Science.gov

Sample records for overlap molecular orbital

  1. Shake for Sigma, Pray for Pi: Classroom Orbital Overlap Analogies

    ERIC Educational Resources Information Center

    Dicks, Andrew P.

    2011-01-01

    An introductory organic classroom demonstration is discussed where analogies are made between common societal hand contact and covalent bond formation. A handshake signifies creation of a [sigma] bond ("head-on" orbital overlap), whereas the action of praying illustrates "sideways" overlap and generation of a [pi] bond. The nature of orbital and…

  2. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

    We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690

  3. Analytical treatment of two-center overlap integral with respect to same screening constants over Slater type orbitals

    NASA Astrophysics Data System (ADS)

    Ćopuroǧlu, Ebru; Mamedov, Bahtiyar A.

    2016-08-01

    By the use of Löwdin- α radial function, an alternative method is introduced for two-center overlap integral over Slater type orbitals (STOs) at same screening constants (SSC). Notice that the overlap integrals with SSC have an important role in accurate evaluation of multicenter multielectron molecular integrals arising in combined Hartree-Fock-Roothaan (CHFR) theory. This approximation provides us simple and efficient expression for the two-center overlap integrals. To show the effectiveness of established formula we have compared our results with available literature data. The method ensures high performance with a very short CPU time.

  4. Visualization of Molecular Orbitals: Formaldehyde

    ERIC Educational Resources Information Center

    Olcott, Richard J.

    1972-01-01

    Describes a computer program that plots a solid" representation of molecular orbital charge density which can be used to analyze wave functions of molecules. Illustrated with diagrams for formaldehyde. (AL)

  5. Imaging molecular orbitals using photoionization

    NASA Astrophysics Data System (ADS)

    Santra, Robin

    2006-10-01

    The interpretation of a recent experiment using high-order harmonic generation [Itatani et al., Nature 432 (2004) 867] as a measurement of the highest occupied molecular orbital of a molecule is conceptually problematic, even if the independent-particle picture is taken seriously. Guided by the relationship between the amplitude for one-photon-induced electron emission and the electron-ion recombination amplitude in the three-step model of high-order harmonic generation, it is argued that synchrotron-based photoionization might be a superior approach to imaging molecular orbitals. Within the Hartree-Fock independent-particle picture, the molecular-frame photoelectron angular distributions, measured as a function of photon energy, could be used to reconstruct all orbitals occupied in the Hartree-Fock ground state of the molecule investigated. It is suggested that laser alignment techniques could be employed to facilitate the measurement of the molecular-frame photoelectron angular distributions.

  6. Generation of a two-center overlap integral over Slater orbitals of higher principal quantum numbers

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1992-01-01

    The expressions for two-center overlap integrals between angular s, p, and d Slater orbitals of arbitrary, higher principal quantum number are explicitly listed. The expressions obtained are extremely compact and independent of the coordinate system. It is further shown that the numerical values of the integrals obtained in this way are free from any numerical instability.

  7. Angular-overlap calculation of the Jahn-Teller stabilization energie for f-orbital degeneracies

    SciTech Connect

    Warren, K.D.

    1980-03-01

    The angular-overlap model is applied to the calculation of the linear Jahn-Teller coupling constants for f-orbital degeneracies. The MX/sub 6/, O/sub h/, chromophore is treated as representative of the highest symmetry commonly occurring in the lanthanide and actinide series, and it is shown that, even when spin-orbit effects are taken into account, 5f orbital degeneracies may lead to significant Jahn-Teller stabilization energies. The operation of this effect for F/sup 1/ GAMMA/sub 8/ states is considered. 2 tables.

  8. Some Observations on Molecular Orbital Theory

    ERIC Educational Resources Information Center

    Journal of Chemical Education, 2005

    2005-01-01

    A few flawed predictions in the context of homonuclear diatomic molecules are presented in order to introduce students to molecular orbital (MO) theory. A common misrepresentation of the relationship between the energy of an atomic orbital and the energy of the MO associated with the atomic orbital is illustrated.

  9. Band Formation in a Molecular Quantum Well via 2D Superatom Orbital Interactions

    SciTech Connect

    Dougherty, D. B.; Feng, Min; Petek, Hrvoje; Yates, John T.; Zhao, Jin

    2012-12-28

    By scanning tunneling microscopy and spectroscopy, we study nearly free electron band formation of the σ*lowest unoccupied molecular orbital of C₆F₆ on a Cu(111) surface. In fractal islands, the lowest unoccupied molecular orbital energy systematically stabilizes with the number of interacting near-neighbor C₆F₆ molecules. Density functional theory calculations reveal the origin of effective intermo- lecular orbital overlap in the previously unrecognized superatom character of the σ*orbital of ₆F₆ molecules. The discovery of superatom orbitals in planar molecules offers a new universal principle for effective band formation, which can be exploited in designing organic semiconductors with nearly free electron properties

  10. Evaluation of VIIRS SST fields through the analysis of overlap regions between consecutive orbits

    NASA Astrophysics Data System (ADS)

    Cayula, Jean-François P.; May, Douglas A.; Arnone, Robert A.; Vandermeulen, Ryan A.

    2015-05-01

    Full-swath Sea Surface Temperature (SST) derived from data acquired by the Visible Infrared Imaging Radiometer Suite (VIIRS) sensor on-board the Suomi-National Polar-orbiting Partnership (S-NPP) satellite produces significant overlap between consecutive orbits at all latitudes. In this study, we use those overlap regions to evaluate VIIRS SST, as inconsistencies between SST values from consecutive orbits are indications of likely degraded quality. The studies investigate two sources of inconsistencies: those resulting from the response of the SST equations when observing a scene from differing view angles and those caused by undetected data contamination. This study will present results for two VIIRS SST products: one from the Naval Oceanographic Office (NAVOCEANO), which is assimilated in the Navy Ocean Models, and the Advanced Clear-Sky Processor for Oceans (ACSPO) product from the National Oceanic and Atmospheric Administration (NOAA) Center for Satellite Applications and Research (STAR). Global statistics based on drifting buoys for both NAVOCEANO and NOAA products complete the analysis.

  11. A Simple Huckel Molecular Orbital Plotter

    ERIC Educational Resources Information Center

    Ramakrishnan, Raghunathan

    2013-01-01

    A program is described and presented to readily plot the molecular orbitals from a Huckel calculation. The main features of the program and the scope of its applicability are discussed through some example organic molecules. (Contains 2 figures.)

  12. Remarkably high mobility ultra-thin-film metal-oxide transistor with strongly overlapped orbitals

    PubMed Central

    Wei Shih, Chen; Chin, Albert; Fu Lu, Chun; Fang Su, Wei

    2016-01-01

    High mobility channel thin-film-transistor (TFT) is crucial for both display and future generation integrated circuit. We report a new metal-oxide TFT that has an ultra-thin 4.5 nm SnO2 thickness for both active channel and source-drain regions, very high 147 cm2/Vs field-effect mobility, high ION/IOFF of 2.3 × 107, small 110 mV/dec sub-threshold slope, and a low VD of 2.5 V for low power operation. This mobility is already better than chemical-vapor-deposition grown multi-layers MoS2 TFT. From first principle quantum-mechanical calculation, the high mobility TFT is due to strongly overlapped orbitals. PMID:26744240

  13. Remarkably high mobility ultra-thin-film metal-oxide transistor with strongly overlapped orbitals

    NASA Astrophysics Data System (ADS)

    Wei Shih, Chen; Chin, Albert; Fu Lu, Chun; Fang Su, Wei

    2016-01-01

    High mobility channel thin-film-transistor (TFT) is crucial for both display and future generation integrated circuit. We report a new metal-oxide TFT that has an ultra-thin 4.5 nm SnO2 thickness for both active channel and source-drain regions, very high 147 cm2/Vs field-effect mobility, high ION/IOFF of 2.3 × 107, small 110 mV/dec sub-threshold slope, and a low VD of 2.5 V for low power operation. This mobility is already better than chemical-vapor-deposition grown multi-layers MoS2 TFT. From first principle quantum-mechanical calculation, the high mobility TFT is due to strongly overlapped orbitals.

  14. Remarkably high mobility ultra-thin-film metal-oxide transistor with strongly overlapped orbitals.

    PubMed

    Shih, Chen Wei; Chin, Albert; Lu, Chun Fu; Su, Wei Fang

    2016-01-01

    High mobility channel thin-film-transistor (TFT) is crucial for both display and future generation integrated circuit. We report a new metal-oxide TFT that has an ultra-thin 4.5 nm SnO2 thickness for both active channel and source-drain regions, very high 147 cm(2)/Vs field-effect mobility, high ION/IOFF of 2.3 × 10(7), small 110 mV/dec sub-threshold slope, and a low VD of 2.5 V for low power operation. This mobility is already better than chemical-vapor-deposition grown multi-layers MoS2 TFT. From first principle quantum-mechanical calculation, the high mobility TFT is due to strongly overlapped orbitals. PMID:26744240

  15. Simple orbital theory for the molecular electrician.

    PubMed

    Ernzerhof, Matthias

    2011-07-01

    Theories of molecular electronic devices (MEDs) are quite involved in general. However, various prominent features of MEDs can be understood drawing only on elementary quantum theory. To support this point of view, we provide a two component orbital theory that enables one to reproduce various important features of MEDs. In this theory, the device orbitals are divided into two components, each of which is obtained from simple rules. To illustrate our two-component model, we apply it to explain, among other things, the conductance suppression in cross-conjugated systems and the dependence of the conductance on the contact position in aromatic systems. PMID:21744885

  16. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

    Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.

    2014-05-14

    The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.

  17. A Comparison of Molecular Vibrational Theory to Huckel Molecular Orbital Theory.

    ERIC Educational Resources Information Center

    Keeports, David

    1986-01-01

    Compares the similar mathematical problems of molecular vibrational calculations (at any intermediate level of sophistication) and molecular orbital calculations (at the Huckel level). Discusses how the generalizations of Huckel treatment of molecular orbitals apply to vibrational theory. (TW)

  18. Seasonal trends of ACSPO VIIRS SST product characterized by the differences in orbital overlaps for various water types

    NASA Astrophysics Data System (ADS)

    Arnone, Robert; Vandermeulen, Ryan; Ignatov, Alexander; Cayula, Jean François

    2015-05-01

    The uncertainty of the Advanced Clear-Sky Processor for Oceans (ACSPO) Sea Surface Temperature (SST) products from the Visible Infrared Imaging Radiometer Suite (VIIRS) satellite is examined using consecutive orbital overlaps in coastal waters of the Gulf of Mexico. The overlapping region on the left and right side of the VIIRS swath at 23-35 degree latitude covers approximately 500 pixels, which occur within 100 minutes and can provide a total of 4 SST products (2 day and 2 night) per day. By assuming the ocean SST should be similar on each side of the swath in this short time period, diel changes are examined and the uncertainty of SST retrieval is determined by comparing with buoy-derived SST. The VIIRS ACSPO product from NOAA STAR was used to determine the difference in SST within the overlapping regions. These SST changes are evaluated between consecutive orbits to validate the accuracy of SST algorithms on each side of the swath at high sensor angles. The SST product differences across the swath can result from surface glint, sensor angular impacts and sensor characteristics such as half angle mirror side (HAM) and calibration. The absolute diurnal SST changes that can occur within 100 minutes are evaluated with the buoy and VIIRS-derived SST. Sensitivity of the SST to water types is evaluated by measuring diurnal differences for open ocean, shelf and coastal waters. The 100 minute VIIRS SST overlap shows the capability to monitor the diurnal ocean heating and cooling which are associated with water mass optical absorption. The seasonal trends of the difference in SST at the overlaps for these water masses were tracked on a monthly basis. The unique capability of using the same VIIRS sensor for self-characterization can provide a method to define the uncertainty of ocean products and characterize the diurnal changes for different water types.

  19. Orbital symmetry and interference effects in molecular high-order harmonic generation

    SciTech Connect

    Lagmago Kamta, G.; Bandrauk, A. D.

    2009-10-15

    We investigate harmonic generation from H{sub 2}{sup +} molecules driven by intense few-cycle laser pulses whose linearly polarization axis makes an arbitrary angle {chi} with respect to the molecular axis. The H{sub 2}{sup +} molecule is considered initially in various orbitals with nodal planes. It is found that a strong enhancement of high-order harmonics (HOHs) occurs when the laser polarization axis overlaps with major axes of electron distribution in the active orbital, while broad suppression of HOHs occurs when the laser polarization axis is parallel to a nodal plane of the active molecular orbital. We show that this harmonic suppression is enhanced by destructive interferences when the nodal and the laser polarization axes are parallel to the internuclear axis, which leads to a shortening of the harmonic cutoff. It follows that the orientation dependence of HOHs intensities mimics the electronic density in active orbitals through the angular dependence of ionization and recombination processes.

  20. Libraries of Extremely Localized Molecular Orbitals. 1. Model Molecules Approximation and Molecular Orbitals Transferability.

    PubMed

    Meyer, Benjamin; Guillot, Benoît; Ruiz-Lopez, Manuel F; Genoni, Alessandro

    2016-03-01

    Despite more and more remarkable computational ab initio results are nowadays continuously obtained for large macromolecular systems, the development of new linear-scaling techniques is still an open and stimulating field of research in theoretical chemistry. In this family of methods, an important role is occupied by those strategies based on the observation that molecules are generally constituted by recurrent functional units with well-defined intrinsic features. In this context, we propose to exploit the notion of extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, or functional groups), are in principle transferable from one molecule to another. Accordingly, the construction of orbital libraries to almost instantaneously build up approximate wave functions and electron densities of very large systems becomes conceivable. In this work, the ELMOs transferability is further investigated in detail and, furthermore, suitable rules to construct model molecules for the computation of ELMOs to be stored in future databanks are also defined. The obtained results confirm the reliable transferability of the ELMOs and show that electron densities obtained from the transfer of extremely localized molecular orbitals are very close to the corresponding Hartree-Fock ones. These observations prompt us to construct new ELMOs databases that could represent an alternative/complement to the already popular pseudoatoms databanks both for determining electron densities and for refining crystallographic structures of very large molecules. PMID:26799516

  1. Molecular orbitals for properties and spectroscopies

    SciTech Connect

    Robert, Vincent; Domingo, Alex; Braunstein, Pierre; Danopoulos, Andreas; Monakhov, Kirill

    2015-12-31

    The description and clarification of spectroscopies and properties goes through ab initio calculations. Wave function based calculations (CASSCF/CASPT2) are particularly appealing since they offer spectroscopic accuracy and means of interpretation. we performed such calculations to elucidate the origin of unusual structural changes and intramolecular electron transfer phenomenon. Based on optimized molecular orbitals and a reading of the multireference wave function, it is suggested that intimate interactions are likely to considerably modify the standard pictures. A so-called PIMA (polarization-induced metalâĹŠarene) interaction similar to the more familiar anion-π interaction is responsible for a significant deviation from sp{sup 3} geometry and an energetic stabilization of 50 kJ/mol in Cr(II) benzyl organometallic complexes. In a similar fashion, it is proposed that the energetic profile of the IVCT (inter valence charge transfer) exhibits strong similarities to the Marcus’ theory, suggesting a response behaviour of the ensemble of electrons as electron transfer occurs in Fe{sup 2+}/Fe{sup 3+} bimetallic compound. The electronic reorganization induced by the IVCT process accounts for 11.8 eV, a very large effect that reduces the transfer energy down to 0.89 eV, in very good agreement with experiments.

  2. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ligands'' with localized surface orbitals perturbed only by these ligands''. These complexes'' are based on a twelve coordinate species with the ligands'' attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  3. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ``ligands`` with localized surface orbitals perturbed only by these ``ligands``. These ``complexes`` are based on a twelve coordinate species with the ``ligands`` attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  4. Molecular-orbital model for metal-sapphire interfacial strength

    NASA Technical Reports Server (NTRS)

    Johnson, K. H.; Pepper, S. V.

    1982-01-01

    Self-consistent-field X-Alpha scattered-wave cluster molecular-orbital models have been constructed for transition and noble metals (Fe, Ni, Cu, and Ag) in contact with a sapphire (Al2O3) surface. It is found that a chemical bond is established between the metal d-orbital electrons and the nonbonding 2p-orbital electrons of the oxygen anions on the Al2O3 surface. An increasing number of occupied metal-sapphire antibonding molecular orbitals explains qualitatively the observed decrease of contact shear strength through the series Fe, Ni, Cu, and Ag.

  5. Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

    PubMed

    Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

    2016-07-12

    We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step. PMID:27267207

  6. Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.

    ERIC Educational Resources Information Center

    Willis, Christopher J.

    1988-01-01

    Described are the energetics involved in the formation of molecular hydrogen using concepts that should be familiar to students beginning the study of molecular orbital theory. Emphasized are experimental data on ionization energies. Included are two-electron atomic and molecular systems. (CW)

  7. MOLECULAR DYNAMICS OF CASCADES OVERLAP IN TUNGSTEN WITH 20-KEV PRIMARY KNOCK-ON ATOMS

    SciTech Connect

    Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.

    2015-04-16

    Molecular dynamics simulations are performed to investigate the mutual influence of two subsequent cascades in tungsten. The influence is studied using 20-keV primary knock-on atoms, to induce one cascade after another separated by 15 ps, in a lattice temperature of 1025 K (i.e. 0.25 of the melting temperature of the interatomic potential). The center of mass of the vacancies at the peak damage during the cascade is taken as the location of the cascade. The distance between this location to that of the next cascade is taken as the overlap parameter. Empirical fits describing the number of surviving vacancies and interstitial atoms as a function of overlap are presented.

  8. Periodic orbits of the hydrogen molecular ion and their quantization

    SciTech Connect

    Duan, Y.; Yuan, J.; Bao, C.

    1995-11-01

    In a classical study of the hydrogen molecular ion beyond the Born-Oppenheimer approximation (BOA), we have found that segments of trajectories resemble that of the Born-Oppenheimer approximation periodic orbits. The importance of this fact to the classical understanding of chemical bonding leads us to a systematic study of the periodic orbits of the planar hydrogen molecular ion within the BOA. Besides introducing a classification scheme for periodic orbits, we discuss the convergence properties of families of periodic orbits and their bifurcation patterns according to their types. Semiclassical calculations of the density of states based on these periodic orbits yield results in agreement with the exact quantum eigenvalues of the hydrogen molecular ion system.

  9. Local Molecular Orbitals from a Projection onto Localized Centers.

    PubMed

    Heßelmann, Andreas

    2016-06-14

    A localization method for molecular orbitals is presented which exploits the locality of the eigenfunctions associated with the largest eigenvalues of the matrix representation of spatially localized functions. Local molecular orbitals are obtained by a projection of the canonical orbitals onto the set of the eigenvectors which correspond to the largest eigenvalues of these matrices. Two different types of spatially localized functions were chosen in this work, a two-parameter smooth-step-type function and the weight functions determined by a Hirshfeld partitioning of the molecular volume. It is shown that the method can provide fairly local occupied molecular orbitals if the positions of the set of local functions are set to the molecular bond centers. The method can also yield reasonably well-localized virtual molecular orbitals, but here, a sensible choice of the positions of the functions are the atomic sites and the locality then depends more strongly on the shape of the set of local functions. The method is tested for a range of polypeptide molecules in two different conformations, namely, a helical and a β-sheet conformation. Futhermore, it is shown that an adequate locality of the occupied and virtual orbitals can also be obtained for highly delocalized systems. PMID:27164445

  10. Dielectric properties of crystalline organic molecular films in the limit of zero overlap

    NASA Astrophysics Data System (ADS)

    D'Avino, Gabriele; Vanzo, Davide; Soos, Zoltán G.

    2016-01-01

    We present the calculation of the static dielectric susceptibility tensor and dipole field sums in thin molecular films in the well-defined limit of zero intermolecular overlap. Microelectrostatic and charge redistribution approaches are applied to study the evolution of dielectric properties from one to a few molecular layers in films of different conjugated molecules with organic electronics applications. Because of the conditional convergence of dipolar interactions, dipole fields depend on the shape of the sample and different values are found in the middle layer of a thick film and in the bulk. The shape dependence is eliminated when depolarization is taken into account, and the dielectric tensor of molecular films converges to the bulk limit within a few molecular layers. We quantify the magnitude of surface effects and interpret general trends among different systems in terms of molecular properties, such as shape, polarizability anisotropy, and supramolecular organization. A connection between atomistic models for molecular dielectrics and simpler theories for polarizable atomic lattices is also provided.

  11. Molecular shield - An orbiting low-density materials laboratory

    NASA Technical Reports Server (NTRS)

    Melfi, L. T., Jr.; Outlaw, R. A.; Hueser, J. E.; Brock, F. J.

    1976-01-01

    Analysis of a molecular shield orbited at 200 km utilizes the kinetic theory of a drifting Maxwellian gas, applied to a hemispherical shell geometry containing internal sources. The molecular shield provides very low gas density conditions for materials experiments at low gravity, while the hemispherical geometry minimizes the internal surface/volume ratio. Deployment of the shield in orbit is described. Contributions to density by shield outgassing, by experiment outgassing, and by interaction with the orbiter are discussed separately. A jettisonable closure plate sealing the hemisphere minimizes any risk of experiment contamination during deployment.

  12. Molecular orbital analysis of dicarbido-transition-metal cluster compounds

    SciTech Connect

    Halet, J.; Mingos, D.M.P.

    1988-01-01

    Molecular orbital calculations on dicarbido-transition-metal carbonyl cluster compounds have shown that the bonding between C/sub 2/ and the metal cage results primarily from electron donation from the C/sub 2/ sigma/sub rho/- and ..pi..-bonding molecular orbitals and back donation from filled metallic molecular orbitals to the C/sub 2/ ..pi..* orbitals. The bonding therefore follows closely the Chatt-Dewar-Ducanson model that has been established previously for ethyne and ethene complexes but not for interstitial moieties. The C-C separation in the dicarbido clusters depends critically on the geometric constraints imposed by the metal cage and the extent of forward and back donation. In these clusters where the carbon atoms are in adjacent trigonal-prismatic sites the calculated formal bond order is between 1.0 and 1.5, which agrees well with the observed C-C bond lengths.

  13. Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

    PubMed

    Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

    2014-01-01

    Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. PMID:24977711

  14. Is There a Need to Discuss Atomic Orbital Overlap When Teaching Hydrogen-Halide Bond Strength and Acidity Trends in Organic Chemistry?

    ERIC Educational Resources Information Center

    Devarajan, Deepa; Gustafson, Samantha J.; Bickelhaupt, F. Matthias; Ess, Daniel H.

    2015-01-01

    Undergraduate organic chemistry textbooks and Internet websites use a variety of approaches for presenting and explaining the impact of halogen atom size on trends in bond strengths and/or acidity of hydrogen halides. In particular, several textbooks and Internet websites explain these trends by invoking decreasing orbital overlap between the…

  15. Molecular and clinical characterization of patients with overlapping 10p deletions.

    PubMed

    Lindstrand, Anna; Malmgren, Helena; Verri, Annapia; Benetti, Elisa; Eriksson, Maud; Nordgren, Ann; Anderlid, Britt-Marie; Golovleva, Irina; Schoumans, Jacqueline; Blennow, Elisabeth

    2010-05-01

    Chromosome 10p terminal deletions have been associated with DiGeorge phenotype, and within the same genomic region haploinsufficiency of GATA3 causes the HDR syndrome (hypoparathyroidism, sensorineural deafness, renal dysplasia). We have performed detailed molecular analysis of four patients with partial overlapping 10p deletions by using FISH-mapping, array-CGH, and custom-designed high-resolution oligonucleotide array. All four patients had mental retardation and speech impairment and three of them showed variable signs of HDR syndrome. In addition, two patients had autistic behaviors and had similar dysmorphic features giving them a striking physical resemblance. A review of the literature identified 10 previously published cases with similar 10p deletions and reliable molecular or molecular cytogenetic mapping data. The combined information of present and previous cases suggests that partial deletions of 10p14-p15 represent a syndrome with a distinct and more severe phenotype than previously assumed. The main characteristics include severe mental retardation, language impairment, autistic behavior, and characteristic clinical features. A critical region involved in mental retardation and speech impairment is defined within 1.6 Mb in 10p15.3. In addition, deletion of 4.3 Mb within 10p14 is associated with autism and characteristic clinical findings. PMID:20425828

  16. Auxiliary functions for molecular integrals with Slater-type orbitals. II. Gauss transform methods

    NASA Astrophysics Data System (ADS)

    Ema, I.; López, R.; Fernández, J. J.; Ramírez, G.; Rico, J. F.

    The Gauss transform of Slater-type orbitals is used to express several types of molecular integrals involving these functions in terms of simple auxiliary functions. After reviewing this transform and the way it can be combined with the shift operator technique, a master formula for overlap integrals is derived and used to obtain multipolar moments associated to fragments of two-center distributions and overlaps of derivatives of Slater functions. Moreover, it is proved that integrals involving two-center distributions and irregular harmonics placed at arbitrary points (which determine the electrostatic potential, field and field gradient, as well as higher order derivatives of the potential) can be expressed in terms of auxiliary functions of the same type as those appearing in the overlap. The recurrence relations and series expansions of these functions are thoroughly studied, and algorithms for their calculation are presented. The usefulness and efficiency of this procedure are tested by developing two independent codes: one for the derivatives of the overlap integrals with respect to the centers of the functions, and another for derivatives of the potential (electrostatic field, field gradient, and so forth) at arbitrary points.0

  17. Exploring chemistry with the fragment molecular orbital method.

    PubMed

    Fedorov, Dmitri G; Nagata, Takeshi; Kitaura, Kazuo

    2012-06-01

    The fragment molecular orbital (FMO) method makes possible nearly linear scaling calculations of large molecular systems, such as water clusters, proteins and DNA. In particular, FMO has been widely used in biochemical applications involving protein-ligand binding and drug design. The method has been efficiently parallelized suitable for petascale computing. Many commonly used wave functions and solvent models have been interfaced with FMO. We review the historical background of FMO, and summarize its method development and applications. PMID:22410762

  18. Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent

    2012-01-01

    From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.

  19. Coulomb-corrected molecular orbital tomography of nitrogen

    NASA Astrophysics Data System (ADS)

    Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang

    2016-03-01

    High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation.

  20. Coulomb-corrected molecular orbital tomography of nitrogen.

    PubMed

    Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang

    2016-01-01

    High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation. PMID:27000666

  1. Coulomb-corrected molecular orbital tomography of nitrogen

    PubMed Central

    Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang

    2016-01-01

    High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation. PMID:27000666

  2. Conformation effects on the molecular orbitals of serine

    NASA Astrophysics Data System (ADS)

    Wang, Ke-Dong; Ma, Peng-Fei; Shan, Xu

    2011-03-01

    This paper calculates the five most stable conformers of serine with Hartree—Fock theory, density functional theory (B3LYP), Møller—Plesset perturbation theory (MP4(SDQ)) and electron propagation theory with the 6-311++G(2d,2p) basis set. The calculated vertical ionization energies for the valence molecular orbitals of each conformer are in agreement with the experimental data, indicating that a range of molecular conformations would coexist in an equilibrium sample. Information of the five outer valence molecular orbitals for each conformer is explored in coordinate and momentum spaces using dual space analysis to investigate the conformational processes, which are generated from the global minimum conformer Ser1 by rotation of C2-C3 (Ser4), C1-C2 (Ser5) and C1-O2 (Ser2 and Ser3). Orbitals 28a, 27a and 26a are identified as the fingerprint orbitals for all the conformational processes. Project supported by the Doctoral Research Fund of Henan Normal University, China (Grant No. 525449).

  3. Temperature measurements in microwave argon plasma source by using overlapped molecular emission spectra

    NASA Astrophysics Data System (ADS)

    Abdel-Fattah, E.; Bazavan, M.; Shindo, H.

    2015-09-01

    The electron excitation temperature Texc, vibrational Tvib, and rotational Trot temperatures were measured in a high-pressure line-shaped microwave plasma source in argon over a wide range of gas pressure and microwave power, by using optical emission spectra. The selected ArI transition lines 5p-4s and 4p-4s were chosen to calculate electron excitation temperature using Boltzmann's plot method. Meanwhile, the emission spectra of hydroxyl OH molecular ( A 2 Σ + - X 2 Π i , Δ ν = 0 ) band and the nitrogen N2 second positive system ( C 3 Π u - B 3 Π g , Δ ν = + 1 ), both second diffraction order, were used to evaluate the vibrational Tvib and rotational Trot temperatures using the method of comparing the measured and calculated spectra with a chi-squared minimization procedure. The components of the overlapped spectrum are greatly influenced by the gas pressure; however, they are independent on microwave power. For temperatures, it was found that the Texc dramatically decreases from 2.5 to 0.75 eV, which qualitatively agrees with T e deduced from zero-global model. Both of Tvib and Trot significantly decrease with as gas pressure increase from 0.4 to 50 Torr. Yet, they behave differently with microwave power.

  4. Ab initio molecular orbital study of adsorption of oxygen, nitrogen, and ethylene on silver-zeolite and silver halides

    SciTech Connect

    Chen, N.; Yang, R.T.

    1996-11-01

    An ab initio molecular orbital study is undertaken on the adsorption of N{sub 2}, O{sub 2}, and C{sub 2}H{sub 4} (adsorbate) on Ag-zeolite and Ag halides (adsorbent). Geometry optimization is performed at the HF/3-21G level, while MP2/3-21G with natural bond orbital calculations are performed to obtain energies, atomic charges, orbital energies, and orbital populations (occupancies). The bonding of adsorbate to adsorbent is discussed in the context of {sigma}-donation (i.e., overlap of the 2p orbitals of the adsorbate molecule with the 5s orbital of Ag) and d-{pi}* back donation (i.e., overlap of the 4d{sub yz} orbitals of Ag with the 2p* antibonding orbitals of the adsorbate). For all adsorbate-adsorbent pairs, the ratio of {sigma}-donation to d-{pi}* back donation is approximately 3:1. Results on occupancy analysis indicate that a considerable electron redistribution from the 4d{sub zy} orbitals to the 4d{sub yz} orbitals occurs in Ag during adsorption and that this redistribution has possibly enhanced the d-{pi}* back donation. Net charge and energy gap ({Delta}{epsilon}) analyses indicate that it is slightly easier for N{sub 2} than O{sub 2} to adsorb, whereas a comparison of N{sub 2} and O{sub 2} adsorption from calculations of the energies of adsorption is inconclusive. However, a fair agreement is obtained in comparison of theory and experiment for energy of adsorption of N{sub 2} and C{sub 2}J{sub 4} on Ag-zeolite. The dispersion energies of adsorption, based on the MP2 correlation energies, are nearly the same for all adsorption pairs, i.e,, approximately 4--5 kcal/mol.

  5. Optimization of selected molecular orbitals in group basis sets.

    PubMed

    Ferenczy, György G; Adams, William H

    2009-04-01

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

  6. Origin of molecular conformational stability: Perspectives from molecular orbital interactions and density functional reactivity theory

    SciTech Connect

    Liu, Shubin E-mail: schauer@unc.edu; Schauer, Cynthia K. E-mail: schauer@unc.edu

    2015-02-07

    To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability.

  7. Intracellular molecular distributions in spacecraft experiments in orbit around Earth

    NASA Astrophysics Data System (ADS)

    Haranas, Ioannis; Gkigkitzis, Ioannis; Zouganelis, George D.

    2012-04-01

    It is possible that the nucleolous inside the cell plays the role of a "gravity receptor". Furthermore, cells up to 10 μm in diameter can demonstrate some effect due to the redistribution of mitochondria or nucleolous. Effects of gravity should be present in various cell systems where larger objects such as the ribosomes move from cell to cell. In this paper we study the effects of gravity on cells. In particular, we examine the resulting intracellular molecular distribution due to Brownian motion and the ordered distribution of molecules under the action of gravity, where n0 is the number per unit volume at certain level, and n is the number per unit volume above that level. This is an experiment that takes place at a certain orbital altitude in a spacecraft in orbit around Earth, where the acceleration due to the central field is corrected for the oblateness and also the rotation of the Earth. We found that equatorial circular and elliptical orbits have the highest n/n0 ratios. This experiment takes place in circular and elliptical orbits, with eccentricities e = 0, 0.1 and involves a bacterial cell at an orbital altitude of 300 km. We found that n/n0 = 1.00299 and 1.0037 respectively, which is still a 0.6-0.7 % higher than n/n0 = 0.0996685 calculated on the surface of the Earth. Examining mitochondria in similar orbital experiments we found that equatorial orbits result to higher n/n0 ratios. In particular, we found that n/n0 = 8.38119, where an elliptical orbit of eccentricity e = 0.1 results to n/n0 = 13.8525. Both are high above 100%, signifying the importance of Brownian motion over gravity. Our results are of interest to biomedical applications. Molecular concentrations are important for various processes such as the embryogenesis, positional homeostasis and its relation to cell energy expenditure, cell torque, cell deformation, and more. These results indicate that statistical molecular distributions play an important role for the recognition of a

  8. A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets

    ERIC Educational Resources Information Center

    Chakraborty, Maharudra; Mukhopadhyay, Subrata; Das, Ranendu Sekhar

    2014-01-01

    A quite simple and inexpensive technique is described here to represent the approximate shapes of atomic orbitals and the molecular orbitals formed by them following the principles of the linear combination of atomic orbitals (LCAO) method. Molecular orbitals of a few simple molecules can also be pictorially represented. Instructors can employ the…

  9. Super-atom molecular orbital excited states of fullerenes.

    PubMed

    Johansson, J Olof; Bohl, Elvira; Campbell, Eleanor E B

    2016-09-13

    Super-atom molecular orbitals are orbitals that form diffuse hydrogenic excited electronic states of fullerenes with their electron density centred at the centre of the hollow carbon cage and a significant electron density inside the cage. This is a consequence of the high symmetry and hollow structure of the molecules and distinguishes them from typical low-lying molecular Rydberg states. This review summarizes the current experimental and theoretical studies related to these exotic excited electronic states with emphasis on femtosecond photoelectron spectroscopy experiments on gas-phase fullerenes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'. PMID:27501970

  10. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    NASA Astrophysics Data System (ADS)

    Lühmann, Dirk-Sören; Weitenberg, Christof; Sengstock, Klaus

    2015-07-01

    In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  11. Analyzing molecular static linear response properties with perturbed localized orbitals

    NASA Astrophysics Data System (ADS)

    Autschbach, Jochen; King, Harry F.

    2010-07-01

    Perturbed localized molecular orbitals (LMOs), correct to first order in an applied static perturbation and consistent with a chosen localization functional, are calculated using analytic derivative techniques. The formalism is outlined for a general static perturbation and variational localization functionals. Iterative and (formally) single-step approaches are compared. The implementation employs an iterative sequence of 2×2 orbital rotations. The procedure is verified by calculations of molecular electric-field perturbations. Boys LMO contributions to the electronic static polarizability and the electric-field perturbation of the ⟨r2⟩ expectation value are calculated and analyzed for ethene, ethyne, and fluoroethene (H2CCHF). For ethene, a comparison is made with results from a Pipek-Mezey localization. The calculations show that a chemically intuitive decomposition of the calculated properties is possible with the help of the LMO contributions and that the polarizability contributions in similar molecules are approximately transferable.

  12. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  13. A low Earth orbit molecular beam space simulation facility

    NASA Technical Reports Server (NTRS)

    Cross, J. B.

    1984-01-01

    A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.

  14. Tomographic Imaging of Molecular Orbitals in Length and Velocity Form

    SciTech Connect

    Zwan, Elmar V. van der; Lein, Manfred

    2007-11-29

    Recently Itatani et al. [Nature 432, 876 (2004)] introduced the new concept of molecular orbital tomography, where high harmonic generation (HHG) is used to image electronic wave functions. We describe an alternative reconstruction form, using momentum instead of dipole matrix elements for the electron recombination step in HHG. We show that using this velocity-form reconstruction, one obtains better results than using the original length-form reconstruction. We provide numerical evidence for our claim that one has to resort to extremely short pulses to perform the reconstruction for an orbital with arbitrary symmetry. The numerical evidence is based on the exact solution of the time-dependent Schroedinger equation for 2D model systems to simulate the experiment. Furthermore we show that in the case of cylindrically symmetric orbitals, such as the N{sub 2} orbital that was reconstructed in the original work, one can obtain the full 3D wave function and not only a 2D projection of it.

  15. Molecular orbital studies on the structure-activity relationships of catechol O-methyltransferase inhibitors.

    PubMed

    Shinagawa, Y

    1992-02-01

    Quantum chemical studies were applied to analyze the activities of catechol O-methyltransferase (COMT) inhibitors. Molecular orbital calculations of inhibitor molecules were made by semi-empirical molecular orbital calculations, CNDO/2 (complete neglect of differential overlap) methods. Regression analysis among theoretical reaction indices based on the frontier electron theory and COMT inhibitory activities were carried out. The COMT inhibitory actions of two series of inhibitors, a series of 1,5-substituted 3,4-dihydroxy benzenes and a series of substituted 3-hydroxy-4-methoxy benzenes, were investigated. The resulting regression equations contain two common reaction indices as regression variables: the electron density on the oxygen atom of the hydroxyl group and the super-delocalizability on the 5th carbon atom of the benzene ring. These two atomic positions are considered to play an important role in the interaction of these inhibitors with COMT. The hydroxyl of atomic position 3 is probably indispensable to the COMT inhibitory action by these inhibitors. PMID:1507526

  16. Why many semiempirical molecular orbital theories fail for liquid water and how to fix them.

    PubMed

    Welborn, Matthew; Chen, Jiahao; Wang, Lee-Ping; Van Voorhis, Troy

    2015-05-01

    Water is an extremely important liquid for chemistry and the search for more accurate force fields for liquid water continues unabated. Neglect of diatomic differential overlap (NDDO) molecular orbital methods provide and intriguing generalization of classical force fields in this regard because they can account both for bond breaking and electronic polarization of molecules. However, we show that most standard NDDO methods fail for water because they give an incorrect description of hydrogen bonding, water's key structural feature. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that PM6 does not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. Finally, we identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry. PMID:25766721

  17. Localization of molecular orbitals: from fragments to molecule.

    PubMed

    Li, Zhendong; Li, Hongyang; Suo, Bingbing; Liu, Wenjian

    2014-09-16

    Conspectus Localized molecular orbitals (LMO) not only serve as an important bridge between chemical intuition and molecular wave functions but also can be employed to reduce the computational cost of many-body methods for electron correlation and excitation. Therefore, how to localize the usually completely delocalized canonical molecular orbitals (CMO) into confined physical spaces has long been an important topic: It has a long history but still remains active to date. While the known LMOs can be classified into (exact) orthonormal and nonorthogonal, as well as (approximate) absolutely localized MOs, the ways for achieving these can be classified into two categories, a posteriori top-down and a priori bottom-up, depending on whether they invoke the global CMOs (or equivalently the molecular density matrix). While the top-down approaches have to face heavy tasks of minimizing or maximizing a given localization functional typically of many adjacent local extrema, the bottom-up ones have to invoke some tedious procedures for first generating a local basis composed of well-defined occupied and unoccupied subsets and then maintaining or resuming the locality when solving the Hartree-Fock/Kohn-Sham (HF/KS) optimization condition. It is shown here that the good of these kinds of approaches can be combined together to form a very efficient hybrid approach that can generate the desired LMOs for any kind of gapped molecules. Specifically, a top-down localization functional, applied to individual small subsystems only, is minimized to generate an orthonormal local basis composed of functions centered on the preset chemical fragments. The familiar notion for atomic cores, lone pairs, and chemical bonds emerges here automatically. Such a local basis is then employed in the global HF/KS calculation, after which a least action is taken toward the final orthonormal localized molecular orbitals (LMO), both occupied and virtual. This last step is very cheap, implying that, after

  18. Molecular orbital analysis of the hydrogen bonded water dimer

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2016-02-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems.

  19. Molecular orbital analysis of the hydrogen bonded water dimer

    PubMed Central

    Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2016-01-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems. PMID:26905305

  20. Molecular diagnosis reveals genetic heterogeneity for the overlapping MKKS and BBS phenotypes.

    PubMed

    Schaefer, Elise; Durand, Myriam; Stoetzel, Corinne; Doray, Bérénice; Viville, Brigitte; Hellé, Sophie; Danse, Jean-Marc; Hamel, Christian; Bitoun, Pierre; Goldenberg, Alice; Finck, Sonia; Faivre, Laurence; Sigaudy, Sabine; Holder, Muriel; Vincent, Marie-Claire; Marion, Vincent; Bonneau, Dominique; Verloes, Alain; Nisand, Israël; Mandel, Jean-Louis; Dollfus, Hélène

    2011-01-01

    Hydrometrocolpos and polydactyly diagnosed in the prenatal period or early childhood may raise diagnostic dilemmas especially in distinguishing McKusick-Kaufman syndrome (MKKS) and the Bardet-Biedl syndrome (BBS). These two conditions can initially overlap. With time, the additional features of BBS appearing in childhood, such as retinitis pigmentosa, obesity, learning disabilities and progressive renal dysfunction allow clear differentiation between BBS and MKKS. Genotype overlap also exists, as mutations in the MKKS-BBS6 gene are found in both syndromes. We report 7 patients diagnosed in the neonatal period with hydrometrocolpos and polydactyly who carry mutations in various BBS genes (BBS6, BBS2, BBS10, BBS8 and BBS12), stressing the importance of wide BBS genotyping in patients with this clinical association for diagnosis, prognosis and genetic counselling. PMID:21044901

  1. Electronic structure and conformation of polymers from cluster molecular orbital and molecular mechanics calculations: Polyimide

    SciTech Connect

    Kafafi, S.A. ); LaFemina, J.P. ); Nauss, J.L. )

    1990-11-21

    Full geometry optimizations using molecular mechanics and the quantum chemical AM1 method have been carried out to determine the minimum energy conformation of pyromellitic dianhydride-oxydianiline polyimide (PMDA-ODA PI). The phenyl-imide twist angle for this compound was determined to be {approximately}30. These computations also provided a quantitative determination of the energy gap (7 eV), electron affinity ({minus}2 eV), and ionization potential (8.97 eV). Computations on the PMDA-ODA PI radical anion provided an estimate of the hopping barrier for an electron to hop from one chain to another (3.2 eV), the mechanism believed responsible for photoconduction. Moreover, the use of qualitative molecular orbital theory (QMOT) arguments provided an interpretation of these results in a simple molecular orbital framework.

  2. On the limits of highest-occupied molecular orbital driven reactions: the frontier effective-for-reaction molecular orbital concept.

    PubMed

    da Silva, Rodrigo R; Ramalho, Teodorico C; Santos, Joana M; Figueroa-Villar, J Daniel

    2006-01-26

    We carried out Hartree-Fock (HF) and density functional theory calculations for 61 compounds, the conjugated bases of carboxylic acids, phenols, and alcohols, and analyzed their acid-base behavior using molecular orbital (MO) energies and their dependence on solvent effects. Despite the well-known correlation between highest-occupied MO (HOMO) energies and pKa, we observed that HOMO energies are inadequate to describe the acid-base behavior of these compounds. Therefore, we established a criterion to identify the best frontier MO for describing pKa values and also to understand why the HOMO approach fails. The MO that fits our criterion provided very good correlations with pKa values, much better than those obtained by HOMO energies. Since they are the frontier molecular orbitals that drive the acid-base reactions in each compound, they were called frontier effective-for-reaction MOs, or FERMOs. By use of the FERMO concept, the reactions that are HOMO driven, and those that are not, can be better explained, independently from the calculation method used, as both HF and Kohn-Sham methodologies lead to the same FERMO. PMID:16420004

  3. The activation strain model and molecular orbital theory

    PubMed Central

    Wolters, Lando P; Bickelhaupt, F Matthias

    2015-01-01

    The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324–343. doi: 10.1002/wcms.1221 PMID:26753009

  4. Charge transfer processes: the role of optimized molecular orbitals.

    PubMed

    Meyer, Benjamin; Domingo, Alex; Krah, Tim; Robert, Vincent

    2014-08-01

    The influence of the molecular orbitals on charge transfer (CT) reactions is analyzed through wave function-based calculations. Characteristic CT processes in the organic radical 2,5-di-tert-butyl-6-oxophenalenoxyl linked with tetrathiafulvalene and the inorganic crystalline material LaMnO3 show that changes in the inner shells must be explicitly taken into account. Such electronic reorganization can lead to a reduction of the CT vertical transition energy up to 66%. A state-specific approach accessible through an adapted CASSCF (complete active space self-consistent field) methodology is capable of reaching good agreement with the experimental spectroscopy of CT processes. A partitioning of the relaxation energy in terms of valence- and inner-shells is offered and sheds light on their relative importance. This work paves the way to the intimate description of redox reactions using quantum chemistry methods. PMID:24781811

  5. Molecular electric moments calculated by using natural orbital functional theory.

    PubMed

    Mitxelena, Ion; Piris, Mario

    2016-05-28

    The molecular electric dipole, quadrupole, and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-ζ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles and multi-reference single and double excitation configuration interaction methods. PMID:27250280

  6. Theoretical analysis of the density within an orbiting molecular shield

    NASA Technical Reports Server (NTRS)

    Hueser, J. E.; Brock, F. J.

    1976-01-01

    An analytical model based on the kinetic theory of a drifting Maxwellian gas is used to determine the nonequilibrium molecular density distribution within a hemispherical shell open aft with its axis parallel to its velocity. Separate numerical results are presented for the primary and secondary density distribution components due to the drifting Maxwellian gas for speed ratios between 2.5 and 10. An analysis is also made of the density component due to gas desorbed from the wall of the hemisphere, and numerical results are presented for the density distribution. It is shown that the adsorption process may be completely ignored. The results are applicable to orbital trajectories in any planet-atmosphere system and interplanetary transfer trajectories. Application to the earth's atmosphere is mentioned briefly.

