Gap (EPG) scaling law was used to calculate the N 2-broadening and N 2-line mixing coefficients. The line broadening and shift coefficients for the A-band of oxygen self-perturbed and perturbed by N 2 are modeled using semiclassical calculations based on the Robert-Bonamy formalism and two intermolecular potentials. These potentials involve electrostatic contributions including the hexadecapole moment of the molecules and (a) a simple dispersion contribution with one adjustable parameter to fit the broadening coefficients or (b) the atom-atom Lennard-Jones model without such adjustable parameters. The first potential leads to very weak broadening coefficients for high J transitions whereas the second potential gives much more improved results at medium and large J values, in reasonable agreement with the experimental data. For the line shifts which mainly arise in our calculation from the electronic state dependence of the isotropic potential, their general trends with increasing J values can be well predicted, especially from the first potential. From the theoretical results, we have derived air-broadening and air-induced shift coefficients with an agreement comparable to that obtained for O 2-O 2 and O 2-N 2.

  7. Accuracy of theoretical calculations of the main parameters of the F2-layer of the daytime ionosphere

    NASA Astrophysics Data System (ADS)

    Pavlov, A. V.; Sitnov, Iu. S.

    1985-10-01

    Pavlov's (1984) method is used to determine the relative errors (due to errors in measuring the input parameters of the model) in theoretical calculations of the main parameters of the daytime F2-layer under quiet conditions. The parameters calculated are the height of the F2-layer maximum and the electron density.

  8. Feeding biomechanics and theoretical calculations of bite force in bull sharks (Carcharhinus leucas) during ontogeny.

    PubMed

    Habegger, Maria L; Motta, Philip J; Huber, Daniel R; Dean, Mason N

    2012-12-01

    Evaluations of bite force, either measured directly or calculated theoretically, have been used to investigate the maximum feeding performance of a wide variety of vertebrates. However, bite force studies of fishes have focused primarily on small species due to the intractable nature of large apex predators. More massive muscles can generate higher forces and many of these fishes attain immense sizes; it is unclear how much of their biting performance is driven purely by dramatic ontogenetic increases in body size versus size-specific selection for enhanced feeding performance. In this study, we investigated biting performance and feeding biomechanics of immature and mature individuals from an ontogenetic series of an apex predator, the bull shark, Carcharhinus leucas (73-285cm total length). Theoretical bite force ranged from 36 to 2128N at the most anterior bite point, and 170 to 5914N at the most posterior bite point over the ontogenetic series. Scaling patterns differed among the two age groups investigated; immature bull shark bite force scaled with positive allometry, whereas adult bite force scaled isometrically. When the bite force of C. leucas was compared to those of 12 other cartilaginous fishes, bull sharks presented the highest mass-specific bite force, greater than that of the white shark or the great hammerhead shark. A phylogenetic independent contrast analysis of anatomical and dietary variables as determinants of bite force in these 13 species indicated that the evolution of large adult bite forces in cartilaginous fishes is linked predominantly to the evolution of large body size. Multiple regressions based on mass-specific standardized contrasts suggest that the evolution of high bite forces in Chondrichthyes is further correlated with hypertrophication of the jaw adductors, increased leverage for anterior biting, and widening of the head. Lastly, we discuss the ecological significance of positive allometry in bite force as a possible

  9. Combinatorial Vibration-Mode Assignment for the FTIR Spectrum of Crystalline Melamine: A Strategic Approach toward Theoretical IR Vibrational Calculations of Triazine-Based Compounds.

    PubMed

    Yuan, Xiaohong; Luo, Kun; Zhang, Keqin; He, Julong; Zhao, Yuanchun; Yu, Dongli

    2016-09-29

    Although polymeric graphitic carbon nitride (g-C3N4) has been widely studied as metal-free photocatalyst, the description of its structure still remains a great challenge. Fourier transform infrared (FTIR) spectroscopy can provide complementary structural information. In this paper, we reconsider the representative crystalline melamine and develop a strategic approach to theoretically calculate the IR vibrations of this triazine-based nitrogen-rich system. IR calculations were based on three different models: a single molecule, a 4-molecule unit cell, and a 32-molecule cluster, respectively. By this comparative study the contribution of the intermolecular weak interactions were elucidated in detail. An accurate and visualized description on the experimental FTIR spectrum has been further presented by a combinatorial vibration-mode assignment based on the calculated potential energy distribution of the 32-molecule cluster. The theoretical approach reported in this study opens the way to the facile and accurate assignment for IR vibrational modes of other complex triazine-based compounds, such as g-C3N4. PMID:27598419

  10. Theoretical grounds of relativistic methods for calculation of spin-spin coupling constants in nuclear magnetic resonance spectra

    NASA Astrophysics Data System (ADS)

    Rusakova, I. L.; Rusakov, Yu Yu; Krivdin, L. B.

    2016-04-01

    The theoretical grounds of the modern relativistic methods for quantum chemical calculation of spin-spin coupling constants in nuclear magnetic resonance spectra are considered. Examples and prospects of application of relativistic calculations of these constants in the structural studies of organic and heteroorganic compounds are discussed. Practical recommendations on relativistic calculations of spin-spin coupling constants using the available software are given. The bibliography includes 622 references.

  11. Theoretical grounds of relativistic methods for calculation of spin–spin coupling constants in nuclear magnetic resonance spectra

    NASA Astrophysics Data System (ADS)

    Rusakova, I. L.; Rusakov, Yu Yu; Krivdin, L. B.

    2016-04-01

    The theoretical grounds of the modern relativistic methods for quantum chemical calculation of spin–spin coupling constants in nuclear magnetic resonance spectra are considered. Examples and prospects of application of relativistic calculations of these constants in the structural studies of organic and heteroorganic compounds are discussed. Practical recommendations on relativistic calculations of spin–spin coupling constants using the available software are given. The bibliography includes 622 references.

  12. REMPI spectroscopy and theoretical calculations of cis and trans 3-fluoro-N-methylaniline

    NASA Astrophysics Data System (ADS)

    Zhang, Lijuan; Liu, Sheng; Dong, Changwu; Cheng, Min; Du, Yikui; Zhu, Qihe; Zhang, Cunhao

    2014-02-01

    The ab initio and density functional theory (DFT) calculations of 3-fluoro-N-methylaniline (3FNMA) reveal that two rotamers, cis and trans 3FNMA, are stable for each of the S0, S1, and D0 states. The vibronic spectra of the two rotamers in the S1 state have been recorded by the one-color resonant two-photon ionization (R2PI) spectroscopy. The band origins of the S1 ← S0 electronic transition of cis and trans 3FNMA are found to be 33 816 ± 3 and 34 023 ± 3 cm-1. The two rotamers display similar vibrational frequencies, and the slight energy difference in some modes reflects the conformation effect due to the relative orientation of the NHCH3 group. Besides, the trans rotamer displays more vibronic features in the low-frequency region, which are active modes mainly involving the CH3 and the NHCH3 groups. By the two-color R2PI spectroscopy, the adiabatic ionization energies (IEs) of cis and trans 3FNMA are determined to be 61 742 ± 10 and 61 602 ± 10 cm-1, respectively. It is derived from the R2PI spectroscopic data that, compared with the trans rotamer, the cis rotamer is more stable by 302 ± 25 cm-1 in the S1 state, but less stable by 45 ± 25 cm-1 in the D0 state. With the aid of theoretical calculations, the substitution and conformation effects on the properties of 3FNMA, including the molecular structures, vibrational frequencies, and the relative stability of the two rotamers, were discussed in detail.

  13. Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations.

    PubMed

    Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng

    2016-08-01

    Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass

  14. Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations.

    PubMed

    Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng

    2016-08-01

    Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass

  15. Conformational analysis of 2-halocyclopentanones by NMR and IR spectroscopies and theoretical calculations.

    PubMed

    Martins, Carina R; Ducati, Lucas C; Tormena, Cláudio F; Rittner, Roberto

    2009-06-01

    The conformational isomerism of 2-chlorocyclopentanone and 2-bromocyclopentanone has been determined through the solvent dependence of the (1)H NMR (3)J(HH) coupling constants, theoretical calculations and infrared data, using the solvation theory for the treatment of NMR data. In 2-chlorocyclopentanone, the energy difference (E(Psi-e)-E(Psi-a)), in the isolated molecule at B3LYP level of theory, between the pseudo-equatorial (Psi-e) and pseudo-axial (Psi-a) conformers is 0.42kcalmol(-1), which decreases in CCl(4) and in acetonitrile solutions, in good agreement with infrared data (nu(CO)), despite the uncertainties of the latter method. The conformational equilibrium for 2-bromocyclopentanone is also between the Psi-e and Psi-a conformations, with an energy difference (E(Psi-e)-E(Psi-a)), in the isolated molecule at B3LYP level of theory, is 0.85kcalmol(-1) which decreases in CCl(4) and in acetonitrile solutions, also in good agreement with infrared data.

  16. Postseismic viscoelastic surface deformation and stress. Part 1: Theoretical considerations, displacement and strain calculations

    NASA Technical Reports Server (NTRS)

    Cohen, S. C.

    1979-01-01

    A model of viscoelastic deformations associated with earthquakes is presented. A strike-slip fault is represented by a rectangular dislocation in a viscoelastic layer (lithosphere) lying over a viscoelastic half-space (asthenosphere). Deformations occur on three time scales. The initial response is governed by the instantaneous elastic properties of the earth. A slower response is associated with viscoelastic relaxation of the lithosphere and a yet slower response is due to viscoelastic relaxation of the asthenosphere. The major conceptual contribution is the inclusion of lithospheric viscoelastic properties into a dislocation model of earthquake related deformations and stresses. Numerical calculations using typical fault parameters reveal that the postseismic displacements and strains are small compared to the coseismic ones near the fault, but become significant further away. Moreover, the directional sense of the deformations attributable to the elastic response, the lithospheric viscoelastic softening, and the asthenospheric viscoelastic flow may differ and depend on location and model details. The results and theoretical arguments suggest that the stress changes accompanying lithospheric relaxation may also be in a different sense than and be larger than the strain changes.

  17. Epoxides, cyclic sulfites, and sulfate from natural pentacyclic triterpenoids: theoretical calculations and chemical transformations.

    PubMed

    García-Granados, Andrés; López, Pilar E; Melguizo, Enrique; Moliz, Juan N; Parra, Andrés; Simeó, Yolanda; Dobado, José A

    2003-06-13

    Several triterpenic derivatives, with the A-ring functionalized, were semisynthesized from oleanolic and maslinic acids. The reactivities of sulfites, sulfate, and epoxides in these triterpene compounds were investigated under different reaction conditions. Moreover, contracted A-ring triterpenes (five-membered rings) were obtained, by different treatments of the sulfate 7. From the epoxide 8, deoxygenated and halohydrin derivatives were semisynthesized with several nucleophiles. Ozonolysis and Beckmann reactions were used to yield 4-aza compounds, from five-membered ring olanediene triterpenes. The X-ray structure of sulfate 7 is given and compared with density functional theory geometries. Theoretical (13)C and (1)H chemical shifts (gauge-invariant atomic orbital method at the B3LYP/6-31G*//B3LYP/6-31G* level) and (3)J(H,H) coupling constants were calculated for compounds 5-9 and 34-36, identifying the (R)- or (S)-sulfur and alpha- or beta-epoxide configurations together with 4-aza or 3-aza structures.

  18. Additional correction for energy transfer efficiency calculation in filter-based Förster resonance energy transfer microscopy for more accurate results

    NASA Astrophysics Data System (ADS)

    Sun, Yuansheng; Periasamy, Ammasi

    2010-03-01

    Förster resonance energy transfer (FRET) microscopy is commonly used to monitor protein interactions with filter-based imaging systems, which require spectral bleedthrough (or cross talk) correction to accurately measure energy transfer efficiency (E). The double-label (donor+acceptor) specimen is excited with the donor wavelength, the acceptor emission provided the uncorrected FRET signal and the donor emission (the donor channel) represents the quenched donor (qD), the basis for the E calculation. Our results indicate this is not the most accurate determination of the quenched donor signal as it fails to consider the donor spectral bleedthrough (DSBT) signals in the qD for the E calculation, which our new model addresses, leading to a more accurate E result. This refinement improves E comparisons made with lifetime and spectral FRET imaging microscopy as shown here using several genetic (FRET standard) constructs, where cerulean and venus fluorescent proteins are tethered by different amino acid linkers.

  19. Molecular structure of cotinine studied by gas electron diffraction combined with theoretical calculations

    NASA Astrophysics Data System (ADS)

    Takeshima, Tsuguhide; Takeuchi, Hiroshi; Egawa, Toru; Konaka, Shigehiro

    2007-09-01

    The molecular structure of cotinine (( S)-1-methyl-5-(3-pyridinyl)-2-pyrrolidinone), the major metabolite of nicotine, has been determined at about 182 °C by gas electron diffraction combined with MP2 and DFT calculations. The diffraction data are consistent with the existence of the (ax, sc), (ax, ap), (eq, sp) and (eq, ap) conformers, where ax and eq indicate the configuration of the pyrrolidinone ring by means of the position (axial and equatorial) of the pyridine ring, and sc, sp and ap distinguish the isomers arising from the internal rotation around the bond connecting the two rings. The (CH 3)NCCC(N) dihedral angles, ϕ, of the (ax, sc) and (eq, sp) conformers were determined independently to be 158(12)° and 129(13)°, respectively, where the numbers in parentheses are three times the standard errors, 3 σ. According to the MP2 calculations, the corresponding dihedral angles for the (ax, ap) and (eq, ap) conformers were assumed to differ by 180° from their syn counterparts. The ratios x(ax, sc)/ x(ax, ap) and x(eq, sp)/ x(eq, ap) were taken from the theoretically estimated free energy differences, Δ G, where x is the abundance of the conformer. The resultant abundances of (ax, sc), (ax, ap), (eq, sp) and (eq, ap) conformers are 34(6)%, 21% (d.p.), 28% (d.p.), and 17% (d.p.), respectively, where d.p. represents dependent parameters. The determined structural parameters ( rg (Å) and ∠ α (°)) of the most abundant conformer, (ax, sc), are as follows: r(N sbnd C) pyrrol = 1.463(5); r(N sbnd C methyl) = 1.457(←); r(N sbnd C( dbnd O)) = 1.384(12); r(C dbnd O) = 1.219(5); < r(C sbnd C) pyrrol> = 1.541(3); r(C pyrrolsbnd C pyrid) = 1.521(←); < r(C sbnd C) pyrid> = 1.396(2); < r(C sbnd N) pyrid> = 1.343(←); ∠(CNC) pyrrol = 113.9(11); ∠CCC pyrrol(-C pyrid) = 103.6(←); ∠NCO = 124.1(13); ∠NC pyrrolC pyrid = 113.1(12); ∠C pyrrolC pyrrolC pyrid = 113.3(←); ∠(CNC) pyrid = 117.1(2); <∠(NCC) pyrid> = 124.4(←); ∠C methylNC( dbnd O) =

  20. Hypertriton calculation with meson-theoretical nucleon-nucleon and hyperon-nucleon interactions

    SciTech Connect

    Miyagawa, K.; Gloeckle, W. Faculty of Liberal Arts and Science, Okayama University of Science, Ridai-cho, Okayama 700 )

    1993-12-01

    Faddeev equations for the coupled [Lambda][ital NN] and [Sigma][ital NN] systems are solved precisely for meson-theoretical nucleon-nucleon and hyperon-nucleon interactions. In this force model the hypertriton is not bound.

  1. A non-empirical, parameter-free, hybrid functional for accurate calculations of optoelectronic properties of finite systems

    NASA Astrophysics Data System (ADS)

    Brawand, Nicholas; Vörös, Márton; Govoni, Marco; Galli, Giulia

    The accurate prediction of optoelectronic properties of molecules and solids is a persisting challenge for current density functional theory (DFT) based methods. We propose a hybrid functional where the mixing fraction of exact and local exchange is determined by a non-empirical, system dependent function. This functional yields ionization potentials, fundamental and optical gaps of many, diverse systems in excellent agreement with experiments, including organic and inorganic molecules and nanocrystals. We further demonstrate that the newly defined hybrid functional gives the correct alignment between the energy level of the exemplary TTF-TCNQ donor-acceptor system. DOE-BES: DE-FG02-06ER46262.

  2. Toward Accurate Modelling of Enzymatic Reactions: All Electron Quantum Chemical Analysis combined with QM/MM Calculation of Chorismate Mutase

    SciTech Connect

    Ishida, Toyokazu

    2008-09-17

    To further understand the catalytic role of the protein environment in the enzymatic process, the author has analyzed the reaction mechanism of the Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM). By introducing a new computational strategy that combines all-electron QM calculations with ab initio QM/MM modelings, it was possible to simulate the molecular interactions between the substrate and the protein environment. The electrostatic nature of the transition state stabilization was characterized by performing all-electron QM calculations based on the fragment molecular orbital technique for the entire enzyme.

  3. AN ACCURATE NEW METHOD OF CALCULATING ABSOLUTE MAGNITUDES AND K-CORRECTIONS APPLIED TO THE SLOAN FILTER SET

    SciTech Connect

    Beare, Richard; Brown, Michael J. I.; Pimbblet, Kevin

    2014-12-20

    We describe an accurate new method for determining absolute magnitudes, and hence also K-corrections, that is simpler than most previous methods, being based on a quadratic function of just one suitably chosen observed color. The method relies on the extensive and accurate new set of 129 empirical galaxy template spectral energy distributions from Brown et al. A key advantage of our method is that we can reliably estimate random errors in computed absolute magnitudes due to galaxy diversity, photometric error and redshift error. We derive K-corrections for the five Sloan Digital Sky Survey filters and provide parameter tables for use by the astronomical community. Using the New York Value-Added Galaxy Catalog, we compare our K-corrections with those from kcorrect. Our K-corrections produce absolute magnitudes that are generally in good agreement with kcorrect. Absolute griz magnitudes differ by less than 0.02 mag and those in the u band by ∼0.04 mag. The evolution of rest-frame colors as a function of redshift is better behaved using our method, with relatively few galaxies being assigned anomalously red colors and a tight red sequence being observed across the whole 0.0 < z < 0.5 redshift range.

  4. Accurate calculation of the x-ray absorption spectrum of water via the GW/Bethe-Salpeter equation

    NASA Astrophysics Data System (ADS)

    Gilmore, Keith; Vinson, John; Kas, Josh; Vila, Fernando; Rehr, John

    2014-03-01

    We calculate x-ray absorption spectra (XAS) of water within the OCEAN code, which combines plane-wave, pseudopotential electronic structure, PAW transition elements, GW self-energy corrections, and the NIST BSE solver. Due to the computational demands of this approach, our initial XAS calculations were limited to 17 molecule super cells. This lead to unphysical, size dependent effects in the calculated spectra. To treat larger systems, we extended the OCEAN interface to support well-parallelized codes such as QuantumESPRESSO. We also implemented an efficient interpolation scheme of Shirley. We applied this large-scale GW/BSE approach to 64 molecule unit cell structures of water obtained from classical DFT/MD and PIMD simulations. In concurrence with previous work, we find the calculated spectrum both qualitatively and quantitatively reproduces the experimental features. The agreement implies that structures based on PIMD, which are similar to the traditional distorted tetrahedral view, are consistent with experimental observations. Supported by the DOE CMCSN through DOE award DE-SC0005180 (Princeton University) and in part by DOE Grant No. DE-FG03-97ER45623 (JJR) with computer support from NERSC.

  5. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    SciTech Connect

    Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  6. Theoretical Fraunhofer light diffraction patterns calculated from three-dimensional sarcomere arrays imaged from isolated cardiac cells at rest.

    PubMed

    Roos, K P; Leung, A F

    1987-08-01

    Sarcomere striation positions have been obtained throughout the volumes of calcium-tolerant resting heart cells by direct computer interfaced high-resolution optical imaging. Each sarcomere position is stored in a three-dimensional (3-D) matrix array from which Fraunhofer light diffraction patterns have been calculated using numerical methods based on Fourier transforms. Diffraction patterns have been calculated from heart cell data arrays oriented normal to a theoretical laser beam. Twelve characteristic features have been identified and described from these diffraction patterns that correlate to diffraction phenomena observed from both cardiac and skeletal muscle. This numerical approach provides the means to directly assess diffraction pattern formulation, the precision of layer line angular separation, layer-line intensity and angular asymmetries, line widths and fine structures in terms of the known diffracting source structures. These results confirm that theoretical calculations can predict real muscle diffraction patterns and their asymmetries.

  7. Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

    PubMed

    Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

    2013-04-01

    The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach.

  8. Theoretical Calculations on Sediment Transport on Titan, and the Possible Production of Streamlined Forms

    NASA Technical Reports Server (NTRS)

    Burr, D. M.; Emery, J. P.; Lorenz, R. D.

    2005-01-01

    The Cassini Imaging Science System (ISS) has been returning images of Titan, along with other Saturnian satellites. Images taken through the 938 nm methane window see down to Titan's surface. One of the purposes of the Cassini mission is to investigate possible fluid cycling on Titan. Lemniscate features shown recently and radar evidence of surface flow prompted us to consider theoretically the creation by methane fluid flow of streamlined forms on Titan. This follows work by other groups in theoretical consideration of fluid motion on Titan's surface.

  9. Phenylalanine and tyrosine methyl ester intramolecular interactions and conformational analysis by (1)H NMR and infrared spectroscopies and theoretical calculations.

    PubMed

    Cormanich, Rodrigo A; Ducati, Lucas C; Tormena, Cláudio F; Rittner, Roberto

    2014-04-01

    Amino acid conformational analysis in solution are scarce, since these compounds present a bipolar zwitterionic structure ((+)H3NCHRCOO(-)) in these media. Also, intramolecular hydrogen bonds have been classified as the sole interactions governing amino acid conformational behavior in the literature. In the present work we propose phenylalanine and tyrosine methyl ester conformational studies in different solvents by (1)H NMR and infrared spectroscopies and theoretical calculations. Both experimental and theoretical results are in agreement and suggest that the conformational behavior of the phenylalanine and tyrosine methyl esters are similar and are dictated by the interplay between steric and hyperconjugative interactions.

  10. Experimental measurements with Monte Carlo corrections and theoretical calculations of neutron inelastic scattering cross section of 115In

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Xiao, Jun; Luo, Xiaobing

    2016-10-01

    The neutron inelastic scattering cross section of 115In has been measured by the activation technique at neutron energies of 2.95, 3.94, and 5.24 MeV with the neutron capture cross sections of 197Au as an internal standard. The effects of multiple scattering and flux attenuation were corrected using the Monte Carlo code GEANT4. Based on the experimental values, the 115In neutron inelastic scattering cross sections data were theoretically calculated between the 1 and 15 MeV with the TALYS software code, the theoretical results of this study are in reasonable agreement with the available experimental results.

  11. Using experimental studies and theoretical calculations to analyze the molecular mechanism of coumarin, p-hydroxybenzoic acid, and cinnamic acid

    NASA Astrophysics Data System (ADS)

    Hsieh, Tiane-Jye; Su, Chia-Ching; Chen, Chung-Yi; Liou, Chyong-Huey; Lu, Li-Hwa

    2005-05-01

    Three natural products, Coumarin ( 1), p-hydroxybenzoic acid ( 2), trans-cinnamic acid ( 3) were isolated from the natural plant of indigenous cinnamon and the structures including relative stereochemistry were elucidated on the basis of spectroscopic data and theoretical calculations. Their sterochemical structures were determined by NMR spectroscopy, mass spectroscopy, and X-ray crystallography. The p-hydroxybenzoic acid complex with water is reported to show the existence of two hydrogen bonds. The two hydrogen bonds are formed in the water molecule of two hydrogen-accepting oxygen of carbonyl group of the p-hydroxybenzoic acid. The intermolecular interaction two hydrogen bond of the model system of the water- p-hydroxybenzoic acid was investigated. An experimental study and a theoretical analysis using the B3LYP/6-31G* method in the GAUSSIAN-03 package program were conducted on the three natural products. The theoretical results are supplemented by experimental data. Optimal geometric structures of three compounds were also determined. The calculated molecular mechanics compared quite well with those obtained from the experimental data. The ionization potentials, highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy, energy gaps, heat of formation, atomization energies, and vibration frequencies of the compounds were also calculated. The results of the calculations show that three natural products are stable molecules with high reactive and various other physical properties. The study also provided an explicit understanding of the sterochemical structure and thermodynamic properties of the three natural products.

  12. Theoretical calculations for mass resolution of a quadrupole ion trap reflectron time-of-flight mass spectrometer.

    PubMed

    Choi, Chang Min; Heo, Jiyoung; Park, Chang Joon; Kim, Nam Joon

    2010-02-01

    We have developed a theoretical method of predicting the mass resolution for a quadrupole ion trap reflectron time-of-flight (QIT-reTOF) mass spectrometer as a function of the spatial and velocity distributions of ions, voltages applied to the electrodes, and dimensions of the instrument. The flight times of ions were calculated using theoretical equations derived with an assumption of uniform electric fields inside the QIT and with the analytical description of the potential including the monopole, dipole, and quadrupole components. The mass resolution was then estimated from the flight-time spread of the ions with finite spatial and velocity distributions inside the QIT. The feasibility of the theoretical method was confirmed by the reasonable agreement of the theoretical resolution with the experimental one measured by varying the extraction voltage of the QIT or the deceleration voltage of the reflectron. We found that the theoretical resolution estimated with the assumption of the uniform electric fields inside the QIT reproduced the experimental one better than that with the analytical description of the potential. The possible applications of this theoretical method include the optimization of the experimental parameters of a given QIT-reTOF mass spectrometer and the design of new instruments with higher mass resolution.

  13. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

    PubMed

    Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun

    2016-04-14

    NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.

  14. Efficient and accurate treatment of weak pairs in local CCSD(T) calculations. II. Beyond the ring approximation

    NASA Astrophysics Data System (ADS)

    Schütz, Martin; Masur, Oliver; Usvyat, Denis

    2014-06-01

    In order to arrive at linear scaling of the computational cost with molecular size, local coupled cluster methods discriminate pairs of local molecular orbitals according to the spatial separation R of the latter. Only strong pairs are treated at the full coupled cluster level, whereas for weak pairs a lower level of theory (usually Møller-Plesset perturbation theory of second order, MP2) is used. Yet an MP2 treatment of weak pairs is inadequate in certain situations (for example, for describing π-stacking), which calls for an improved but still inexpensive method for dealing with the weak pairs. In a previous contribution, we proposed as a substituent for MP2 the LrCCD3 method, which is based on ring coupled cluster doubles (ring-CCD) and includes all third-order diagrams with energy contributions decaying not quicker than R-6. In the present work, we explore a still more accurate method, which is based on the same principles. It turned out to be essential to abandon the restriction to ring-CCD, i.e., to include further CCD diagrams beyond the ring approximation. The occurring intermediates turn out to be formally very similar to LMP2 density matrices, such that an efficient evaluation of these non-ring CCD diagrams is possible. Furthermore, a computationally cheap a posteriori estimate for the fourth-order singles contribution to the weak pair energy, which also exhibits a decay behavior of R-6, is introduced. The resulting method, denoted as LCCD[S]-R-6, indeed provides a substantial improvement in accuracy over the previous LrCCD3 method at a relatively modest additional computational cost.

  15. Toward Accurate Reaction Energetics for Molecular Line Growth at Surface: Quantum Monte Carlo and Density Functional Theory Calculations

    SciTech Connect

    Kanai, Y; Takeuchi, N

    2009-10-14

    We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

  16. Theoretical calculations of emission of wolframite and scheelite-type tungstate crystals

    SciTech Connect

    Nikolaenko, T.; Hizhnyi, Y.; Nedilko, S.

    2009-01-21

    Tungstate crystals AWO{sub 4} (A = Zn,Cd,Pb) are well-known scintillation materials for various applications in science and technology. In recent years the optical properties of these crystals were intensively studied experimentally and theoretically. However, the origin of luminescence in lead, cadmium and zinc tungstates is still the subject of discussion. According to generally accepted view, the centers of luminescence in AWO{sub 4} crystals are in some or other way related to the tungstate anionic groups. We developed a cluster approach in theoretical investigation of the electronic structure of AWO{sub 4} tungstate crystals based on the configuration interaction (CI) computation in which the lattice vibrations were taken into account.

  17. Ocean color spectrum calculations. [theoretical models relating oceanographic parameters to upwelling radiances

    NASA Technical Reports Server (NTRS)

    Mccluney, W. R.

    1974-01-01

    The development is considered of procedures for measuring a number of subsurface oceanographic parameters using remotely sensed ocean color data. It is proposed that the first step in this effort should be the development of adequate theoretical models relating the desired oceanographic parameters to the upwelling radiances to be observed. A portion of a contributory theoretical model is shown to be described by a modified single scattering approach based upon a simple treatment of multiple scattering. The resulting quasi-single scattering model can be used to predict the upwelling distribution of spectral radiance emerging from the sea. The shape of the radiance spectrum predicted by this model for clear ocean water shows encouraging agreement with measurments made at the edge of the Sargasso Sea off Cape Hatteras.

  18. Recombination of W19 + ions with electrons: Absolute rate coefficients from a storage-ring experiment and from theoretical calculations

    NASA Astrophysics Data System (ADS)

    Badnell, N. R.; Spruck, K.; Krantz, C.; Novotný, O.; Becker, A.; Bernhardt, D.; Grieser, M.; Hahn, M.; Repnow, R.; Savin, D. W.; Wolf, A.; Müller, A.; Schippers, S.

    2016-05-01

    Experimentally measured and theoretically calculated rate coefficients for the recombination of W19 +([Kr ] 4 d10 4 f9 ) ions with free electrons (forming W18 +) are presented. At low electron-ion collision energies, the merged-beam rate coefficient is dominated by strong, mutually overlapping, recombination resonances as already found previously for the neighboring charge-state ions W18 + and W20 +. In the temperature range where W19 + is expected to form in a collisionally ionized plasma, the experimentally derived recombination rate coefficient deviates by up to a factor of about 20 from the theoretical rate coefficient obtained from the Atomic Data and Analysis Structure database. The present calculations, which employ a Breit-Wigner redistributive partitioning of autoionizing widths for dielectronic recombination via multi-electron resonances, reproduce the experimental findings over the entire temperature range.

  19. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

    DOE PAGES

    Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; Parks, Jerry M.

    2016-07-08

    In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted

  20. Weighting Strategies for Single-Step Genomic BLUP: An Iterative Approach for Accurate Calculation of GEBV and GWAS.

    PubMed

    Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy

    2016-01-01

    former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861

  1. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

    PubMed

    Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M

    2016-08-01

    Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and

  2. Weighting Strategies for Single-Step Genomic BLUP: An Iterative Approach for Accurate Calculation of GEBV and GWAS

    PubMed Central

    Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy

    2016-01-01

    . Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.

  3. Weighting Strategies for Single-Step Genomic BLUP: An Iterative Approach for Accurate Calculation of GEBV and GWAS

    PubMed Central

    Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy

    2016-01-01

    . Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861

  4. Weighting Strategies for Single-Step Genomic BLUP: An Iterative Approach for Accurate Calculation of GEBV and GWAS.

    PubMed

    Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy

    2016-01-01

    former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.

  5. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

    PubMed

    Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M

    2016-08-01

    Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and

  6. Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User's Guide

    USGS Publications Warehouse

    Bales, Jerad D.; Nardi, Mark R.

    2007-01-01

    In order to standardize methods and facilitate rapid calculation and archival of stream-metabolism variables, the Stream Metabolism Program was developed to calculate gross primary production, net ecosystem production, respiration, and selected other variables from continuous measurements of dissolved-oxygen concentration, water temperature, and other user-supplied information. Methods for calculating metabolism from continuous measurements of dissolved-oxygen concentration and water temperature are fairly well known, but a standard set of procedures and computation software for all aspects of the calculations were not available previously. The Stream Metabolism Program addresses this deficiency with a stand-alone executable computer program written in Visual Basic.NET?, which runs in the Microsoft Windows? environment. All equations and assumptions used in the development of the software are documented in this report. Detailed guidance on application of the software is presented, along with a summary of the data required to use the software. Data from either a single station or paired (upstream, downstream) stations can be used with the software to calculate metabolism variables.

  7. The Calculation of Theoretical Chromospheric Models and the Interpretation of the Solar Spectrum

    NASA Technical Reports Server (NTRS)

    Avrett, Eugene H.

    1998-01-01

    Since the early 1970s we have been developing the extensive computer programs needed to construct models of the solar atmosphere and to calculate detailed spectra for use in the interpretation of solar observations. This research involves two major related efforts: work by Avrett and Loeser on the Pandora computer program for non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Rurucz on the detailed synthesis of the solar spectrum based on opacity data or over 58 million atomic and molecular lines. our goals are: to determine models of the various features observed on the Sun (sunspots, different components of quiet and active regions, and flares) by means of physically realistic models, and to calculate detailed spectra at all wavelengths that match observations of those features. These two goals are interrelated: discrepancies between calculated and observed spectra are used to determine improvements in the structure of the models, and in the detailed physical processes used in both the model calculations and the spectrum calculations. The atmospheric models obtained in this way provide not only the depth variation of various atmospheric parameters, but also a description of the internal physical processes that are responsible for non-radiative heating, and for solar activity in general.

  8. Accurate and highly efficient calculation of the highly excited pure OH stretching resonances of O(1D)HCl, using a combination of methods.

    PubMed

    Bian, Wensheng; Poirier, Bill

    2004-09-01

    Accurate calculation of the energies and widths of the resonances of HOCl--an important intermediate in the O(1D)HCl reactive system--poses a challenging benchmark for computational methods. The need for very large direct product basis sets, combined with an extremely high density of states, results in difficult convergence for iterative methods. A recent calculation of the highly excited OH stretch mode resonances using the filter diagonalization method, for example, required 462,000 basis functions, and 180,000 iterations. In contrast, using a combination of new methods, we are able to compute the same resonance states to higher accuracy with a basis less than half the size, using only a few hundred iterations-although the CPU cost per iteration is substantially greater. Similar performance enhancements are observed for calculations of the high-lying bound states, as reported in a previous paper [J. Theo. Comput. Chem. 2, 583 (2003)].

  9. Theoretical Calculation for the Ionization of Molecules by Short Strong Laser Pulses

    SciTech Connect

    Nagy, L.; Borbely, S.

    2011-10-03

    We have developed several calculation methods for the ionization of atoms and molecules by strong and ultrashort laser pulses, based on the numerical solution of the time dependent Schroedinger equation (TDSE) in the momentum space. We have performed calculations within the strong field approximation (Volkov) and using iterative and direct methods for solving the TDSE. The investigated molecules are H{sub 2}{sup +} and H{sub 2}O. In case of the ionization of diatomic molecules the interference effects in the ejected electron spectra due to the coherent addition of the waves associated to the electrons ejected from the vicinity of different nuclei were also analysed.

  10. 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.

  11. Theoretical Calculation on the Coercivity of Single Acicular γ-Fe2O3 Particle

    NASA Astrophysics Data System (ADS)

    Kuo, P. C.; Chang, C. Y.

    1985-03-01

    The chain-of-spheres model is modified by taking crystal anisotropy into account. Coercivity of isolated single-domain particle due to mixed anisotropies of shape and crystal is treated in detail for various should be deleted particle axis orientation. Calculations on the single acicular γ-Fe2O3 particle are found in good agreement with experimental results by Knowles.

  12. Calculation of theoretical lubrication regimes in two-piece first metatarsophalangeal prostheses.

    PubMed

    Joyce, T J

    2008-01-01

    The key joint of the forefoot during gait is the first metatarsophalangeal joint. It plays an important role in propelling the human form but can be subject to a number of diseases which can lead to its replacement with an artificial joint. Some of these designs of prosthesis employ a two-piece ball and socket arrangement and are available with a range of biomaterial couples including ceramic-on-ceramic, metal-on-metal and metal-on-polymer. Calculation of predicted lubrication regimes applicable to these implant designs was undertaken. Modelling the ball and socket implant as an equivalent ball-on-plane model and employing elastohydrodynamic theory allowed the minimum film thickness to be calculated and in turn the lambda ratio to indicate the lubrication regime. The calculations were undertaken for a 50 to 1500 N range of loading values, a 0 to 30 mm/s range of entraining velocities, and a 3 to 15 mm radius range of sizes. Calculations showed that the ceramic-on-ceramic and metal-on-metal implants could operate under fluid film lubrication, whereas the metal-on-polymer combination operated in the boundary lubrication regime. It was also recognized that manufacturing capabilities are critical to the radial clearances and values of surface roughness that can be achieved, and thus the predicted lubrication regime.

  13. Comparison between Theoretical Calculation and Experimental Results of Excitation Functions for Production of Relevant Biomedical Radionuclides

    SciTech Connect

    Menapace, E.; Birattari, C.; Bonardi, M.L.; Groppi, F.; Morzenti, S.; Zona, C.

    2005-05-24

    The radionuclide production for biomedical applications has been brought up in the years, as a special nuclear application, at INFN LASA Laboratory, particularly in co-operation with the JRC-Ispra of EC. Mainly scientific aspects concerning radiation detection and the relevant instruments, the measurements of excitation functions of the involved nuclear reactions, the requested radiochemistry studies and further applications have been investigated. On the side of the nuclear data evaluations, based on nuclear model calculations and critically selected experimental data, the appropriate competence has been developed at ENEA Division for Advanced Physics Technologies. A series of high specific activity accelerator-produced radionuclides in no-carrier-added (NCA) form, for uses in metabolic radiotherapy and for PET radiodiagnostics, are investigated. In this work, last revised measurements and model calculations are reviewed for excitation functions of natZn(d,X)64Cu, 66Ga reactions, referring to irradiation experiments at K=38 variable energy Cyclotron of JRC-Ispra. Concerning the reaction data for producing 186gRe and 211At/211gPo (including significant emission spectra) and 210At, most recent and critically selected experimental results are considered and discussed in comparison with model calculations paying special care to pre-equilibrium effects estimate and to the appropriate overall parameterization. Model calculations are presented for 226Ra(p,2n)225Ac reaction, according to the working program of the ongoing IAEA CRP on the matter.

  14. Calculations of band gaps in polyaniline from theoretical studies of oligomers

    SciTech Connect

    Kwon, O.; McKee, M.L.

    2000-03-02

    Geometries and band gaps of polyaniline oligomers up to decamer have been systematically calculated and analyzed using various computational techniques such as molecular mechanics, semiempirical, and ab initio methods. On the basis of fully optimized geometries of neural and charged forms of polyaniline oligomers, excitation energies are calculated at the semiempirical ZINDO (INDO/S) level and extrapolated to the band gap value of the infinite chain. Band gaps are also approximately by extrapolating the HOMO/LUMO difference calculated at the density functional level (B3LYP/6--31G*). The SINDO//AM1 band gaps in the reduced and oxidized form of polyaniline (4.3 and 2.7 eV) are in good agreement with experimental values (3.8 {+-} 2 and 1.8 {+-} 3 eV, respectively). The doped form of polyaniline (two positive charges per four aniline units) has been computed with a spin-unrestricted method (UAM1) and the band gap approximated from an extrapolation of the tetramer and octamer. The calculated band gap of 1.3 eV (UZINDO//UAM1) is in good agreement with experiment (1.5 eV). The influence of ring torsional angle and interchain interaction on the band gap of the polyaniline system are also discussed.

  15. A theoretical study of blue phosphorene nanoribbons based on first-principles calculations

    SciTech Connect

    Xie, Jiafeng; Si, M. S. Yang, D. Z.; Zhang, Z. Y.; Xue, D. S.