  7. Sulfur at nickel-alumina interfaces - Molecular orbital theory

    NASA Technical Reports Server (NTRS)

    Hong, S. Y.; Anderson, Alfred B.; Smialek, James L.

    1990-01-01

    Previous studies on Al-Ni alloys containing sulfur as an impurity suggest that, when S is in the interface between a metal and an oxide scale, it weakens the chemical bonding between them. This paper investigates factors responsible for this effect, using a molecular orbital theory to predict sulfur structures and electronic properties on the Ni-Al2O3 interface. It is shown that, in absence of S, the basal plane of Al2O3 will bind strongly through the Al(3+) cation surface to Ni (111). When segregated S impurity is present on the Ni surface, there are too few interfacial AlS bonds to effect good adhesion, leading to an inhibition of the oxide scale adhesion in NiCrAl alloys.

  8. Molecular electric moments calculated by using natural orbital functional theory

    NASA Astrophysics Data System (ADS)

    Mitxelena, Ion; Piris, Mario

    2016-05-01

    The molecular electric dipole, quadrupole, and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-ζ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles and multi-reference single and double excitation configuration interaction methods.

  9. P and N compensation in diamond molecular orbital theory

    NASA Astrophysics Data System (ADS)

    Anderson, Alfred B.; Kostadinov, Lubomir N.

    1997-01-01

    Cluster models and the atom superposition and electron delocalization molecular orbital theory calculations lead to an explanation for the ability of nitrogen to cause phosphorous incorporation in low pressure grown diamond films as observed recently by Cao and coworkers. The theory shows that substitutional N compensates substitutional P, creating stable P+-N- disubstitutional pairs. These ionized systems are calculated to be deep donors, which explains the absence of measurable electrical conductivity or phosphorous induced luminescence. The possibility of creating donor P defects by the annealing reaction P-N+N→P+N-N is discussed. The issues of atom size and electronegativity and their influence on donor capability are addressed. It is shown that the difference between substitutional P, a shallow donor, and substitutional N, a deep donor, is predominantly due to the larger size of P; its lower electronegativity makes a relatively small contribution.

  10. Overlapping molecular pathological themes link Charcot-Marie-Tooth neuropathies and hereditary spastic paraplegias.

    PubMed

    Timmerman, Vincent; Clowes, Virginia E; Reid, Evan

    2013-08-01

    In this review we focus on Charcot-Marie-Tooth (CMT) neuropathies and hereditary spastic paraplegias (HSPs). Although these diseases differ in whether they primarily affect the peripheral or central nervous system, both are genetically determined, progressive, long axonopathies that affect motor and sensory pathways. This commonality suggests that there might be similarities in the molecular pathology underlying these conditions, and here we compare the molecular genetics and cellular pathology of the two groups. PMID:22285450

  11. Imprinting disorders: a group of congenital disorders with overlapping patterns of molecular changes affecting imprinted loci.

    PubMed

    Eggermann, Thomas; Perez de Nanclares, Guiomar; Maher, Eamonn R; Temple, I Karen; Tümer, Zeynep; Monk, David; Mackay, Deborah J G; Grønskov, Karen; Riccio, Andrea; Linglart, Agnès; Netchine, Irène

    2015-01-01

    Congenital imprinting disorders (IDs) are characterised by molecular changes affecting imprinted chromosomal regions and genes, i.e. genes that are expressed in a parent-of-origin specific manner. Recent years have seen a great expansion in the range of alterations in regulation, dosage or DNA sequence shown to disturb imprinted gene expression, and the correspondingly broad range of resultant clinical syndromes. At the same time, however, it has become clear that this diversity of IDs has common underlying principles, not only in shared molecular mechanisms, but also in interrelated clinical impacts upon growth, development and metabolism. Thus, detailed and systematic analysis of IDs can not only identify unifying principles of molecular epigenetics in health and disease, but also support personalisation of diagnosis and management for individual patients and families. PMID:26583054

  12. The Pairwise Correlated Generalized Valence Bond Model of Electronic Structure I; The Estimation of Pair Energies from Orbital Overlaps

    PubMed Central

    Petersson, G. A.

    1974-01-01

    A new method for the accurate a priori calculation of atomic and molecular energies is proposed. The new method agrees with experiment to within less than 1 kcal/mole in all cases examined thus far, and is applicable to excited states and to transition states for chemical reactions. Since the new method corrects the results of generalized valence bond calculations for the effects of electron pair correlations, we call the new method the pairwise correlated generalized valence bond method. PMID:16592172

  13. Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

  14. Orbital tomography: Molecular band maps, momentum maps and the imaging of real space orbitals of adsorbed molecules

    PubMed Central

    Offenbacher, Hannes; Lüftner, Daniel; Ules, Thomas; Reinisch, Eva Maria; Koller, Georg; Puschnig, Peter; Ramsey, Michael G.

    2015-01-01

    The frontier orbitals of molecules are the prime determinants of their chemical, optical and electronic properties. Arguably, the most direct method of addressing the (filled) frontier orbitals is ultra-violet photoemission spectroscopy (UPS). Although UPS is a mature technique from the early 1970s on, the angular distribution of the photoemitted electrons was thought to be too complex to be analysed quantitatively. Recently angle resolved UPS (ARUPS) work on conjugated molecules both, in ordered thick films and chemisorbed monolayers, has shown that the angular (momentum) distribution of the photocurrent from orbital emissions can be simply understood. The approach, based on the assumption of a plane wave final state is becoming known as orbital tomography. Here we will demonstrate, with selected examples of pentacene (5A) and sexiphenyl (6P), the potential of orbital tomography. First it will be shown how the full angular distribution of the photocurrent (momentum map) from a specific orbital is related to the real space orbital by a Fourier transform. Examples of the reconstruction of 5A orbitals will be given and the procedure for recovering the lost phase information will be outlined. We then move to examples of sexiphenyl where we interrogate the original band maps of thick sexiphenyl in the light of our understanding of orbital tomography that has developed since then. With comparison to theoretical simulations of the molecular band maps, the molecular conformation and orientation will be concluded. New results for the sexiphenyl monolayer on Al(1 1 0) will then be presented. From the band maps it will be concluded that the molecule is planarised and adopts a tilted geometry. Finally the momentum maps down to HOMO-11 will be analysed and real space orbitals reconstructed. PMID:26752804

  15. Abundant Genetic Overlap between Blood Lipids and Immune-Mediated Diseases Indicates Shared Molecular Genetic Mechanisms

    PubMed Central

    Andreassen, Ole A.; Desikan, Rahul S.; Wang, Yunpeng; Thompson, Wesley K.; Schork, Andrew J.; Zuber, Verena; Doncheva, Nadezhda T.; Ellinghaus, Eva; Albrecht, Mario; Mattingsdal, Morten; Franke, Andre; Lie, Benedicte A.; Mills, Ian; Aukrust, Pål; McEvoy, Linda K.; Djurovic, Srdjan; Karlsen, Tom H.; Dale, Anders M.

    2015-01-01

    Epidemiological studies suggest a relationship between blood lipids and immune-mediated diseases, but the nature of these associations is not well understood. We used genome-wide association studies (GWAS) to investigate shared single nucleotide polymorphisms (SNPs) between blood lipids and immune-mediated diseases. We analyzed data from GWAS (n~200,000 individuals), applying new False Discovery Rate (FDR) methods, to investigate genetic overlap between blood lipid levels [triglycerides (TG), low density lipoproteins (LDL), high density lipoproteins (HDL)] and a selection of archetypal immune-mediated diseases (Crohn’s disease, ulcerative colitis, rheumatoid arthritis, type 1 diabetes, celiac disease, psoriasis and sarcoidosis). We found significant polygenic pleiotropy between the blood lipids and all the investigated immune-mediated diseases. We discovered several shared risk loci between the immune-mediated diseases and TG (n = 88), LDL (n = 87) and HDL (n = 52). Three-way analyses differentiated the pattern of pleiotropy among the immune-mediated diseases. The new pleiotropic loci increased the number of functional gene network nodes representing blood lipid loci by 40%. Pathway analyses implicated several novel shared mechanisms for immune pathogenesis and lipid biology, including glycosphingolipid synthesis (e.g. FUT2) and intestinal host-microbe interactions (e.g. ATG16L1). We demonstrate a shared genetic basis for blood lipids and immune-mediated diseases independent of environmental factors. Our findings provide novel mechanistic insights into dyslipidemia and immune-mediated diseases and may have implications for therapeutic trials involving lipid-lowering and anti-inflammatory agents. PMID:25853426

  16. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    SciTech Connect

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  17. Towards simple orbital-dependent density functionals for molecular dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Igor Ying; Richter, Patrick; Scheffler, Matthias

    2015-03-01

    Density functional theory (DFT) is one of the leading first-principles electronic-structure theories. However, molecular dissociation remains a challenge, because it requires a well-balanced description of the drastically different electronic structure at different bond lengths. One typical and well-documented case is the dissociation of both H2+ and H2, for which all popular DFT functionals fail. We start from the Bethe-Goldstone equation to propose a simple orbital-dependent correlation functional which generalizes the linear adiabatic connection approach. The resulting scheme is based on second-order perturbation theory (PT2), but includes the self-consistent coupling of electron-hole pairs, which ensures the correct H2 dissociation limit and gives a finite correlation energy for systems with a (near)-degenerate energy gap. This coupling PT2-like (CPT2) approximation delivers a significant improvement over all existing functionals for both H2 and H2+ dissociation. We will demonstrate the reason for this improvement analytically for H2 in a minimal basis.

  18. [Applications of the Fragment Molecular Orbital Method in Drug Discovery].

    PubMed

    Ishikawa, Takeshi

    2016-01-01

      Recently, ab initio quantum mechanical calculations have been applied to large molecules, including biomolecular systems. The fragment molecular orbital (FMO) method is one of the most efficient approaches for the quantum mechanical investigation of such molecules. In the FMO method, dividing a target molecule into small fragments reduces computational effort. The clear definition of inter-fragment interaction energy (IFIE) as an expression of total energy is another valuable feature of the FMO method because it provides the ability to analyze interactions in biomolecules. Thus, the FMO method is expected to be useful for drug discovery. This study demonstrates applications of the FMO method related to drug discovery. First, IFIE, according to FMO calculations, was used in the optimization of drug candidates for the development of anti-prion compounds. The second example involved interaction analysis of the human immunodeficiency virus type 1 (HIV-1) protease and a drug compound that used a novel analytical method for dispersion interaction, i.e., fragment interaction analysis based on LMP2 (FILM). PMID:26725679

  19. Amide N-oxides: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

    There are no known examples of amide N-oxides. The present study employs ab initio molecular orbital calculations at the 6-3G ∗ level to explore potential target molecules in this class. Bridgehead bicyclic lactams appear to be attractive targets for oxidation to form the corresponding N-oxides because they have reduced (or zero) amide resonance energy. The amide N-oxide linkage is predicted to have a ca. 9-10 kcal/mol rotational barrier due to eclipsing of nonbonded oxygen atoms in the transition state. The linkage has a nearly flat conformational ( ΦON-CO) profile in the range 120-240° and this suggests that a very sterically hindered acyclic amide N-oxide may be a practical synthetic target. The oxidation of strained amides is calculated to be highly exothermic if dimethyldioxirane is employed. This reagent is predicted to react appreciably exothermically with normal, stable amides such as N, N-dimethylacetamide, thus offering the potential for generating and studying such relatively unstable amide N-oxides at low temperatures.

  20. Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods.

    PubMed

    Gilbert, Kathleen M; Skawinski, William J; Misra, Milind; Paris, Kristina A; Naik, Neelam H; Buono, Ronald A; Deutsch, Howard M; Venanzi, Carol A

    2004-11-01

    Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte > MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the

  1. Dependence of the conductance change on the molecular orbitals in Ag and Au electrodes

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Sung; Kim, Taekyeong

    2016-01-01

    The conductance change in single-molecule junctions due to the molecular orbitals and the metal's Fermi energy was investigated by using a scanning tunneling microscopy break-junction technique with Ag and Au electrodes. 4,4'-diaminobiphenyl and 4,4'-dicyanobiphenyl as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) junctions were used. The amine-linked HOMO-conducting junction had a lower conductance, and cyano-linked LUMO-conducting junction had a higher conductance for Ag electrode compared to Au electrode. These results are attributed to the difference between the metal electrode Fermi energy and the molecular orbital level in the metal-molecule junction. Furthermore, 2,7-diaminofluorene exhibited a higher conductance but the identical molecular plateau length for the Ag electrodes compared to that of 4,4'-diaminobiphenyl indicating that the twist angle of the molecular backbone affects the conductance.

  2. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  3. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  4. Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Hashimoto, Hideki; Yoda, Takeshi; Kobayashi, Takayoshi; Young, Andrew J.

    2002-02-01

    Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6-C7 bond to be ±48.7 and -84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.

  5. Hybridization of organic molecular orbitals with substrate states at interfaces: PTCDA on silver.

    PubMed

    Ziroff, J; Forster, F; Schöll, A; Puschnig, P; Reinert, F

    2010-06-11

    We demonstrate the application of orbital k-space tomography for the analysis of the bonding occurring at metal-organic interfaces. Using angle-resolved photoelectron spectroscopy, we probe the spatial structure of the highest occupied molecular orbital and the former lowest unoccupied molecular orbital (LUMO) of one monolayer 3, 4, 9, 10-perylene-tetracarboxylic-dianhydride (PTCDA) on Ag(110) and (111) surfaces and, in particular, the influence of the hybridization between the orbitals and the electronic states of the substrate. We are able to quantify and localize the substrate contribution to the LUMO and thus prove the metal-molecule hybrid character of this complex state. PMID:20867234

  6. Moving Beyond the Single Center--Ways to Reinforce Molecular Orbital Theory in an Inorganic Course

    ERIC Educational Resources Information Center

    Cass, Marion E.; Hollingsworth, William E.

    2004-01-01

    It is suggested that molecular theory should be taught earlier in the inorganic chemistry curriculum even in the introductory chemistry course in order to integrate molecular orbital arguments more effectively throughout the curriculum. The method of teaching relies on having access to molecular modeling software as having access to such software…

  7. Quantifying the relative molecular orbital alignment for molecular junctions with similar chemical linkage to electrodes

    NASA Astrophysics Data System (ADS)

    Bâldea, Ioan

    2014-11-01

    Estimating the relative alignment between the frontier molecular orbitals (MOs) that dominates the charge transport through single-molecule junctions represents a challenge for theory. This requires approaches beyond the widely employed framework provided by the density functional theory, wherein the Kohn-Sham ‘orbitals’ are treated as if they were real MOs, which is not the case. In this paper, we report results obtained by means of quantum chemical calculations, including the equation-of-motion coupled-cluster singles and doubles, which is the state-of-the-art of quantum chemistry for medium-size molecules like those considered here. These theoretical results are validated against data on the MO energy offset relative to the electrodes’ Fermi energy extracted from experiments for junctions based on 4,4’-bipyridine and 1,4-dicyanobenzene.

  8. Polarization and molecular-orbital dependence of strong-field enhanced ionization

    NASA Astrophysics Data System (ADS)

    Lai, Wei; Guo, Chunlei

    2016-04-01

    In this work we perform a polarization dependence study of enhanced ionization (EI) in diatomic molecules. We find that EI exists when the field polarization is parallel to the molecular axis but disappears when polarization is perpendicular. We further study EI with circular polarization and find that EI exists with circular polarization indicating that rescattering does not play a significant role for EI. Furthermore, we study molecular orbital effect on EI. We find that EI exists in σ type but not π type outmost molecular orbitals.

  9. Molecular orbital model of optical centers in bismuth-doped glasses.

    PubMed

    Kustov, E F; Bulatov, L I; Dvoyrin, V V; Mashinsky, V M

    2009-05-15

    Spectroscopic properties of optical fibers with a bismuth-doped silicate glass core are explained on the basis of molecular orbital theory and a solution of the Schrödinger equation, which takes into account the exchange, the spin-orbital, and the glass field potential interactions of s, p, and d electron shells of bismuth with s(sigma), p(sigma), and p(pi) orbits of oxygen atoms. The approach can explain the IR luminescence properties of other optical centers formed by other atoms with the same structure of electron shells as the bismuth atom. The model of transitions based on intramolecular charge transfer between molecular orbital and metallic states is proposed. PMID:19448817

  10. {open_quotes}Neglect of diatomic differential overlap{close_quotes} in nonempirical quantum chemical orbital theories. V. A calculus of error concerning the justification of the neglect of diatomic differential overlap (NDDO) approximation

    SciTech Connect

    Neymeyr, K.

    1995-03-05

    Several types of approximations have been used for the justification of the Neglect of Diatomic Differential Overlap (NDDO) in Part IV but control of the introduced error remains insufficient. Analytic formulas describing the induced error for all types of approximations are given. Numerically lower bounds for these errors can be derived from the discussion on diatomic molecules. Far-reaching consequences on the applicability of NDDO will be discussed. 7 refs., 6 tabs.

  11. Growth mechanism, electronic spectral investigation and molecular orbital studies of L-prolinium phosphate.

    PubMed

    Liu, Xiaojing; Sun, Xin; Xu, Xijin; Sun, Ping

    2015-11-01

    By using atomic force microscopy, birth and spread has proved to be the primary growth mechanism for L-prolinium phosphate (LPP). The phenomenon of newly formed islands expanding to the edge of the preceding terrace was observed. The optimized molecular structure and the molecular properties were calculated by density functional theory method. Natural bond orbital analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of LPP leading to high NLO activity. Molecular electrostatic potential, frontier molecular orbital analysis and thermodynamic properties were investigated to get a better insight of the molecular properties. Global and local reactivity descriptors were computed to predict the reactivity and reactive sites on the molecules. Non-linear optical (NLO) properties such as the total dipole moment (μ) and first order hyperopolarizability (β) were also calculated to predict NLO behavior. PMID:26067937

  12. Intramolecular charge ordering in the multi molecular orbital system (TTM-TTP)I3

    NASA Astrophysics Data System (ADS)

    Bonnet, Marie-Laure; Robert, Vincent; Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu

    2010-06-01

    Starting from the structure of the (TTM-TTP)I3 molecular-based material, we examine the characteristics of frontier molecular orbitals using ab initio (CASSCF/CASPT2) configurations interaction calculations. It is shown that the singly occupied and second-highest-occupied molecular orbitals are close to each other, i.e., this compound should be regarded as a two-orbital system. By dividing virtually the [TTM-TTP] molecule into three fragments, an effective model is constructed to rationalize the origin of this picture. In order to investigate the low-temperature, symmetry breaking experimentally observed in the crystal, the electronic distribution in a pair of [TTM-TTP] molecules is analyzed from CASPT2 calculations. Our inspection supports and explains the speculated intramolecular charge ordering which is likely to give rise to low-energy magnetic properties.

  13. Solution of multi-center molecular integrals of Slater-type orbitals

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1989-01-01

    The troublesome multi-center molecular integrals of Slater-type orbitals (STO) in molecular physics calculations can be evaluated by using the Fourier transform and proper coupling of the two center exchange integrals. A numerical integration procedure is then readily rendered to the final expression in which the integrand consists of well known special functions of arguments containing the geometrical arrangement of the nuclear centers and the exponents of the atomic orbitals. A practical procedure was devised for the calculation of a general multi-center molecular integrals coupling arbitrary Slater-type orbitals. Symmetry relations and asymptotic conditions are discussed. Explicit expressions of three-center one-electron nuclear-attraction integrals and four-center two-electron repulsion integrals for STO of principal quantum number n=2 are listed. A few numerical results are given for the purpose of comparison.

  14. Fragmented Molecular Orbital with Diffusion Monte Carlo for large molecular systems

    NASA Astrophysics Data System (ADS)

    Benali, Anouar; Pruitt, Spencer R.; Fedorov, Dmitri G.

    Performing accurate quantum mechanics (QM) calculations on larger and larger systems, while maintaining a high level of accuracy is an ongoing effort in many ab initio fields. Many different attempts have been made to develop highly scalable and accurate methods. The fragment molecular orbital (FMO) method is an ab initio method capable of taking advantage of modern supercomputers, such as the Blue Gene Q system Mira at the Argonne National Laboratory Leadership Computing Facility (ALCF). FMO is based on dividing molecules into fragments and performing ab initio calculations on fragments, their dimers and, optionally, trimers. This decomposition makes it possible to perform QM calculations of real size biological molecules. In contrast to many other fragment-based methods, the effect of the environment is rigorously accounted for by computing the electrostatic potential (ESP) due to remaining fragments that are not explicitly included in a given monomer, dimer, or trimer calculation. The use of highly accurate levels of theory, such as Diffusion Monte Carlo (DMC-QMC), in conjunction with FMO allows for the goal of highly scalable and accurate all electron calculations demonstrated in this study, on a variety of relevant systems (H2O)[3-6] and protein using GAMESS and QMCPACK.

  15. Terazulene Isomers: Polarity Change of OFETs through Molecular Orbital Distribution Contrast.

    PubMed

    Yamaguchi, Yuji; Takubo, Maki; Ogawa, Keisuke; Nakayama, Ken-Ichi; Koganezawa, Tomoyuki; Katagiri, Hiroshi

    2016-09-01

    Intermolecular orbital coupling is fundamentally important to organic semiconductor performance. Recently, we reported that 2,6':2',6″-terazulene (TAz1) exhibited excellent performance as an n-type organic field-effect transistor (OFET) via molecular orbital distribution control. To validate and develop this concept, here we present three other terazulene regioisomers, which have three azulene molecules connected at the 2- or 6-position along the long axis of the azulene, thus constructing a linear expanded π-conjugation system: 2,2':6',2″-terazulene (TAz2), 2,2':6',6″-terazulene (TAz3), and 6,2':6',6″-terazulene (TAz4). TAz2 and TAz3 exhibit ambipolar characteristics; TAz4 exhibits clear n-type transistor behavior as an OFET. The lowest unoccupied molecular orbitals (LUMOs) of all terazulenes are fully delocalized over the entire molecule. In contrast, the highest occupied molecular orbitals (HOMOs) of TAz2 and TAz3 are delocalized over the 2,2'-biazulene units; the HOMOs of TAz4 are localized at one end of the azulene unit. These findings confirm that terazulene isomers which are simple hydrocarbon compounds are versatile materials with a tunable-polarity FET characteristic that depends on the direction of the azulene unit and the related contrast of the molecular orbital distribution in the terazulene backbone. PMID:27511286

  16. Molecular orbital ordering in titania and the associated semiconducting behavior

    SciTech Connect

    Park, Joseph; Ok, Kyung-Chul; Park, Jin-Seong; Du Ahn, Byung; Hun Lee, Je; Park, Jae-Woo; Chung, Kwun-Bum

    2011-10-03

    RF-sputtered TiO{sub x} layers were thermally treated and the associated thin-film transistor properties were studied. X-ray diffraction and x-ray absorption spectroscopy analyses indicate that as-grown amorphous TiO{sub x} films crystallize to anatase at temperatures above 450 deg. C in air. Thin-film transistors incorporating anatase active layers exhibit n-type behavior, with field effect mobility values near 0.11 cm{sup 2}/Vs when annealed at 550 deg. C. Such a phenomenon is suggested to originate from the ordering of Ti 3d orbitals upon crystallization, and the mobility enhancement at higher annealing temperatures may be attributed to the reduced grain boundary scattering of carriers by virtue of enlarged average grain size.

  17. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.

    PubMed

    Pruitt, Spencer R; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, Mark S

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Møller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed. PMID:26913837

  18. Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals.

    PubMed

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-08-17

    An energy decomposition analysis (EDA) separates a calculated interaction energy into as many interpretable contributions as possible; for instance, permanent and induced electrostatics, Pauli repulsions, dispersion and charge transfer. The challenge is to construct satisfactory definitions of all terms in the chemically relevant regime where fragment densities overlap, rendering unique definitions impossible. Towards this goal, we present an improved EDA for Kohn-Sham density functional theory (DFT) with properties that have previously not been simultaneously attained. Building on the absolutely localized molecular orbital (ALMO)-EDA, this second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above. These contributions moreover all have non-trivial complete basis set limits. We apply the EDA to the water dimer, the T-shaped and parallel-displaced benzene dimer, the p-biphthalate dimer "anti-electrostatic" hydrogen bonding complex, the biologically relevant binding of adenine and thymine in stacked and hydrogen-bonded configurations, the triply hydrogen-bonded guanine-cytosine complex, the interaction of Cl(-) with s-triazine and with the 1,3-dimethyl imidazolium cation, which is relevant to the study of ionic liquids, and the water-formaldehyde-vinyl alcohol ter-molecular radical cationic complex formed in the dissociative photoionization of glycerol. PMID:27492057

  19. Pyrite oxidation and reduction - Molecular orbital theory considerations. [for geochemical redox processes

    NASA Technical Reports Server (NTRS)

    Luther, George W., III

    1987-01-01

    In this paper, molecular orbital theory is used to explain a heterogeneous reaction mechanism for both pyrite oxidation and reduction. The mechanism demonstrates that the oxidation of FeS2 by Fe(3+) may occur as a result of three important criteria: (1) the presence of a suitable oxidant having a vacant orbital (in case of liquid phase) or site (solid phase) to bind to the FeS2 via sulfur; (2) the initial formation of a persulfido (disulfide) bridge between FeS2 and the oxidant, and (3) an electron transfer from a pi(asterisk) orbital in S2(2-) to a pi or pi(asterisk) orbital of the oxidant.

  20. Molecular Orbitals of NO, NO[superscript+], and NO[superscript-]: A Computational Quantum Chemistry Experiment

    ERIC Educational Resources Information Center

    Orenha, Renato P.; Galembeck, Sérgio E.

    2014-01-01

    This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

  1. Multi-electron coincidence spectroscopy: double photoionization from molecular inner-shell orbitals

    NASA Astrophysics Data System (ADS)

    Hikosaka, Y.; Lablanquie, P.; Penent, F.; Nakano, M.; Ito, K.

    2014-04-01

    We have studied double photoionization from molecular inner-shell orbitals and investigated the properties of the resultant double core-hole states in molecules, by multi-electron coincidence spectroscopy with a magnetic bottle electron spectrometer. A brief summary of our previous studies is presented.

  2. Extending electron orbital precession to the molecular case: Use of orbital alignment for observation of wavepacket dynamics

    SciTech Connect

    Martay, Hugo E. L.; England, Duncan G.; McCabe, David J.; Walmsley, Ian A.

    2011-04-15

    The complexity of ultrafast molecular photoionization presents an obstacle to the modeling of pump-probe experiments. Here, a simple optimized model of atomic rubidium is combined with a molecular dynamics model to predict quantitatively the results of a pump-probe experiment in which long-range rubidium dimers are first excited, then ionized after a variable delay. The method is illustrated by the outline of two proposed feasible experiments and the calculation of their outcomes. Both of these proposals use Feshbach {sup 87}Rb{sub 2} molecules. We show that long-range molecular pump-probe experiments should observe spin-orbit precession given a suitable pump pulse, and that the associated high-frequency beat signal in the ionization probability decays after a few tens of picoseconds. If the molecule was to be excited to only a single fine-structure state, then a low-frequency oscillation in the internuclear separation would be detectable through the time-dependent ionization cross section, giving a mechanism that would enable observation of coherent vibrational motion in this molecule.

  3. Atomlike, Hollow-Core–Bound Molecular Orbitals of C₆₀

    SciTech Connect

    Feng, Min; Zhao, Jin; Petek, Hrvoje

    2008-04-17

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The atomic electron orbitals that underlie molecular bonding originate from the central Coulomb potential of the atomic core. We used scanning tunneling microscopy and density functional theory to explore the relation between the nearly spherical shape and unoccupied electronic structure of buckminsterfullerene (C60) molecules adsorbed on copper surfaces. Besides the known p* antibonding molecular orbitals of the carbon-atom framework, above 3.5 electron volts we found atomlike orbitals bound to the core of the hollow C60 cage. These “superatom” states hybridize like the s and p orbitals of hydrogen and alkali atoms into diatomic molecule-like dimers and free-electron bands of one-dimensional wires and two-dimensional quantum wells in C60 aggregates. We attribute the superatom states to the central potential binding an electron to its screening charge, a property expected for hollow-shell molecules derived from layered materials.

  4. Orbital Exponent Optimization in Elementary VB Calculations of the Chemical Bond in the Ground State of Simple Molecular Systems

    ERIC Educational Resources Information Center

    Magnasco, Valerio

    2008-01-01

    Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and…

  5. Orbital Models Made of Plastic Soda Bottles

    NASA Astrophysics Data System (ADS)

    Samoshin, Vyacheslav V.

    1998-08-01

    The models for demonstration of shape and direction of atomic and molecular orbitals, their overlaps, interactions, and hybridizations may be easily constructed from plastic soda bottles. For such models one may attach the screw caps to the faces of wooden or plastic tetrahedrons, trigonal prisms, or cubes (by screws, glue, wire). When the bottles are screwed into the lids, the models of sp3, sp2, or sp hybridized atoms are obtained. The orbital overlap leading to s bond formation is imitated by insertion of a smaller bottle into a larger one with the bottom cut off. Rubber or plastic rings put on pairs of "p orbitals" mimic pi bond formations.

  6. The dynamical evolution of molecular clouds near the Galactic Centre - I. Orbital structure and evolutionary timeline

    NASA Astrophysics Data System (ADS)

    Kruijssen, J. M. Diederik; Dale, James E.; Longmore, Steven N.

    2015-02-01

    We recently proposed that the star-forming potential of dense molecular clouds in the Central Molecular Zone (CMZ, i.e. the central few 100 pc) of the Milky Way is intimately linked to their orbital dynamics, potentially giving rise to an absolute-time sequence of star-forming clouds. In this paper, we present an orbital model for the gas stream(s) observed in the CMZ. The model is obtained by integrating orbits in the empirically constrained gravitational potential and represents a good fit (χ _red^2=2.0) to the observed position-velocity distribution of dense (n > several 103 cm-3) gas, reproducing all of its key properties. The orbit is also consistent with observational constraints not included in the fitting process, such as the 3D space velocities of Sgr B2 and the Arches and Quintuplet clusters. It differs from previous, parametric models in several respects: (1) the orbit is open rather than closed due to the extended mass distribution in the CMZ, (2) its orbital velocity (100-200 km s-1) is twice as high as in previous models, and (3) Sgr A* coincides with the focus of the (eccentric) orbit rather than being offset. Our orbital solution supports the recently proposed scenario in which the dust ridge between G0.253+0.016 (`the Brick') and Sgr B2 represents an absolute-time sequence of star-forming clouds, of which the condensation was triggered by the tidal compression during their most recent pericentre passage. We position the clouds on a common timeline and find that their pericentre passages occurred 0.30-0.74 Myr ago. Given their short free-fall times (tff ˜ 0.34 Myr), the quiescent cloud G0.253+0.016 and the vigorously star-forming complex Sgr B2 are separated by a single free-fall time of evolution, implying that star formation proceeds rapidly once collapse has been initiated. We provide the complete orbital solution, as well as several quantitative predictions of our model (e.g. proper motions and the positions of star formation `hotspots'). The

  7. Communication through molecular bridges: different bridge orbital trends result in common property trends.

    PubMed

    Proppe, Jonny; Herrmann, Carmen

    2015-02-01

    Common trends in communication through molecular bridges are ubiquitous in chemistry, such as the frequently observed exponential decay of conductance/electron transport and of exchange spin coupling with increasing bridge length, or the increased communication through a bridge upon closing a diarylethene photoswitch. For antiferromagnetically coupled diradicals in which two equivalent spin centers are connected by a closed-shell bridge, the molecular orbitals (MOs) whose energy splitting dominates the coupling strength are similar in shape to the MOs of the dithiolated bridges, which in turn can be used to rationalize conductance. Therefore, it appears reasonable to expect the observed common property trends to result from common orbital trends. We illustrate based on a set of model compounds that this assumption is not true, and that common property trends result from either different pairs of orbitals being involved, or from orbital energies not being the dominant contribution to property trends. For substituent effects, an effective modification of the π system can make a comparison difficult. PMID:25382464

  8. Rotation and Anisotropic Molecular Orbital Effect in a Single H2TPP Molecule Transistor

    NASA Astrophysics Data System (ADS)

    Sakata, Shuichi; Yoshida, Kenji; Kitagawa, Yuichi; Ishii, Kazuyuki; Hirakawa, Kazuhiko

    2013-12-01

    Electron transport through a single molecule is determined not only by the intrinsic properties of the molecule but also by the configuration of the molecule with respect to the lead electrodes. Here, we show how electron transport through a single H2TPP molecule is modulated by changes in the configuration. The Coulomb stability diagram of a single H2TPP molecule transistor exhibited a few different patterns in different measurement scans. Furthermore, the sample exhibited negative differential resistance, the magnitude of which changed with the pattern in the Coulomb stability diagram. Such behavior can be explained by the rotation of the molecule with anisotropic molecular orbitals in the gap electrodes induced by electrical stress. Moreover, we find that the energy separations between molecular orbitals are also affected by the rotation, confirming that the metal-molecule interface configuration renormalizes the electronic levels in the molecule.

  9. Effect of vacuum processing on outgassing within an orbiting molecular shield

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.

    1982-01-01

    The limiting hydrogen number density in an orbiting molecular shield is highly dependent on the outgassing rates from the materials of construction for the shield, experimental apparatus, and other hardware contained within the shield. Ordinary degassing temperatures used for ultrahigh vacuum studies (less than 450 C) are not sufficient to process metals so that the contribution to the number density within the shield due to outgassing is less than the theoretically attainable level (approximately 200 per cu. cm). Pure aluminum and type 347 stainless steel were studied as candidate shield materials. Measurements of their hydrogen concentration and diffusion coefficients were made, and the effects of high temperature vacuum processing (greater than 600 C) on their resulting outgassing rates was determined. The densities in a molecular shield due to the outgassing from either metal were substantially less ( 0.003) than the density due to the ambient atomic hydrogen flux at an orbital altitude of 500 km.

  10. Thermal Analysis Investigation of Dapoxetine and Vardenafil Hydrochlorides using Molecular Orbital Calculations

    PubMed Central

    Attia, Ali Kamal; Souaya, Eglal R.; Soliman, Ethar A.

    2015-01-01

    Purpose: Thermal analysis techniques have been used to study the thermal behavior of dapoxetine and vardenafil hydrochlorides and confirmed using semi-empirical molecular orbital calculations. Methods: Thermogravimetric analysis, derivative thermogravimetry, differential thermal analysis and differential scanning calorimetry were used to determine the thermal behavior and purity of the drugs under investigation. Thermodynamic parameters such as activation energy, enthalpy, entropy and Gibbs free energy were calculated. Results: Thermal behavior of DAP and VAR were confirmed using by semi-empirical molecular orbital calculations. The purity values were found to be 99.97% and 99.95% for dapoxetine and vardenafil hydrochlorides, respectively. The purity of dapoxetine and vardenafil hydrochlorides is similar to that found by reported methods according to DSC data. Conclusion: Thermal analysis justifies its application in quality control of pharmaceutical compounds due to its simplicity, sensitivity and low operational costs. PMID:26819925

  11. Semiempirical molecular orbital estimation of the relative stability of bianthryls produced by anthracene pyrolysis

    SciTech Connect

    Mulholland, J.A.; Mukherjee, J.; Wornat, M.J.; Sarofim, A.F.; Rutledge, G.C. . Dept. of Chemical Engineering)

    1993-08-01

    The pyrolysis of pure anthracene at temperatures between 1,200 and 1,500 K produced all six bianthryl isomers whose relative yields appear to be related to steric factors. To evaluate the hypothesis that thermodynamic factors govern the product distribution of bianthryls in this system, the relative enthalpies and entropies of biaryl isomers were estimated by molecular orbital modeling, using the semiempirical AM1 (Austin Model 1). Computational analysis of several isomer sets demonstrates that the relative stabilities of a large number of biaryl isomers are determined largely by steric interactions caused by structural features defined as bays, coves, and fjords. These steric factors affect both the degree of biaryl twist in the preferred conformation and the freedom of internal rotation. Molecular orbital modeling supports the hypothesis that a thermodynamic distribution of bianthryl isomers is produced by anthracene pyrolysis.

  12. On-orbit free molecular flow aerodynamic characteristics of a proposal space operations center configuration

    NASA Astrophysics Data System (ADS)

    Romere, P. O.

    1982-03-01

    A proposed configuration for a Space Operations Center is presented in its eight stages of buildup. The on orbit aerodynamic force and moment characteristics were calculated for each stage based upon free molecular flow theory. Calculation of the aerodynamic characteristics was accomplished through the use of an orbital aerodynamic computer program, and the computation method is described with respect to the free molecular theory used. The aerodynamic characteristics are presented in tabulated form for each buildup stage at angles of attack from 0 to 360 degrees and roll angles from -60 to +60 degrees. The reference altitude is 490 kilometers, however, the data should be applicable for altitudes below 490 kilometers down to approximately 185 kilometers.

  13. On-orbit free molecular flow aerodynamic characteristics of a proposal space operations center configuration

    NASA Technical Reports Server (NTRS)

    Romere, P. O.

    1982-01-01

    A proposed configuration for a Space Operations Center is presented in its eight stages of buildup. The on orbit aerodynamic force and moment characteristics were calculated for each stage based upon free molecular flow theory. Calculation of the aerodynamic characteristics was accomplished through the use of an orbital aerodynamic computer program, and the computation method is described with respect to the free molecular theory used. The aerodynamic characteristics are presented in tabulated form for each buildup stage at angles of attack from 0 to 360 degrees and roll angles from -60 to +60 degrees. The reference altitude is 490 kilometers, however, the data should be applicable for altitudes below 490 kilometers down to approximately 185 kilometers.

  14. Classification of compounds with distinct or overlapping multi-target activities and diverse molecular mechanisms using emerging chemical patterns.

    PubMed

    Namasivayam, Vigneshwaran; Hu, Ye; Balfer, Jenny; Bajorath, Jürgen

    2013-06-24

    The emerging chemical patterns (ECP) approach has been introduced for compound classification. Thus far, only very few ECP applications have been reported. Here, we further investigate the ECP methodology by studying complex classification problems. The analysis involves multi-target data sets with systematically organized subsets of compounds having distinct or overlapping target activities and, in addition, data sets containing classes of specifically active compounds with different mechanism-of-action. In systematic classification trials focusing on individual compound subsets or mechanistic classes, ECP calculations utilizing numerical descriptors achieve moderate to high sensitivity, dependent on the data set, and consistently high specificity. Accurate ECP predictions are already obtained on the basis of very small learning sets with only three positive training instances, which distinguishes the ECP approach from many other machine learning techniques. PMID:23692475

  15. Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates

    USGS Publications Warehouse

    Sherman, David M.

    1986-01-01

    A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

  16. The interaction of hydrogen with an Fe vacancy: a molecular orbital simulation

    NASA Astrophysics Data System (ADS)

    Irigoyen, B.; Ferullo, R.; Castellani, N.; Juan, A.

    1996-05-01

    The semi-empirical atom superposition and electron delocalization molecular orbital (ASED-MO) theory was used to study the H - Fe interaction present during the adsorption of monotomic hydrogen on Fe(110) and the subsequent absorption of the hydrogen atom in a bulk Fe vacancy. For that purpose calculations were carried out using clusters with 53 and 50 atoms, respectively. Results indicate that, in general, the hydrogen - iron interaction is stronger near the surface and near the vacancy.

  17. Molecular orbital calculations of octahedral molybdenum cluster complexes with the DV-X{alpha} method

    SciTech Connect

    Imoto, Hideo; Saito, Taro; Adachi, Hirohiko

    1995-04-26

    Discrete variational-{Chi}{alpha} molecular orbital methods were applied to octahedral cluster complexes, [Mo{sub 6}X{sub 8}-(PH{sub 3}){sub 6}](X = S and Se). This structure is of interest due to its role in superconductivity of Chevrel plates. Level energies are discussed and factors contributing to their separations are categorized. Agreement with empirical XPS data is excellent.

  18. Spectral studies and molecular orbital PPP-calculations of some azo-dyes

    NASA Astrophysics Data System (ADS)

    Shalabi, A. S.; Dessouki, H. A.; Issa, Y. M.; Ahmed, I. S.

    2002-10-01

    The UV, IR and 1H-NMR spectra of some 4-( R-phenyl azo) 1-hydroxy 2-naphthoic acid derivatives are studied. The effects of substituent groups and the solvent polarity on electronic spectral, IR bands and 1H-NMR proton chemical shifts are considered, the molecular orbital calculations obtained are rationalized quantitatively with that obtained practically using the PPP-model with configuration interaction (CI).

  19. Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

    SciTech Connect

    Kress, Joel David; Ticknor, Christopher; Collins, Lee A.

    2015-09-16

    Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

  20. Pseudo-symmetry analysis of the d-block molecular orbitals in four-coordinate complexes.

    PubMed

    Falceto, Andrés; Casanova, David; Alemany, Pere; Alvarez, Santiago

    2013-06-01

    A rigorous definition of the concept of pseudo-symmetry, which is as important to chemistry as the concepts of symmetry implemented through group theory, should allow us to apply those group theoretical tools to molecules that are significantly distorted from those ideal symmetries best known and understood by the chemical community. In this paper, we consider four-coordinate transition-metal complexes with geometries along the interconversion path between the square and the tetrahedron and show how their molecular orbitals can be expressed in terms of either the tetrahedral or tetragonal symmetry groups. Furthermore, we analyze how the intensity of a d-d absorption band can be related to the degree of symmetry loss of the d-block molecular orbitals by means of their decomposition in terms of contributions from different pseudo-symmetry representations. As a final example, we also show how the substitution of a single ligand in a square planar complex affects the symmetry of the molecular orbitals and the absorption intensity associated to an electronic transition. PMID:23668721

  1. Molecular orbital study of some eight-coordinate sulfur chelate complexes of molybdenum

    SciTech Connect

    Perkins, P.G.; Schultz, F.A.

    1983-03-30

    A number of molybdenum complexes involving the formal oxidation states Mo(IV) and Mo(V) have been studied by a self-consistent-field molecular orbital technique. All the complexes were of dodecahedral geometry and had eight sulfurs chelated to the central metal atom. In all, a series of five tetrakis complexes was studied, including the ligands dithiocarbamate (dtc), thioxanthate (txn), 1,1-dicyano-2,2-ethylenedithiolate (i-mnt), 1-cyano-1-carbethoxy-2,2-ethylenedithiolate (ced), and 1,1-dicarbethoxy-2,2-ethylenedithiolate (ded). The 4d orbitals were included on molybdenum, and the empty 3d levels on all sulfur atoms. The results show that the highest occupied molecular orbital in each case has over 90% metal d/sub xy/ character. Further, the energy of this orbital is linearly related to the reversible half-wave potentials for Mo(IV) ..-->.. Mo(V) and Mo(V) ..-->.. Mo(VI) oxidations of the complexes. A further irreversible oxidation observed experimentally also is closely related to the calculated energy levels. Relationships between the calculated results and Mo 3d/sub 5///sub 2/ X-ray photoelectron binding energies, EPR parameters, and charge-transfer absorption energies are discussed. Electrochemical and spectroscopic properties of these MoS/sub 8/ complexes can be understood in terms of a manifold of orbital energies that retain approximately constant spacings between one another and that move up or down in absolute energy in response to the charge donated or withdrawn by the ligands.

  2. Libraries of Extremely Localized Molecular Orbitals. 2. Comparison with the Pseudoatoms Transferability.

    PubMed

    Meyer, Benjamin; Guillot, Benoît; Ruiz-Lopez, Manuel F; Jelsch, Christian; Genoni, Alessandro

    2016-03-01

    Due to both technical and methodological difficulties, determining and analyzing charge densities of very large molecular systems represents a serious challenge that, in the crystallographers community, has been mainly tackled by observing that the so-called pseudoatoms of the electron density multipole expansions are reliably transferable from molecule to molecule. This has led to the construction of pseudoatoms databanks that have allowed successful refinements of crystallographic structures of macromolecules, while taking into account their corresponding reconstructed electron distributions. A recent alternative/complement to the previous approach is represented by techniques based on extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, and functional groups), are also in principle exportable from system to system. The ELMOs transferability has been already tested in detail, and, in this work, it has been compared to the one of the pseudoatoms. To accomplish this task, electron distributions obtained both through the transfer of pseudoatoms and through the transfer of extremely localized molecular orbitals have been analyzed, especially taking into account topological properties and similarity indexes. The obtained results indicate that all the considered reconstruction methods give completely reasonable and similar charge densities, and, consequently, the new ELMOs libraries will probably represent new useful tools not only for refining crystal structures but also for computing approximate electronic properties of very large molecules. PMID:26799595

  3. Depopulation of Single-Phthalocyanine Molecular Orbitals upon Pyrrolic-Hydrogen Abstraction on Graphene.

    PubMed

    Néel, Nicolas; Lattelais, Marie; Bocquet, Marie-Laure; Kröger, Jörg

    2016-02-23

    Single-molecule chemistry with a scanning tunneling microscope has preponderantly been performed on metal surfaces. The molecule-metal hybridization, however, is often detrimental to genuine molecular properties and obscures their changes upon chemical reactions. We used graphene on Ir(111) to reduce the coupling between Ir(111) and adsorbed phthalocyanine molecules. By local electron injection from the tip of a scanning tunneling microscope the two pyrrolic H atoms were removed from single phthalocyanines. The detachment of the H atom pair induced a strong modification of the molecular electronic structure, albeit with no change in the adsorption geometry. Spectra and maps of the differential conductance combined with density functional calculations unveiled the entire depopulation of the highest occupied molecular orbital upon H abstraction. Occupied π states of intact molecules are proposed to be emptied via intramolecular electron transfer to dangling σ states of H-free N atoms. PMID:26812093

  4. An analytical molecular orbital approach in tetrathiafulvalene tetracyanoquinodimethane (TTF-TCNQ)

    NASA Astrophysics Data System (ADS)

    Tada, Tomofumi; Aoki, Yuriko; Imamura, Akira

    In low-dimensional molecular crystals exhibiting the Peierls instability, intercolumnar interactions play an important role in electrical conduction. In this work, we propose an efficient method based on molecular orbital theory for studying the Peierls instability in molecular crystals composed of mixed-valence complexes. A perturbational approach to general N-merized systems is incorporated and applied to tetrathiafulvalene tetracyanoquinodimethane (TTF-TCNQ) crystals. From the results of the calculations, a mixed state of several commensurate distortions is proposed as another aspect of the incommensurate distortion in TTF-TCNQ under atmospheric pressure, and TTF+0.5-TCNQ-0.5 crystal is found to be expected as an electronic conductor under high pressure.

  5. Transport properties of lithium hydride at extreme conditions from orbital-free molecular dynamics

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Ticknor, C.; Kress, J. D.; Collins, L. A.; Lambert, F.

    2013-02-01

    We have performed a systematic study of lithium hydride (LiH), using orbital-free molecular dynamics, with a focus on mass transport properties such as diffusion and viscosity by extending our previous studies at the lower end of the warm, dense matter regime to cover a span of densities from ambient to 10-fold compressed and temperatures from 10 eV to 10 keV. We determine analytic formulas for self- and mutual-diffusion coefficients, and viscosity, which are in excellent agreement with our molecular dynamics results, and interpolate smoothly between liquid and dense plasma regimes. In addition, we find the orbital-free calculations begin to agree with the Brinzinskii-Landau formula above about 250 eV at which point the medium becomes fully ionized. A binary-ion model based on a bare Coulomb interaction within a neutralizing background with the effective charges determined from a regularization prescription shows good agreement above about 100 eV with the orbital-free results. Finally, we demonstrate the validity of a pressure-based mixing rule in determining the transport properties from the pure-species quantities.

  6. Effects of the Shuttle Orbiter fuselage and elevon on the molecular distribution of water vapor from the flash evaporator system

    NASA Technical Reports Server (NTRS)

    Richmond, R. G.; Kelso, R. M.

    1980-01-01

    A concern has arisen regarding the emissive distribution of water molecules from the shuttle orbiter flash evaporator system (FES). The role of the orbiter fuselage and elevon in affecting molecular scattering distributions was nuclear. The effect of these components were evaluated. Molecular distributions of the water vapor effluents from the FE were measured. These data were compared with analytically predicted values and the resulting implications were calculated.

  7. A molecular orbital study of H interaction with an edge dislocation in Fe bcc

    NASA Astrophysics Data System (ADS)

    Irigoyen, B.; Ferullo, R.; Castellani, N.; Juan, A.

    1997-07-01

    We have calculated the total energy curve for an H atom near an edge dislocation interacting with the surface. We have used a cluster to simulate the Fe(100) surface and an edge (100) dislocation. The semi-empirical method based on atom superposition and electron delocalization molecular orbital (ASED-MO) theory was employed. In the ground state, the distorted cluster expands while the H occupies an eccentric position. The H energy in that position is 0.15 eV lower than at the surface. The electronic structure was analysed by local density of states (LDOS). The width of the metal band is increased near the dislocation void because of a higher hybridization and the interaction with the H 1s orbital.

  8. Molecular orbital calculations of possible pinning centers for magnetic flux in copper oxide superconductors

    NASA Astrophysics Data System (ADS)

    Fukushima, Kimichika

    1993-07-01

    Cluster calculations using the molecular orbital method were performed to search for impurities which would act as pinning centers for magnetic flux in copper oxide superconductors. Electronic structures were first investigated for interstitial helium atoms and for He atoms (including He clusters) substituted for oxygen and copper atoms. Calculations were then done for F atoms substituted for O atoms, and C, Mg, Al, Zn, Ga, and Cd atoms substituted for Cu. With these impurities, the energies of orbitals mainly attributable to the impurities differ from the Fermi energy. The Mulliken populations show that most charge carriers do not exist on the impurity sites (though some charge carriers enter the C sites), so it can be expected that the impurities considered here will act as pinning centers.

  9. Angiostrongylus cantonensis and A. malaysiensis Broadly Overlap in Thailand, Lao PDR, Cambodia and Myanmar: A Molecular Survey of Larvae in Land Snails.

    PubMed

    Rodpai, Rutchanee; Intapan, Pewpan M; Thanchomnang, Tongjit; Sanpool, Oranuch; Sadaow, Lakkhana; Laymanivong, Sakhone; Aung, Win Papa; Phosuk, Issarapong; Laummaunwai, Porntip; Maleewong, Wanchai

    2016-01-01

    Angiostrongylus cantonensis is a zoonotic nematode parasite causing human eosinophilic meningitis (or meningoencephalitis) worldwide. A closely related species, Angiostrongylus malaysiensis, might also be a human pathogen. Larvae were obtained from land snails in Lao PDR, Cambodia, Myanmar and Thailand. We sequenced two nuclear gene regions (nuclear ribosomal ITS2 and SSU rRNA) and a portion of one mitochondrial gene (COI) from these larvae. Angiostrongylus cantonensis and A. malaysiensis were identified. This is the first report of the molecular identification of the two Angiostrongylus species in Lao PDR, Cambodia and Myanmar. The regional distributions of the two species broadly overlap. Phylogenetic relationships were inferred including data from Angiostrongylus species deposited in public databases. All the gene regions we sequenced have potential value in distinguishing between species of Angiostrongylus. The COI gene exhibited the greatest intraspecific variation in the study region (five haplotypes in A. cantonensis and four in A. malaysiensis) and might be suitable for more detailed phylogeographic studies. PMID:27513930

  10. Angiostrongylus cantonensis and A. malaysiensis Broadly Overlap in Thailand, Lao PDR, Cambodia and Myanmar: A Molecular Survey of Larvae in Land Snails

    PubMed Central

    Rodpai, Rutchanee; Intapan, Pewpan M.; Thanchomnang, Tongjit; Sanpool, Oranuch; Sadaow, Lakkhana; Laymanivong, Sakhone; Aung, Win Papa; Phosuk, Issarapong; Laummaunwai, Porntip

    2016-01-01

    Angiostrongylus cantonensis is a zoonotic nematode parasite causing human eosinophilic meningitis (or meningoencephalitis) worldwide. A closely related species, Angiostrongylus malaysiensis, might also be a human pathogen. Larvae were obtained from land snails in Lao PDR, Cambodia, Myanmar and Thailand. We sequenced two nuclear gene regions (nuclear ribosomal ITS2 and SSU rRNA) and a portion of one mitochondrial gene (COI) from these larvae. Angiostrongylus cantonensis and A. malaysiensis were identified. This is the first report of the molecular identification of the two Angiostrongylus species in Lao PDR, Cambodia and Myanmar. The regional distributions of the two species broadly overlap. Phylogenetic relationships were inferred including data from Angiostrongylus species deposited in public databases. All the gene regions we sequenced have potential value in distinguishing between species of Angiostrongylus. The COI gene exhibited the greatest intraspecific variation in the study region (five haplotypes in A. cantonensis and four in A. malaysiensis) and might be suitable for more detailed phylogeographic studies. PMID:27513930

  11. Multi-Orbital Molecular Compound (TTM-TTP)I3: Effective Model and Fragment Decomposition

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent; Ishibashi, Shoji; Seo, Hitoshi

    2011-01-01

    The electronic structure of the molecular compound (TTM-TTP)I3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.

  12. Detection of a Molecular Disk Orbiting the Nearby, "old," Classical T Tauri Star MP Muscae

    NASA Astrophysics Data System (ADS)

    Kastner, Joel H.; Hily-Blant, Pierry; Sacco, G. G.; Forveille, Thierry; Zuckerman, B.

    2010-11-01

    We have used the Atacama Pathfinder Experiment 12 m telescope to detect circumstellar CO emission from MP Muscae (MP Mus; K1 IVe), a nearby (D ~ 100 pc), actively accreting, ~7 Myr old pre-main-sequence (pre-MS) star. The CO emission line profile measured for MP Mus is indicative of an orbiting disk with radius ~120 AU, assuming that the central star mass is 1.2 M sun and the disk inclination is i ~ 30°. The inferred disk molecular gas mass is ~3 M ⊕. MP Mus thereby joins TW Hya and V4046 Sgr as the only late-type (low-mass), pre-MS star systems within ~100 pc of Earth that are known to retain orbiting, molecular disks. We also report the nondetection (with the Institut de Radio Astronomie Millimetrique 30 m telescope) of CO emission from another 10 nearby (D <~ 100 pc), dusty, young (age ~10-100 Myr) field stars of spectral type A-G. We discuss the implications of these results for the timescales for stellar and Jovian planet accretion from, and dissipation of, molecular disks around young stars. This research is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, proposal number 385.C-0143, with the Atacama Pathfinder Experiment (APEX).

  13. DETECTION OF A MOLECULAR DISK ORBITING THE NEARBY, 'OLD', CLASSICAL T TAURI STAR MP MUSCAE

    SciTech Connect

    Kastner, Joel H.; Sacco, G. G.; Hily-Blant, Pierry; Forveille, Thierry; Zuckerman, B.

    2010-11-10

    We have used the Atacama Pathfinder Experiment 12 m telescope to detect circumstellar CO emission from MP Muscae (MP Mus; K1 IVe), a nearby (D {approx} 100 pc), actively accreting, {approx}7 Myr old pre-main-sequence (pre-MS) star. The CO emission line profile measured for MP Mus is indicative of an orbiting disk with radius {approx}120 AU, assuming that the central star mass is 1.2 M {sub sun} and the disk inclination is i {approx} 30{sup 0}. The inferred disk molecular gas mass is {approx}3 M {sub +}. MP Mus thereby joins TW Hya and V4046 Sgr as the only late-type (low-mass), pre-MS star systems within {approx}100 pc of Earth that are known to retain orbiting, molecular disks. We also report the nondetection (with the Institut de Radio Astronomie Millimetrique 30 m telescope) of CO emission from another 10 nearby (D {approx_lt} 100 pc), dusty, young (age {approx}10-100 Myr) field stars of spectral type A-G. We discuss the implications of these results for the timescales for stellar and Jovian planet accretion from, and dissipation of, molecular disks around young stars.

  14. Molecular Dynamics Modeling of the Thermal Conductivity of Irradiated SiC as a Function of Cascade Overlap

    SciTech Connect

    Crocombette, J.-P.; Dumazer, Guillaume; Hoang, Nguyen Q.; Gao, Fei; Weber, William J.

    2007-01-15

    SiC thermal conductivity is known to decrease under irradiation. To understand this effect, we study the variation of the thermal conductivity of cubic SiC with defect accumulation induced by displacement cascades. We use an empirical potential of the Tersoff type in the framework of non-equilibrium molecular dynamics. The conductivity of SiC is found to decrease with dose, in very good quantitative agreement with low temperature irradiation experiments. The results are analyzed in view of the amorphization states that are created by the cascade accumulation simulations. The calculated conductivity values at lower doses are close to the smallest measured values after high temperature irradiation, indicating that the decrease of the conductivity observed at lower doses is related to the creation of point defects. A subsequent decrease takes place upon further cascade accumulation. It is characteristic of the amorphization of the material and is experimentally observed for low temperature irradiation only.

  15. Multicenter molecular integrals for Slater orbitals of higher principal quantum numbers

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1989-01-01

    As was shown earlier by Tai (1979), by using the Fourier-transform technique and properly coupling a pair of two-center exchange integrals, the multicenter molecular integrals can be cast into a simple expression upon which numerical procedures can be directly applied. In this paper, the procedure of Tai is extended to integrals involving orbitals with arbitrarily higher principal quantum number. The derivation is outlined, and the explicit expressions are presented for a three-center nuclear attraction integral and a four-center two-electron Coulomb repulsion integral of arbitrary higher states.

  16. Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Yuan, Dingwang; Yu, Arthur; Czap, Gregory; Wu, Ruqian; Ho, W.

    2015-05-01

    A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j =0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom.

  17. Molecular-orbital coefficients for dinuclear polymethyne dyes in the effective additive parameter method

    SciTech Connect

    Dyadyusha, G.G.; Ushomirskii, M.M.

    1986-09-01

    A method previously proposed for determining the energy structure of a polymethyne dye with any terminal groups is used in considering formulas for the molecularorbital coefficients and the differences in the distribution on the atoms in the polymethyne chain for localized and delocalized energy levels, as well as the accuracy in calculating the molecular-orbital coefficients by means of a finite number of effective additive parameters. It is found that the localized states are important to the electron-density distribution on the chain atoms characteristic of the polymethyne dyes.

  18. Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule.

    PubMed

    Li, Shaowei; Yuan, Dingwang; Yu, Arthur; Czap, Gregory; Wu, Ruqian; Ho, W

    2015-05-22

    A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j=0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom. PMID:26047242

  19. Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Watanabe, Hirofumi; Okiyama, Yoshio; Nakano, Tatsuya; Tanaka, Shigenori

    2010-11-01

    We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17 β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation.

  20. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme

    NASA Astrophysics Data System (ADS)

    Okiyama, Yoshio; Fukuzawa, Kaori; Yamada, Haruka; Mochizuki, Yuji; Nakano, Tatsuya; Tanaka, Shigenori

    2011-06-01

    Basis set superposition error (BSSE) correction with counterpoise (CP) procedure under the environmental electrostatic potential is newly introduced to interfragment interaction energy (IFIE), which is important for interaction analysis in the fragment molecular orbital method. The CP correction for IFIE is applied to a stacked dimer of base pair and a protein-ligand complex of estrogen receptor and 17β-estradiol with scaled third-order Møller-Plesset perturbation theory. The BSSEs amount to about quarter of IFIE for hydrogen-bonding and electrostatic interactions and half or even more for dispersion interactions. Estimation of IFIE with the CP correction is therefore preferred for the quantitative discussion.

  1. Radical damage in lipids investigated with the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Green, Mandy C.; Nakata, Hiroya; Fedorov, Dmitri G.; Slipchenko, Lyudmila V.

    2016-05-01

    To quantify the thermodynamics for hydrogen abstraction lipids, the fragment molecular orbital method (FMO) is used to calculate structures and energies of the reactants and products. The analytic second derivative is developed for the open-shell Hartree-Fock formulation of FMO and used to calculate zero point energy corrections. The accuracy of FMO is evaluated for a lipid model and the errors in reaction energies are found not to exceed 0.5 kcal/mol. The reaction energies determined for multiple sites in two lipids are used to discuss likely sites and pathways of radical initiation in membranes.

  2. The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method.

    PubMed

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

    We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets. PMID:19894991

  3. Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Kato, Koichiro; Fukuzawa, Kaori; Mochizuki, Yuji

    2015-06-01

    We have applied the four-body corrected fragment molecular orbital (FMO4) calculations to analyze the interaction between a designed peptide motif (Glu1-Ser2-Gln3-Glu4-Ser5) and the hydroxyapatite (HA) solid mimicked by a cluster model consisting of 1408 atoms. To incorporate statistical fluctuations, a total of 30 configurations were generated through classical molecular dynamics simulation with water molecules and were subjected to FMO4 calculations at the MP2 level. It was found that Ser5 plays a leading role in interacting with the phosphate moieties of HA via charge transfer and also that negatively charged Glu1 and Glu4 provide electrostatic stabilizations with the calcium ions.

  4. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

  5. Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

    ERIC Educational Resources Information Center

    Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

  6. Orbital alignment at the internal interface of arylthiol functionalized CdSe molecular hybrids

    SciTech Connect

    Li, Zhi; Schlaf, Rudy; Mazzio, Katherine A.; Okamoto, Ken; Luscombe, Christine K.

    2015-04-21

    Organic-inorganic nanoparticle molecular hybrid materials are interesting candidates for improving exciton separation in organic solar cells. The orbital alignment at the internal interface of cadmium selenide (ArS-CdSe) hybrid materials functionalized with covalently attached arylthiolate moieties was investigated through X-ray photoemission spectroscopy (XPS) and ultraviolet photoemission spectroscopy (UPS). A physisorbed interface between arylthiol (ArSH) ligands and CdSe nanoparticles was also investigated for comparison. This interface was created via a multi-step thin film deposition procedure in-vacuo, where the surface was characterized after each experimental step. This enabled the direct comparison of ArSH/CdSe interfaces produced via physisorption and ArS-CdSe covalently attached hybrid materials, which rely on a chemical reaction for their synthesis. All material depositions were performed using an electrospray deposition, which enabled the direct injection of solution-originating molecular species into the vacuum system. This method allows XPS and UPS measurements to be performed immediately after deposition without exposure to the atmosphere. Transmission electron microscopy was used to determine the morphology and particle size of the deposited materials. Ultraviolet-visible spectroscopy was used to estimate the optical band gap of the CdSe nanoparticles and the HOMO-LUMO gap of the ArSH ligands. These experiments showed that hybridization via covalent bonds results in an orbital realignment at the ArSH/CdSe interface in comparison to the physisorbed interface. The orbital alignment within the hybrid caused a favorable electron injection barrier, which likely facilitates exciton-dissociation while preventing charge-recombination.

  7. Molecular orbitals vs. relativistic orbitals in t2g honeycomb lattices: SrRu2O6 as compared to Na2IrO3, RuCl3, and Li2RuO3

    NASA Astrophysics Data System (ADS)

    Mazin, Igor; Streltsov, Sergey; Foyevtseva, Kateryna

    t2g states on a honeycomb lattice tend to form non-dispersive localized states even if large intersite hopping is present. In the nonrelativistic case, these are molecular orbitals (MO) localized on metal hexagons, if the ligand-assisted nearest and next nearest neighbor hoppings, t1' and t2', dominate, or dimers (DO), if the direct overlap, t1, dominates. In the ultrarelativistic limit t2 g form effective relativistic orbitals (RO), jeff = 3/3 2 2, which are atomically localized if t1'is the dominant hopping. On the first glance, the three regimes are defined by the conditions t1' >>t1 , λ or t1 >>t1' , λ or λ >>t1 ,t1' . In reality, the latter condition is never fulfilled, especially in ruthenates, yet not only Na2IrO3, but also RuCl3 appear to be in a regime dominated by RO, even though the residual effect of MO critically influences magnetic interactions, while Li2RuO3, not far removed from RuCl3 in the parameter space, is firmly in the DO regime. Most surprisingly, SrRu2O6, which is even closer to RuCl3, happens to be fully in the MO regime, with negligible spin-orbit effects. In this talk, we will show that an additional, decisive factor is the doping level per site. The principal difference between Na2IrO3 or RuCl3, Li2RuO3, and SrRu2O6 is that the first two have one t2 ghole per site, the second one two holes, and the last three electrons. In particular, the total dominance of MO in the latter compound fully explains its unique and unexpected magnetic properties. This work was supported by ONR (IIM) and CRDF (IIM and SVS).

  8. INVESTIGATION OF THE CORRELATION BETWEEN THE ENERGY OF THE HIGHESTOCCUPIED MOLECULAR ORBITAL (HOMO) AND THE LOGARITHM OF THE OH RATECONSTANT OF HYDROFLUOROCARBONS AND HYDROFLUOROETHERS

    EPA Science Inventory

    A regression based model was developed to determine whether highest occupied molecular orbital (HOMO) energies, calculated using Kohn-Sham orbital density functional theory (DFT) could be used to estimate the OH rate constants of hydrofluorocarbons (HFCS) and hydrofluoroethers (H...

  9. Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

    SciTech Connect

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M.

    2014-10-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

  10. Conformational stability, spectroscopic and computational studies, hikes' occupied molecular orbital, lowest unoccupied molecular orbital, natural bond orbital analysis and thermodynamic parameters of anticancer drug on nanotube-A review.

    PubMed

    Ghasemi, A S; Mashhadban, F; Hoseini-Alfatemi, S M; Sharifi-Rad, J

    2015-01-01

    Today the use of nanotubes (CNTs) is widely spread a versatile vector for drug delivery that can officiate as a platform for transporting a variety of bioactive molecules, such as drugs. In the present study, the interaction between the nanotube and anticancer drugs is investigated. Density functional theory (DFT) calculations were using the Gauss view and the complexes were optimized by B3LYP method using B3LYP/6-31G (d, p) and B3LYP/6-311++G (d, p) basis set in the gas phase and water solution at 298.15K. The calculated hikes' occupied molecular orbital (HOMO) and the lowest unoccupied (LUMO) energies Show that charge transfer occurs within the molecule. Furthermore, the effects of interactions on the natural bond orbital analysis (NBO) have been used to a deeper investigation into the studied compounds. These factors compete against each other to determine the adsorption behavior of the tube computer simulation is seen to be capable to optimize anticancer drug design. This review article mainly concentrates on the different protocols of loading anticancer drugs onto CNTs as well as how to control the anticancer drug release and cancer treatment. PMID:26718433

  11. Molecular Orbital Simulations of Metal 1s2p Resonant Inelastic X-ray Scattering.

    PubMed

    Guo, Meiyuan; Källman, Erik; Sørensen, Lasse Kragh; Delcey, Mickaël G; Pinjari, Rahul V; Lundberg, Marcus

    2016-07-28

    For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s→3d) excitation can be followed by monitoring the dipole-allowed Kα (2p→1s) or Kβ (3p→1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)6](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)6](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)6](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems. PMID:27398775

  12. Fourier transform photoelectron diffraction and its application to molecular orbitals and surface structure

    SciTech Connect

    Zhou, Xin

    1998-11-30

    Photoemission intensities from the molecular orbitals of c(2x2)CO/Pt(111) over a wide photon energy range were measured and analyzed by the same methods developed for structural studies using core levels. The 4{sigma} orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5{sigma} orbital lies between the C atom and the Pt surface. The C 1s photoelectron diffraction was used to determine the adsorption geometry. The earlier ambiguity that multiple scattering is needed to correctly model a {chi} curve while single scattering is sufficient for understanding major peaks in the ARPEFS-FTS is clarified by studying the clean Ni(111) surface. In the normal emission case, several different combinations of scattering events have similar path length differences (PLDs), and can either cancel each other or enhance the corresponding FT peak. In the off-normal case the degeneracy is greatly reduced due to the lower degree of symmetry. In normal emission AR PEFS, up to third order multiple scattering is needed to describe fully both the {chi} curve and its FT spectrum. To improve the spectral resolution in the ARPEFS-FT analysis, several new spectral analysis methods are introduced. With both autocorrelation autoregression (ACAR) and autocorrelation eigenvector (ACE), we can produce a reliable power spectrum by following the order-closing procedure. The best spectra are usually obtained when the autocorrelation sequence is computed with lags up to half the data range. A simple way of determining surface adsorption sites is proposed as follows: First use a single scattering cluster for possible adsorption sites to construct the geometrical PLDs from the strong backscattering events; then compare these PLDs with those obtained from the ARPEFS-FT analysis of the experimental data. After the preferred adsorption site is determined, fine tune the interlayer distances according to the positional R-factor.

  13. Investigations into the molecular-level adhesion characteristics of hydroxyapatite-coated and anodized titanium surfaces using the molecular orbital approach.

    PubMed

    Saju, K K; Jayadas, N H; Vidyanand, S; James, J

    2011-03-01

    It has been established that the adhesion of cells on to the surfaces of orthopaedic implants depends on the ability of the surfaces to accommodate protein molecules. Hydroxyapatite coating and anodizing are the most common methods to make TiAl6V4 implants (Ti) more biocompatible. In this paper Spartan 02, a molecular dynamics software, is used to analyze and predict the bonding characteristics of Extra cellular matrix protein sequence arginine-glycine-aspartic acid (RGD) on a Hyrdoxyapatite (HA) coated Ti and an anodized Ti surface based on the property of its constituent atoms, their polarity (net electrostatic charge, Qr), the energies of the molecular orbital E_HOMO (energy of the highest occupied molecular orbital), and E_LUMO (energy of the lowest unoccupied molecular orbital). The results show favourable criterion for formation of bonding between the HOMO orbital of the HA coated and anodized surfaces and LUMO orbital of the glycine strand from the RGD unit. The mechanism of bonding of individual atoms to form primary calcium oxide compounds is likely only in the case of HA coated surfaces . The surface texture of the anodized Ti with inherent porosities appear more responsible for the adsorption of proteins on to them by mechanical interlocking than the formation of any intermediate calcium oxide compounds. PMID:21485326

  14. Design principle for increasing charge mobility of π-conjugated polymers using regularly localized molecular orbitals

    PubMed Central

    Terao, Jun; Wadahama, Akihisa; Matono, Akitoshi; Tada, Tomofumi; Watanabe, Satoshi; Seki, Shu; Fujihara, Tetsuaki; Tsuji, Yasushi

    2013-01-01

    The feasibility of using π-conjugated polymers as next-generation electronic materials is extensively studied; however, their charge mobilities are lower than those of inorganic materials. Here we demonstrate a new design principle for increasing the intramolecular charge mobility of π-conjugated polymers by covering the π-conjugated chain with macrocycles and regularly localizing π-molecular orbitals to realize an ideal orbital alignment for charge hopping. Based on theoretical predictions, insulated wires containing meta-junctioned poly(phenylene–ethynylene) as the backbone units were designed and synthesized. The zigzag wires exhibited higher intramolecular charge mobility than the corresponding linear wires. When the length of the linear region of the zigzag wires was increased to 10 phenylene–ethynylene units, the intramolecular charge mobility increased to 8.5 cm2 V−1 s−1. Theoretical analysis confirmed that this design principle is suitable for obtaining ideal charge mobilities in π-conjugated polymer chains and that it provides the most effective pathways for inter-site hopping processes. PMID:23575695

  15. Predicting the solid solubility limit in high-entropy alloys using the molecular orbital approach

    NASA Astrophysics Data System (ADS)

    Sheikh, Saad; Klement, Uta; Guo, Sheng

    2015-11-01

    High-entropy alloys (HEAs) are currently at the research frontier of metallic materials. Understanding the solid solubility limit in HEAs, such a highly concentrated multicomponent alloy system, is scientifically intriguing. It is also technically important to achieve desirable mechanical properties by controlling the formation of topologically or geometrically closed packed phases. Previous approaches to describe the solid solubilities in HEAs could not accurately locate the solubility limit and have to utilize at least two parameters. Here, we propose to use a single parameter, the average energy of d-orbital levels, Md, to predict the solid solubility limit in HEAs. It is found that Md can satisfactorily describe the solid solubilities in fcc structured HEAs containing 3 d transition metals, and also in bcc structured HEAs. This finding will greatly simplify the alloys design and lends more flexibility to control the mechanical properties of HEAs. When 4 d transition metals are alloyed, Md alone cannot describe the solid solubility limit in fcc structured HEAs, due to the large increase of the bond strength that can be gauged by the bond order, Bo. The potential opportunities and challenges with applying the molecular orbital approach to HEAs are discussed.

  16. Enhanced Magnetoresistance in Molecular Junctions by Geometrical Optimization of Spin-Selective Orbital Hybridization.

    PubMed

    Rakhmilevitch, David; Sarkar, Soumyajit; Bitton, Ora; Kronik, Leeor; Tal, Oren

    2016-03-01

    Molecular junctions based on ferromagnetic electrodes allow the study of electronic spin transport near the limit of spintronics miniaturization. However, these junctions reveal moderate magnetoresistance that is sensitive to the orbital structure at their ferromagnet-molecule interfaces. The key structural parameters that should be controlled in order to gain high magnetoresistance have not been established, despite their importance for efficient manipulation of spin transport at the nanoscale. Here, we show that single-molecule junctions based on nickel electrodes and benzene molecules can yield a significant anisotropic magnetoresistance of up to ∼200% near the conductance quantum G0. The measured magnetoresistance is mechanically tuned by changing the distance between the electrodes, revealing a nonmonotonic response to junction elongation. These findings are ascribed with the aid of first-principles calculations to variations in the metal-molecule orientation that can be adjusted to obtain highly spin-selective orbital hybridization. Our results demonstrate the important role of geometrical considerations in determining the spin transport properties of metal-molecule interfaces. PMID:26926769

  17. New methods for accelerating the convergence of molecular electronic integrals over exponential type orbitals

    NASA Astrophysics Data System (ADS)

    Safouhi, Hassan; Hoggan, Philip

    2003-01-01

    This review on molecular integrals for large electronic systems (MILES) places the problem of analytical integration over exponential-type orbitals (ETOs) in a historical context. After reference to the pioneering work, particularly by Barnett, Shavitt and Yoshimine, it focuses on recent progress towards rapid and accurate analytic solutions of MILES over ETOs. Software such as the hydrogenlike wavefunction package Alchemy by Yoshimine and collaborators is described. The review focuses on convergence acceleration of these highly oscillatory integrals and in particular it highlights suitable nonlinear transformations. Work by Levin and Sidi is described and applied to MILES. A step by step description of progress in the use of nonlinear transformation methods to obtain efficient codes is provided. The recent approach developed by Safouhi is also presented. The current state of the art in this field is summarized to show that ab initio analytical work over ETOs is now a viable option.

  18. Molecular orbital studies in oxidation: Sulfate formation and metal-metal oxide adhesion

    NASA Technical Reports Server (NTRS)

    Anderson, A. B.

    1985-01-01

    The chemical mechanisms for sulfate formation from sodium chloride and sulfur trioxide, which is a product of jet fuel combustion was determined. Molten sodium sulfate leads to hot corrosion of the protective oxide layers on turbine blades. How yttrium dopants in nidkel-aluminum alloys used in turbine blades reduce the spalling rate of protective alumina films and enhance their adhesion was also determined. Two other fulfate mechanisms were deduced and structure of carbon monoxide on a clean chronium and clean platinum-titanium alloys surfaces was determined. All studies were by use of the atom superposition and electron delocalization molecular orbital (ASED-MO) theory. Seven studies were completed. Their titles and abstracts are given.

  19. Orbital-free Molecular Dynamics Simulations to Characterize the Liquid-vapor Critical Point of Aluminum

    NASA Astrophysics Data System (ADS)

    Chakraborty, Debajit; Karasiev, Valentin; Trickey, Samuel

    Aluminum is frequently used in warm-dense matter (WDM) experiments. However, experimental diagnostic limitations make computational exploration of the Al liquid-vapor transition important. The elevated temperaure and low-density make ab initio molecular dynamics (AIMD) with Kohn-Sham (KS) density functional theory (DFT) searches for the divergent compressibility extremely time consuming. Orbital free DFT (OFDFT) in principle is a cost-effective alternative. Here we report on calculations utilizing the PROFESS@QuantumEspresso interface to explore suitable pseudo-potentials, the limitations of our wholly constraint-based VT84F non-ineracting free-energy functional as exposed in the low-density regime, and possible extensions or extrapolations via tunable non-interacting free energy functionals. Work supported by U.S. Dept. of Energy, Grant DE-SC0002139.

  20. Oxygen evolution on a SrFeO3 anode - Mechanistic considerations from molecular orbital theory

    NASA Technical Reports Server (NTRS)

    Mehandru, S. P.; Anderson, Alfred B.

    1989-01-01

    Various pathways proposed in the literature for the evolution of O2 in electrochemical oxidations are explored using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory and the cluster models of the SrFeO3 surface as a prototype material. Calculations indicate that oxygen atoms can be easily formed on the (100) surface as well as on the edge cation sites of a SrFeO3 anode by the discharge of OH(-), followed by its deprotonation and electron transfer to the electrode. The O atoms can form O2 on the edge and corner sites, where the Fe(4+) is coordinated to four and three bulk oxygen anions, respectively. The calculations strongly disfavor mechanisms involving coupling of oxygen atoms adsorbed on different cations as well as a mechanism featuring an ozone intermediate.

  1. Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits).

    PubMed

    Taguchi, Naoki; Mochizuki, Yuji; Nakano, Tatsuya; Amari, Shinji; Fukuzawa, Kaori; Ishikawa, Takeshi; Sakurai, Minoru; Tanaka, Shigenori

    2009-01-29

    We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion. PMID:19127982

  2. AM1 and ab initio molecular orbital study of water dimer

    SciTech Connect

    Dannenberg, J.J.

    1988-12-01

    Several structures for the water dimer, including trifurcated structures similar to the optimized AM1 geometry, have been calculated by using the MP4/6-311G** level of ab initio molecular orbital theory. The relative energies of the structures become quite close at the higher levels of calculation. The best trifurcated is only 0.2 kcal/mol higher than the optimized HF/6-31G* structure and only 0.4 kcal/mol higher than the lowest energy structure found (optimized by using AM1 with the H bond constrained to be linear). It appears likely that the potential surface of the water dimer is extremely flat. The experimental geometry, which corresponds to the minimum on the free energy surface, is likely to be dominated by entropy contributions.

  3. Hyperfine Parameters for Aluminum Hydride: An ab Initio Molecular Orbital Study

    NASA Astrophysics Data System (ADS)

    Gee, Myrlene; Wasylishen, Roderick E.

    2001-06-01

    An extensive ab initio molecular orbital study of the 27Al nuclear spin-rotation and nuclear quadrupolar coupling constants in aluminum hydride, AlH, has been performed. The 27Al nuclear spin-rotation constant (C⊥), calculated to be approximately 300 kHz, was neglected in a previous analysis of the hyperfine structure in the microwave spectrum (M. Goto and S. Saito, Astrophys. J.452, L147-148 (1995)). Unfortunately, the ab initio calculations do not provide a definitive value for the aluminum nuclear quadrupolar coupling constant, but suggest a value of -49±4 MHz. It is apparent that the microwave study of AlH should be repeated.

  4. Defect-induced discriminative modulation of the highest occupied molecular orbital energies of graphene

    SciTech Connect

    Yuan, Wenjuan E-mail: luojunkink@126.com; Yang, Hongping; Zhu, Jing; Luo, Jun E-mail: luojunkink@126.com

    2015-11-15

    Defects are capable of modulating various properties of graphene, and thus controlling defects is useful in the development of graphene-based devices. Here we present first-principles calculations, which reveal a new avenue for defect engineering of graphene: the modulation by defects on the highest occupied molecular orbital (HOMO) energy of a charged monolayer graphene quantum dot (GQD) is discriminative. When the charge of a GQD increases its HOMO energy also increases. Importantly, when the GQD contains one particular class of defects its HOMO energy is sometimes higher and sometimes lower than that of the corresponding GQD without any defects, but when the GQD contains another class of defects its HOMO energy is always higher or lower than that of the corresponding intact GQD as its excess charge reaches a critical value. This discriminative modulation could allow defect engineering to control secondary electron ejection in graphene, leading to a new way to develop graphene-based devices.

  5. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

    PubMed Central

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2010-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations. PMID:19618944

  6. Development of the four-body corrected fragment molecular orbital (FMO4) method

    NASA Astrophysics Data System (ADS)

    Nakano, Tatsuya; Mochizuki, Yuji; Yamashita, Katsumi; Watanabe, Chiduru; Fukuzawa, Kaori; Segawa, Katsunori; Okiyama, Yoshio; Tsukamoto, Takayuki; Tanaka, Shigenori

    2012-01-01

    The four-body corrected fragment molecular orbital (FMO4) method was implemented at the second-order Møller-Plesset perturbation (MP2) level. A series of accuracy tests relative to the previous two-body and three-body treatments were performed. As expected, FMO4 provided better accuracy in total energies in comparison with the reference values by regular MO calculations. A nonconventional fragmentation by separating main and side chains in amino acid residues was examined for Ala-pentamer and Chignolin, where the four-body corrections were shown to be substantial. A large complex of HIV-1 protease (total 198 residues) with lopinavir was calculated as well. Furthermore, this new FMO scheme was successfully applied to adamantane-shaped clusters with three-dimensional bonding framework.

  7. Hybrid RHF/MP2 Geometry Optimizations with the Effective Fragment Molecular Orbital Method

    PubMed Central

    Christensen, Anders S.; Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2014-01-01

    The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two. PMID:24558430

  8. Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

    PubMed Central

    Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be kcal mol−1 for MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively. PMID:23593259

  9. Overlap in Bibliographic Databases.

    ERIC Educational Resources Information Center

    Hood, William W.; Wilson, Concepcion S.

    2003-01-01

    Examines the topic of Fuzzy Set Theory to determine the overlap of coverage in bibliographic databases. Highlights include examples of comparisons of database coverage; frequency distribution of the degree of overlap; records with maximum overlap; records unique to one database; intra-database duplicates; and overlap in the top ten databases.…

  10. Communication: Unambiguous comparison of many-electron wavefunctions through their overlaps

    NASA Astrophysics Data System (ADS)

    Plasser, Felix; González, Leticia

    2016-07-01

    A simple and powerful method for comparing many-electron wavefunctions constructed at different levels of theory is presented. By using wavefunction overlaps, it is possible to analyze the effects of varying wavefunction models, molecular orbitals, and one-electron basis sets. The computation of wavefunction overlaps eliminates the inherent ambiguity connected to more rudimentary wavefunction analysis protocols, such as visualization of orbitals or comparing selected physical observables. Instead, wavefunction overlaps allow processing the many-electron wavefunctions in their full inherent complexity. The presented method is particularly effective for excited state calculations as it allows for automatic monitoring of changes in the ordering of the excited states. A numerical demonstration based on multireference computations of two test systems, the selenoacrolein molecule and an iridium complex, is presented.

  11. Communication: Unambiguous comparison of many-electron wavefunctions through their overlaps.

    PubMed

    Plasser, Felix; González, Leticia

    2016-07-14

    A simple and powerful method for comparing many-electron wavefunctions constructed at different levels of theory is presented. By using wavefunction overlaps, it is possible to analyze the effects of varying wavefunction models, molecular orbitals, and one-electron basis sets. The computation of wavefunction overlaps eliminates the inherent ambiguity connected to more rudimentary wavefunction analysis protocols, such as visualization of orbitals or comparing selected physical observables. Instead, wavefunction overlaps allow processing the many-electron wavefunctions in their full inherent complexity. The presented method is particularly effective for excited state calculations as it allows for automatic monitoring of changes in the ordering of the excited states. A numerical demonstration based on multireference computations of two test systems, the selenoacrolein molecule and an iridium complex, is presented. PMID:27421390

  12. Molecular orbital (SCF-Xα-SW) theory of metal-metal charge transfer processes in minerals - II. Application to Fe2+ --> Ti4+ charge transfer transitions in oxides and silicates

    USGS Publications Warehouse

    Sherman, David M.

    1987-01-01

    A molecular orbital description, based on Xα-Scattered wave calculations on a (FeTiO10)14− cluster, is given for Fe2+ → Ti4+ charge transfer transitions in minerals. The calculated energy for the lowest Fe2+ → Ti4+ metal-metal charge transfer transition is 18040 cm−1 in reasonable agreement with energies observed in the optical spectra of Fe-Ti oxides and silicates. As in the case of Fe2+ → Fe3+ charge transfer in mixed-valence iron oxides and silicates, Fe2+ → Ti4+ charge transfer is associated with Fe-Ti bonding across shared polyhedral edges. Such bonding results from the overlap of the Fe(t 2g ) and Ti(t 2g ) 3d orbitals.

  13. Estimation of Molecular Acidity via Electrostatic Potential at the Nucleus and Valence Natural Atomic Orbitals

    PubMed Central

    Liu, Shubin; Pedersen, Lee G.

    2009-01-01

    An effective approach of estimating molecular pKa values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pKa values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pKa data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pKa values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules. PMID:19317439

  14. Computational study of the vibrational spectroscopic studies, natural bond orbital, frontier molecular orbital and second-order non-linear optical properties of acetophenone thiosemicarbazone molecule

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Hong; Mei, Zheng; Zhang, Xian-Zhou

    2014-01-01

    The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist Nsbnd H…N and Nsbnd H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z = 8, a = 16.0735 Å, b = 7.1719 Å, c = 7.8725 Å, ρ = 0.808 g/cm3.

  15. Computational study of the vibrational spectroscopic studies, natural bond orbital, frontier molecular orbital and second-order non-linear optical properties of acetophenone thiosemicarbazone molecule.

    PubMed

    Li, Xiao-Hong; Mei, Zheng; Zhang, Xian-Zhou

    2014-01-24

    The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist N-H…N and N-H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z=8, a=16.0735 Å, b=7.1719 Å, c=7.8725 Å, ρ=0.808 g/cm(3). PMID:24084483

  16. Spectroscopic studies and molecular orbital calculations of charge transfer complexation between 3,5-dimethylpyrazole with DDQ in acetonitrile

    NASA Astrophysics Data System (ADS)

    Habeeb, Moustafa M.; Al-Attas, Amirah S.; Al-Raimi, Doaa S.

    2015-05-01

    Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589 nm, respectively. Job's method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi-Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded.

  17. General contraction of Gaussian basis sets. Part 2: Atomic natural orbitals and the calculation of atomic and molecular properties

    NASA Technical Reports Server (NTRS)

    Almloef, Jan; Taylor, Peter R.

    1989-01-01

    A recently proposed scheme for using natural orbitals from atomic configuration interaction (CI) wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outmost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital (ANO) sets.

  18. General contraction of Gaussian basis sets. II - Atomic natural orbitals and the calculation of atomic and molecular properties

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Taylor, Peter R.

    1990-01-01

    A recently proposed scheme for using natural orbitals from atomic configuration interaction wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outermost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital sets.

  19. Prediction for thermodynamic function of dioxins for gas phase using semi-empirical molecular orbital method with PM3 Hamiltonian.

    PubMed

    Saito, N; Fuwa, A

    2000-01-01

    In this investigation, respective thermodynamic parameters of heats of formation, standard entropy and specific heat capacity at constant pressure for PCDDs, PCDFs, Co-PCB and PCBs as well as polychlorinated-benzenes and polychlorinated-phenols have been evaluated by quantum chemical calculation using a semi-empirical molecular orbital method with the PM3 Hamiltonian and statistical thermodynamic correlation. PMID:10665426

  20. Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    ERIC Educational Resources Information Center

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

  1. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    NASA Astrophysics Data System (ADS)

    Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

    2015-03-01

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  2. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    SciTech Connect

    Wyrick, Jonathan; Bartels, Ludwig; Einstein, T. L.

    2015-03-14

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species’ diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  3. Arsia Mons Overlapping Flows

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site]

    This VIS image shows overlapping flows with different suface textures. In the middle of the image there is a round, darker feature -- a small volcano. To the left of the volcano a graben cuts across the lava flows.

    Image information: VIS instrument. Latitude -18.5, Longitude 244.5 East (115.5 West). 17 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  4. Molecular modeling benzo[a]pyrene N2-dG adducts in the two overlapping active sites of the Y-family DNA polymerase Dpo4.

    PubMed

    Chandani, Sushil; Loechler, Edward L

    2007-01-01

    The potent, ubiquitous environmental mutagen/carcinogen benzo[a]pyrene (B[a]P) induces a single major adduct [+ta]-B[a]P-N2-dG, whose bypass in most cases results in either no mutation (dCTP insertion) or a G-->T mutation (dATP insertion). Translesion synthesis (TLS) of [+ta]-B[a]P-N2-dG generally requires DNA polymerases (DNAPs) in the Y-family, which exist in cells to bypass DNA damage caused by chemicals and radiation. A molecular dynamics (MD) study is described with dCTP opposite [+ta]-B[a]P-N2-dG in Dpo4, which is the best studied Y-family DNAP from a structural point of view. Two orientations of B[a]P-N2-dG (BPmi5 and BPmi3) are considered, along with two orientations of the dCTP (AS1 and AS2), as outlined next. Based on NMR studies, the pyrene moiety of B[a]P-N2-dG is in the minor groove, when paired with dC, and can point toward either the base on the 5'-side (BPmi5) or the 3'-side (BPmi3). Based on published X-ray structures, Dpo4 appears to have two partially overlapping active sites. The architecture of active site 1 (AS1) is similar to all other families of DNAPs (e.g., the shape of the dNTP). Active site 2 (AS2), however, is non-canonical (e.g., the beta- and gamma-phosphates in AS2 are approximately where the alpha- and beta-phosphates are in AS1). In the Dpo4 models generated herein, using the BPmi3 orientation the pyrene moiety of [+ta]-B[a]P-N2-dG points toward the duplex region of the DNA, and is accommodated without distortions in AS1, but with distortions in AS2. Considering the BPmi5 orientation, the pyrene moiety points toward the ss-region of DNA in Dpo4, and sits in a hole defined by the fingers and little fingers domain ("chimney"); BPmi5 is accommodated in AS2 without significant distortions, but poorly in AS1. In summary, when dCTP is paired with [+ta]-B[a]P-N2-dG in the two overlapping active sites in Dpo4, the pyrene in the BPmi3 orientation is accommodated better in active site 1 (AS1), while the pyrene in the BPmi5 orientation is

  5. Efficient and Flexible Computation of Many-Electron Wave Function Overlaps

    PubMed Central

    2016-01-01

    A new algorithm for the computation of the overlap between many-electron wave functions is described. This algorithm allows for the extensive use of recurring intermediates and thus provides high computational efficiency. Because of the general formalism employed, overlaps can be computed for varying wave function types, molecular orbitals, basis sets, and molecular geometries. This paves the way for efficiently computing nonadiabatic interaction terms for dynamics simulations. In addition, other application areas can be envisaged, such as the comparison of wave functions constructed at different levels of theory. Aside from explaining the algorithm and evaluating the performance, a detailed analysis of the numerical stability of wave function overlaps is carried out, and strategies for overcoming potential severe pitfalls due to displaced atoms and truncated wave functions are presented. PMID:26854874

  6. Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method.