    2014-08-21

    Based on first-principles calculations, we present a quantum confinement mechanism for the band gaps of blue phosphorene nanoribbons (BPNRs) as a function of their widths. The BPNRs considered have either armchair or zigzag shaped edges on both sides with hydrogen saturation. Both the two types of nanoribbons are shown to be indirect semiconductors. An enhanced energy gap of around 1 eV can be realized when the ribbon's width decreases to ∼10 Å. The underlying physics is ascribed to the quantum confinement effect. More importantly, the parameters to describe quantum confinement are obtained by fitting the calculated band gaps with respect to their widths. The results show that the quantum confinement in armchair nanoribbons is stronger than that in zigzag ones. This study provides an efficient approach to tune the band gap in BPNRs.

  16. Method and Basis Set Analysis of Oxorhenium(V) Complexes for Theoretical Calculations

    PubMed Central

    Demoin, Dustin Wayne; Li, Yawen; Jurisson, Silvia S.; Deakyne, Carol A.

    2012-01-01

    A variety of method and basis set combinations has been evaluated for monooxorhenium(V) complexes with N, O, P, S, Cl, and Se donor atoms. The geometries and energies obtained are compared to both high-level computations and literature structures. These calculations show that the PBE0 method outperforms the B3LYP method with respect to both structure and energetics. The combination of 6-31G** basis set on the nonmetal atoms and LANL2TZ effective core potential on the rhenium center gives reliable equilibrium structures with minimal computational resources for both model and literature compounds. Single-point energy calculations at the PBE0/LANL2TZ,6-311+G* level of theory are recommended for energetics. PMID:23087847

  17. Theoretical Calculations of Refractive Properties for Hg3Te2Cl2 Crystals.

    PubMed

    Bokotey, O V

    2016-12-01

    This paper reviews the optical properties, such as refractive index, optical dielectric constant, and reflection coefficient of the Hg3Te2Cl2 crystals. The applications of the Hg3X2Y2 crystals as electronic, optical, and optoelectronic devices are very much determined by the nature and magnitude of these fundamental material properties. The origin of chemical bonding in the crystals is very important for definition of the physical and chemical properties. The main structural feature of the Hg3X2Y2 crystals is the presence of covalent pyramids [XHg3] and linear X-Hg-X groups. Optical properties are calculated according to the model proposed by Harrison. The refractive index in the spectral region far from the absorption edge is determined within the generalized single-oscillator model. The calculated results are found to be in good agreement with experimental data. PMID:27184964

  18. Theoretical Calculations of Refractive Properties for Hg3Te2Cl2 Crystals

    NASA Astrophysics Data System (ADS)

    Bokotey, O. V.

    2016-05-01

    This paper reviews the optical properties, such as refractive index, optical dielectric constant, and reflection coefficient of the Hg3Te2Cl2 crystals. The applications of the Hg3X2Y2 crystals as electronic, optical, and optoelectronic devices are very much determined by the nature and magnitude of these fundamental material properties. The origin of chemical bonding in the crystals is very important for definition of the physical and chemical properties. The main structural feature of the Hg3X2Y2 crystals is the presence of covalent pyramids [XHg3] and linear X-Hg-X groups. Optical properties are calculated according to the model proposed by Harrison. The refractive index in the spectral region far from the absorption edge is determined within the generalized single-oscillator model. The calculated results are found to be in good agreement with experimental data.

  19. Synthesis, structure, theoretical calculations and biological activity of sulfonate active ester new derivatives

    NASA Astrophysics Data System (ADS)

    Ghazzali, Mohamed; Khattab, Sherine A. N.; Elnakady, Yasser A.; Al-Mekhlafi, Fahd A.; Al-Farhan, Khalid; El-Faham, Ayman

    2013-08-01

    A series of naphthyl and tolyl sulfonate ester were synthesized and characterized by H NMR. X-ray single crystal diffraction experiments established the molecular structure of three new sulfonate esters derivatives, and spectral data agree with these in solution. The observed hydrogen bonding is discussed on the basis of crystal structural analyses and DFT/MP2 geometry optimization quantum calculations. Antimicrobial activities were screened for selected compounds against three human cancer cell lines and Mosquito Culex pipiens larvae.

  20. Theoretical analysis of three methods for calculating thermal insulation of clothing from thermal manikin.

    PubMed

    Huang, Jianhua

    2012-07-01

    There are three methods for calculating thermal insulation of clothing measured with a thermal manikin, i.e. the global method, the serial method, and the parallel method. Under the condition of homogeneous clothing insulation, these three methods yield the same insulation values. If the local heat flux is uniform over the manikin body, the global and serial methods provide the same insulation value. In most cases, the serial method gives a higher insulation value than the global method. There is a possibility that the insulation value from the serial method is lower than the value from the global method. The serial method always gives higher insulation value than the parallel method. The insulation value from the parallel method is higher or lower than the value from the global method, depending on the relationship between the heat loss distribution and the surface temperatures. Under the circumstance of uniform surface temperature distribution over the manikin body, the global and parallel methods give the same insulation value. If the constant surface temperature mode is used in the manikin test, the parallel method can be used to calculate the thermal insulation of clothing. If the constant heat flux mode is used in the manikin test, the serial method can be used to calculate the thermal insulation of clothing. The global method should be used for calculating thermal insulation of clothing for all manikin control modes, especially for thermal comfort regulation mode. The global method should be chosen by clothing manufacturers for labelling their products. The serial and parallel methods provide more information with respect to the different parts of clothing.

  1. Theoretical Study of the Inverting Mechanism in a Processive Cellobiohydrolase with Quantum Mechanical Calculations

    SciTech Connect

    Kim, S.; Payne, C. M.; Himmel, M. E.; Crowley, M. F.; Paton, R. S.; Beckham, G. T.

    2012-01-01

    The Hypocrea jecorina Family 6 cellobiohydrolase (Cel6A) is one of most efficient enzymes for cellulose deconstruction to soluble sugars and is thus of significant current interest for the growing biofuels industry. Cel6A is known to hydrolyze b(1,4)-glycosidic linkages in cellulose via an inverting mechanism, but there are still questions that remain regarding the role of water and the catalytic base. Here we study the inverting, single displacement, hydrolytic reaction mechanism in Cel6A using density functional theory (DFT) calculations. The computational model used to follow the reaction is a truncated active site model with several explicit waters based on structural studies of H. jecorina Cel6A. Proposed mechanisms are evaluated with several density functionals. From our calculations, the role of the water in nucleophilic attack on the anomeric carbon, and the roles of several residues in the active site loops are elucidated explicitly for the first time. We also apply quantum mechanical calculations to understand the proton transfer reaction which completes the catalytic cycle.

  2. Theoretical study of small sodium-potassium alloy clusters through genetic algorithm and quantum chemical calculations.

    PubMed

    Silva, Mateus X; Galvão, Breno R L; Belchior, Jadson C

    2014-05-21

    Genetic algorithm is employed to survey an empirical potential energy surface for small Na(x)K(y) clusters with x + y ≤ 15, providing initial conditions for electronic structure methods. The minima of such empirical potential are assessed and corrected using high level ab initio methods such as CCSD(T), CR-CCSD(T)-L and MP2, and benchmark results are obtained for specific cases. The results are the first calculations for such small alloy clusters and may serve as a reference for further studies. The validity and choice of a proper functional and basis set for DFT calculations are then explored using the benchmark data, where it was found that the usual DFT approach may fail to provide the correct qualitative result for specific systems. The best general agreement to the benchmark calculations is achieved with def2-TZVPP basis set with SVWN5 functional, although the LANL2DZ basis set (with effective core potential) and SVWN5 functional provided the most cost-effective results. PMID:24691391

  3. Theoretical calculations on structural and electronic properties of BGaAsBi alloys

    NASA Astrophysics Data System (ADS)

    Aslan, Metin; Yalcin, Battal G.; Ustundag, Mehmet; Bagci, Sadik

    2015-11-01

    The structural and electronic properties of cubic B x Ga1- x As1- y Bi y alloys with bismuth (Bi) concentration of 0.0625, 0.125, 0.1875 and 0.25 are studied with various boron (B) compositions by means of density functional theory (DFT) within the Wu-Cohen (WC) exchange correlation potential based on generalized gradient approximation (GGA). For all studied alloy structures, we have implemented geometric optimization before the volume optimization calculations. The obtained equilibrium lattice constants and band gap of studied quaternary alloys are investigated for the first time in literature. While the lattice constant behavior changes linearly with boron concentration, increasing small amount of bismuth concentration alter the lattice constant nonlinearly. The present calculation shows that the band gap decreases with increasing bismuth concentration and direct band gap semiconductor alloy became an indirect band gap with increasing boron concentration. From the band offset calculation we have shown that increasing B and Bi concentration in host GaAs reduced the valance band offset in a heterostructure formed by GaAs and studied alloys.

  4. Theoretical calculation of the longitudinal spherical aberration of rigid and soft contact lenses.

    PubMed

    Cox, I

    1990-04-01

    Although previous investigators have attempted to calculate the longitudinal spherical aberration inherent in soft and rigid contact lenses both on and off the eye, the use of inappropriate assumptions on which to base their calculations has left the problem unresolved. In this study, the longitudinal spherical aberration of both soft and rigid contact lenses was calculated surface by surface both in air and on the eye using a two-dimensional, exact ray tracing program. The erroneous assumptions made by previous investigators were avoided by using an elliptical model for the anterior corneal surface and assuming that the posterior surfaces of soft lenses aligned exactly with the anterior corneal surface after flexure onto the eye. The results demonstrated that, with a 6-mm pupil, contact lenses induce significant levels of spherical aberration in the ocular system for soft lenses of back vertex power greater than +3.00 D or -6.00 D and for rigid lenses of powers more positive than -3.00 D. It is suggested that visual disturbance due to induced spherical aberration has not been a major clinical problem in the past because these conditions fall outside those experienced by a large proportion of the contact lens-wearing public.

  5. Theoretical calculation of a composite pulse for 2H broadband excitation by average Hamiltonian theory

    PubMed Central

    Shen, Ming; Roopchand, Rabia; Amoureux, Jean-Paul; Chen, Qun

    2015-01-01

    Quadrupolar echo NMR spectroscopy of solids often requires RF pulse excitation that covers spectral widths exceeding 100 kHz. In a recent work we found out that a four pulse, composite pulse COM-II ( 90180¯90135¯45 ), provided robust broadband excitation for deuterium quadrupolar echo spectroscopy. Moreover, when combined with an eight step phase cycle, spectral distortions arising from finite pulse widths were greatly supressed. In this paper we report on a theoretical analysis COM-II with 8-step phase cycle by average Hamiltonian theory. This treatment is combined with the fictitious spin-1 operator formalism, and the mechanism of the 8-step phase cycling that minimizes the spectral distortions is discussed. PMID:26681896

  6. Calculation of theoretical and empirical nutrient N critical loads in the mixed conifer ecosystems of southern California.

    PubMed

    Breiner, Joan; Gimeno, Benjamin S; Fenn, Mark

    2007-01-01

    Edaphic, foliar, and hydrologic forest nutrient status indicators from 15 mixed conifer forest stands in the Sierra Nevada, San Gabriel Mountains, and San Bernardino National Forest were used to estimate empirical or theoretical critical loads (CL) for nitrogen (N) as a nutrient. Soil acidification response to N deposition was also evaluated. Robust empirical relationships were found relating N deposition to plant N uptake (N in foliage), N fertility (litter C/N ratio), and soil acidification. However, no consistent empirical CL were obtained when the thresholds for parameters indicative of N excess from other types of ecosystems were used. Similarly, the highest theoretical CL for nutrient N calculated using the simple mass balance steady state model (estimates ranging from 1.4-8.8 kg N/ha/year) was approximately two times lower than the empirical observations. Further research is needed to derive the thresholds for indicators associated with the impairment of these mixed conifer forests exposed to chronic N deposition within a Mediterranean climate. Further development or parameterization of models for the calculation of theoretical critical loads suitable for these ecosystems will also be an important aspect of future critical loads research. PMID:17450298

  7. Synthesis, spectral, optical properties and theoretical calculations on schiff bases ligands containing o-tolidine

    NASA Astrophysics Data System (ADS)

    Arroudj, S.; Bouchouit, M.; Bouchouit, K.; Bouraiou, A.; Messaadia, L.; Kulyk, B.; Figa, V.; Bouacida, S.; Sofiani, Z.; Taboukhat, S.

    2016-06-01

    This paper explores the synthesis, structure characterization and optical properties of two new schiff bases. These compounds were obtained by condensation of o-tolidine with salicylaldehyde and cinnamaldehyde. The obtained ligands were characterized by UV, 1H and NMR. Their third-order NLO properties were measured using the third harmonic generation technique on thin films at 1064 nm. The electric dipole moment (μ), the polarizability (α) and the first hyperpolarizability (β) were calculated using the density functional B3LYP method with the lanl2dz basis set. For the results, the title compound shows nonzero β value revealing second order NLO behaviour.

  8. Determination of Structural and Electronic Parameters of Antimony Complex, from Theoretical Calculations

    NASA Astrophysics Data System (ADS)

    Catikkas, Berna; Kosar, Ismail

    2016-06-01

    In this study, ground states of antimony (Sbv) with organic ligands complexes were studied by using density functional theory hybrid methods in order to obtain structural, electronic and vibrational spectral parameters. The mapping molecular electrostatic potential surface of the molecules computed to information about the charge density distribution of the molecules and its chemical reactivity. Frontier molecule orbital properties, HOMO and LUMO energies, global descriptors, and the total density of state diagram analysis were performed by using the time-dependent density functional theory. For the learning nonlinear optical properties, polarizability and hyperpolarizability tensors of the molecule were calculated.

  9. Proton transfer in acetaldehyde and acetaldehyde-water clusters: Vacuum ultraviolet photoionization experiment and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Kostko, Oleg; Troy, Tyler P.; Bandyopadhyay, Biswajit; Ahmed, Musahid

    2015-03-01

    Acetaldehyde, a probable human carcinogen and of environmental importance, upon solvation provides a test bed for understanding proton transfer pathways and catalytic mechanisms. In this study, we report on single photon vacuum ultraviolet photoionization of small acetaldehyde and acetaldehyde-water clusters. Appearance energies of protonated clusters are extracted from the experimental photoionization efficiency curves and compared to electronic structure calculations. The comparison of experimental data to computational results provides mechanistic insight into the fragmentation mechanisms of the observed mass spectra. Using deuterated water for isotopic tagging, we observe that proton transfer is mediated via acetaldehyde and not water in protonated acetaldehyde-water clusters.

  10. Correlation of theoretical calculations and experimental measurements of damage around a shaft in salt

    SciTech Connect

    Munson, D.E.; Holcomb, D.J.; DeVries, K.L.; Brodsky, N.S.

    1994-12-31

    Cross-hole ultrasonic measurements were made in the immediate wall of the Air Intake Shaft of the Waste Isolation Pilot Plant facility. These measurements show that compressional wave speed markedly decreases at the shaft wall and then increases with radial distance from the shaft to eventually become that of solid or undamaged salt. This behavior is indicative of deformation damage or microfractures in the salt. These in situ data are compared to both laboratory measurements of wave speed as a function of volume dilatancy and to calculations based on the Multimechanism Deformation Coupled Fracture model, with reasonable agreement.

  11. The calculation of theoretical chromospheric models and the interpretation of solar spectra from rockets and spacecraft

    NASA Technical Reports Server (NTRS)

    Avrett, E. H.

    1985-01-01

    Solar chromospheric models are described. The models included are based on the observed spectrum, and on the assumption of hydrostatic equilibrium. The calculations depend on realistic solutions of the radiative transfer and statistical equilibrium equations for optically thick lines and continua, and on including the effects of large numbers of lines throughout the spectrum. Although spectroheliograms show that the structure of the chromosphere is highly complex, one-dimensional models of particular features are reasonably successful in matching observed spectra. Such models were applied to the interpretation of chromospheric observations.

  12. The calculation of theoretical chromospheric models and the interpretation of solar spectra from rockets and spacecraft

    NASA Technical Reports Server (NTRS)

    Avrett, E. H.

    1986-01-01

    Calculated results based on two chromospheric flare models F1 and F2 of Machado, et al., (1980) are presented. Two additional models are included: F1*, which has enhanced temperatures relative to the weak-flare model F1 in the upper photosphere and low chromosphere, and F3 which has enhanced temperatures relative to the strong flare model F2 in the upper chromosphere. Each model is specified by means of a given variation of the temperature as a function of column mass. The corresponding variation of particle density and the geometrical height scale are determined by assuming hydrostatic equilibrium. The coupled equations of statistical equilibrium is solved as is radiative transfer for H, H-, He I-II, C I-IV, Si I-II, Mg I-II, Fe, Al, O I-II, Na, and Ca II. The overall absorption and emission of radiation by lines throughout the spectrum is determined by means of a reduced set of opacities sampled from a compilation of over 10 to the 7th power individual lines. That the white flight flare continuum may arise by extreme chromospheric overheating as well as by an enhancement of the minimum temperature region is also shown. The radiative cooling rate calculations for our brightest flare model suggest that chromospheric overheating provides enhanced radiation that could cause significant heating deep in the flare atmosphere.

  13. ``Phantom'' Modes in Ab Initio Tunneling Calculations: Implications for Theoretical Materials Optimization, Tunneling, and Transport

    NASA Astrophysics Data System (ADS)

    Barabash, Sergey V.; Pramanik, Dipankar

    2015-03-01

    Development of low-leakage dielectrics for semiconductor industry, together with many other areas of academic and industrial research, increasingly rely upon ab initio tunneling and transport calculations. Complex band structure (CBS) is a powerful formalism to establish the nature of tunneling modes, providing both a deeper understanding and a guided optimization of materials, with practical applications ranging from screening candidate dielectrics for lowest ``ultimate leakage'' to identifying charge-neutrality levels and Fermi level pinning. We demonstrate that CBS is prone to a particular type of spurious ``phantom'' solution, previously deemed true but irrelevant because of a very fast decay. We demonstrate that (i) in complex materials, phantom modes may exhibit very slow decay (appearing as leading tunneling terms implying qualitative and huge quantitative errors), (ii) the phantom modes are spurious, (iii) unlike the pseudopotential ``ghost'' states, phantoms are an apparently unavoidable artifact of large numerical basis sets, (iv) a presumed increase in computational accuracy increases the number of phantoms, effectively corrupting the CBS results despite the higher accuracy achieved in resolving the true CBS modes and the real band structure, and (v) the phantom modes cannot be easily separated from the true CBS modes. We discuss implications for direct transport calculations. The strategy for dealing with the phantom states is discussed in the context of optimizing high-quality high- κ dielectric materials for decreased tunneling leakage.

  14. Practical method for highly accurate large-scale surface calculations. [of linearized muffin-tin orbital technique for chemisorption and magnetism

    NASA Technical Reports Server (NTRS)

    Fernando, G. W.; Cooper, B. R.; Ramana, M. V.; Krakauer, H.; Ma, C. Q.

    1986-01-01

    An accurate and efficient film linearized muffin-tin orbital (FLMTO) technique for surface electronic-structure calculations is presented which uses only 60-70 basis functions, as opposed to the 300 functions used in the linear augmented plane-wave method. Calculations for three different (3d and 4d) transition-metal films resulted in high quality results for five-layer slabs of Cu(001), Fe(001), and Ru(001), in addition to good results for the work functions and projected density of states. By retaining the LMTO small basis size, computer time and memory are reduced, making practical the study of systems with a larger number of atoms in the two-dimensional unit cell.

  15. Refinement of the experimental energy levels of higher {sup 2}D Rydberg states of the lithium atom with very accurate quantum mechanical calculations

    SciTech Connect

    Sharkey, Keeper L.; Bubin, Sergiy; Adamowicz, Ludwik

    2011-05-21

    Very accurate variational non-relativistic calculations are performed for four higher Rydberg {sup 2}D states (1s{sup 2}nd{sup 1}, n= 8, ..., 11) of the lithium atom ({sup 7}Li). The wave functions of the states are expanded in terms of all-electron explicitly correlated Gaussian functions and finite nuclear mass is used. The exponential parameters of the Gaussians are optimized using the variational method with the aid of the analytical energy gradient determined with respect to those parameters. The results of the calculations allow for refining the experimental energy levels determined with respect to the {sup 2}S 1s{sup 2}2s{sup 1} ground state.

  16. The reaction mechanism of allene oxide synthase: Interplay of theoretical QM/MM calculations and experimental investigations.

    PubMed

    Cho, Kyung-Bin; Lai, Wenzhen; Hamberg, Mats; Raman, C S; Shaik, Sason

    2011-03-01

    A combined theoretical and experimental study highlights the reaction mechanism of allene oxide synthase (AOS) and its possible link to hydroperoxide lyase (HPL) pathway. A previously published study (Lee et al., Nature 455 (2008) 363) has shown that the F137 residue is of central importance in differentiating between the AOS and HPL pathways after initial identical steps. In the experimental part of this study, we show that wild-type AOS from Arabidopsis or rice in fact produces both AOS and HPL products in a ratio of about 80:15, something that was found only in trace amounts before. Theoretical calculations successfully map the whole AOS pathway with 13(S)-hydroperoxy linolenic and linoleic acid as substrates. Subsequent calculations investigated the effects of in silico F137L mutation at the suggested diverging point of the two pathways. The results show that QM/MM calculations can reasonably reproduce three out of four experimentally available cases, and confirm that the pathways are energetically very close to each other, thus making a switch from one path to other plausible under different circumstances.

  17. Synthesis, crystal structure, biological activity and theoretical calculations of novel isoxazole derivatives

    NASA Astrophysics Data System (ADS)

    Jin, R. Y.; Sun, X. H.; Liu, Y. F.; Long, W.; Chen, B.; Shen, S. Q.; Ma, H. X.

    2016-01-01

    Series of isoxazole derivatives were synthesized by substituted chalcones and 2-chloro-6-fluorobenzene formaldehyde oxime with 1,3-dipolar cycloaddition. The target compounds were determined by melting point, IR, 1H NMR, elemental analyses and HRMS. The crystal structure of compound 3a was detected by X-ray diffraction and it crystallizes in the triclinic space group p2(1)/c with z = 4. The molecular geometry of compound 3a was optimized using density functional theory (DFT/B3LYP) method with the 6-31G+(d,p) basis set in the ground state. From the optimized geometry of the molecule, FT-IR, FT-Raman, HOMO-LUMO and natural bond orbital (NBO) were calculated at B3LYP/6-31G+(d,p) level. Finally, the antifungal activity of the synthetic compounds were evaluated against Pythium solani, Gibberella nicotiancola, Fusarium oxysporium f.sp. niveum and Gibberella saubinetii.

  18. Reaction cross-section calculations using new experimental and theoretical level structure data for deformed nuclei

    SciTech Connect

    Hoff, R.W.; Gardner, D.G.; Gardner, M.A.

    1984-10-05

    A technique for modeling quasiparticle excitation energies and rotational parameters in odd-odd deformed nuclei has been used to construct sets of discrete states with energy 0 to 1.5 MeV in /sup 176/Lu and /sup 236/Np. These data were used as part of the input for calculation of isomer production cross-section ratios in the /sup 175/Lu(n,..gamma..)/sup 176/Lu and /sup 237/Np(n,2n)/sup 236/Np reactions. In order to achieve agreement with experiment, it has been found necessary to include in the modeled set many rotational bands (35 to 95), which are comprised of hundreds of levels with their gamma-ray branching ratios. It is essential that enough bands be included to produce a representative selection of K quantum numbers in the de-excitation cascade. 20 refs., 3 figs., 3 tabs.

  19. a Theoretical Calculation of Microlensing Signatures Caused by Free-Floating Planets Towards the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Hamolli, L.; Hafizi, M.; Nucita, A. A.

    2013-08-01

    Free-floating planets (FFPs) are recently drawing a special interest of the scientific community. Gravitational microlensing is up to now the exclusive method for the investigation of FFPs, including their spatial distribution function and mass function. In this paper, we examine the possibility that the future Euclid space-based observatory may allow to discover a substantial number of microlensing events caused by FFPs. Based on latest results about the free-floating planet (FFP) mass function in the mass range [10-5, 10-2]M⊙, we calculate the optical depth towards the Galactic bulge as well as the expected microlensing rate and find that Euclid may be able to detect hundreds to thousands of these events per month. Making use of a synthetic population, we also investigate the possibility of detecting parallax effect in simulated microlensing events due to FFPs and find a significant efficiency for the parallax detection that turns out to be around 30%.

  20. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    PubMed

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  1. Calibrating the High Density Magnetic Port within Tissue Expanders to Achieve more Accurate Dose Calculations for Postmastectomy Patients with Immediate Breast Reconstruction

    NASA Astrophysics Data System (ADS)

    Jones, Jasmine; Zhang, Rui; Heins, David; Castle, Katherine

    In postmastectomy radiotherapy, an increasing number of patients have tissue expanders inserted subpectorally when receiving immediate breast reconstruction. These tissue expanders are composed of silicone and are inflated with saline through an internal metallic port; this serves the purpose of stretching the muscle and skin tissue over time, in order to house a permanent implant. The issue with administering radiation therapy in the presence of a tissue expander is that the port's magnetic core can potentially perturb the dose delivered to the Planning Target Volume, causing significant artifacts in CT images. Several studies have explored this problem, and suggest that density corrections must be accounted for in treatment planning. However, very few studies accurately calibrated commercial TP systems for the high density material used in the port, and no studies employed fusion imaging to yield a more accurate contour of the port in treatment planning. We compared depth dose values in the water phantom between measurement and TPS calculations, and we were able to overcome some of the inhomogeneities presented by the image artifact by fusing the KVCT and MVCT images of the tissue expander together, resulting in a more precise comparison of dose calculations at discrete locations. We expect this method to be pivotal in the quantification of dose distribution in the PTV. Research funded by the LS-AMP Award.

  2. Infrared spectra and theoretical calculations for Fe, Ru, and Os metal hydrides and dihydrogen complexes.

    PubMed

    Wang, Xuefeng; Andrews, Lester

    2009-01-22

    Laser-ablated iron, ruthenium, and osmium atoms react with hydrogen in excess argon, neon and pure hydrogen to produce the FeH(2) molecule, and the FeH(2)(H(2))(3), RuH(H(2))(4), RuH(2)(H(2))(4), and (H(2))MH complexes (M = Fe, Ru, Os), as identified through infrared spectra with D(2) and HD substitution. DFT frequency calculations support the assignment of absorptions observed experimentally. The FeH(2) molecule has a quintet ground state with a quasi-linear structure, and is repulsive to the addition of one more H(2) ligand: however, with three more H(2) ligands, stable triplet and singlet state FeH(2)(H(2))(3) supercomplexes can be formed. The quintet FeH(2) molecule and FeH(2)(H(2))(3) supercomplex undergo reversible near-ultraviolet photochemical rearrangement in solid neon and hydrogen. The RuH(2) molecule has a bent triplet ground state and forms the stable singlet RuH(2)(H(2))(4) supercomplex, but only the latter is observed in these experiments. In like fashion RuH has a quartet ground state and the doublet RuH(H(2))(4) complex is trapped in solid hydrogen. All three (H(2))MH complexes with lower energy than MH(3) are trapped, and no absorptions are observed for MH(3) molecules.

  3. Theoretical calculations on the conformation of cyclopentadienyl coordination in Ru nitrosyl and thionitrosyl complexes

    SciTech Connect

    Burns, R.M.; Hubbard, J.L.; McCullough, E.A. Jr.

    1995-12-01

    X-ray structural characterization of a series of CpRu(NE)LL` complexes (Cp = cyclopentadieny), C{sub 5}R{sub 5}; L, L` = ligand; E = O, S) reveals systematic trends in the coordination conformation of the cyclopentadienyl ligand. The thionitrosyl complex (C{sub 5}(CH{sub 3}){sub 5})Ru(NS)Cl{sub 2} exhibits a slipped (eta-3,eta-2 Cp ring, with the central C(skeletal)-CH{sub 3} bond of the more tightly bound eta-3 portion eclipsing the Ru-N-S vector. With NO derivatives, ring {open_quotes}slippage{close_quotes} is not significant, but ring orientation is variable depending upon the L and L` ligand set. NMR spectroscopy measurements show that the barriers to changes in ring conformation become very low in solution. For catalytic purposes, it is of interest to fix the Cp geometry with respect to rotation. Ab initio SCF and DFT calculations have been performed, using the NWChem suite of computer codes, developed at Pacific Northwest Laboratory, to explore three questions: By what mechanism does the choice of ligand affect the Cp orientation? What is the barrier to rotation of the Cp? By what mechanism does salvation affect the barriers to Cp rotation?

  4. Adherence of Molecules to Silica Glass Surface: Experimental Results and Theoretical Calculations

    NASA Astrophysics Data System (ADS)

    Rivera, Edison; Prado, Miguel Oscar; Nuñez, Matias

    The adherence of molecules to surfaces is used in a wide scope of technological applications. In this work we study the attachment of molecules onto porous silica glass surface obtained from a Vycor glass, after glass- glass phase separation and leaching of the soluble phase with water. Nitrogen adsorption at 77 K was used for the determination of the specific surface area (BET area) and pore size distribution on the leached glass. The adherence onto the glass surface, of model molecules methylene blue (MB) and eosine yellow (EY), with positive and negative electrical charges respectively, was studied. The adsorption kinetics was determined from aqueous solutions using UV-VIS spectroscopy. It was found that the silica glass surface as prepared in this work is selective for positively charged molecules at pH≈5.20, an adsorption of 1 mg MB per gram of glass was found for methylene blue, and almost null adsorption for eosine yellow. First principles calculations were performed using the Density Functional Theory in order to model the interaction between both molecules and the glass surface.

  5. Infrared spectra and theoretical calculations for Fe, Ru, and Os metal hydrides and dihydrogen complexes.

    PubMed

    Wang, Xuefeng; Andrews, Lester

    2009-01-22

    Laser-ablated iron, ruthenium, and osmium atoms react with hydrogen in excess argon, neon and pure hydrogen to produce the FeH(2) molecule, and the FeH(2)(H(2))(3), RuH(H(2))(4), RuH(2)(H(2))(4), and (H(2))MH complexes (M = Fe, Ru, Os), as identified through infrared spectra with D(2) and HD substitution. DFT frequency calculations support the assignment of absorptions observed experimentally. The FeH(2) molecule has a quintet ground state with a quasi-linear structure, and is repulsive to the addition of one more H(2) ligand: however, with three more H(2) ligands, stable triplet and singlet state FeH(2)(H(2))(3) supercomplexes can be formed. The quintet FeH(2) molecule and FeH(2)(H(2))(3) supercomplex undergo reversible near-ultraviolet photochemical rearrangement in solid neon and hydrogen. The RuH(2) molecule has a bent triplet ground state and forms the stable singlet RuH(2)(H(2))(4) supercomplex, but only the latter is observed in these experiments. In like fashion RuH has a quartet ground state and the doublet RuH(H(2))(4) complex is trapped in solid hydrogen. All three (H(2))MH complexes with lower energy than MH(3) are trapped, and no absorptions are observed for MH(3) molecules. PMID:19099441

  6. Effective theory for the nonrigid rotor in an electromagnetic field: Toward accurate and precise calculations of E 2 transitions in deformed nuclei

    NASA Astrophysics Data System (ADS)

    Coello Pérez, E. A.; Papenbrock, T.

    2015-07-01

    We present a model-independent approach to electric quadrupole transitions of deformed nuclei. Based on an effective theory for axially symmetric systems, the leading interactions with electromagnetic fields enter as minimal couplings to gauge potentials, while subleading corrections employ gauge-invariant nonminimal couplings. This approach yields transition operators that are consistent with the Hamiltonian, and the power counting of the effective theory provides us with theoretical uncertainty estimates. We successfully test the effective theory in homonuclear molecules that exhibit a large separation of scales. For ground-state band transitions of rotational nuclei, the effective theory describes data well within theoretical uncertainties at leading order. To probe the theory at subleading order, data with higher precision would be valuable. For transitional nuclei, next-to-leading-order calculations and the high-precision data are consistent within the theoretical uncertainty estimates. We also study the faint interband transitions within the effective theory and focus on the E 2 transitions from the 02+ band (the "β band") to the ground-state band. Here the predictions from the effective theory are consistent with data for several nuclei, thereby proposing a solution to a long-standing challenge.

  7. Effective theory for the nonrigid rotor in an electromagnetic field: Toward accurate and precise calculations of E2 transitions in deformed nuclei

    SciTech Connect

    Coello Pérez, Eduardo A.; Papenbrock, Thomas F.

    2015-07-27

    In this paper, we present a model-independent approach to electric quadrupole transitions of deformed nuclei. Based on an effective theory for axially symmetric systems, the leading interactions with electromagnetic fields enter as minimal couplings to gauge potentials, while subleading corrections employ gauge-invariant nonminimal couplings. This approach yields transition operators that are consistent with the Hamiltonian, and the power counting of the effective theory provides us with theoretical uncertainty estimates. We successfully test the effective theory in homonuclear molecules that exhibit a large separation of scales. For ground-state band transitions of rotational nuclei, the effective theory describes data well within theoretical uncertainties at leading order. To probe the theory at subleading order, data with higher precision would be valuable. For transitional nuclei, next-to-leading-order calculations and the high-precision data are consistent within the theoretical uncertainty estimates. In addition, we study the faint interband transitions within the effective theory and focus on the E2 transitions from the 02+ band (the “β band”) to the ground-state band. Here the predictions from the effective theory are consistent with data for several nuclei, thereby proposing a solution to a long-standing challenge.

  8. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH{sub 2}{sup +}

    SciTech Connect

    Li, Y. Q.; Zhang, P. Y.; Han, K. L.

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.

  9. ELECTRON-ION RECOMBINATION OF Fe XII FORMING Fe XI: LABORATORY MEASUREMENTS AND THEORETICAL CALCULATIONS

    SciTech Connect

    Novotny, O.; Hahn, M.; Lestinsky, M.; Savin, D. W.; Badnell, N. R.; Bernhardt, D.; Mueller, A.; Schippers, S.; Grieser, M.; Krantz, C.; Repnow, R.; Wolf, A.

    2012-07-01

    We have measured electron-ion recombination for Fe XII forming Fe XI using a merged-beam configuration at the heavy-ion storage ring TSR located at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany. The measured merged-beam recombination rate coefficient (MBRRC) for collision energies from 0 to 1500 eV is presented. This work uses a new method for determining the absolute MBRRC based on a comparison of the ion beam decay rate with and without the electron beam on. For energies below 75 eV, the spectrum is dominated by dielectronic recombination (DR) resonances associated with 3s {yields} 3p and 3p {yields} 3d core excitations. At higher energies, we observe contributions from 3 {yields} N' and 2 {yields} N' core excitation DR. We compare our experimental results to state-of-the-art multi-configuration Breit-Pauli (MCBP) calculations and find significant differences, both in resonance energies and strengths. We have extracted the DR contributions from the measured MBRRC data and transformed them into a plasma recombination rate coefficient (PRRC) for temperatures in the range of 10{sup 3}-10{sup 7} K. We show that the previously recommended DR data for Fe XII significantly underestimate the PRRC at temperatures relevant for both photoionized plasmas (PPs) and collisionally ionized plasmas (CPs). This is contrasted with our MCBP PRRC results, which agree with the experiment to within 30% at PP temperatures and even better at CP temperatures. We find this agreement despite the disagreement shown by the detailed comparison between our MCBP and experimental MBRRC results. Last, we present a simple parameterized form of the experimentally derived PRRC for easy use in astrophysical modeling codes.

  10. NR2 and P3+: Accurate, Efficient Electron-Propagator Methods for Calculating Valence, Vertical Ionization Energies of Closed-Shell Molecules.

    PubMed

    Corzo, H H; Galano, Annia; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V

    2015-08-20

    Two accurate and computationally efficient electron-propagator (EP) methods for calculating the valence, vertical ionization energies (VIEs) of closed-shell molecules have been identified through comparisons with related approximations. VIEs of a representative set of closed-shell molecules were calculated with EP methods using 10 basis sets. The most easily executed method, the diagonal, second-order (D2) EP approximation, produces results that steadily rise as basis sets are improved toward values based on extrapolated coupled-cluster singles and doubles plus perturbative triples calculations, but its mean errors remain unacceptably large. The outer valence Green function, partial third-order and renormalized partial third-order methods (P3+), which employ the diagonal self-energy approximation, produce markedly better results but have a greater tendency to overestimate VIEs with larger basis sets. The best combination of accuracy and efficiency with a diagonal self-energy matrix is the P3+ approximation, which exhibits the best trends with respect to basis-set saturation. Several renormalized methods with more flexible nondiagonal self-energies also have been examined: the two-particle, one-hole Tamm-Dancoff approximation (2ph-TDA), the third-order algebraic diagrammatic construction or ADC(3), the renormalized third-order (3+) method, and the nondiagonal second-order renormalized (NR2) approximation. Like D2, 2ph-TDA produces steady improvements with basis set augmentation, but its average errors are too large. Errors obtained with 3+ and ADC(3) are smaller on average than those of 2ph-TDA. These methods also have a greater tendency to overestimate VIEs with larger basis sets. The smallest average errors occur for the NR2 approximation; these errors decrease steadily with basis augmentations. As basis sets approach saturation, NR2 becomes the most accurate and efficient method with a nondiagonal self-energy. PMID:26226061

  11. NR2 and P3+: Accurate, Efficient Electron-Propagator Methods for Calculating Valence, Vertical Ionization Energies of Closed-Shell Molecules.

    PubMed

    Corzo, H H; Galano, Annia; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V

    2015-08-20

    Two accurate and computationally efficient electron-propagator (EP) methods for calculating the valence, vertical ionization energies (VIEs) of closed-shell molecules have been identified through comparisons with related approximations. VIEs of a representative set of closed-shell molecules were calculated with EP methods using 10 basis sets. The most easily executed method, the diagonal, second-order (D2) EP approximation, produces results that steadily rise as basis sets are improved toward values based on extrapolated coupled-cluster singles and doubles plus perturbative triples calculations, but its mean errors remain unacceptably large. The outer valence Green function, partial third-order and renormalized partial third-order methods (P3+), which employ the diagonal self-energy approximation, produce markedly better results but have a greater tendency to overestimate VIEs with larger basis sets. The best combination of accuracy and efficiency with a diagonal self-energy matrix is the P3+ approximation, which exhibits the best trends with respect to basis-set saturation. Several renormalized methods with more flexible nondiagonal self-energies also have been examined: the two-particle, one-hole Tamm-Dancoff approximation (2ph-TDA), the third-order algebraic diagrammatic construction or ADC(3), the renormalized third-order (3+) method, and the nondiagonal second-order renormalized (NR2) approximation. Like D2, 2ph-TDA produces steady improvements with basis set augmentation, but its average errors are too large. Errors obtained with 3+ and ADC(3) are smaller on average than those of 2ph-TDA. These methods also have a greater tendency to overestimate VIEs with larger basis sets. The smallest average errors occur for the NR2 approximation; these errors decrease steadily with basis augmentations. As basis sets approach saturation, NR2 becomes the most accurate and efficient method with a nondiagonal self-energy.

  12. Theoretical investigations on molecular structure, vibrational spectra, HOMO, LUMO, NBO analysis and hyperpolarizability calculations of thiophene-2-carbohydrazide

    NASA Astrophysics Data System (ADS)

    Balachandran, V.; Janaki, A.; Nataraj, A.