    PubMed

    Brorsen, Kurt R; Zahariev, Federico; Nakata, Hiroya; Fedorov, Dmitri G; Gordon, Mark S

    2014-12-01

    The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO-DFT gradient, which lacks response terms, the FMO-DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO-DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn-Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO-DFT is a nonvariational method and the FMO-DFT gradient is unique compared to standard DFT gradients in that the FMO-DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories. PMID:26583213

  7. Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Fedorov, Dmitri G.; Kitaura, Kazuo

    2004-08-01

    The fragment molecular orbital (FMO) method was combined with the second order Møller-Plesset (MP2) perturbation theory. The accuracy of the method using the 6-31G* basis set was tested on (H2O)n, n=16,32,64; α-helices and β-strands of alanine n-mers, n=10,20,40; as well as on (H2O)n, n=16,32,64 using the 6-31++G** basis set. Relative to the regular MP2 results that could be afforded, the FMO2-MP2 error in the correlation energy did not exceed 0.003 a.u., the error in the correlation energy gradient did not exceed 0.000 05 a.u./bohr and the error in the correlation contribution to dipole moment did not exceed 0.03 debye. An approximation reducing computational load based on fragment separation was introduced and tested. The FMO2-MP2 method demonstrated nearly linear scaling and drastically reduced the memory requirements of the regular MP2, making possible calculations with several thousands basis functions using small Pentium clusters. As an example, (H2O)64 with the 6-31++G** basis set (1920 basis functions) can be run in 1 Gbyte RAM and it took 136 s on a 40-node Pentium4 cluster.

  8. A rational reduction of CI expansions: combining localized molecular orbitals and selected charge excitations.

    PubMed

    Krah, Tim; Ben Amor, Nadia; Maynau, Daniel; Berger, J A; Robert, Vincent

    2014-07-01

    Based on localized molecular orbitals, the proposed method reduces large configuration interaction (CI) spaces while maintaining agreement with reference values. Our strategy concentrates the numerical effort on physically pertinent CI-contributions and is to be considered as a tool to tackle large systems including numerous open-shells. To show the efficiency of our method we consider two 4-electron parent systems. First, we illustrate our approach by describing the van der Waals interactions in the (H2)2 system. By systematically including local correlation, dispersion and charge transfer mechanisms, we show that 90% of the reference full CI dissociation energy of the H2 dimer is reproduced using only 3% of the full CI space. Second, the conformational cis/trans rotation barrier of the butadiene molecule is remarkably reproduced (97% of the reference value) with less than 1% of the reference space. This work paves the way to numerical strategies which afford the electronic structure determination of large open-shell systems avoiding the exponential limitation. At the same time, a physical analysis of the contents of the wave function is offered. PMID:24935105

  9. Structures of Si-Carbohydrate Aqueous Complexes: Comparison of NMR Spectra and Molecular Orbital Results

    NASA Astrophysics Data System (ADS)

    Kubicki, J. D.; Heaney, P. J.

    2002-12-01

    Researchers recently have made the discovery that hypercoordinate Si-sorbitol complexes will readily form in biologically relevant fluids, and they have reported the first evidence for a transient organosilicon complex generated within the life cycle of an organism. These interpretations are based upon peak assignments of Si-29 NMR spectra that invoke Si-polyol complexes with Si in five- and six-fold coordination states. However, ab initio analyses of the proposed organosilicon structures do not reproduce the experimentally observed chemical shifts. We have successfully modeled one of the observed Si-29 chemical shifts with a 5-fold Si-disorbitol complex involving 5-membered ring configurations (i.e., Si-O-C-C-O), which yielded Si-29 chemical shifts that closely matched the observed values in the -100 to -102 ppm range. Likewise, Si-29 NMR peaks near -144 ppm were well fit by a model in which a 6-fold Si was complexed to three sorbitol molecules in a 5-membered ring configuration. The ability to simulate observed NMR signals using molecular orbital calculations provides strong support for the controversial role of hypercoordinate organosilicon species in the uptake and transport of silica by biological systems. The existence of such complexes in turn may explain other puzzles in Si biogeochemistry, such as the persistence of monomeric silica in concentrated biological fluids and the biofractionation of Si isotopes and Ge.

  10. An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane

    PubMed Central

    Song, Lingchun; Mo, Yirong; Gao, Jiali

    2009-01-01

    An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H12 such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method. PMID:20047006

  11. An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane.

    PubMed

    Song, Lingchun; Mo, Yirong; Gao, Jiali

    2009-01-01

    An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H(12) such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method. PMID:20047006

  12. The Space Shuttle Orbiter molecular environment induced by the supplemental flash evaporator system

    NASA Technical Reports Server (NTRS)

    Ehlers, H. K. F.

    1985-01-01

    The water vapor environment of the Space Shuttle Orbiter induced by the supplemental flash evaporator during the on-orbit flight phase has been analyzed based on Space II model predictions and orbital flight measurements. Model data of local density, column density, and return flux are presented. Results of return flux measurements with a mass spectrometer during STS-2 and of direct flux measurements during STS-4 are discussed and compared with model predictions.

  13. Combined fragment molecular orbital cluster in molecule approach to massively parallel electron correlation calculations for large systems.

    PubMed

    Findlater, Alexander D; Zahariev, Federico; Gordon, Mark S

    2015-04-16

    The local correlation "cluster-in-molecule" (CIM) method is combined with the fragment molecular orbital (FMO) method, providing a flexible, massively parallel, and near-linear scaling approach to the calculation of electron correlation energies for large molecular systems. Although the computational scaling of the CIM algorithm is already formally linear, previous knowledge of the Hartree-Fock (HF) reference wave function and subsequent localized orbitals is required; therefore, extending the CIM method to arbitrarily large systems requires the aid of low-scaling/linear-scaling approaches to HF and orbital localization. Through fragmentation, the combined FMO-CIM method linearizes the scaling, with respect to system size, of the HF reference and orbital localization calculations, achieving near-linear scaling at both the reference and electron correlation levels. For the 20-residue alanine α helix, the preliminary implementation of the FMO-CIM method captures 99.6% of the MP2 correlation energy, requiring 21% of the MP2 wall time. The new method is also applied to solvated adamantine to illustrate the multilevel capability of the FMO-CIM method. PMID:25794346

  14. Density functional calculation of superatomic molecular orbitals in C60: First truly converged results on a real grid mesh

    NASA Astrophysics Data System (ADS)

    Drake, Kyle; Bonacum, Jason; Zhang, Guo-Ping

    2014-03-01

    The molecular structure of Buckminster fullerene (C60) allows for electron delocalization in all of the pi-bonding electrons of the molecule. This coupled with the symmetry of the molecule allows for the formation of super-atomic molecular orbitals (SAMOs) similar to those observed in aluminum clusters. The SAMOs behave as if the molecule that they belong to is a single atom. We compute the eigenstates of C60 compulationally using density functional theory (DFT) and a grid mesh. Using larger radii also allows us to accurately describe SAMOs and test the convergence of our data. The results are interesting because for the first time, we can show the true converged super atomic orbitals in C60. Indiana State University SURE Program, Department of Energy, Indiana State University Department of Physics, and Indiana State University Center for Student Creativity and Research.

  15. Mixed ab initio quantum mechanics/molecular mechanics methods using frozen orbitals with applications to peptides and proteins

    NASA Astrophysics Data System (ADS)

    Philipp, Dean Michael

    Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.

  16. Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.

    PubMed

    Heifetz, Alexander; Aldeghi, Matteo; Chudyk, Ewa I; Fedorov, Dmitri G; Bodkin, Mike J; Biggin, Philip C

    2016-04-15

    The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available. PMID:27068972

  17. Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method

    PubMed Central

    Ohno, Kazuki; Orita, Masaya; Inoue, Masayuki; Shiba, Tomoo; Harada, Shigeharu; Honma, Teruki; Balogun, Emmanuel Oluwadare; da Rocha, Josmar Rodrigues; Montanari, Carlos Alberto; Kita, Kiyoshi; Sekijima, Masakazu

    2015-01-01

    Background Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives. Methodology/Principal Findings Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. Conclusions/Significance FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs. PMID:25961853

  18. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    SciTech Connect

    Roemelt, Michael

    2015-07-28

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  19. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    NASA Astrophysics Data System (ADS)

    Roemelt, Michael

    2015-07-01

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  20. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors.

    PubMed

    Roemelt, Michael

    2015-07-28

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method. PMID:26233112

  1. Using Atomic Orbitals and Kinesthetic Learning to Authentically Derive Molecular Stretching Vibrations

    ERIC Educational Resources Information Center

    Bridgeman, Adam J.; Schmidt, Timothy W.; Young, Nigel A.

    2013-01-01

    The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many…

  2. Many-body exchange-repulsion in polarizable molecular mechanics. I. Orbital-based approximations and applications to hydrated metal cation complexes.

    PubMed

    Chaudret, Robin; Gresh, Nohad; Parisel, Olivier; Piquemal, Jean-Philip

    2011-11-15

    We have quantified the extent of the nonadditivity of the short-range exchange-repulsion energy, E(exch-rep), in several polycoordinated complexes of alkali, alkaline-earth, transition, and metal cations. This was done by performing ab initio energy decomposition analyses of interaction energies in these complexes. The magnitude of E(exch-rep(n-body, n > 2)) was found to be strongly cation-dependent, ranging from close to zero for some alkali metal complexes to about 6 kcal/mol for the hexahydrated Zn(2+) complex. In all cases, the cation-water molecules, E(exch-rep(three-body)), has been found to be the dominant contribution to many-body exchange-repulsion effects, higher order terms being negligible. As the physical basis of this effect is discussed, a three-center exponential term was introduced in the SIBFA (Sum of Interactions Between Fragments Ab initio computed) polarizable molecular mechanics procedure to model such effects. The three-body correction is added to the two-center (two-body) overlap-like formulation of the short-range repulsion contribution, E(rep), which is grounded on simplified integrals obtained from localized molecular orbital theory. The present term is computed on using mostly precomputed two-body terms and, therefore, does not increase significantly the computational cost of the method. It was shown to match closely E(three-body) in a series of test cases bearing on the complexes of Ca(2+), Zn(2+), and Hg(2+). For example, its introduction enabled to restore the correct tetrahedral versus square planar preference found from quantum chemistry calculations on the tetrahydrate of Hg(2+) and [Hg(H(2)O)(4)](2+). PMID:21793002

  3. Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

    NASA Astrophysics Data System (ADS)

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

  4. Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states

    SciTech Connect

    Pinjari, Rahul V.; Delcey, Mickaël G.; Guo, Meiyuan; Lundberg, Marcus; Odelius, Michael

    2014-09-28

    The metal L-edge (2p → 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d{sup 5}) model systems with well-known electronic structure, viz., atomic Fe{sup 3+}, high-spin [FeCl{sub 6}]{sup 3−} with ligand donor bonding, and low-spin [Fe(CN){sub 6}]{sup 3−} that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

  5. Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

    PubMed

    Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

    2016-07-12

    We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design. PMID:27248370

  6. Preparation and Characterization of [pi]-Stacking Quinodimethane Oligothiophenes. Predicting Semiconductor Behavior and Bandwidths from Crystal Structures and Molecular Orbital Calculations

    SciTech Connect

    Janzen, Daron E.; Burand, Michael W.; Ewbank, Paul C.; Pappenfus, Ted M.; Higuchi, Hiroyuki; da Silva, Demetrio A.; Young, Victor G.; Bredas, Jean-Luc; Mann, Kent R.

    2010-11-16

    A series of new quinodimethane-substituted terthiophene and quaterthiophene oligomers has been investigated for comparison with a previously studied quinoid oligothiophene that has demonstrated high mobilities and ambipolar transport behavior in thin-film transistor devices. Each new quinoidal thiophene derivative shows a reversible one-electron oxidation between 0.85 and 1.32 V, a quasi-reversible one-electron second oxidation between 1.37 and 1.96 V, and a reversible two-electron reduction between -0.05 and -0.23 V. The solution UV-vis-NIR spectrum of each compound is dominated by an intense epsilon congruent with 100,000 M{sup -1} cm{sup -1} low energy pi-pi transition that has a lambda(max) ranging between 648 and 790 nm. All X-ray crystal structures exhibit very planar quinoidal backbones and short intermolecular pi-stacking distances (3.335-3.492 A). Structures exhibit a single pi-stacking distance with parallel cofacial stacking (sulfur atoms of equivalent rings pointed in the same direction) or with alternating distances and antiparallel cofacial stacking (sulfur atoms of equivalent rings pointed in the opposite direction). Examples of the layered and herringbone-packing motifs are observed for both the parallel and the antiparallel cofacial stacking. Analysis of the X-ray structures and molecular orbital calculations indicates that all of these compounds have one-dimensional electronic band structures as a result of the pi-stacking. For structures with a unique pi-stacking distance, a simple geometric overlap parameter calculated from the shape of the molecule and the slip from perfect registry in the pi-stack correlates well with the transfer integrals (t) calculated using molecular orbital theory. The calculated valence (633 meV) and conduction (834 meV) bandwidths for a quinoid quaterthiophene structure are similar to those calculated for the benchmark pentacene and indicate that both hole and electron mobilities could be significant.

  7. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets.

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-01

    We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions. PMID:27434607

  8. Introducing PROFESS 3.0: An advanced program for orbital-free density functional theory molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Chen, Mohan; Xia, Junchao; Huang, Chen; Dieterich, Johannes M.; Hung, Linda; Shin, Ilgyou; Carter, Emily A.

    2015-05-01

    Orbital-free density functional theory (OFDFT) is a linear-scaling first-principles quantum mechanics method used to calculate the ground-state energy of a given system. Here we present a new version of PRinceton Orbital-Free Electronic Structure Software (PROFESS) with new features. First, PROFESS 3.0 provides a set of new kinetic energy density functionals (KEDFs) which are designed to model semiconductors or transition metals. Specifically, PROFESS 3.0 includes the Huang-Carter (HC) KEDF [1], a density decomposition method with fixed localized electronic density [2], the Wang-Govind-Carter (WGC) decomposition KEDF [3], and the Enhanced von Weizsäcker (EvW)-WGC KEDF [4]. Other major new functions are included, such as molecular dynamics with different statistical mechanical ensembles and spin-polarized density optimizers.

  9. Formation of giant molecular clouds in global spiral structures: The role of orbital dynamics and cloud-cloud collisions

    NASA Technical Reports Server (NTRS)

    Roberts, W. W., Jr.; Stewart, G. R.

    1987-01-01

    The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes.

  10. Molecular structure, vibrational spectroscopic, hyperpolarizability, natural bond orbital analysis, frontier molecular orbital analysis and thermodynamic properties of 2,3,4,5,6-pentafluorophenylacetic acid.

    PubMed

    Balachandran, V; Karunakaran, V

    2014-06-01

    The FT-IR (4000-400cm(-)(1)) and FT-Raman spectra (3500-100cm(-)(1)) of 2,3,4,5,6-pentafluorophenylacetic acid (PAA) have been recorded. Density functional theory calculation with LSDA/6-31+G(d,p) and B3LYP/6-31+G(d,p) basis sets have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman intensities and bonding features of the title compound. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of PAA are calculated using B3LYP/6-31+G(d,p) method on the finite-field approach. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The stability of molecule has been analyzed by using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within this molecule. Mulliken population analysis on atomic charges is also calculated. Thermodynamic properties (heat capacity, enthalpy, Gibb's free energy and entropy) of the title compound at different temperatures were calculated. PMID:24662720

  11. Theoretical and experimental studies of the molecular orbital bonding coefficients for Cu2+ ion in cesium hydrogen oxalate single crystals

    NASA Astrophysics Data System (ADS)

    Kalfaoǧlu, Emel; Karabulut, Bünyamin

    2016-03-01

    Electron paramagnetic resonance (EPR) and optical absorption spectra of Cu2+ ions in cesium hydrogen oxalate single crystals have been investigated at room temperature. The spin-Hamiltonian parameters (g and A), have been determined. Crystalline field around the Cu2+ ion is almost axially symmetric. The results show a single paramagnetic site which confirms the triclinic crystal symmetry. Molecular orbital bonding coefficients are studied from the EPR and optical data. Theoretical octahedral field parameter and the tetragonal field parameters have been evaluated from the superposition model. Using these parameters, various bonding parameters are analyzed and the nature of bonding in the complex is discussed. The theoretical results are supported by experimental results.

  12. Molecular orbital (SCF-Xα-SW) theory of metal-metal charge transfer processes in minerals

    USGS Publications Warehouse

    Sherman, David M.

    1987-01-01

    Electronic transitions between the Fe-Fe bonding and Fe-Fe antibonding orbitals results in the optically-induced intervalence charge transfer bands observed in the electronic spectra of mixed valence minerals. Such transitions are predicted to be polarized along the metal-metal bond direction, in agreement with experimental observations.

  13. Demystifying Introductory Chemistry. Part 2: Bonding and Molecular Geometry Without Orbitals--the Electron Domain Model.

    ERIC Educational Resources Information Center

    Gillespie, Ronald J.; And Others

    1996-01-01

    Presents an alternative approach to bonding and geometry--the electron domain model--which avoids some of the problems with the conventional approach. Discusses difficulties with the orbital model at the introductory level, electron spin and the Pauli exclusion principle, electron pair domains, nonequivalent domains, multiple bonds, and origins…

  14. Molecular Orbital Study of the Formation of Intramolecular Hydrogen Bonding of a Ligand Molecule in a Protein Aromatic Hydrophobic Pocket.

    PubMed

    Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi

    2016-01-01

    The natural product argadin is a cyclopentapeptide chitinase inhibitor that binds to chitinase B (ChiB) from the pathogenic bacteria Serratia marcescens. N(ω)-Acetyl-L-arginine and L-aminoadipic acid of argadin form intramolecular ionic hydrogen bonds in the aromatic hydrophobic pocket of ChiB. We performed ab initio molecular orbital and density functional theory calculations to elucidate the role of this intramolecular hydrogen bonding on intermolecular interactions between argadin and ChiB. We found that argadin accrues large stabilization energies from the van der Waals dispersion interactions, such as CH-π, π-π, and π-lone pair interactions, in the aromatic hydrophobic pocket of ChiB, although intramolecular hydrogen bonding within argadin might result in loss of entropy. The intramolecular ionic hydrogen bonding formation canceled local molecular charges and provided good van der Waals interactions with surrounding aromatic residues. PMID:27373666

  15. Orbital-free molecular dynamics simulations of a warm dense mixture: Examination of the excess-pressure matching rule

    SciTech Connect

    Danel, J-F.; Kazandjian, L.; Zerah, G.

    2009-06-15

    A form of the linear mixing rule involving the equality of excess pressures is tested with various mole fractions and various types of orbital-free molecular dynamics simulations. For all the cases considered, this mixing rule yields, within statistical error, the pressure of a mixture of helium and iron obtained by a direct simulation. In an attempt to interpret the robustness of the mixing rule, we show that it can be derived from thermodynamic stability if the system is regarded as a mixture of independent effective average atoms. The success of the mixing rule applied with equations of state including various degrees of approximation leads us to suggest its use in the thermodynamic domain where quantum molecular dynamics can be implemented.

  16. Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

    PubMed

    Nishimoto, Yoshio; Nakata, Hiroya; Fedorov, Dmitri G; Irle, Stephan

    2015-12-17

    The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well. PMID:26623658

  17. Molecular docking, TG/DTA, molecular structure, harmonic vibrational frequencies, natural bond orbital and TD-DFT analysis of diphenyl carbonate by DFT approach

    NASA Astrophysics Data System (ADS)

    Xavier, S.; Periandy, S.; Carthigayan, K.; Sebastian, S.

    2016-12-01

    Vibrational spectral analysis of Diphenyl Carbonate (DPC) is carried out by using FT-IR and FT-Raman spectroscopic techniques. It is found that all vibrational modes are in the expected region. Gaussian computational calculations were performed using B3LYP method with 6-311++G (d, p) basis set. The computed geometric parameters are in good agreement with XRD data. The observation shows that the structure of the carbonate group is unsymmetrical by ∼5° due to the attachment of the two phenyl rings. The stability of the molecule arising from hyperconjugative interaction and charge delocalization are analyzed by Natural Bond Orbital (NBO) study and the results show the lone pair transition has higher stabilization energy compared to all other. The 1H and 13C NMR chemical shifts are calculated using the Gauge-Including Atomic Orbital (GIAO) method with B3LYP/6-311++G (d, p) method. The chemical shifts computed theoretically go very closer to the experimental results. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies and Molecular electrostatic potential (MEP) exhibit the high reactivity nature of the molecule. The non-linear optical property of the DPC molecule predicted theoretically found to be good candidate for NLO material. TG/DTA analysis was made and decomposition of the molecule with respect to the temperature was studied. DPC having the anthelmintic activity is docked in the Hemoglobin of Fasciola hepatica protein. The DPC has been screened to antimicrobial activity and found to exhibit antibacterial effects.

  18. Illusion induced overlapped optics.

    PubMed

    Zang, XiaoFei; Shi, Cheng; Li, Zhou; Chen, Lin; Cai, Bin; Zhu, YiMing; Zhu, HaiBin

    2014-01-13

    The traditional transformation-based cloak seems like it can only hide objects by bending the incident electromagnetic waves around the hidden region. In this paper, we prove that invisible cloaks can be applied to realize the overlapped optics. No matter how many in-phase point sources are located in the hidden region, all of them can overlap each other (this can be considered as illusion effect), leading to the perfect optical interference effect. In addition, a singular parameter-independent cloak is also designed to obtain quasi-overlapped optics. Even more amazing of overlapped optics is that if N identical separated in-phase point sources covered with the illusion media, the total power outside the transformation region is N2I0 (not NI0) (I0 is the power of just one point source, and N is the number point sources), which seems violating the law of conservation of energy. A theoretical model based on interference effect is proposed to interpret the total power of these two kinds of overlapped optics effects. Our investigation may have wide applications in high power coherent laser beams, and multiple laser diodes, and so on. PMID:24515019

  19. Molecular quantum magnetism with strong spin-orbit coupling in inorganic solid Ba3Yb2Zn5O11

    NASA Astrophysics Data System (ADS)

    Park, Sang-Youn; Ji, Sungdae; Park, Jae-Hoon; Do, Seunghwan; Choi, Kwang-Yong; Jang, Dongjin; Schmidt, Burkhard; Brando, Manuel; Butch, Nicholas

    The molecular magnet, assembly of finite number of spins which are isolated from environment, is a model system to study the quantum information process such as the qubit or spintronic devices. In past decades, the molecular magnet has been mostly realized in organic material, however, it has difficulty synthesizing materials or controlling their properties, meanwhile tremendous endeavors to search inorganic molecular magnet are continuing. Here, we propose Ba3Yb2Zn5O11 as a candidate of inorganic molecular magnet. This material consists of an alternating 3D-array of small and large tetrahedron containing antiferromagnetically coupled four pseudospin-1/2 Yb ions, and magnetic properties are described by an isolated tetrahedron without long-range magnetic ordering. Inelastic neutron scattering measurement with external magnetic field reveals that extraordinarily huge Dzyaloshinsky-Moriya (DM) interaction originating from strong spin-orbit coupling in Yb isospin is the key to explain energy level of tetrahedron in addition to Heisenberg exchange interaction and Zeeman effect. Magnetization measurement shows the Landau-Zener transition between avoided crossing levels caused by DM interaction.

  20. Molecular Orbital Calculations on the Interaction of PF3 and CO with Ni and Cu Atoms

    NASA Astrophysics Data System (ADS)

    Itoh, H.; Ertl, G.

    1982-04-01

    The interaction of Ni and Cu atoms with PF3 and CO ligands was investigated by means of ab initio MO calculations. Coupling occurs mainly through the HOMO (8a1 for PF3 and 5 a for CO) levels with the metal 4s and 3dz2 orbitals, if the 3dn-1 4s1 electronic configuration of the metal atom is considered. The estimated M-PF3 bond lengths are 2.0 Å for Ni and 2.5 Å for Cu. Calculations with Ni(3d10) revealed for PF3 a more pronounced electron transfer to the ligand than for CO. The results are consistent with experimental UPS data for mononuclear complexes as well as corresponding adsorption systems. In particular, split-off d-states observed in UPS data for adsorbed PF3 are attributed to the pronounced lowering of the 3d-orbital energy of the metal atom upon interaction with this electropositive ligand.

  1. Overlap among Environmental Databases.

    ERIC Educational Resources Information Center

    Miller, Betty

    1981-01-01

    Describes the methodology and results of a study comparing the overlap of Enviroline, Pollution, and the Environmental Periodicals Bibliography files through searches on acid rain, asbestos and water, diesel, glass recycling, Lake Erie, Concorde, reverse osmosis wastewater treatment cost, and Calspan. Nine tables are provided. (RBF)

  2. Direct observation of collective modes coupled to molecular orbital-driven charge transfer

    NASA Astrophysics Data System (ADS)

    Ishikawa, Tadahiko; Hayes, Stuart A.; Keskin, Sercan; Corthey, Gastón; Hada, Masaki; Pichugin, Kostyantyn; Marx, Alexander; Hirscht, Julian; Shionuma, Kenta; Onda, Ken; Okimoto, Yoichi; Koshihara, Shin-ya; Yamamoto, Takashi; Cui, Hengbo; Nomura, Mitsushiro; Oshima, Yugo; Abdel-Jawad, Majed; Kato, Reizo; Miller, R. J. Dwayne

    2015-12-01

    Correlated electron systems can undergo ultrafast photoinduced phase transitions involving concerted transformations of electronic and lattice structure. Understanding these phenomena requires identifying the key structural modes that couple to the electronic states. We report the ultrafast photoresponse of the molecular crystal Me4P[Pt(dmit)2]2, which exhibits a photoinduced charge transfer similar to transitions between thermally accessible states, and demonstrate how femtosecond electron diffraction can be applied to directly observe the associated molecular motions. Even for such a complex system, the key large-amplitude modes can be identified by eye and involve a dimer expansion and a librational mode. The dynamics are consistent with the time-resolved optical study, revealing how the electronic, molecular, and lattice structures together facilitate ultrafast switching of the state.

  3. Bonding, Backbonding, and Spin-Polarized Molecular Orbitals:Basis for Magnetism and Semiconducting Transport in V[TCNE]x~;;2

    SciTech Connect

    Kortright, Jeffrey B; Kortright, Jeffrey B; Lincoln, Derek M; Edelstein, Ruth Shima; Epstein, Arthur J

    2008-05-20

    X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (MCD) at the V L2,3 and C and N K edges reveal bonding/backbonding interactions in films of the 400 K magnetic semiconductor V[TCNE]x~;;2. In V spectra, dxy-like orbitals are modeled assuming V2+ in an octahedral ligand field, while dz2 and dx2-y2 orbitals involved in strong covalent bonding cannot be modeled by atomic calculations. C and N MCD, and differences in XAS from neutral TCNE molecules, reveal spin-polarized molecular orbitals in V[TCNE]x~;;2 associated with backbonding interactions that yield its novel properties.

  4. Specific interactions between lactose repressor protein and DNA affected by ligand binding: ab initio molecular orbital calculations.

    PubMed

    Ohyama, Tatsuya; Hayakawa, Masato; Nishikawa, Shin; Kurita, Noriyuki

    2011-06-01

    Transcription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti-inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti-inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. PMID:21328406

  5. How amino and nitro substituents direct electrophilic aromatic substitution in benzene: an explanation with Kohn-Sham molecular orbital theory and Voronoi deformation density analysis.

    PubMed

    Stasyuk, O A; Szatylowicz, H; Krygowski, T M; Fonseca Guerra, C

    2016-04-28

    The substituent effect of the amino and nitro groups on the electronic system of benzene has been investigated quantum chemically using quantitative Kohn-Sham molecular orbital theory and a corresponding energy decomposition analysis (EDA). The directionality of electrophilic substitution in aniline can accurately be explained with the amount of contribution of the 2pz orbitals on the unsubstituted carbon atoms to the highest occupied π orbital. For nitrobenzene, the molecular π orbitals cannot explain the regioselectivity of electrophilic substitution as there are two almost degenerate π orbitals with nearly the same 2pz contributions on the unsubstituted carbon atoms. The Voronoi deformation density analysis has been applied to aniline and nitrobenzene to obtain an insight into the charge rearrangements due to the substituent. This analysis method identified the orbitals involved in the C-N bond formation of the π system as the cause for the π charge accumulation at the ortho and para positions in the case of the NH2 group and the largest charge depletion at these same positions for the NO2 substituent. Furthermore, we showed that it is the repulsive interaction between the πHOMO of the phenyl radical and the πHOMO of the NH2 radical that is responsible for pushing up the πHOMO of aniline and therefore activating this π orbital of the phenyl ring towards electrophilic substitution. PMID:26800159

  6. DFT calculations of molecular excited states using an orbital-dependent nonadiabatic exchange kernel

    SciTech Connect

    Ipatov, A. N.

    2010-02-15

    A density functional method for computing molecular excitation spectra is presented that uses a frequency-dependent kernel and takes into account the nonlocality of exchange interaction. Owing to its high numerical stability and the use of a nonadiabatic (frequency-dependent) exchange kernel, the proposed approach provides a qualitatively correct description of the asymptotic behavior of charge-transfer excitation energies.

  7. Length-dependence of intramolecular electron transfer in σ-bonded rigid molecular rods: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Karna, Shashi P.

    2002-01-01

    The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

  8. Controlling the Interference of Multiple Molecular Orbitals in High-Harmonic Generation

    SciTech Connect

    Woerner, H. J.; Bertrand, J. B.; Hockett, P.; Corkum, P. B.; Villeneuve, D. M.

    2010-06-11

    We demonstrate a new method to investigate the origin of spectral structures in high-harmonic generation. We report detailed measurements of high-harmonic spectra in aligned nitrogen and carbon dioxide molecules. Varying the wavelength and intensity of the generating laser field, we show that the minimum in aligned N{sub 2} molecules is nearly unaffected, whereas the minimum in aligned CO{sub 2} molecules shifts over more than 15 eV. Our quantitative analysis shows that both the interference of multiple orbitals and their structural characteristics affect the position of the minimum. Our method provides a simple approach to the investigation of the high-harmonic generation process in more complex molecules.

  9. Rings of C2H in the Molecular Disks Orbiting TW Hya and V4046 Sgr

    NASA Astrophysics Data System (ADS)

    Kastner, J. H.; Qi, C.; Gorti, U.; Hily-Blant, P.; Oberg, K.; Forveille, T.; Andrews, S.; Wilner, D.

    2016-01-01

    We have used the Submillimeter Array (SMA) to image, at ~1'' resolution, C2H(3-2) emission from the molecule-rich circumstellar disks orbiting the nearby, classical T Tauri star systems TW Hya and V4046 Sgr. The SMA imaging reveals that the C2H emission exhibits a ring-like morphology within each disk; the radius of the inner hole of the C2H ring within the V4046 Sgr disk (~70 AU) is somewhat larger than than of its counterpart within the TW Hya disk (~45 AU). We suggest that, in each case, the C2H emission likely traces irradiation of the tenuous surface layers of the outer disks by high-energy photons from the central stars.

  10. Energetics of the Preyssler anion's molecular orbitals: quantifying the effect of the encapsulated-cation's charge.

    PubMed

    Chiang, Ming-Hsi; Antonio, Mark R; Soderholm, L

    2004-11-01

    The ground state electronic properties of metal-exchanged Preyssler heteropolyoxoanions [M(n+)P(5)W(30)O(110)](n-15), in which the encapsulated M(n+) ions are the spherical, diamagnetic ions Na(+), Ca(2+), Sr(2+), Y(3+), La(3+) and Th(4+), are studied using a combination of electrochemical, optical, and NMR experiments. We have designed experiments that focus on the influence of the charge (n) of the encapsulated cations, which themselves have no redox response, and its effect upon the W-O framework MOs. As n increases, the cluster anions accept electrons into their LUMOs with increasing ease, and their lowest-energy LMCT bands reveal a corresponding blue shift, which is indicative of an increase of the LUMO-HOMO energy splitting with increasing n. (183)W NMR spectra are used to identify the atomic origin of the LUMO states, which are shown to be composed primarily of orbitals from the ring of 5 W atoms near M(n+). The cation charge correlates directly and linearly with the half-wave potentials of the first redox couples, the LMCT band energies, and the W chemical shifts. We have combined this suite of experimental results to construct an energy level diagram of the frontier MOs for the Preyssler cluster anions. In so doing, we provide a fundamental perspective that is not otherwise available on the cation's role with specific regard to the electronic behavior of the W-O orbitals. These results are expected to provide benchmarking information as theorists begin to study these large POM systems. PMID:15510277

  11. The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model.

    PubMed

    Nishimoto, Yoshio; Fedorov, Dmitri G

    2016-08-10

    The energy and its analytic gradient are formulated for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) and the polarizable continuum model (PCM). The accuracy is demonstrated in comparison with unfragmented calculations and numerical gradients. The instability in the description of proteins using density functional theory (DFT) and DFTB is analyzed for both unfragmented and FMO methods. The cause of the instability is shown to be charged residues, and the problem is particularly severe in the gas phase when long-range functionals are not used. Adding solvent effects considerably increases the gap between occupied and virtual orbitals and stabilizes convergence. The pair interaction energies calculated using FMO-DFT and FMO-DFTB in solution are shown to correlate, whereas the latter method is 4840 times faster than the former for a protein consisting of 1961 atoms. The structures of five proteins (containing up to 3578 atoms) optimized using FMO-DFTB/PCM agree reasonably well with experiment. PMID:27215663

  12. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    NASA Astrophysics Data System (ADS)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  13. Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Tagami, Ayumu; Ishibashi, Nobuhiro; Kato, Dai-ichiro; Taguchi, Naoki; Mochizuki, Yuji; Watanabe, Hirofumi; Ito, Mika; Tanaka, Shigenori

    2009-04-01

    Bioluminescence spectra of firefly Luciola cruciata were theoretically analyzed on the basis of the fragment molecular orbital (FMO) method. The CIS(D) and PR-CIS(Ds) methods were employed for the calculations of emission energies of wild-type and mutant luciferase-oxyluciferin systems, and various multi-layer FMO calculations were performed changing the sizes of the luciferase protein and of the chromophore to which the excited-state calculations were applied. We have thus reproduced the experimental emission energies of wild-type and mutant luciferase systems with good accuracy, which provides useful information concerning the roles of protein environment for the color tuning of the bioluminescence spectra of firefly.

  14. Discriminative modulation of the highest occupied molecular orbital energies of graphene and carbon nanotubes induced by charging.

    PubMed

    Yang, Hongping; Yam, Chi-Yung; Zhang, Aihua; Xu, Zhiping; Luo, Jun; Zhu, Jing

    2015-03-21

    The highest occupied molecular orbital (HOMO) energies of carbon nanotubes (CNTs) and graphene are crucial in fundamental and applied research of carbon nanomaterials, and so their modulation is desired. Our first-principles calculations reveal that the HOMO energies of CNTs and graphene can both be raised by negatively charging, and that the rate of increase of the HOMO energy of a CNT is much greater and faster than that of graphene with the same number of C atoms. This discriminative modulation holds true regardless of the number of C atoms and the CNT type, and so is universal. This work provides a new opportunity to develop all-carbon devices with CNTs and graphene as different functional elements. PMID:25692228

  15. Ab initio molecular orbital studies of low-energy, metastable isomers of the ubiquitous cyclopropenylidene. [in interstellar space

    NASA Technical Reports Server (NTRS)

    Defrees, D. J.; Mclean, A. D.

    1986-01-01

    The discovery of cyclopropenylidene in space suggests that other C3H2 isomers may be present, and a tentative detection of one such isomer, propargylene (HCCCH), has been reported. Ab initio molecular orbital theory has been used to characterize five low-lying, metastable isomers of cyclopropenylidene. Extended calculations including the electron correlation energy, show that the lowest in energy is singlet propadienylidene, followed by propargylene; the singlet and triplet of the latter are too close in energy to allow an assignment of the ground state; triplet propadienylidene is at a significantly higher energy. Rotational frequencies computed to an expected accuracy of + or - 1 -2 percent do not confirm the tentative detection of propargylene in space, although the discrepancy between theory and the observation is not so great as to unequivocally rule out this possibility.

  16. Large Orbital Magnetic Moment Measured in the [TpFe(III)(CN)3](-) Precursor of Photomagnetic Molecular Prussian Blue Analogues.

    PubMed

    Jafri, Sadaf Fatima; Koumousi, Evangelia S; Sainctavit, Philippe; Juhin, Amélie; Schuler, Vivien; Bun U, Oana; Mitcov, Dmitri; Dechambenoit, Pierre; Mathonière, Corine; Clérac, Rodolphe; Otero, Edwige; Ohresser, Philippe; Cartier Dit Moulin, Christophe; Arrio, Marie-Anne

    2016-07-18

    Photomagnetism in three-dimensional Co/Fe Prussian blue analogues is a complex phenomenon, whose detailed mechanism is not yet fully understood. Recently, researchers have been able to prepare molecular fragments of these networks using a building block synthetic approach from mononuclear precursors. The main objective in this strategy is to isolate the smallest units that show an intramolecular electron transfer to have a better understanding of the electronic processes. A prior requirement to the development of this kind of system is to understand to what extent electronic and magnetic properties are inherited from the corresponding precursors. In this work, we investigate the electronic and magnetic properties of the FeTp precursor (N(C4H9)4)[TpFe(III)(CN)3], (Tp being tris-pyrazolyl borate) of a recently reported binuclear cyanido-bridged Fe/Co complex. X-ray absorption spectroscopy and X-ray magnetic circular dichroism measurements at the Fe L2,3 edges (2p → 3d) supported by ligand field multiplet calculations have allowed to determine the spin and orbit magnetic moments. Inaccuracy of the spin sum rule in the case of low-spin Fe(III) ion was demonstrated. An exceptionally large value of the orbital magnetic moment is found (0.9 μB at T = 2 K and B = 6.5 T) that is likely to play an important role in the magnetic and photomagnetic properties of molecular Fe/Co Prussian blue analogues. PMID:27385292

  17. An energy decomposition analysis for second-order Møller–Plesset perturbation theory based on absolutely localized molecular orbitals

    SciTech Connect

    Thirman, Jonathan Head-Gordon, Martin

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller–Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  18. Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method

    SciTech Connect

    Yoshida, Norio

    2014-06-07

    The three-dimensional reference interaction site model (3D-RISM) method was efficiently implemented in the fragment molecular orbital (FMO) method. The method is referred to as the FMO/3D-RISM method, and allows us to treat electronic structure of the whole of a macromolecule, such as a protein, as well as the solvent distribution around a solute macromolecule. The formalism of the FMO/3D-RISM method, for the computationally available form and variational expressions, are proposed in detail. A major concern leading to the implementation of the method was decreasing the computational costs involved in calculating the electrostatic potential, because the electrostatic potential is calculated on numerous grid points in three-dimensional real space in the 3D-RISM method. In this article, we propose a procedure for decreasing the computational costs involved in calculating the electrostatic potential in the FMO method framework. The strategy involved in this procedure is to evaluate the electrostatic potential and the solvated Fock matrix in different manners, depending on the distance between the solute and the solvent. The electrostatic potential is evaluated directly in the vicinity of the solute molecule by integrating the molecular orbitals of monomer fragments of the solute molecule, whereas the electrostatic potential is described as the sum of multipole interactions when an analog of the fast multipole method is used. The efficiency of our method was demonstrated by applying it to a water trimer system and three biomolecular systems. The FMO/3D-RISM calculation can be performed within a reasonable computational time, retaining the accuracy of some physical properties.

  19. Localized and Spectroscopic Orbitals: Squirrel Ears on Water.

    ERIC Educational Resources Information Center

    Martin, R. Bruce

    1988-01-01

    Reexamines the electronic structure of water considering divergent views. Discusses several aspects of molecular orbital theory using spectroscopic molecular orbitals and localized molecular orbitals. Gives examples for determining lowest energy spectroscopic orbitals. (ML)

  20. COL11A2 mutation associated with autosomal recessive Weissenbacher-Zweymuller syndrome: molecular and clinical overlap with otospondylomegaepiphyseal dysplasia (OSMED).

    PubMed

    Harel, Tamar; Rabinowitz, Ronen; Hendler, Netta; Galil, Aharon; Flusser, Hagit; Chemke, Juan; Gradstein, Libe; Lifshitz, Tova; Ofir, Rivka; Elbedour, Khalil; Birk, Ohad S

    2005-01-01

    Autosomal recessive Weissenbacher-Zweymuller syndrome (WZS) is a skeletal dysplasia characterized by rhizomelic dwarfism and severe hearing loss. Mutations in the COL11A2 gene have been implicated in causing the autosomal dominant form of this syndrome as well as non-ocular Stickler syndrome and the autosomal recessive syndrome otospondylomegaepiphyseal dysplasia (OSMED). In a consanguineous Bedouin tribe living in Southern Israel, five individuals affected by autosomal recessive WZS were available for genetic analysis. Homozygosity of a mutation in the COL11A2 gene was found in all affected individuals. This finding lends molecular support to the clinical notion that autosomal recessive WZS and OSMED are a single entity. PMID:15558753

  1. HUNTing the Overlap

    SciTech Connect

    Iancu, Costin; Parry, Husbands; Hargrove, Paul

    2005-07-08

    Hiding communication latency is an important optimization for parallel programs. Programmers or compilers achieve this by using non-blocking communication primitives and overlapping communication with computation or other communication operations. Using non-blocking communication raises two issues: performance and programmability. In terms of performance, optimizers need to find a good communication schedule and are sometimes constrained by lack of full application knowledge. In terms of programmability, efficiently managing non-blocking communication can prove cumbersome for complex applications. In this paper we present the design principles of HUNT, a runtime system designed to search and exploit some of the available overlap present at execution time in UPC programs. Using virtual memory support, our runtime implements demand-driven synchronization for data involved in communication operations. It also employs message decomposition and scheduling heuristics to transparently improve the non-blocking behavior of applications. We provide a user level implementation of HUNT on a variety of modern high performance computing systems. Results indicate that our approach is successful in finding some of the overlap available at execution time. While system and application characteristics influence performance, perhaps the determining factor is the time taken by the CPU to execute a signal handler. Demand driven synchronization at execution time eliminates the need for the explicit management of non-blocking communication. Besides increasing programmer productivity, this feature also simplifies compiler analysis for communication optimizations.

  2. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states.

    PubMed

    Jacovella, U; Agner, J A; Schmutz, H; Deiglmayr, J; Merkt, F

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C2H2 (+) in selected rotational levels of the (2)Πu,3/2 and (2)Πu,1/2 spin-orbit components of the vibronic ground state. PMID:27394102

  3. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states

    NASA Astrophysics Data System (ADS)

    Jacovella, U.; Agner, J. A.; Schmutz, H.; Deiglmayr, J.; Merkt, F.

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C 2 H2 + in selected rotational levels of the 2Πu,3/2 and 2Πu,1/2 spin-orbit components of the vibronic ground state.

  4. Stereochemical diversity of {MNO}(10) complexes: molecular orbital analyses of nickel and copper nitrosyls.

    PubMed

    Conradie, Jeanet; Ghosh, Abhik

    2014-05-19

    The great majority of {NiNO}(10) complexes are characterized by short Ni-N(O) distances of 1.60-1.65 Å and linear NO units. Against this backdrop, the {CuNO}(10) unit in the recently reported [Cu(CH3NO2)5(NO)](2+) cation (1) has a CuNO angle of about 120° and a very long 1.96 Å Cu-N(O) bond. According to DFT calculations, metal-NO bonding in 1 consists of a single Cu(dz(2))-NO(π*) σ-interaction and essentially no metal(dπ)-NO(π*) π-bonding, which explains both the bent CuNO geometry and the long, weak Cu-N(O) bond. This σ-interaction is strongly favored by a ligand trans to the NO; indeed such a trans ligand may be critical for the existence and stability of a {CuNO}(10) unit. By contrast, {NiNO}(10) complexes exhibit a strong avoidance of such trans ligands. Thus, a five-coordinate {NiNO}(10) complex appears to favor a trigonal-bipyramidal structure with the NO in an equatorial position, as in the case of [Ni(bipy)2(NO)](+) (6). An unusual set of Ni(d)-NO(π*) orbital interactions accounts for the strongly bent NiNO geometry for this complex. PMID:24796643

  5. Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

    SciTech Connect

    Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F. Ingrosso, Francesca

    2014-07-21

    In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the

  6. Intraparticle Molecular Orbital Engineering of Semiconducting Polymer Nanoparticles as Amplified Theranostics for in Vivo Photoacoustic Imaging and Photothermal Therapy.

    PubMed

    Lyu, Yan; Fang, Yuan; Miao, Qingqing; Zhen, Xu; Ding, Dan; Pu, Kanyi

    2016-04-26

    Optical theranostic nanoagents that seamlessly and synergistically integrate light-generated signals with photothermal or photodynamic therapy can provide opportunities for cost-effective precision medicine, while the potential for clinical translation requires them to have good biocompatibility and high imaging/therapy performance. We herein report an intraparticle molecular orbital engineering approach to simultaneously enhance photoacoustic brightness and photothermal therapy efficacy of semiconducting polymer nanoparticles (SPNs) for in vivo imaging and treatment of cancer. The theranostic SPNs have a binary optical component nanostructure, wherein a near-infrared absorbing semiconducting polymer and an ultrasmall carbon dot (fullerene) interact with each other to induce photoinduced electron transfer upon light irradiation. Such an intraparticle optoelectronic interaction augments heat generation and consequently enhances the photoacoustic signal and maximum photothermal temperature of SPNs by 2.6- and 1.3-fold, respectively. With the use of the amplified SPN as the theranostic nanoagent, it permits enhanced photoacoustic imaging and photothermal ablation of tumor in living mice. Our study thus not only introduces a category of purely organic optical theranostics but also highlights a molecular guideline to amplify the effectiveness of light-intensive imaging and therapeutic nanosystems. PMID:26959505

  7. Energy of the Lowest Unoccupied Molecular Orbital, Thiol Reactivity, and Toxicity of Three Monobrominated Water Disinfection Byproducts

    PubMed Central

    Pals, Justin A.; Wagner, Elizabeth D.; Plewa, Michael J.