    2014-01-01

    The Fourier-Transform infrared and Fourier-Transform Raman spectra of thiophene-2-carbohydrazide (TCH) was recorded in the region 4000-400 cm-1 and 3500-100 cm-1. Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of TCH were carried out by DFT (B3LYP) method with 6-311++G(d,p) as basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Stability of the molecule arising from hyper conjugative interaction and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecule have also been constructed.

  13. Theoretical investigations on molecular structure, vibrational spectra, HOMO, LUMO, NBO analysis and hyperpolarizability calculations of thiophene-2-carbohydrazide.

    PubMed

    Balachandran, V; Janaki, A; Nataraj, A

    2014-01-24

    The Fourier-Transform infrared and Fourier-Transform Raman spectra of thiophene-2-carbohydrazide (TCH) was recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1). Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of TCH were carried out by DFT (B3LYP) method with 6-311++G(d,p) as basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Stability of the molecule arising from hyper conjugative interaction and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecule have also been constructed. PMID:24060478

  14. Lead-chromium carbonyl complexes incorporated with group 8 metals: synthesis, reactivity, and theoretical calculations.

    PubMed

    Shieh, Minghuey; Chu, Yen-Yi; Hsu, Miao-Hsing; Ke, Wei-Ming; Lin, Chien-Nan

    2011-01-17

    The trichromium-lead complex [Pb{Cr(CO)5}3](2-) (1) was isolated from the reaction of PbCl2 and Cr(CO)6 in a KOH/MeOH solution, and the new mixed chromium-iron-lead complex [Pb{Cr(CO)5}{Fe(CO)4}2](2-) (3) was synthesized from the reaction of PbCl2 and Cr(CO)6 in a KOH/MeOH solution followed by the addition of Fe(CO)5. X-ray crystallography showed that 3 consisted of a central Pb atom bound in a trigonal-planar environment to two Fe(CO)4 and one Cr(CO)5 fragments. When complex 1 reacted with 1.5 equiv of Mn(CO)5Br, the Cr(CO)4-bridged dimeric lead-chromium carbonyl complex [Pb2Br2Cr4(CO)18](2-) (4) was produced. However, a similar reaction of 3 or the isostructural triiron-lead complex [Pb{Fe(CO)4}3](2-) (2) with Mn(CO)5Br in MeCN led to the formation of the Fe3Pb2-based trigonal-bipyramidal complexes [Fe3(CO)9{PbCr(CO)5}2](2-) (6) and [Fe3(CO)9{PbFe(CO)4}2](2-) (5), respectively. On the other hand, the Ru3Pb2-based trigonal-bipyramidal complex [Ru3(CO)9{PbCr(CO)5}2](2-) (7) was obtained directly from the reaction of PbCl2, Cr(CO)6, and Ru3(CO)12 in a KOH/MeOH solution. X-ray crystallography showed that 5 and 6 each had an Fe3Pb2 trigonal-bipyramidal core geometry, with three Fe(CO)3 groups occupying the equatorial positions and two PbFe(CO)4 or PbCr(CO)5 units in the axial positions, while 7 displayed a Ru3Pb2 trigonal-bipyramidal geometry with three equatorial Ru(CO)3 groups and two axial PbCr(CO)5 units. The complexes 3-7 were characterized spectroscopically, and their nature, formation, and electrochemistry were further examined by molecular orbital calculations at the B3LYP level of density functional theory.

  15. Theoretical calculation and experiment of microwave electromagnetic property of Ni(C) nanocapsules

    NASA Astrophysics Data System (ADS)

    Dan-Feng, Zhang; Zhi-Feng, Hao; Bi, Zeng; Yan-Nan, Qian; Ying-Xin, Huang; Zhen-Da, Yang

    2016-04-01

    With the combination of the dielectric loss of the carbon layer with the magnetic loss of the ferromagnetic metal core, carbon-coated nickel (Ni(C)) nanoparticles are expected to be the promising microwave absorbers. Microwave electromagnetic parameters and reflection loss in a frequency range of 2 GHz-18 GHz for paraffin-Ni(C) composites are investigated. The values of relative complex permittivity and permeability, the dielectric and magnetic loss tangent of paraffin-Ni(C) composites are measured, respectively, when the weight ratios of Ni(C) nanoparticles are equal to 10 wt%, 40 wt%, 50 wt%, 70 wt%, and 80 wt% in paraffin-Ni(C) composites. The results reveal that Ni(C) nanoparticles exhibit a peak of magnetic loss at about 13 GHz, suggesting that magnetic loss and a natural resonance could be found at that frequency. Based on the measured complex permittivity and permeability, the reflection losses of paraffin-Ni(C) composites with different weight ratios of Ni(C) nanoparticles and coating thickness values are simulated according to the transmission line theory. An excellent microwave absorption is obtained. To be proved by the experimental results, the reflection loss of composite with a coating thickness of 2 mm is measured by the Arch method. The results indicate that the maximum reflection loss reaches -26.73 dB at 12.7 GHz, and below -10 dB, the bandwidth is about 4 GHz. The fact that the measured absorption position is consistent with the calculated results suggests that a good electromagnetic match and a strong microwave absorption can be established in Ni(C) nanoparticles. The excellent Ni(C) microwave absorber is prepared by choosing an optimum layer number and the weight ratio of Ni(C) nanoparticles in paraffin-Ni(C) composites. Project supported by the Science and Technology Program of Guangdong Province, China (Grant Nos. 2014B010106005, 2013B051000077, and 2015A050502047) and the Science and Technology Program of Guangzhou City, China (Grant No

  16. Analysis and calculation of electronic properties and light absorption of defective sulfur-doped silicon and theoretical photoelectric conversion efficiency.

    PubMed

    Jiang, He; Chen, Changshui

    2015-04-23

    Most material properties can be traced to electronic structures. Black silicon produced from SF6 or sulfur powder via irradiation with femtosecond laser pulses displays decreased infrared absorption after annealing, with almost no corresponding change in visible light absorption. The high-intensity laser pulses destroy the original crystal structure, and the doping element changes the material performance. In this work, the structural and electronic properties of several sulfur-doped silicon systems are investigated using first principle calculations. Depending on the sulfur concentration (level of doping) and the behavior of the sulfur atoms in the silicon lattice, different states or an absence of states are exhibited, compared with the undoped system. Moreover, the visible-infrared light absorption intensities are structure specific. The results of our theoretical calculations show that the conversion efficiency of sulfur-doped silicon solar cells depends on the sulfur concentrations. Additionally, two types of defect configurations exhibit light absorption characteristics that differ from the other configurations. These two structures produce a rapid increase in the theoretical photoelectric conversion efficiency in the range of the specific chemical potential studied. By controlling the positions of the atomic sulfur and the sulfur concentration in the preparation process, an efficient photovoltaic (PV) material may be obtainable.

  17. Analysis and calculation of electronic properties and light absorption of defective sulfur-doped silicon and theoretical photoelectric conversion efficiency.

    PubMed

    Jiang, He; Chen, Changshui

    2015-04-23

    Most material properties can be traced to electronic structures. Black silicon produced from SF6 or sulfur powder via irradiation with femtosecond laser pulses displays decreased infrared absorption after annealing, with almost no corresponding change in visible light absorption. The high-intensity laser pulses destroy the original crystal structure, and the doping element changes the material performance. In this work, the structural and electronic properties of several sulfur-doped silicon systems are investigated using first principle calculations. Depending on the sulfur concentration (level of doping) and the behavior of the sulfur atoms in the silicon lattice, different states or an absence of states are exhibited, compared with the undoped system. Moreover, the visible-infrared light absorption intensities are structure specific. The results of our theoretical calculations show that the conversion efficiency of sulfur-doped silicon solar cells depends on the sulfur concentrations. Additionally, two types of defect configurations exhibit light absorption characteristics that differ from the other configurations. These two structures produce a rapid increase in the theoretical photoelectric conversion efficiency in the range of the specific chemical potential studied. By controlling the positions of the atomic sulfur and the sulfur concentration in the preparation process, an efficient photovoltaic (PV) material may be obtainable. PMID:25798659

  18. Structural determination of vanillin, isovanillin and ethylvanillin by means of gas electron diffraction and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Egawa, Toru; Kameyama, Akiyo; Takeuchi, Hiroshi

    2006-08-01

    The molecular structures of vanillin (4-hydroxy-3-methoxybenzaldehyde), isovanillin (3-hydroxy-4-methoxybenzaldehyde) and ethylvanillin (3-ethoxy-4-hydroxybenzaldehyde) were determined by means of gas electron diffraction. Among them, vanillin and ethylvanillin have a vanilla odor but isovanillin smells differently. The nozzle temperatures were 125, 173 and 146 °C, for vanillin, isovanillin and ethylvanillin, respectively. The results of MP2 and B3LYP calculations with the 6-31G** basis set were used as supporting information. The MP2 calculations predicted that vanillin and isovanillin have two stable conformers and ethylvanillin has four stable conformers. The electron diffraction data were found to be consistent with these conformational compositions. The determined structural parameters ( rg and ∠ α) of vanillin are as follows: < r(C-C) ring>=1.397(4) Å; r(C 1-C aldehyde)=1.471(←) Å; r(C 3-O Me)=1.374(9) Å; r(C 4-O H)=1.361(←) Å; r(O-C Me)=1.428(←) Å; r(C dbnd6 O)=1.214(8) Å; < r(C-H)>=1.110(11) Å; r(O-H)=0.991(←) Å; ∠C 6-C 1-C 2=120.6(2)°; ∠C 1-C 2-C 3=118.8(←)°; ∠C 1-C 6-C 5=120.1(←)°; ∠C 2-C 1-C aldehyde=122.7(18)°; ∠C 1-C dbnd6 O=119.4(16)°; ∠C 4-C 3-O Me=112.2(12)°; ∠C 3-C 4-O H=119.1(←)°; ∠C 3-O-C=121.7(29)°. Those of isovanillin are as follows: < r(C-C) ring>=1.402(4) Å; r(C 1-C aldehyde)=1.479(←) Å; r(C 4-O Me)=1.369(9) Å; r(C 3-O H)=1.357(←) Å; r(O-C Me)=1.422(←) Å; r(C dbnd6 O)=1.221(9) Å; < r(C-H)>=1.114(14) Å; r(O-H)=0.995(←) Å; ∠C 6-C 1-C 2=120.2(3)°; ∠C 1-C 2-C 3=119.0(←)°; ∠C 1-C 6-C 5=119.9(←)°; ∠C 2-C 1-C aldehyde=124.6(25)°; ∠C 1-C dbnd6 O=121.3(24)°; ∠C 3-C 4-O Me=114.4(12)°; ∠C 4-C 3-O H=121.2(←)°; ∠C 4-O-C=123.8(26)°. Those of ethylvanillin are as follows: < r(C-C) ring>=1.397(6) Å; r(C 1-C aldehyde)=1.471(←) Å; r(C 3-O Et)=1.365(13) Å; r(C 4-O H)=1.352(←) Å; r(O-C Et)=1.427(←) Å; r(C-C Et)=1.494(21) Å; r(C dbnd6 O)=1.206(9) Å; < r

  19. Amorphous Solid Simulation and Trial Fabrication of the Organic Field-Effect Transistor of Tetrathienonaphthalenes Prepared by Using Microflow Photochemical Reactions: A Theoretical Calculation-Inspired Investigation.

    PubMed

    Yamamoto, Atsushi; Matsui, Yasunori; Asada, Toshio; Kumeda, Motoki; Takagi, Kenichiro; Suenaga, Yu; Nagae, Kunihiko; Ohta, Eisuke; Sato, Hiroyasu; Koseki, Shiro; Naito, Hiroyoshi; Ikeda, Hiroshi

    2016-04-15

    The p-type organic semiconductor (OSC) material tetrathieno[2,3-a:3',2'-c:2″,3″-f:3‴,2‴-h]naphthalene (2TTN) and its alkyl-substituted derivatives C(n)-2TTNs (n = 6, 8, and 10) have been developed based on the results of theoretical calculation-inspired investigation. A hole mobility for amorphous C(n)-2TTNs (10(-2)-10(-3) cm(2) V(-1) s(-1)) was accurately predicted by using a novel statistical method in which the geometric mean of the mobilities for many individual small molecular flocks in an amorphous solid was obtained by using molecular mechanical molecular dynamics simulations and quantum chemical calculations. The simulation also suggests that upon increasing the length of alkyl chains in C(n)-2TTNs the mobilities become smaller as a consequence of a decrease in transfer integral values. C(n)-2TTNs are synthesized in a microflow reactor through photoreactions of the corresponding precursors. C(n)-2TTNs are then utilized in the fabrication of organic field-effect transistors (OFETs). Although spin-coated thin films of C(n)-2TTNs are crystalline, the hole mobilities (10(-2)-10(-3) cm(2) V(-1) s(-1)) of trial OFETs decrease upon elongation of the alkyl chains. This finding parallels the results of theoretical simulation. The simulation method for amorphous solids developed in this effort should become a useful tool in studies aimed at designing new OSC materials. PMID:27010327

  20. An accurate symplectic calculation of the inboard magnetic footprint from statistical topological noise and field errors in the DIII-D

    NASA Astrophysics Data System (ADS)

    Punjabi, Alkesh; Ali, Halima

    2011-02-01

    Any canonical transformation of Hamiltonian equations is symplectic, and any area-preserving transformation in 2D is a symplectomorphism. Based on these, a discrete symplectic map and its continuous symplectic analog are derived for forward magnetic field line trajectories in natural canonical coordinates. The unperturbed axisymmetric Hamiltonian for magnetic field lines is constructed from the experimental data in the DIII-D [J. L. Luxon and L. E. Davis, Fusion Technol. 8, 441 (1985)]. The equilibrium Hamiltonian is a highly accurate, analytic, and realistic representation of the magnetic geometry of the DIII-D. These symplectic mathematical maps are used to calculate the magnetic footprint on the inboard collector plate in the DIII-D. Internal statistical topological noise and field errors are irreducible and ubiquitous in magnetic confinement schemes for fusion. It is important to know the stochasticity and magnetic footprint from noise and error fields. The estimates of the spectrum and mode amplitudes of the spatial topological noise and magnetic errors in the DIII-D are used as magnetic perturbation. The discrete and continuous symplectic maps are used to calculate the magnetic footprint on the inboard collector plate of the DIII-D by inverting the natural coordinates to physical coordinates. The combination of highly accurate equilibrium generating function, natural canonical coordinates, symplecticity, and small step-size together gives a very accurate calculation of magnetic footprint. Radial variation of magnetic perturbation and the response of plasma to perturbation are not included. The inboard footprint from noise and errors are dominated by m =3, n =1 mode. The footprint is in the form of a toroidally winding helical strip. The width of stochastic layer scales as 1/2 power of amplitude. The area of footprint scales as first power of amplitude. The physical parameters such as toroidal angle, length, and poloidal angle covered before striking, and the

  1. A Theoretical Study of Bulk and Surface Diffusion Processes for Semiconductor Materials Using First Principles Calculations

    NASA Astrophysics Data System (ADS)

    Roehl, Jason L.

    Diffusion of point defects on crystalline surfaces and in their bulk is an important and ubiquitous phenomenon affecting film quality, electronic properties and device functionality. A complete understanding of these diffusion processes enables one to predict and then control those processes. Such understanding includes knowledge of the structural, energetic and electronic properties of these native and non-native point defect diffusion processes. Direct experimental observation of the phenomenon is difficult and microscopic theories of diffusion mechanisms and pathways abound. Thus, knowing the nature of diffusion processes, of specific point defects in given materials, has been a challenging task for analytical theory as well as experiment. The recent advances in computing technology have been a catalyst for the rise of a third mode of investigation. The advent of tremendous computing power, breakthroughs in algorithmic development in computational applications of electronic density functional theory now enables direct computation of the diffusion process. This thesis demonstrates such a method applied to several different examples of point defect diffusion on the (001) surface of gallium arsenide (GaAs) and the bulk of cadmium telluride (CdTe) and cadmium sulfide (CdS). All results presented in this work are ab initio, total-energy pseudopotential calculations within the local density approximation to density-functional theory. Single particle wavefunctions were expanded in a plane-wave basis and reciprocal space k-point sampling was achieved by Monkhorst-Pack generated k-point grids. Both surface and bulk computations employed a supercell approach using periodic boundary conditions. Ga adatom adsorption and diffusion processes were studied on two reconstructions of the GaAs(001) surface including the c(4x4) and c(4x4)-heterodimer surface reconstructions. On the GaAs(001)- c(4x4) surface reconstruction, two distinct sets of minima and transition sites were

  2. Magnetic coupling constants of self-assembled Cu(II) [3×3] grids: alternative spin model from theoretical calculations.

    PubMed

    Calzado, Carmen J; Ben Amor, Nadia; Maynau, Daniel

    2014-07-14

    This paper reports a theoretical analysis of the electronic structure and magnetic properties of a ferromagnetic Cu(II) [3×3] grid. A two-step strategy, combining calculations on the whole grid and on binuclear fragments, has been employed to evaluate all the magnetic interactions in the grid. The calculations confirm an S = 7/2 ground state, which is in accordance with the magnetisation versus field curve and the thermal dependence of the magnetic moment data. Only the first-neighbour coupling terms present non-negligible amplitudes, all of them in agreement with the structure and arrangement of the Cu 3d magnetic orbitals. The results indicate that the dominant interaction in the system is the antiferromagnetic coupling between the ring and the central Cu sites (J3 = J4 ≈ -31 cm(-1)). In the ring two different interactions can be distinguished, J1 = 4.6 cm(-1) and J2 = -0.1 cm(-1), in contrast to the single J model employed in the magnetic data fit. The calculated J values have been used to determine the energy level distribution of the Heisenberg magnetic states. The effective magnetic moment versus temperature plot resulting from this ab initio energy profile is in good agreement with the experimental curve and the fitting obtained with the simplified spin model, despite the differences between these two spin models. This study underlines the role that the theoretical evaluations of the coupling constants can play on the rationalisation of the magnetic properties of these complex polynuclear systems.

  3. Accurately Modelling the Absorption of a Mixture of Gases at Low- to Medium-resolution in Exoplanetary and Brown Dwarf Atmospheric Radiative Transfer Calculations

    NASA Astrophysics Data System (ADS)

    Garland, Ryan; Irwin, Patrick Gerard Joseph

    2016-10-01

    Exoplanetary and brown dwarf atmospheres are extremely diverse environments ranging over many different temperatures, pressures, and compositions. In order to model the spectra produced by the these objects, a commonplace approach in exoplanetary science is to use cross-sections of individual gases to quickly calculate the atmospheric opacities. However, when combining multiple gases with non-monochromatic absorption coefficients, the multiplication property of transmission does not hold. The resulting spectra are hence unreliable. Extensive work was carried out on Solar System radiative transfer models to find an efficient alternative to line-by-line calculations of opacity which was more accurate than combining cross-sections, resulting in many band models and the correlated-k method. Here we illustrate the effect of using cross-sections to model typical brown dwarf and exoplanetary atmospheres (e.g. HD189733b), and compare them to the spectra calculated using the correlated-k method. We verify our correlated-k method using a line-by-line model. For the same objects, we also present the effects of pressure broadening on the resulting spectra. Considering both the method of calculation (i.e. cross-section or correlated-k) and the treatment of pressure broadening, we show that the differences in the spectra are immediately obvious and hugely significant. Entire spectral features can appear or disappear, changing the morphology of the spectra. For the inspected brown dwarfs, these spectral features can vary by up to three orders of magnitude in luminosity. For our exoplanets, the transit depth can vary by up to 1%. We conclude that each effect would change the retrieved system parameters (i.e. temperature and abundances) considerably.

  4. Laser sputtering generation of B/sub 2/ for ESR matrix isolation studies: comparison with ab initio CI theoretical calculations

    SciTech Connect

    Knight, L.B. Jr.; Gregory, B.W.; Cobranchi, S.T.; Feller, D.; Davidson, E.R.

    1987-06-10

    The /sup 11/B/sub 2/ molecule has been trapped in neon and argon matrices at 5 +/- 1 K for ESR (electron spin resonance) investigations. Laser sputtering from solid boron was used to generate the B/sub 2/ molecule whose ground electronic state has been established experimentally for the first time to be /sup 3/..sigma../sub g//sup -/. The ESR nuclear hyperfine parameters for B/sub 2/ and B atoms have been compared with the results of ab initio CI theoretical calculations. Good agreement between theory and experiment is found for the dipolar component of the A tensor but not for the small and difficult to calculate isotropic hfs. Reasons that make the Fermi contact term especially difficult to calculate in this particular case are presented. The argon matrix ESR results yield the following magnetic parameters for /sup 11/B/sub 2/ in its ground electronic state: g/sub parallel/ = g/sub perpendicular/ = 2.0015 (4); A/sub parallel/ = +/- 11 (1) MHz and A/sub perpendicular/ = +/- 27.4 (3) MHz for /sup 11/B and the zero field parameter; and the D value is 3633 (3) MHz. As discussed, the most reasonable signs for the A values are A/sub parallel/ < O and A/sub perpendicular/ > 0. The neon matrix value of D was found to be 3840 (3) MHz and A/sub perpendicular/ in neon is +/- 26.6 (3) MHz.

  5. Theoretical calculations of X-ray absorption spectra of a copper mixed ligand complex using computer code FEFF9

    NASA Astrophysics Data System (ADS)

    Gaur, A.; Shrivastava, B. D.

    2014-09-01

    The terms X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) refer, respectively, to the structure in the X-ray absorption spectrum at low and high energies relative to the absorption edge. Routine analysis of EXAFS experiments generally makes use of simplified models and several many-body parameters, e.g. mean free paths, many-body amplitude factors, and Debye-Waller factors, as incorporated in EXAFS analysis software packages like IFEFFIT which includes Artemis. Similar considerations apply to XANES, where the agreement between theory and experiment is often less satisfactory. The recently available computer code FEFF9 uses the real-space Green's function (RSGF) approach to calculate dielectric response over a broad spectrum including the dominant low-energy region. This code includes improved treatments of many-body effects such as inelastic losses, core-hole effects, vibrational amplitudes, and the extension to full spectrum calculations of optical constants including solid state effects. In the present work, using FEFF9, we have calculated the X-ray absorption spectrum at the K-edge of copper in a complex, viz., aqua (diethylenetriamine) (isonicotinato) copper(II), the crystal structure of which is unknown. The theoretical spectrum has been compared with the experimental spectrum, recorded by us at the XAFS beamline 11.1 at ELETTRA synchrotron source, Italy, in both XANES and EXAFS regions.

  6. Investigation of attractive and repulsive interactions associated with ketones in supercritical CO2, based on Raman spectroscopy and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Kajiya, Daisuke; Saitow, Ken-ichi

    2013-08-01

    Carbonyl compounds are solutes that are highly soluble in supercritical CO2 (scCO2). Their solubility governs the efficiency of chemical reactions, and is significantly increased by changing a chromophore. To effectively use scCO2 as solvent, it is crucial to understand the high solubility of carbonyl compounds, the solvation structure, and the solute-solvent intermolecular interactions. We report Raman spectroscopic data, for three prototypical ketones dissolved in scCO2, and four theoretical analyses. The vibrational Raman spectra of the C=O stretching modes of ketones (acetone, acetophenone, and benzophenone) were measured in scCO2 along the reduced temperature Tr = T/Tc = 1.02 isotherm as a function of the reduced density ρr = ρ/ρc in the range 0.05-1.5. The peak frequencies of the C=O stretching modes shifted toward lower energies as the fluid density increased. The density dependence was analyzed by using perturbed hard-sphere theory, and the shift was decomposed into attractive and repulsive energy components. The attractive energy between the ketones and CO2 was up to nine times higher than the repulsive energy, and its magnitude increased in the following order: acetone < acetophenone < benzophenone. The Mulliken charges of the three solutes and CO2 molecules obtained by using quantum chemistry calculations described the order of the magnitude of the attractive energy and optimized the relative configuration between each solute and CO2. According to theoretical calculations for the dispersion energy, the dipole-induced-dipole interaction energy, and the frequency shift due to their interactions, the experimentally determined attractive energy differences in the three solutes were attributed to the dispersion energies that depended on a chromophore attached to the carbonyl groups. It was found that the major intermolecular interaction with the attractive shift varied from dipole-induced dipole to dispersion depending on the chromophore in the ketones in

  7. Density functional computational thermochemistry: Accurate determination of the enthalpy of formation of perfluoropropane from DFT and ab initio calculations on isodesmic reactions

    NASA Astrophysics Data System (ADS)

    Ventura, Oscar N.; Segovia, Marc

    2005-02-01

    The experimental enthalpy of formation of perfluoropropane (C 3F 8), reported originally as -1729 kJ/mol and latter corrected to -1784.7 kJ/mol, is reexamined at the light of density functional and model chemistry (G3, CBS-4, CBS-Q) calculations of several isodesmic reactions relating C 3F 8 to smaller fluoroalkanes. The average enthalpy of formation of C 3F 8 obtained from all reactions studied was -1739 ± 12 kJ/mol at the DFT level and -1748 ± 12 kJ/mol at the ab initio level, thus ruling out the larger experimental value. A value of -1732 ± 5 kJ/mol is recommended from careful analysis of the theoretical results.

  8. Effective theory for the nonrigid rotor in an electromagnetic field: Toward accurate and precise calculations of E2 transitions in deformed nuclei

    DOE PAGES

    Coello Pérez, Eduardo A.; Papenbrock, Thomas F.

    2015-07-27

    In this paper, we present a model-independent approach to electric quadrupole transitions of deformed nuclei. Based on an effective theory for axially symmetric systems, the leading interactions with electromagnetic fields enter as minimal couplings to gauge potentials, while subleading corrections employ gauge-invariant nonminimal couplings. This approach yields transition operators that are consistent with the Hamiltonian, and the power counting of the effective theory provides us with theoretical uncertainty estimates. We successfully test the effective theory in homonuclear molecules that exhibit a large separation of scales. For ground-state band transitions of rotational nuclei, the effective theory describes data well within theoreticalmore » uncertainties at leading order. To probe the theory at subleading order, data with higher precision would be valuable. For transitional nuclei, next-to-leading-order calculations and the high-precision data are consistent within the theoretical uncertainty estimates. In addition, we study the faint interband transitions within the effective theory and focus on the E2 transitions from the 02+ band (the “β band”) to the ground-state band. Here the predictions from the effective theory are consistent with data for several nuclei, thereby proposing a solution to a long-standing challenge.« less

  9. Electron-ion recombination of Fe{sup 12+} forming Fe{sup 11+}: Laboratory measurements and theoretical calculations

    SciTech Connect

    Hahn, M.; Novotný, O.; Savin, D. W.; Badnell, N. R.; Grieser, M.; Krantz, C.; Repnow, R.; Wolf, A.; Lestinsky, M.; Müller, A.; Schippers, S.

    2014-06-10

    We have measured dielectronic recombination (DR) for Fe{sup 12+} forming Fe{sup 11+} using the heavy ion storage ring TSR located at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany. Using our results, we have calculated a plasma rate coefficient from these data that can be used for modeling astrophysical and laboratory plasmas. For the low temperatures characteristic of photoionized plasmas, the experimentally derived rate coefficient is orders of magnitude larger than the previously recommended atomic data. The existing atomic data were also about 40% smaller than our measurements at temperatures relevant for collisionally ionized plasmas. Recent state-of-the-art theory has difficulty reproducing the detailed energy dependence of the DR spectrum. However, for the Maxwellian plasma rate coefficient, recent theoretical results agree with our measurements to within about 30% for both photoionized and collisionally ionized plasmas.

  10. Predicting the viscosity and electrical conductivity of ionic liquids on the basis of theoretically calculated ionic volumes

    NASA Astrophysics Data System (ADS)

    Wileńska, Dorota; Anusiewicz, Iwona; Freza, Sylwia; Bobrowski, Maciej; Laux, Edith; Uhl, Stefanie; Keppner, Herbert; Skurski, Piotr

    2015-03-01

    Selected physical properties of the ionic liquids might be quantitatively predicted based on the volumes of the ions these systems are composed of. It is demonstrated that the ionic volumes calculated using relatively simple theoretical quantum chemistry methods can be utilised to estimate the viscosities and electrical conductivities of various commonly used ionic liquids. The fitting formulas of the exponential form are offered and their predictive usefulness is verified. The quality of such predictions is discussed on the basis of several ionic liquids involving [Tf2N]‑ and [BF4]‑ anions and 16 various cations. The dependence of the viscosity and electrical conductivity of the ionic liquids on the temperature is also investigated and the temperature-dependent equations are derived and compared to the experimentally measured values.

  11. Synthesis, NMR characterization, X-ray structural analysis and theoretical calculations of amide and ester derivatives of the coumarin scaffold

    NASA Astrophysics Data System (ADS)

    Matos, Maria J.; Uriarte, Eugenio; Santana, Lourdes; Vilar, Santiago

    2013-06-01

    Compounds 1 (4-methyl-N-(coumarin-3-yl)benzamide) and 2 ((coumarin-3-yl)-4-methylbenzoate) were synthesized by linking the coumarin system (3-aminocoumarin or 3-hydroxycoumarin, respectively) to a p-toluoylchloride. 1H and 13C NMR and X-ray diffractometry determined the molecular structures of both derivatives. The X-ray results were compared to those obtained by conformational analysis followed by semiempirical methodologies (AM1 and PM3). The theoretical calculations yielded results reproducing the whole three-dimensional (3D) structure of both molecules in a good agreement with X-ray structural analysis. The global structures of the two compounds are very similar in the two studied environments, meaning that the structural determination in the gas phase can be extrapolated. A comparative study between compounds 1 and 2, based on the structural results, was carried out.

  12. A combined study based on experimental analyses and theoretical calculations on properties of poly (lactic acid) under annealing treatment

    NASA Astrophysics Data System (ADS)

    Loued, W.; Wéry, J.; Dorlando, A.; Alimi, K.

    2015-02-01

    In this paper, the significance of annealing, in two different atmospheres (air and vacuum), on the surface characteristics of poly (lactic acid) (PLA) films was investigated. X-ray diffraction (XRD) measurements correlated to atomic force microscopy (AFM) observations of the cast PLA films show that thermal treatment under air atmosphere is responsible for a significant increase of crystallinity with the increase of temperature. However, band gap energy of the title compound is slightly affected by annealing at different temperatures. As for the untreated PLA, the molecular geometry was optimized using density functional theory (DFT/B3LYP) method with 6-31g (d) basis set in ground state. From the optimized geometry, HOMO and LUMO energies and quantum chemical parameters were performed at B3LYP/6-31g (d). The theoretical results, applied to simulated optical spectra of the compound, were compared to the observed ones. On the basis of theoretical vibrational analyses, the thermodynamic properties were calculated at different temperatures, revealing the correlation between internal energy (U), enthalpy (H), entropy (S), Free energy (G) and temperatures.

  13. Molecular structures of benzoic acid and 2-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations.

    PubMed

    Aarset, Kirsten; Page, Elizabeth M; Rice, David A

    2006-07-20

    The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d,p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+G(d,p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol(-1) lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond. PMID:16836466

  14. Structural determination of carvone, a component of spearmint, by means of gas electron diffraction augmented by theoretical calculations

    NASA Astrophysics Data System (ADS)

    Egawa, Toru; Kachi, Yukari; Takeshima, Tsuguhide; Takeuchi, Hiroshi; Konaka, Shigehiro

    2003-10-01

    The molecular structure and conformation of carvone, a compound with a minty odor, were investigated by means of gas electron diffraction supported by theoretical calculations. Electron diffraction patterns were recorded by heating the nozzle up to 128 °C to obtain enough scattering intensity. The infrared spectrum was also measured by using an absorption cell with a path length of 10 m. The obtained molecular scattering intensities were analyzed with the aid of theoretical calculations and infrared spectroscopy. It was revealed that the experimental data are well reproduced by assuming that carvone consists of a mixture of three conformers that have the isopropenyl group in the equatorial position and mutually differ in the torsional angle around the single bond connecting the ring and the isopropenyl group. It was also found that the puckering amplitude of the ring of carvone is close to those of menthol and isomenthol, a minty compound and its nonminty isomer. The determined structural parameters ( rg and ∠ α) of the most abundant conformer of carvone are as follows: < r(C-C)>=1.520(3) Å; < r(CC)>=1.360(5) Å; r(CO)=1.225(5) Å; < r(C-H)>=1.104(4)Å; <∠CC-C>=121.1(5)°; <∠C-C-C>=110.4(5)°; ∠C-CO-C=117.1(14)°; <∠C-C-H>=111.1(13)°. Angle brackets denote average values and parenthesized values are the estimated limits of error (3 σ) referring to the last significant digit.

  15. Ionizing Collisions of Electrons with Radical Species OH, H2 O2 and HO2; Theoretical Calculations

    NASA Astrophysics Data System (ADS)

    Joshipura, K. N.; Pandya, S. H.; Vaishnav, B. G.; Patel, U. R.

    2016-05-01

    In this paper we present our calculated total ionization cross sections (TICS) of electron impact on radical targets OH, H2 O2 and HO2 at energies from threshold to 2000 eV. Reactive species such as these pose difficulties in measurements of electron scattering cross sections. No measured data have been reported in this regard except an isolated TICS measurement on OH radical, and hence the present work on the title radicals hold significance. These radical species are present in an environment in which water molecules undergo dissociation (neutral or ionic) in interactions with photons or electrons. The embedding environments could be quite diverse, ranging from our atmosphere to membranes of living cells. Ionization of OH, H2 O2 or HO2 can give rise to further chemistry in the relevant bulk medium. Therefore, it is appropriate and meaningful to examine electron impact ionization of these radicals in comparison with that of water molecules, for which accurate da are available. For the OH target single-centre scattering calculations are performed by starting with a 4-term complex potential, that describes simultaneous elastic plus inelastic scattering. TICS are obtained from the total inelastic cross sections in the complex scattering potential - ionization contribution formalism , a well established method. For H2 O2 and HO2 targets, we employ the additivity rule with overlap or screening corrections. Detailed results will be presented in the Conference.

  16. Accurate calculations of spectroscopic properties for the 13 Λ-S states and the 23 Ω states of BO radical including the spin-orbit coupling effect.

    PubMed

    Zhu, Zunlue; Yu, Wei; Wang, Shuai; Sun, Jinfeng; Shi, Deheng

    2014-10-15

    The spectroscopic properties of 23 Ω states generated from the 13 Λ-S states of BO radical are studied for the first time for internuclear separations from about 0.07 to 1.0nm. Of the 13 Λ-S states, each of the F(2)Π, 1(2)Φ and 1(2)Δ states is found to possess the double well. Each of the 1(4)Π, C(2)Π, 1(2)Σ(-) and 2(2)Σ(-) states possesses one well with one barrier. The A(2)Π, 1(4)Π and F(2)Π are the inverted states with the spin-orbit coupling effect taken into account. All the states possess the deep well except for the 1(2)Φ. The potential energy curves (PECs) are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections are included into the calculations. The PECs are extrapolated to the complete basis set limit. The spin-orbit coupling effect is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. The spectroscopic parameters are evaluated, and compared with the available measurements and other theoretical results. The Franck-Condon factors and radiative lifetimes of the transitions from the B(2)Σ(+), C(2)Π, D(2)Σ(+), 1(2)Σ(-) and 1(4)Π Λ-S states to the ground state are calculated for several low vibrational levels, and some necessary discussion is made. Analyses show that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. PMID:24820321

  17. Peak clustering in two-dimensional gas chromatography with mass spectrometric detection based on theoretical calculation of two-dimensional peak shapes: the 2DAid approach.

    PubMed

    van Stee, Leo L P; Brinkman, Udo A Th

    2011-10-28

    A method is presented to facilitate the non-target analysis of data obtained in temperature-programmed comprehensive two-dimensional (2D) gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-ToF-MS). One main difficulty of GC×GC data analysis is that each peak is usually modulated several times and therefore appears as a series of peaks (or peaklets) in the one-dimensionally recorded data. The proposed method, 2DAid, uses basic chromatographic laws to calculate the theoretical shape of a 2D peak (a cluster of peaklets originating from the same analyte) in order to define the area in which the peaklets of each individual compound can be expected to show up. Based on analyte-identity information obtained by means of mass spectral library searching, the individual peaklets are then combined into a single 2D peak. The method is applied, amongst others, to a complex mixture containing 362 analytes. It is demonstrated that the 2D peak shapes can be accurately predicted and that clustering and further processing can reduce the final peak list to a manageable size.

  18. How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.

    SciTech Connect

    Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    2003-03-01

    Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

  19. The calculation of accurate 17O hyperfine coupling constants in the hydroxyl radical: A difficult problem for current quantum chemical methods

    NASA Astrophysics Data System (ADS)

    Wetmore, Stacey D.; Eriksson, Leif A.; Boyd, Russell J.

    1998-12-01

    The hyperfine coupling constants (HFCCs) in the hydroxyl radical are investigated through comparison of results obtained from a variety of quantum chemical methods. The couplings obtained from the multi-reference configuration interaction (MRCI) wave function, built upon the restricted open-shell Hartree-Fock (ROHF) reference determinant, are investigated in terms of the basis set, the configuration selection energy threshold, and the size of the reference space. Overall results which converge to the experimental couplings are obtained for hydrogen, but not for oxygen. In particular, the MRCI method shows no improvement over density functional theory (the B3LYP functional), for the calculation of Aiso(17O). On the other hand, results in excellent agreement with experiment are obtained through the use of the quadratic configuration interaction (QCISD) method based on the unrestricted HF (UHF) reference determinant with the identical basis sets. Examination of UHF and ROHF based coupled-cluster methods, CCSD and CCSD(T), indicates that once a high enough level of electron correlation is included, the oxygen HFCC is independent of the form of the reference determinant. Unlike the ROHF-CCSD method, which yields reliable results once the effects of triple excitations have been taken into account, the MRCI wave function cannot easily be adjusted to account for the inadequacies of the ROHF reference determinant in order to accurately predict 17O HFCCs.

  20. Coagulation Behavior of Graphene Oxide on Nanocrystallined Mg/Al Layered Double Hydroxides: Batch Experimental and Theoretical Calculation Study.

    PubMed

    Zou, Yidong; Wang, Xiangxue; Ai, Yuejie; Liu, Yunhai; Li, Jiaxing; Ji, Yongfei; Wang, Xiangke

    2016-04-01

    Graphene oxide (GO) has attracted considerable attention because of its remarkable enhanced adsorption and multifunctional properties. However, the toxic properties of GO nanosheets released into the environment could lead to the instability of biological system. In aqueous phase, GO may interact with fine mineral particles, such as chloridion intercalated nanocrystallined Mg/Al layered double hydroxides (LDH-Cl) and nanocrystallined Mg/Al LDHs (LDH-CO3), which are considered as coagulant molecules for the coagulation and removal of GO from aqueous solutions. Herein the coagulation of GO on LDHs were studied as a function of solution pH, ionic strength, contact time, temperature and coagulant concentration. The presence of LDH-Cl and LDH-CO3 improved the coagulation of GO in solution efficiently, which was mainly attributed to the surface oxygen-containing functional groups of LDH-Cl and LDH-CO3 occupying the binding sites of GO. The coagulation of GO by LDH-Cl and LDH-CO3 was strongly dependent on pH and ionic strength. Results of theoretical DFT calculations indicated that the coagulation of GO on LDHs was energetically favored by electrostatic interactions and hydrogen bonds, which was further evidenced by FTIR and XPS analysis. By integrating the experimental results, it was clear that LDH-Cl could be potentially used as a cost-effective coagulant for the elimination of GO from aqueous solutions, which could efficiently decrease the potential toxicity of GO in the natural environment. PMID:26978487

  1. Coagulation Behavior of Graphene Oxide on Nanocrystallined Mg/Al Layered Double Hydroxides: Batch Experimental and Theoretical Calculation Study.

    PubMed

    Zou, Yidong; Wang, Xiangxue; Ai, Yuejie; Liu, Yunhai; Li, Jiaxing; Ji, Yongfei; Wang, Xiangke

    2016-04-01

    Graphene oxide (GO) has attracted considerable attention because of its remarkable enhanced adsorption and multifunctional properties. However, the toxic properties of GO nanosheets released into the environment could lead to the instability of biological system. In aqueous phase, GO may interact with fine mineral particles, such as chloridion intercalated nanocrystallined Mg/Al layered double hydroxides (LDH-Cl) and nanocrystallined Mg/Al LDHs (LDH-CO3), which are considered as coagulant molecules for the coagulation and removal of GO from aqueous solutions. Herein the coagulation of GO on LDHs were studied as a function of solution pH, ionic strength, contact time, temperature and coagulant concentration. The presence of LDH-Cl and LDH-CO3 improved the coagulation of GO in solution efficiently, which was mainly attributed to the surface oxygen-containing functional groups of LDH-Cl and LDH-CO3 occupying the binding sites of GO. The coagulation of GO by LDH-Cl and LDH-CO3 was strongly dependent on pH and ionic strength. Results of theoretical DFT calculations indicated that the coagulation of GO on LDHs was energetically favored by electrostatic interactions and hydrogen bonds, which was further evidenced by FTIR and XPS analysis. By integrating the experimental results, it was clear that LDH-Cl could be potentially used as a cost-effective coagulant for the elimination of GO from aqueous solutions, which could efficiently decrease the potential toxicity of GO in the natural environment.

  2. Studies on the s-cis-trans isomerism for some furan derivatives through IR and NMR spectroscopies and theoretical calculations.

    PubMed

    Rittner, Roberto; Ducati, Lucas C; Tormena, Cláudio F; Cormanich, Rodrigo A; Fiorin, Barbara C; Braga, Carolyne B; Abraham, Raymond J

    2013-02-15

    The s-cis-trans isomerism of two furan derivatives [2-acetyl- (AF) and 2-acetyl-5-methylfuran, (AMF)] was analyzed, using data from the deconvolution of their carbonyl absorption band in two solvents (CH(2)Cl(2) and CH(3)CN). These infrared data showed that the O,O-trans conformers predominate in the less polar solvent (CH(2)Cl(2)), but these equilibria change in a more polar solvent (CH(3)CN) leading to a slight predominance of the O,O-cis conformers, in agreement with the theoretical calculations. The later results were obtained using B3LYP-IEFPCM/6-31++g(3df,3p) level of theory, which taking into account the solvent effects at IEFPCM (Integral Equation Formalism Polarizable Continuum Model). Low temperature (13)CNMR spectra in CD(2)Cl(2) (ca. -75 °C) showed pairs of signals for each carbon, due to the known high energy barrier for the cis-trans interconversion leading to a large predominance of the trans isomers, which decreases in acetone-d(6). This was confirmed by their (1)HNMR spectra at the same temperatures. Moreover, despite the larger hyperconjugative interactions for the O,O-cis isomers, obtained from NBO data, these isomers are destabilized by the their Lewis energy.

  3. Probing silicon and aluminium chemical environments in silicate and aluminosilicate glasses by solid state NMR spectroscopy and accurate first-principles calculations

    NASA Astrophysics Data System (ADS)

    Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Caurant, Daniel; Charpentier, Thibault

    2014-01-01

    Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO2·20Na2O·20CaO (CSN), 60SiO2·20Al2O3·20CaO (CAS), 78SiO2·11Al2O3·11Na2O (NAS) and 60SiO2·10Al2O3·10Na2O·20CaO (CASN) have been investigated by 27Al and 29Si solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the 29Si and 27Al NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both 29Si and 27Al increases of about +5 ppm for each Al added in the second sphere and (ii) both the 27Al and 29Si isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, 27Al and 29Si NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from 27Al and 29Si NMR.

  4. Microwave and infrared spectra, adjusted r0 structural parameters, conformational stabilities, vibrational assignments, and theoretical calculations of cyclobutylcarboxylic acid chloride.

    PubMed

    Klaassen, Joshua J; Darkhalil, Ikhlas D; Deodhar, Bhushan S; Gounev, Todor K; Gurusinghe, Ranil M; Tubergen, Michael J; Groner, Peter; Durig, James R

    2013-08-01

    The FT-microwave spectrum of cyclobutylcarboxylic acid chloride, c-C4H7C(O)Cl, has been recorded and 153 transitions for the (35)Cl and (37)Cl isotopologues have been assigned for the gauche-equatorial (g-Eq) conformation. The ground state rotational constants were determined for (35)Cl [(37)Cl]: A = 4349.8429(25) [4322.0555(56)] MHz, B = 1414.8032(25) [1384.5058(25)] MHz, and C = 1148.2411(25) [1126.3546(25)] MHz. From these rotational constants and ab initio predicted parameters, adjusted r0 parameters are reported with distances (Å) rCα-C = 1.491(4), rC═O = 1.193(3), rCα-Cβ = 1.553(4), rCα-Cβ' = 1.540(4), rCγ-Cβ = 1.547(4), rCγ-Cβ' = 1.546(4), rC-Cl = 1.801(3) and angles (deg) τCγCβCβ'Cα = 30.9(5). Variable temperature (-70 to -100 °C) infrared spectra (4000 to 400 cm(-1)) were recorded in liquid xenon and the g-Eq conformer was determined the most stable form, with enthalpy differences of 91 ± 9 cm(-1) (1.09 ± 0.11 kJ/mol) for the gauche-axial (g-Ax) form and 173 ± 17 cm(-1) (2.07 ± 0.20 kJ/mol) for the trans-equatorial (t-Eq) conformer. The relative amounts at ambient temperature are 54% g-Eq, 35 ± 1% g-Ax, and 12 ± 1% t-Eq forms. Vibrational assignments have been provided for the three conformers and theoretical calculations were carried out. The results are discussed and compared to corresponding properties of related molecules.

  5. Bis(alpha-diimine)iron complexes: electronic structure determination by spectroscopy and broken symmetry density functional theoretical calculations.

    PubMed

    Muresan, Nicoleta; Lu, Connie C; Ghosh, Meenakshi; Peters, Jonas C; Abe, Megumi; Henling, Lawrence M; Weyhermöller, Thomas; Bill, Eckhard; Wieghardt, Karl

    2008-06-01

    The electronic structure of a family comprising tetrahedral (alpha-diimine)iron dichloride, and tetrahedral bis(alpha-diimine)iron compounds has been investigated by Mossbauer spectroscopy, magnetic susceptibility measurements, and X-ray crystallography. In addition, broken-symmetry density functional theoretical (B3LYP) calculations have been performed. A detailed understanding of the electronic structure of these complexes has been obtained. A paramagnetic (St=2), tetrahedral complex [FeII(4L)2], where (4L)1- represents the diamagnetic monoanion N-tert-butylquinolinylamide, has been synthesized and characterized to serve as a benchmark for a Werner-type complex containing a tetrahedral FeIIN4 geometry and a single high-spin ferrous ion. In contrast to the most commonly used description of the electronic structure of bis(alpha-diimine)iron(0) complexes as low-valent iron(0) species with two neutral alpha-diimine ligands, it is established here that they are, in fact, complexes containing two (alpha-diiminato)1-* pi radical monoanions and a high-spin ferrous ion (in tetrahedral N4 geometry) (SFe=2). Intramolecular antiferromagnetic coupling between the pi radical ligands (Srad=1/2) and the ferrous ion (SFe=2) yields the observed St=1 ground state. The study confirms that alpha-diimines are redox noninnocent ligands with an energetically low-lying antibonding pi* lowest unoccupied molecular orbital which can accept one or two electrons from a transition metal ion. The (alpha-diimine)FeCl2 complexes (St=2) are shown to contain a neutral alpha-diimine ligand, a high spin ferrous ion, and two chloride ligands. PMID:18442239

  6. Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: application to H2O, N2H+, NO2+, and C2H2.

    PubMed

    Huang, Xinchuan; Valeev, Edward F; Lee, Timothy J

    2010-12-28

    One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar

  7. Theoretical calculations of a model of NOS indazole inhibitors: interaction of aromatic compounds with Zn-porphyrins.

    PubMed

    Elguero, José; Alkorta, Ibon; Claramunt, Rosa M; López, Concepción; Sanz, Dionísia; María, Dolores Santa

    2009-12-01

    We report a theoretical approach, at the M05-2x/6-311+G(d) level, to explain the affinity of indazoles for nitric oxide synthases using a simplified model of porphyrin. The theoretical E(rel)=E(i) stacking-E(i) apical values correlate with the experimental inhibition percents allowing to predict that 3,7-dinitro-1H-indazole should be a good NOS inhibitor.

  8. Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

    NASA Astrophysics Data System (ADS)

    Speranskiy, Kirill; Kurnikova, Maria

    2004-07-01

    We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602 (2002)]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.

  9. Low temperature rate constants for the N + CN → N2 + C reaction: two-dimensional quantum capture calculations on an accurate potential energy surface.

    PubMed

    Ma, Jianyi; Guo, Hua; Dawes, Richard

    2012-09-21

    The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.

  10. MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO{sup +}(H{sub 2}O) cluster using accurate potential energy and dipole moment surfaces

    SciTech Connect

    Homayoon, Zahra

    2014-09-28

    A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO{sup +}(H{sub 2}O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO{sup +}(H{sub 2}O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water “antisymmetric” stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

  11. Comparasion of Experimental obtained Data from Kashima maps and Theoretical Calculated by IRI 2012 and by IRI Plus 2015 Data

    NASA Astrophysics Data System (ADS)

    Güzel, Esat; Canyilmaz, Murat; Akdoǧan, Tayfun

    2016-07-01

    In this study, Ionosphere F2-region critical frequency (fof2) changes obtained from maps created from the Kashima ground station from 90º N to 90º S latitude and 30, 35, 40, 45 degrees East longitude on 8 December 1978 were examined in comparison with the values obtained from the International Reference Ionosphere (IRI 2012) and International Reference Ionosphere Plus (IRI plus 2015). When the experimental data are examined, It was observed that the critical frequency values increase from the poles to the equator and pits occur at the equator and hills occur between 20° N and 20° S latitudes. Critical frequency (fof2) changes in the theoretical data are same as experimental data but pits occur at 10° N and hills occur between 20° N and 10° S latitudes. The critical frequency values have decreased in the experimental data and have increased in the theoretical data when going from 30 to 45 longitudes.

  12. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

    PubMed

    Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

    2008-06-14

    Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

  13. NOTE: How accurate is a CT-based dose calculation on a pencil beam TPS for a patient with a metallic prosthesis?

    NASA Astrophysics Data System (ADS)

    Roberts, Ralph

    2001-09-01

    The accuracy of a CT-based dose calculation on a treatment planning system (TPS) for a radiotherapy patient with a metallic prosthesis has not previously been reported. In this study, the accuracy of the CT-based inhomogeneity correction on a pencil beam TPS (Helax TMS) was determined in a phantom containing a metallic prosthesis. A steel prosthesis phantom and a titanium prosthesis phantom were investigated. The phantoms were CT-scanned and dose plans produced on the TPS, using the CT images to provide density information for the inhomogeneity corrections. Verification measurements were performed on a linear accelerator for 6 and 15 MV x-rays. Measured dose profiles at three different depths were compared to the calculations of the TPS. For the titanium prosthesis and for 6 MV x-rays, the TPS overestimated the beam attenuation by approximately 20% at 15 and 20 cm depths in the phantom. This is due to a limitation in the density allocation of this TPS: any Hounsfield number (HN) above a certain threshold is allocated the density of steel. For the steel prosthesis, the TPS performed the correct mapping of HN to mass density. The dose calculation was within 6% for 6 MV x-rays at 15 and 20 cm depths. However, the accuracy of dose calculation varied with beam energy and depth, with large errors in the region close to the prosthesis. The TPS overestimated the dose by 11% for 6 MV and 15% for 15 MV x-rays at 11 cm depth, 2.5 cm beyond the steel prosthesis. These results highlight the limitations in the density allocation of this TPS and demonstrate shortcomings in the pencil beam dose calculation.

  14. Theoretical study on flueggenines A and B: A comparison of calculated spectroscopic properties with IR, UV and ECD experimental data

    NASA Astrophysics Data System (ADS)

    Zhou, Chang-Xin; Mo, Jian-Xia; Wang, Xue-Yao; Zhang, Jian; Gan, Li-She

    2011-03-01

    Using DFT at the B3LYP/6-31+G (d) level, DFT-D at the wb97xd/tzvpp level and TD-DFT at the B3LYP/aug-cc-pVDZ level, computational analysis of the first examples of naturally occurring dimeric indolizidine alkaloids, flueggenines A and B, accomplished the simulation and interpretation of their IR, UV and ECD spectra. Compared with the experimental ones, the calculated IR and UV spectra allowed the reinforcement of the carbon skeletons and functional groups. Calculation of the ECD spectra assured the formerly assigned absolute configurations for flueggenines A and B.

  15. Explicitly correlated benchmark calculations on C8H8 isomer energy separations: how accurate are DFT, double-hybrid, and composite ab initio procedures?

    NASA Astrophysics Data System (ADS)

    Karton, Amir; Martin, Jan M. L.

    2012-10-01

    Accurate isomerization energies are obtained for a set of 45 C8H8 isomers by means of the high-level, ab initio W1-F12 thermochemical protocol. The 45 isomers involve a range of hydrocarbon functional groups, including (linear and cyclic) polyacetylene, polyyne, and cumulene moieties, as well as aromatic, anti-aromatic, and highly-strained rings. Performance of a variety of DFT functionals for the isomerization energies is evaluated. This proves to be a challenging test: only six of the 56 tested functionals attain root mean square deviations (RMSDs) below 3 kcal mol-1 (the performance of MP2), namely: 2.9 (B972-D), 2.8 (PW6B95), 2.7 (B3PW91-D), 2.2 (PWPB95-D3), 2.1 (ωB97X-D), and 1.2 (DSD-PBEP86) kcal mol-1. Isomers involving highly-strained fused rings or long cumulenic chains provide a 'torture test' for most functionals. Finally, we evaluate the performance of composite procedures (e.g. G4, G4(MP2), CBS-QB3, and CBS-APNO), as well as that of standard ab initio procedures (e.g. MP2, SCS-MP2, MP4, CCSD, and SCS-CCSD). Both connected triples and post-MP4 singles and doubles are important for accurate results. SCS-MP2 actually outperforms MP4(SDQ) for this problem, while SCS-MP3 yields similar performance as CCSD and slightly bests MP4. All the tested empirical composite procedures show excellent performance with RMSDs below 1 kcal mol-1.

  16. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    1991-11-15

    The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.

  17. Theoretical calculation of bulk properties of ionic crystals from the cluster approach: Application to NaF

    SciTech Connect

    Recio, J.M.; Luana, V.; Pueyo, L. ); Bermejo, M. )

    1990-11-01

    The Theory of Electronic Separability is applied to the calculation of the ground state total energy and related bulk properties of simple ionic crystals. The work is based on a general equation of this theory that gives the total energy of the crystal in terms of additive energies of conjugate clusters. The properties of the NaF crystal analyzed in this work include equilibrium geometry, cohesive energy, elastic constants, and external pressure effects on these quantities.

  18. X-ray structures of the anticoagulants coumatetralyl and chlorophacinone. Theoretical calculations and SAR investigations on thirteen anticoagulant rodenticides

    NASA Astrophysics Data System (ADS)

    Dolmella, A.; Gatto, S.; Girardi, E.; Bandoli, G.

    1999-12-01

    Coumatetralyl and chlorophacinone, two substances related to 4-hydroxycoumarin (HC) and to 1,3-indandione (ID), respectively, show activity as anticoagulant rodenticides. In the present study we have investigated the solid-state structures of coumatetralyl and chlorophacinone by means of X-ray single-crystal and powder diffraction, along with thermal analysis. The crystal structures of the two compounds have been used as input geometries for a series of computational chemistry efforts, involving other anticoagulant derivatives as well. Thus, ab initio, semiempirical molecular orbital, molecular mechanics and molecular dynamics/simulated annealing calculations have been performed on thirteen anticoagulant rodenticides. In particular, the annealing calculations have been made to assess the conformational freedom of the compounds under scrutiny. All the generated conformers have been classified into families. The classification has first been made empirically, and then validated by means of a cluster analysis. A number of structural and physico-chemical parameters derived from the calculations has been used in turn for structure-activity relationships (SARs) investigations. In the latter, we have assessed how the selected parameters affect toxicity. The results seem to be consistent with a three-dimensional biophore model, in which higher toxicity is predicted for the more voluminous rodenticides. We suggest that these compounds better fit the active site of the target enzyme vitamin K 2,3-epoxide reductase (KO-reductase).

  19. Singularity of proton transport in salts of orthoperiodic and orthotellurium acids: theoretical modeling using density functional calculations.

    PubMed

    Zyubina, Tatiana S; Shilov, Gennady V; Dobrovolsky, Yury A; Leonova, Ludmila S; Mebel, Alexander M

    2004-07-21

    Density functional B3LYP calculations have been performed to investigate proton transport in orthoperiodic and orthotellurium acids, their salts MIO(6)H(4)(M = Li, Rb, Cs) and CsH(5)TeO(6), dimers of the salt*acid type MIO(6)H(4)*H(5)IO(6)(M = Rb, Cs), CsIO(6)H(4)*H(6)TeO(6), CsHSO(4)*H(6)TeO(6), Cs(2)SO(4)*H(6)TeO(6), and also in double-substituted and binary salts Rb(2)H(3)IO(6) and Rb(4)H(2)I(2)O(10). It has been shown that the energy of salt dimerization is 33-35 kcal mol(-1) and the activation barrier for proton migration between the neighboring octahedrons of the salt*acid --> acid*salt type is calculated to be 3-13 kcal mol(-1). The activation energy of the proton migration along the octahedron, 20-30 kcal mol(-1), is comparable with the barrier for water molecule separation. Quantum-chemical calculations correlate with the results of X-ray and electrochemical studies.

  20. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.

  1. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol. PMID:19603962

  2. Full-dimensional quantum calculations of vibrational levels of NH4+ and isotopomers on an accurate ab initio potential energy surface

    DOE PAGES

    Hua -Gen Yu; Han, Huixian; Guo, Hua

    2016-03-29

    Vibrational energy levels of the ammonium cation (NH4+) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4+ and ND4+ exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.

  3. Full-Dimensional Quantum Calculations of Vibrational Levels of NH4(+) and Isotopomers on An Accurate Ab Initio Potential Energy Surface.

    PubMed

    Yu, Hua-Gen; Han, Huixian; Guo, Hua

    2016-04-14

    Vibrational energy levels of the ammonium cation (NH4(+)) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4(+) and ND4(+) exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm(-1).

  4. Vibrational spectra, theoretical calculations, and two-dimensional potential energy surface for the ring-puckering vibrations of 2,4,7-trioxa[3.3.0]octane.

    PubMed

    Chun, Hye Jin; Meinander, Niklas; Villarreal, John R; Laane, Jaan

    2015-01-15

    2,4,7-Trioxa[3.3.0]octane (247TOO) is an unusual bicyclic molecule which can exist in four different conformational forms which are determined by the directions of the two ring- puckering motions. The vibrational assignments of 247TOO have been made based on its infrared and Raman spectra and theoretical density functional theory (DFT) calculations. The two ring-puckering motions (in-phase and out-of-phase) were observed in the Raman spectra of the liquid at 249 and 205 cm(-1) and these values correspond well to the DFT values of 247 and 198 cm(-1). Ab initio calculations were utilized to calculate the structures and conformational energies for the four energy minima and the barriers to interconversion and the data was utilized to generate a two-dimensional potential energy surface (PES) for the two ring-puckering motions. The resulting quantum state energies for this PES were then calculated in order to better understand the patterns that are produced when the PES has four energy minima at different energy values. The wave functions corresponding to the different quantum states were also calculated. The NMR spectrum of 247TOO showed the presence of the two lowest energy conformations, consistent with the results of the ab initio calculations. PMID:25514365

  5. Vibrational spectra, theoretical calculations, and two-dimensional potential energy surface for the ring-puckering vibrations of 2,4,7-trioxa[3.3.0]octane.

    PubMed

    Chun, Hye Jin; Meinander, Niklas; Villarreal, John R; Laane, Jaan

    2015-01-15

    2,4,7-Trioxa[3.3.0]octane (247TOO) is an unusual bicyclic molecule which can exist in four different conformational forms which are determined by the directions of the two ring- puckering motions. The vibrational assignments of 247TOO have been made based on its infrared and Raman spectra and theoretical density functional theory (DFT) calculations. The two ring-puckering motions (in-phase and out-of-phase) were observed in the Raman spectra of the liquid at 249 and 205 cm(-1) and these values correspond well to the DFT values of 247 and 198 cm(-1). Ab initio calculations were utilized to calculate the structures and conformational energies for the four energy minima and the barriers to interconversion and the data was utilized to generate a two-dimensional potential energy surface (PES) for the two ring-puckering motions. The resulting quantum state energies for this PES were then calculated in order to better understand the patterns that are produced when the PES has four energy minima at different energy values. The wave functions corresponding to the different quantum states were also calculated. The NMR spectrum of 247TOO showed the presence of the two lowest energy conformations, consistent with the results of the ab initio calculations.

  6. Theoretical calculations of stability constants and pKa values of metal complexes in solution: application to pyridoxamine-copper(II) complexes and their biological implications in AGE inhibition.

    PubMed

    Casasnovas, Rodrigo; Ortega-Castro, Joaquín; Donoso, Josefa; Frau, Juan; Muñoz, Francisco

    2013-10-14

    Accurate prediction of thermodynamic constants of chemical reactions in solution is one of the current challenges in computational chemistry. We report a scheme for predicting stability constants (log β) and pKa values of metal complexes in solution by means of calculating free energies of ligand- and proton-exchange reactions using Density Functional Theory calculations in combination with a continuum solvent model. The accuracy of the predicted log β and pKa values (mean absolute deviations of 1.4 and 0.2 units respectively) is equivalent to the experimental uncertainties. This theoretical methodology provides direct knowledge of log β and pKa values of major and minor species, so it is of potential use in combination with experimental techniques to obtain a detailed description of the microscopic equilibria. In particular, the proposed methodology is shown to be especially useful for obtaining the real acidity constants of those chelates where the metal-ligand coordination changes as a result of ligand deprotonation. The stability and acidity constants of pyridoxamine-Cu(2+) chelates calculated with the proposed methodology show that pyridoxamine is an efficient scavenging agent of Cu(2+) under physiological pH conditions. This is of special interest as Cu(2+) overload is involved in the formation of advanced glycation end-products (AGEs) and their associated degenerative medical conditions. PMID:23999915

  7. A Initio Calculations Performed on Carbon Monoxide Adsorption on the IRON(100) Surface and Complementing Theoretical Techniques

    NASA Astrophysics Data System (ADS)

    Meehan, Timothy Erickson

    1992-01-01

    Unrestricted Hartree-Fock calculations were performed on Fe_{x}CO clusters to model the CO(alpha_1), CO(alpha_2), and CO( alpha_3) adsorptions on the Fe(100) surface. Clusters of FeCO(C_{4v}) and a multiplicity of 5, Fe_2 CO(C_{2v}) and a multiplicity of 7, and Fe_2CO(C _{s}) and a multiplicity of 7, were constructed to model, respectively, the adsorption for the on top site, bridging site, and tilted CO structure at the 4-fold site. The CO position was optimized with respect to the Fe bulk distances using gradient techniques and the partial geometry optimization. CO stretching frequencies were calculated for each optimized geometry, and we find no evidence supporting CO adsorption in the bridging site. Using a full basis set the calculated CO stretching frequencies for the FeCO(C_{4v}), Fe_2CO(C_ {2v}), and the Fe_2 CO(C_{s}) clusters are 1992, 1767, and 771 cm^{ -1}, respectively. The CSOV analysis was executed to analyze the major orbital interactions between the CO and Fe_{x} clusters. For both Fe_2CO clusters, the CO pi^* perpendicular to the Fe _2 axis had a more significant contribution involving the pi backdonation from the Fe_2 clusters. Furthermore, the spin minority d electrons are mainly responsible for the pi backdonation. Due to problems with SCF convergence incurred during the Fe_{x}CO studies, we were forced to investigate a number of different techniques to achieve SCF convergence. Therefore, techniques that generate starting guesses of the eigenvectors for the SCF procedure and techniques used to accelerate SCF convergence are reviewed. The standard guesses of H _{core} and charge build -up are examined, and we introduce a new incremental cluster method for generating starting guesses for large clusters. The standard techniques of extrapolation, DIIS, damping, level shifting, restrict, and symmetry blocking are examined, and we also developed the hacker method and partial geometry optimization as new techniques to achieve SCF convergence. Results

  8. Application of vibrational spectroscopy supported by theoretical calculations in identification of amorphous and crystalline forms of cefuroxime axetil.

    PubMed

    Talaczyńska, Alicja; Lewandowska, Kornelia; Jelińska, Anna; Garbacki, Piotr; Podborska, Agnieszka; Zalewski, Przemysław; Oszczapowicz, Irena; Sikora, Adam; Kozak, Maciej; Cielecka-Piontek, Judyta

    2015-01-01

    FT-IR and Raman scattering spectra of cefuroxime axetil were proposed for identification studies of its crystalline and amorphous forms. An analysis of experimental spectra was supported by quantum-chemical calculations performed with the use of B3LYP functional and 6-31G(d,p) as a basis set. The geometric structure of a cefuroxime axetil molecule, HOMO and LUMO orbitals, and molecular electrostatic potential were also determined by using DFT (density functional theory). The benefits of applying FT-IR and Raman scattering spectroscopy for characterization of drug subjected to degradation were discussed.

  9. A Modular Class of Fluorescent Difluoroboranes: Synthesis, Structure, Optical Properties, Theoretical Calculations and Applications for Biological Imaging.

    PubMed

    Bachollet, Sylvestre P J T; Volz, Daniel; Fiser, Béla; Münch, Stephan; Rönicke, Franziska; Carrillo, Jokin; Adams, Harry; Schepers, Ute; Gómez-Bengoa, Enrique; Bräse, Stefan; Harrity, Joseph P A

    2016-08-22

    Ten borylated bipyridines (BOBIPYs) have been synthesized and selected structural modifications have been made that allow useful structure-optical property relationships to be gathered. These systems have been further investigated using DFT calculations and spectroscopic measurements, showing blue to green fluorescence with quantum yields up to 41 %. They allow full mapping of the structure to determine where selected functionalities can be implemented, to tune the optical properties or to incorporate linking groups. The best derivative was thus functionalised with an alkyne linker, which would enable further applications through click chemistry and in this optic, the stability of the fluorophores has been evaluated. PMID:27465819

  10. Theoretical calculations of rotationally inelastic collisions of He with NaK(A {sup 1}Σ{sup +}): Transfer of population, orientation, and alignment

    SciTech Connect

    Malenda, R. F.; Price, T. J.; Stevens, J.; Uppalapati, S. L.; Fragale, A.; Weiser, P. M.; Kuczala, A.; Hickman, A. P.; Talbi, D.

    2015-06-14

    We have performed extensive calculations to investigate thermal energy, rotationally inelastic collisions of NaK (A{sup 1}Σ{sup +}) with He. We determined a potential energy surface using a multi-reference configuration interaction wave function as implemented by the GAMESS electronic structure code, and we have performed coupled channel scattering calculations using the Arthurs and Dalgarno formalism. We also calculate the Grawert coefficients B{sub λ}(j, j′) for each j → j′ transition. These coefficients are used to determine the probability that orientation and alignment are preserved in collisions taking place in a cell environment. The calculations include all rotational levels with j or j′ between 0 and 50, and total (translational and rotational) energies in the range 0.0002–0.0025 a.u. (∼44–550 cm{sup −1}). The calculated cross sections for transitions with even values of Δj tend to be larger than those for transitions with odd Δj, in agreement with the recent experiments of Wolfe et al. (J. Chem. Phys. 134, 174301 (2011)). The calculations of the energy dependence of the cross sections and the calculations of the fraction of orientation and alignment preserved in collisions also exhibit distinctly different behaviors for odd and even values of Δj. The calculations also indicate that the average fraction of orientation or alignment preserved in a transition becomes larger as j increases. We interpret this behavior using the semiclassical model of Derouard, which also leads to a simple way of visualizing the distribution of the angles between the initial and final angular momentum vectors j and j′. Finally, we compare the exact quantum results for j → j′ transitions with results based on the simpler, energy sudden approximation. That approximation is shown to be quite accurate.

  11. Accurate spectroscopic calculations of the 17 Λ-S and 59 Ω states of the AsP molecule including the spin-orbit coupling effect

    NASA Astrophysics Data System (ADS)

    Shi, Deheng; Liu, Qionglan; Wang, Shuai; Sun, Jinfeng; Zhu, Zunlue

    2015-01-01

    The potential energy curves (PECs) of 59 Ω states generated from the 17 Λ-S states (X1Σ+, a3Σ+, 15Σ+, b3Δ, c3Π, 15Π, 25Σ+, 23Δ, 23Π, 33Σ+, A1Π, 23Σ+, 35Σ+, 17Σ+, 15Δ, 25Δ, and 25Π) of AsP molecule are studied for the first time for internuclear separations from about 0.10 to 1.10 nm. All the Λ-S states are contributed to the first three dissociation channels of AsP molecule except for the A1Π. The 23Σ+, 35Σ+, 17Σ+, 15Δ, 25Δ, and 25Π are found to be the repulsive states. The a3Σ+, 15Π, b3Δ, 17Σ+, 15Δ, 25Δ, and 25Π are found to be the inverted states. Each of the 33Σ+, c3Π, 23Π, 15Π, and 15Σ+ states has one potential barrier. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with Davidson correction. Core-valence correlation and scalar relativistic corrections are included. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling effect is accounted for. All these PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated for the bound states involved, and are compared with available measurements. Excellent agreement has been found between the present results and the measurements. It shows that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters is not obvious for all the Λ-S bound states except for few ones such as 15Σ+ and c3Π.

  12. Theoretical calculation of the dehydrogenation of ethanol on a Rh/CeO2(111) surface.

    PubMed

    Chen, Hui-Lung; Liu, Shih-Hung; Ho, Jia-Jen

    2006-08-01

    We applied periodic density-functional theory (DFT) to investigate the dehydrogenation of ethanol on a Rh/CeO2 (111) surface. Ethanol is calculated to have the greatest energy of adsorption when the oxygen atom of the molecule is adsorbed onto a Ce atom in the surface, relative to other surface atoms (Rh or O). Before forming a six-membered ring of an oxametallacyclic compound (Rh-CH2CH2O-Ce(a)), two hydrogen atoms from ethanol are first eliminated; the barriers for dissociation of the O-H and the beta-carbon (CH2-H) hydrogens are calculated to be 12.00 and 28.57 kcal/mol, respectively. The dehydrogenated H atom has the greatest adsorption energy (E(ads) = 101.59 kcal/mol) when it is adsorbed onto an oxygen atom of the surface. The dehydrogenation continues with the loss of two hydrogens from the alpha-carbon, forming an intermediate species Rh-CH2CO-Ce(a), for which the successive barriers are 34.26 and 40.84 kcal/mol. Scission of the C-C bond occurs at this stage with a dissociation barrier Ea = 49.54 kcal/mol, to form Rh-CH(2(a)) + 4H(a) + CO(g). At high temperatures, these adsorbates desorb to yield the final products CH(4(g)), H(2(g)), and CO(g). PMID:16869591

  13. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations.

    PubMed

    Mishra, Sandeep Kumar; Suryaprakash, N

    2015-06-21

    The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

  14. Thermodynamic properties and solidification kinetics of intermetallic Ni7Zr2 alloy investigated by electrostatic levitation technique and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Li, L. H.; Hu, L.; Yang, S. J.; Wang, W. L.; Wei, B.

    2016-01-01

    The thermodynamic properties, including the density, volume expansion coefficient, ratio of specific heat to emissivity of intermetallic Ni7Zr2 alloy, have been measured using the non-contact electrostatic levitation technique. These properties vary linearly with temperature at solid and liquid states, even down to the obtained maximum undercooling of 317 K. The enthalpy, glass transition, diffusion coefficient, shear viscosity, and surface tension were obtained by using molecular dynamics simulations. Ni7Zr2 has a relatively poor glass forming ability, and the glass transition temperature is determined as 1026 K. The inter-diffusivity of Ni7Zr2 alloy fitted by Vogel-Fulcher-Tammann law yields a fragility parameter of 8.49, which indicates the fragile nature of this alloy. Due to the competition of increased thermodynamic driving force and decreased atomic diffusion, the dendrite growth velocity of Ni7Zr2 compound exhibits double-exponential relationship to the undercooling. The maximum growth velocity is predicted to be 0.45 m s-1 at the undercooling of 335 K. Theoretical analysis reveals that the dendrite growth is a diffusion-controlled process and the atomic diffusion speed is only 2.0 m s-1.

  15. Theoretical calculation of the stress-strain behavior of dual-phase metals with randomly oriented spheroidal inclusions

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, A.; Weng, G. J.

    1996-08-01

    A simple model is developed to determine the overall response of dual-phase metals with an inclusion/matrix microgeometry. The inclusions are taken to be spheroidal in shape and are randomly oriented and homogeneously dispersed in the matrix. No restriction is placed on whether the inclusions are harder or softer (in the sense of flow stress) than the matrix, and as with most dual-phase metals, both phases are capable of undergoing plastic flow. The yielding process of the inclusions is now orientation dependent and sequential, and the overall elastoplastic response of the two-phase system is found to be strongly dependent upon the inclusion shape and concentration, even more so than on the corresponding elastic behavior. Disc-shaped inclusions generally give a superior reinforcing effect when the matrix is the softer phase, whereas spherical inclusions are more effective when the matrix is the harder one. As compared to the condition when the inclusions are strictly elastic, the plasticity of inclusions is found to translate into noticeable reduction in the flow stress of the composite. Comparison of the theoretical prediction with the experimental data for a ferrite/austenite system further shows a reasonable agreement.

  16. The molecular recognition of β-cyclodextrin modified CdSe quantum dots with tyrosine enantiomers: Theoretical calculation and experimental study

    NASA Astrophysics Data System (ADS)

    Cao, Yujuan; Wu, Shuangshuang; Liang, Yaozhen; Yu, Ying

    2013-01-01

    In the present work, the molecular recognition of mono-(6-mercapto)-β-cyclodextrin modified CdSe quantum dots (β-CD/CdSe QDs) with tyrosine enantiomers were investigated with theoretical calculation and fluorescence spectroscopy. The inclusion processes and the most probable structures of the inclusion complexes were simulated using PM3 energy scanning and optimization method. The trends of stability of the two inclusion complexes deduced from their calculated stabilization energies were studied. Moreover, the fluorescence spectra of β-CD/CdSe QDs in the presence of tyrosine enantiomers as well as the effect of ionic strength on the complexation of β-CD/CdSe QDs-tyrosine were discussed. The experimental results indicated that the β-CD/CdSe QDs have better enantioselectivity to L-tyrosine than that to D-tyrosine, and good linearity between the fluorescence intensity of β-CD/CdSe QDs and L-tyrosine over the concentration range from 0.10 × 10-4 mol/L to 4.00 × 10-4 mol/L with relative coefficient of 0.9909 was obtained. The experimental data agrees well with that obtained from theoretical calculation, indicating that β-cyclodextrin modified CdSe quantum dots contained good inclusion capability and fluorescence property, it has good potential application in the field of biological diagnosis, analysis, etc.

  17. Interaction of curcumin with Al(III) and its complex structures based on experiments and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Jiang, Teng; Wang, Long; Zhang, Sui; Sun, Ping-Chuan; Ding, Chuan-Fan; Chu, Yan-Qiu; Zhou, Ping

    2011-10-01

    Curcumin has been recognized as a potential natural drug to treat the Alzheimer's disease (AD) by chelating baleful metal ions, scavenging radicals and preventing the amyloid β (Aβ) peptides from the aggregation. In this paper, Al(III)-curcumin complexes with Al(III) were synthesized and characterized by liquid-state 1H, 13C and 27Al nuclear magnetic resonance (NMR), mass spectroscopy (MS), ultraviolet spectroscopy (UV) and generalized 2D UV-UV correlation spectroscopy. In addition, the density functional theory (DFT)-based UV and chemical shift calculations were also performed to view insight into the structures and properties of curcumin and its complexes. It was revealed that curcumin could interact strongly with Al(III) ion, and form three types of complexes under different molar ratios of [Al(III)]/[curcumin], which would restrain the interaction of Al(III) with the Aβ peptide, reducing the toxicity effect of Al(III) on the peptide.

  18. Feature Article: Thermodynamic properties from ab-initio calculations: New theoretical developments, and applications to various materials systems

    NASA Astrophysics Data System (ADS)

    Fähnle, Manfred; Drautz, Ralf; Lechermann, Frank; Singer, Reinhard; Diaz-Ortiz, Alejandro; Dosch, Helmut

    2005-05-01

    The cover picture from the Feature Article [1] depicts the calculated landscape of lowest formation energies for the ternary compound system Ni-Fe-Al. The figure shows for each composition the difference in the formation energy (in meV/atom) for the respective homogeneous configuration with lowest energy on the bcc and the fcc parent lattice. The phases on the fcc lattice dominate the Ni- and Al-rich regions of the Gibbs triangle.The first author Manfred Fähnle is Professor at the University of Stuttgart and member of the theory group of the department of Prof. Schütz at the Max-Planck-Institut für Metallforschung in Stuttgart. In 1980 he was awarded with the Otto-Hahn medal of the Max-Planck Society and in 1985 he received the Academy Award for Physics of the University of Göttingen. His present research interests are the static and dynamic properties of bulk and nanostructured magnetic systems, as well as the ab-initio statistical mechanics of alloys.

  19. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine--its vibrational spectra and theoretical calculations.

    PubMed

    Marchewka, M K; Drozd, M; Janczak, J

    2011-08-15

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2(1)/c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H···O hydrogen bonds with O···O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H···O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double CC bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  20. Synthesis, molecular structure, theoretical calculation, DNA/protein interaction and cytotoxic activity of manganese(III) complex with 8-hydroxyquinoline.

    PubMed

    Thamilarasan, V; Sengottuvelan, N; Sudha, A; Srinivasan, P; Siva, A

    2015-01-01

    Manganese(III) complex (1) [Mn(8-hq)3] (where 8-hq=8-hydroxyquinoline) has been synthesized and characterized by elemental, spectral (UV-vis, FT-IR) and thermal analysis. The structure of complex (1) has been determined by single crystal X-ray diffraction studies and the configuration around manganese(III) ion was elongated octahedral coordination geometry. Density functional theory calculations were performed for ligand and its complex. Binding studies of ligand and complex 1 with calf thymus DNA (CT-DNA) was investigated by absorption, fluorescence, circular dichroic (CD) spectroscopy and viscosity measurements. Absorption spectral studies revealed that ligand and complex 1 binds to DNA groove and its intrinsic binding strength has been found to be 2.57×10(4) and 2.91×10(4)M(-1). A molecular docking study confirm that the complex 1 is a minor groove binder and was stabilized through hydrogen bonding interactions. Complex 1 exhibits a good binding propensity to bovine serum albumin (BSA) protein. The in vitro cytotoxicity study of complex 1 on breast cancer cell line (MCF-7) indicate that it has the potential to act as effective anticancer drug, with IC50 values of 3.25μM. The ligand and its complex have been screened for antimicrobial activities and the complex showed better antimicrobial activity than the free ligand.