    2016-01-01

    Disinfection of drinking water protects public health against waterborne pathogens. However, during disinfection, toxic disinfection byproducts (DBPs) are formed. Exposure to DBPs was associated with increased risk of bladder cancer in humans. DBPs are generated at concentrations below their carcinogenic potencies; it is unclear how exposure leads to adverse health outcomes. We used computational estimates of the energy of the lowest unoccupied molecular orbital (ELUMO) to predict thiol reactivity and additive toxicity among soft electrophile DBPs. Bromoacetic acid (BAA) was identified as non-thiol-reactive, which was supported by in chemico and in vitro data. Bromoacetonitrile (BAN) and bromoacetamide (BAM) were thiol-reactive. Genotoxicity induced by these compounds was reduced by increasing the thiol pool with N-acetyl l-cysteine (NAC), while NAC had little effect on BAA. BAN and BAM shared depletion of glutathione (GSH) or cellular thiols as a molecular initiating event (MIE), whereas BAA induces toxicity through another pathway. Binary mixtures of BAM and BAN expressed a potentiating effect in genotoxicity. We found that soft electrophile DBPs could be an important predictor of common mechanism groups that demonstrated additive toxicity. In silico estimates of ELUMO could be used to identify the most relevant DBPs that are the forcing factors of the toxicity of finished drinking waters. PMID:26854864

  8. The continuous and discrete molecular orbital x-ray bands from Xeq+ (12≤q≤29) +Zn collisions

    PubMed Central

    Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie

    2016-01-01

    In this paper, the x-ray emissions are measured by the interaction of 1500–3500 keV Xeq+ (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xeq+ ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9–1.32 keV over the energy range studied and are proportional to v1/2 (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field. PMID:27469425

  9. The continuous and discrete molecular orbital x-ray bands from Xeq+ (12≤q≤29) +Zn collisions

    NASA Astrophysics Data System (ADS)

    Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie

    2016-07-01

    In this paper, the x-ray emissions are measured by the interaction of 1500–3500 keV Xeq+ (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xeq+ ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9–1.32 keV over the energy range studied and are proportional to v1/2 (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field.

  10. Energy of the Lowest Unoccupied Molecular Orbital, Thiol Reactivity, and Toxicity of Three Monobrominated Water Disinfection Byproducts.

    PubMed

    Pals, Justin A; Wagner, Elizabeth D; Plewa, Michael J

    2016-03-15

    Disinfection of drinking water protects public health against waterborne pathogens. However, during disinfection, toxic disinfection byproducts (DBPs) are formed. Exposure to DBPs was associated with increased risk of bladder cancer in humans. DBPs are generated at concentrations below their carcinogenic potencies; it is unclear how exposure leads to adverse health outcomes. We used computational estimates of the energy of the lowest unoccupied molecular orbital (ELUMO) to predict thiol reactivity and additive toxicity among soft electrophile DBPs. Bromoacetic acid (BAA) was identified as non-thiol-reactive, which was supported by in chemico and in vitro data. Bromoacetonitrile (BAN) and bromoacetamide (BAM) were thiol-reactive. Genotoxicity induced by these compounds was reduced by increasing the thiol pool with N-acetyl l-cysteine (NAC), while NAC had little effect on BAA. BAN and BAM shared depletion of glutathione (GSH) or cellular thiols as a molecular initiating event (MIE), whereas BAA induces toxicity through another pathway. Binary mixtures of BAM and BAN expressed a potentiating effect in genotoxicity. We found that soft electrophile DBPs could be an important predictor of common mechanism groups that demonstrated additive toxicity. In silico estimates of ELUMO could be used to identify the most relevant DBPs that are the forcing factors of the toxicity of finished drinking waters. PMID:26854864

  11. Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.

    PubMed

    Chang, Le; Ishikawa, Takeshi; Kuwata, Kazuo; Takada, Shoji

    2013-05-30

    Accurate computational estimate of the protein-ligand binding affinity is of central importance in rational drug design. To improve accuracy of the molecular mechanics (MM) force field (FF) for protein-ligand simulations, we use a protein-specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO-RESP method to two proteins, dodecin, and lysozyme, we found that protein-specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO-RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities. PMID:23420697

  12. Fragment Molecular Orbital Method Applied to Lead Optimization of Novel Interleukin-2 Inducible T-Cell Kinase (ITK) Inhibitors.

    PubMed

    Heifetz, Alexander; Trani, Giancarlo; Aldeghi, Matteo; MacKinnon, Colin H; McEwan, Paul A; Brookfield, Frederick A; Chudyk, Ewa I; Bodkin, Mike; Pei, Zhonghua; Burch, Jason D; Ortwine, Daniel F

    2016-05-12

    Inhibition of inducible T-cell kinase (ITK), a nonreceptor tyrosine kinase, may represent a novel treatment for allergic asthma. In our previous reports, we described the discovery of sulfonylpyridine (SAP), benzothiazole (BZT), indazole (IND), and tetrahydroindazole (THI) series as novel ITK inhibitors and how computational tools such as dihedral scans and docking were used to support this process. X-ray crystallography and modeling were applied to provide essential insight into ITK-ligand interactions. However, "visual inspection" traditionally used for the rationalization of protein-ligand affinity cannot always explain the full complexity of the molecular interactions. The fragment molecular orbital (FMO) quantum-mechanical (QM) method provides a complete list of the interactions formed between the ligand and protein that are often omitted from traditional structure-based descriptions. FMO methodology was successfully used as part of a rational structure-based drug design effort to improve the ITK potency of high-throughput screening hits, ultimately delivering ligands with potency in the subnanomolar range. PMID:26950250

  13. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    SciTech Connect

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

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  14. Studies of the molecular geometry, vibrational spectra, Frontier molecular orbital, nonlinear optical and thermodynamics properties of Aceclofenac by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  15. A Ring of C2H in the Molecular Disk Orbiting TW Hya

    NASA Astrophysics Data System (ADS)

    Kastner, Joel H.; Qi, Chunhua; Gorti, Uma; Hily-Blant, Pierre; Oberg, Karin; Forveille, Thierry; Andrews, Sean; Wilner, David

    2015-06-01

    We have used the Submillimeter Array to image, at ˜1.″5 resolution, C2H N=3\\to 2 emission from the circumstellar disk orbiting the nearby (D = 54 pc), ˜8 Myr-old, ˜0.8 {{M}⊙ } classical T Tauri star TW Hya. The SMA imaging reveals that the C2H emission exhibits a ring-like morphology. Based on a model in which the C2H column density follows a truncated radial power-law distribution, we find that the inner edge of the ring lies at ˜45 AU, and that the ring extends to at least ˜120 AU. Comparison with previous (single-dish) observations of C2H N=4\\to 3 emission indicates that the C2H molecules are subthermally excited and, hence, that the emission arises from the relatively warm (T≳ 40 K), tenuous (n\\ll {{10}7} cm-3) upper atmosphere of the disk. Based on these results and comparisons of the SMA C2H map with previous submillimeter and scattered-light imaging, we propose that the C2H emission most likely traces particularly efficient photo-destruction of small grains and/or photodesorption and photodissociation of hydrocarbons derived from grain ice mantles in the surface layers of the outer disk. The presence of a C2H ring in the TW Hya disk hence likely serves as a marker of dust grain processing and radial and vertical grain size segregation within the disk.

  16. Molecular orbital analysis of the inverse halogen dependence of nuclear magnetic shielding in LaX₃, X = F, Cl, Br, I.

    PubMed

    Moncho, Salvador; Autschbach, Jochen

    2010-12-01

    The NMR nuclear shielding tensors for the series LaX(3), with X = F, Cl, Br and I, have been computed using two-component relativistic density functional theory based on the zeroth-order regular approximation (ZORA). A detailed analysis of the inverse halogen dependence (IHD) of the La shielding was performed via decomposition of the shielding tensor elements into contributions from localized and delocalized molecular orbitals. Both spin-orbit and paramagnetic shielding terms are important, with the paramagnetic terms being dominant. Major contributions to the IHD can be attributed to the La-X bonding orbitals, as well as to trends associated with the La core and halogen lone pair orbitals, the latter being related to X-La π donation. An 'orbital rotation' model for the in-plane π acceptor f orbital of La helps to rationalize the significant magnitude of deshielding associated with the in-plane π donation. The IHD goes along with a large increase in the shielding tensor anisotropy as X becomes heavier, which can be associated with trends for the covalency of the La-X bonds, with a particularly effective transfer of spin-orbit coupling induced spin density from iodine to La in LaI(3). PMID:20586110

  17. Exploring the Nature of the H[subscript 2] Bond. 1. Using Spreadsheet Calculations to Examine the Valence Bond and Molecular Orbital Methods

    ERIC Educational Resources Information Center

    Halpern, Arthur M.; Glendening, Eric D.

    2013-01-01

    A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital-configuration interaction (MO-CI) treatments of H[subscript 2]. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several…

  18. Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole.

    PubMed

    Muthu, S; Uma Maheswari, J; Srinivasan, S; Isac paulraj, E

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N(6)-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials. PMID:23831980

  19. Electric field gradients in Hg compounds: molecular orbital (MO) analysis and comparison of 4-component and 2-component (ZORA) methods.

    PubMed

    Arcisauskaite, Vaida; Knecht, Stefan; Sauer, Stephan P A; Hemmingsen, Lars

    2012-12-14

    We examine the performance of Density Functional Theory (DFT) approaches based on the Zeroth-Order Regular Approximation (ZORA) Hamiltonian (with and without inclusion of spin-orbit coupling) for predictions of electric field gradients (EFGs) at the heavy atom Hg nucleus. This is achieved by comparing with benchmark DFT and CCSD-T data (Arcisauskaite et al., Phys. Chem. Chem. Phys., 2012, 14, 2651-2657) obtained from 4-component Dirac-Coulomb Hamiltonian calculations. The investigated set of molecules comprises linear HgL(2) (L = Cl, Br, I, CH(3)) and bent HgCl(2) mercury compounds as well as the trigonal planar [HgCl(3)](-) system. In 4-component calculations we used the dyall.cv3z basis set for Hg, Br, I and the cc-pCVTZ basis set for H, C, Cl, whereas in ZORA calculations we used the QZ4P basis set for all the atoms. ZORA-4 reproduces the fully relativistic 4-component DFT reference values within 6% for all studied Hg compounds and employed functionals (BH&H, BP86, PBE0), whereas scalar relativistic (SR)-ZORA-4 results show deviations of up to 15%. Compared to our 4-component CCSD-T benchmark the BH&H functional performs best at both 4-component and ZORA levels. We furthermore observe that changes in the largest component of the diagonalised EFG tensor, V(zz), of linear HgCl(2) show a slightly stronger dependence than the r(-3) scaling upon bond length r(Hg-Cl) alterations. The 4-component/BH&H V(zz) value of -9.26 a.u. for a bent HgCl(2) (∠Cl-Hg-Cl = 120°) is close to -9.60 a.u. obtained for the linear HgCl(2) structure. Thus a point charge model for EFG calculations completely fails in this case. By means of a projection analysis of molecular orbital (MO) contributions to V(zz) in terms of the atomic constituents, we conclude that this is due to the increased importance of the Hg 5d orbitals upon bending HgCl(2) compared to the linear HgCl(2) structure. Changing ligand leads to only minor changes in V(zz) (from -9.60 a.u. (HgCl(2)) to -8.85 a.u. (HgI(2)) at

  20. The Fourier transform method and the SD-bar approach for the analytical and numerical treatment of multicenter overlap-like quantum similarity integrals

    SciTech Connect

    Safouhi, Hassan . E-mail: hassan.safouhi@ualberta.ca; Berlu, Lilian

    2006-07-20

    Molecular overlap-like quantum similarity measurements imply the evaluation of overlap integrals of two molecular electronic densities related by Dirac delta function. When the electronic densities are expanded over atomic orbitals using the usual LCAO-MO approach (linear combination of atomic orbitals), overlap-like quantum similarity integrals could be expressed in terms of four-center overlap integrals. It is shown that by introducing the Fourier transform of delta Dirac function in the integrals and using the Fourier transform approach combined with the so-called B functions, one can obtain analytic expressions of the integrals under consideration. These analytic expressions involve highly oscillatory semi-infinite spherical Bessel functions, which are the principal source of severe numerical and computational difficulties. In this work, we present a highly efficient algorithm for a fast and accurate numerical evaluation of these multicenter overlap-like quantum similarity integrals over Slater type functions. This algorithm is based on the SD-bar approach due to Safouhi. Recurrence formulae are used for a better control of the degree of accuracy and for a better stability of the algorithm. The numerical result section shows the efficiency of our algorithm, compared with the alternatives using the one-center two-range expansion method, which led to very complicated analytic expressions, the epsilon algorithm and the nonlinear D-bar transformation.

  1. Molecular orbital theory on cellulolytic reactivity between pNP-cellooligosccharides and beta-glucosidase from Cellulomonas uda CS1-1.

    PubMed

    Yoon, Min-Ho; Nam, Yun-Kyu; Choi, Woo-Young; Sung, Nack-Do

    2007-11-01

    A beta-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters (Km and Vmax) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified beta-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion (H3O+), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion (SH+) protonated to the S molecule and the HOMO energy of the H2O2 molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via SN1 and SN2 reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that Km has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively. PMID:18092462

  2. A proposal for the proper use of pseudopotentials in molecular orbital cluster model studies of chemisorption

    NASA Technical Reports Server (NTRS)

    Bagus, P. S.; Bauschlicher, C. W., Jr.; Nelin, C. J.; Laskowski, B. C.; Seel, M.

    1984-01-01

    The interaction of CO with Cu5, Ni5, and Al4 are treated as model systems for molecular adsorption on metal surfaces. The effect of the use of pseudopotentials for the metal atoms is studied by considering three types of clusters. In the first case, all of the metal electrons are explicitly included in the wave function; an all electron (AE) treatment. In the second case, the metal atom which directly interacts with the CO is described by AE but the remaining metal atoms include a pseudopotential for their core electrons. Finally, in the third case, all of the metal atoms in the cluster have a pseudopotential treatment for the core electrons. The AE cluster results are taken as reference values for the two pseudopotential treatments. The mixed cluster results are in excellent agreement with those of the all AE clusters; however, the results for the all pseudopotential cluster of Ni5CO or of Cu5CO are qualitatively different. The pseudopotential treatment for all of the metal atoms often leads to results that contain serious errors and it is not a reliable approach.

  3. Conformational effects, molecular orbitals, and reaction activities of bis(phthalocyaninato) lanthanum double-deckers: density functional theory calculations.

    PubMed

    Qi, Dongdong; Zhang, Lijuan; Wan, Liang; Zhang, Yuexing; Bian, Yongzhong; Jiang, Jianzhuang

    2011-08-01

    The conformational effects on the frontier molecular orbital energy and stability for reduced, neutral, and oxidized bis(phthalocyaninato) lanthanum double-deckers have been revealed on the basis of density functional theory calculations. Calculation results indicate that the frontier orbital coupling degree changes along with the molecular conformation of the double-decker compound, first decreasing along with the increase of rotation angle β from 0 to 20° and then increasing along with the increase of rotation angle β from 20 to 45°. In addition, the stability for the three forms of double-decker changes in the same order, but first increasing and then decreasing along with the change of the rotation angle β in the range of 0 to 45° with a rotation energy barrier of (31.3 ± 3.1) kJ mol(-1) at 20°. This reveals that the rotation of the two phthalocyanine rings for the reduced, neutral, and oxidized bis(phthalocyaninato) lanthanum double-deckers are able to occur at room temperature. Nevertheless, the superior coordination reaction activity of the neutral bis(phthalocyaninato) lanthanum double-decker complex over their reduced form in forming sandwich-type tris(phthalocyaninato) lanthanum triple-decker compounds has also been clearly clarified on the basis of comparative calculations on the Fukui function of [La(Pc)(2)] and [La(Pc)(2)](-) using the DFT method. Fukui function analysis reveals the reaction center of the 18-electron-π-conjugated core in the bis(phthalocyaninato) lanthanum double-decker molecule against both electrophilic and radical attack. Nevertheless, the larger global chemical softness (S) for the neutral [La(Pc)(2)] than the reduced form [La(Pc)(2)](-) indicates the higher reaction activity of the former form over the latter one. This explains well the experimental findings that only the neutral instead of the reduced form of bis(tetrapyrrole) rare earth double-decker complexes, containing at least one phthalocyanine ligand, could be

  4. Development of Prediction Models for the Reactivity of Organic Compounds with Ozone in Aqueous Solution by Quantum Chemical Calculations: The Role of Delocalized and Localized Molecular Orbitals.

    PubMed

    Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs

    2015-08-18

    Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to

  5. Overlap extension PCR cloning.

    PubMed

    Bryksin, Anton; Matsumura, Ichiro

    2013-01-01

    Rising demand for recombinant proteins has motivated the development of efficient and reliable cloning methods. Here we show how a beginner can clone virtually any DNA insert into a plasmid of choice without the use of restriction endonucleases or T4 DNA ligase. Chimeric primers encoding plasmid sequence at the 5' ends and insert sequence at the 3' ends are designed and synthesized. Phusion(®) DNA polymerase is utilized to amplify the desired insert by PCR. The double-stranded product is subsequently employed as a pair of mega-primers in a PCR-like reaction with circular plasmids. The original plasmids are then destroyed in restriction digests with Dpn I. The product of the overlap extension PCR is used to transform competent Escherichia coli cells. Phusion(®) DNA polymerase is used for both the amplification and fusion reactions, so both steps can be monitored and optimized in the same way. PMID:23996437

  6. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein–Zernike self-consistent field approach

    SciTech Connect

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-07

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S{sub N}2 reaction (Cl{sup −} + CH{sub 3}Cl → ClCH{sub 3} + Cl{sup −}) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  7. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

    NASA Astrophysics Data System (ADS)

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  8. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

    PubMed

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF. PMID:26156461

  9. Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method.

    PubMed

    Nakata, Hiroya; Fedorov, Dmitri G; Zahariev, Federico; Schmidt, Michael W; Kitaura, Kazuo; Gordon, Mark S; Nakamura, Shinichiro

    2015-03-28

    Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented. PMID:25833559

  10. Molecular structure, vibrational spectra (FTIR and FT Raman) and natural bond orbital analysis of 4-Aminomethylpiperidine: DFT study

    NASA Astrophysics Data System (ADS)

    Mahalakshmi, G.; Balachandran, V.

    2014-10-01

    The FT-IR and FT-Raman spectra of 4-Aminomethylpiperidine have been recorded using Perkin Elmer Spectrophotometer and Nexus 670 spectrophotometer. The equilibrium geometrical parameters, various bonding features, the vibrational wavenumbers, the infrared intensities and the Raman scattering activities were calculated using Hartree-Fock and density functional method (B3LYP) with 6-311+G(d,p) basis set. Detailed interpretations of the vibrational spectra have been carried out with the aid of the normal coordinate analysis. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of intra molecular hydrogen bonds, electron delocalization and steric effects. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of 4-Aminomethylpiperidine (4AMP) were calculated. The theoretical UV-Visible spectrum of the compound was computed in the region 200-400 nm by time-dependent TD-DFT approach. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. The dipole moment (μ) and polarizability (α), anisotropy polarizability (Δα) and hyperpolarizability (β) of the molecule have been reported.

  11. Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

    SciTech Connect

    Nakata, Hiroya; Fedorov, Dmitri G.; Zahariev, Federico; Schmidt, Michael W.; Gordon, Mark S.; Kitaura, Kazuo; Nakamura, Shinichiro

    2015-03-28

    Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

  12. Electronic levels and electrical response of periodic molecular structures from plane-wave orbital-dependent calculations

    NASA Astrophysics Data System (ADS)

    Li, Yanli; Dabo, Ismaila

    2011-10-01

    Plane-wave electronic-structure predictions based upon orbital-dependent density-functional theory (OD-DFT) approximations, such as hybrid density-functional methods and self-interaction density-functional corrections, are severely affected by computational inaccuracies in evaluating electron interactions in the plane-wave representation. These errors arise from divergence singularities in the plane-wave summation of electrostatic and exchange interaction contributions. Auxiliary-function corrections are reciprocal-space countercharge corrections that cancel plane-wave singularities through the addition of an auxiliary function to the point-charge electrostatic kernel that enters into the expression of interaction terms. At variance with real-space countercharge corrections that are employed in the context of density-functional theory (DFT), reciprocal-space corrections are computationally inexpensive, making them suited to more demanding OD-DFT calculations. Nevertheless, there exists much freedom in the choice of auxiliary functions and various definitions result in different levels of performance in eliminating plane-wave inaccuracies. In this work we derive exact point-charge auxiliary functions for the description of molecular structures of arbitrary translational symmetry, including the yet unaddressed one-dimensional case. In addition, we provide a critical assessment of different reciprocal-space countercharge corrections and demonstrate the improved accuracy of point-charge auxiliary functions in predicting the electronic levels and electrical response of conjugated polymers from plane-wave OD-DFT calculations.

  13. Molecular orbital calculations of proton transfer involving amines as models for the clastic binding of opiates with their receptor

    SciTech Connect

    Bennett, L.K.; Beamer, R.L.

    1986-08-01

    Semi-empirical (CNDO) molecular orbital calculations, based on a previously reported ammonia-amine model system, were performed on an extended series of methyl-, ethyl-, and propylamines as models for the analgesic receptor. Methyl-, dimethyl-, and trimethylamines were chosen to represent the opiate molecules. Interatomic distances were varied within normally expected biological values. The results for the larger systems are similar to more elaborate calculations previously reported using smaller molecules. At internuclear distances of greater than 0.275 nm, the potential energy curves had two minima. At 0.2731 nm, the optimized N-N distance, the depth of the minima in the potential energy curve were not as great. Energy differences as well as population differences suggest deviation from the currently stated clastic binding theories mechanism for the analgesic response of the tertiary amines. The dimethylamine energy profile and population data indicate that the hypothesis of N-demethylated opiate as the active molecule needs further consideration and investigation. Investigation of larger systems is also indicated to develop increasingly realistic models for the analgesic response.

  14. Characterization of methyl methacrylate oligomers using secondary ion mass spectrometry, APCI mass spectrometry and molecular orbital theory

    NASA Astrophysics Data System (ADS)

    Takeuchi, T.; Iwai, K.; Momoji, K.; Miyamoto, I.; Saiki, K.; Hashimoto, K.

    2003-01-01

    The ionization efficiency and fragmentation mechanism of methyl methacrylate (MMA) oligomers (3-mer˜8-mer) were investigated by using secondary ion mass spectrometry (SIMS) and APCI mass spectrometry (APCI-MS). Protonation and fragmentation mechanisms of MMA oligomers were clarified by using molecular orbital (MO) methods. MMA oligomers were synthesized in anionic polymerization, and the oligomers were fractionated into 3-mer˜8-mer using gel permeation chromatography (GPC). In SIMS of MMA oligomers (3-mer˜8-mer), [MH] +, [MH-CH 3OH] +, [MH-methyl formate] + and [MH-2CH 3OH-methyl formate] + appeared. The peak intensities of adduct ions [M+Li] +, [M+Na] + and [M+K] + increased with the increase of the polymerization degree. The optimized geometries and H +, Li +, Na + and K + affinities of MMA monomer (1-mer), dimer (2-mer), and trimer (3-mer) were calculated using the PM3 and ab initio MO methods. The calculated H +, Li +, Na + and K + affinities increased in order of 1-mer, 2-mer and 3-mer of MMA.

  15. Design of Acceptors with Suitable Frontier Molecular Orbitals to Match Donors via Substitutions on Perylene Diimide for Organic Solar Cells

    PubMed Central

    Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa

    2016-01-01

    A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The –CN substituent can improve the electron transport properties of PDI-BI. The –CH3 group in different positions slightly affects the electron transport properties of PDI-BI. PMID:27187370

  16. Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nakata, Hiroya; Fedorov, Dmitri G.; Zahariev, Federico; Schmidt, Michael W.; Kitaura, Kazuo; Gordon, Mark S.; Nakamura, Shinichiro

    2015-03-01

    Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

  17. Understanding the molecular basis of toxin promiscuity: the analgesic sea anemone peptide APETx2 interacts with acid-sensing ion channel 3 and hERG channels via overlapping pharmacophores.

    PubMed

    Jensen, Jonas E; Cristofori-Armstrong, Ben; Anangi, Raveendra; Rosengren, K Johan; Lau, Carus H Y; Mobli, Mehdi; Brust, Andreas; Alewood, Paul F; King, Glenn F; Rash, Lachlan D

    2014-11-13

    The sea anemone peptide APETx2 is a potent and selective blocker of acid-sensing ion channel 3 (ASIC3). APETx2 is analgesic in a variety of rodent pain models, but the lack of knowledge of its pharmacophore and binding site on ASIC3 has impeded development of improved analogues. Here we present a detailed structure-activity relationship study of APETx2. Determination of a high-resolution structure of APETx2 combined with scanning mutagenesis revealed a cluster of aromatic and basic residues that mediate its interaction with ASIC3. We show that APETx2 also inhibits the off-target hERG channel by reducing the maximal current amplitude and shifting the voltage dependence of activation to more positive potentials. Electrophysiological screening of selected APETx2 mutants revealed partial overlap between the surfaces on APETx2 that mediate its interaction with ASIC3 and hERG. Characterization of the molecular basis of these interactions is an important first step toward the rational design of more selective APETx2 analogues. PMID:25337890

  18. Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST.

    PubMed

    Nakata, Ayako; Bowler, David R; Miyazaki, Tsuyoshi

    2014-11-11

    Multisite local orbitals, which are formed from linear combinations of pseudoatomic orbitals from a target atom and its neighbor atoms, have been introduced in the large-scale density functional theory calculation code CONQUEST. Multisite local orbitals correspond to local molecular orbitals so that the number of required local orbitals can be minimal. The multisite support functions are determined by using the localized filter diagonalization (LFD) method [ Phys. Rev. B 2009 , 80 , 205104 ]. Two new methods, the double cutoff method and the smoothing method, are introduced to the LFD method to improve efficiency and stability. The Hamiltonian and overlap matrices with multisite local orbitals are constructed by efficient sparse-matrix multiplications in CONQUEST. The investigation of the calculated energetic and geometrical properties and band structures of bulk Si, Al, and DNA systems demonstrate the accuracy and the computational efficiency of the present method. The representability of both occupied and unoccupied band structures with the present method has been also confirmed. PMID:26584368

  19. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule

    NASA Astrophysics Data System (ADS)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-01

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists Csbnd H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  20. An extension to artifact-free projection overlaps

    SciTech Connect

    Lin, Jianyu

    2015-05-15

    Purpose: In multipinhole single photon emission computed tomography, the overlapping of projections has been used to increase sensitivity. Avoiding artifacts in the reconstructed image associated with projection overlaps (multiplexing) is a critical issue. In our previous report, two types of artifact-free projection overlaps, i.e., projection overlaps that do not lead to artifacts in the reconstructed image, were formally defined and proved, and were validated via simulations. In this work, a new proposition is introduced to extend the previously defined type-II artifact-free projection overlaps so that a broader range of artifact-free overlaps is accommodated. One practical purpose of the new extension is to design a baffle window multipinhole system with artifact-free projection overlaps. Methods: First, the extended type-II artifact-free overlap was theoretically defined and proved. The new proposition accommodates the situation where the extended type-II artifact-free projection overlaps can be produced with incorrectly reconstructed portions in the reconstructed image. Next, to validate the theory, the extended-type-II artifact-free overlaps were employed in designing the multiplexing multipinhole spiral orbit imaging systems with a baffle window. Numerical validations were performed via simulations, where the corresponding 1-pinhole nonmultiplexing reconstruction results were used as the benchmark for artifact-free reconstructions. The mean square error (MSE) was the metric used for comparisons of noise-free reconstructed images. Noisy reconstructions were also performed as part of the validations. Results: Simulation results show that for noise-free reconstructions, the MSEs of the reconstructed images of the artifact-free multiplexing systems are very similar to those of the corresponding 1-pinhole systems. No artifacts were observed in the reconstructed images. Therefore, the testing results for artifact-free multiplexing systems designed using the

  1. On the accuracy limits of orbital expansion methods: Explicit effects of k-functions on atomic and molecular energies

    NASA Astrophysics Data System (ADS)

    Valeev, Edward F.; Allen, Wesley D.; Hernandez, Rigoberto; Sherrill, C. David; Schaefer, Henry F.

    2003-05-01

    For selected first- and second-row atoms, correlation-optimized Gaussian k functions have been determined and used in the construction of septuple-ζ basis sets for the correlation-consistent cc-pVXZ and aug-cc-pVXZ series. Restricted Hartree-Fock (RHF) and second-order Møller-Plesset (MP2) total and pair energies were computed for H, N, O, F, S, H2, N2, HF, H2O, and (H2O)2 to demonstrate the consistency of the new septuple-ζ basis sets as extensions of the established (aug)-cc-pVXZ series. The pV7Z and aug-pV7Z sets were then employed in numerous extrapolation schemes on the test species to probe the accuracy limits of the conventional MP2 method vis-à-vis explicitly correlated (MP2-R12/A) benchmarks. For (singlet, triplet) pairs, (X+1/2)-n functional forms with n=(3, 5) proved best for extrapolations. The (mean abs. relative error, std. dev.) among the 73 singlet pair energies in the dataset is (1.96%, 0.54%) and (1.72%, 0.51%) for explicit computations with the pV7Z and aug-pV7Z basis sets, respectively, but only (0.07%, 0.09%) after two-point, 6Z/7Z extrapolations with the (X+1/2)-3 form. The effects of k functions on molecular relative energies were examined by application of the septuple-ζ basis sets to the barrier to linearity and the dimerization energy of water. In the former case, an inherent uncertainty in basis set extrapolations persists which is comparable in size to the error (≈20 cm-1) in explicit aug-pV7Z computations, revealing fundamental limits of orbital expansion methods in the domain of subchemical accuracy (0.1 kcal mol-1).

  2. Structures, molecular orbitals and UV-vis spectra investigations on Br2C6H4: a computational study.

    PubMed

    Wang, Tsang-Hsiu; Hsu, Chen-Shuo; Huang, Wen-Lin; Lo, Yih-Hsing

    2013-11-01

    The dibromobenzenes (1,2-, 1,3- and 1,4-Br2C6H4) have been studied by theoretical methods. The structures of these species are optimized and the structural characteristics are determined by density functional theory (DFT) and the second order Møller-Plesset perturbation theory (MP2) levels. The geometrical structures of Br2C6H4 show a little distortion of benzene ring due to the substitution of highly electronegativity of bromine atoms. The electronegativity of bromine atoms in 1,4-Br2C6H4 is predicted to be more negative than 1,2- and 1,3-Br2C6H4. In addition, dipole moment and frontier molecular orbitals (FMOs) of these Br2C6H4 are performed as well. The 1,4-Br2C6H4 is slightly more reactive than 1,2- and 1,3-Br2C6H4 because of its small HOMO-LUMO energy gap. The simulated UV-vis spectra are investigated by time-dependent density functional theory (TD-DFT) approach, which are in excellent agreement with the available experimental value. Our calculations show that a few of absorption features are between 140nm and 250nm, which is in ultraviolet C range, and the red shift of 1,3- and 1,4-Br2C6H4 are predicted. Moreover, the UV absorption features of these Br2C6H4 in water or methanol are predicted to be more intense than in gas phase due to solvent effect. PMID:23892349

  3. Positron-attachment to small molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

    SciTech Connect

    Tachikawa, Masanori

    2015-12-31

    To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.

  4. A molecular orbital study of a model of the Mg2+ coordination complex of the self splicing reaction of ribosomal RNA

    NASA Technical Reports Server (NTRS)

    McCourt, M.; Shibata, M.; McIver, J. W.; Rein, R.

    1988-01-01

    Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.

  5. Lunar Reconnaissance Orbiter Orbit Determination Accuracy Analysis

    NASA Technical Reports Server (NTRS)

    Slojkowski, Steven E.

    2014-01-01

    LRO definitive and predictive accuracy requirements were easily met in the nominal mission orbit, using the LP150Q lunar gravity model. center dot Accuracy of the LP150Q model is poorer in the extended mission elliptical orbit. center dot Later lunar gravity models, in particular GSFC-GRAIL-270, improve OD accuracy in the extended mission. center dot Implementation of a constrained plane when the orbit is within 45 degrees of the Earth-Moon line improves cross-track accuracy. center dot Prediction accuracy is still challenged during full-Sun periods due to coarse spacecraft area modeling - Implementation of a multi-plate area model with definitive attitude input can eliminate prediction violations. - The FDF is evaluating using analytic and predicted attitude modeling to improve full-Sun prediction accuracy. center dot Comparison of FDF ephemeris file to high-precision ephemeris files provides gross confirmation that overlap compares properly assess orbit accuracy.

  6. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes

    SciTech Connect

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  7. Overlapping clusters for distributed computation.

    SciTech Connect

    Mirrokni, Vahab; Andersen, Reid; Gleich, David F.

    2010-11-01

    Scalable, distributed algorithms must address communication problems. We investigate overlapping clusters, or vertex partitions that intersect, for graph computations. This setup stores more of the graph than required but then affords the ease of implementation of vertex partitioned algorithms. Our hope is that this technique allows us to reduce communication in a computation on a distributed graph. The motivation above draws on recent work in communication avoiding algorithms. Mohiyuddin et al. (SC09) design a matrix-powers kernel that gives rise to an overlapping partition. Fritzsche et al. (CSC2009) develop an overlapping clustering for a Schwarz method. Both techniques extend an initial partitioning with overlap. Our procedure generates overlap directly. Indeed, Schwarz methods are commonly used to capitalize on overlap. Elsewhere, overlapping communities (Ahn et al, Nature 2009; Mishra et al. WAW2007) are now a popular model of structure in social networks. These have long been studied in statistics (Cole and Wishart, CompJ 1970). We present two types of results: (i) an estimated swapping probability {rho}{infinity}; and (ii) the communication volume of a parallel PageRank solution (link-following {alpha} = 0.85) using an additive Schwarz method. The volume ratio is the amount of extra storage for the overlap (2 means we store the graph twice). Below, as the ratio increases, the swapping probability and PageRank communication volume decreases.

  8. Orbit Determination of the Lunar Reconnaissance Orbiter

    NASA Technical Reports Server (NTRS)

    Mazarico, Erwan; Rowlands, D. D.; Neumann, G. A.; Smith, D. E.; Torrence, M. H.; Lemoine, F. G.; Zuber, M. T.

    2011-01-01

    We present the results on precision orbit determination from the radio science investigation of the Lunar Reconnaissance Orbiter (LRO) spacecraft. We describe the data, modeling and methods used to achieve position knowledge several times better than the required 50-100m (in total position), over the period from 13 July 2009 to 31 January 2011. In addition to the near-continuous radiometric tracking data, we include altimetric data from the Lunar Orbiter Laser Altimeter (LOLA) in the form of crossover measurements, and show that they strongly improve the accuracy of the orbit reconstruction (total position overlap differences decrease from approx.70m to approx.23 m). To refine the spacecraft trajectory further, we develop a lunar gravity field by combining the newly acquired LRO data with the historical data. The reprocessing of the spacecraft trajectory with that model shows significantly increased accuracy (approx.20m with only the radiometric data, and approx.14m with the addition of the altimetric crossovers). LOLA topographic maps and calibration data from the Lunar Reconnaissance Orbiter Camera were used to supplement the results of the overlap analysis and demonstrate the trajectory accuracy.

  9. Effect of Intermolecular Hydrogen Bonding on the Nuclear Quadrupole Interaction in Imidazole and its Derivatives as Studied by ab initio Molecular Orbital Calculations

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

    Ab initio Hartree-Fock molecular orbital calculations were applied to the crystalline imidazole and its derivatives in order to examine systematically the effect of possible N-H---N type hydrogen bond-ing on the nuclear quadrupole interaction parameters in these materials. The nitrogen quadrupole coupling constant (QCC) and the asymmetry parameter (η) of the electric field gradient (EFG) were found to depend strongly on the size of the molecular clusters, from single molecule, to dimer, trimer and to the infinite molecular chain, i.e., crystalline state, implying that the intermolecular N-H -N hydrogen bond affects significantly the electronic structure of imidazole molecule. A certain correla-tion between the QCC of 14N and the N-H bond distance R was also found and interpreted on the basis of the molecular orbital theory. However, we found that the value of the calculated EFG at the hy-drogen position of the N-H group, or the corresponding QCC value of 2 H, increases drastically as R-3 when R is shorter than about 0.1 nm, due probably to the inapplicability of the Gaussian basis sets to the very short chemical bond as revealed in the actual imidazole derivatives. We suggested that the ob-served N-H distances in imidazole derivatives should be re-examined.

  10. Spectral, electrochemical and molecular orbital studies on solvatochromic mixed ligand copper(II) complexes of malonate and diamine derivatives

    NASA Astrophysics Data System (ADS)

    Taha, Ali

    2003-04-01

    Solvatochromic mixed ligand complexes of copper(II) with malonate and diamine derivatives, Cu n(RMal)(diam) nXm (where n=1 or 2, m=1-4, RMal, malonic acid (H 2Mal), diethylmalonate (HDEtMal) or diethylethoxyethylenemalonate (DEtEMal), and diam, ethylenediamine (en), 1,3-propylenediamine (1,3-pn), N, N, N'-trimethylethylenediamine (Me 3en), N, N, N'-triethylethylenediamine (Et 3en), N, N, N', N'-tetramethylethylenediamine (Me 4en), N, N, N', N'-tetramethylpropylenediamine (Me 4pn), or N-methyl-1,4-diazacycloheptane (medach); and X=ClO 4- or Cl -), has been synthesized and characterized by spectroscopic, magnetic, molar conductance and electrochemical measurements. The mass spectra along with the analytical data of the complexes show peaks with m/ e corresponding to a bridged binuclear structure for the chloride complexes, while perchlorate complexes showed either mononuclear structure for DEtMal and DEtEMal or bridged binuclear structure for Mal complexes. These results correspond to IR spectral data, which indicated that the modes of ester and carboxylato coordination sites are mono- and/or bidentate. The d-d absorption bands in weak donor solvents suggest square-planar and distorted square pyramidal-trigonal bipyramid geometries for the perchlorate and chloride complexes; respectively. On the other hand, an octahedral structure is identified for complexes in strong donor solvents. Perchlorate complexes show a drastic color change from violet to green as the donation ability of solvent increases, whereas chloride complexes are highly affected by the acceptor properties of the solvent. Cyclic voltammetric measurements on the complexes, proposed a quasi-reversible or irreversible and mainly diffusion controlled reduction process. Such behavior has been explained according to the ECE mechanism. A linear correlation has been found between the Cu(II) reduction potential and the spectral data. Molecular orbital calculations were performed for the ligands on the bases of

  11. Methane conversion and Fischer-Tropsch catalysis over MoS sub 2 : Predictions and interpretations from molecular orbital theory

    SciTech Connect

    Anderson, A.B.; Yu, J. )

    1989-09-01

    An atom superposition and electron delocalization molecular orbital study has been made of a variety of CH{sub n} and CO reactions over coordinatively unsaturated Mo{sup IV} edge cations in MoS{sub 2}. CH{sub 3}, formed by oxidative insertion of an edge Mo into a CH{sub 4} bond, is found to dehydrogenate easily by means of H transfer to an adjacent Mo. The process is activated by the formation of a strong double bond between CH{sub 2} and Mo. Coupling of 2 CH{sub 3}, CH{sub 3} + CH{sub 2}, and 2 CH{sub 2} are found to proceed with high barriers, a consequence of electron promotion to the Fermi level during C-C bond formation, yielding unstable C{sub 2} species. Coupling to strongly adsorbed ethylene proceeds with the lowest barrier, and if ethylene forms hydrogenation to ethane is possible, although ethane formation from 2 CH{sub 4} is thermodynamically forbidden so none of these CH{sub n} coupling schemes will be productive in the absence of stabilizing ancillary reactions. CO is found to bind relatively weakly to fivefold coordinated Mo and strongly to fourfold coordinated sites. In the presence of a second adjacent fourfold coordinated Mo, CO easily tilts to the di-{sigma} bridging orientation and dissociates with a low barrier. In the Fischer-Tropsch process hydrogenation to CH{sub 3}(a) and H{sub 2}O(g) is expected. CO is found to insert into the Mo-CH{sub 3} bond, as found by Klier and co-workers, with a low barrier, and subsequent hydrogenations to form C{sub 2}H{sub 6} + H{sub 2}O or CH{sub 3}CH{sub 2}OH are found to be favorable. It is proposed that the selectivity toward alcohol formation over alkali-doped MoS{sub 2} (the DOW process) may stem from the ability of the alkali cations to bond to O from the CO insertions process, thus blocking hydrogenation to H{sub 2}O, which would lead to alkane products.

  12. Structures and stabilities of small silicon clusters: Ab initio molecular-orbital calculations of Si7-Si11

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaolei; Zeng, X. C.

    2003-02-01

    Ab initio all-electron molecular-orbital calculations have been carried out to study the structure and relative stability of small silicon clusters (Sin, n=7-11). A number of low-energy geometric isomers are optimized at the second-order Møller-Plesset (MP2) MP2/6-31G(d) level. Harmonic vibrational analysis has been performed to assure that the optimized geometries are stable. The total energies of stable isomers are computed at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level. The calculated binding energies per atom at both the MP2/6-31G(d) and CCSD(T)/6-31G(d) levels agree with the experiments. For Si7, Si8, and Si10, the lowest-energy structures are the same as those predicted previously from the all-electron optimization at the Hartree-Fock (HF) HF/6-31G(d) level [Raghavachari and Rohlfing, J. Chem. Phys. 89, 2219 (1988)]. For Si9, the lowest-energy isomer is same as that predicted based on density-functional plane-wave pseudopotential method [Vasiliev, Ogut, and Chelikowsky, Phys. Rev. Lett. 78, 4805 (1997)]. Particular attention has been given to Si11 because several low-energy geometric isomers were found nearly isoenergetic. On the basis of MP2/6-311G(2d)//CCSD(T)/6-311G(2d) calculation, we identified that the C2v isomer, a tricapped trigonal prism with two additional caps on side trigonal faces, is most likely the global-minimum structure. However, another competitive geometric isomer for the global minimum is also found on basis of the MP2/6-311G(2d)//CCSD(T)/6-311G(2d) calculation. Additionally, calculations of the binding energy and the cluster polarizability offer more insights into relatively strong stability of two magic-number clusters Si6 and Si10.

  13. Ab initio molecular orbital study of XO{sub 2}{sup +} (X = F, Cl, Br, I) systems

    SciTech Connect

    Alcami, M.; Mo, O.; Yanez, M.; Cooper, I.L.

    1999-04-15

    The depletion of stratospheric ozone has resulted in an increasing interest in the study of the possible reaction mechanisms responsible for its depletion. The structures and relative stabilities of the cationic forms of the halogen dioxides have been studied by means of ab initio molecular orbital calculations. For fluorine- and chlorine-containing compounds the geometries and the harmonic vibrational frequencies of all possible isomers were calculated at the QCISD/6-311+G(2d) level of theory. For bromine- and iodine-containing compounds the effective core-potential basis sets of Hay and Wadt, modified to include a set of diffuse functions and two sets of polarization functions, were employed. For all systems the final energies were obtained at the QCISD(T)/6-311+G(3df) level of theory. In addition, multiconfiguration-based methods have also been used. The relative stabilities of structures XOO{sup +} and OXO{sup +} are greatly reduced relative to those observed for the corresponding neutral species. In fact, for Cl and I derivatives, the lowest energy isomer corresponds to the symmetric OXO{sup +} open-chain species. The corresponding cyclic structures arise as local minima on the respective potential energy surfaces, but they lie much higher in energy than the OXO{sup +} open-chain form or the XOO{sup +} isomer. There are significant differences in bonding between XOO{sup +} and OXO{sup +}, the X-O interaction in OXO{sup +} being more covalent than in XOO{sup +}. There are also trends along the series that reflect the pronounced disparity between the electron affinity of F{sup +} and those of the heavier atoms of the group. FOO{sup +} species can be viewed as F({sup 2}P)-O{sub 2}{sup +} complexes, whereas XOO{sup +}(X = Br, I) species can be regarded as X{sup +}({sup 3}P)-O{sub 2} complexes. The OXO{sup +} open-chain species have an electron charge distribution similar to that of the ozone molecule, reflecting the same number of valence electrons in each case.

  14. A multifacet mechanism for the OH+HNO3 reaction: An ab initio molecular orbital/statistical theory study

    NASA Astrophysics Data System (ADS)

    Xia, W. S.; Lin, M. C.

    2001-03-01

    The mechanism for the OH+HNO3 reaction has been studied by ab initio molecular orbital calculations at the G2M(cc3) level of theory. Four complexes and four transition states have been found and confirmed by intrinsic reaction coordinate analyses. The commonly assumed six-membered ring complex formed by hydrogen bonding of the OH radical with HNO3, -ON(O)OH…OH-, was found to be stable by 8.1 kcal/mol; its decomposition producing NO3+H2O was predicted to have a barrier of 11.6 kcal/mol. A five-membered ring complex, -ON(O)OH…O(H)-, with the H atom of the OH radical placed out of the ring plane, was found to have a stability of 5.3 kcal/mol; it fragments to form NO3+H2O with a barrier of 6.6 kcal/mol. Two additional complexes, which are the mirror image of each other with a 7.4 kcal/mol binding energy, were found to be related to the OH exchange reaction with a 13.3 kcal/mol barrier above the complexes. The direct abstraction process producing H2O2 and NO2 was predicted to have a large barrier of 24.4 kcal/mol, insignificant to atmospheric chemistry. The rate constant has been calculated at 200-1500 K and 0-760 Torr. The results show that the reaction has strong pressure and tunneling effects below room temperature. In addition, the rate constants for the decay of OH and OD (in OD+DNO3) evaluated by kinetic modeling compare reasonably well with experimental data below room temperature. The unusually pronounced kinetic isotope effect observed experimentally, kH/kD⩾10, could be accounted for by the combination of the greater tunneling rate in the H system and the large redissociation rate of stabilized complexes in the D system. The rate constant predicted for the production of H2O and NO3 in the temperature range 750-1500 K can be effectively represented by the expression k=1.45×10-23 T3.5 exp(+839/T) cm3/s.

  15. AC Stark effect in a spin-orbit mixed quantum states in a five-level molecular system coupled by three lasers

    NASA Astrophysics Data System (ADS)

    Qi, Jianbing

    2016-05-01

    The interaction of the spin orbital motion of electrons can mix quantum states with different spin multiplicity. Thus the mixed states can carry both characteristics of the two states depending on the mixing coefficients. The spin-orbit coupled rovibrational levels in diatomic alkali are ubiquitous. These levels are classified as singlet states (if the total spin is zero) and triplet states (if the total spin is one), respectively. A transition from a singlet level can only go to singlet levels and a triplet only to triplet levels. The spin-orbit coupled states can be used as a gateway to access some normally prohibited transitions. By coupling the mixed states to an auxiliary quantum state with lasers, the coupling coefficient of two mixed singlet-triplet molecular states can be modified by ac Stark effect via varying the Rabi frequency of the coupling lasers and the detuning of the laser frequency, We use density matrix equations and a five-level molecular model to show that a coupled singlet-triplet pair of rovibrational levels can be used as a channel to enhance the probability of accessing target quantum states.

  16. Formation of Molecular-Orbital Bands in a Twisted Hubbard Tube: Implications for Unconventional Superconductivity in K2Cr3As3

    NASA Astrophysics Data System (ADS)

    Zhong, Hanting; Feng, Xiao-Yong; Chen, Hua; Dai, Jianhui

    2015-11-01

    We study a twisted Hubbard tube modeling the [CrAs ]∞ structure of quasi-one-dimensional superconductors A2Cr3 As3 (A =K , Rb, Cs). The molecular-orbital bands emerging from the quasi-degenerate atomic orbitals are exactly solved. An effective Hamiltonian is derived for a region where three partially filled bands intersect the Fermi energy. The deduced local interactions among these active bands show a significant reduction compared to the original atomic interactions. The resulting three-channel Luttinger liquid shows various interaction-induced instabilities including two kinds of spin-triplet superconducting instabilities due to gapless spin excitations, with one of them being superseded by the spin-density-wave phase in the intermediate Hund's coupling regime. The implications of these results for the alkali chromium arsenides are discussed.

  17. On the Neuberger overlap operator

    NASA Astrophysics Data System (ADS)

    Boriçi, Artan

    1999-04-01

    We compute Neuberger's overlap operator by the Lanczos algorithm applied to the Wilson-Dirac operator. Locality of the operator for quenched QCD data and its eigenvalue spectrum in an instanton background are studied.

  18. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

    PubMed

    Ferenczy, György G

    2013-04-01

    Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. PMID:23281055

  19. Equation of state of a dense plasma by orbital-free and quantum molecular dynamics: Examination of two isothermal-isobaric mixing rules

    NASA Astrophysics Data System (ADS)

    Danel, J.-F.; Kazandjian, L.

    2015-01-01

    We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C2H3 and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm 3 for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm 3 for orbital-free molecular dynamics. Simulations for the full C2H3 mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot.

  20. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    NASA Astrophysics Data System (ADS)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  1. Oxygen Radical Scavenger Activity, EPR, NMR, Molecular Mechanics and Extended-Hückel Molecular Orbital Investigation of the Bis(Piroxicam)Copper(II) Complex.

    PubMed

    Cini, R; Pogni, R; Basosi, R; Donati, A; Rossi, C; Sabadini, L; Rollo, L; Lorenzini, S; Gelli, R; Marcolongo, R

    1995-01-01

    The oxygen radical scavenger activity (ORSA) of [Cu(II)(Pir)(2)] (HPir = Piroxicam = 4-hydroxy -2- methyl -N-2- pyridyl -2H- 1,2-benzothiazine -3- carboxamide 1,1-dioxide) was determined by chemiluminescence of samples obtained by mixing human neutrophils (from healthy subjects) and [Cu(II)(Pir)(2)(DMF)(2)] (DMF = N,N -dimethylformammide) in DMSO/GLY/PBS (2:1:2, v/v) solution (DMSO = dimethylsulfoxide, GLY = 1,2,3-propantriol, PBS = Dulbecco's buffer salt solution). The ratio of the residual radicals, for the HPir (1.02.10(-4)M) and [Cu(II)(Pir)(2)(DMF)(2)] (1.08.10(-5)M)/HPir (8.01.10-(-5)M) systems was higher than 12 (not stimulated) [excess of piroxicam was added (Cu/Pir molar ratio approximately 1:10) in order to have most of the metal complexed as bischelate]. In contrast, the ratio of residual radicals for the CuCl(2) (1.00.10(-5)M) and [Cu(II)(Pir)(2)(DMF)(2)] (1.08.10(-5)M)/Hpir (8.01.10(-5)M)system was 5. The [Cu(II)(Pir)(2)] compound is therefore a stronger radical scavenger than either HPir or CuCl(2). A molecular mechanics (MM) analysis of the gas phase structures of neutral HPir, its zwitterionic (HPir(+-)) and anionic (Pir(-)) forms, and some Cu(II)-piroxicam complexes based on X-ray structures allowed calculation of force constants. The most stable structure for HPir has a ZZZ conformation similar to that found in the Cu(II) (and Cd(II) complexes) in the solid state as well as in the gas phase. The structure is stabilized by a strong H bond which involves the N(amide)-H and O(enolic) groups. The MM simulation for the [Cu(II)(Pir)(2)(DMF)(2)] complex showed that two high repulsive intramolecular contacts exist between a pyridyl hydrogen atom of one Pir(-) molecule with the O donor of the other ligand. These interactions activate a transition toward a pseudo-tetrahedral geometry, in the case the apical ligands are removed. On refluxing a suspension of [Cu(II)(Pir)(2)(DMF)(2)] in acetone a brown microcystalline solid with the Cu(Pir)(2).0.5DMF

  2. Charge Redistribution and Transport in Molecular Contacts

    NASA Astrophysics Data System (ADS)

    Corso, Martina; Ondráček, Martin; Lotze, Christian; Hapala, Prokop; Franke, Katharina J.; Jelínek, Pavel; Pascual, J. Ignacio

    2015-09-01

    The forces between two single molecules brought into contact, and their connection with charge transport through the molecular junction, are studied here using non contact AFM, STM, and density functional theory simulations. A carbon monoxide molecule approaching an acetylene molecule (C2 H2 ) initially feels weak attractive electrostatic forces, partly arising from charge reorganization in the presence of molecular . We find that the molecular contact is chemically passive, and protects the electron tunneling barrier from collapsing, even in the limit of repulsive forces. However, we find subtle conductance and force variations at different contacting sites along the C2 H2 molecule attributed to a weak overlap of their respective frontier orbitals.

  3. 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.

  4. Altimetry, Orbits and Tides

    NASA Technical Reports Server (NTRS)

    Colombo, O. L.

    1984-01-01

    The nature of the orbit error and its effect on the sea surface heights calculated with satellite altimetry are explained. The elementary concepts of celestial mechanics required to follow a general discussion of the problem are included. Consideration of errors in the orbits of satellites with precisely repeating ground tracks (SEASAT, TOPEX, ERS-1, POSEIDON, amongst past and future altimeter satellites) are detailed. The theoretical conclusions are illustrated with the numerical results of computer simulations. The nature of the errors in this type of orbits is such that this error can be filtered out by using height differences along repeating (overlapping) passes. This makes them particularly valuable for the study and monitoring of changes in the sea surface, such as tides. Elements of tidal theory, showing how these principles can be combined with those pertinent to the orbit error to make direct maps of the tides using altimetry are presented.

  5. Mass Transport Properties of LiD-U Mixtures from Orbital Free Molecular Dynamics Simulations and a Pressure-Matching Mixing Rule

    SciTech Connect

    Burakovsky, Leonid; Kress, Joel D.; Collins, Lee A.

    2012-05-31

    Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD){sub x}U{sub (1-x)} compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, {rho}, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk{sub B}T/V + P{sub e}, is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species {alpha}, D{sub {alpha}}, the mutual diffusion coefficient for species {alpha} and {beta}, D{alpha}{beta}, and the shear viscosity, {eta}, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.

  6. Seeding for pervasively overlapping communities

    NASA Astrophysics Data System (ADS)

    Lee, Conrad; Reid, Fergal; McDaid, Aaron; Hurley, Neil

    2011-06-01

    In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms specifically designed to detect overlapping communities do not perform well in such highly overlapping settings. Here, we consider one class of these algorithms, those which optimize a local fitness measure, typically by using a greedy heuristic to expand a seed into a community. We perform synthetic benchmarks which indicate that an appropriate seeding strategy becomes more important as the extent of community overlap increases. We find that distinct cliques provide the best seeds. We find further support for this seeding strategy with benchmarks on a Facebook network and the yeast interactome.

  7. Traveling-molecular-orbital-expansion studies of electron capture in collisions of fully stripped ions (Z = 6--9) with H and H/sub 2/

    SciTech Connect

    Kimura, M.; Lane, N.F.

    1987-01-01

    The traveling-molecular-orbital-expansion description has been employed to investigate electron capture in collisions of fully stripped ions (Z = 6--9) with H and H/sub 2/ in the energy regime from 0.14 to 9 keV/amu. The pseudopotential method was used to represent the H/sub 2/ /sup +/ core which enables us to treat the H/sub 2/ molecule as an atom having an ionization potential for H/sub 2/..-->..H/sub 2/ /sup +/. Features of the adiabatic potentials and corresponding radial coupling matrix elements at the ''reaction window'' as well as the quantitative results of relatively small-scale close-coupling calculations provide a rationale for the interpretation of a recent measurement for these systems by Meyer et al. (Phys. Rev. A 32, 3310 (1985)). For collisions of O/sup 8+/ with H, an extended molecular-orbital-expansion approach has been employed (i) to seek an understanding of the discrepancy evident in two recent independent large-scale calculations for n = 6 partial cross sections, and (ii) to obtain a quantitative test for the mechanism suggested in this paper.

  8. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of 3-hydroxy-6-methyl-2-nitropyridine

    NASA Astrophysics Data System (ADS)

    Karnan, M.; Balachandran, V.; Murugan, M.

    2012-10-01

    The optimized molecular structure and corresponding vibrational assignments of 3-hydroxy-6-methyl-2-nitropyridine have been investigated using density functional theory (DFT) B3LYP method with 6-311++G(d,p), 6-311++G(2d,2p) and 6-311++G(3d,3p) basis sets. Investigation of the relative orientation of the hydroxyl group with respect to the nitro group has shown that two conformers (O-cis) and (O-trans) exist. The vibrational analysis of the stable conformer of the title compound is performed by means of infrared absorption and Raman spectroscopy in combination with theoretical simulations. The molecular stability and bond strength were investigated by applying the natural bond orbital (NBO) analysis. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with electrostatic potential (ESP). The isotropic chemical shift computed by 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the HMNP calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations.

  9. Bridge-mediated excitation energy transfer pathways through protein media: a Slater determinant-based electronic coupling calculation combined with localized molecular orbitals.

    PubMed

    Kawatsu, Tsutomu; Matsuda, Kenji; Hasegawa, Jun-ya

    2011-10-01

    A computational method for calculating electronic coupling and pathway of electron transfer (ET) has been extended to that for excitation energy transfer (EET). A molecular orbital (MO)-based description has been generalized to one based on Slater determinants. This approach reduces the approximations used for the Green's function method from the perturbation of chemical-bond interactions to the perturbation of the configuration interactions. It is, therefore, reasonable to apply this method to EET, which involves the transfer of an electron-hole pair. To represent EET donor, acceptor, and bridge states, we adopted recently developed localized molecular orbitals (LMOs) for constructing locally excited determinants. The LMO approach provides a chemically meaningful interpretation of how each local excitation on the bridge contributes to the total electronic coupling of the EET. We applied the method to six model peptides and calculated their electronic couplings as well as the direct and through-peptide terms. Although the through-peptide term is usually negligibly small compared with the direct term, it can dominate the EET reaction in appropriate situations. The direct term dominates in long-range interactions because the indirect term decays in shorter distances. PMID:21861486

  10. A Bayesian variable selection procedure to rank overlapping gene sets

    PubMed Central

    2012-01-01

    Background Genome-wide expression profiling using microarrays or sequence-based technologies allows us to identify genes and genetic pathways whose expression patterns influence complex traits. Different methods to prioritize gene sets, such as the genes in a given molecular pathway, have been described. In many cases, these methods test one gene set at a time, and therefore do not consider overlaps among the pathways. Here, we present a Bayesian variable selection method to prioritize gene sets that overcomes this limitation by considering all gene sets simultaneously. We applied Bayesian variable selection to differential expression to prioritize the molecular and genetic pathways involved in the responses to Escherichia coli infection in Danish Holstein cows. Results We used a Bayesian variable selection method to prioritize Kyoto Encyclopedia of Genes and Genomes pathways. We used our data to study how the variable selection method was affected by overlaps among the pathways. In addition, we compared our approach to another that ignores the overlaps, and studied the differences in the prioritization. The variable selection method was robust to a change in prior probability and stable given a limited number of observations. Conclusions Bayesian variable selection is a useful way to prioritize gene sets while considering their overlaps. Ignoring the overlaps gives different and possibly misleading results. Additional procedures may be needed in cases of highly overlapping pathways that are hard to prioritize. PMID:22554182

  11. The Energy of Substituted Ethanes. Asymmetry Orbitals

    PubMed Central

    Salem, Lionel; Hoffmann, Roald; Otto, Peter

    1973-01-01

    The leading terms in the energy of a general substituted ethane are derived in explicit form as a function of the torsional angle θ, the substituent electronegativities, and their mutual overlaps. The energy is found to be the sum of all four overlaps between pairs of asymmetry orbitals, and satisfies the requisite symmetry properties. PMID:16592060

  12. Molecular cloning and characterization of genes for antibodies generated by orbital tissue-infiltrating B-cells in Graves` ophthalmopathy

    SciTech Connect

    Jaume, J.C.; Portolano, S.; Prummel, M.F.; McLachlan, S.M.; Rapoport, B.

    1994-02-01

    Graves` ophthalmopathy is a distressing autoimmune disease of unknown etiology. Analysis of the genes for antibodies secreted by orbital tissue-infiltrating plasma cells might provide insight into the pathogenesis of this disease. The authors, therefore, constructed an immunoglobulin heavy (H) chain and an immunoglobulin k light (L) chain cDNA library from the orbital tissue of a patient with active Graves` ophthalmopathy. Analysis of 15 H (IgG1) and 15 L (k) chains revealed a restricted spectrum of variable region genes. Fourteen of 15 variable k genes were about 94% homologous to the closest known germline gene, KL012. Thirteen of 15 H chain genes were 91% and 90% homologous to the closest germline genes, DP10 and hv1263, respectively. Remarkably, these germline genes also code for other autoantibodies to striated muscle (KL012) and thyroid peridase (KL012 and hv1263). These studies raise the possibility that particular germline genes may be associated with autoimmunity in humans. Further, the present study opens the way to identifying ocular autoantigens that may be the target of an humoral immune response. 29 refs., 4 figs., 1 tab.

  13. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  14. Hydrogen bonded C-H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2016-03-01

    Hydrogen bonded C-H···Y complexes formed by H2O, H2S molecules, hydrogen halides, and halogen-ions with methane, halogen substituted methane as well as with the C2H2 and NCH molecules were studied at the MP2/aug-cc-pVDZ level. The structure of NBOs corresponding to lone pair of acceptor Y, n Y, and vacant anti-σ-bond C-H of proton donor was analyzed and estimates of second order perturbation energy E(2) characterizing donor-acceptor n Y → σ C-H * charge-transfer interaction were obtained. Computational results for complexes of methane and its halogen substituted derivatives show that for each set of analogous structures, the EnY→σ*C-H (2) energy tends to grow with an increase in the s-component percentage in the lone pair NBO of acceptor Y. Calculations for different C···Y distances show that the equilibrium geometries of complexes lie in the region where the E(2) energy is highest and it changes symbatically with the length of the covalent E-H bond when the R(C···Y) distance is varied. The performed analysis allows us to divide the hydrogen bonded complexes into two groups, depending on the pattern of overlapping for NBOs of the hydrogen bridge.

  15. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of Isoxanthopterin

    NASA Astrophysics Data System (ADS)

    Prabavathi, N.; Nilufer, A.; Krishnakumar, V.

    2013-10-01

    The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0), related properties (β, α0 and Δα) and the Mulliken charges of the molecule were also computed using DFT calculations. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. Information about the charge density distribution of the molecule and its chemical reactivity has been obtained by mapping molecular electrostatic potential surface. In addition, the non-linear optical properties were discussed from the dipole moment values and excitation wavelength in the UV-visible region.

  16. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of Isoxanthopterin.

    PubMed

    Prabavathi, N; Nilufer, A; Krishnakumar, V

    2013-10-01

    The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0), related properties (β, α0 and Δα) and the Mulliken charges of the molecule were also computed using DFT calculations. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. Information about the charge density distribution of the molecule and its chemical reactivity has been obtained by mapping molecular electrostatic potential surface. In addition, the non-linear optical properties were discussed from the dipole moment values and excitation wavelength in the UV-visible region. PMID:23751224

  17. Vibrational spectra and ab initio molecular orbital calculations of the novel anti-cancer drug combretastatin A-4 prodrug

    NASA Astrophysics Data System (ADS)

    James, C.; Pettit, G. R.; Nielsen, O. F.; Jayakumar, V. S.; Joe, I. Hubert

    2008-10-01

    The NIR-FT Raman and FT-IR spectral studies of the novel antineoplastic and antiangiogenesis substance comprestatin A-4 prodrug (CA4P) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of CA4P have been investigated with the help of B3LYP density functional theory (DFT) method. The most preferred cis-configuration for its bioactivity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization and mesomeric effects have been analyzed using natural bond orbital (NBO) analysis. Detailed assignments of the vibrational spectra have been made with the aid of theoretically predicted vibrational frequencies. The optimized geometry shows near-planarity of phenyl rings and perpendicular conformation of meta substituted methoxy group. The vibrational analysis confirms the differently acting ring modes, steric repulsion, π conjugation and back-donation.

  18. Clique graphs and overlapping communities

    NASA Astrophysics Data System (ADS)

    Evans, T. S.

    2010-12-01

    It is shown how to construct a clique graph in which properties of cliques of a fixed order in a given graph are represented by vertices in a weighted graph. Various definitions and motivations for these weights are given. The detection of communities or clusters is used to illustrate how a clique graph may be exploited. In particular a benchmark network is shown where clique graphs find the overlapping communities accurately while vertex partition methods fail.

  19. Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

    NASA Astrophysics Data System (ADS)

    Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

    2013-01-01

    In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

  20. Vibrational spectra, molecular structure, natural bond orbital, first order hyperpolarizability, thermodynamic analysis and normal coordinate analysis of Salicylaldehyde p-methylphenylthiosemicarbazone by density functional method.

    PubMed

    Porchelvi, E Elamurugu; Muthu, S

    2015-01-01

    The thiosemicarbazone compound, Salicylaldehyde p-methylphenylthiosemicarbazone (abbreviated as SMPTSC) was synthesized and characterized by FTIR, FT-Raman and UV. Density functional (DFT) calculations have been carried out for the title compound by performing DFT level of theory using B3LYP/6-31++G(d,p) basis set. The molecular geometry and vibrational frequencies were calculated and compared with the experimental data. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. Thearomaticities of the phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Mulliken population analysis on atomic charges is also calculated. The molecule orbital contributions are studied by density of energy states (DOSs). PMID:25033238

  1. Using simple molecular orbital calculations to predict disease: fast DFT methods applied to enzymes implicated in PKU, Parkinson's disease and Obsessive Compulsive Disorder

    NASA Astrophysics Data System (ADS)

    Hofto, Laura; Hofto, Meghan; Cross, Jessica; Cafiero, Mauricio

    2007-09-01

    Many diseases can be traced to point mutations in the DNA coding for specific enzymes. These point mutations result in the change of one amino acid residue in the enzyme. We have developed a model using simple molecular orbital calculations which can be used to quantitatively determine the change in interaction between the enzyme's active site and necessary ligands upon mutation. We have applied this model to three hydroxylase proteins: phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase, and we have obtained excellent correlation between our results and observed disease symptoms. Furthermore, we are able to use this agreement as a baseline to screen other mutations which may also cause onset of disease symptoms. Our focus is on systems where the binding is due largely to dispersion, which is much more difficult to model inexpensively than pure electrostatic interactions. Our calculations are run in parallel on a sixteen processor cluster of 64-bit Athlon processors.

  2. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods. PMID:27308221

  3. Hydration effects on enzyme-substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Ando, Hiroyuki; Shigeta, Yasuteru; Baba, Takeshi; Watanabe, Chiduru; Okiyama, Yoshio; Mochizuki, Yuji; Nakano, Masayoshi

    2015-02-01

    Fragment molecular orbital calculations were successfully applied to a nylon oligomer hydrolase, NylB, to investigate the hydration effects on an enzyme-substrate binding structure. Statistically corrected inter-fragment interaction energy analyses were performed on this system to quantitatively characterise the interactions between the substrate, 6-aminohexanoate linear dimer (ALD), and the amino acid residues, such as Asp181, Ser112, and Ile 345, which are regarded as important for enzyme-substrate complex formation by NylB. We found that the direct interaction between ALD and NylB is weakened by hydration, because water molecules cause charge translation or polarisation of ALD or each amino acid residue. However, including the interaction energy between ALD and water molecules greatly stabilises this complex. These results indicate the importance of the hydration effects in enzyme-substrate complex formation.

  4. Theoretical study on the electronic absorption spectra and molecular orbitals of ten novel ruthenium sensitizers derived from N3 and K8.

    PubMed

    Guo, Ping; Ma, Ruimin; Guo, Lianshun; Yang, Linlin; Liu, Jifeng; Zhang, Xianxi; Pan, Xu; Dai, Songyuan

    2010-11-01

    Ten novel sensitizer candidates Ru2, Ru4, Ru5, Ru6, Ru7, Ru8, Ru9, Ru10, Ru11 and Ru12 derived from the sensitizers N3 and K8 were designed and studied using the density functional theory and time-dependent density functional theory calculations. The influences of the C=C double bonds between the carboxyl groups and the bipyridine ring as well as the numbers and positions of the -CN groups adjacent to the carboxyl groups on the properties of the sensitizer candidates were discussed. The energy levels and the spatial distributions of the frontier molecular orbitals as well as the electronic absorption spectra of these complexes were compared with those of N3 and K8. Ru10 and Ru7 were found promising to provide superior photon-to-current conversion efficiency to those of N3 and K8 in ruthenium complex sensitized solar cells. PMID:21036083

  5. Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

    PubMed Central

    Sure, Rebecca; Brandenburg, Jan Gerit

    2015-01-01

    Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221

  6. Molecular orbital (SCF-X-α-SW) theory of Fe2+-Mn3+, Fe3+-Mn2+, and Fe3+-Mn3+ charge transfer and magnetic exchange in oxides and silicates

    USGS Publications Warehouse

    Sherman, David M.

    1990-01-01

    Metal-metal charge-transfer and magnetic exchange interactions have important effects on the optical spectra, crystal chemistry, and physics of minerals. Previous molecular orbital calculations have provided insight on the nature of Fe2+-Fe3+ and Fe2+-Ti4+ charge-transfer transitions in oxides and silicates. In this work, spin-unrestricted molecular orbital calculations on (FeMnO10) clusters are used to study the nature of magnetic exchange and electron delocalization (charge transfer) associated with Fe3+-Mn2+, Fe3+-Mn3+, and Fe2+-Mn3+ interactions in oxides and silicates. 

  7. Development of a Silicon Carbide Molecular Beam Nozzle for Simulation Planetary Flybys and Low-Earth Orbit

    NASA Technical Reports Server (NTRS)

    Patrick, E. L.; Earle, G. D.; Kasprzak, W. T.; Mahaffy, Paul R.

    2008-01-01

    From commercial origins as a molybdenum molecular beam nozzle, a ceramic nozzle of silicon carbide (SiC) was developed for space environment simulation. The nozzle is mechanically stable under extreme conditions of temperature and pressure. A heated, continuous, supersonically-expanded hydrogen beam with a 1% argon seed produced an argon beam component of nearly 4 km/s, with an argon flux exceeding 1x1014 /cm2.s. This nozzle was part of a molecular beam machine used in the Atmospheric Experiments Branch at NASA Goddard Space Flight Center to characterize the performance of the University of Texas at Dallas Ram Wind Sensor (RWS) aboard the Air Force Communications/Navigation Outage Forecasting System (C/NOFS) launched in the Spring of 2008.

  8. Precise Orbit Determination of the Lunar Reconnaissance Orbiter and inferred gravity field information

    NASA Astrophysics Data System (ADS)

    Maier, A.; Baur, O.; Krauss, S.

    2014-04-01

    This contribution deals with Precise Orbit Determination of the Lunar Reconnaissance Orbiter, which is tracked with optical laser ranges in addition to radiometric Doppler range-rates and range observations. The optimum parameterization is assessed by overlap analysis tests that indicate the inner precision of the computed orbits. Information about the very long wavelengths of the lunar gravity field is inferred from the spacecraft positions. The NASA software packages GEODYN II and SOLVE were used for orbit determination and gravity field recovery [1].

  9. Conformational and Molecular Structures of α,β-Unsaturated Acrylonitrile Derivatives: Photophysical Properties and Their Frontier Orbitals.

    PubMed

    Percino, María Judith; Cerón, Margarita; Rodríguez, Oscar; Soriano-Moro, Guillermo; Castro, María Eugenia; Chapela, Víctor M; Siegler, Maxime A; Pérez-Gutiérrez, Enrique

    2016-01-01

    We report single crystal X-ray diffraction (hereafter, SCXRD) analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylamino)phenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z)-3-(4-(diphenylamino)-phenyl)-2-(pyridin-3-yl)prop-2-enenitrile (I), (2Z)-3-(4-(diphenylamino)phenyl)-2-(pyridin-4-yl)-prop-2-enenitrile (II) and (2Z)-3-(9-ethyl-9H-carbazol-3-yl)-2-(pyridin-2-yl)enenitrile (III). SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z' = 2 and C2/c with Z' = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z' = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z'). It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV). Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide) in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported. PMID:27043499

  10. Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

    NASA Astrophysics Data System (ADS)

    Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

    From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

  11. Hospital mergers and market overlap.

    PubMed Central

    Brooks, G R; Jones, V G

    1997-01-01

    OBJECTIVE: To address two questions: What are the characteristics of hospitals that affect the likelihood of their being involved in a merger? What characteristics of particular pairs of hospitals affect the likelihood of the pair engaging in a merger? DATA SOURCES/STUDY SETTING: Hospitals in the 12 county region surrounding the San Francisco Bay during the period 1983 to 1992 were the focus of the study. Data were drawn from secondary sources, including the Lexis/Nexis database, the American Hospital Association, and the Office of Statewide Health Planning and Development of the State of California. STUDY DESIGN: Seventeen hospital mergers during the study period were identified. A random sample of pairs of hospitals that did not merge was drawn to establish a statistically efficient control set. Models constructed from hypotheses regarding hospital and market characteristics believed to be related to merger likelihood were tested using logistic regression analysis. DATA COLLECTION: See Data Sources/Study Setting. PRINCIPAL FINDINGS: The analysis shows that the likelihood of a merger between a particular pair of hospitals is positively related to the degree of market overlap that exists between them. Furthermore, market overlap and performance difference interact in their effect on merger likelihood. In an analysis of individual hospitals, conditions of rivalry, hospital market share, and hospital size were not found to influence the likelihood that a hospital will engage in a merger. CONCLUSIONS: Mergers between hospitals are not driven directly by considerations of market power or efficiency as much as by the existence of specific merger opportunities in the hospitals' local markets. Market overlap is a condition that enables a merger to occur, but other factors, such as the relative performance levels of the hospitals in question and their ownership and teaching status, also play a role in influencing the likelihood that a merger will in fact take place. PMID

  12. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

    PubMed

    Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition. PMID:25791682

  13. The continuous and discrete molecular orbital x-ray bands from Xe(q+) (12≤q≤29) +Zn collisions.

    PubMed

    Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie

    2016-01-01

    In this paper, the x-ray emissions are measured by the interaction of 1500-3500 keV Xe(q+) (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xe(q+) ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9-1.32 keV over the energy range studied and are proportional to v(1/2) (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field. PMID:27469425

  14. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

    NASA Astrophysics Data System (ADS)

    Zobač, Vladimír; Lewis, James P.; Abad, Enrique; Mendieta-Moreno, Jesús I.; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  15. Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems

    SciTech Connect

    Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi

    2015-01-22

    In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.

  16. Intermolecular Hybridization Creating Nanopore Orbital in a Supramolecular Hydrocarbon Sheet.

    PubMed

    Zhang, Yi-Qi; Björk, Jonas; Barth, Johannes V; Klappenberger, Florian

    2016-07-13

    Molecular orbital engineering is a key ingredient for the design of organic devices. Intermolecular hybridization promises efficient charge carrier transport but usually requires dense packing for significant wave function overlap. Here we use scanning tunneling spectroscopy to spatially resolve the electronic structure of a surface-confined nanoporous supramolecular sheet of a prototypical hydrocarbon compound featuring terminal alkyne (-CCH) groups. Surprisingly, localized nanopore orbitals are observed, with their electron density centered in the cavities surrounded by the functional moieties. Density functional theory calculations reveal that these new electronic states originate from the intermolecular hybridization of six in-plane π-orbitals of the carbon-carbon triple bonds, exhibiting significant electronic splitting and an energy downshift of approximately 1 eV. Importantly, these nanopore states are distinct from previously reported interfacial states. We unravel the underlying connection between the formation of nanopore orbital and geometric arrangements of functional groups, thus demonstrating the generality of applying related orbital engineering concepts in various types of porous organic structures. PMID:27253516

  17. Orbit to orbit transportation

    NASA Technical Reports Server (NTRS)

    Bergeron, R. P.

    1980-01-01

    Orbital transfer vehicle propulsion options for SPS include both chemical (COTV) and electrical (EOTV) options. The proposed EOTV construction method is similar to that of the SPS and, by the addition of a transmitting antenna, may serve as a demonstration or precursor satellite option. The results of the studies led to the selection of a single stage COTV for crew and priority cargo transfer. An EOTV concept is favored for cargo transfer because of the more favorable orbital burden factor over chemical systems. The gallium arsenide solar array is favored over the silicon array because of its self annealing characteristics of radiation damage encountered during multiple transitions through the Van Allen radiation belt. Transportation system operations are depicted. A heavy lift launch vehicle (HLLV) delivers cargo and propellants to LEO, which are transferred to a dedicated EOTV by means of an intraorbit transfer vehicle (IOTV) for subsequent transfer to GEO. The space shuttle is used for crew transfer from Earth to LEO. At the LEO base, the crew module is removed from the shuttle cargo bay and mated to a COTV for transfer to GEO. Upon arrival at GEO, the SPS construction cargo is transferred from the EOTV to the SPS construction base by IOTV. Crew consumables and resupply propellants are transported to GEO by the EOTV. Transportation requirements are dominated by the vast quantity of materials to be transported to LEO and GEO.

  18. [Asthma-COPD overlap syndrome].

    PubMed

    Odler, Balázs; Müller, Veronika

    2016-08-01

    Obstructive lung diseases represent a major health problem worldwide due to their high prevalence associated with elevated socioeconomic costs. Bronchial asthma and chronic obstructive pulmonary disease are chronic obstructive ventilatory disorders with airway inflammation, however they are separate nosological entities based on thedifferent development, diagnostic and therapeutic approaches, and prognostic features. However, these diseases may coexist and can be defined as the coexistence of increased variability of airflow in a patient with incompletely reversible airway obstruction. This phenotype is called asthma - chronic obstructive pulmonary disease overlap syndrome. The syndrome is a clinical and scientific challenge as the majority of these patients have been excluded from the clinical and pharmacological trials, thus well-defined clinical characteristics and therapeutic approaches are lacking. The aim of this review is to summarize the currently available literature focusing on pathophysiological and clinical features, and discuss possible therapeutic approaches of patients with asthma - chronic obstructive pulmonary disease overlap syndrome. Orv. Hetil., 2016, 157(33), 1304-1313. PMID:27523313

  19. Item Overlap Correlations: Definitions, Interpretations, and Implications.

    ERIC Educational Resources Information Center

    Hsu, Louis M.

    1994-01-01

    Item overlap coefficient (IOC) formulas are discussed, providing six warnings about their calculation and interpretation and some explanations of why item overlap influences the Minnesota Multiphasic Personality Inventory and the Millon Clinical Multiaxial Inventory factor structures. (SLD)

  20. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... overlap does not already exists, if: (1) The total area of overlap with that station would not be... modified NCE-FM station other than a Class D (secondary) station will not be accepted if the proposed operation would involve overlap of signal strength contours with any other station licensed by...

  1. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... overlap does not already exists, if: (1) The total area of overlap with that station would not be... modified NCE-FM station other than a Class D (secondary) station will not be accepted if the proposed operation would involve overlap of signal strength contours with any other station licensed by...

  2. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... overlap does not already exists, if: (1) The total area of overlap with that station would not be... modified NCE-FM station other than a Class D (secondary) station will not be accepted if the proposed operation would involve overlap of signal strength contours with any other station licensed by...

  3. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... overlap does not already exists, if: (1) The total area of overlap with that station would not be... modified NCE-FM station other than a Class D (secondary) station will not be accepted if the proposed operation would involve overlap of signal strength contours with any other station licensed by...

  4. Orbital pseudotumor

    MedlinePlus

    ... Names Idiopathic orbital inflammatory syndrome (IOIS) Images Skull anatomy References Goodlick TA, Kay MD, Glaser JS, Tse DT, Chang WJ. Orbital disease and neuro-ophthalmology. In: Tasman W, Jaeger EA, eds. Duane’s ...

  5. Kepler's Orbit

    NASA Video Gallery

    Kepler does not orbit the Earth, rather it orbits the Sun in concert with the Earth, slowly drifting away from Earth. Every 61 Earth years, Kepler and Earth will pass by each other. Throughout the ...

  6. Orbital cellulitis

    MedlinePlus

    ... Haemophilus influenzae B) vaccine. The bacteria Staphylococcus aureus , Streptococcus pneumoniae , and beta-hemolytic streptococci may also cause orbital cellulitis. Orbital cellulitis infections in children may get worse very quickly and can lead ...

  7. Structure investigation of three hydrazones Schiff's bases by spectroscopic, thermal and molecular orbital calculations and their biological activities

    NASA Astrophysics Data System (ADS)

    Belal, Arafa A. M.; Zayed, M. A.; El-Desawy, M.; Rakha, Sh. M. A. H.

    2015-03-01

    Three Schiff's bases AI (2(1-hydrazonoethyl)phenol), AII (2, 4-dibromo 6-(hydrazonomethyl)phenol) and AIII (2(hydrazonomethyl)phenol) were prepared as new hydrazone compounds via condensation reactions with molar ratio (1:1) of reactants. Firstly by reaction of 2-hydroxy acetophenone solution and hydrazine hydrate; it gives AI. Secondly condensation between 3,5-dibromo-salicylaldehyde and hydrazine hydrate gives AII. Thirdly condensation between salicylaldehyde and hydrazine hydrate gives AIII. The structures of AI-AIII were characterized by elemental analysis (EA), mass (MS), FT-IR and 1H NMR spectra, and thermal analyses (TG, DTG, and DTA). The activation thermodynamic parameters, such as, ΔE∗, ΔH∗, ΔS∗ and ΔG∗ were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bond responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their anti-microbial potential.

  8. Structure investigation of three hydrazones Schiff's bases by spectroscopic, thermal and molecular orbital calculations and their biological activities.

    PubMed

    Belal, Arafa A M; Zayed, M A; El-Desawy, M; Rakha, Sh M A H

    2015-03-01

    Three Schiff's bases AI (2(1-hydrazonoethyl)phenol), AII (2, 4-dibromo 6-(hydrazonomethyl)phenol) and AIII (2(hydrazonomethyl)phenol) were prepared as new hydrazone compounds via condensation reactions with molar ratio (1:1) of reactants. Firstly by reaction of 2-hydroxy acetophenone solution and hydrazine hydrate; it gives AI. Secondly condensation between 3,5-dibromo-salicylaldehyde and hydrazine hydrate gives AII. Thirdly condensation between salicylaldehyde and hydrazine hydrate gives AIII. The structures of AI-AIII were characterized by elemental analysis (EA), mass (MS), FT-IR and (1)H NMR spectra, and thermal analyses (TG, DTG, and DTA). The activation thermodynamic parameters, such as, ΔE(∗), ΔH(∗), ΔS(∗) and ΔG(∗) were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bond responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their anti-microbial potential. PMID:25437844

  9. Hemodynamics in coronary arteries with overlapping stents.

    PubMed

    Rikhtegar, Farhad; Wyss, Christophe; Stok, Kathryn S; Poulikakos, Dimos; Müller, Ralph; Kurtcuoglu, Vartan

    2014-01-22

    Coronary artery stenosis is commonly treated by stent placement via percutaneous intervention, at times requiring multiple stents that may overlap. Stent overlap is associated with increased risk of adverse clinical outcome. While changes in local blood flow are suspected to play a role therein, hemodynamics in arteries with overlapping stents remain poorly understood. In this study we analyzed six cases of partially overlapping stents, placed ex vivo in porcine left coronary arteries and compared them to five cases with two non-overlapping stents. The stented vessel geometries were obtained by micro-computed tomography of corrosion casts. Flow and shear stress distribution were calculated using computational fluid dynamics. We observed a significant increase in the relative area exposed to low wall shear stress (WSS<0.5 Pa) in the overlapping stent segments compared both to areas without overlap in the same samples, as well as to non-overlapping stents. We further observed that the configuration of the overlapping stent struts relative to each other influenced the size of the low WSS area: positioning of the struts in the same axial location led to larger areas of low WSS compared to alternating struts. Our results indicate that the overlap geometry is by itself sufficient to cause unfavorable flow conditions that may worsen clinical outcome. While stent overlap cannot always be avoided, improved deployment strategies or stent designs could reduce the low WSS burden. PMID:24275438

  10. Overlapping Structures in Sensory-Motor Mappings

    PubMed Central

    Earland, Kevin; Lee, Mark; Shaw, Patricia; Law, James

    2014-01-01

    This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots. PMID:24392118

  11. Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid

    NASA Astrophysics Data System (ADS)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    2014-11-01

    The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  12. A Localized Molecular Orbital Study of the Halogen Substitution Effect on (103)Rh NMR Shielding in [Cp*RhX2]2, Where X = Cl, Br, or I.

    PubMed

    Mirzaeva, Irina V; Mainichev, Dmitry A; Kozlova, Svetlana G

    2016-03-24

    (103)Rh NMR parameters and the bonding structure of three complexes of [Cp*RhX2]2, where X = Cl, Br, or I, have been studied with the help of natural bond orbitals (NBOs) and natural localized molecular orbitals (NLMOs). The complexes of [Cp*RhX2]2, where X = Cl, Br, or I, have similar bonding structures, with the major difference being in the degree of covalency of the Rh-X bonds. The decomposition of (103)Rh NMR shielding into diamagnetic, paramagnetic, and spin-orbit terms shows that normal halogen dependence (NHD) of the (103)Rh NMR shift is defined mostly by the paramagnetic term, with the spin-orbit term being significantly smaller. The decomposition of (103)Rh shielding into spin-free NBO and NLMO contributions shows that (103)Rh shielding is dominated by Rh d-orbital deshielding contributions. We explain the NHD of the (103)Rh NMR shift with the increase in the energies of the virtual antibonding Rh-X orbitals along the X = Cl, Br, and I series. PMID:26927955

  13. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method.

    PubMed

    Nagata, Takeshi; Fedorov, Dmitri G; Li, Hui; Kitaura, Kazuo

    2012-05-28

    A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order Møller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 Å for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed. PMID:22667545

  14. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2(+)) Cation.

    PubMed

    Dietrick, Scott M; Iyengar, Srinivasan S

    2012-12-11

    A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted. PMID:26593181

  15. Structure, electronic and magnetic properties of hexagonal boron nitride sheets doped by 5d transition metal atoms: First-principles calculations and molecular orbital analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Zhaofu; Geng, Zhaohui; Cai, Danyun; Pan, Tongxi; Chen, Yixin; Dong, Liyuan; Zhou, Tiege

    2015-01-01

    A first-principles calculation based on density functional theory is carried out to reveal the geometry, electronic structures and magnetic properties of hexagonal boron nitride sheets (h-BNSs) doped by 5d transitional mental atoms (Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au and Hg) at boron-site (B5d) and nitrogen-site (N5d). Results of pure h-BNS, h-BNS with B vacancy (VB) and N vacancy (VN) are also given for comparison. It is shown that all the h-BNSs doped with 5d atoms possess a C3v local symmetry except for NLu and NHg which have a clear deviation. For the same 5d dopant, the binding energy of B5d is larger than that of N5d, which indicates the substitution of a 5d atom for B is preferred. The total densities of states are presented, where impurity energy levels exist. Besides, the total magnetic moments (TMMs) change regularly with the increment of the 5d atomic number. Theoretical analyses by molecular orbital under C3v symmetry explain the impurity energy levels and TMMs.

  16. High-T c superconductivity in potassium-doped fullerene, K xC 60, via coupled C 60 (pπ) cluster molecular orbitals and dynamic Jahn-Teller coupling

    NASA Astrophysics Data System (ADS)

    Johnson, K. H.; McHenry, M. E.; Clougherty, D. P.

    1991-11-01

    Recently observed superconductivity at 18 K in potassium-doped fullerene, K xC 60, may be due to Cooper pairing of partially occupied icosahedral C 60 cluster t 1u (pπ) molecular orbitals, induced by cooperative dynamic Jahn-Teller coupling of these orbitals to “soft-mode” vibrations of the C 60 molecules, leading to a BCS-like mechanism. Predicted are a nonvanishing isotope effect and Tc increasing to 30 K or more with optimization of doping, and significant effects with pressure.

  17. Polynomials for evaluation of two-center overlap integrals

    NASA Astrophysics Data System (ADS)

    Petrov, Dimitar

    2016-05-01

    Expressions of products AkBk, where Ak and Bk are incomplete gamma functions, are given for evaluation of two-center overlap integrals (TCOIs) over unnormalized Slater-type orbitals (STOs). The polynomials of AkBk have been derived after the method proposed by Lofthus and pertain to two-center bonds of σ, π, δ, and φ axial symmetries. The functions of AkBk have been arranged in pairs of s, p, d, and f STOs with principal quantum numbers between 1 and 5. The contributions of these functions to various TCOIs have been evaluated and discussed. The formulae are applicable as input matrices for computations of TCOIs.

  18. Geostationary orbit determination using SATRE

    NASA Astrophysics Data System (ADS)

    Lei, Hui; Li, ZhiGang; Yang, XuHai; Wu, WenJun; Cheng, Xuan; Yang, Ying; Feng, ChuGang

    2011-09-01

    A new strategy of precise orbit determination (POD) for GEO (Geostationary Earth Orbit) satellite using SATRE (SAtellite Time and Ranging Equipment) is presented. Two observation modes are proposed and different channels of the same instruments are used to construct different observation modes, one mode receiving time signals from their own station and the other mode receiving time signals from each other for two stations called pairs of combined observations. Using data from such a tracking network in China, the results for both modes are compared. The precise orbit determination for the Sino-1 satellite using the data from 6 June 2005 to 13 June 2005 has been carried out in this work. The RMS (Root-Mean-Square) of observing residuals for 3-day solutions with the former mode is better than 9.1 cm. The RMS of observing residuals for 3-day solutions with the latter mode is better than 4.8 cm, much better than the former mode. Orbital overlapping (3-day orbit solution with 1-day orbit overlap) tests show that the RMS of the orbit difference for the former mode is 0.16 m in the radial direction, 0.53 m in the along-track direction, 0.97 m in the cross-track direction and 1.12 m in the 3-dimension position and the RMS of the orbit difference for the latter mode is 0.36 m in the radial direction, 0.89 m in the along-track direction, 1.18 m in the cross-track direction and 1.52 m in the 3-dimension position, almost the same as the former mode. All the experiments indicate that a meter-level accuracy of orbit determination for geostationary satellite is achievable.

  19. Solving Partial Differential Equations on Overlapping Grids

    SciTech Connect

    Henshaw, W D

    2008-09-22

    We discuss the solution of partial differential equations (PDEs) on overlapping grids. This is a powerful technique for efficiently solving problems in complex, possibly moving, geometry. An overlapping grid consists of a set of structured grids that overlap and cover the computational domain. By allowing the grids to overlap, grids for complex geometries can be more easily constructed. The overlapping grid approach can also be used to remove coordinate singularities by, for example, covering a sphere with two or more patches. We describe the application of the overlapping grid approach to a variety of different problems. These include the solution of incompressible fluid flows with moving and deforming geometry, the solution of high-speed compressible reactive flow with rigid bodies using adaptive mesh refinement (AMR), and the solution of the time-domain Maxwell's equations of electromagnetism.

  20. [Orbital inflammation].