  1. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Marchewka, M. K.; Drozd, M.; Janczak, J.

    2011-08-01

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  2. Theoretical calculations and experimental verification for the pumping effect caused by the dynamic micro-tapered angle

    NASA Astrophysics Data System (ADS)

    Cai, Yufei; Zhang, Jianhui; Zhu, Chunling; Huang, Jun; Jiang, Feng

    2016-05-01

    The atomizer with micro cone apertures has advantages of ultra-fine atomized droplets, low power consumption and low temperature rise. The current research of this kind of atomizer mainly focuses on the performance and its application while there is less research of the principle of the atomization. Under the analysis of the dispenser and its micro-tapered aperture's deformation, the volume changes during the deformation and vibration of the micro-tapered aperture on the dispenser are calculated by coordinate transformation. Based on the characters of the flow resistance in a cone aperture, it is found that the dynamic cone angle results from periodical changes of the volume of the micro-tapered aperture of the atomizer and this change drives one-way flows. Besides, an experimental atomization platform is established to measure the atomization rates with different resonance frequencies of the cone aperture atomizer. The atomization performances of cone aperture and straight aperture atomizers are also measured. The experimental results show the existence of the pumping effect of the dynamic tapered angle. This effect is usually observed in industries that require low dispersion and micro- and nanoscale grain sizes, such as during production of high-pressure nozzles and inhalation therapy. Strategies to minimize the pumping effect of the dynamic cone angle or improve future designs are important concerns. This research proposes that dynamic micro-tapered angle is an important cause of atomization of the atomizer with micro cone apertures.

  3. PCM/TD-DFT analysis of 1-bromo-2,3-dichlorobenzene - A combined study of experimental (FT-IR and FT-Raman) and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Arivazhagan, M.; Muniappan, P.; Meenakshi, R.; Rajavel, G.

    2013-03-01

    This study represents an integral approach towards understanding the electronic and structural aspects of 1-bromo-2,3-dichlorobenzene (BDCB). The experimental spectral bands were structurally assigned with the theoretical calculation, and the thermodynamic properties of the studied compound were obtained from the theoretically calculated frequencies. The relationship between the structure and absorption spectrum and effects of solvents have been discussed. It turns that the hybrid PBE1PBE functional with 6-311+G(d,p) basis provide reliable λmax when solvent effects are included in the model. The NBO analysis reveals that the studied compound presents a structural characteristic of electron-transfer within the compound. The frontier molecular orbitals (HOMO-LUMO) are responsible for the electron polarization and electron-transfer properties. The reactivity sites are identified by mapping the electron density into electrostatic potential surface (MESP). Besides, 13C and 1H have been calculated using the gauge-invariant atomic orbital (GIAO) method. The thermodynamic properties at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. Furthermore, the studied compound can be used as a good nonlinear optical material due to the higher value of first hyper polarizability (5.7 times greater than that of urea (0.37289 × 10-30 esu)). Finally, it is worth to mentioning that solvent induces a considerable red shift of the absorption maximum going from the gas phase, and a slight blue shift of the transition S0 → S1 going from less polar to more polar solvents.

  4. Screening nitrogen-rich bases and oxygen-rich acids by theoretical calculations for forming highly stable salts.

    PubMed

    Zhang, Xueli; Gong, Xuedong

    2014-08-01

    Nitrogen-rich heterocyclic bases and oxygen-rich acids react to produce energetic salts with potential application in the field of composite explosives and propellants. In this study, 12 salts formed by the reaction of the bases 4-amino-1,2,4-trizole (A), 1-amino-1,2,4-trizole (B), and 5-aminotetrazole (C), upon reaction with the acids HNO3 (I), HN(NO2 )2 (II), HClO4 (III), and HC(NO2 )3 (IV), are studied using DFT calculations at the B97-D/6-311++G** level of theory. For the reactions with the same base, those of HClO4 are the most exothermic and spontaneous, and the most negative Δr Gm in the formation reaction also corresponds to the highest decomposition temperature of the resulting salt. The ability of anions and cations to form hydrogen bonds decreases in the order NO3 (-) >N(NO2 )2 (-) >ClO4 (-) >C(NO2 )3 (-) , and C(+) >B(+) >A(+) . In particular, those different cation abilities are mainly due to their different conformations and charge distributions. For the salts with the same anion, the larger total hydrogen-bond energy (EH,tot ) leads to a higher melting point. The order of cations and anions on charge transfer (q), second-order perturbation energy (E2 ), and binding energy (Eb ) are the same to that of EH,tot , so larger q leads to larger E2 , Eb , and EH,tot . All salts have similar frontier orbitals distributions, and their HOMO and LUMO are derived from the anion and the cation, respectively. The molecular orbital shapes are kept as the ions form a salt. To produce energetic salts, 5-aminotetrazole and HClO4 are the preferred base and acid, respectively.

  5. Theoretical Calculations and Simulations of Interaction of X-Rays with High-Z Nanomoities for Use in Cancer Radiotherapy

    NASA Astrophysics Data System (ADS)

    Lim, Sara N.; Pradhan, Anil K.; Nahar, Sultana N.

    2013-06-01

    When used with X-ray radiotherapy, heavy elements (high atomic number Z or HZ) such as gold(Au) and platinum(Pt) have the potential to greatly sensitize and enhance the damage to tumor tissues. While HZ radiosensitization has been shown to be higly effective in reducing tumor sizes, much work still needs to be done to determine the ideal X-ray energy/energy spectrum. The likelihood of photoelectric absorption of X-rays that result in the production of cell-killing Auger electrons relative to the photon scatter in an HZ sensitized tumor has to be determined for treatments using X-rays from various sources and energies to assess their efficacy. In this report, we present computations that outline the dependence of photoelectric absorption on X-ray energy. The relative X-ray absorption by a radiosensitized tumor was calculated to contrast the efficacy of different X-ray sources in Auger electron production at different tumor depths. Enhanced photoabsorption of low-energy X-rays from broadband sources in the keV range is shown to be much higher than from those in the MeV range. In addition, with the use of the Monte Carlo code package Geant4, we present the total X-ray energy deposited into a radiosensitized tumor located at different depths in a phantom. The enhancement in radiation dose deposition will also be analysed at the microscopic cellular level to determine the HZ radiosensitizer concentration required. Potential use of monochromatic X-rays for more precise HZ radiosensitization will also be described.

  6. Infrared and Raman spectra, theoretical calculations, conformations, and two-dimensional potential energy surface of 2-cyclopenten-1-one ethylene ketal.

    PubMed

    Sheu, Hong-Li; Meinander, Niklas; Laane, Jaan

    2015-03-01

    The infrared and Raman spectra of the bicyclic spiro molecule 2-cyclopenten-1-one ethylene ketal (CEK) have been recorded. Density functional theory (DFT) calculations were used to compute the theoretical spectra, and these agree well with the experimental spectra. The structures and conformational energies for the two pairs of conformational minima, which can be defined in terms of ring-bending (x) and ring-twisting (τ) vibrational coordinates, have also been calculated. Utilizing the results from ab initio MP2/cc-PVTZ computations, a two-dimensional potential energy surface (PES) was calculated. The energy levels and wave functions for this PES were then calculated, and the characteristics of these were analyzed. At lower energies, all of the quantum states are doubly degenerate and correspond to either the lower-energy conformation L or to conformation H, which is 154 cm(-1) higher in energy. At energies above the barrier to interconversion of 264 cm(-1), the wave functions show that the quantum levels have significant probabilities for both conformations. PMID:25133325

  7. Interaction of O2 with CH4, CF4, and CCl4 by Molecular Beam Scattering Experiments and Theoretical Calculations.

    PubMed

    Cappelletti, David; Aquilanti, Vincenzo; Bartocci, Alessio; Nunzi, Francesca; Tarantelli, Francesco; Belpassi, Leonardo; Pirani, Fernando

    2016-07-14

    Gas phase collisions of O2 by CH4, CF4, and CCl4 have been investigated with the molecular beam technique by measuring both the integral cross section value, Q, and its dependence on the collision velocity, v. The adopted experimental conditions have been appropriate to resolve the oscillating "glory" pattern, a quantum interference effect controlled by the features of the intermolecular interaction, for all the three case studies. The analysis of the Q(v) data, performed by adopting a suitable representation of the intermolecular potential function, provided the basic features of the anisotropic potential energy surfaces at intermediate and large separation distances and information on the relative role of the physically relevant types of contributions to the global interaction. The present work demonstrates that while O2-CH4 and O2-CF4 are basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreaciable intermolecular bond stabilization by charge transfer is operative in O2-CCl4. Ab initio calculations of the strength of the interaction, coupled with detailed analysis of electronic charge displacement promoted by the formation of the dimer, fully rationalizes the experimental findings. This investigation indicates that the interactions of O2, when averaged over its relative orientations, are similar to that of a noble gas (Ng), specifically Ar. We also show that the binding energy in the basic configurations of the prototypical Ng-CF4,CCl4 systems [ Cappelletti , D. ; Chem. Eur. J. 2015 , 21 , 6234 - 6240 ] can be reconstructed by using the interactions in Ng-F and Ng-Cl systems, previously characterized by molecular beam scattering experiments of state-selected halogen atom beams. This information is fundamental to approach the modeling of the weak intermolecular halogen bond. On the basis of the electronic polarizability, this also confirms [ Aquilanti , V. ; Angew. Chem., Int. Ed. 2005 , 44 , 2356 - 2360 ] that O2

  8. A pH dependent Raman and surface enhanced Raman spectroscopic studies of citrazinic acid aided by theoretical calculations

    NASA Astrophysics Data System (ADS)

    Sarkar, Sougata; Chowdhury, Joydeep; Dutta, Soumen; Pal, Tarasankar

    2016-12-01

    calculations for these prescribed model systems were also carried out to have a plausible understanding of their equilibrium geometries and the vibrational wavenumbers. An idea about the molecular orientation of the adsorbate over nanocolloidal gold substrate is also documented.

  9. A pH dependent Raman and surface enhanced Raman spectroscopic studies of citrazinic acid aided by theoretical calculations.

    PubMed

    Sarkar, Sougata; Chowdhury, Joydeep; Dutta, Soumen; Pal, Tarasankar

    2016-12-01

    A pH dependent normal Raman scattering (NRS) and surface enhanced Raman scattering (SERS) spectral patterns of citrazinic acid (CZA), a biologically important molecule, have been investigated. The acid, with different pKa values (~4 and ~11) for the two different functional groups (-COOH and -OH groups), shows interesting range of color changes (yellow at pH~14 and brown at pH~2) with the variation in solution pH. Thus, depending upon the pH of the medium, CZA molecule can exist in various protonated and/or deprotonated forms. Here we have prescribed the existence different possible forms of CZA at different pH (Forms "C", "H" and "Dprot" at pH~14 and Forms "A", "D", and "P" at pH~2 respectively). The NRS spectra of these solutions and their respective SERS spectra over gold nanoparticles were recorded. The spectra clearly differ in their spectral profiles. For example the SERS spectra recorded with the CZA solution at pH~2 shows blue shift for different bands compared to its NRS window e.g. 406 to 450cm(-1), 616 to 632cm(-1), 1332 to 1343cm(-1) etc. Again, the most enhanced peak at ~1548cm(-1) in NRS while in the SERS window this appears at ~1580cm(-1). Similar observation was also made for CZA at pH~14. For example, the 423cm(-1) band in the NRS profile experience a blue shift and appears at ~447cm(-1) in the SERS spectrum as well as other bands at ~850, ~1067 and ~1214cm(-1) in the SERS window are markedly enhanced. It is also worth noting that the SERS spectra at the different pH also differ from each other. These spectral differences indicate the existence of various adsorptive forms of the CZA molecule depending upon the pH of the solution. Therefore based on the experimental findings we propose different possible molecular forms of CZA at different pH (acidic and alkaline) conditions. For example forms 'A', 'D' and 'P' existing in acidic pH (pH~2) and three other deprotonated forms 'C', 'H' and 'Dprot' in alkaline pH (pH~14). The DFT calculations for these

  10. Ion-molecule reactions involving HCO+ and N2H+: Isotopologue equilibria from new theoretical calculations and consequences for interstellar isotope fractionation

    NASA Astrophysics Data System (ADS)

    Mladenović, M.; Roueff, E.

    2014-06-01

    Aims: We revisit with new augmented accuracy the theoretical dynamics of basic isotope exchange reactions involved in the 12C/13C, 16O/18O, and 14N/15N balance because these reactions have already been studied experimentally in great detail. Methods: Electronic structure methods were employed to explore potential energy surfaces, full-dimensional rovibrational calculations to compute rovibrational energy levels that are numerically exact, and chemical network models to estimate the abundance ratios under interstellar conditions. Results: New exothermicities, derived for HCO+ reacting with CO, provide rate coefficients markedly different from previous theoretical values in particular at low temperatures, resulting in new abundance ratios relevant for carbon chemistry networks. In concrete terms, we obtain a reduction in the abundance of H12C18O+ and an increase in the abundance of H13C16O+ and D13C16O+. In all studied cases, the reaction of the ion with a neutral polarizable molecule proceeds through the intermediate proton-bound complex found to be very stable. For the complexes OCH+··· CO, OCH+··· OC, COHOC+, N2··· HCO+, N2H+··· OC, and N2HN2+, we also calculated vibrational frequencies and dissociation energies. Conclusions: The linear proton-bound complexes possess sizeable dipole moments, which may facilitate their detection.

  11. An Atomistic-Scale Study for Thermal Conductivity and Thermochemical Compatibility in (DyY)Zr2O7 Combining an Experimental Approach with Theoretical Calculation

    NASA Astrophysics Data System (ADS)

    Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard

    2016-02-01

    Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy3+ and Y3+on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke’s model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases.

  12. An Atomistic-Scale Study for Thermal Conductivity and Thermochemical Compatibility in (DyY)Zr2O7 Combining an Experimental Approach with Theoretical Calculation.

    PubMed

    Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard

    2016-01-01

    Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy(3+) and Y(3+)on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke's model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases. PMID:26888438

  13. An Atomistic-Scale Study for Thermal Conductivity and Thermochemical Compatibility in (DyY)Zr2O7 Combining an Experimental Approach with Theoretical Calculation

    PubMed Central

    Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard

    2016-01-01

    Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy3+ and Y3+on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke’s model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases. PMID:26888438

  14. Theoretical calculation of the OH vibrational overtone spectra of 1-n alkane diols (n = 2-4): origin of disappearing hydrogen-bonded OH peak.

    PubMed

    Cheng, Yu-Lung; Chen, Hui-Yi; Takahashi, Kaito

    2011-06-01

    In this theoretical study, we simulated the vibrational overtone spectrum of ethylene glycol (EG), 1-3 propanediol (PD), and 1-4 butanediol (BD). Using the local mode model along with the potential energy curve and dipole moment function calculated by B3LYP/6-31+G(d,p) and QCISD/6-311++G(3df,3pd), we obtained the theoretical peak position and integrated absorption coefficient. Furthermore, the vibrational spectra was simulated using a Voigt function using homogeneous and inhomogenous width obtained from quantum chemical calculation methods. Previously, Howard and Kjaergaard recorded the second and third overtone photoacoustic spectra of the three aforementioned alkane diols in the gas phase and observed that the intramolecular hydrogen bonded OH peak becomes difficult to observe as the intramolecular hydrogen bonding strength increased, that is, as the chain length was increased. In this paper we show that the disappearance of the hydrogen-bonded OH peak for the OH stretching overtone excitation for BD is partly due to the increase in homogeneous width due to the increase in the hydrogen bond strength and partly due to the decrease in the relative population of the intramolecular hydrogen-bonded conformers as the chain length is increased. This latter feature is a consequence of the unfavorable strained geometry needed to form the intramolecular hydrogen bond in longer alkane chains. PMID:21568300

  15. An Atomistic-Scale Study for Thermal Conductivity and Thermochemical Compatibility in (DyY)Zr2O7 Combining an Experimental Approach with Theoretical Calculation.

    PubMed

    Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard

    2016-02-18

    Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy(3+) and Y(3+)on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke's model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases.

  16. Calculation of Temperature Rise in Calorimetry.

    ERIC Educational Resources Information Center

    Canagaratna, Sebastian G.; Witt, Jerry

    1988-01-01

    Gives a simple but fuller account of the basis for accurately calculating temperature rise in calorimetry. Points out some misconceptions regarding these calculations. Describes two basic methods, the extrapolation to zero time and the equal area method. Discusses the theoretical basis of each and their underlying assumptions. (CW)

  17. Prediction of {sup 2}D Rydberg energy levels of {sup 6}Li and {sup 7}Li based on very accurate quantum mechanical calculations performed with explicitly correlated Gaussian functions

    SciTech Connect

    Bubin, Sergiy; Sharkey, Keeper L.; Adamowicz, Ludwik

    2013-04-28

    Very accurate variational nonrelativistic finite-nuclear-mass calculations employing all-electron explicitly correlated Gaussian basis functions are carried out for six Rydberg {sup 2}D states (1s{sup 2}nd, n= 6, Horizontal-Ellipsis , 11) of the {sup 7}Li and {sup 6}Li isotopes. The exponential parameters of the Gaussian functions are optimized using the variational method with the aid of the analytical energy gradient determined with respect to these parameters. The experimental results for the lower states (n= 3, Horizontal-Ellipsis , 6) and the calculated results for the higher states (n= 7, Horizontal-Ellipsis , 11) fitted with quantum-defect-like formulas are used to predict the energies of {sup 2}D 1s{sup 2}nd states for {sup 7}Li and {sup 6}Li with n up to 30.

  18. SU-E-J-100: The Combination of Deformable Image Registration and Regions-Of-Interest Mapping Technique to Accomplish Accurate Dose Calculation On Cone Beam Computed Tomography for Esophageal Cancer

    SciTech Connect

    Huang, B-T; Lu, J-Y

    2015-06-15

    Purpose: We introduce a new method combined with the deformable image registration (DIR) and regions-of-interest mapping (ROIM) technique to accurately calculate dose on daily CBCT for esophageal cancer. Methods: Patients suffered from esophageal cancer were enrolled in the study. Prescription was set to 66 Gy/30 F and 54 Gy/30 F to the primary tumor (PTV66) and subclinical disease (PTV54) . Planning CT (pCT) were segmented into 8 substructures in terms of their differences in physical density, such as gross target volume (GTV), venae cava superior (SVC), aorta, heart, spinal cord, lung, muscle and bones. The pCT and its substructures were transferred to the MIM software to readout their mean HU values. Afterwards, a deformable planning CT to daily KV-CBCT image registration method was then utilized to acquire a new structure set on CBCT. The newly generated structures on CBCT were then transferred back to the treatment planning system (TPS) and its HU information were overridden manually with mean HU values obtained from pCT. Finally, the treatment plan was projected onto the CBCT images with the same beam arrangements and monitor units (MUs) to accomplish dose calculation. Planning target volume (PTV) and organs at risk (OARs) from both of the pCT and CBCT were compared to evaluate the dose calculation accuracy. Results: It was found that the dose distribution in the CBCT showed little differences compared to the pCT, regardless of whether PTV or OARs were concerned. Specifically, dose variation in GTV, PTV54, PTV66, SVC, lung and heart were within 0.1%. The maximum dose variation was presented in the spinal cord, which was up to 2.7% dose difference. Conclusion: The proposed method combined with DIR and ROIM technique to accurately calculate dose distribution on CBCT for esophageal cancer is feasible.

  19. Structures of Plutonium(IV) and Uranium(VI) with N,N-Dialkyl Amides from Crystallography, X-ray Absorption Spectra, and Theoretical Calculations.

    PubMed

    Acher, Eléonor; Hacene Cherkaski, Yanis; Dumas, Thomas; Tamain, Christelle; Guillaumont, Dominique; Boubals, Nathalie; Javierre, Guilhem; Hennig, Christoph; Solari, Pier Lorenzo; Charbonnel, Marie-Christine

    2016-06-01

    The structures of plutonium(IV) and uranium(VI) ions with a series of N,N-dialkyl amides ligands with linear and branched alkyl chains were elucidated from single-crystal X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS), and theoretical calculations. In the field of nuclear fuel reprocessing, N,N-dialkyl amides are alternative organic ligands to achieve the separation of uranium(VI) and plutonium(IV) from highly concentrated nitric acid solution. EXAFS analysis combined with XRD shows that the coordination structure of U(VI) is identical in the solution and in the solid state and is independent of the alkyl chain: two amide ligands and four bidentate nitrate ions coordinate the uranyl ion. With linear alkyl chain amides, Pu(IV) also adopt identical structures in the solid state and in solution with two amides and four bidentate nitrate ions. With branched alkyl chain amides, the coordination structure of Pu(IV) was more difficult to establish unambiguously from EXAFS. Density functional theory (DFT) calculations were consequently performed on a series of structures with different coordination modes. Structural parameters and Debye-Waller factors derived from the DFT calculations were used to compute EXAFS spectra without using fitting parameters. By using this methodology, it was possible to show that the branched alkyl chain amides form partly outer-sphere complexes with protonated ligands hydrogen bonded to nitrate ions. PMID:27171842

  20. Measuring the absolute disintegration rate of a radioactive gas with a moveable endplate discharge counter (MEP) and theoretical calculation of wall effect

    SciTech Connect

    Jaffey, A.H.; Gray, J.; Bentley, W.C.; Lerner, J.L.

    1987-09-01

    A precision built moveable endplate Geiger-Mueller counter was used to measure the absolute disintegration rate of a beta-emitting radioactive gas. A Geiger-Mueller counter used for measuring gaseous radioactivity has <100% counting efficiency owing to two factors: (1) ''end effect,'' due to decreased and distorted fields at the ends where wire-insulator joints are placed, and (2) ''wall effect,'' due to non-ionization by beta particles emitted near to and heading into the wall. The end effect was evaluated by making one end of the counter movable and measuring counting rates at a number of endplate positions. Much of the wall effect was calculated theoretically, based on known data for primary ionization of electrons as a function of energy and gas composition. Corrections were then made for the ''shakeoff'' effect in beta decay and for backscattering of electrons from the counter wall. Measurements and calculations were made for a sample of /sup 85/Kr (beta energy, 0.67 MeV). The wall effect calculation is readily extendable to other beta energies.

  1. Interaction analysis of HIV-1 antibody 2G12 and Man9GlcNAc2 ligand: Theoretical calculations by fragment molecular orbital and MD methods

    NASA Astrophysics Data System (ADS)

    Koyama, Yuka; Ueno-Noto, Kaori; Takano, Keiko

    2013-07-01

    In HIV-1 infection, human antibody 2G12 is capable of recognizing the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. To investigate the ligand binding mechanisms of antibody 2G12 with glycans aiming for the contribution to the medications, we carried out classical molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the antibody 2G12 complex with its high-mannose ligand. We found that Mannose D1 of the ligand had the largest binding affinity with the antibody, which was well consistent with experimental reports. Furthermore, significant roles of Mannose 4 and 4‧ in the ligand binding were theoretically indicated.

  2. Theoretical oxidation state analysis of Ru-(bpy){sub 3}: Influence of water solvation and Hubbard correction in first-principles calculations

    SciTech Connect

    Reeves, Kyle G.; Kanai, Yosuke

    2014-07-14

    Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations.

  3. Theoretical oxidation state analysis of Ru-(bpy)3: Influence of water solvation and Hubbard correction in first-principles calculations

    NASA Astrophysics Data System (ADS)

    Reeves, Kyle G.; Kanai, Yosuke

    2014-07-01

    Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations.

  4. A critical evaluation of the s-cis-trans isomerism of 2-acetylpyrrole and its N-methyl derivative through infrared and NMR spectroscopies and theoretical calculations.

    PubMed

    Ducati, Lucas C; Braga, Carolyne B; Rittner, Roberto; Tormena, Cláudio F

    2013-12-01

    Literature data are controversial regarding the conformational equilibria of 2-acetylpyrrole (AP) and its N-methyl derivative (AMP). Now, a detailed study through infrared spectroscopy and theoretical calculations has shown that previous data were erroneously interpreted, since only a N,O-cis conformer is present in solution and that it is the stable conformer in the isolated state (ΔE(trans-cis) = 5.05 kcal mol(-1), for AP; ΔE(trans-cis) = 7.14 kcal mol(-1), for AMP). Carbonyl and NH absorption data in different solvents, supported by theoretical results taking into account the solvent effects [at IEFPCM-B3LYP/6-311++G(3df,3p) level of theory] clearly demonstrated that only the N,O-cis conformer is present in solution. However, a doublet was observed for AP, in CCl4, which can be attributed to this conformer and the lowest wavenumber component to the cis dimer form, stabilized through intermolecular hydrogen bonds (NH · · · OC). The overall preference for the N,O-cis conformer, in AP and AMP, as interpreted by the NBO analysis, indicated that the hyperconjugative effect is the main contribution to stabilize this rotamer, overcoming the possible steric repulsion. (13)C NMR experiments at low temperature in two different solvents (CS2/CDCl2 and acetone-d6) confirmed the occurrence of a single conformer since no separated signals were observed.

  5. Comparison between angular dependent NEXAFS analysis and theoretical calculations of molecular orientation of new functional mixed aromatic molecules deposited onto Au/Si(1 1 1)

    NASA Astrophysics Data System (ADS)

    Battocchio, C.; Polzonetti, G.; Gambino, L.; Tuccitto, N.; Licciardello, A.; Marletta, G.

    2006-05-01

    Self-assembled mixed component aromatic layers on gold, prepared from solutions of 4'(4-mercaptophenyl)-2,2':6',2″-terpyridine (MPTP) and mercaptobenzene (MB), have been investigated by means of angular dependent NEXAFS spectroscopy at the C K-edge and N K-edge. For such a system, angular dependent NEXAFS data analysis provides information on the molecular arrangement in excellent agreement with theoretical calculations. The presence of mercaptobenzene molecule forces the terpyridine-containing molecule to an organized molecular arrangement. Analysis of the angular dependence of a few selected resonances of both the C K-edge and N K-edge spectra, i.e. the π ∗ C dbnd C, the π ∗ C dbnd N and the π ∗ N-C, for the mixed layer (MPTP/MB) and for the terpyridine (MPTP), allowed to establish that in the mixed conditions the three external pyridine rings are arranged in a geometry in which they stand up respect to the Au surface and they are nearly coplanar to each other, in a completely similar fashion to the MPTP sample itself. The presence of MB in the mixed system induces a tilting up of the phenyl ring of MPTP, as evidenced by the calculations, but seems to leave virtually unaffected the arrangement of the three external pyridine rings.

  6. Fluorescence excitation and ultraviolet absorption spectra and theoretical calculations for benzocyclobutane: Vibrations and structure of its excited S{sub 1}(π,π{sup *}) electronic state

    SciTech Connect

    Shin, Hee Won; Ocola, Esther J.; Laane, Jaan; Kim, Sunghwan

    2014-01-21

    The fluorescence excitation spectra of jet-cooled benzocyclobutane have been recorded and together with its ultraviolet absorption spectra have been used to assign the vibrational frequencies for this molecule in its S{sub 1}(π,π{sup *}) electronic excited state. Theoretical calculations at the CASSCF(6,6)/aug-cc-pVTZ level of theory were carried out to compute the structure of the molecule in its excited state. The calculated structure was compared to that of the molecule in its electronic ground state as well as to the structures of related molecules in their S{sub 0} and S{sub 1}(π,π{sup *}) electronic states. In each case the decreased π bonding in the electronic excited states results in longer carbon-carbon bonds in the benzene ring. The skeletal vibrational frequencies in the electronic excited state were readily assigned and these were compared to the ground state and to the frequencies of five similar molecules. The vibrational levels in both S{sub 0} and S{sub 1}(π,π{sup *}) states were remarkably harmonic in contrast to the other bicyclic molecules. The decreases in the frequencies of the out-of-plane skeletal modes reflect the increased floppiness of these bicyclic molecules in their S{sub 1}(π,π{sup *}) excited state.

  7. A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis.

    PubMed

    Astani, Elahe K; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L

    2016-07-01

    A theoretical study at the level of density functional theory (DFT) was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond interactions, in the active site of enzyme human androsterone sulphotransferase (SULT2A1/ADT). Geometry optimization, interaction energy, (2)H, (14)N, and (17)O electric field gradient (EFG) tensors, (1)H, (13)C, (17)O, and (15)N chemical shielding (CS) tensors, Natural Bonding Orbital (NBO) analysis, and quantum theory of atoms in molecules (QTAIM) analysis of this active site were investigated. It was found that androsterone (ADT) is able to form hydrogen bonds with residues Ser80, Ile82, and His99 of the active site. The interaction energy calculations and NBO analysis revealed that the ADT molecule forms the strongest hydrogen bond with Ser80. Results revealed that ADT interacts with the other residues through electrostatic and Van der Waals interactions. Results showed that these hydrogen bonds influence on the calculated (2)H, (14)N, and (17)O quadrupole coupling constants (QCCs), as well as (1)H, (13)C, (17)O, and (15)N CS tensors. The magnitude of the QCC and CS changes at each nucleus depends directly on its amount of contribution to the hydrogen bond interaction. PMID:27337388

  8. Determination by ultraviolet absorption spectrometry and theoretical calculation of dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one.

    PubMed

    Zhang, Shufang; Zhang, Xiaoyan; Tang, Ke; Zhou, Zhengyu

    2009-08-15

    The dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one was determined by ultraviolet absorption spectrometry method based on the absorption spectra of 1,2,3,9-tetrahydro-4H-carbazol-4-one at different pH in ethanol-water mixed solvents. The results show that the pK(b) was a good linear function of the volume fraction of ethanol in the concentration range studied. The dissociation constant of 1, 2, 3,9-tetrahydro-4H-carbazol-4-one in water were determined by extrapolation to be 14.04 under the condition of this experiment. The accurate pK(b) calculations of 1,2,3,9-tetrahydro-4H-carbazol-4-one have been investigated using the combination of the extended clusters-continuum model with the polarizable continuum solvation model (PCM). The calculations are performed at the B3LYP/6-31G levels. The formation of molecular clusters by means of the 1,2,3,9-tetrahydro-4H-carbazol-4-one wrapped up with water molecules leads to the weakness of the interaction between the polar solvents and the 1,2,3,9-tetrahydro-4H-carbazol-4-one, hence, the accuracy of pK(b) has been enhanced. The dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one in water were calculated to be 14.10 and agreed well with experimental data.

  9. PREFACE: Proceedings of the First International Workshop on the Theoretical Calculation of ELNES and XANES (TEX2008) (Nagoya, Japan, 2-4 July 2008) Proceedings of the First International Workshop on the Theoretical Calculation of ELNES and XANES (TEX2008) (Nagoya, Japan, 2-4 July 2008)

    NASA Astrophysics Data System (ADS)

    Tanaka, Isao; Mizoguchi, Teruyasu; Yamamoto, Tomoyuki

    2009-03-01

    Both electron energy loss near edge structure (ELNES) spectroscopy and x-ray absorption near edge structure (XANES) spectroscopy provide information on the local structural and chemical environments of selected elements of interest. Recent technological progress in scanning transmission electron microscopy has enabled ELNES measurements with atomic column spatial resolution. Very dilute concentrations (nanograms per milliliter or ppb level) of dopants can be observed using third-generation synchrotron facilities when x-ray fluorescence is measured with highly efficient detectors. With such technical developments, ELNES and XANES have become established as essential tools in a large number of fields of natural science, including condensed matter physics, chemistry, mineralogy and materials science. In addition to these developments in experimental methodology, notable progress in reproducing spectra using theoretical methods has recently been made. Using first-principles methods, one can analyze and interpret spectra without reference to experiment. This is quite important since we are often interested in the analysis of exotic materials or specific atoms located at lattice discontinuities such as surfaces and interfaces, where appropriate experimental data are difficult to obtain. Using the structures predicted by reliable first-principles calculations, one can calculate theoretical ELNES and XANES spectra without too much difficulty even in such cases. Despite the fact that ELNES and XANES probe the same phenomenon—essentially the electric dipole transition from a core orbital to an unoccupied band—there have not been many opportunities for researchers in the two areas to meet and discuss. Theoretical calculations of ELNES spectra have been mainly confined to the electron microscopy community. On the other hand, the theory of XANES has been developed principally by researchers in the x-ray community. Publications describing the methods have been written more

  10. Studies on adsorption of mono- and multi-chromophoric hemicyanine dyes on silver nanoparticles by surface-enhanced resonance raman and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Biswas, Nandita; Thomas, Susy; Kapoor, Sudhir; Mishra, Amaresh; Wategaonkar, Sanjay; Mukherjee, Tulsi

    2008-11-01

    Structural and vibrational properties of mono- and multichromophoric hemicyanine (HC) dyes in solution and adsorbed on silver-coated films have been investigated using optical absorption and resonance Raman scattering techniques, with interpretations aided by theoretical calculations. This is the first report on the Raman spectroscopic studies of multichromophoric HC derivatives. The structure of the monomer, N-propyl-4-(p-N,N-dimethylamino styryl)pyridinium bromide (HC3), and its charged and neutral silver complexes (HC3-Ag) in the ground electronic (S0) state were optimized using density functional calculations with the B3LYP method using the 6-31G* and LANL2DZ basis sets. The ground state structure of N-hexyl-4-(p-N,N-dimethylamino styryl)pyridinium bromide (HC6) and multichromophoric HC dyes were computed using the HF /6-31G* method. The negligible shift or broadening observed in the electronic absorption and resonance Raman spectra in solution with increasing size of the HC chromophore suggests that the excitations are localized within individual monomer units in bis and tetra chromophores. However, in the tris chromophore, considerable redshift and broadening were observed, indicating a significant electronic interaction between the nonbonded electrons of the N atom and the aromatic π-system that is supported by the calculated excitation energies using the time-dependent density functional theory method. The effect of HC dye concentration on the electronic absorption spectra of the silver-coated film showed significant broadening, which was attributed to the formation of H- and J-aggregates in addition to the formation of a metal-molecule complex. A considerable redshift along various vibrations observed in the surface-enhanced resonance Raman scattering (SERRS) spectra of the HC derivatives indicates that adsorption on the silver surface leads to a considerable interaction of the electron rich moiety of HC derivatives with the silver surface. The

  11. Theoretical Modeling of the Chirality Discrimination of Enantiomers by Nanotubular Cyclic Peptides using Gas-Phase Photoelectron Spectroscopy: An ONIOM Spectroscopic Calculations.

    PubMed

    Farrokhpour, H; Karachi, S; Chermahini, A Najafi

    2016-09-01

    In the present work, the chirality recognition of the enantiomers of a chiral molecule (1-phenyl-1-propanol) interacting with a nanotubular cyclic peptide (E-type cyclic decapeptide) was investigated by their ionization in the gas phase, theoretically. The absolute energy difference between the interaction of the S- and R-enantiomer with the cyclic peptide, calculated at the M06-2X/6-311++G(d, p) level of theory, was 4.70 kcal·mol(-1). Two different schemes of "Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)" method such as (quantum mechanics (QM):molecular mechanics (MM)) and (QM:QM) were employed to study the effect of the interaction on the gas-phase ionization energies of the enantiomers and cyclic peptide, separately. The symmetry-adapted cluster/configuration interaction (SAC-CI) methodology was used for the calculation of the ionization energies. It was found that the difference between the interactions of R- and S-enantiomer with the cyclic peptide caused different changes in the photoelectron spectrum of each enantiomer so that these changes could be used for the chirality discrimination of the enantiomers in the gas phase. Similarly, the photoelectron spectrum of the cyclic peptide interacting with the R and S-enantiomer were calculated, separately, and it was observed that the difference in the interaction with the R- and S-enantiomer created different changes in the spectrum of cyclic peptide. Finally, it was shown that the difference in the interaction of cyclic peptide with the enantiomers of a chiral molecule in the gas phase can be used for the identification of enantiomers in the gas phase by the direct ionization. PMID:27500312

  12. Accurate calculation of the absolute free energy of binding for drug molecules† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02678d Click here for additional data file.

    PubMed Central

    Aldeghi, Matteo; Heifetz, Alexander; Bodkin, Michael J.; Knapp, Stefan

    2016-01-01

    Accurate prediction of binding affinities has been a central goal of computational chemistry for decades, yet remains elusive. Despite good progress, the required accuracy for use in a drug-discovery context has not been consistently achieved for drug-like molecules. Here, we perform absolute free energy calculations based on a thermodynamic cycle for a set of diverse inhibitors binding to bromodomain-containing protein 4 (BRD4) and demonstrate that a mean absolute error of 0.6 kcal mol–1 can be achieved. We also show a similar level of accuracy (1.0 kcal mol–1) can be achieved in pseudo prospective approach. Bromodomains are epigenetic mark readers that recognize acetylation motifs and regulate gene transcription, and are currently being investigated as therapeutic targets for cancer and inflammation. The unprecedented accuracy offers the exciting prospect that the binding free energy of drug-like compounds can be predicted for pharmacologically relevant targets. PMID:26798447

  13. Photo-deactivation pathways of a double H-bonded photochromic Schiff base investigated by combined theoretical calculations and experimental time-resolved studies.

    PubMed

    Randino, Carlos; Ziółek, Marcin; Gelabert, Ricard; Organero, Juan Angel; Gil, Michal; Moreno, Miquel; Lluch, José M; Douhal, Abderrazzak

    2011-09-01

    The photophysics of N,N'-bis(salicylidene)-p-phenylenediamine (BSP) is analyzed both theoretically and experimentally. The alternative intramolecular proton-transfer reactions lead to three different tautomers. We performed DFT and TDDFT calculations to analyze the topography of the reactions connecting the three tautomers. Deactivation paths through a Conical Intersection (CI) region are also analyzed to explain the low fluorescence quantum yield of the phototautomers. The complex molecular structure of BSP provides a large number of deactivation paths, almost all of them energetically available following the initial photoexcitation. Femtosecond (fs) time-resolved emission studies in solution and flash photolysis experiments (nano to millisecond regime) were performed to get detailed information on the time domain of the full photocycle. The picture that emerges by combining theoretical and experimental results shows a very fast (less than 100 fs) photoinduced single proton transfer process leading to a phototautomer where a single proton has moved. This species may deactivate through a low-energy CI leading in about 20 ps to a rotameric form in the ground state that has a lifetime of several tens of microseconds in solution. This process competes with another deactivation path taking place prior to the proton-transfer reaction which involves a low-energy CI leading to a rotamer of the enol structure. In the flash photolysis studies, the rotamer of the enol structure was directly identified by the positive transient absorption band in the 250-260 nm and its lifetime in n-hexane (10 ms) is almost 3 orders of magnitude longer than the lifetime of the photochrome (around 40 μs). Our findings do not exclude a double proton transfer reaction in the excited enol form to give a tautomer in less than 100 fs during the first (impulsive) phase of the reaction which reverts back to the photoproducts of the simple proton transfer in 1-3 ps.

  14. Stontium-90 contamination in vegetation from radioactive waste seepage areas at ORNL, and theoretical calculations of /sup 90/Sr accumulation by deer

    SciTech Connect

    Garten, C.T. Jr.; Lomax, R.D.