    PubMed

    Mouriaux, F; Coffin-Pichonnet, S; Robert, P-Y; Abad, S; Martin-Silva, N

    2014-12-01

    Orbital inflammation is a generic term encompassing inflammatory pathologies affecting all structures within the orbit : anterior (involvement up to the posterior aspect of the globe), diffuse (involvement of intra- and/or extraconal fat), apical (involvement of the posterior orbit), myositis (involvement of only the extraocular muscles), dacryoadenitis (involvement of the lacrimal gland). We distinguish between specific inflammation and non-specific inflammation, commonly referred to as idiopathic inflammation. Specific orbital inflammation corresponds to a secondary localization of a "generalized" disease (systemic or auto-immune). Idiopathic orbital inflammation corresponds to uniquely orbital inflammation without generalized disease, and thus an unknown etiology. At the top of the differential diagnosis for specific or idiopathic orbital inflammation are malignant tumors, represented most commonly in the adult by lympho-proliferative syndromes and metastases. Treatment of specific orbital inflammation begins with treatment of the underlying disease. For idiopathic orbital inflammation, treatment (most often corticosteroids) is indicated above all in cases of visual loss due to optic neuropathy, in the presence of pain or oculomotor palsy. PMID:25455557

  1. Enzymatic assembly of overlapping DNA fragments.

    PubMed

    Gibson, Daniel G

    2011-01-01

    Three methods for assembling multiple, overlapping DNA molecules are described. Each method shares the same basic approach: (i) an exonuclease removes nucleotides from the ends of double-stranded (ds) DNA molecules, exposing complementary single-stranded (ss) DNA overhangs that are specifically annealed; (ii) the ssDNA gaps of the joined molecules are filled in by DNA polymerase, and the nicks are covalently sealed by DNA ligase. The first method employs the 3'-exonuclease activity of T4 DNA polymerase (T4 pol), Taq DNA polymerase (Taq pol), and Taq DNA ligase (Taq lig) in a two-step thermocycled reaction. The second method uses 3'-exonuclease III (ExoIII), antibody-bound Taq pol, and Taq lig in a one-step thermocycled reaction. The third method employs 5'-T5 exonuclease, Phusion® DNA polymerase, and Taq lig in a one-step isothermal reaction and can be used to assemble both ssDNA and dsDNA. These assembly methods can be used to seamlessly construct synthetic and natural genes, genetic pathways, and entire genomes and could be very useful for molecular engineering tools. PMID:21601685

  2. Overlap in Facebook Profiles Reflects Relationship Closeness.

    PubMed

    Castañeda, Araceli M; Wendel, Markie L; Crockett, Erin E

    2015-01-01

    We assessed the association between self-reported Inclusion of Other in the Self (IOS) and Facebook overlap. Ninety-two participants completed online measures of IOS and investment model constructs. Researchers then recorded Facebook data from participants' profile pages. Results from multilevel models revealed that IOS predicted Facebook overlap. Furthermore, Facebook overlap was associated with commitment and investment in ways comparable to self-reported IOS. These findings suggest that overlap in Facebook profiles can be used to measure relationship closeness. PMID:25635533

  3. Experimental investigation of the EPR parameters and molecular orbital bonding coefficients for VO2+ ion in NaH2PO4·2H2O single crystals

    NASA Astrophysics Data System (ADS)

    Kalfaoğlu, Emel; Karabulut, Bünyamin

    2016-09-01

    Electron paramagnetic resonance (EPR) spectra of VO2+ ions in NaH2PO4·2H2O single crystal have been studied. The spin-Hamiltonian parameters and molecular orbital bonding coefficients were calculated. The angular variation of the EPR spectra shows two different VO2+ complexes. These are located in different chemical environment and each environment contains four magnetically inequivalent VO2+ sites. The crystal field around VO2+ ion is approximately axially symmetric since a strong V=O bond distorts the crystal lattice. Spin Hamiltonian parameters and molecular orbital bonding coefficients were calculated from the EPR data and the nature of bonding in the complex was discussed together.

  4. The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n-butane conformation and SN2 reaction: RCl+Cl -

    NASA Astrophysics Data System (ADS)

    Humbel, Stéphane; Sieber, Stefan; Morokuma, Keiji

    1996-08-01

    A new theoretical method, called IMOMO (integrated MO (molecular orbital)+MO), for integration of two different levels of MO approximation is presented. Only the active or more difficult part of a molecule is treated at a higher level of approximation and the rest of the molecule at a lower level of approximation. The integrated total energy and energy derivatives are defined from three different calculations, and the structure of transition state as well as the equilibrium structure can be optimized using the integrated energy. Any combination of any molecular orbital approximations (ab initio, density functional to semi-empirical) can be used. Test calculations in the IMOMO method have been performed and compared with normal MO calculations for the conformation energy of ethane and n-butane and the SN2 reaction of ethyl, propyl, isobutyl, and neopentyl chloride with Cl-. The results indicate that these methods have a tremendous potential for theoretical study of larger molecules, in particular for transition states.

  5. Ab initio molecular orbital calculations of DNA radical ions. 5. Scaling of calculated electron affinities and ionization potentials to experimental values

    SciTech Connect

    Sevilla, M.D.; Colson, A.O. ); Besler, B. )

    1995-01-19

    Ab initio molecular orbital calculations of the electron affinities (EAs) and ionization potentials (IPs) of the DNA bases are presented in this work. Comparisons of calculated and experimental values are made for a series of compounds of size and/or structure similar to the DNA bases. Excellent correlations between calculated and experimental values are found for both Koopmans EAs at the 6-31G[sup *] and D95v levels and calculated vertical EAs of the model compounds. Several basis sets are considered: 6-31G[sup *], 6-31+G(d), and D95v. Calculations at 6-31G[sup *] and 6-31+G(d) using both ROHF and ROMP2 theories show a consistent difference between calculated vertical and adiabatic EAs. This allows for a good estimate of DNA base adiabatic EAs. i.e., -0.7, -0.3, 0.2, 0.3, and 0.4 eV; from the vertical EAs -1.23, -0.74, -0.40, -0.32, and -0.19 eV for G, A, C, T, and U respectively. While EAs must be scaled, we find that Koopmans IPs calculated at the simple 3-21G level predict vertical IPs of the DNA bases with only a 0.15 eV average absolute deviation from the experimentally reported values and calculations at MP2/6-31+G(d)//6-31G[sup *] for the adiabatic ionization potentials of the DNA bases are all within 0.1 eV of experiment. 41 refs., 2 figs., 5 tabs.

  6. Crystal Field Theory and the Angular Overlap Model Applied to Hydrides of Main Group Elements.

    ERIC Educational Resources Information Center

    Moore, E. A.

    1990-01-01

    Described is how crystal field theory and the angular overlap model can be applied to very simple molecules which can then be used to introduce such concepts as bonding orbitals, MO diagrams, and Walsh diagrams. The main-group compounds are used as examples and a switch to the transition metal complexes. (KR)

  7. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Prohibited overlap. 73.509 Section 73.509 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Noncommercial Educational FM Broadcast Stations § 73.509 Prohibited overlap. (a) An application for a new or modified NCE-FM station...

  8. Restoration and reconstruction from overlapping images

    NASA Technical Reports Server (NTRS)

    Reichenbach, Stephen E.; Kaiser, Daniel J.; Hanson, Andrew L.; Li, Jing

    1997-01-01

    This paper describes a technique for restoring and reconstructing a scene from overlapping images. In situations where there are multiple, overlapping images of the same scene, it may be desirable to create a single image that most closely approximates the scene, based on all of the data in the available images. For example, successive swaths acquired by NASA's planned Moderate Imaging Spectrometer (MODIS) will overlap, particularly at wide scan angles, creating a severe visual artifact in the output image. Resampling the overlapping swaths to produce a more accurate image on a uniform grid requires restoration and reconstruction. The one-pass restoration and reconstruction technique developed in this paper yields mean-square-optimal resampling, based on a comprehensive end-to-end system model that accounts for image overlap, and subject to user-defined and data-availability constraints on the spatial support of the filter.

  9. Neural overlap in processing music and speech

    PubMed Central

    Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L.

    2015-01-01

    Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing. PMID:25646513

  10. Neural overlap in processing music and speech.

    PubMed

    Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L

    2015-03-19

    Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing. PMID:25646513

  11. Motor Protein Accumulation on Antiparallel Microtubule Overlaps

    NASA Astrophysics Data System (ADS)

    Kuan, Hui-Shun; Betterton, Meredith D.

    2016-05-01

    Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying the motion of Xklp1 motors on reconstituted antiparallel microtubule overlaps demonstrated that motors recruited to the overlap walk toward the plus end of individual microtubules and frequently switch between filaments. We study a model of this system that couples the totally asymmetric simple exclusion process (TASEP) for motor motion with switches between antiparallel filaments and binding kinetics. We determine steady-state motor density profiles for fixed-length overlaps using exact and approximate solutions of the continuum differential equations and compare to kinetic Monte Carlo simulations. Overlap motor density profiles and motor trajectories resemble experimental measurements. The phase diagram of the model is similar to the single-filament case for low switching rate, while for high switching rate we find a new low density-high density-low density-high density phase. The overlap center region, far from the overlap ends, has a constant motor density as one would naively expect. However, rather than following a simple binding equilibrium, the center motor density depends on total overlap length, motor speed, and motor switching rate. The size of the crowded boundary layer near the overlap ends is also dependent on the overlap length and switching rate in addition to the motor speed and bulk concentration. The antiparallel microtubule overlap geometry may offer a previously unrecognized mechanism for biological regulation of protein concentration and consequent activity.

  12. Motor Protein Accumulation on Antiparallel Microtubule Overlaps.

    PubMed

    Kuan, Hui-Shun; Betterton, Meredith D

    2016-05-10

    Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying the motion of Xklp1 motors on reconstituted antiparallel microtubule overlaps demonstrated that motors recruited to the overlap walk toward the plus end of individual microtubules and frequently switch between filaments. We study a model of this system that couples the totally asymmetric simple exclusion process for motor motion with switches between antiparallel filaments and binding kinetics. We determine steady-state motor density profiles for fixed-length overlaps using exact and approximate solutions of the continuum differential equations and compare to kinetic Monte Carlo simulations. Overlap motor density profiles and motor trajectories resemble experimental measurements. The phase diagram of the model is similar to the single-filament case for low switching rate, while for high switching rate we find a new (to our knowledge) low density-high density-low density-high density phase. The overlap center region, far from the overlap ends, has a constant motor density as one would naïvely expect. However, rather than following a simple binding equilibrium, the center motor density depends on total overlap length, motor speed, and motor switching rate. The size of the crowded boundary layer near the overlap ends is also dependent on the overlap length and switching rate in addition to the motor speed and bulk concentration. The antiparallel microtubule overlap geometry may offer a previously unrecognized mechanism for biological regulation of protein concentration and consequent activity. PMID:27166811

  13. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

    SciTech Connect

    Habasaki, Junko; Ngai, K. L.

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO{sub 3}), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, T{sub B} (or T{sub c}) and the glass transition temperature T{sub g}, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, N{sub B}, within the first minimum of the pair correlation function, g(r){sub min}, increases. On crossing T{sub B} (>T{sub g}), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at T{sub g}. The glass transition temperature, T{sub g}, is characterized by the saturation of the total number of “bonds,” N{sub B} and the corresponding decrease in degree of freedom, F = [(3N − 6) − N{sub B}], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at T{sub g}, the number of bonds shows a remarkable change at around T{sub B}. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, f{sub g}, of each coordination polyhedron, which can be defined by f{sub g} = [(3N{sub V} − 6) − N{sub b}]. Here, 3N{sub v} is the degree of freedom of N{sub V} vertices of the polyhedron, and N{sub b} is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion

  14. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

    NASA Astrophysics Data System (ADS)

    Habasaki, Junko; Ngai, K. L.

    2015-04-01

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO3), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, TB (or Tc) and the glass transition temperature Tg, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, NB, within the first minimum of the pair correlation function, g(r)min, increases. On crossing TB (>Tg), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at Tg. The glass transition temperature, Tg, is characterized by the saturation of the total number of "bonds," NB and the corresponding decrease in degree of freedom, F = [(3N - 6) - NB], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at Tg, the number of bonds shows a remarkable change at around TB. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, fg, of each coordination polyhedron, which can be defined by fg = [(3NV - 6) - Nb]. Here, 3Nv is the degree of freedom of NV vertices of the polyhedron, and Nb is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion in the cage is found to be correlated with the fluctuation of Nb of cation-cation (or anion-anion) pairs in the polyhedron, although the

  15. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations--Existence of infinite overlapping networks in a fragile ionic liquid.

    PubMed

    Habasaki, Junko; Ngai, K L

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO3), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, TB (or Tc) and the glass transition temperature Tg, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, NB, within the first minimum of the pair correlation function, g(r)min, increases. On crossing TB (>Tg), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at Tg. The glass transition temperature, Tg, is characterized by the saturation of the total number of "bonds," NB and the corresponding decrease in degree of freedom, F = [(3N - 6) - NB], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at Tg, the number of bonds shows a remarkable change at around TB. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, fg, of each coordination polyhedron, which can be defined by fg = [(3NV - 6) - Nb]. Here, 3Nv is the degree of freedom of NV vertices of the polyhedron, and Nb is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion in the cage is found to be correlated with the fluctuation of Nb of cation-cation (or anion-anion) pairs in the polyhedron, although the

  16. Evaluation of multicenter one-electron integrals of noninteger u screened Coulomb type potentials and their derivatives over noninteger n Slater orbitals.

    PubMed

    Guseinov, I I; Mamedov, B A

    2004-07-22

    Multicenter integrals over noninteger n Slater type orbitals with integer and noninteger values of indices u of screened Coulomb type potentials, f(u)(eta,r)=r(u-1)e(-etar), and their first and second derivatives with respect to Cartesian coordinates of the nuclei of a molecule are described. Using complete orthonormal sets of Psi(alpha) exponential type orbitals and rotation transformation of two-center overlap integrals, these integrals are expressed through the noncentral potential functions depending on the molecular auxiliary functions A(k) and B(k). The series expansion formulas derived for molecular integrals of screened Coulomb potentials and their derivatives are especially useful for the computation of multicenter electronic attraction, electric field, and electric field gradient integrals. The convergence of series is tested for arbitrary values of parameters of potentials and orbitals. PMID:15260714

  17. Orbiter's Skeleton

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The structure of NASA's Mars Reconnaissance Orbiter spacecraft is constructed from composite panels of carbon layers over aluminum honeycomb, lightweight yet strong. This forms a basic structure or skeleton on which the instruments, electronics, propulsion and power systems can be mounted. The propellant tank is contained in the center of the orbiter's structure. This photo was taken at Lockheed Martin Space Systems, Denver, during construction of the spacecraft.

  18. Ab initio base fragment molecular orbital studies of influenza viral hemagglutinin HA1 full-domains in complex with sialoside receptors

    PubMed Central

    Sawada, Toshihiko; Hashimoto, Tomohiro; Tokiwa, Hiroaki; Suzuki, Tohru; Nakano, Hirofumi; Ishida, Hideharu; Kiso, Makoto; Suzuki, Yasuo

    2009-01-01

    Mutations in avian influenza A viral hemagglutinin HA1 domain may alter the binding specificity of HA for α-sialosaccharide receptors, shifting the virus's host range from birds to humans. The amino acid mutations can occur at the sialoside binding site, as well as the antigenic site, far from the binding site. Thus, a theoretical study involving the in silico prediction of HA-sialosaccharide binding may require quantum chemical analysis of HA1 full domain complexed with sialosides, balancing a computational cost with model size of HA1-sialoside complex. In addition, there is no insight to relationship between the model size of HA1-sialoside complex and its binding energy. In this study, H3 subtype HA1 full domains complexed with avian- and human-type Neu5Acα(2-3 and 2-6)Gal receptor analogs was investigated by ab initio based fragment molecular orbital (FMO) method at the level of second-order Møller–Plesset perturbation (MP2)/6-31G. Using this approach, we found avian H3 HA1 to bind to avian α2-3 receptor more strongly than to human α2-6 receptor in gas phase, by a value of 15.3-16.5 kcal/mol. This binding benefit was larger than that in the small model complex. Analysis of the interfragment interaction energies (IFIEs) between Neu5Ac-Gal receptor and amino acid residues on the full domain of H3 HA1 also confirmed the higher avian H3-avian α2-3 binding specificity. It was particularly important to evaluate the IFIEs of amino acid residues in a 13Å radius around Neu5Ac-Gal to take account of long-range electrostatic interactions in the larger HA1-sialoside complex model. These results suggest suitable size of HA1-sialoside complex is significant to estimate HA1-sialoside binding energy and IFIE analysis with FMO method. PMID:19565017

  19. Molecular orbital calculation and spectroscopic study of the photochemical generation of Bis(2,2{prime}-bipyridine)rhodium(I) from Bis(2,2{prime}-bipyridine)(oxalato)rhodium(III)

    SciTech Connect

    Shinozaki, Kazuteru; Takahashi, Naoto

    1996-06-19

    A planar complex, [Rh(bpy){sub 2}]{sup +} (bpy=2,2{sup {prime}}-bipyridine), was obtained from [Rh(ox)(bpy){sub 2}]{sup +} (ox=oxalato) by photoirradiation. A rate constant k for the photoreaction was evaluated as 1 x 10{sup 8} s{sup {minus}1} in simple first-order kinetics, whereas a ligand dissociation, a reorganization of the coordinated bpy, and a two-electron transfer were involved in the reaction. The process of the Rh(I) complex generation was investigated in terms of a discrete variational(DV)-X{alpha} molecular orbital calculation on [Rh(ox)(HN=CHCH=NH){sub 2}]{sup +} instead of [Rh(ox)(bpy){sub 2}]{sup +}. From the calculation, using the transition-state method, it was predicted that a transition of the ox {pi}{sup *} orbital to the metal 4d{sub z}{sup 2} orbital caused the ligand dissociation and the reorganization of the coordinated bpy occurred in the ox {pi} to Rh 4d{sub x{sup 2}-y{sup 2}} excited state stabilized by the ox elimination. Upon release of the ligand and a change from octahedral to square-planar geometry, the electron density on the metal increased and the Rh 4d orbital acquired a d{sup 8} electronic configuration.

  20. Charge Redistribution and Transport in Molecular Contacts.

    PubMed

    Corso, Martina; Ondráček, Martin; Lotze, Christian; Hapala, Prokop; Franke, Katharina J; Jelínek, Pavel; Pascual, J Ignacio

    2015-09-25

    The forces between two single molecules brought into contact, and their connection with charge transport through the molecular junction, are studied here using non contact AFM, STM, and density functional theory simulations. A carbon monoxide molecule approaching an acetylene molecule (C_{2}H_{2}) initially feels weak attractive electrostatic forces, partly arising from charge reorganization in the presence of molecular . We find that the molecular contact is chemically passive, and protects the electron tunneling barrier from collapsing, even in the limit of repulsive forces. However, we find subtle conductance and force variations at different contacting sites along the C_{2}H_{2} molecule attributed to a weak overlap of their respective frontier orbitals. PMID:26451568

  1. Correlated edge overlaps in multiplex networks.

    PubMed

    Baxter, Gareth J; Bianconi, Ginestra; da Costa, Rui A; Dorogovtsev, Sergey N; Mendes, José F F

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions. PMID:27575144

  2. Correlated edge overlaps in multiplex networks

    NASA Astrophysics Data System (ADS)

    Baxter, Gareth J.; Bianconi, Ginestra; da Costa, Rui A.; Dorogovtsev, Sergey N.; Mendes, José F. F.

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions.

  3. 4,5-Dicyano-3,6-diethylbenzo-1,2-diselenete, a highly stable 1,2-diselenete: its preparation, structural characterization, calculated molecular orbitals, and complexation with tetrakis(triphenylphosphine)palladium.

    PubMed

    Kimura, Takeshi; Nakahodo, Tsukasa; Fujihara, Hisashi; Suzuki, Eiichi

    2014-05-01

    The first isolable benzo-1,2-diselenete, 4,5-dicyano-3,6-diethylbenzo-1,2-diselenete (4), was prepared by the reaction of 4,5-(o-xylylenediseleno)-3,6-diethylphthalonitrile (3) with aluminum chloride in toluene. X-ray crystallographic analysis demonstrated that 4 contains a trapezoidal diselenide ring rather than a benzo-1,2-diselenone structure. In crystal form, 4 undergoes self-assembly and generates structures based on layered molecular sheets since the unit cell contains only one molecule. While the cyclic voltammogram of 4 exhibited only one irreversible peak (Ep = 1.59 V) during oxidation and two quasireversible couples during reduction, three peaks were observed in the differential pulse voltammogram of the reduction couples (E1/2 = -1.19, -0.75, and -0.69 V). Although a THF solution of 4 in the presence of sodium metal was EPR silent, various signals were readily observed in its (1)H, (13)C, and (77)Se NMR spectra. Molecular orbital calculations for 4 demonstrated that the HOMO orbital is primarily localized at the two selenium atoms and four of the benzene carbon atoms while the LUMO orbital is situated solely on the diselenete ring. It appears that the HOMO and LUMO orbitals of 4 receive significant stabilization from the nitrile groups compared to the level of stabilization in the unsubstituted benzo-1,2-diselenete (BDS). The reaction of 4 with tetrakis(triphenylphosphine)palladium in benzene was found to produce a dinuclear palladium complex (8), and the structure of this complex was determined by X-ray crystallographic analysis. The central four membered ring of 8 consists of the Pd1, Se2, Pd2, and Se3 atoms and is not planar but rather adopts a folded arrangement. PMID:24724937

  4. Orbital cellulitis.

    PubMed Central

    Martin-Hirsch, D P; Habashi, S; Hinton, A H; Kotecha, B

    1992-01-01

    Orbital cellulitis is an emergency. It may cause blindness and progress to life-threatening sequelae such as brain abscess, meningitis and cavernous sinus thrombosis. Successful management is dependent upon urgent referral and immediate treatment. Although isolated eyelid erythema and swelling usually indicate primary infection anterior to the orbital septum, they may also be the first signs of an underlying frontal or ethmoidal sinusitis. The condition always requires emergency referral to both an ophthalmologist and otorhinolaryngologist. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:1388488

  5. Orbital Debris

    NASA Technical Reports Server (NTRS)

    Kessler, D. J. (Compiler); Su, S. Y. (Compiler)

    1985-01-01

    Earth orbital debris issues and recommended future activities are discussed. The workshop addressed the areas of environment definition, hazards to spacecraft, and space object management. It concluded that orbital debris is a potential problem for future space operations. However, before recommending any major efforts to control the environment, more data are required. The most significant required data are on the population of debris smaller than 4 cm in diameter. New damage criteria are also required. When these data are obtained, they can be combined with hypervelocity data to evaluate the hazards to future spacecraft. After these hazards are understood, then techniques to control the environment can be evaluated.

  6. Vanishing rainbows near orbiting and the energy dependence of rainbow scattering - Relation to properties of the potential. [molecular beam scattering cross sections

    NASA Technical Reports Server (NTRS)

    Greene, E. F.; Hall, R. B.; Mason, E. A.

    1975-01-01

    The energy threshold behavior of elastic rainbow scattering near the transition to orbiting is derived. Analysis of the energy dependence of the rainbow angle shows that the full range from high energies down to orbiting can be fitted with two parameters. Thus, measurements of the rainbow angle can give essentially only two pieces of information about the potential. For potentials of common shapes, such measurements are sensitive to regions of the potential just beyond the minimum and give information about the shape of the potential in this range. However, neither a minimum nor a point of inflection in the potential is necessary for rainbow scattering.

  7. Numerical evaluation of two-center integrals over Slater type orbitals

    NASA Astrophysics Data System (ADS)

    Kurt, S. A.; Yükçü, N.

    2016-03-01

    Slater Type Orbitals (STOs) which one of the types of exponential type orbitals (ETOs) are used usually as basis functions in the multicenter molecular integrals to better understand physical and chemical properties of matter. In this work, we develop algorithms for two-center overlap and two-center two-electron hybrid and Coulomb integrals which are calculated with help of translation method for STOs and some auxiliary functions by V. Magnasco's group. We use Mathematica programming language to produce algorithms for these calculations. Numerical results for some quantum numbers are presented in the tables. Consequently, we compare our obtained numerical results with the other known literature results and other details of evaluation method are discussed.

  8. H-atom ionization by elliptically polarized microwave fields: The overlap criterion

    SciTech Connect

    Sacha, K.; Zakrzewski, J.

    1997-07-01

    The threshold for H-atom ionization by elliptically polarized microwave fields is discussed within the classical-mechanics framework using the Chirikov overlap criterion. It is shown that the trends observed in the recent experiment [M. R. W. Bellermann {ital et al.} Phys. Rev. Lett. {bold 76}, 892 (1996)] are qualitatively reproduced by the theory; the origin of the remaining discrepancy is discussed. Increased stability of some orbits with respect to the perturbation due to the elliptically polarized microwaves has been related to vanishing widths of the corresponding resonance islands. Analytic Chirikov overlap prediction is compared with results of numerical simulations. {copyright} {ital 1997} {ital The American Physical Society}

  9. Automatic segmentation of overlapping and touching chromosomes

    NASA Astrophysics Data System (ADS)

    Yuan, Zhiqiang; Chen, Xiaohua; Zhang, Renli; Yu, Chang

    2001-09-01

    This paper describes a technique to segment overlapping and touching chromosomes of human metaphase cells. Automated chromosome classification has been an important pattern recognition problem for decades, numerous attempts were made in the past to characterize chromosome band patterns. But successful separation between touching and overlapping chromosomes is vital for correct classification. Since chromosomes are non-rigid objects, common methods for separation between touching chromosomes are not usable. We proposed a method using shape concave and convex information, topology analysis information, and band pale paths for segmentation of touching and overlapping chromosomes. To detect shape concave and convex information, we should first pre-segment the chromosomes and get the edge of overlapping and touching chromosomes. After filtering the original image using edge-preserving filter, we adopt the Otsu's segmentation method and extract the boundary of chromosomes. Hence the boundary can be used for segment the overlapping and touching chromosomes by detecting the concave and convex information based on boundary information. Most of the traditional boundary-based algorithms detect corners based on two steps: the first step is to acquire the smoothed version of curvature at every point along the contour, and the second step is to detect the positions where curvature maximal occur and threshold the curvature as corner points. Recently wavelet transform has been adopted into corner detection algorithms. Since the metaphase overlapping chromosomes has multi-scale corners, we adopt a multi-scale corner detection method based on Hua's method for corner detection. For touching chromosomes, it is convenient to split them using pale paths. Starting from concave corner points, a search algorithm is represented. The searching algorithm traces three pixels into the object in the direction of the normal vector in order to avoid stopping at the initial boundary until it

  10. The role of orbital dynamics and cloud-cloud collisions in the formation of giant molecular clouds in global spiral structures

    NASA Technical Reports Server (NTRS)

    Roberts, William W., Jr.; Stewart, Glen R.

    1987-01-01

    The role of orbit crowding and cloud-cloud collisions in the formation of GMCs and their organization in global spiral structure is investigated. Both N-body simulations of the cloud system and a detailed analysis of individual particle orbits are used to develop a conceptual understanding of how individual clouds participate in the collective density response. Detailed comparisons are made between a representative cloud-particle simulation in which the cloud particles collide inelastically with one another and give birth to and subsequently interact with young star associations and stripped down simulations in which the cloud particles are allowed to follow ballistic orbits in the absence of cloud-cloud collisions or any star formation processes. Orbit crowding is then related to the behavior of individual particle trajectories in the galactic potential field. The conceptual picture of how GMCs are formed in the clumpy ISMs of spiral galaxies is formulated, and the results are compared in detail with those published by other authors.

  11. Comparisons of Satellite-Deduced Overlapping Cloud Properties and CALIPSO CloudSat Data

    NASA Technical Reports Server (NTRS)

    Chang, Fu-Lung; Minnis, Patrick; Lin, Bing; Sun-Mack, Sunny

    2010-01-01

    Introduction to the overlapped cloud properties derived from polar-orbiting (MODIS) and geostationary (GOES-12, -13, Meteosat-8, -9, etc.) meteorological satellites, which are produced at the NASA Langley Research Center (LaRC) cloud research & development team (NASA lead scientist: Dr. Patrick Minnis). Comparison of the LaRC CERES MODIS Edition-3 overlapped cloud properties to the CALIPSO and the CloudSat active sensing data. High clouds and overlapped clouds occur frequently as deduced by CALIPSO (44 & 25%), CloudSat (25 & 4%), and MODIS (37 & 6%). Large fractions of optically-thin cirrus and overlapped clouds are deduced from CALIPSO, but much smaller fractions are from CloudSat and MODIS. For overlapped clouds, the averaged upper-layer CTHs are about 12.8 (CALIPSO), 10.9 (CloudSat) and 10 km (MODIS), and the averaged lower-layer CTHs are about 3.6 (CALIPSO), 3.2 (CloudSat) and 3.9 km (MODIS). Based on comparisons of upper and lower-layer cloud properties as deduced from the MODIS, CALIPSO and CloudSat data, more enhanced passive satellite methods for retrieving thin cirrus and overlapped cloud properties are needed and are under development.

  12. Detecting overlapping communities in massive networks

    NASA Astrophysics Data System (ADS)

    Sun, Bing-Jie; Shen, Hua-Wei; Cheng, Xue-Qi

    2014-12-01

    Community detection is an essential work for network analysis. However, few methods could be used as off-the-shelf tools to detect communities in real-world networks for two main reasons: Real networks often contain millions of nodes or even hundreds of millions of nodes while most methods cannot handle networks at this scale. One node often belongs to multiple communities, posing another big challenge. In this paper, we circumvent the tricky problem of detecting overlapping communities using a two-stage framework, balancing efficiency and accuracy. Given a network, we first focus on efficiently finding its coarse-grained communities. Starting from them, we next obtain overlapping communities by optimizing a principled objective function. In this divide-and-conquer way, the framework achieves a much better performance than detecting overlapping communities from scratch. Extensive tests on synthetic and real networks demonstrate that it outperforms state-of-the-art methods in terms of both efficiency and accuracy.

  13. Generating Composite Overlapping Grids on CAD Geometries

    SciTech Connect

    Henshaw, W.D.

    2002-02-07

    We describe some algorithms and tools that have been developed to generate composite overlapping grids on geometries that have been defined with computer aided design (CAD) programs. This process consists of five main steps. Starting from a description of the surfaces defining the computational domain we (1) correct errors in the CAD representation, (2) determine topology of the patched-surface, (3) build a global triangulation of the surface, (4) construct structured surface and volume grids using hyperbolic grid generation, and (5) generate the overlapping grid by determining the holes and the interpolation points. The overlapping grid generator which is used for the final step also supports the rapid generation of grids for block-structured adaptive mesh refinement and for moving grids. These algorithms have been implemented as part of the Overture object-oriented framework.

  14. A new mathematical formulation of the line-by-line method in case of weak line overlapping

    NASA Technical Reports Server (NTRS)

    Ishov, Alexander G.; Krymova, Natalie V.

    1994-01-01

    A rigorous mathematical proof is presented for multiline representation on the equivalent width of a molecular band which consists in the general case of n overlapping spectral lines. The multiline representation includes a principal term and terms of minor significance. The principal term is the equivalent width of the molecular band consisting of the same n nonoverlapping spectral lines. The terms of minor significance take into consideration the overlapping of two, three and more spectral lines. They are small in case of the weak overlapping of spectral lines in the molecular band. The multiline representation can be easily generalized for optically inhomogeneous gas media and holds true for combinations of molecular bands. If the band lines overlap weakly the standard formulation of line-by-line method becomes too labor-consuming. In this case the multiline representation permits line-by-line calculations to be performed more effectively. Other useful properties of the multiline representation are pointed out.

  15. Temporal niche overlap among insectivorous small mammals.

    PubMed

    Vieira, Emerson M; Paise, Gabriela

    2011-12-01

    Being active in the same environment at different times exposes animals to the effects of very different environmental factors, both biotic and abiotic. In the present study, we used live traps equipped with timing devices to evaluate the potential role of biotic factors (competition and food abundance) on overall overlap in the temporal niche axis of 4 insectivorous small mammals in high-elevation grassland fields ('campos de altitude') of southern Brazil. Based on resources availability (invertebrates), data on animal captures were pooled in 2 seasons: 'scarcity' (June 2001-September 2001) and 'abundance' (November 2001-May 2002) seasons. We tested for non-random structure in temporal niche overlap among the species in each season. These species were the rodents Oxymycterus nasutus (Waterhouse, 1837), Deltamys sp., Akodon azarae (Fischer, 1829), and the marsupial Monodelphis brevicaudis Olfers, 1818. The studied community was mainly diurnal with crepuscular peaks. Simulations using the Pianka index of niche overlap indicated that the empirical assemblage-wide overlap was not significantly different from randomly generated patterns in the abundance season but significantly greater than expected by chance alone in the scarcity season. All the species showed an increase in temporal niche breadth during the abundance season, which appears to be related to longer daylength and high nocturnal temperatures. Patterns on both temporal niche overlap and temporal niche breadth were the opposite to those that we were expecting in the case of diel activity patterns determined by competition for dietary resources. Therefore, we conclude that competition did not seem to be preponderant for determining patterns of temporal niche overlap by the studied community. PMID:22182329

  16. Sub-Plate Overlap Code Documentation

    NASA Technical Reports Server (NTRS)

    Taff, L. G.; Bucciarelli, B.; Zarate, N.

    1997-01-01

    An expansion of the plate overlap method of astrometric data reduction to a single plate has been proposed and successfully tested. Each plate is (artificially) divided into sub-plates which can then be overlapped. This reduces the area of a 'plate' over which a plate model needs to accurately represent the relationship between measured coordinates and standard coordinates. Application is made to non-astrographic plates such as Schmidt plates and to wide-field astrographic plates. Indeed, the method is completely general and can be applied to any type of recording media.

  17. Dynamics of overlapping structures in modular networks.

    PubMed

    Almendral, J A; Leyva, I; Li, D; Sendiña-Nadal, I; Havlin, S; Boccaletti, S

    2010-07-01

    Modularity is a fundamental feature of real networks, being intimately bounded to their functionality, i.e., to their capability of performing parallel tasks in a coordinated way. Although the modular structure of real graphs has been intensively studied, very little is known on the interactions between functional modules of a graph. Here, we present a general method based on synchronization of networking oscillators, that is able to detect overlapping structures in multimodular environments. We furthermore report the full analytical and theoretical description on the relationship between the overlapping dynamics and the underlying network topology. The method is illustrated by means of a series of applications. PMID:20866697

  18. On the rotation of co-orbital bodies in eccentric orbits

    NASA Astrophysics Data System (ADS)

    Leleu, A.; Robutel, P.; Correia, A. C. M.

    2016-06-01

    We investigate the resonant rotation of co-orbital bodies in eccentric and planar orbits. We develop a simple analytical model to study the impact of the eccentricity and orbital perturbations on the spin dynamics. This model is relevant in the entire domain of horseshoe and tadpole orbit, for moderate eccentricities. We show that there are three different families of spin-orbit resonances, one depending on the eccentricity, one depending on the orbital libration frequency, and another depending on the pericenter's dynamics. We can estimate the width and the location of the different resonant islands in the phase space, predicting which are the more likely to capture the spin of the rotating body. In some regions of the phase space the resonant islands may overlap, giving rise to chaotic rotation.

  19. Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis of 4-4'-(1H-1,2,4-triazol-1-yl methylene) dibenzonitrile based on abinitio and DFT methods.

    PubMed

    Sheela, N R; Muthu, S; Sampathkrishnan, S

    2014-01-01

    The Fourier transform infrared (FTIR) and FT Raman (FTR) of 4-4'-(1H-1, 2, 4-triazol-1-yl methylene) dibenzonitrile (4-HTMDBN) have been recorded and analyzed. The equilibrium geometry harmonic vibrational frequencies have been investigated with the help of standard HF and DFT methods with 6-31G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). Theoretical simulations of the FTIR and FTR spectra of the title compound have been calculated. The (1)H and (13)C Nuclear Magnetic Resonance (NMR) chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. The stability of the molecule has been analyzed using natural bond orbital (NBO) analysis. The linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using HF/DFT/6-31G(d,p) methods on the finite field approach. UV-Vis spectrum of the compound is recorded and the electronic properties such as HOMO and LUMO energies, are performed. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), electrophilicity index (ω), hardness (η) and chemical potential (ρ) are all correlated with the HOMO and LUMO energies with their molecular properties. Mulliken population analysis on atomic charges, molecular electrostatic potential maps (MEP) and thermodynamical properties of title compound at different temperature have been calculated. PMID:24184626

  20. Orbit determination and gravity field recovery from Doppler tracking data to the Lunar Reconnaissance Orbiter

    NASA Astrophysics Data System (ADS)

    Maier, Andrea; Baur, Oliver

    2016-03-01

    We present results for Precise Orbit Determination (POD) of the Lunar Reconnaissance Orbiter (LRO) based on two-way Doppler range-rates over a time span of ~13 months (January 3, 2011 to February 9, 2012). Different orbital arc lengths and various sets of empirical parameters were tested to seek optimal parametrization. An overlap analysis covering three months of Doppler data shows that the most precise orbits are obtained using an arc length of 2.5 days and estimating arc-wise constant empirical accelerations in along track direction. The overlap analysis over the entire investigated time span of 13 months indicates an orbital precision of 13.79 m, 14.17 m, and 1.28 m in along track, cross track, and radial direction, respectively, with 21.32 m in total position. We compare our orbits to the official science orbits released by the US National Aeronautics and Space Administration (NASA). The differences amount to 9.50 m, 6.98 m, and 1.50 m in along track, cross track, and radial direction, respectively, as well as 12.71 m in total position. Based on the reconstructed LRO orbits, we estimated lunar gravity field coefficients up to spherical harmonic degree and order 60. The results are compared to gravity field solutions derived from data collected by other lunar missions.

  1. Eye and orbit ultrasound

    MedlinePlus

    Echography - eye orbit; Ultrasound - eye orbit; Ocular ultrasonography; Orbital ultrasonography ... ophthalmology department of a hospital or clinic. Your eye is numbed with medicine (anesthetic drops). The ultrasound ...

  2. Payload/orbiter contamination control requirement study

    NASA Technical Reports Server (NTRS)

    Bareiss, L. E.; Rantanen, R. O.; Ress, E. B.

    1974-01-01

    A study was conducted to determine and quantify the expected particulate and molecular on-orbit contaminant environment for selected space shuttle payloads as a result of major shuttle orbiter contamination sources. Individual payload susceptibilities to contamination are reviewed. The risk of payload degradation is identified and preliminary recommendations are provided concerning the limiting factors which may depend on operational activities associated with the payload/orbiter interface or upon independent payload functional activities. A basic computer model of the space shuttle orbiter which includes a representative payload configuration is developed. The major orbiter contamination sources, locations, and flux characteristics based upon available data have been defined and modeled.

  3. Power divergences in overlapping Wilson lines

    NASA Astrophysics Data System (ADS)

    Berwein, Matthias

    2016-01-01

    We discuss the divergence structure of Wilson line operators with partially overlapping segments on the basis of the cyclic Wilson loop as an explicit example. The generalized exponentiation theorem is used to show the exponentiation and factorization of power divergences for certain linear combinations of associated loop functions.

  4. Overlapping Community Detection based on Network Decomposition

    NASA Astrophysics Data System (ADS)

    Ding, Zhuanlian; Zhang, Xingyi; Sun, Dengdi; Luo, Bin

    2016-04-01

    Community detection in complex network has become a vital step to understand the structure and dynamics of networks in various fields. However, traditional node clustering and relatively new proposed link clustering methods have inherent drawbacks to discover overlapping communities. Node clustering is inadequate to capture the pervasive overlaps, while link clustering is often criticized due to the high computational cost and ambiguous definition of communities. So, overlapping community detection is still a formidable challenge. In this work, we propose a new overlapping community detection algorithm based on network decomposition, called NDOCD. Specifically, NDOCD iteratively splits the network by removing all links in derived link communities, which are identified by utilizing node clustering technique. The network decomposition contributes to reducing the computation time and noise link elimination conduces to improving the quality of obtained communities. Besides, we employ node clustering technique rather than link similarity measure to discover link communities, thus NDOCD avoids an ambiguous definition of community and becomes less time-consuming. We test our approach on both synthetic and real-world networks. Results demonstrate the superior performance of our approach both in computation time and accuracy compared to state-of-the-art algorithms.

  5. Liberal Education: An Overlapping Pragmatic Consensus.

    ERIC Educational Resources Information Center

    Paris, David C.; Kimball, Bruce A.

    2000-01-01

    Suggests in Bruce Kimball's thesis that a pragmatic consensus was emerging about the understanding of liberal education offers that it might be best understood by comparing it to J. Rawl's idea of an "overlapping consensus." States that by comparing and contrasting these ideas that the emerging consensus is pragmatic in nature. (CMK)

  6. Overlapping Community Detection based on Network Decomposition

    PubMed Central

    Ding, Zhuanlian; Zhang, Xingyi; Sun, Dengdi; Luo, Bin

    2016-01-01

    Community detection in complex network has become a vital step to understand the structure and dynamics of networks in various fields. However, traditional node clustering and relatively new proposed link clustering methods have inherent drawbacks to discover overlapping communities. Node clustering is inadequate to capture the pervasive overlaps, while link clustering is often criticized due to the high computational cost and ambiguous definition of communities. So, overlapping community detection is still a formidable challenge. In this work, we propose a new overlapping community detection algorithm based on network decomposition, called NDOCD. Specifically, NDOCD iteratively splits the network by removing all links in derived link communities, which are identified by utilizing node clustering technique. The network decomposition contributes to reducing the computation time and noise link elimination conduces to improving the quality of obtained communities. Besides, we employ node clustering technique rather than link similarity measure to discover link communities, thus NDOCD avoids an ambiguous definition of community and becomes less time-consuming. We test our approach on both synthetic and real-world networks. Results demonstrate the superior performance of our approach both in computation time and accuracy compared to state-of-the-art algorithms. PMID:27066904

  7. Autism and ADHD: Overlapping and Discriminating Symptoms

    ERIC Educational Resources Information Center

    Mayes, Susan Dickerson; Calhoun, Susan L.; Mayes, Rebecca D.; Molitoris, Sarah

    2012-01-01

    Children with ADHD and autism have some similar features, complicating a differential diagnosis. The purpose of our study was to determine the degree to which core ADHD and autistic symptoms overlap in and discriminate between children 2-16 years of age with autism and ADHD. Our study demonstrated that 847 children with autism were easily…

  8. Overlapping Community Detection based on Network Decomposition.

    PubMed

    Ding, Zhuanlian; Zhang, Xingyi; Sun, Dengdi; Luo, Bin

    2016-01-01

    Community detection in complex network has become a vital step to understand the structure and dynamics of networks in various fields. However, traditional node clustering and relatively new proposed link clustering methods have inherent drawbacks to discover overlapping communities. Node clustering is inadequate to capture the pervasive overlaps, while link clustering is often criticized due to the high computational cost and ambiguous definition of communities. So, overlapping community detection is still a formidable challenge. In this work, we propose a new overlapping community detection algorithm based on network decomposition, called NDOCD. Specifically, NDOCD iteratively splits the network by removing all links in derived link communities, which are identified by utilizing node clustering technique. The network decomposition contributes to reducing the computation time and noise link elimination conduces to improving the quality of obtained communities. Besides, we employ node clustering technique rather than link similarity measure to discover link communities, thus NDOCD avoids an ambiguous definition of community and becomes less time-consuming. We test our approach on both synthetic and real-world networks. Results demonstrate the superior performance of our approach both in computation time and accuracy compared to state-of-the-art algorithms. PMID:27066904

  9. Stochastic Cooling with Schottky Band Overlap

    SciTech Connect

    Lebedev, Valeri

    2006-03-20

    Optimal use of stochastic cooling is essential to maximize the antiproton stacking rate for Tevatron Run II. Good understanding and characterization of the cooling is important for the optimization. The paper is devoted to derivation of the Fokker-Plank equations justified in the case of near or full Schottky base overlap for both longitudinal and transverse coolings.

  10. Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N'-hydroxy-pyrimidine-2-carboximidamide by DFT approach.

    PubMed

    Jasmine, N Jeeva; Muthiah, P Thomas; Arunagiri, C; Subashini, A

    2015-06-01

    The FT-IR, FT-Raman, (1)H, (13)C NMR and UV-Visible spectral measurements of N'-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure. PMID:25756689

  11. Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N‧-hydroxy-pyrimidine-2-carboximidamide by DFT approach

    NASA Astrophysics Data System (ADS)

    Jeeva Jasmine, N.; Thomas Muthiah, P.; Arunagiri, C.; Subashini, A.

    2015-06-01

    The FT-IR, FT-Raman, 1H, 13C NMR and UV-Visible spectral measurements of N‧-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure.

  12. The biology of race: searching for no overlap.

    PubMed

    Jackson, Myles W

    2014-01-01

    With the rise of molecular genetics and the cornucopia of techniques it provides, a number of biomedical researchers in both the public and private sectors have turned to the human genome to search for variations among the world's populations, with the purpose of tracing human evolution and migration patterns and predicting genetic disorders. The human genome also offers insight into an individual's genealogy, which has never before been charted with such precision. Whereas 18th- and 19th-century scholars fetishized external characteristics in order to classify humans,more recent scholars have turned to the internal sequence of the genome. But how does one define populations? Should they be based on race? Can one speak of race at the molecular level? This essay explores the history of the biology of race with a view to compare and contrast modern molecular biological studies with the more pernicious actions of early-20th-century eugenicists. The key linking the two practices is the search for biological entities that do not overlap among the races. A critical difference is that modern studies use molecular biology to include previously excluded populations in the treatment of certain diseases. While the intentions are quite different, a number of scholars feel that genetic essentialism might be the end result. PMID:25345704

  13. Orbit analysis

    SciTech Connect

    Michelotti, L.

    1995-01-01

    The past fifteen years have witnessed a remarkable development of methods for analyzing single particle orbit dynamics in accelerators. Unlike their more classic counterparts, which act upon differential equations, these methods proceed by manipulating Poincare maps directly. This attribute makes them well matched for studying accelerators whose physics is most naturally modelled in terms of maps, an observation that has been championed most vigorously by Forest. In the following sections the author sketchs a little background, explains some of the physics underlying these techniques, and discusses the best computing strategy for implementing them in conjunction with modeling accelerators.

  14. High-Resolution Soft X-Ray Spectral Analysis in the CK Region of Titanium Carbide (TiC) using the DV-X alpha Molecular Orbital Method

    SciTech Connect

    Shimomura, Kenta; Muramatsu, Yasuji; Denlinger, Jonathan D.; Gullikson, Eric M.