    1987-06-01

    This report describes data obtained during a preliminary characterization of /sup 90/Sr levels in browse vegetation from the vicinity of seeps adjacent to ORNL solid waste storage areas (SWSA) where deer (Odocoileus virginianus) were suspected to accumulate /sup 90/Sr through the food chain. The highest strontium concentrations in plant samples were found at seeps associated with SWSA-5. Strontium-90 concentrations in honeysuckle and/or blackberry shoots from two seeps in SWSA-5 averaged 39 and 19 nCi/g dry weight (DW), respectively. The maximum concentration observed was 90 nCi/g DW. Strontium-90 concentrations in honeysuckle and blackberry shoots averaged 7.4 nCi/g DW in a study area south of SWSA-4, and averaged 1.0 nCi/g DW in fescue grass from a seepage area located on SWSA-4. A simple model (based on metabolic data for mule deer) has been used to describe the theoretical accumulation of /sup 90/Sr in bone of whitetail deer following ingestion of contaminated vegetation. These model calculations suggest that if 30 pCi /sup 90/Sr/g deer bone is to be the accepted screening level for retaining deer killed on the reservation, then 5-pCi /sup 90/Sr/g DW vegetation should be considered as a possible action level in making decisions about the need for remedial measures, because unrestricted access and full utilization of vegetation contaminated with <5 pCi/g DW results in calculated steady-state (maximum) /sup 90/Sr bone concentrations of <30 pCi/g in a 45-kg buck.

  15. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations.

    PubMed

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-01

    The vibrational and reorientational motions of NH3 ligands and ClO4(-) anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385cm(-1), associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR≈10(-12)-10(-13)s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5kJmol(-1), in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TC(c)=137.6K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6](2+) cation and ClO4(-) anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models. PMID:25459713

  16. Cadmium(II) and Copper(II) coordination polymers based on 5-(Pyrazinyl) tetrazolate ligand: Structure, photoluminescence, theoretical calculations and magnetism

    SciTech Connect

    Chen, Hui-Fen; Yang, Wen-Bin; Lin, Lang; Guo, Xiang-Guang; Dui, Xue-jing; Wu, Xiao-Yuan; Lu, Can-Zhong; Zhang, Cui-Juan

    2013-05-01

    Two μ₂-tetrazolyl bridged metal complexes, ([CdI(PTZ)(H₂O)]·H₂O)ₙ1 and ([Cu(PTZ)₂]·H₂O)ₙ2 (HPTZ=5-(pyrazinyl) tetrazolate), were hydrothermally synthesized and fully characterized by X-ray crystallography, elemental analyses and spectrum techniques. In 1, cadmium ions are bridged by tridentate μ₂-κ²N2,N5:κ¹N1 chelating PTZ⁻ ligand and halide linkers into an infinite 1D chain, while in 2 copper ions are connected by tridentate μ₂-κ²N7,N12:κ¹N8 and bidentate μ₂-κ¹N1:κ¹N2 chelating-bridging PTZ⁻ ligands to form a 1D castellated chain structure. Compound 1 displays phosphorescence with a lifetime of ~7.74 ms in the visible region, and the origin of the luminescent emission is primary assigned to the combination of ligand-centered emission, metal-to-ligand charge transfer and ligand-to-ligand charge transfer, which has been probed by the density of states (DOS) calculations. Magnetic measurement reveals that compound 2 displays an anti-ferromagnetic ordering. - Graphical abstract: Two new complexes based on 5-(pyrazinyl) tertrazolate, namely ([CdI(PTZ)(H2O)]·H2O)n and ([Cu(PTZ)2]·H2O)n have been synthesized and characterized. Compound 1 exhibits interesting green luminescence. Compound 2 displays an anti-ferromagnetic ordering. Highlights: • We report two novel 1D μ₂-tetrazolyl bridged Cd(II) and Cu(II) compounds. • The cadmium(II) compound exhibits a green luminescence. • Theoretical calculations were conducted to elucidate the green luminescence. • The Cu(II) compound exhibits an anti-ferromagnetic ordering.

  17. Calculation of broadband time histories of ground motion, Part II: Kinematic and dynamic modeling using theoretical Green's functions and comparison with the 1994 northridge earthquake

    USGS Publications Warehouse

    Hartzell, S.; Guatteri, Mariagiovanna; Mai, P.M.; Liu, P.-C.; Fisk, M. R.

    2005-01-01

    In the evolution of methods for calculating synthetic time histories of ground motion for postulated earthquakes, kinematic source models have dominated to date because of their ease of application. Dynamic models, however, which incorporate a physical relationship between important faulting parameters of stress drop, slip, rupture velocity, and rise time, are becoming more accessible. This article compares a class of kinematic models based on the summation of a fractal distribution of subevent sizes with a dynamic model based on the slip-weakening friction law. Kinematic modeling is done for the frequency band 0.2 to 10.0. Hz, dynamic models are calculated from 0.2 to 2.0. Hz. The strong motion data set for the 1994 Northridge earthquake is used to evaluate and compare the synthetic time histories. Source models are propagated to the far field by convolution with 1D and 3D theoretical Green’s functions. In addition, the kinematic model is used to evaluate the importance of propagation path effects: velocity structure, scattering, and nonlinearity. At present, the kinematic model gives a better broadband fit to the Northridge ground motion than the simple slip-weakening dynamic model. In general, the dynamic model overpredicts rise times and produces insufficient shorter-period energy. Within the context of the slip-weakening model, the Northridge ground motion requires a short slip-weakening distance, on the order of 0.15 m or less. A more complex dynamic model including rate weakening or one that allows shorter rise times near the hypocenter may fit the data better.

  18. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-01

    The vibrational and reorientational motions of NH3 ligands and ClO4- anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385 cm-1, associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR ≈ 10-12-10-13 s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5 kJ mol-1, in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TCc = 137.6 K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311 + G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6]2+ cation and ClO4- anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models.

  19. Detection of Structural Changes upon One-Electron Oxidation and Reduction of Stilbene Derivatives by Time-Resolved Resonance Raman Spectroscopy during Pulse Radiolysis and Theoretical Calculations.

    PubMed

    Fujitsuka, Mamoru; Cho, Dae Won; Choi, Jungkweon; Tojo, Sachiko; Majima, Tetsuro

    2015-07-01

    Stilbene (St) derivatives have been investigated for many years because of their interesting photochemical reactions such as cis-trans isomerization in the excited states and charged states and their relation to poly(p-phenylenevinylene)s. To clarify their charged state properties, structural information is indispensable. In the present study, radical cations and radical anions of St derivatives were investigated by radiation chemical methods. Absorption spectra of radical ion states were obtained by transient absorption measurements during pulse radiolysis; theoretical calculations that included the solvent effect afforded reasonable assignments. The variation in the peak position was explained by using HOMO and LUMO energy levels. Structural changes upon one-electron oxidation and reduction were detected by time-resolved resonance Raman measurements during pulse radiolysis. Significant downshifts were observed with the CC stretching mode of the ethylenic groups, indicative of the decrease in the bonding order. It was confirmed that the downshifts observed with reduction were larger than those with oxidation. On the other hand, the downshift caused by oxidation depends significantly on the electron-donating or electron-withdrawing nature of the substituents.

  20. Detection of Structural Changes upon One-Electron Oxidation and Reduction of Stilbene Derivatives by Time-Resolved Resonance Raman Spectroscopy during Pulse Radiolysis and Theoretical Calculations.

    PubMed

    Fujitsuka, Mamoru; Cho, Dae Won; Choi, Jungkweon; Tojo, Sachiko; Majima, Tetsuro

    2015-07-01

    Stilbene (St) derivatives have been investigated for many years because of their interesting photochemical reactions such as cis-trans isomerization in the excited states and charged states and their relation to poly(p-phenylenevinylene)s. To clarify their charged state properties, structural information is indispensable. In the present study, radical cations and radical anions of St derivatives were investigated by radiation chemical methods. Absorption spectra of radical ion states were obtained by transient absorption measurements during pulse radiolysis; theoretical calculations that included the solvent effect afforded reasonable assignments. The variation in the peak position was explained by using HOMO and LUMO energy levels. Structural changes upon one-electron oxidation and reduction were detected by time-resolved resonance Raman measurements during pulse radiolysis. Significant downshifts were observed with the CC stretching mode of the ethylenic groups, indicative of the decrease in the bonding order. It was confirmed that the downshifts observed with reduction were larger than those with oxidation. On the other hand, the downshift caused by oxidation depends significantly on the electron-donating or electron-withdrawing nature of the substituents. PMID:26052901

  1. New algorithms for field-theoretic block copolymer simulations: Progress on using adaptive-mesh refinement and sparse matrix solvers in SCFT calculations

    NASA Astrophysics Data System (ADS)

    Sides, Scott; Jamroz, Ben; Crockett, Robert; Pletzer, Alexander

    2012-02-01

    Self-consistent field theory (SCFT) for dense polymer melts has been highly successful in describing complex morphologies in block copolymers. Field-theoretic simulations such as these are able to access large length and time scales that are difficult or impossible for particle-based simulations such as molecular dynamics. The modified diffusion equations that arise as a consequence of the coarse-graining procedure in the SCF theory can be efficiently solved with a pseudo-spectral (PS) method that uses fast-Fourier transforms on uniform Cartesian grids. However, PS methods can be difficult to apply in many block copolymer SCFT simulations (eg. confinement, interface adsorption) in which small spatial regions might require finer resolution than most of the simulation grid. Progress on using new solver algorithms to address these problems will be presented. The Tech-X Chompst project aims at marrying the best of adaptive mesh refinement with linear matrix solver algorithms. The Tech-X code PolySwift++ is an SCFT simulation platform that leverages ongoing development in coupling Chombo, a package for solving PDEs via block-structured AMR calculations and embedded boundaries, with PETSc, a toolkit that includes a large assortment of sparse linear solvers.

  2. FROM THE HISTORY OF PHYSICS: How Gamow calculated the temperature of the background radiation or a few words about the fine art of theoretical physics

    NASA Astrophysics Data System (ADS)

    Chernin, Artur D.

    1994-08-01

    In a paper published in 1953, i.e., more than a decade before the observational discovery of the cosmic microwave background radiation, George Gamow predicted theoretically the temperature of this radiation. He estimated it to be 7 K, which is very close to the subsequently measured value of about 3 K. Gamow found the present temperature of the background radiation on the basis of general formulas of cosmological dynamics. This prediction was in no way related to primordial nucleosynthesis.This circumstance has and is still causing misunderstanding in those cases in which the authors have raised doubts about Gamow's results, although an actual error has never been demonstrated. A detailed analysis makes it possible to understand how Gamow's calculation is possible. The problem lies in the fact that Gamow makes a certain additional implicit assumption which allows him to dispense with information on nucleosynthesis. This assumption is discussed in the context of the state of cosmology in the period from the fifties to the seventies, and of the current status of this branch of science.

  3. 3D models of slow motions in the Earth's crust and upper mantle in the source zones of seismically active regions and their comparison with highly accurate observational data: II. Results of numerical calculations

    NASA Astrophysics Data System (ADS)

    Molodenskii, S. M.; Molodenskii, M. S.; Begitova, T. A.

    2016-09-01

    In the first part of the paper, a new method was developed for solving the inverse problem of coseismic and postseismic deformations in the real (imperfectly elastic, radially and horizontally heterogeneous, self-gravitating) Earth with hydrostatic initial stresses from highly accurate modern satellite data. The method is based on the decomposition of the sought parameters in the orthogonalized basis. The method was suggested for estimating the ambiguity of the solution of the inverse problem for coseismic and postseismic deformations. For obtaining this estimate, the orthogonal complement is constructed to the n-dimensional space spanned by the system of functional derivatives of the residuals in the system of n observed and model data on the coseismic and postseismic displacements at a variety of sites on the ground surface with small variations in the models. Below, we present the results of the numerical modeling of the elastic displacements of the ground surface, which were based on calculating Green's functions of the real Earth for the plane dislocation surface and different orientations of the displacement vector as described in part I of the paper. The calculations were conducted for the model of a horizontally homogeneous but radially heterogeneous selfgravitating Earth with hydrostatic initial stresses and the mantle rheology described by the Lomnitz logarithmic creep function according to (M. Molodenskii, 2014). We compare our results with the previous numerical calculations (Okado, 1985; 1992) for the simplest model of a perfectly elastic nongravitating homogeneous Earth. It is shown that with the source depths starting from the first hundreds of kilometers and with magnitudes of about 8.0 and higher, the discrepancies significantly exceed the errors of the observations and should therefore be taken into account. We present the examples of the numerical calculations of the creep function of the crust and upper mantle for the coseismic deformations. We

  4. Accurate benchmark calculation of the reaction barrier height for hydrogen abstraction by the hydroperoxyl radical from methane. Implications for C(n)H(2n+2) where n = 2 --> 4.

    PubMed

    Aguilera-Iparraguirre, Jorge; Curran, Henry J; Klopper, Wim; Simmie, John M

    2008-07-31

    The CH4 + HO2(*) reaction is studied by using explicitly correlated coupled-cluster theory with singles and doubles (CCSD-R12) in a large 19s14p8d6f4g3h basis (9s6p4d3f for H) to approach the basis-set limit at the coupled-cluster singles-doubles level. A correction for connected triple excitations is obtained from the conventional CCSD(T) coupled-cluster approach in the correlation-consistent quintuple-zeta basis (cc-pV5Z). The highly accurate results for the methane reaction are used to calibrate the calculations of the hydroperoxyl-radical hydrogen abstraction from other alkanes. For the alkanes C(n)H(2n+2) with n = 2 --> 4, the reactions are investigated at the CCSD(T) level in the correlation-consistent triple-zeta (cc-pVTZ) basis. The results are adjusted to the benchmark methane reaction and compared with those from other approaches that are commonly used in the field such as CBS-QB3, CBS-APNO, and density functional theory. Rate constants are computed in the framework of transition state theory, and the results are compared with previous values available. PMID:18610940

  5. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    PubMed

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  6. Accurate thermochemical properties for energetic materials applications. II. Heats of formation of imidazolium-, 1,2,4-triazolium-, and tetrazolium-based energetic salts from isodesmic and lattice energy calculations.

    PubMed

    Gutowski, Keith E; Rogers, Robin D; Dixon, David A

    2007-05-10

    A computational approach to the prediction of the heats of formation (DeltaH(f)degrees' s of solid-state energetic salts from electronic structure and volume-based thermodynamics (VBT) calculations is described. The method uses as its starting point reliable DeltaH(f)degrees' s for energetic precursor molecules and ions. The DeltaH(f)degrees' s of more complex energetics species such as substituted imidazole, 1,2,4-triazole, and tetrazole molecules and ions containing amino, azido, and nitro (including methyl) substituents are calculated using an isodesmic approach at the MP2/complete basis set level. On the basis of comparisons to experimental data for neutral analogues, this isodesmic approach is accurate to <3 kcal/mol for the predicted cation and anion DeltaH(f)degrees' s. The DeltaH(f)degrees' s of the energetic salts in the solid state are derived from lattice energy (U(L)) calculations using a VBT approach. Improved values for the alpha and beta parameters of 19.9 (kcal nm)/mol and 37.6 kcal/mol for the U(L) equation were obtained on the basis of comparisons to experimental U(L)' s for a series of 23 salts containing ammonium, alkylammonium, and hydrazinium cations. The total volumes are adjusted to account for differences between predicted and experimental total volumes due to different shapes of the ions (flat vs spherical). The predicted DeltaH(f)degrees' s of the energetic salts are estimated to have error bars of 6-7 kcal/mol, on the basis of comparisons to established experimental DeltaH(f)degrees' s of a subset of the salts studied. Energetic salts with the highest positive DeltaH(f)degrees' s are predicted for azido-containing cations, coupled with heterocyclic anions containing nitro substituents. The substitution of functional groups on carbon versus nitrogen atoms of the heterocyclic cations has interesting stabilization and destabilization effects, respectively.

  7. Theoretical Issues

    SciTech Connect

    Marc Vanderhaeghen

    2007-04-01

    The theoretical issues in the interpretation of the precision measurements of the nucleon-to-Delta transition by means of electromagnetic probes are highlighted. The results of these measurements are confronted with the state-of-the-art calculations based on chiral effective-field theories (EFT), lattice QCD, large-Nc relations, perturbative QCD, and QCD-inspired models. The link of the nucleon-to-Delta form factors to generalized parton distributions (GPDs) is also discussed.

  8. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  9. Synthesis, characterization and theoretical calculations of (1,2-diaminocyclohexane)(1,3-diaminopropane)gold(III) chloride complexes: in vitro cytotoxic evaluations against human cancer cell lines.

    PubMed

    Al-Jaroudi, Said S; Altaf, Muhammad; Al-Saadi, Abdulaziz A; Kawde, Abdel-Nasser; Altuwaijri, Saleh; Ahmad, Saeed; Isab, Anvarhusein A

    2015-10-01

    The gold(III) complexes of the type (1,2-diaminocyclohexane)(1,3-diaminopropane)gold(III) chloride, [(DACH)Au(pn)]Cl3, [where DACH = cis-, trans-1,2- and S,S-1,2-diaminocyclohexane and pn = 1,3-diaminopropane] have been synthesized and characterized using various spectroscopic and analytical techniques including elemental analysis, UV-Vis and FTIR spectroscopy; solution as well as solid-state NMR measurements. The solid-state (13)C NMR shows that 1,2-diaminocyclohexane (1,2-DACH) and 1,3-diaminopropane (pn) are strongly bound to the gold(III) center via N donor atoms. The stability of the mixed diamine ligand gold(III) was checked by UV-Vis spectroscopy and NMR measurements. The molecular structure of compound 1 (containing cis-1,2-DACH) was determined by X-ray diffraction analysis. The structure of 1 consists of [(cis-DACH)Au(pn)](3+) complex ion and chloride counter ions. Each gold atom in the complex ion adopts a distorted square-planar geometry. The structural details and relative stabilities of the four possible isomers of the complexes were also estimated at the B3LYP/LANL2DZ level of theoretical calculations. The computational study demonstrates that trans- conformations are slightly more stable than the cis- conformations. The antiproliferative effects and cytotoxic properties of the mixed ligand gold(III) complexes were evaluated in vitro on human gastric SGC7901 and prostate PC3 cancer cells using MTT assay. The antiproliferative study of the gold(III) complexes on PC3 and SGC7901 cells indicate that complex 3 (containing 1S,2S-(+)-1,2-(DACH)) is the most effective antiproliferative agent. The IC50 data reveal that the in vitro cytotoxicity of complex 3 against SGC7901 cancer cells manifested similar and very pronounced cytotoxic effects with respect to cisplatin. Moreover, the electrochemical behavior, and the interaction of complex 3 with two well-known model proteins, namely, hen egg white lysozyme and bovine serum albumin is also reported. PMID

  10. Synthesis, characterization and theoretical calculations of (1,2-diaminocyclohexane)(1,3-diaminopropane)gold(III) chloride complexes: in vitro cytotoxic evaluations against human cancer cell lines.

    PubMed

    Al-Jaroudi, Said S; Altaf, Muhammad; Al-Saadi, Abdulaziz A; Kawde, Abdel-Nasser; Altuwaijri, Saleh; Ahmad, Saeed; Isab, Anvarhusein A

    2015-10-01

    The gold(III) complexes of the type (1,2-diaminocyclohexane)(1,3-diaminopropane)gold(III) chloride, [(DACH)Au(pn)]Cl3, [where DACH = cis-, trans-1,2- and S,S-1,2-diaminocyclohexane and pn = 1,3-diaminopropane] have been synthesized and characterized using various spectroscopic and analytical techniques including elemental analysis, UV-Vis and FTIR spectroscopy; solution as well as solid-state NMR measurements. The solid-state (13)C NMR shows that 1,2-diaminocyclohexane (1,2-DACH) and 1,3-diaminopropane (pn) are strongly bound to the gold(III) center via N donor atoms. The stability of the mixed diamine ligand gold(III) was checked by UV-Vis spectroscopy and NMR measurements. The molecular structure of compound 1 (containing cis-1,2-DACH) was determined by X-ray diffraction analysis. The structure of 1 consists of [(cis-DACH)Au(pn)](3+) complex ion and chloride counter ions. Each gold atom in the complex ion adopts a distorted square-planar geometry. The structural details and relative stabilities of the four possible isomers of the complexes were also estimated at the B3LYP/LANL2DZ level of theoretical calculations. The computational study demonstrates that trans- conformations are slightly more stable than the cis- conformations. The antiproliferative effects and cytotoxic properties of the mixed ligand gold(III) complexes were evaluated in vitro on human gastric SGC7901 and prostate PC3 cancer cells using MTT assay. The antiproliferative study of the gold(III) complexes on PC3 and SGC7901 cells indicate that complex 3 (containing 1S,2S-(+)-1,2-(DACH)) is the most effective antiproliferative agent. The IC50 data reveal that the in vitro cytotoxicity of complex 3 against SGC7901 cancer cells manifested similar and very pronounced cytotoxic effects with respect to cisplatin. Moreover, the electrochemical behavior, and the interaction of complex 3 with two well-known model proteins, namely, hen egg white lysozyme and bovine serum albumin is also reported.

  11. Theoretical calculations of spin-Hamiltonian parameters for the square planer CuCl4 2 - cluster in Cs2ZrCl6 crystal

    NASA Astrophysics Data System (ADS)

    Liu, Gang; Mei, Yang; Zhang, Xin-Xin; Zheng, Wen-Chen

    2015-05-01

    The high-order perturbation formulas based on a two-mechanism model (where in addition to the contributions from the crystal-field (CF) mechanism in the usually-applied CF theory, those from the generally-neglected charge-transfer (CT) mechanism are also contained) are employed to calculate the spin-Hamiltonian parameters (g factors g//, g⊥ and the hyperfine structure constants A//, A⊥) of the square planar CuCl4 2 - clusters in Cs2ZrCl6 crystal. The needed CF energy levels in the calculations are obtained from the observed optical spectra. The calculated results show reasonable agreement with the experimented values. The negative sign of A// and positive sign of A⊥ are proposed from the calculations. The calculations also suggest that one should take account of the contributions due to both the CF and CT mechanisms for the exact and rational calculations of spin-Hamiltonian parameters of Cu2+-Cl- combination in crystals.

  12. Theoretical calculations of structural, electronic, and elastic properties of CdSe1‑x Te x : A first principles study

    NASA Astrophysics Data System (ADS)

    M, Shakil; Muhammad, Zafar; Shabbir, Ahmed; Muhammad Raza-ur-rehman, Hashmi; M, A. Choudhary; T, Iqbal

    2016-07-01

    The plane wave pseudo-potential method was used to investigate the structural, electronic, and elastic properties of CdSe1‑x Te x in the zinc blende phase. It is observed that the electronic properties are improved considerably by using LDA+U as compared to the LDA approach. The calculated lattice constants and bulk moduli are also comparable to the experimental results. The cohesive energies for pure CdSe and CdTe binary and their mixed alloys are calculated. The second-order elastic constants are also calculated by the Lagrangian theory of elasticity. The elastic properties show that the studied material has a ductile nature.

  13. Theoretical dissociation energies for ionic molecules

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

    1986-01-01

    Ab initio calculations at the self-consistent-field and singles plus doubles configuration-interaction level are used to determine accurate spectroscopic parameters for most of the alkali and alkaline-earth fluorides, chlorides, oxides, sulfides, hydroxides, and isocyanides. Numerical Hartree-Fock (NHF) calculations are performed on selected systems to ensure that the extended Slater basis sets employed for the diatomic systems are near the Hartree-Fock limit. Extended Gaussian basis sets of at least triple-zeta plus double polarization equality are employed for the triatomic system. With this model, correlation effects are relatively small, but invariably increase the theoretical dissociation energies. The importance of correlating the electrons on both the anion and the metal is discussed. The theoretical dissociation energies are critically compared with the literature to rule out disparate experimental values. Theoretical (sup 2)Pi - (sup 2)Sigma (sup +) energy separations are presented for the alkali oxides and sulfides.

  14. Synthesis, molecular structure and spectroscopic characterization of (E)-1-((2-hydroxynaphthalen-1-yl) methyleneamino)-5-(4-methoxybenzoyl)-4-(4-methoxyphenyl) pyrimidine-2(1H)-one with experimental techniques and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Ceylan, Ümit; Hacıyusufoğlu, Mehmet Emin; Yalçınc, Şerife Pınar; Sönmez, Mehmet; Aygün, Muhittin

    2016-04-01

    A new Schiff base compound, (E)-1-((2-hydroxynaphthalen-1-yl) methyleneamino)-5-(4-methoxybenzoyl)-4-(4-methoxyphenyl) pyrimidine-2(1H)-one, formula sum is given by C30H23N3O5, was synthesized and characterized by experimentally and theoretically. Optimized molecular structure was obtained using X-ray diffraction in the ground state. FT-IR, NMR and UV-Vis frequencies have been measured and compared with theoretically obtained data by using by DFT/B3LYP method with 6-31G(d) and 6-311++G(d,p) basis set. In addition, molecular electrostatic potential (MEP), dipole moments, NBO analysis, atomic charges, HOMO-LUMO and molecular electrostatic potential were computed. The calculated results show that the optimized geometry can well reproduce the crystal structure parameters, and the theoretical vibrational frequencies, 1H and 13C NMR chemical shifts show good agreement with experimental values.

  15. A New Method for Simultaneous Measurement of the Integrated Reflectivity of Crystals at Multiple Orders of Reflection and Comparison with New Theoretical Calculations

    SciTech Connect

    S.G. Lee; J.G. Bak; Y.S. Jung; M. Bitter; K.W. Hill; G. Hoelzer; O. Wehrhan; E. Foerster

    2003-04-09

    This paper describes a new method for the simultaneous measurement of the integrated reflectivity of a crystal for multiple orders of reflection at a predefined Bragg angle. The technique is demonstrated with a mica crystal for Bragg angles of 43{sup o}, 47{sup o}, and 50{sup o}. The measured integrated reflectivity for Bragg reflections up to the 24th order is compared with new theoretical predictions, which are also presented in this paper.

  16. Theoretical study of the formation of mercury (Hg2+) complexes in solution using an explicit solvation shell in implicit solvent calculations.

    PubMed

    Afaneh, Akef T; Schreckenbach, Georg; Wang, Feiyue

    2014-09-25

    The structures and harmonic vibrational frequencies of water clusters (H2O)n, n = 1-10, have been computed using the M06-L/, B3LYP/, and CAM-BLYP/cc-pVTZ levels of theories. On the basis of the literature and our results, we use three hexamer structures of the water molecules to calculate an estimated "experimental" average solvation free energy of [Hg(H2O)6](2+). Aqueous formation constants (log K) for Hg(2+) complexes, [Hg(L)m(H2O)n](2-mq), L = Cl(-), HO(-), HS(-), and S(2-), are calculated using a combination of experimental (solvation free energies of ligands and Hg(2+)) and calculated gas- and liquid-phase free energies. A combined approach has been used that involves attaching n explicit water molecules to the Hg(2+) complexes such that the first coordination sphere is complete, then surrounding the resulting (Hg(2+)-Lm)-(OH2)n cluster by a dielectric continuum, and using suitable thermodynamic cycles. This procedure significantly improves the agreement between the calculated log K values and experiment. Thus, for some neutral and anionic Hg(II) complexes, particularly Hg(II) metal ion surrounded with homo- or heteroatoms, augmenting implicit solvent calculations with sufficient explicit water molecules to complete the first coordination sphere is required-and adequate-to account for strong short-range hydrogen bonding interactions between the anion and the solvent. Calculated values for formation constants of Hg(2+) complexes with S(2-) and SH(-) are proposed. Experimental measurements of these log K values have been lacking or controversial.

  17. Comparison of aerodynamic coefficients obtained from theoretical calculations wind tunnel tests and flight tests data reduction for the alpha jet aircraft

    NASA Technical Reports Server (NTRS)

    Guiot, R.; Wunnenberg, H.

    1980-01-01

    The methods by which aerodynamic coefficients are determined and discussed. These include: calculations, wind tunnel experiments and experiments in flight for various prototypes of the Alpha Jet. A comparison of obtained results shows good correlation between expectations and in-flight test results.

  18. Intramolecular CH⋯π and CH⋯O interactions in the conformational stability of benzyl methyl ether studied by matrix-isolation infrared spectroscopy and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Shin-ya, Kei; Takahashi, Osamu; Katsumoto, Yukiteru; Ohno, Keiichi

    2007-02-01

    Contributions of the intramolecular CH⋯π and CH⋯O interactions to the molecular conformation of benzyl methyl ether (BME) have been investigated by matrix-isolation infrared (IR) spectroscopy combined with quantum chemical calculations. Comparative investigations have been carried out for propylbenzene. Quantum chemical calculations predict that there are two conformers for BME; for the ET conformer the methyl ether and the phenyl groups lie in the plane of the benzene ring, while for the AG conformer they are out of the plane. Comparison between the observed and calculated spectra for BME reveals that the ET and AG conformers coexist in an Ar matrix. By measuring matrix-isolation IR spectra of BME deposited at different gas temperatures, the enthalpy difference (Δ H (AG - ET)) between ET and AG conformers was determined to be -1.03 ± 0.06 kJ mol -1. The experimental and calculation results indicate that the AG conformer of BME is stabilized by the intramolecular CH⋯π and CH⋯O interactions.

  19. Accurate thermoelastic tensor and acoustic velocities of NaCl

    NASA Astrophysics Data System (ADS)

    Marcondes, Michel L.; Shukla, Gaurav; da Silveira, Pedro; Wentzcovitch, Renata M.

    2015-12-01

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.

  20. Accurate thermoelastic tensor and acoustic velocities of NaCl

    SciTech Connect

    Marcondes, Michel L.; Shukla, Gaurav; Silveira, Pedro da; Wentzcovitch, Renata M.

    2015-12-15

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.

  1. Theoretical characterization of the potential energy surface for H + N2 yields HN2. III - Calculations for the excited state surfaces

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1991-01-01

    Additional calculations which characterize potential energy sources (PESs) for the excited 3A-double-prime state, for a bound 2(2A-prime) state, for HN2(+), and for the Rydberg states associated with HN2(+). It is anticipated that these excited state PESs will be important in interpreting and designing experiments to characterize the ground state HN2 species via neutralized ion beam techniques.

  2. Spectroscopic [FT-IR and FT-Raman] and theoretical [UV-Visible and NMR] analysis on α-Methylstyrene by DFT calculations

    NASA Astrophysics Data System (ADS)

    Karthikeyan, N.; Joseph Prince, J.; Ramalingam, S.; Periandy, S.

    2015-05-01

    In the present research work, the FT-IR, FT-Raman and 13C and 1H NMR spectra of the α-Methylstyrene were recorded. The observed fundamental frequencies in finger print as well as functional group regions were assigned according to their uniqueness region. The Gaussian computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The impact of the presence of vinyl group in phenyl structure of the compound is investigated. The modified vibrational pattern of the molecule associated vinyl group was analyzed. Moreover, 13C NMR and 1H NMR were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed.

  3. Theoretical Calculation of Jet Fuel Thermochemistry. 1; Tetrahydrodicylopentadiene (JP10) Thermochemistry Using the CBS-QB3 and G3(MP2)//B3LYP Methods

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.; Jaffe, Richard L.

    2010-01-01

    High-level ab initio calculations have been performed on the exo and endo isomers of gas-phase tetrahydrodicyclopentadiene (THDCPD), a principal component of the jet fuel JP10, using the Gaussian Gx and Gx(MPx) composite methods, as well as the CBS-QB3 method, and using a variety of isodesmic and homodesmotic reaction schemes. The impetus for this work is to help resolve large discrepancies existing between literature measurements of the formation enthalpy Delta (sub f)H deg (298) for exo-THDCPD. We find that use of the isodesmic bond separation reaction C10H16 + 14CH4 yields 12C2H6 yields results for the exo isomer (JP10) in between the two experimentally accepted values, for the composite methods G3(MP2), G3(MP2)//B3LYP, and CBS-QB3. Application of this same isodesmic bond separation scheme to gas-phase adamantane yields a value for Delta (sub f)H deg (298) within 5 kJ/mol of experiment. Isodesmic bond separation calculations for the endo isomer give a heat of formation in excellent agreement with the experimental measurement. Combining our calculated values for the gas-phase heat of formation with recent measurements of the heat of vaporization yields recommended values for Delta (sub f)H deg (298)liq of -126.4 and -114.7 kJ/mol for the exo and endo isomers, respectively.

  4. Spectroscopic characteristic (FT-IR, FT-Raman, UV, 1H and 13C NMR), theoretical calculations and biological activity of alkali metal homovanillates

    NASA Astrophysics Data System (ADS)

    Samsonowicz, M.; Kowczyk-Sadowy, M.; Piekut, J.; Regulska, E.; Lewandowski, W.

    2016-04-01

    The structural and vibrational properties of lithium, sodium, potassium, rubidium and cesium homovanillates were investigated in this paper. Supplementary molecular spectroscopic methods such as: FT-IR, FT-Raman in the solid phase, UV and NMR were applied. The geometrical parameters and energies were obtained from density functional theory (DFT) B3LYP method with 6-311++G** basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned. Geometric and magnetic aromaticity indices, atomic charges, dipole moments, HOMO and LUMO energies were also calculated. The microbial activity of investigated compounds was tested against Bacillus subtilis (BS), Pseudomonas aeruginosa (PA), Escherichia coli (EC), Staphylococcus aureus (SA) and Candida albicans (CA). The relationship between the molecular structure of tested compounds and their antimicrobial activity was studied. The principal component analysis (PCA) was applied in order to attempt to distinguish the biological activities of these compounds according to selected band wavenumbers. Obtained data show that the FT-IR spectra can be a rapid and reliable analytical tool and a good source of information for the quantitative analysis of the relationship between the molecular structure of the compound and its biological activity.

  5. Assessment of a Cost-Effective Approach to the Calculation of Kinetic and Thermodynamic Properties of Methyl Methacrylate Homopolymerization: A Comprehensive Theoretical Study.

    PubMed

    Zhang, Guozhen; Konstantinov, Ivan A; Arturo, Steven G; Yu, Decai; Broadbelt, Linda J

    2014-12-01

    In this work, we carried out a comprehensive density functional theory (DFT) study on the basis of a trimer-to-tetramer radical reaction model to assess a cost-effective approach to perform the calculation of kinetic and thermodynamic properties of methyl methacrylate (MMA) free-radical homopolymerization. By comparing results from several different functionals (PBE, M06-2X, wB97XD, KMLYP, and MPW1B95), in conjunction with a series of basis sets (6-31G(d,p), 6-31+G(d,p), 6-31G(2df,p), 6-311G(d,p), 6-311+G(d,p), 6-311+G(2df,p), 6-311+G(2df,2p)), we show that calculations using M06-2X/6-311+G(2df,p)//B3LYP/6-31G(2df,p) provide an activation energy of 5.25 kcal mol(-1) for the homopropagation step, which is within 1 kcal mol(-1) of the experimental value. However, this method predicts a heat of polymerization of 17.37 kcal mol(-1) that is larger than the experimental value by 3.5 kcal mol(-1). MPW1B95/6-311+G(2df,p) on the B3LYP/6-31G(2df,p) geometries produces a heat of polymerization value within 1 kcal mol(-1) of experimental data, yet overestimates the activation energy by 3 kcal mol(-1). In addition, we evaluated the performance of ONIOM MO:MO calculations on the geometry optimization of species comprising our MMA polymerization model and found that ONIOM(B3LYP/6-31G(2df,p):B3LYP/6-31G(d)) is capable of producing geometries in very good agreement with the full B3LYP/6-31G(2df,p) calculations. Subsequent calculations of energies using M06-2X/6-311+G(2df,p) based on the ONIOM geometries provided an activation energy value comparable to that based on the full B3LYP/6-31G(2df,p) geometries.

  6. Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force.

    PubMed

    Makowska, Joanna; Makowski, Mariusz; Liwo, Adam; Chmurzyński, Lech

    2005-02-01

    The potentials of mean force (PMFs) were determined for systems forming cationic and anionic homocomplexes composed of acetic acid, phenol, isopropylamine, n-butylamine, imidazole, and 4(5)-methylimidazole, and their conjugated bases or acids, respectively, in three solvents with different polarity and hydrogen-bonding propensity: acetonitrile (AN), dimethyl sulfoxide (DMSO), and water (H(2)O). For each pair and each solvent a series of umbrella-sampling molecular dynamics simulations with the AMBER force field, explicit solvent, and counterions added to maintain a zero net charge of a system were carried out and the PMF was calculated by using the Weighted Histogram Analysis Method (WHAM). Subsequently, homoconjugation-equilibrium constants were calculated by numerical integration of the respective PMF profiles. In all cases but imidazole stable homocomplexes were found to form in solution, which was manifested as the presence of contact minima corresponding to hydrogen-bonded species in the PMF curves. The calculated homoconjugation constants were found to be greater for complexes with the OHO bridge (acetic acid and phenol) than with the NHN bridge and they were found to decrease with increasing polarity and hydrogen-bonding propensity of the solvent (i.e., in the series AN > DMSO > H(2)O), both facts being in agreement with the available experimental data. It was also found that interactions with counterions are manifested as the broadening of the contact minimum or appearance of additional minima in the PMF profiles of the acetic acid-acetate, phenol/phenolate system in acetonitrile, and the 4(5)-methylimidazole/4(5)-methylimidzole cation conjugated base system in dimethyl sulfoxide.

  7. Theoretical calculation of oxygen equilibrium isotope fractionation factors involving various NOy molecules, radOH, and H2O and its implications for isotope variations in atmospheric nitrate

    NASA Astrophysics Data System (ADS)

    Walters, Wendell W.; Michalski, Greg

    2016-10-01

    The oxygen stable isotope composition (δ18O) of nitrogen oxides [NOx = nitric oxide (NO) + nitrogen dioxide (NO2)] and their oxidation products (NOy = NOx + nitric acid (HNO3) + particulate nitrate (p-NO3-) + nitrate radical (NO3) + dinitrogen pentoxide (N2O5) + nitrous acid (HONO) + …) have been shown to be a useful tool for inferring the proportion of NOx that is oxidized by ozone (O3). However, isotopic fractionation processes may have an influence on δ18O of various NOy molecules and other atmospheric O-bearing molecules pertinent to NOx oxidation chemistry. Here we have evaluated the impacts of O isotopic exchange involving NOy molecules, the hydroxyl radical (radOH), and water (H2O) using reduced partition function ratios (xβ) calculated by hybrid density functional theory. Assuming atmospheric isotopic equilibrium is achieved between NO and NO2 during the daytime, and NO2, NO3, and N2O5 during the nighttime, δ18O-δ15N compositions were predicted for the major atmospheric nitrate formation pathways using our calculated exchange fractionation factors and isotopic mass-balance. Our equilibrium model predicts that various atmospheric nitrate formation pathways, including NO2 + radOH → HNO3, N2O5 + H2O + surface → 2HNO3, and NO3 + R → HNO3 + Rrad will yield distinctive δ18O-δ15N compositions. Our calculated δ18O-δ15N compositions match well with previous atmospheric nitrate measurements, and will potentially help better understand the role oxidation chemistry plays on the N and O isotopic composition of atmospheric nitrate.

  8. Two-dimensional Fröhlich interaction in transition-metal dichalcogenide monolayers: Theoretical modeling and first-principles calculations

    NASA Astrophysics Data System (ADS)

    Sohier, Thibault; Calandra, Matteo; Mauri, Francesco

    2016-08-01

    We perform ab initio calculations of the coupling between electrons and small-momentum polar-optical phonons in monolayer transition-metal dichalcogenides of the 2 H type: MoS2,MoSe2,MoTe2,WS2 , and WSe2. The polar-optical coupling with longitudinal optical phonons, or Fröhlich interaction, is fundamentally affected by the dimensionality of the system. In a plane-wave framework with periodic boundary conditions, the Fröhlich interaction is affected by the spurious interaction between the two-dimensional (2D) material and its periodic images. To overcome this difficulty, we perform density functional perturbation theory calculations with a truncated Coulomb interaction in the direction perpendicular to the plane of the 2D material. We show that the two-dimensional Fröhlich interaction is much stronger than assumed in previous ab initio studies. We provide analytical models depending on the effective charges and dielectric properties of the materials to interpret our ab initio calculations. Screening is shown to play a fundamental role in the phonon-momentum dependency of the polar-optical coupling, with a crossover between two regimes depending on the dielectric properties of the material relative to its environment. The Fröhlich interaction is screened by the dielectric environment in the limit of small phonon momenta and sharply decreases due to stronger screening by the monolayer at finite momenta. The small-momentum regime of the ab initio Fröhlich interaction is reproduced by a simple analytical model, for which we provide the necessary parameters. At larger momenta, however, direct ab initio calculations of electron-phonon interactions are necessary to capture band-specific effects. We compute and compare the carrier relaxation times associated with the scattering by both LO and A1 phonon modes. While both modes are capable of relaxing carriers on time scales under the picosecond at room temperature, their absolute importance and relative importance vary

  9. Calculation of the Residual Blood Volume after Acute, Non-Ongoing Hemorrhage Using Serial Hematocrit Measurements and the Volume of Isotonic Fluid Infused: Theoretical Hypothesis Generating Study.

    PubMed

    Oh, Won Sup; Chon, Sung-Bin

    2016-05-01

    Fluid resuscitation, hemostasis, and transfusion is essential in care of hemorrhagic shock. Although estimation of the residual blood volume is crucial, the standard measuring methods are impractical or unsafe. Vital signs, central venous or pulmonary artery pressures are inaccurate. We hypothesized that the residual blood volume for acute, non-ongoing hemorrhage was calculable using serial hematocrit measurements and the volume of isotonic solution infused. Blood volume is the sum of volumes of red blood cells and plasma. For acute, non-ongoing hemorrhage, red blood cell volume would not change. A certain portion of the isotonic fluid would increase plasma volume. Mathematically, we suggest that the residual blood volume after acute, non-ongoing hemorrhage might be calculated as 0·25N/[(Hct1/Hct2)-1], where Hct1 and Hct2 are the initial and subsequent hematocrits, respectively, and N is the volume of isotonic solution infused. In vivo validation and modification is needed before clinical application of this model.

  10. Calculation of the Residual Blood Volume after Acute, Non-Ongoing Hemorrhage Using Serial Hematocrit Measurements and the Volume of Isotonic Fluid Infused: Theoretical Hypothesis Generating Study

    PubMed Central

    2016-01-01

    Fluid resuscitation, hemostasis, and transfusion is essential in care of hemorrhagic shock. Although estimation of the residual blood volume is crucial, the standard measuring methods are impractical or unsafe. Vital signs, central venous or pulmonary artery pressures are inaccurate. We hypothesized that the residual blood volume for acute, non-ongoing hemorrhage was calculable using serial hematocrit measurements and the volume of isotonic solution infused. Blood volume is the sum of volumes of red blood cells and plasma. For acute, non-ongoing hemorrhage, red blood cell volume would not change. A certain portion of the isotonic fluid would increase plasma volume. Mathematically, we suggest that the residual blood volume after acute, non-ongoing hemorrhage might be calculated as 0·25N/[(Hct1/Hct2)–1], where Hct1 and Hct2 are the initial and subsequent hematocrits, respectively, and N is the volume of isotonic solution infused. In vivo validation and modification is needed before clinical application of this model. PMID:27134507

  11. Determination of ionization energies of CnN (n=4-12): Vacuum-ultraviolet (VUV) photoionization experiments and theoretical calculations

    SciTech Connect

    Kostko, Oleg; Zhou, Jia; Sun, Bian Jian; Lie, Jie Shiuan; Chang, Agnes H.H.; Kaiser, Ralf I.; Ahmed, Musahid

    2010-06-10

    Results from single photon vacuum ultraviolet photoionization of astrophysically relevant CnN clusters, n = 4 - 12, in the photon energy range of 8.0 eV to 12.8 eV are presented. The experimental photoionization efficiency curves, combined with electronic structure calculations, provide improved ionization energies of the CnN species. A search through numerous nitrogen-terminated CnN isomers for n=4-9 indicates that the linear isomer has the lowest energy, and therefore should be the most abundant isomer in the molecular beam. Comparison with calculated results also shed light on the energetics of the linear CnN clusters, particularly in the trends of the even-carbon and the odd-carbon series. These results can help guide the search of potential astronomical observations of these neutral molecules together with their cations in highly ionized regions or regions with a high UV/VUV photon flux (ranging from the visible to VUV with flux maxima in the Lyman- region) in the interstellar medium.

  12. Determination of ionization energies of CnN (n=4-12): Vacuum-ultraviolet (VUV) photoionization experiments and theoretical calculations

    SciTech Connect

    Kostko, Oleg; Zhou, Jia; Sun, Bian Jian; Lie, Jie Shiuan; Chang, Agnes H.H.; Kaiser, Ralf I.; Ahmed, Musahid

    2010-03-02

    Results from single photon vacuum ultraviolet photoionization of astrophysically relevant CnN clusters, n = 4 - 12, in the photon energy range of 8.0 eV to 12.8 eV are presented. The experimental photoionization efficiency curves, combined with electronic structure calculations, provide improved ionization energies of the CnN species. A search through numerous nitrogen-terminated CnN isomers for n=4-9 indicates that the linear isomer has the lowest energy, and therefore should be the most abundant isomer in the molecular beam. Comparison with calculated results also shed light on the energetics of the linear CnN clusters, particularly in the trends of the even-carbon and the odd-carbon series. These results can help guide the search of potential astronomical observations of these neutral molecules together with their cations in highly ionized regions or regions with a high UV/VUV photon flux (ranging from the visible to VUV with flux maxima in the Lyman-a region) in the interstellar medium.

  13. Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

    SciTech Connect

    Cao, Jun

    2015-06-28

    In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.

  14. Carbon p-electron induced magnetic ordering in Zn-implanted 6H-SiC: experimental observation and theoretical calculation

    NASA Astrophysics Data System (ADS)

    Li, Qiang; Xu, Juping; Liu, Jiandang; Ye, Bangjiao

    2016-05-01

    We observed clear ferromagnetic ordering in 6H-SiC crystal bombarded with zinc ions, and presented a detailed investigation of magnetic properties in this sample. The magnetization of Zn-implanted 6H-SiC fell and rose with annealing temperature from 500 °C to 1100 °C. Meanwhile, amount of oxygen penetrated lattices and combined with Si-bonds after 1100 °C annealing. Using ab initio calculations based on density functional theory, we confirm that Zn ions play a role in the origin of ferromagnetism, while the localized moment is mainly comes from C2p electrons surrounding the foreign particle (which is Zn in this work). Silicon vacancies can provide localized moment about 2.0 μB/VSi and form stable ferromagnetic interaction at room temperature. Oxygen may facilitate this coupling and no need of VC-mediation any more. The calculations are consistent with experimental results. We concluded that the dangling C2p bonds are fundamental cause of magnetic ordering in whatever microstructures in 6H-SiC crystal. The type of foreign impurities is not crucial factor for the magnetic origin in such carbon-based materials.

  15. Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations.

    PubMed

    Cao, Jun

    2015-06-28

    In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π(*) transition induces a cleavage of the C-N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π(*) excitation of the imine chromophore results in a cleavage of the C-C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N-O bond cleavages on both S1((1)ππ(*)) and S2((1)nNπ(*)) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.

  16. Theoretical investigations of half-metallic ferromagnetism in new Half-Heusler YCrSb and YMnSb alloys using first-principle calculations

    NASA Astrophysics Data System (ADS)

    Atif Sattar, M.; Rashid, Muhammad; Hashmi, M. Raza; Ahmad, S. A.; Imran, Muhammad; Hussain, Fayyaz

    2016-10-01

    Structural, electronic, and magnetic properties of new predicted half-Heusler YCrSb and YMnSb compounds within the ordered MgAgAs C1b-type structure are investigated by employing first-principal calculations based on density functional theory. Through the calculated total energies of three possible atomic placements, we find the most stable structures regarding YCrSb and YMnSb materials, where Y, Cr(Mn), and Sb atoms occupy the (0.5, 0.5, 0.5), (0.25, 0.25, 0.25), and (0, 0, 0) positions, respectively. Furthermore, structural properties are explored for the non-magnetic and ferromagnetic and anti-ferromagnetic states and it is found that both materials prefer ferromagnetic states. The electronic band structure shows that YCrSb has a direct band gap of 0.78 eV while YMnSb has an indirect band gap of 0.40 eV in the majority spin channel. Our findings show that YCrSb and YMnSb materials exhibit half-metallic characteristics at their optimized lattice constants of 6.67 Å and 6.56 Å, respectively. The half-metallicities associated with YCrSb and YMnSb are found to be robust under large in-plane strains which make them potential contenders for spintronic applications.

  17. Carbon p-electron induced magnetic ordering in Zn-implanted 6H–SiC: experimental observation and theoretical calculation

    NASA Astrophysics Data System (ADS)

    Li, Qiang; Xu, Juping; Liu, Jiandang; Ye, Bangjiao

    2016-05-01

    We observed clear ferromagnetic ordering in 6H–SiC crystal bombarded with zinc ions, and presented a detailed investigation of magnetic properties in this sample. The magnetization of Zn-implanted 6H–SiC fell and rose with annealing temperature from 500 °C to 1100 °C. Meanwhile, amount of oxygen penetrated lattices and combined with Si-bonds after 1100 °C annealing. Using ab initio calculations based on density functional theory, we confirm that Zn ions play a role in the origin of ferromagnetism, while the localized moment is mainly comes from C2p electrons surrounding the foreign particle (which is Zn in this work). Silicon vacancies can provide localized moment about 2.0 μB/VSi and form stable ferromagnetic interaction at room temperature. Oxygen may facilitate this coupling and no need of VC-mediation any more. The calculations are consistent with experimental results. We concluded that the dangling C2p bonds are fundamental cause of magnetic ordering in whatever microstructures in 6H–SiC crystal. The type of foreign impurities is not crucial factor for the magnetic origin in such carbon-based materials.

  18. TAD- THEORETICAL AERODYNAMICS PROGRAM

    NASA Technical Reports Server (NTRS)

    Barrowman, J.

    1994-01-01

    This theoretical aerodynamics program, TAD, was developed to predict the aerodynamic characteristics of vehicles with sounding rocket configurations. These slender, axisymmetric finned vehicle configurations have a wide range of aeronautical applications from rockets to high speed armament. Over a given range of Mach numbers, TAD will compute the normal force coefficient derivative, the center-of-pressure, the roll forcing moment coefficient derivative, the roll damping moment coefficient derivative, and the pitch damping moment coefficient derivative of a sounding rocket configured vehicle. The vehicle may consist of a sharp pointed nose of cone or tangent ogive shape, up to nine other body divisions of conical shoulder, conical boattail, or circular cylinder shape, and fins of trapezoid planform shape with constant cross section and either three or four fins per fin set. The characteristics computed by TAD have been shown to be accurate to within ten percent of experimental data in the supersonic region. The TAD program calculates the characteristics of separate portions of the vehicle, calculates the interference between separate portions of the vehicle, and then combines the results to form a total vehicle solution. Also, TAD can be used to calculate the characteristics of the body or fins separately as an aid in the design process. Input to the TAD program consists of simple descriptions of the body and fin geometries and the Mach range of interest. Output includes the aerodynamic characteristics of the total vehicle, or user-selected portions, at specified points over the mach range. The TAD program is written in FORTRAN IV for batch execution and has been implemented on an IBM 360 computer with a central memory requirement of approximately 123K of 8 bit bytes. The TAD program was originally developed in 1967 and last updated in 1972.

  19. Detection of the nanomolar level of total Cr[(iii) and (vi)] by functionalized gold nanoparticles and a smartphone with the assistance of theoretical calculation models

    NASA Astrophysics Data System (ADS)

    Chen, Wenwen; Cao, Fengjing; Zheng, Wenshu; Tian, Yue; Xianyu, Yunlei; Xu, Peng; Zhang, Wei; Wang, Zhuo; Deng, Ke; Jiang, Xingyu

    2015-01-01

    We report a method for rapid, effective detection of both Cr(iii) and Cr(vi) (in the form of Cr3+ and Cr2O72-, the main species of chromium in the natural environment) by making use of meso-2,3-dimercaptosuccinic acid (DMSA)-functionalized gold nanoparticles (Au NPs). The limit of detection (LOD) is 10 nM with the naked eye and the assay can be applied in detecting chromium in polluted soil from Yun-Nan Province in Southwest China. We use density functional theory to calculate the change of the Gibbs free energy (ΔG) of the interactions between the DMSA-Au NP system and various metal ions, which shows that DMSA-Au NPs have high specificity for both Cr3+ and Cr2O72-.We report a method for rapid, effective detection of both Cr(iii) and Cr(vi) (in the form of Cr3+ and Cr2O72-, the main species of chromium in the natural environment) by making use of meso-2,3-dimercaptosuccinic acid (DMSA)-functionalized gold nanoparticles (Au NPs). The limit of detection (LOD) is 10 nM with the naked eye and the assay can be applied in detecting chromium in polluted soil from Yun-Nan Province in Southwest China. We use density functional theory to calculate the change of the Gibbs free energy (ΔG) of the interactions between the DMSA-Au NP system and various metal ions, which shows that DMSA-Au NPs have high specificity for both Cr3+ and Cr2O72-. Electronic supplementary information (ESI) available: ΔG of the interactions between the DMSA-AuNPs and various metal ions, models of the metal ions (Mn+) and six water molecules, DLS results for DMSA-Au NPs before and after adding Cr3+, Cr2O72-, Cr3+ and Cr2O72- mixtures, comparison of the performance of different sensors. See DOI: 10.1039/c4nr06726f

  20. Structural, magnetic, and redox diversity of first-row transition metal complexes of a pyridine-based macrocycle: well-marked trends supported by theoretical DFT calculations.

    PubMed

    Drahoš, Bohuslav; Herchel, Radovan; Trávníček, Zdeněk

    2015-04-01

    A series of first-row transition metal complexes with 15-membered pyridine-based macrocycle (3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1(18),14,16-triene = L) was prepared ([M(II)(L)Cl2], where M = Mn, Co, Ni, Zn (1, 3, 4, 6); [Fe(III)(L)Cl2]Cl (2), [Cu(II)(L)Cl]Cl (5)) and thoroughly characterized. Depending on the complexated metal atom, the coordination number varies from 7 (Mn, Fe, Co), through 5 + 2 for Ni and 4 + 1 for Cu, to 5 for Zn accompanied by changes in the coordination geometry from the pentagonal bipyramid (1-4) to the square pyramid (5 and 6). Along the series, the metal-oxygen distances were prolonged in such manner that their bonding character was investigated, apart from X-ray structural analysis, also by ab initio calculations (Mayer's bond order, electron localization function), which confirmed that, in 4 and 5, two and one oxygen donor atoms are semicoordinated, respectively, and one and two oxygen atoms are uncoordinated in 5, and 6, respectively. On the basis of the temperature variable magnetic susceptibility measurements, 1 and 2 behave as expected for 3d(5) high-spin configuration with negligible zero-field splitting (ZFS). On the other hand, a large axial ZFS (D(Co) ≈ 40 cm(-1), D(Ni) ≈ -6.0 cm(-1)) was found for 3 and 4, and rhombic ZFS (E/D ≈ 0.15) for 4. Antiferromagnetic exchange coupling was observed for 4 and 5 (J(Ni) = -0.48 cm(-1), and J(Cu) = -2.43 cm(-1), respectively). The obtained results correlate well with ab initio calculations of ZFS parameters as well as J-values, which indicate that the antiferromagnetic exchange is mediated by hydrogen bonds. The complexes were also investigated by cyclic voltammetry in water or acetonitrile. A quasi-reversible couple Mn(II)/Mn(III) at 1.13/0.97 V, an almost reversible couple Fe(II)/Fe(III) at 0.51/0.25 V, and a one-step/multistep reduction/oxidation of Cu(II) complex 5 at -0.33 V/0.06-0.61 V were detected. PMID:25761063

  1. Synthesis, crystal structure, theoretical calculations and antimicrobial properties of [Pt(tetramethylthiourea)4] [Pt(CN)4]·4H2O

    NASA Astrophysics Data System (ADS)

    Sadaf, Haseeba; Isab, Anvarhusein A.; Ahmad, Saeed; Espinosa, Arturo; Mas-Montoya, Míriam; Khan, Islam Ullah; Ejaz; Rehman, Seerat-ur; Ali, Muhammad Akhtar Javed; Saleem, Muhammad; Ruiz, José; Janiak, Christoph

    2015-04-01

    A new platinum(II) complex, [Pt(Tmtu)4][Pt(CN)4]·4H2O (1) was synthesized by reaction of K2[PtCl4], KCN and tetramethylthiourea (Tmtu). Its structure was determined by X-ray crystallography. The [Pt(CN)4]2- anion shows regular square planar geometry at platinum, while in the [Pt(Tmtu)4]2+ cation the geometry at platinum is somewhat distorted. Hydrogen bonding between water molecules and the cyanide nitrogen of [Pt(CN)4]2- ions stabilizes the structure and leads to a supramolecular 2D network. DFT calculations support the experimentally found dinuclear (homocoordinated) ion-pair structure 1 as the most stable in comparison to noncovalent dimer [Pt(CN)2(Tmtu)2]222 that could, in turn, be involved in the formation sequence of 1. Antimicrobial activities of the complex were evaluated by minimum inhibitory concentration and the results showed that the complex exhibited moderate activities against gram-negative bacteria (Escherichiacoli, Pseudomonas aeruginosa) and molds (Aspergillus niger,Penicilliumcitrinum).

  2. Molecular modeling, theoretical calculations and property evaluation of three muscarinic agonists. X-ray structures of LU 25-109 and WAL 2014

    NASA Astrophysics Data System (ADS)

    Dolmella, A.; Bandoli, G.; Cavallin, M.

    2000-08-01

    LU 25-109 ( II) and WAL 2014 (talsaclidine, III) are two M1 muscarinic agonists chemically related to the natural substance arecoline ( I). All these compounds have beneficial effects on memory and cognition in animals and humans, and they have been proposed in the treatment of Alzheimer's disease, but only III will likely find a place in therapy. In this work we have investigated the solid state structures of II and III, and the X-ray structures of the two molecules and of the parent compound I have been used to input a series of computational chemistry efforts. In particular, the X-ray geometries have been manipulated to model 20 molecular structures ( 1- 20) which have been submitted to ab initio, semiempirical quantum mechanics and molecular mechanics calculations. The conformational space accessible to the 20 structures has been assessed by means of potential energy maps. The reactivities of 1- 20 have been estimated by examining at the graphics terminal the composition and the extension of the frontier orbitals (HOMOs and LUMOs) and of the molecular electrostatic potential. The information obtained has been interpreted to explain the different degrees of activity shown by I- III. Our data indicate that III has better in vivo activity for its intermediate size, less polar surface, conformational rigidity and orientation of reactive domains.

  3. Theoretical and experimental tests of a chromosomal fingerprint for densely ionizing radiation based on F ratios calculated from stable and unstable chromosome aberrations

    NASA Technical Reports Server (NTRS)

    Lucas, J. N.; Deng, W.; Oram, S. W.; Hill, F. S.; Durante, M.; George, K.; Wu, H.; Owens, C. L.; Yang, T.

    1999-01-01

    In the present study, F ratios for both stable chromosome aberrations, i.e. ratios of translocations to pericentric inversions, and unstable aberrations, i.e. dicentrics and centric rings, were measured using fluorescence in situ hybridization. F ratios for stable aberrations measured after exposure to low (2.89 Gy 60Co gamma rays) and high-LET (0.25 Gy 56Fe ions; 1.25 Gy 56Fe ions; 3.0 Gy 12C ions) radiation were 6.5 +/- 1.5, 4.7 +/- 1.6, 9.3 +/- 2.5 and 10.4 +/- 3.0, respectively. F ratios for unstable aberrations measured after low (2.89 Gy 60Co gamma rays) and high-LET (0.25 Gy 56Fe ions; 3.0 Gy 12C ions) radiations were 6.5 +/- 1.6, 6.3 +/- 2.3 and 11.1 +/- 3.7, respectively. No significant difference between the F ratios for low- and high-LET radiation was found. Further tests on the models for calculation of the F ratio proposed by Brenner and Sachs (Radiat. Res. 140, 134-142, 1994) showed that the F ratio may not be straightforward as a practical fingerprint for densely ionizing radiation.

  4. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    NASA Astrophysics Data System (ADS)

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-11-01

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol-1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB

  5. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    SciTech Connect

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-11-14

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non

  6. Enhanced Adsorption of Hydroxyl- and Amino-Substituted Aromatic Chemicals to Nitrogen-Doped Multiwall Carbon Nanotubes: A Combined Batch and Theoretical Calculation Study.

    PubMed

    Zuo, Linzi; Guo, Yong; Li, Xiao; Fu, Heyun; Qu, Xiaolei; Zheng, Shourong; Gu, Cheng; Zhu, Dongqiang; Alvarez, Pedro J J

    2016-01-19

    A large effort is being made to develop nanosorbents with tunable surface chemistry for enhanced adsorption affinity and selectivity toward target organic contaminants. Heteroatom N-doped multiwall carbon nanotubes (N-MCNT) were synthesized by chemical vapor deposition of pyridine and were further investigated for the adsorptive removal of several aromatic chemicals varying in electronic donor and acceptor ability from aqueous solutions using a batch technique. Compared with commercial nondoped multiwall carbon nanotubes (MCNT), N-MCNT had similar specific surface area, morphology, and pore-size distribution but more hydrophilic surfaces and more surface defects due to the doping of graphitic and pyridinic N atoms. N-MCNT exhibited enhanced adsorption (2-10 folds) for the π-donor chemicals (2-naphthol and 1-naphthalmine) at pH ∼6 but similar adsorption for the weak π-donor chemical (naphthalene) and even lower adsorption (up to a 2-fold change) for the π-acceptor chemical (1,3-dinitrobenzene). The enhanced adsorption of 2-naphthol and 1-naphthalmine to N-MCNT was mainly attributed to the favored π-π electron-donor-acceptor (EDA) interaction between the π-donor adsorbate molecule and the polarized N-heterocyclic aromatic ring (π-acceptor) on N-MCNT. The proposed adsorption enhancement mechanisms were further tested through the pH effects on adsorption and the density function theory (DFT) calculation. The results show for the first time that the adsorptive interaction of π-donor aromatic compounds with carbon nanomaterials can be facilitated by N-doping.

  7. 2,2,6,6-Tetramethyl-1-oxopiperidinetribromide and two forms of 1-hydroxy-2,2,6,6-tetramethylpiperidinium bromide salt: Syntheses, crystal structures and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Judith Percino, M.; Cerón, Margarita; Soriano-Moro, Guillermo; Pacheco, José A.; Eugenia Castro, M.; Chapela, Víctor M.; Bonilla-Cruz, José; Saldivar-Guerra, Enrique

    2016-01-01

    The reaction of the nitroxy radical 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) with Br2 has been investigated with CCl4 and hexane to obtain TEMPO-Br salts: 2,2,6,6-tetramethylpiperidine-1-oxopiperidine tribromide [TEMPO] [Br3- ] (I), and the 1-hydroxy-2,2,6,6-tetramethylpiperidinium bromide salts [TEMPH+OHBr-] (II and III). The salt I was isolated in crystalline form directly from the synthesis and II and III by only changing the solvent. The crystals of I belong to the orthorhombic crystal systems with space group Cmc21, a = 10.5596(4) Å, b = 14.0464(4) Å, c = 9.4202(5), and with asymmetric unit of Z = 4. Crystals II belong to Pnna a = 11.9860(3) Å, b = 23.6720(9) Å, c = 7.7051(3) Å while III belongs to Cmc21 with a = 10.2686(3) Å, b = 10.7661(3) Å, c = 10.0274(2) Å; the asymmetric unit of II and III was Z = 8 and Z = 4, respectively. The crystal structure of I shows the Br3- ion as [Br-Br-Br]- for each molecule of TEMPO. The crystal structure of II shows a weak intermolecular hydrogen bond between -N-H⋯Br(1) and O(1)H⋯Br(2) due to the presence of the -N+HOH- moiety. In contrast, crystal III shows intermolecular hydrogen bonding between O(1)H⋯Br(1)⋯HN(1) due to the -N+HOH- moiety. The resulting compounds were characterized by FT-IR and UV-vis spectroscopy. The structural parameters have been compared with the related hydroxylaminotrichlorosilane known from the literature and with results of DFT calculations.

  8. Different Interaction Mechanisms of Eu(III) and (243)Am(III) with Carbon Nanotubes Studied by Batch, Spectroscopy Technique and Theoretical Calculation.

    PubMed

    Wang, Xiangxue; Yang, Shubin; Shi, Weiqun; Li, Jiaxing; Hayat, Tasawar; Wang, Xiangke

    2015-10-01

    Herein the sorption of Eu(III) and (243)Am(III) on multiwalled carbon nanotubes (CNTs) are studied, and the results show that Eu(III) and (243)Am(III) could form strong inner-sphere surface complexes on CNT surfaces. However, the sorption of Eu(III) on CNTs is stronger than that of (243)Am(III) on CNTs, suggesting the difference in the interaction mechanisms or properties of Eu(III) and (243)Am(III) with CNTs, which is quite different from the results of Eu(III) and (243)Am(III) interaction on natural clay minerals and oxides. On the basis of the results of density functional theory calculations, the binding energies of Eu(III) on CNTs are much higher than those of (243)Am(III) on CNTs, indicating that Eu(III) could form stronger complexes with the oxygen-containing functional groups of CNTs than (243)Am(III), which is in good agreement with the experimental results of higher sorption capacity of CNTs for Eu(III). The oxygen-containing functional groups contribute significantly to the uptake of Eu(III) and (243)Am(III), and the binding affinity increases in the order of ≡S-OH < ≡S-COOH < ≡S-COO(-). This paper highlights the interaction mechanism of Eu(III) and (243)Am(III) with different oxygen-containing functional groups of CNTs, which plays an important role for the potential application of CNTs in the preconcentration, removal, and separation of trivalent lanthanides and actinides in environmental pollution cleanup. PMID:26371690

  9. Enhanced Adsorption of Hydroxyl- and Amino-Substituted Aromatic Chemicals to Nitrogen-Doped Multiwall Carbon Nanotubes: A Combined Batch and Theoretical Calculation Study.

    PubMed

    Zuo, Linzi; Guo, Yong; Li, Xiao; Fu, Heyun; Qu, Xiaolei; Zheng, Shourong; Gu, Cheng; Zhu, Dongqiang; Alvarez, Pedro J J

    2016-01-19

    A large effort is being made to develop nanosorbents with tunable surface chemistry for enhanced adsorption affinity and selectivity toward target organic contaminants. Heteroatom N-doped multiwall carbon nanotubes (N-MCNT) were synthesized by chemical vapor deposition of pyridine and were further investigated for the adsorptive removal of several aromatic chemicals varying in electronic donor and acceptor ability from aqueous solutions using a batch technique. Compared with commercial nondoped multiwall carbon nanotubes (MCNT), N-MCNT had similar specific surface area, morphology, and pore-size distribution but more hydrophilic surfaces and more surface defects due to the doping of graphitic and pyridinic N atoms. N-MCNT exhibited enhanced adsorption (2-10 folds) for the π-donor chemicals (2-naphthol and 1-naphthalmine) at pH ∼6 but similar adsorption for the weak π-donor chemical (naphthalene) and even lower adsorption (up to a 2-fold change) for the π-acceptor chemical (1,3-dinitrobenzene). The enhanced adsorption of 2-naphthol and 1-naphthalmine to N-MCNT was mainly attributed to the favored π-π electron-donor-acceptor (EDA) interaction between the π-donor adsorbate molecule and the polarized N-heterocyclic aromatic ring (π-acceptor) on N-MCNT. The proposed adsorption enhancement mechanisms were further tested through the pH effects on adsorption and the density function theory (DFT) calculation. The results show for the first time that the adsorptive interaction of π-donor aromatic compounds with carbon nanomaterials can be facilitated by N-doping. PMID:26669961

  10. Torsional energy levels of CH{sub 3}OH{sup +}/CH{sub 3}OD{sup +}/CD{sub 3}OD{sup +} studied by zero-kinetic energy photoelectron spectroscopy and theoretical calculations

    SciTech Connect

    Dai, Zuyang; Gao, Shuming; Wang, Jia; Mo, Yuxiang

    2014-10-14

    The torsional energy levels of CH{sub 3}OH{sup +}, CH{sub 3}OD{sup +}, and CD{sub 3}OD{sup +} have been determined for the first time using one-photon zero kinetic energy photoelectron spectroscopy. The adiabatic ionization energies for CH{sub 3}OH, CH{sub 3}OD, and CD{sub 3}OD are determined as 10.8396, 10.8455, and 10.8732 eV with uncertainties of 0.0005 eV, respectively. Theoretical calculations have also been performed to obtain the torsional energy levels for the three isotopologues using a one-dimensional model with approximate zero-point energy corrections of the torsional potential energy curves. The calculated values are in good agreement with the experimental data. The barrier height of the torsional potential energy without zero-point energy correction was calculated as 157 cm{sup −1}, which is about half of that of the neutral (340 cm{sup −1}). The calculations showed that the cation has eclipsed conformation at the energy minimum and staggered one at the saddle point, which is the opposite of what is observed in the neutral molecule. The fundamental C–O stretch vibrational energy level for CD{sub 3}OD{sup +} has also been determined. The energy levels for the combinational excitation of the torsional vibration and the fundamental C–O stretch vibration indicate a strong torsion-vibration coupling.

  11. Accurate adiabatic correction in the hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-01

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10-12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10-7 cm-1, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  12. Accurate adiabatic correction in the hydrogen molecule

    SciTech Connect

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  13. Accurate adiabatic correction in the hydrogen molecule.

    PubMed

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10(-12) at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10(-7) cm(-1), which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels. PMID:25494728

  14. SU-C-BRB-06: Utilizing 3D Scanner and Printer for Dummy Eye-Shield: Artifact-Free CT Images of Tungsten Eye-Shield for Accurate Dose Calculation

    SciTech Connect

    Park, J; Lee, J; Kim, H; Kim, I; Ye, S

    2015-06-15

    Purpose: To evaluate the effect of a tungsten eye-shield on the dose distribution of a patient. Methods: A 3D scanner was used to extract the dimension and shape of a tungsten eye-shield in the STL format. Scanned data was transferred into a 3D printer. A dummy eye shield was then produced using bio-resin (3D systems, VisiJet M3 Proplast). For a patient with mucinous carcinoma, the planning CT was obtained with the dummy eye-shield placed on the patient’s right eye. Field shaping of 6 MeV was performed using a patient-specific cerrobend block on the 15 x 15 cm{sup 2} applicator. The gantry angle was 330° to cover the planning target volume near by the lens. EGS4/BEAMnrc was commissioned from our measurement data from a Varian 21EX. For the CT-based dose calculation using EGS4/DOSXYZnrc, the CT images were converted to a phantom file through the ctcreate program. The phantom file had the same resolution as the planning CT images. By assigning the CT numbers of the dummy eye-shield region to 17000, the real dose distributions below the tungsten eye-shield were calculated in EGS4/DOSXYZnrc. In the TPS, the CT number of the dummy eye-shield region was assigned to the maximum allowable CT number (3000). Results: As compared to the maximum dose, the MC dose on the right lens or below the eye shield area was less than 2%, while the corresponding RTP calculated dose was an unrealistic value of approximately 50%. Conclusion: Utilizing a 3D scanner and a 3D printer, a dummy eye-shield for electron treatment can be easily produced. The artifact-free CT images were successfully incorporated into the CT-based Monte Carlo simulations. The developed method was useful in predicting the realistic dose distributions around the lens blocked with the tungsten shield.

  15. A Theoretical Trombone

    ERIC Educational Resources Information Center

    LoPresto, Michael C.

    2014-01-01

    What follows is a description of a theoretical model designed to calculate the playing frequencies of the musical pitches produced by a trombone. The model is based on quantitative treatments that demonstrate the effects of the flaring bell and cup-shaped mouthpiece sections on these frequencies and can be used to calculate frequencies that…

  16. Accurate Cross Sections for Microanalysis

    PubMed Central

    Rez, Peter

    2002-01-01

    To calculate the intensity of x-ray emission in electron beam microanalysis requires a knowledge of the energy distribution of the electrons in the solid, the energy variation of the ionization cross section of the relevant subshell, the fraction of ionizations events producing x rays of interest and the absorption coefficient of the x rays on the path to the detector. The theoretical predictions and experimental data available for ionization cross sections are limited mainly to K shells of a few elements. Results of systematic plane wave Born approximation calculations with exchange for K, L, and M shell ionization cross sections over the range of electron energies used in microanalysis are presented. Comparisons are made with experimental measurement for selected K shells and it is shown that the plane wave theory is not appropriate for overvoltages less than 2.5 V. PMID:27446747

  17. Monte Carlo and theoretical calculations of the first four perturbation coefficients in the high temperature series expansion of the free energy for discrete and core-softened potential models

    NASA Astrophysics Data System (ADS)

    Zhou, Shiqi; Solana, J. R.

    2013-06-01

    The first four perturbation coefficients in the expansion of the Helmholtz free energy in power series of the inverse of the reduced temperature for a number of potential models with hard-sphere cores plus core-softened and discontinuous tails are obtained from Monte Carlo simulations. The potential models considered include square-well, double square-well, and square-shoulder plus square-well, with different potential parameters. These simulation data are used to evaluate the performance of a traditional macroscopic compressibility approximation (MCA) for the second order coefficient and a recent coupling parameter series expansion (CPSE) for the first four coefficients. Comprehensive comparison indicates the incapability of the MCA for the second order coefficient in most non-stringent situations, and significance of the CPSE in accurately calculating these four coefficients.

  18. Monte Carlo and theoretical calculations of the first four perturbation coefficients in the high temperature series expansion of the free energy for discrete and core-softened potential models.

    PubMed

    Zhou, Shiqi; Solana, J R

    2013-06-28

    The first four perturbation coefficients in the expansion of the Helmholtz free energy in power series of the inverse of the reduced temperature for a number of potential models with hard-sphere cores plus core-softened and discontinuous tails are obtained from Monte Carlo simulations. The potential models considered include square-well, double square-well, and square-shoulder plus square-well, with different potential parameters. These simulation data are used to evaluate the performance of a traditional macroscopic compressibility approximation (MCA) for the second order coefficient and a recent coupling parameter series expansion (CPSE) for the first four coefficients. Comprehensive comparison indicates the incapability of the MCA for the second order coefficient in most non-stringent situations, and significance of the CPSE in accurately calculating these four coefficients.

  19. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  20. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  1. An Accurate Temperature Correction Model for Thermocouple Hygrometers 1

    PubMed Central

    Savage, Michael J.; Cass, Alfred; de Jager, James M.

    1982-01-01

    Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques. In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38°C). The model based on calibration at two temperatures is superior to that based on only one calibration. The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25°C, if the calibration slopes are corrected for temperature. PMID:16662241

  2. An accurate temperature correction model for thermocouple hygrometers.

    PubMed

    Savage, M J; Cass, A; de Jager, J M

    1982-02-01

    Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques.In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38 degrees C). The model based on calibration at two temperatures is superior to that based on only one calibration.The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25 degrees C, if the calibration slopes are corrected for temperature.

  3. An accurate temperature correction model for thermocouple hygrometers.

    PubMed

    Savage, M J; Cass, A; de Jager, J M

    1982-02-01

    Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques.In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38 degrees C). The model based on calibration at two temperatures is superior to that based on only one calibration.The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25 degrees C, if the calibration slopes are corrected for temperature. PMID:16662241

  4. SMARTIES: Spheroids Modelled Accurately with a Robust T-matrix Implementation for Electromagnetic Scattering

    NASA Astrophysics Data System (ADS)

    Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.

    2016-03-01

    SMARTIES calculates the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. This suite of MATLAB codes provides a fully documented implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. Included are scripts that cover a range of scattering problems relevant to nanophotonics and plasmonics, including calculation of far-field scattering and absorption cross-sections for fixed incidence orientation, orientation-averaged cross-sections and scattering matrix, surface-field calculations as well as near-fields, wavelength-dependent near-field and far-field properties, and access to lower-level functions implementing the T-matrix calculations, including the T-matrix elements which may be calculated more accurately than with competing codes.

  5. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH₃)₂)₆](ClO₄)₂ supported by theoretical (DFT) calculations.

    PubMed

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-15

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made. PMID:25795611

  6. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH3)2)6](ClO4)2 supported by theoretical (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-01

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5c = 222.9 K on cooling and at TC5h = 225.4 K on heating) the CH3 groups perform fast (τR ≈ 10-12-10-13 s) reorientational motions. These motions start to slow down below TC5c Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6]2+ cation and ClO4- anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made.

  7. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH₃)₂)₆](ClO₄)₂ supported by theoretical (DFT) calculations.

    PubMed

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-15

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made.

  8. Kinetics of the reaction of the heaviest hydrogen atom with H2, the 4Heμ + H2 → 4HeμH + H reaction: experiments, accurate quantal calculations, and variational transition state theory, including kinetic isotope effects for a factor of 36.1 in isotopic mass.

    PubMed

    Fleming, Donald G; Arseneau, Donald J; Sukhorukov, Oleksandr; Brewer, Jess H; Mielke, Steven L; Truhlar, Donald G; Schatz, George C; Garrett, Bruce C; Peterson, Kirk A

    2011-11-14

    The neutral muonic helium atom (4)Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of (4)Heμ with molecular hydrogen, (4)Heμ + H(2) → (4)HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, k(Heμ), are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for k(Heμ) are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for k(Heμ) on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H(2) and Mu + H(2) reactions in a novel study of kinetic isotope effects for the H + H(2) reactions over a factor of 36.1 in isotopic mass of the atomic reactant.

  9. A theoretical trombone

    NASA Astrophysics Data System (ADS)

    LoPresto, Michael C.

    2014-09-01

    What follows is a description of a theoretical model designed to calculate the playing frequencies of the musical pitches produced by a trombone. The model is based on quantitative treatments that demonstrate the effects of the flaring bell and cup-shaped mouthpiece sections on these frequencies and can be used to calculate frequencies that compare well to both the desired frequencies of the musical pitches and those actually played on a real trombone.

  10. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  11. Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations.

    PubMed

    Armentano, Donatella; De Munno, Giovanni; Di Donna, Leonardo; Sindona, Giovanni; Giorgi, Gianluca; Salvini, Laura; Napoli, Anna

    2004-02-01

    Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

  12. A Multispectrum Analysis of the v2 Band of H12C14N: Part II. Theoretical Calculations of Self-Broadening, Self-Induced Shifts, and Their Temperature Dependences

    SciTech Connect

    Bouanich, J P.; Boulet, C; Predoi-Cross, A; Sharpe, Steven W.; Sams, Robert L.; Smith, Mary A.; Rinsland, Curtis P.; Benner, D C.; Devi, V M.

    2005-04-07

    A semiclassical theory based upon the Robert-Bonamy formalism has been developed in order to explain the experimental measurements of self-broadening, self-induced pressure shift coefficients in the v1, v2, 2v2 bands of H12C14N and the 2v1 band of H13C14N as well as the temperature dependences of these parameters with special emphasis on the v2 band. Our calculations include only electrostatic interactions and neglect the vibrational dependence of the isotropic part of the intermolecular potential, which probably has a weak contribution to the HCN self-shifts for the bands investigated in this study. The agreement between theory and measurements is good in the cases of self-broadening coefficients and their variation with temperature, as well as the self-shift coefficients determined at room temperature. However, the observed temperature dependence of self-shift coefficients in the v2 band is different from that derived theoretically.

  13. Exact calculations of nuclear-recoil energies from prompt gamma decays resulting from neutron capture

    SciTech Connect

    Kinney, J.H.

    1981-07-20

    The results of an accurate determination of the recoil spectrum from (n, ..gamma..) reactions in molybdenum are presented. The recoil spectrum has been calculated from nuclear level structure data and measured branching ratios. Angular correlations between successive gammas have been accounted for using the standard theoretical techniques of Racah algebra and the density matrix formalism.

  14. Two Polymorphic Forms of a Six-Coordinate Mononuclear Cobalt(II) Complex with Easy-Plane Anisotropy: Structural Features, Theoretical Calculations, and Field-Induced Slow Relaxation of the Magnetization.

    PubMed

    Roy, Subhadip; Oyarzabal, Itziar; Vallejo, Julia; Cano, Joan; Colacio, Enrique; Bauza, Antonio; Frontera, Antonio; Kirillov, Alexander M; Drew, Michael G B; Das, Subrata

    2016-09-01

    A mononuclear cobalt(II) complex [Co(3,5-dnb)2(py)2(H2O)2] {3,5-Hdnb = 3,5-dinitrobenzoic acid; py = pyridine} was isolated in two polymorphs, in space groups C2/c (1) and P21/c (2). Single-crystal X-ray diffraction analyses reveal that 1 and 2 are not isostructural in spite of having equal formulas and ligand connectivity. In both structures, the Co(II) centers adopt octahedral {CoN2O4} geometries filled by pairs of mutually trans terminal 3,5-dnb, py, and water ligands. However, the structures of 1 and 2 disclose distinct packing patterns driven by strong intermolecular O-H···O hydrogen bonds, leading to their 0D→2D (1) or 0D→1D (2) extension. The resulting two-dimensional layers and one-dimensional chains were topologically classified as the sql and 2C1 underlying nets, respectively. By means of DFT theoretical calculations, the energy variations between the polymorphs were estimated, and the binding energies associated with the noncovalent interactions observed in the crystal structures were also evaluated. The study of the direct-current magnetic properties, as well as ab initio calculations, reveal that both 1 and 2 present a strong easy-plane magnetic anisotropy (D > 0), which is larger for the latter polymorph (D is found to exhibit values between +58 and 117 cm(-1) depending on the method). Alternating current dynamic susceptibility measurements show that these polymorphs exhibit field-induced slow relaxation of the magnetization with Ueff values of 19.5 and 21.1 cm(-1) for 1 and 2, respectively. The analysis of the whole magnetic data allows the conclusion that the magnetization relaxation in these polymorphs mainly takes place through a virtual excited state (Raman process). It is worth noting that despite the notable difference between the supramolecular networks of 1 and 2, they exhibit almost identical magnetization dynamics. This fact suggests that the relaxation process is intramolecular in nature and that the virtual state involved in the

  15. Two Polymorphic Forms of a Six-Coordinate Mononuclear Cobalt(II) Complex with Easy-Plane Anisotropy: Structural Features, Theoretical Calculations, and Field-Induced Slow Relaxation of the Magnetization.

    PubMed

    Roy, Subhadip; Oyarzabal, Itziar; Vallejo, Julia; Cano, Joan; Colacio, Enrique; Bauza, Antonio; Frontera, Antonio; Kirillov, Alexander M; Drew, Michael G B; Das, Subrata

    2016-09-01

    A mononuclear cobalt(II) complex [Co(3,5-dnb)2(py)2(H2O)2] {3,5-Hdnb = 3,5-dinitrobenzoic acid; py = pyridine} was isolated in two polymorphs, in space groups C2/c (1) and P21/c (2). Single-crystal X-ray diffraction analyses reveal that 1 and 2 are not isostructural in spite of having equal formulas and ligand connectivity. In both structures, the Co(II) centers adopt octahedral {CoN2O4} geometries filled by pairs of mutually trans terminal 3,5-dnb, py, and water ligands. However, the structures of 1 and 2 disclose distinct packing patterns driven by strong intermolecular O-H···O hydrogen bonds, leading to their 0D→2D (1) or 0D→1D (2) extension. The resulting two-dimensional layers and one-dimensional chains were topologically classified as the sql and 2C1 underlying nets, respectively. By means of DFT theoretical calculations, the energy variations between the polymorphs were estimated, and the binding energies associated with the noncovalent interactions observed in the crystal structures were also evaluated. The study of the direct-current magnetic properties, as well as ab initio calculations, reveal that both 1 and 2 present a strong easy-plane magnetic anisotropy (D > 0), which is larger for the latter polymorph (D is found to exhibit values between +58 and 117 cm(-1) depending on the method). Alternating current dynamic susceptibility measurements show that these polymorphs exhibit field-induced slow relaxation of the magnetization with Ueff values of 19.5 and 21.1 cm(-1) for 1 and 2, respectively. The analysis of the whole magnetic data allows the conclusion that the magnetization relaxation in these polymorphs mainly takes place through a virtual excited state (Raman process). It is worth noting that despite the notable difference between the supramolecular networks of 1 and 2, they exhibit almost identical magnetization dynamics. This fact suggests that the relaxation process is intramolecular in nature and that the virtual state involved in the

  16. Universality: Accurate Checks in Dyson's Hierarchical Model

    NASA Astrophysics Data System (ADS)

    Godina, J. J.; Meurice, Y.; Oktay, M. B.

    2003-06-01

    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  17. Theoretical and experimental study of valence photoelectron spectrum of D,L-alanine amino acid.

    PubMed

    Farrokhpour, H; Fathi, F; De Brito, A Naves

    2012-07-01

    In this work, the He-I (21.218 eV) photoelectron spectrum of D,L-alanine in the gas phase is revisited experimentally and theoretically. To support the experiment, the high level ab initio calculations were used to calculate and assign the photoelectron spectra of the four most stable conformers of gaseous alanine, carefully. The symmetry adapted cluster/configuration interaction (SAC-CI) method based on single and double excitation operators (SD-R) and its more accurate version, termed general-R, was used to separately calculate the energies and intensities of the ionization bands of the L- and D-alanine conformers. The intensities of ionization bands were calculated based on the monopole approximation. Also, natural bonding orbital (NBO) calculations were employed for better spectral band assignment. The relative electronic energy, Gibbs free energy, and Boltzmann population ratio of the conformers were calculated at the experimental temperature (403 K) using several theoretical methods. The theoretical photoelectron spectrum of alanine was calculated by summing over the spectra of individual D and L conformers weighted by different population ratios. Finally, the population ratio of the four most stable conformers of alanine was estimated from the experimental photoelectron spectrum using theoretical calculations for the first time.

  18. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

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

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  19. Theoretical geology

    NASA Astrophysics Data System (ADS)

    Mikeš, Daniel

    2010-05-01

    Theoretical geology Present day geology is mostly empirical of nature. I claim that geology is by nature complex and that the empirical approach is bound to fail. Let's consider the input to be the set of ambient conditions and the output to be the sedimentary rock record. I claim that the output can only be deduced from the input if the relation from input to output be known. The fundamental question is therefore the following: Can one predict the output from the input or can one predict the behaviour of a sedimentary system? If one can, than the empirical/deductive method has changes, if one can't than that method is bound to fail. The fundamental problem to solve is therefore the following: How to predict the behaviour of a sedimentary system? It is interesting to observe that this question is never asked and many a study is conducted by the empirical/deductive method; it seems that the empirical method has been accepted as being appropriate without question. It is, however, easy to argument that a sedimentary system is by nature complex and that several input parameters vary at the same time and that they can create similar output in the rock record. It follows trivially from these first principles that in such a case the deductive solution cannot be unique. At the same time several geological methods depart precisely from the assumption, that one particular variable is the dictator/driver and that the others are constant, even though the data do not support such an assumption. The method of "sequence stratigraphy" is a typical example of such a dogma. It can be easily argued that all the interpretation resulting from a method that is built on uncertain or wrong assumptions is erroneous. Still, this method has survived for many years, nonwithstanding all the critics it has received. This is just one example of the present day geological world and is not unique. Even the alternative methods criticising sequence stratigraphy actually depart from the same

  20. ELECTRON-ION RECOMBINATION OF Mg{sup 6+} FORMING Mg{sup 5+} AND OF Mg{sup 7+} FORMING Mg{sup 6+}: LABORATORY MEASUREMENTS AND THEORETICAL CALCULATIONS

    SciTech Connect

    Lestinsky, M.; Hahn, M.; Novotny, O.; Savin, D. W.; Badnell, N. R.; Bernhardt, D.; Mueller, A.; Schippers, S.; Bing, D.; Grieser, M.; Hoffmann, J.; Jordon-Thaden, B.; Krantz, C.; Orlov, D. A.; Repnow, R.; Shornikov, A.; Wolf, A.

    2012-10-10

    We have measured electron-ion recombination for C-like Mg{sup 6+} forming Mg{sup 5+}, and for B-like Mg{sup 7+} forming Mg{sup 6+}. These studies were performed using a merged electron-ion beam arrangement at the TSR heavy ion storage ring located in Heidelberg, Germany. Both primary ions have metastable levels with significant lifetimes. Using a simple cascade model we estimate the population fractions in these metastable levels. For the Mg{sup 6+} results, we find that the majority of the stored ions are in a metastable level, while for Mg{sup 7+} the metastable fraction is insignificant. We present the Mg{sup 6+} merged beams recombination rate coefficient for DR via N = 2 {yields} N' = 2 core electron excitations ({Delta}N = 0 DR) and for Mg{sup 7+} via 2 {yields} 2 and 2 {yields} 3 core excitations. Taking the estimated metastable populations into account, we compare our results to state-of-the-art multiconfiguration Breit-Pauli theoretical calculations. Significant differences are found at low energies where theory is known to be unreliable. Moreover, for both ions we observe a discrepancy between experiment and theory for {Delta}N = 0 DR involving capture into high-n Rydberg levels and where the stabilization is primarily due to a radiative transition of the excited core electron. This is consistent with previous DR experiments on M-shell iron ions which were performed at TSR. The large metastable content of the Mg{sup 6+} ion beam precludes generating a plasma recombination rate coefficient (PRRC). However, this is not an issue for Mg{sup 7+} and we present an experimentally derived Mg{sup 7+} PRRC for plasma temperatures from 400 K to 10{sup 7} K with an estimated uncertainty of less than 27% at a 90% confidence level. We also provide a fit to our experimentally derived PRRC for use in plasma modeling codes.

  1. Accurate band-to-band registration of AOTF imaging spectrometer using motion detection technology

    NASA Astrophysics Data System (ADS)

    Zhou, Pengwei; Zhao, Huijie; Jin, Shangzhong; Li, Ningchuan

    2016-05-01

    This paper concerns the problem of platform vibration induced band-to-band misregistration with acousto-optic imaging spectrometer in spaceborne application. Registrating images of different bands formed at different time or different position is difficult, especially for hyperspectral images form acousto-optic tunable filter (AOTF) imaging spectrometer. In this study, a motion detection method is presented using the polychromatic undiffracted beam of AOTF. The factors affecting motion detect accuracy are analyzed theoretically, and calculations show that optical distortion is an easily overlooked factor to achieve accurate band-to-band registration. Hence, a reflective dual-path optical system has been proposed for the first time, with reduction of distortion and chromatic aberration, indicating the potential of higher registration accuracy. Consequently, a spectra restoration experiment using additional motion detect channel is presented for the first time, which shows the accurate spectral image registration capability of this technique.

  2. Theoretical approximations and experimental extinction coefficients of biopharmaceuticals.

    PubMed

    Miranda-Hernández, Mariana P; Valle-González, Elba R; Ferreira-Gómez, David; Pérez, Néstor O; Flores-Ortiz, Luis F; Medina-Rivero, Emilio

    2016-02-01

    UV spectrophotometric measurement is a widely accepted and standardized routine analysis for quantitation of highly purified proteins; however, the reliability of the results strictly depends on the accuracy of the employed extinction coefficients. In this work, an experimental estimation of the differential refractive index (dn/dc), based on dry weight measurements, was performed in order to determine accurate extinction coefficients for four biotherapeutic proteins and one synthetic copolymer after separation in a size-exclusion ultra-performance liquid chromatograph coupled to an ultraviolet, multiangle light scattering and refractive index (SE-UPLC-UV-MALS-RI) multidetection system. The results showed small deviations with respect to theoretical values, calculated from the specific amino acid sequences, for all the studied immunoglobulins. Nevertheless, for proteins like etanercept and glatiramer acetate, several considerations, such as glycan content, partial specific volume, polarizability, and higher order structure, should be considered to properly calculate theoretical extinction coefficient values. Herein, these values were assessed with simple approximations. The precision of the experimentally obtained extinction coefficients, and its convergence towards the theoretical values, makes them useful for characterization and comparability exercises. Also, these values provide insight into the absorbance and scattering properties of the evaluated proteins. Overall, this methodology is capable of providing accurate extinction coefficients useful for development studies.

  3. Accurate measurements of the collision stopping powers for 5 to 30 MeV electrons

    NASA Astrophysics Data System (ADS)

    MacPherson, Miller Shawn

    Accurate knowledge of electron stopping powers is crucial for accurate radiation dosimetry and radiation transport calculations. Current values for stopping powers are based on a theoretical model, with estimated uncertainties of 0.5-1% (1σ) for electron energies greater than 100 keV. This work presents the first measurements of electron collision stopping powers capable of testing the theoretical values within these stated uncertainties. A large NaI spectrometer was used to measure the change in electron energy when an absorbing disk of known thickness was placed in an electron beam. Monte Carlo simulations of the experiment were performed to account for the effects of surrounding materials. Energy differences between the calculated and measured spectra were used to determine corrections to the soft collision component of the theoretical stopping powers employed by the Monte Carlo simulations. Four different elemental materials were studied: Be, Al, Cu, and Ta. This provided a wide range of atomic numbers and densities over which to test the theory. In addition, stopping powers were measured for graphite (both standard and pyrolytic), A-150 tissue equivalent plastic, C-552 air equivalent plastic, and water. The incident electron energies ranged from 5 to 30 MeV. Generally, the measured stopping powers agree with the theoretical values within the experimental uncertainties, which range from 0.4% to 0.7% (1σ). Aluminum, however, exhibits a 0.7% discrepancy at higher electron energies. Furthermore, these measurements have established that the grain density stopping power is appropriate for graphite, contrary to the recommendations of ICRU Report 37. This removes a 0.2% uncertainty in air kerma calibrations, and impacts on dosimetric quantities determined via graphite calorimetry, such as ɛG for Fricke dosimetry and (W/ e)air for ion chamber measurements.

  4. Accurate Molecular Polarizabilities Based on Continuum Electrostatics

    PubMed Central

    Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.

    2013-01-01

    A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034

  5. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139

  6. Accurate phase-shift velocimetry in rock

    NASA Astrophysics Data System (ADS)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  7. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  8. Precise and accurate isotopic measurements using multiple-collector ICPMS

    NASA Astrophysics Data System (ADS)

    Albarède, F.; Telouk, Philippe; Blichert-Toft, Janne; Boyet, Maud; Agranier, Arnaud; Nelson, Bruce

    2004-06-01

    New techniques of isotopic measurements by a new generation of mass spectrometers equipped with an inductively-coupled-plasma source, a magnetic mass filter, and multiple collection (MC-ICPMS) are quickly developing. These techniques are valuable because of (1) the ability of ICP sources to ionize virtually every element in the periodic table, and (2) the large sample throughout. However, because of the complex trajectories of multiple ion beams produced in the plasma source whether from the same or different elements, the acquisition of precise and accurate isotopic data with this type of instrument still requires a good understanding of instrumental fractionation processes, both mass-dependent and mass-independent. Although physical processes responsible for the instrumental mass bias are still to be understood more fully, we here present a theoretical framework that allows for most of the analytical limitations to high precision and accuracy to be overcome. After a presentation of unifying phenomenological theory for mass-dependent fractionation in mass spectrometers, we show how this theory accounts for the techniques of standard bracketing and of isotopic normalization by a ratio of either the same or a different element, such as the use of Tl to correct mass bias on Pb. Accuracy is discussed with reference to the concept of cup efficiencies. Although these can be simply calibrated by analyzing standards, we derive a straightforward, very general method to calculate accurate isotopic ratios from dynamic measurements. In this study, we successfully applied the dynamic method to Nd and Pb as examples. We confirm that the assumption of identical mass bias for neighboring elements (notably Pb and Tl, and Yb and Lu) is both unnecessary and incorrect. We further discuss the dangers of straightforward standard-sample bracketing when chemical purification of the element to be analyzed is imperfect. Pooling runs to improve precision is acceptable provided the pooled

  9. Quantum Chemical Calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Arnold, James O. (Technical Monitor)

    1997-01-01

    The current methods of quantum chemical calculations will be reviewed. The accent will be on the accuracy that can be achieved with these methods. The basis set requirements and computer resources for the various methods will be discussed. The utility of the methods will be illustrated with some examples, which include the calculation of accurate bond energies for SiF$_n$ and SiF$_n^+$ and the modeling of chemical data storage.

  10. Methods for Melting Temperature Calculation

    NASA Astrophysics Data System (ADS)

    Hong, Qi-Jun

    Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly. We propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments. We propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which

  11. Research on the Rapid and Accurate Positioning and Orientation Approach for Land Missile-Launching Vehicle

    PubMed Central

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-01-01

    Getting a land vehicle’s accurate position, azimuth and attitude rapidly is significant for vehicle based weapons’ combat effectiveness. In this paper, a new approach to acquire vehicle’s accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle’s accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm’s iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system’s working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249

  12. Research on the rapid and accurate positioning and orientation approach for land missile-launching vehicle.

    PubMed

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-01-01

    Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249

  13. Accurate spectral modeling for infrared radiation

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Gupta, S. K.

    1977-01-01

    Direct line-by-line integration and quasi-random band model techniques are employed to calculate the spectral transmittance and total band absorptance of 4.7 micron CO, 4.3 micron CO2, 15 micron CO2, and 5.35 micron NO bands. Results are obtained for different pressures, temperatures, and path lengths. These are compared with available theoretical and experimental investigations. For each gas, extensive tabulations of results are presented for comparative purposes. In almost all cases, line-by-line results are found to be in excellent agreement with the experimental values. The range of validity of other models and correlations are discussed.

  14. Accurate basis set truncation for wavefunction embedding

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  15. Accurate determination of characteristic relative permeability curves

    NASA Astrophysics Data System (ADS)

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  16. Spectroscopically Accurate Line Lists for Application in Sulphur Chemistry

    NASA Astrophysics Data System (ADS)

    Underwood, D. S.; Azzam, A. A. A.; Yurchenko, S. N.; Tennyson, J.

    2013-09-01

    Monitoring sulphur chemistry is thought to be of great importance for exoplanets. Doing this requires detailed knowledge of the spectroscopic properties of sulphur containing molecules such as hydrogen sulphide (H2S) [1], sulphur dioxide (SO2), and sulphur trioxide (SO3). Each of these molecules can be found in terrestrial environments, produced in volcano emissions on Earth, and analysis of their spectroscopic data can prove useful to the characterisation of exoplanets, as well as the study of planets in our own solar system, with both having a possible presence on Venus. A complete, high temperature list of line positions and intensities for H32 2 S is presented. The DVR3D program suite is used to calculate the bound ro-vibration energy levels, wavefunctions, and dipole transition intensities using Radau coordinates. The calculations are based on a newly determined, spectroscopically refined potential energy surface (PES) and a new, high accuracy, ab initio dipole moment surface (DMS). Tests show that the PES enables us to calculate the line positions accurately and the DMS gives satisfactory results for line intensities. Comparisons with experiment as well as with previous theoretical spectra will be presented. The results of this study will form an important addition to the databases which are considered as sources of information for space applications; especially, in analysing the spectra of extrasolar planets, and remote sensing studies for Venus and Earth, as well as laboratory investigations and pollution studies. An ab initio line list for SO3 was previously computed using the variational nuclear motion program TROVE [2], and was suitable for modelling room temperature SO3 spectra. The calculations considered transitions in the region of 0-4000 cm-1 with rotational states up to J = 85, and includes 174,674,257 transitions. A list of 10,878 experimental transitions had relative intensities placed on an absolute scale, and were provided in a form suitable

  17. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  18. Calculation of delayed-neutron energy spectra in a QRPA-Hauser-Feshbach model

    SciTech Connect

    Kawano, Toshihiko; Moller, Peter; Wilson, William B

    2008-01-01

    Theoretical {beta}-delayed-neutron spectra are calculated based on the Quasiparticle Random-Phase Approximation (QRPA) and the Hauser-Feshbach statistical model. Neutron emissions from an excited daughter nucleus after {beta} decay to the granddaughter residual are more accurately calculated than in previous evaluations, including all the microscopic nuclear structure information, such as a Gamow-Teller strength distribution and discrete states in the granddaughter. The calculated delayed-neutron spectra agree reasonably well with those evaluations in the ENDF decay library, which are based on experimental data. The model was adopted to generate the delayed-neutron spectra for all 271 precursors.

  19. Synthesis, crystal structures and theoretical calculations of new 1-[2-(5-chloro-2-benzoxazolinone-3-yl)acetyl]-3,5-diphenyl-4,5-dihydro-(1H)-pyrazoles

    NASA Astrophysics Data System (ADS)

    Gökşen, Umut Salgın; Alpaslan, Yelda Bingöl; Kelekçi, Nesrin Gökhan; Işık, Şamil; Ekizoğlu, Melike

    2013-05-01

    1-[2-(5-Chloro-2-benzoxazolinone-3-yl)acetyl]-3-phenyl-5-(3-methoxyphenyl)-4,5-dihydro-(1H)-pyrazole (5a), 1-[2-(5-chloro-2-benzoxazolinone-3-yl)acetyl]-3-phenyl-5-(3,4-dimethoxyphenyl)-4,5-dihydro-(1H)-pyrazole (5b) and 1-[2-(5-chloro-2-benzoxazolinone-3-yl)acetyl]-3-(4-methylphenyl)-5-(2,3-dimethoxyphenyl)-4,5-dihydro-(1H)-pyrazole (5c) were synthesized. The crystal and molecular structures of the compounds 5a, 5b and 5c were determined by elemental analyses, IR, 1H NMR, ESI-MS and single-crystal X-ray diffraction. DFT method with 6-31G(d,p) basis set was used to calculate the optimized geometrical parameters, vibrational frequencies and chemical shift values. The calculated vibrational frequencies and chemical shift values were compared with experimental IR and 1H NMR values. The results represented that there was a good agreement between experimental and calculated values of the compounds 5a-5c. In addition, DFT calculations of the compounds, molecular electrostatic potentials (MEPs) and frontier molecular orbitals were performed at B3LYP/6-31G(d,p) level of theory. Furthermore, compounds were tested against three Gram-positive bacteria: Staphylococcus aureus ATCC 29213 (American Type Culture Collection), methicillin resistant S. aureus (MRSA) ATCC 43300 and Enterococcus faecalis ATCC 29212; two Gram negative bacteria: Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853; and three fungi: Candida albicans ATCC 90028, Candida krusei ATCC 6258 and Candida parapsilosis ATCC 90018. In general, all of the compounds were found to be slightly active against tested microorganisms.

  20. Synthesis, spectroscopy, electrochemistry and thermogravimetry of copper(II) tridentate Schiff base complexes, theoretical study of the structures of compounds and kinetic study of the tautomerism reactions by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Kianfar, Ali Hossein; Ramazani, Shapour; Fath, Roghaye Hashemi; Roushani, Mahmoud

    2013-03-01

    Attempts to spectroscopic and structural study of copper complexes, some Cu(II) Schiff base complexes were synthesized and characterized by means of electronic, IR, 1HNMR spectra and elemental analysis. The thermal analyses of the complexes were investigated and the first order kinetic parameters were derived for them. The cyclic voltammetric studies in acetonitrile were proposed a monomeric structure for complexes. The structures of compounds were determined by ab initio calculations. In the solid state, the ligands exist as keto-amine/enol-imine tautomeric forms with an intramolecular hydrogen bond (Nsbnd H⋯O) between amine and carbonyl group. The kinetic studies of the tautomerism and equilibrium constant of the reactions were calculated using transition state theory. The optimized molecular geometry and atomic charges were calculated using MP2 method with 6-31G(d) basis set for H, C, N and O atoms and LANL2DZ for the Cu atom. The results suggested that, in the complexes, Cu(II) ion is in pseudo square-planar NO3 coordination geometry. Also the bond lengths and angles were studied and compared.

  1. Theoretical study of hole initiated impact ionization in bulk silicon and GaAs using a wave-vector-dependent numerical transition rate formulation within an ensemble Monte Carlo calculation

    NASA Technical Reports Server (NTRS)

    Oguzman, Ismail H.; Wang, Yang; Kolnik, Jan; Brennan, Kevin F.

    1995-01-01

    In this paper, calculations of the hole initiated interband impact ionization rate in bulk silicon and GaAs are presented based on an ensemble Monte Carlo simulation with the inclusion of a wave-vector-dependent numerical transition rate formulation. The ionization transition rate is determined for each of the three valence bands, heavy, light, and split-off, using Fermi's golden rule with a two-body, screened Coulomb interaction. The dielectric function used within the calculation is assumed to be wave-vector-dependent. Calculations of the field-dependent impact ionization rate as well as the quantum yield are presented. It is found from both the quantum yield results and examination of the hole distribution function that the effective threshold energy for hole initiated impact ionization is relatively soft, similar to that predicted for the corresponding electron initiated ionization events occur more frequently than either heavy or split-offf initiated ionization events in bulk silicon over the applied electric field strengths examined here, 250-500 kV/cm. Conversely,in GaAs, the vast majority of hole initated ionization events originate from holes within the split-off band.

  2. Assessing the performance of popular QM methods for calculation of conformational energies of trialanine

    NASA Astrophysics Data System (ADS)

    Li, Yongxiu; Zhang, Saiqun; Zhang, John Z. H.; He, Xiao

    2016-05-01

    Accurate description of the conformational energies of the amino acids is essential for molecular dynamics simulation of protein structures. In this study, we compute the relative energies at 51 conformations for a trialanine tetrapeptide at different levels of theory. The computed energies at various theoretical levels, including the semiempirical DFTB method, HF, DFT, MP2 and CCSD(T), are compared with each other. The calculated energies from density-fitting local CCSD(T)/CBS (complete basis set) calculations are taken as the benchmark. The accuracy of the theoretical methods is highly dependent on the electronic correlation and dispersion corrections as well as the size of the basis sets. The involvement of the empirical dispersion energies in HF and DFT methods consistently improves their performance. Considering both the accuracy and computational efficiency, the Minnesota density functional M06-L-D and M06-2X-D are efficient and accurate for modeling of trialanine structures.

  3. Theoretical assessment of graphene-metal contacts.

    PubMed

    Janthon, Patanachai; Viñes, Francesc; Kozlov, Sergey M; Limtrakul, Jumras; Illas, Francesc

    2013-06-28

    Graphene-metal contacts have emerged as systems of paramount importance in the synthesis of high-quality and large-size patches of graphene and as vital components of nanotechnological devices. Herein, we study the accuracy of several density functional theory methods using van der Waals functionals or dispersive forces corrections when describing the attachment of graphene on Ni(111). Two different experimentally observed chemisorption states, top-fcc and bridge-top, were put under examination, together with the hcp-fcc physisorption state. Calculated geometric, energetic, and electronic properties were compared to experimental data. From the calculations, one finds that (i) predictions made by different methodologies differ significantly and (ii) optB86b-vdW functional and Grimme dispersion correction seem to provide the best balanced description of stability of physisorption and chemisorption states, the attachment strength of the latter on Ni(111) surface, the graphene-Ni(111) separation, and the bandstructure of chemisorbed graphene. The collation suggests that accurate and affordable theoretical studies on technologies based on graphene-metal contacts are already at hand.

  4. Space Service Market (Theoretical Aspect)

    NASA Astrophysics Data System (ADS)

    Prisniakov, V. F.; Prisniakova, L. M.

    The authors propose a mathematical model of the demand and supply in the market economics and in the market of space services, in particular. A theoretical demand formula and a real curve demand are compared. The market equilibrium price is defined. The space market dynamics is studied. The calculations are carried out for the parameters which are close to the market of space services.

  5. Theoretical molecular studies of astrophysical interest

    NASA Technical Reports Server (NTRS)

    Flynn, George

    1991-01-01

    When work under this grant began in 1974 there was a great need for state-to-state collisional excitation rates for interstellar molecules observed by radio astronomers. These were required to interpret observed line intensities in terms of local temperatures and densities, but, owing to lack of experimental or theoretical values, estimates then being used for this purpose ranged over several orders of magnitude. A problem of particular interest was collisional excitation of formaldehyde; Townes and Cheung had suggested that the relative size of different state-to-state rates (propensity rules) was responsible for the anomalous absorption observed for this species. We believed that numerical molecular scattering techniques (in particular the close coupling or coupled channel method) could be used to obtain accurate results, and that these would be computationally feasible since only a few molecular rotational levels are populated at the low temperatures thought to prevail in the observed regions. Such calculations also require detailed knowledge of the intermolecular forces, but we thought that those could also be obtained with sufficient accuracy by theoretical (quantum chemical) techniques. Others, notably Roy Gordon at Harvard, had made progress in solving the molecular scattering equations, generally using semi-empirical intermolecular potentials. Work done under this grant generalized Gordon's scattering code, and introduced the use of theoretical interaction potentials obtained by solving the molecular Schroedinger equation. Earlier work had considered only the excitation of a diatomic molecule by collisions with an atom, and we extended the formalism to include excitation of more general molecular rotors (e.g., H2CO, NH2, and H2O) and also collisions of two rotors (e.g., H2-H2).

  6. Theoretical studies of condensed-phase chemistry

    NASA Astrophysics Data System (ADS)

    Johnson, Michael Andrew

    1999-12-01

    The material presented here can be divided into two categories, (i)chemistry of energetic materials, or (ii)interfacial quantum chemistry. The work in Chapters 2 and 3 was performed as part of a program to simulate accidental fires and explosions. Combustion simulations rely on a great deal of chemical information such as enthalpy changes and reaction barriers for hundreds of chemical reactions, and Chapter 2 proposes a strategy for efficient calculation of these parameters. Also important in the simulation of combustion is the ability to track physical properties through phase changes. Chapter 3 emphasizes the importance of polarization in the crystal phase of DMNA; this knowledge is vital to the development of accurate molecular dynamics force fields for simulating thermophysical properties of explosive materials. Chapters 4, 5, and 6, are devoted to forefront theoretical research in the field of interfacial chemistry. As an example of chemistry at the solid-vacuum interface, the catalytic production of methyl radicals over lithium-doped magnesium oxide is considered. A new mechanism is proposed for the catalytic coupling of methane that is more consistent with available experimental data than the previously proposed Ito- Lunsford mechanism. The final two chapters describe in great detail the interactions of water with the magnesium oxide (100) surface. Applied is a novel theoretical approach that combines an embedded quantum cluster for modeling the crystal surface with a dielectric continuum representation of the solution phase. Validation of this approach is achieved by demonstrating that it can reasonably model complicated many-body interactions at solid-liquid interfaces. Attention is then focused on the challenging problem regarding the chemical reactivity of the MgO-water interface. Presented are both experimental and theoretical studies that provide new evidence for dissociative chemisorption of water molecules at the MgO(100) interface with bulk water

  7. Frozen core potential scheme with a relativistic electronic Hamiltonian: Theoretical connection between the model potential and all-electron treatments

    NASA Astrophysics Data System (ADS)

    Seino, Junji; Tarumi, Moto; Nakai, Hiromi

    2014-01-01

    This Letter proposes an accurate scheme using frozen core orbitals, called the frozen core potential (FCP) method, to theoretically connect model potential calculations to all-electron (AE) ones. The present scheme is based on the Huzinaga-Cantu equation combined with spin-free relativistic Douglas-Kroll-Hess Hamiltonians. The local unitary transformation scheme for efficiently constructing the Hamiltonian produces a seamless extension to the FCP method in a relativistic framework. Numerical applications to coinage diatomic molecules illustrate the high accuracy of this FCP method, as compared to AE calculations. Furthermore, the efficiency of the FCP method is also confirmed by these calculations.

  8. Accurate documentation and wound measurement.

    PubMed

    Hampton, Sylvie

    This article, part 4 in a series on wound management, addresses the sometimes routine yet crucial task of documentation. Clear and accurate records of a wound enable its progress to be determined so the appropriate treatment can be applied. Thorough records mean any practitioner picking up a patient's notes will know when the wound was last checked, how it looked and what dressing and/or treatment was applied, ensuring continuity of care. Documenting every assessment also has legal implications, demonstrating due consideration and care of the patient and the rationale for any treatment carried out. Part 5 in the series discusses wound dressing characteristics and selection.

  9. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    PubMed Central

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe− using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm−1 or 153.236(34) meV. The fine structures of Fe− were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm−1 accuracy. PMID:27138292

  10. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-05-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe‑ using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm‑1 or 153.236(34) meV. The fine structures of Fe‑ were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm‑1 accuracy.

  11. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.

    PubMed

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe(-) using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm(-1) or 153.236(34) meV. The fine structures of Fe(-) were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm(-1) accuracy. PMID:27138292

  12. Theoretical calculation of performance enhancement in lattice-matched SiGeSn/GeSn p-channel tunneling field-effect transistor with type-II staggered tunneling junction

    NASA Astrophysics Data System (ADS)

    Wang, Hongjuan; Han, Genquan; Wang, Yibo; Peng, Yue; Liu, Yan; Zhang, Chunfu; Zhang, Jincheng; Hu, Shengdong; Hao, Yue

    2016-04-01

    In this work, a lattice-matched SiGeSn/GeSn heterostructure p-channel tunneling field-effect transistor (hetero-PTFET) with a type-II staggered tunneling junction (TJ) is investigated theoretically. Lattice matching and type-II band alignment at the Γ-point is obtained at the SiGeSn/GeSn interface by tuning Sn and Si compositions. A steeper subthreshold swing (SS) and a higher on state current (I ON) are demonstrated in SiGeSn/GeSn hetero-PTFET than in GeSn homo-PTFET. Si0.31Ge0.49Sn0.20/Ge0.88Sn0.12 hetero-PTFET achieves a 2.3-fold higher I ON than Ge0.88Sn0.12 homo-PTFET at V DD of 0.3 V. Hetero-PTFET achieves a more abrupt hole profile and a higher carrier density near TJ than the homo-PTFET, which contributes to the significantly enhanced band-to-band tunneling (BTBT) rate and tunneling current in hetero-PTFET.

  13. Design Calculations for Thermoelectric Generators

    NASA Technical Reports Server (NTRS)

    Zeldin, B.

    1983-01-01

    Nine simplified analytic models based on average properties accurately predict heat rates for silicon/germanium thermoelectric generators. Solutions from simplified models were compared with those obtained using sophisticated numerical analysis. Maximum errors in calculated heat rate range from about 4 percent to about 0.2 percent. Models also used to calculate power delivered to load and thermodynamic efficiency.

  14. A theoretical study of the mechanism of the atmospherically relevant reaction of chlorine atoms with methyl nitrate, and calculation of the reaction rate coefficients at temperatures relevant to the troposphere.

    PubMed

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

    2015-03-21

    The reaction between atomic chlorine (Cl) and methyl nitrate (CH3ONO2) is significant in the atmosphere, as Cl is a key oxidant, especially in the marine boundary layer, and alkyl nitrates are important nitrogen-containing organic compounds, which are temporary reservoirs of the reactive nitrogen oxides NO, NO2 and NO3 (NOx). Four reaction channels HCl + CH2ONO2, CH3OCl + NO2, CH3Cl + NO3 and CH3O + ClNO2 were considered. The major channel is found to be the H abstraction channel, to give the products HCl + CH2ONO2. For all channels, geometry optimization and frequency calculations were carried out at the M06-2X/6-31+G** level, while relative electronic energies were improved to the UCCSD(T*)-F12/CBS level. The reaction barrier (ΔE(‡)0K) and reaction enthalpy (ΔH(RX)298K) of the H abstraction channel were computed to be 0.61 and -2.30 kcal mol(-1), respectively, at the UCCSD(T*)-F12/CBS//M06-2X/6-31+G** level. Reaction barriers (ΔE(‡)0K) for the other channels are more positive and these pathways do not contribute to the overall reaction rate coefficient in the temperature range considered (200-400 K). Rate coefficients were calculated for the H-abstraction channel at various levels of variational transition state theory (VTST) including tunnelling. Recommended ICVT/SCT rate coefficients in the temperature range 200-400 K are presented for the first time for this reaction. The values obtained in the 200-300 K region are particularly important as they will be valuable for atmospheric modelling calculations involving reactions with methyl nitrate. The implications of the results to atmospheric chemistry are discussed. Also, the enthalpies of formation, ΔHf,298K, of CH3ONO2 and CH2ONO2 were computed to be -29.7 and 19.3 kcal mol(-1), respectively, at the UCCSD(T*)-F12/CBS level.

  15. SPLASH: Accurate OH maser positions

    NASA Astrophysics Data System (ADS)

    Walsh, Andrew; Gomez, Jose F.; Jones, Paul; Cunningham, Maria; Green, James; Dawson, Joanne; Ellingsen, Simon; Breen, Shari; Imai, Hiroshi; Lowe, Vicki; Jones, Courtney

    2013-10-01

    The hydroxyl (OH) 18 cm lines are powerful and versatile probes of diffuse molecular gas, that may trace a largely unstudied component of the Galactic ISM. SPLASH (the Southern Parkes Large Area Survey in Hydroxyl) is a large, unbiased and fully-sampled survey of OH emission, absorption and masers in the Galactic Plane that will achieve sensitivities an order of magnitude better than previous work. In this proposal, we request ATCA time to follow up OH maser candidates. This will give us accurate (~10") positions of the masers, which can be compared to other maser positions from HOPS, MMB and MALT-45 and will provide full polarisation measurements towards a sample of OH masers that have not been observed in MAGMO.

  16. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  17. Accurate thickness measurement of graphene.

    PubMed

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  18. Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach.

    PubMed

    Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti

    2016-01-01

    The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems. PMID:26651397

  19. Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach.

    PubMed

    Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti

    2016-01-01

    The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems.

  20. MEMS Calculator

    National Institute of Standards and Technology Data Gateway

    SRD 166 MEMS Calculator (Web, free access)   This MEMS Calculator determines the following thin film properties from data taken with an optical interferometer or comparable instrument: a) residual strain from fixed-fixed beams, b) strain gradient from cantilevers, c) step heights or thicknesses from step-height test structures, and d) in-plane lengths or deflections. Then, residual stress and stress gradient calculations can be made after an optical vibrometer or comparable instrument is used to obtain Young's modulus from resonating cantilevers or fixed-fixed beams. In addition, wafer bond strength is determined from micro-chevron test structures using a material test machine.