    2008-10-31

    We used the DV-X alpha method to analyze the high-resolution soft X-ray emission and absorption spectra in the CK region of titanium carbide (TiC). The spectral profiles of the X-ray emission and absorption can be ssuscfucelly reproduced by the occupied and unoccupied density of states (DOS ), respectively, in the C2p orbitals of the center carbon atoms in a Ti62C63 cluster model, suggesting that the center carbon atom in a large cluster model expanded to the cubic-structured 53 (= 125) atoms provides sufficient DOS for the X-ray spectral analysis of rock-salt structured metal carbides.

  15. Quantitative Structure-Cytotoxicity Relationship of Bioactive Heterocycles by the Semi-empirical Molecular Orbital Method with the Concept of Absolute Hardness

    NASA Astrophysics Data System (ADS)

    Ishihara, Mariko; Sakagami, Hiroshi; Kawase, Masami; Motohashi, Noboru

    The relationship between the cytotoxicity of N-heterocycles (13 4-trifluoromethylimidazole, 15 phenoxazine and 12 5-trifluoromethyloxazole derivatives), O-heterocycles (11 3-formylchromone and 20 coumarin derivatives) and seven vitamin K2 derivatives against eight tumor cell lines (HSC-2, HSC-3, HSC-4, T98G, HSG, HepG2, HL-60, MT-4) and a maximum of 15 chemical descriptors was investigated using CAChe Worksystem 4.9 project reader. After determination of the conformation of these compounds and approximation to the molecular form present in vivo (biomimetic) by CONFLEX5, the most stable structure was determined by CAChe Worksystem 4.9 MOPAC (PM3). The present study demonstrates the best relationship between the cytotoxic activity and molecular shape or molecular weight of these compounds. Their biological activities can be estimated by hardness and softness, and by using η-χ activity diagrams.

  16. Vacuum structure as seen by overlap fermions

    SciTech Connect

    Ilgenfritz, E.-M.; Koller, K.; Koma, Y.; Schierholz, G.; Streuer, T.; Weinberg, V.

    2007-02-27

    Three complementary views on the QCD vacuum structure, all based on eigenmodes of the overlap operator, are reported in their interrelation: (i) spectral density, localization and chiral properties of the modes, (ii) the possibility of filtering the field strength with the aim to detect selfdual and antiselfdual domains and (iii) the various faces of the topological charge density, with and without a cutoff {lambda}cut = O({lambda}QCD). The techniques are tested on quenched SU(3) configurations.

  17. A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

    SciTech Connect

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix, based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.

  18. Function approximation using adaptive and overlapping intervals

    SciTech Connect

    Patil, R.B.

    1995-05-01

    A problem common to many disciplines is to approximate a function given only the values of the function at various points in input variable space. A method is proposed for approximating a function of several to one variable. The model takes the form of weighted averaging of overlapping basis functions defined over intervals. The number of such basis functions and their parameters (widths and centers) are automatically determined using given training data and a learning algorithm. The proposed algorithm can be seen as placing a nonuniform multidimensional grid in the input domain with overlapping cells. The non-uniformity and overlap of the cells is achieved by a learning algorithm to optimize a given objective function. This approach is motivated by the fuzzy modeling approach and a learning algorithms used for clustering and classification in pattern recognition. The basics of why and how the approach works are given. Few examples of nonlinear regression and classification are modeled. The relationship between the proposed technique, radial basis neural networks, kernel regression, probabilistic neural networks, and fuzzy modeling is explained. Finally advantages and disadvantages are discussed.

  19. Burnout-depression overlap: a review.

    PubMed

    Bianchi, Renzo; Schonfeld, Irvin Sam; Laurent, Eric

    2015-03-01

    Whether burnout is a form of depression or a distinct phenomenon is an object of controversy. The aim of the present article was to provide an up-to-date review of the literature dedicated to the question of burnout-depression overlap. A systematic literature search was carried out in PubMed, PsycINFO, and IngentaConnect. A total of 92 studies were identified as informing the issue of burnout-depression overlap. The current state of the art suggests that the distinction between burnout and depression is conceptually fragile. It is notably unclear how the state of burnout (i.e., the end stage of the burnout process) is conceived to differ from clinical depression. Empirically, evidence for the distinctiveness of the burnout phenomenon has been inconsistent, with the most recent studies casting doubt on that distinctiveness. The absence of consensual diagnostic criteria for burnout and burnout research's insufficient consideration of the heterogeneity of depressive disorders constitute major obstacles to the resolution of the raised issue. In conclusion, the epistemic status of the seminal, field-dominating definition of burnout is questioned. It is suggested that systematic clinical observation should be given a central place in future research on burnout-depression overlap. PMID:25638755

  20. Mass and charge overlaps in beamline implantation into compound semiconductor materials

    SciTech Connect

    Current, M. I.; Eddy, R.; Hudak, C.; Serfass, J.; Mount, G.

    2012-11-06

    Mass overlaps occurring as a result of extraction of ions from an arc discharge and gas collisions, producing molecular break up and charge exchange in the accelerator beamline, are examined for ion implantation into compound semiconductors. The effects of the choice of plasma gas elements for Be{sup +} implants are examined as an example.

  1. Mass and charge overlaps in beamline implantation into compound semiconductor materials

    NASA Astrophysics Data System (ADS)

    Current, M. I.; Eddy, R.; Hudak, C.; Serfass, J.; Mount, G.

    2012-11-01

    Mass overlaps occurring as a result of extraction of ions from an arc discharge and gas collisions, producing molecular break up and charge exchange in the accelerator beamline, are examined for ion implantation into compound semiconductors. The effects of the choice of plasma gas elements for Be+ implants are examined as an example.

  2. Optimizing packing fraction in granular media composed of overlapping spheres.

    PubMed

    Roth, Leah K; Jaeger, Heinrich M

    2016-01-28

    What particle shape will generate the highest packing fraction when randomly poured into a container? In order to explore and navigate the enormous search space efficiently, we pair molecular dynamics simulations with artificial evolution. Arbitrary particle shape is represented by a set of overlapping spheres of varying diameter, enabling us to approximate smooth surfaces with a resolution proportional to the number of spheres included. We discover a family of planar triangular particles, whose packing fraction of ϕ ∼ 0.73 is among the highest experimental results for disordered packings of frictionless particles. We investigate how ϕ depends on the arrangement of spheres comprising an individual particle and on the smoothness of the surface. We validate the simulations with experiments using 3D-printed copies of the simplest member of the family, a planar particle consisting of three overlapping spheres with identical radius. Direct experimental comparison with 3D-printed aspherical ellipsoids demonstrates that the triangular particles pack exceedingly well not only in the limit of large system size but also when confined to small containers. PMID:26592541

  3. Orbital Winch

    NASA Technical Reports Server (NTRS)

    Hoyt, Robert (Inventor); Slostad, Jeffrey T. (Inventor); Frank, Scott (Inventor); Barnes, Ian M. (Inventor)

    2016-01-01

    Orbital winch having: lower and upper frames; spool having upper and lower flanges with lower flange attached to lower frame; axial tether guide mounted to upper frame; secondary slewing ring coaxial with spool and rotatably mounted to upper frame, wherein secondary slewing ring's outer surface has gearing; upper tether guide mounted to inner surface of secondary slewing ring; linear translation means having upper end mounted to upper frame and lower end mounted on lower frame; primary slewing ring rotatably mounted within linear translation means allowing translation axially between flanges, wherein primary slewing ring's outer surface has gearing; lower tether guide mounted on primary slewing ring's inner surface; pinion rod having upper end mounted to upper frame and lower end mounted to lower frame, wherein pinion rod's teeth engage primary and secondary slewing rings' outer surface teeth; and tether passing through axial, upper, and lower tether guides and winding around spool.

  4. Analysis of Bonding Patterns in the Valence Isoelectronic series O3, S3, SO2 and OS2 in Terms of Oriented Quasi-Atomic Molecular Orbitals

    SciTech Connect

    Glezakou, Vassiliki Alexandra; Elbert, Stephen T; Xantheas, Sotiris S; Ruedenberg, Klaus

    2010-08-26

    A novel analysis of the chemical bonding pattern in the valence isoelectronic series of triatomic molecules O3, S3, SO2 and OS2 is reported. The analysis is based on examining the bond order matrix elements between the Oriented Localized Molecular Orbitals (OLMOs) that are localized on the three individual left (L), center (C) and right (R) atoms. The analysis indicates that there is a (L-C) and (C-R) π-bonding interaction and a (L-R) π-antibonding interaction. This finding supports the previously proposed "partial biradical" interpretation of these triatomic systems, which had recently been challenged.

  5. Energy stabilization of the s -symmetry superatom molecular orbital by endohedral doping of C 82 fullerene with a lanthanum atom

    SciTech Connect

    Feng, Min; Shi, Yongliang; Lin, Chungwei; Zhao, Jin; Liu, Fupin; Yang, Shangfeng; Petek, Hrvoje

    2013-08-01

    Energy stabilization of the superatom molecular orbitals (SAMOs) in fullerenes is investigated with the goal of involving their nearly free-electron bands in practical charge transport applications. Combining low-temperature scanning tunneling microscopy-based spectroscopic methods and density functional theory calculations on an endohedral metallofullerene La@C82, we confirm that the s-SAMO of C82 fullerene is stabilized by as much as 2 eV with respect to that of C60 by endohedral doping with the La atom. On the copper metal substrate, the s-SAMO energy is further lowered to just 1 eV above the Fermi level, making the applications of s-SAMO state in transport more plausible. We conclude that in an endohedral metallofullerene, the s-SAMO state is stabilized through the hybridization with the s-symmetry valence state of the metal atom and the stabilization energy correlates with the ionization potential of the free atom.

  6. Communications overlapping in fast multipole particle dynamics methods

    SciTech Connect

    Kurzak, Jakub; Pettitt, B. Montgomery . E-mail: pettitt@uh.edu

    2005-03-01

    In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating electrostatic interactions due to the operation counts. However when applied to small particle systems and taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared with optimized Ewald methods.

  7. Theoretical analysis of an all-photonic multifunctional molecular logic device: Using TD-DFT//DFT to assess photochromic activity of multimeric photochrome

    NASA Astrophysics Data System (ADS)

    Belfon, Kellon A. A.; Gough, Jonathan D.

    2013-10-01

    The structures and properties of a single-molecule photochromic switch consisting of 3 photochromic moieties is investigated. Using time-dependent density functional theory (TD-DFT) we calculated the λmax within ± 30 nm (± 0.18 eV) and produced spectra that were similar. The charge-transfer (CT) character of the molecular orbitals (MO) was assessed via the overlap between the occupied and virtual orbitals (Λ diagnostic) and did not suffer from CT failure. The MOs were consistent with photochemically productive photochromes. The MO and their contribution to different excited states paralleled both the observed activity and observed inactivity of the photochrome.

  8. Influence of slice overlap on positron emission tomography image quality

    NASA Astrophysics Data System (ADS)

    McKeown, Clare; Gillen, Gerry; Dempsey, Mary Frances; Findlay, Caroline

    2016-02-01

    PET scans use overlapping acquisition beds to correct for reduced sensitivity at bed edges. The optimum overlap size for the General Electric (GE) Discovery 690 has not been established. This study assesses how image quality is affected by slice overlap. Efficacy of 23% overlaps (recommended by GE) and 49% overlaps (maximum possible overlap) were specifically assessed. European Association of Nuclear Medicine (EANM) guidelines for calculating minimum injected activities based on overlap size were also reviewed. A uniform flood phantom was used to assess noise (coefficient of variation, (COV)) and voxel accuracy (activity concentrations, Bq ml-1). A NEMA (National Electrical Manufacturers Association) body phantom with hot/cold spheres in a background activity was used to assess contrast recovery coefficients (CRCs) and signal to noise ratios (SNR). Different overlap sizes and sphere-to-background ratios were assessed. COVs for 49% and 23% overlaps were 9% and 13% respectively. This increased noise was difficult to visualise on the 23% overlap images. Mean voxel activity concentrations were not affected by overlap size. No clinically significant differences in CRCs were observed. However, visibility and SNR of small, low contrast spheres (⩽13 mm diameter, 2:1 sphere to background ratio) may be affected by overlap size in low count studies if they are located in the overlap area. There was minimal detectable influence on image quality in terms of noise, mean activity concentrations or mean CRCs when comparing 23% overlap with 49% overlap. Detectability of small, low contrast lesions may be affected in low count studies—however, this is a worst-case scenario. The marginal benefits of increasing overlap from 23% to 49% are likely to be offset by increased patient scan times. A 23% overlap is therefore appropriate for clinical use. An amendment to EANM guidelines for calculating injected activities is also proposed which better reflects the effect overlap size has

  9. Orbiter Camera Payload System

    NASA Technical Reports Server (NTRS)

    1980-01-01

    Components for an orbiting camera payload system (OCPS) include the large format camera (LFC), a gas supply assembly, and ground test, handling, and calibration hardware. The LFC, a high resolution large format photogrammetric camera for use in the cargo bay of the space transport system, is also adaptable to use on an RB-57 aircraft or on a free flyer satellite. Carrying 4000 feet of film, the LFC is usable over the visible to near IR, at V/h rates of from 11 to 41 milliradians per second, overlap of 10, 60, 70 or 80 percent and exposure times of from 4 to 32 milliseconds. With a 12 inch focal length it produces a 9 by 18 inch format (long dimension in line of flight) with full format low contrast resolution of 88 lines per millimeter (AWAR), full format distortion of less than 14 microns and a complement of 45 Reseau marks and 12 fiducial marks. Weight of the OCPS as supplied, fully loaded is 944 pounds and power dissipation is 273 watts average when in operation, 95 watts in standby. The LFC contains an internal exposure sensor, or will respond to external command. It is able to photograph starfields for inflight calibration upon command.

  10. Strong orbital interaction in a weak CH-π hydrogen bonding system.

    PubMed

    Li, Jianfu; Zhang, Rui-Qin

    2016-01-01

    For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms "bonding" and "antibonding" orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least -1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex. PMID:26927609

  11. Orbit Determination of the SELENE Satellites Using Multi-Satellite Data Types and Evaluation of SELENE Gravity Field Models

    NASA Technical Reports Server (NTRS)

    Goossens, S.; Matsumoto, K.; Noda, H.; Araki, H.; Rowlands, D. D.; Lemoine, F. G.

    2011-01-01

    The SELENE mission, consisting of three separate satellites that use different terrestrial-based tracking systems, presents a unique opportunity to evaluate the contribution of these tracking systems to orbit determination precision. The tracking data consist of four-way Doppler between the main orbiter and one of the two sub-satellites while the former is over the far side, and of same-beam differential VLBI tracking between the two sub-satellites. Laser altimeter data are also used for orbit determination. The contribution to orbit precision of these different data types is investigated through orbit overlap analysis. It is shown that using four-way and VLBI data improves orbit consistency for all satellites involved by reducing peak values in orbit overlap differences that exist when only standard two-way Doppler and range data are used. Including laser altimeter data improves the orbit precision of the SELENE main satellite further, resulting in very smooth total orbit errors at an average level of 18m. The multi-satellite data have also resulted in improved lunar gravity field models, which are assessed through orbit overlap analysis using Lunar Prospector tracking data. Improvements over a pre-SELENE model are shown to be mostly in the along-track and cross-track directions. Orbit overlap differences are at a level between 13 and 21 m with the SELENE models, depending on whether l-day data overlaps or I-day predictions are used.

  12. Cenozoic Motion of Greenland - Overlaps and Seaways

    NASA Astrophysics Data System (ADS)

    Lawver, L. A.; Norton, I. O.; Gahagan, L.

    2014-12-01

    Using the seafloor magnetic anomalies found in the Labrador Sea, North Atlantic and Eurasian basin to constrain the Cenozoic motion of Greenland, we have produced a new model for the tectonic evolution of the region. The aeromagnetic data collected by the Naval Research Lab [Brozena et al., 2003] in the Eurasian Basin and Canadian data from the Labrador Sea have been re-evaluated using new gridding algorithms and profile modeling using ModMag (Mendel et al., 2005). As a consequence, we have changed the published correlations, mostly prior to Chron C6 [19.05 Ma]. Presently published seafloor magnetic anomalies from the Labrador Sea assume that seafloor spreading ceased at C13 [33.06 Ma] but such an assumption produces an unacceptable overlap of Kronprins Christian Land of northeast Greenland with Svalbard, up to 140 km of overlap in some models. Our new model does not need any "unacceptable" overlap but does produce a slight amount of Eocene compression on Svalbard as is found on land there. Our model allows for an Early Eocene seaway between Ellesmere Island and northwest Greenland that may have connected the Labrador Sea through Baffin Bay and ultimately to the nascent Eurasian Basin, although its depth or even its essential existence is unknowable. During the Miocene, there is no room for a deepwater seaway in Fram Strait until at least the very end of the Early Miocene and perhaps not until Middle Miocene. Brozena, J. and six others, 2003. New aerogeophysical study of the Eurasia Basin and Lomonosov Ridge: Implications for basin development. Geology 31, 825-828. Mendel, V., M. Munschy and D.Sauter, 2005, MODMAG, a MATLAB program to model marine magnetic anomalies, Comp. Geosci., 31, .589-597

  13. Shaft drill bit with overlapping cutter arrangement

    SciTech Connect

    Cunningham, R.A.; Pessier, R.C.

    1981-02-03

    An earth boring drill bit for large diameter shafts has an improved cutter arrangement. The drill bit has a cutter support member with a number of cutters mounted to it for disintegrating the earth formation face. At least one inner cutter is mounted near the center for cutting the center area. A number of gage cutters are mounted at the periphery to cut the gage area of the shaft. A number of intermediate cutters are spaced between the inner and gage cutters. Each intermediate cutter overlaps onehalf of its width with an adjacent intermediate cutter.

  14. Technology initiatives with government/business overlap

    NASA Astrophysics Data System (ADS)

    Knapp, Robert H., Jr.

    2015-03-01

    Three important present-day technology development settings involve significant overlap between government and private sectors. The Advanced Research Project Agency for Energy (ARPA-E) supports a wide range of "high risk, high return" projects carried out in academic, non-profit or private business settings. The Materials Genome Initiative (MGI), based in the White House, aims at radical acceleration of the development process for advanced materials. California public utilities such as Pacific Gas & Electric operate under a structure of financial returns and political program mandates that make them arms of public policy as much as independent businesses.

  15. Improvement of overlapping nuclear track densitometry.

    PubMed

    Ghergherehchi, M; Kim, S Y; Afarideh, H; Kim, Y S; Chai, J S

    2015-03-01

    Detection of tracks produced by α particles, protons or nuclear fission fragments in plastic detectors, viz., solid-state nuclear track detectors, constitutes a very important tool in various areas. It is not easy for humans to count CR-39 nuclear tracks manually, especially when the track density is very high. An automated computer program called KTTMS2, written in C++ and running with a user friendly interface, has been developed for recognition and parametric measurements of etched tracks in images captured from the surface of solid-state nuclear track detectors. Well-known edge detection methods were applied to estimate the precision and accuracy of nuclear track densitometry using the CR-39 detector. Among the various routine edge detection methods, the Canny method was chosen because it was the most accurate technique. Because accuracy becomes more important as the track density increases, this allows more overlapping tracks to be detected. KTTMS2 (the proposed system) has an efficiency of 95% and can identify the noise as a background track (5%). Experimental results showed that the error percentage was reduced from 7.63% to 3.23% for high-density tracks when the count was adjusted by the estimated overlapping tracks. PMID:25581623

  16. Serial FBG sensor network allowing overlapping spectra

    NASA Astrophysics Data System (ADS)

    Abbenseth, S.; Lochmann, S.; Ahrens, A.; Rehm, B.

    2016-05-01

    For structure or material monitoring low impact serial fiber Bragg grating (FBG) networks have attracted increasing research interest. Common sensor networks using wavelength division multiplexing (WDM) for FBG interrogation are limited in their efficiency by the spectral width of their light source, the FBG tuning range and the spectral guard bands. Overlapping spectra are strictly forbidden in this case. Applying time division multiplexing (TDM) or active resonator schemes may overcome these restrictions. However, they introduce other substantial disadvantages like signal roundtrip dependency or sophisticated control of active resonating structures. Code division multiplexing (CDM) as a means of FBG interrogation by simple autocorrelation of appropriate codes has been shown to be superior in this respect. However, it came at the cost of a second spectrometer introducing additional equalization efforts. We demonstrate a new serial FBG sensor network utilizing CDM signal processing for efficient sensor interrogation without the need of a second spectrometer and additional state of polarization (SOP) controlling components. It allows overlapping spectra even when all sensing FBGs are positioned at the same centre wavelength and it shows a high degree of insensitivity to SOP. Sequence inversed keyed (SIK) serial signal processing utilizing quasi-orthogonal balanced codes ensures simple and quick sensor interrogation with high signal-to-interference/noise ratio.

  17. Preparation, optical and electrochemical properties, and molecular orbital calculations of tetraazaporphyrinato ruthenium (II) bis(4-methylpyridine) fused with one to four diphenylthiophene units.

    PubMed

    Kimura, Takeshi; Murakami, Naoko; Suzuki, Eiichi; Furuyama, Taniyuki; Nakahodo, Tsukasa; Fujihara, Hisashi; Kobayashi, Nagao

    2016-05-01

    2,5-Diphenyl-3,4-dicyanothiophene (1) and phthalonitrile (2) were mixed and treated with ruthenium (III) trichloride, 4-methylpyridine, and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in 2-ethoxyethanol at 135°C, to produce low-symmetrical tetraazaporphyrins (TAPs) (3), (4), (5), and (6) with one to three thiophene rings. Two thiophene-annelated tetraazaporphyrins were isolated as opposite and adjacent isomers 4 and 5. The structure of 3 was determined by X-ray crystallography, showing that the thiophene ring linked at the 3,4-positions on the tetraazaporphyrin scaffold deviates from the mean plane of the four central pyrrole nitrogen atoms (N1-N3-N5-N7). Optical and electrochemical properties of the products were examined by UV-vis and magnetic circular dichroism (MCD) spectroscopy, together with cyclic voltammetry. In the (1)H NMR spectra, the signals of 4-methylpyridine coordinating to the central ruthenium atom appeared at a higher magnetic field than those of uncoordinated 4-methylpyridine itself due to the shielding effect of the TAP ring. Increasing the number of fused thiophene rings resulted in 1) lower magnetic field shifts of the signals of axially coordinated 4-methylpyridine in the (1)H NMR spectra, 2) lower energy shifts of the Q band absorption in the UV-vis spectra, and 3) decreasing (cathodic shift) of the first oxidation potentials. The structures of simplified model compounds were optimized using the DFT method with the Gaussian 09 program at the B3LYP/LANL2DZ level for the Ru atom and the B3LYP/6-31G (d, p) level for the C, H, N, and S atoms. The optimized structures were utilized to calculate the NMR shielding constants, the HOMO and LUMO orbital energies, and the electronic absorption spectra. PMID:26876817

  18. Unique human orbital morphology compared with that of apes.

    PubMed

    Denion, Eric; Hitier, Martin; Guyader, Vincent; Dugué, Audrey-Emmanuelle; Mouriaux, Frédéric

    2015-01-01

    Humans' and apes' convergent (front-facing) orbits allow a large overlap of monocular visual fields but are considered to limit the lateral visual field extent. However, humans can greatly expand their lateral visual fields using eye motion. This study aimed to assess whether the human orbital morphology was unique compared with that of apes in avoiding lateral visual field obstruction. The orbits of 100 human skulls and 120 ape skulls (30 gibbons; 30 orangutans; 30 gorillas; 30 chimpanzees and bonobos) were analyzed. The orbital width/height ratio was calculated. Two orbital angles representing orbital convergence and rearward position of the orbital margin respectively were recorded using a protractor and laser levels. Humans have the largest orbital width/height ratio (1.19; p < 0.001). Humans and gibbons have orbits which are significantly less convergent than those of chimpanzees/bonobos, gorillas and orangutans (p < 0.001). These elements suggest a morphology favoring lateral vision in humans. More specifically, the human orbit has a uniquely rearward temporal orbital margin (107.1°; p < 0.001), suitable for avoiding visual obstruction and promoting lateral visual field expansion through eye motion. Such an orbital morphology may have evolved mainly as an adaptation to open-country habitat and bipedal locomotion. PMID:26111067

  19. Unique human orbital morphology compared with that of apes

    PubMed Central

    Denion, Eric; Hitier, Martin; Guyader, Vincent; Dugué, Audrey-Emmanuelle; Mouriaux, Frédéric

    2015-01-01

    Humans’ and apes’ convergent (front-facing) orbits allow a large overlap of monocular visual fields but are considered to limit the lateral visual field extent. However, humans can greatly expand their lateral visual fields using eye motion. This study aimed to assess whether the human orbital morphology was unique compared with that of apes in avoiding lateral visual field obstruction. The orbits of 100 human skulls and 120 ape skulls (30 gibbons; 30 orangutans; 30 gorillas; 30 chimpanzees and bonobos) were analyzed. The orbital width/height ratio was calculated. Two orbital angles representing orbital convergence and rearward position of the orbital margin respectively were recorded using a protractor and laser levels. Humans have the largest orbital width/height ratio (1.19; p < 0.001). Humans and gibbons have orbits which are significantly less convergent than those of chimpanzees / bonobos, gorillas and orangutans (p < 0.001). These elements suggest a morphology favoring lateral vision in humans. More specifically, the human orbit has a uniquely rearward temporal orbital margin (107.1°; p < 0.001), suitable for avoiding visual obstruction and promoting lateral visual field expansion through eye motion. Such an orbital morphology may have evolved mainly as an adaptation to open-country habitat and bipedal locomotion. PMID:26111067

  20. Phonological and Orthographic Overlap Effects in Fast and Masked Priming

    PubMed Central

    Frisson, Steven; Bélanger, Nathalie N.; Rayner, Keith

    2014-01-01

    We investigated how orthographic and phonological information is activated during reading, using a fast priming task, and during single word recognition, using masked priming. Specifically, different types of overlap between prime and target were contrasted: high orthographic and high phonological overlap (track-crack), high orthographic and low phonological overlap (bear-gear), or low orthographic and high phonological overlap (fruit-chute). In addition, we examined whether (orthographic) beginning overlap (swoop-swoon) yielded the same priming pattern as end (rhyme) overlap (track-crack). Prime durations were 32 and 50ms in the fast priming version, and 50ms in the masked priming version, and mode of presentation (prime and target in lower case) was identical. The fast priming experiment showed facilitatory priming effects when both orthography and phonology overlapped, with no apparent differences between beginning and end overlap pairs. Facilitation was also found when prime and target only overlapped orthographically. In contrast, the masked priming experiment showed inhibition for both types of end overlap pairs (with and without phonological overlap), and no difference for begin overlap items. When prime and target only shared principally phonological information, facilitation was only found with a long prime duration in the fast priming experiment, while no differences were found in the masked priming version. These contrasting results suggest that fast priming and masked priming do not necessarily tap into the same type of processing. PMID:24365065

  1. Phonological and orthographic overlap effects in fast and masked priming.

    PubMed

    Frisson, Steven; Bélanger, Nathalie N; Rayner, Keith

    2014-01-01

    We investigated how orthographic and phonological information is activated during reading, using a fast priming task, and during single-word recognition, using masked priming. Specifically, different types of overlap between prime and target were contrasted: high orthographic and high phonological overlap (track-crack), high orthographic and low phonological overlap (bear-gear), or low orthographic and high phonological overlap (fruit-chute). In addition, we examined whether (orthographic) beginning overlap (swoop-swoon) yielded the same priming pattern as end (rhyme) overlap (track-crack). Prime durations were 32 and 50 ms in the fast priming version and 50 ms in the masked priming version, and mode of presentation (prime and target in lower case) was identical. The fast priming experiment showed facilitatory priming effects when both orthography and phonology overlapped, with no apparent differences between beginning and end overlap pairs. Facilitation was also found when prime and target only overlapped orthographically. In contrast, the masked priming experiment showed inhibition for both types of end overlap pairs (with and without phonological overlap) and no difference for begin overlap items. When prime and target only shared principally phonological information, facilitation was only found with a long prime duration in the fast priming experiment, while no differences were found in the masked priming version. These contrasting results suggest that fast priming and masked priming do not necessarily tap into the same type of processing. PMID:24365065

  2. Theoretical analysis (NBO, NPA, Mulliken Population Method) and molecular orbital studies (hardness, chemical potential, electrophilicity and Fukui function analysis) of (E)-2-((4-hydroxy-2-methylphenylimino)methyl)-3-methoxyphenol

    NASA Astrophysics Data System (ADS)

    Demircioğlu, Zeynep; Kaştaş, Çiğdem Albayrak; Büyükgüngör, Orhan

    2015-07-01

    The molecular structure and spectroscopic properties of (E)-2-((4-hydroxy-2-methylphenylimino)methyl)-3-methoxyphenol, were characterized by X-ray diffraction, FT-IR and UV-Vis spectroscopy. All of theoretical calculations and optimized geometric parameters have been calculated by using density functional theory (DFT) with hybrid method B3LYP by 6-31G(d,p) basis set. The title compound of C15H15N1O3 have been analyzed according to electronic and energetics behaviors for enol-imine and keto-amine tautomers. Both these tautomers engender six-membered ring due to intramolecular hydrogen bonded interactions. Two types of intramolecular hydrogen bonds (a) strong O-H⋯N interactions in enol-imine form and (b) N-H⋯O interactions in keto-amine form are compared particularly. The theoretical vibrational frequencies have been found in good agreement with the corresponding experimental data. A study on the electronic and optical properties, absorption wavelengths, excitation energy, dipole moment, molecular electrostatic potential (MEP) and frontier molecular orbital energies are performed using DFT method. Additionally, geometry optimizations in solvent media were performed with the same level of theory by the polarizable continuum model (PCM). The effect of solvents on the tautomeric stability has been investigated. Mulliken Population Method and natural population analysis (NPA) have been studied. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. The local reactivity of the molecule has been studied using the Fukui function. NLO properties related to polarizability and hyperpolarizability are also discussed.

  3. Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in Cu(A) Sites of Cytochrome c Oxidase.

    PubMed

    Zitare, Ulises; Alvarez-Paggi, Damián; Morgada, Marcos N; Abriata, Luciano A; Vila, Alejandro J; Murgida, Daniel H

    2015-08-10

    The Cu(A) site of cytochrome c oxidase is a redox hub that participates in rapid electron transfer at low driving forces with two redox cofactors in nearly perpendicular orientations. Spectroscopic and electrochemical characterizations performed on first and second-sphere mutants have allowed us to experimentally detect the reversible switching between two alternative electronic states that confer different directionalities to the redox reaction. Specifically, the M160H variant of a native Cu(A) shows a reversible pH transition that allows to functionally probe both states in the same protein species. Alternation between states exerts a dramatic impact on the kinetic redox parameters, thereby suggesting this effect as the mechanism underlying the efficiency and directionality of Cu(A) electron transfer in vivo. These findings may also prove useful for the development of molecular electronics. PMID:26118421

  4. Mitigating fluorescence spectral overlap in wide-field endoscopic imaging

    PubMed Central

    Hou, Vivian; Nelson, Leonard Y.; Seibel, Eric J.

    2013-01-01

    Abstract. The number of molecular species suitable for multispectral fluorescence imaging is limited due to the overlap of the emission spectra of indicator fluorophores, e.g., dyes and nanoparticles. To remove fluorophore emission cross-talk in wide-field multispectral fluorescence molecular imaging, we evaluate three different solutions: (1) image stitching, (2) concurrent imaging with cross-talk ratio subtraction algorithm, and (3) frame-sequential imaging. A phantom with fluorophore emission cross-talk is fabricated, and a 1.2-mm ultrathin scanning fiber endoscope (SFE) is used to test and compare these approaches. Results show that fluorophore emission cross-talk could be successfully avoided or significantly reduced. Near term, the concurrent imaging method of wide-field multispectral fluorescence SFE is viable for early stage cancer detection and localization in vivo. Furthermore, a means to enhance exogenous fluorescence target-to-background ratio by the reduction of tissue autofluorescence background is demonstrated. PMID:23966226

  5. Communications Overlapping in Fast Multipole Particle Dynamics Methods

    SciTech Connect

    Kurzak, Jakub; Pettitt, Bernard M.

    2005-03-01

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating electrostatic interactions due to the operation counts. However when applied to small particle systems and taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared with optimized Ewald methods.

  6. A Review of Journal Coverage Overlap with an Extension to the Definition of Overlap.

    ERIC Educational Resources Information Center

    Gluck, Myke

    1990-01-01

    Examines the definition of journal coverage overlap in abstracting and indexing services during the past 30 years of research and expands the definition using a matrix of dissimilarity values. Multidimensional scaling analysis is applied to graphically demonstrate this definition and a naive secondary tool selection algorithm is presented. (43…

  7. Grid adaptation using chimera composite overlapping meshes

    NASA Technical Reports Server (NTRS)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1994-01-01

    The objective of this paper is to perform grid adaptation using composite overlapping meshes in regions of large gradient to accurately capture the salient features during computation. The chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using trilinear interpolation. Application to the Euler equations for shock reflections and to shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well-resolved.

  8. Grid adaptation using Chimera composite overlapping meshes

    NASA Technical Reports Server (NTRS)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1993-01-01

    The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.

  9. Parkinsonism and frontotemporal dementia: the clinical overlap.

    PubMed

    Espay, Alberto J; Litvan, Irene

    2011-11-01

    Frontotemporal dementia is commonly associated with parkinsonism in several sporadic (i.e., progressive supranuclear palsy, corticobasal degeneration) and familial neurodegenerative disorders (i.e., frontotemporal dementia associated with parkinsonism and MAPT or progranulin mutations in chromosome 17). The clinical diagnosis of these disorders may be challenging in view of overlapping clinical features, particularly in speech, language, and behavior. The motor and cognitive phenotypes can be viewed within a spectrum of clinical, pathologic, and genetic disorders with no discrete clinicopathologic correlations but rather lying within a dementia-parkinsonism continuum. Neuroimaging and cerebrospinal fluid analysis can be helpful, but the poor specificity of clinical and imaging features has enormously challenged the development of biological markers that could differentiate these disorders premortem. This gap is critical to bridge in order to allow testing of novel biological therapies that may slow the progression of these proteinopathies. PMID:21892619

  10. Competitive STDP Learning of Overlapping Spatial Patterns.

    PubMed

    Krunglevicius, Dalius

    2015-08-01

    Spike-timing-dependent plasticity (STDP) is a set of Hebbian learning rules firmly based on biological evidence. It has been demonstrated that one of the STDP learning rules is suited for learning spatiotemporal patterns. When multiple neurons are organized in a simple competitive spiking neural network, this network is capable of learning multiple distinct patterns. If patterns overlap significantly (i.e., patterns are mutually inclusive), however, competition would not preclude trained neuron's responding to a new pattern and adjusting synaptic weights accordingly. This letter presents a simple neural network that combines vertical inhibition and Euclidean distance-dependent synaptic strength factor. This approach helps to solve the problem of pattern size-dependent parameter optimality and significantly reduces the probability of a neuron's forgetting an already learned pattern. For demonstration purposes, the network was trained for the first ten letters of the Braille alphabet. PMID:26079753

  11. Recombining overlapping BACs into single large BACs.

    PubMed

    Kotzamanis, George; Kotsinas, Athanassios

    2015-01-01

    BAC clones containing the entire genomic region of a gene including the long-range regulatory elements are very useful for gene functional analysis. However, large genes often span more than the insert of a BAC clone, and single BACs covering the entire region of interest are not available. Here, we describe a general system for linking two or more overlapping BACs into a single clone. Two rounds of homologous recombination are used. In the first, the BAC inserts are subcloned into the pBACLink vectors. In the second, the two BACs are combined together. Multiple BACs in a contig can be combined by alternating use of the pBACLInk vectors, resulting in several BAC clones containing as much of the genomic region of a gene as required. Such BACs can then be used in gene expression studies and/or gene therapy applications. PMID:25239744

  12. Overlapped Fourier coding for optical aberration removal

    PubMed Central

    Horstmeyer, Roarke; Ou, Xiaoze; Chung, Jaebum; Zheng, Guoan; Yang, Changhuei

    2014-01-01

    We present an imaging procedure that simultaneously optimizes a camera’s resolution and retrieves a sample’s phase over a sequence of snapshots. The technique, termed overlapped Fourier coding (OFC), first digitally pans a small aperture across a camera’s pupil plane with a spatial light modulator. At each aperture location, a unique image is acquired. The OFC algorithm then fuses these low-resolution images into a full-resolution estimate of the complex optical field incident upon the detector. Simultaneously, the algorithm utilizes redundancies within the acquired dataset to computationally estimate and remove unknown optical aberrations and system misalignments via simulated annealing. The result is an imaging system that can computationally overcome its optical imperfections to offer enhanced resolution, at the expense of taking multiple snapshots over time. PMID:25321982

  13. Grid adaption using Chimera composite overlapping meshes

    NASA Technical Reports Server (NTRS)

    Kao, Kai-Hsiung; Liou, Meng-Sing; Chow, Chuen-Yen

    1993-01-01

    The objective of this paper is to perform grid adaptation using composite over-lapping meshes in regions of large gradient to capture the salient features accurately during computation. The Chimera grid scheme, a multiple overset mesh technique, is used in combination with a Navier-Stokes solver. The numerical solution is first converged to a steady state based on an initial coarse mesh. Solution-adaptive enhancement is then performed by using a secondary fine grid system which oversets on top of the base grid in the high-gradient region, but without requiring the mesh boundaries to join in any special way. Communications through boundary interfaces between those separated grids are carried out using tri-linear interpolation. Applications to the Euler equations for shock reflections and to a shock wave/boundary layer interaction problem are tested. With the present method, the salient features are well resolved.

  14. Projected seniority-two orbital optimization of the antisymmetric product of one-reference orbital geminal

    NASA Astrophysics Data System (ADS)

    Boguslawski, Katharina; Tecmer, Paweł; Limacher, Peter A.; Johnson, Paul A.; Ayers, Paul W.; Bultinck, Patrick; De Baerdemacker, Stijn; Van Neck, Dimitri

    2014-06-01

    We present a new, non-variational orbital-optimization scheme for the antisymmetric product of one-reference orbital geminal wave function. Our approach is motivated by the observation that an orbital-optimized seniority-zero configuration interaction (CI) expansion yields similar results to an orbital-optimized seniority-zero-plus-two CI expansion [L. Bytautas, T. M. Henderson, C. A. Jimenez-Hoyos, J. K. Ellis, and G. E. Scuseria, J. Chem. Phys. 135, 044119 (2011)]. A numerical analysis is performed for the C2 and LiF molecules, for the CH2 singlet diradical as well as for the symmetric stretching of hypothetical (linear) hydrogen chains. For these test cases, the proposed orbital-optimization protocol yields similar results to its variational orbital optimization counterpart, but prevents symmetry-breaking of molecular orbitals in most cases.

  15. Detecting overlapping instances in microscopy images using extremal region trees.

    PubMed

    Arteta, Carlos; Lempitsky, Victor; Noble, J Alison; Zisserman, Andrew

    2016-01-01

    In many microscopy applications the images may contain both regions of low and high cell densities corresponding to different tissues or colonies at different stages of growth. This poses a challenge to most previously developed automated cell detection and counting methods, which are designed to handle either the low-density scenario (through cell detection) or the high-density scenario (through density estimation or texture analysis). The objective of this work is to detect all the instances of an object of interest in microscopy images. The instances may be partially overlapping and clustered. To this end we introduce a tree-structured discrete graphical model that is used to select and label a set of non-overlapping regions in the image by a global optimization of a classification score. Each region is labeled with the number of instances it contains - for example regions can be selected that contain two or three object instances, by defining separate classes for tuples of objects in the detection process. We show that this formulation can be learned within the structured output SVM framework and that the inference in such a model can be accomplished using dynamic programming on a tree structured region graph. Furthermore, the learning only requires weak annotations - a dot on each instance. The candidate regions for the selection are obtained as extremal region of a surface computed from the microscopy image, and we show that the performance of the model can be improved by considering a proxy problem for learning the surface that allows better selection of the extremal regions. Furthermore, we consider a number of variations for the loss function used in the structured output learning. The model is applied and evaluated over six quite disparate data sets of images covering: fluorescence microscopy, weak-fluorescence molecular images, phase contrast microscopy and histopathology images, and is shown to exceed the state of the art in performance. PMID:25980675

  16. Proteomics Analysis Reveals Overlapping Functions of Clustered Protocadherins*

    PubMed Central

    Han, Meng-Hsuan; Lin, Chengyi; Meng, Shuxia; Wang, Xiaozhong

    2010-01-01

    The three tandem-arrayed protocadherin (Pcdh) gene clusters, namely Pcdh-α, Pcdh-β, and Pcdh-γ, play important roles in the development of the vertebrate central nervous system. To gain insight into the molecular action of PCDHs, we performed a systematic proteomics analysis of PCDH-γ-associated protein complexes. We identified a list of 154 non-redundant proteins in the PCDH-γ complexes. This list includes nearly 30 members of clustered Pcdh-α, -β, and -γ families as core components of the complexes and additionally over 120 putative PCDH-associated proteins. We validated a selected subset of PCDH-γ-associated proteins using specific antibodies. Analysis of the identities of PCDH-associated proteins showed that the majority of them overlap with the proteomic profile of postsynaptic density preparations. Further analysis of membrane protein complexes revealed that several validated PCDH-γ-associated proteins exhibit reduced levels in Pcdh-γ-deficient brain tissues. Therefore, PCDH-γs are required for the integrity of the complexes. However, the size of the overall complexes and the abundance of many other proteins remained unchanged, raising a possibility that PCDH-αs and PCDH-βs might compensate for PCDH-γ function in complex formation. As a test of this idea, RNA interference knockdown of both PCDH-αs and PCDH-γs showed that PCDHs have redundant functions in regulating neuronal survival in the chicken spinal cord. Taken together, our data provide evidence that clustered PCDHs coexist in large protein complexes and have overlapping functions during vertebrate neural development. PMID:19843561

  17. Geometrical constraint experimental determination of Raman lidar overlap profile.

    PubMed

    Li, Jian; Li, Chengcai; Zhao, Yiming; Li, Jing; Chu, Yiqi

    2016-06-20

    A simple experimental method to determine the overlap profile of Raman lidar is presented in this paper. Based on Mie and Raman backscattering signals and a geometrically constrained condition, the overlap profile of a Raman lidar system can be determined. Our approach simultaneously retrieves the lidar ratio of aerosols, which is one of the most important sources of uncertainty in the overlap profile determination. The results indicate that the overlap factor is significantly influenced by the lidar ratio in experimental methods. A representative case study indicates that the correction of the overlap profile obtained by this method is practical and feasible. PMID:27409119

  18. Orbit determination and prediction study for Dynamic Explorer 2

    NASA Technical Reports Server (NTRS)

    Smith, R. L.; Nakai, Y.; Doll, C. E.

    1983-01-01

    Definitive orbit determination accuracy and orbit prediction accuracy for the Dynamic Explorer-2 (DE-2) are studied using the trajectory determination system for the period within six weeks of spacecraft reentry. Baseline accuracies using standard orbit determination models and methods are established. A promising general technique for improving the orbit determination accuracy of high drag orbits, estimation of random drag variations at perigee passages, is investigated. This technique improved the fit to the tracking data by a factor of five and improved the solution overlap consistency by a factor of two during a period in which the spacecraft perigee altitude was below 200 kilometers. The results of the DE-2 orbit predictions showed that improvement in short term prediction accuracy reduces to the problem of predicting future drag scale factors: the smoothness of the solar 10.7 centimeter flux density suggests that this may be feasible.

  19. Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domain.

    PubMed

    Lehman, William; Medlock, Greg; Li, Xiaochuan Edward; Suphamungmee, Worawit; Tu, An-Yue; Schmidtmann, Anja; Ujfalusi, Zoltán; Fischer, Stefan; Moore, Jeffrey R; Geeves, Michael A; Regnier, Michael

    2015-04-01

    The ends of coiled-coil tropomyosin molecules are joined together by nine to ten residue-long head-to-tail "overlapping domains". These short four-chained interconnections ensure formation of continuous tropomyosin cables that wrap around actin filaments. Molecular Dynamics simulations indicate that the curvature and bending flexibility at the overlap is 10-20% greater than over the rest of the molecule, which might affect head-to-tail filament assembly on F-actin. Since the penultimate residue of striated muscle tropomyosin, Ser283, is a natural target of phosphorylating enzymes, we have assessed here if phosphorylation adjusts the mechanical properties of the tropomyosin overlap domain. MD simulations show that phosphorylation straightens the overlap to match the curvature of the remainder of tropomyosin while stiffening it to equal or exceed the rigidity of canonical coiled-coil regions. Corresponding EM data on phosphomimetic tropomyosin S283D corroborate these findings. The phosphorylation-induced change in mechanical properties of tropomyosin likely results from electrostatic interactions between C-terminal phosphoSer283 and N-terminal Lys12 in the four-chain overlap bundle, while promoting stronger interactions among surrounding residues and thus facilitating tropomyosin cable assembly. The stiffening effect of D283-tropomyosin noted correlates with previously observed enhanced actin-tropomyosin activation of myosin S1-ATPase, suggesting a role for the tropomyosin phosphorylation in potentiating muscle contraction. PMID:25726728

  20. Molecular orbital calculations, experimental and theoretical UV spectra of granulatimides and didemnimides, biologically active polycyclic heteroaromatic alkaloids from the ascidian Didemnum granulatum

    NASA Astrophysics Data System (ADS)

    Camargo, A. J.; Oliveira, J. H. H. L.; Trsic, M.; Berlinck, R. G. S.

    2001-01-01

    A detailed computational study was performed for compounds granulatimide, isogranulatimide, and didemnimides A, D, and E, using the semiempirical Austin model 1 quantum chemical method. The electronic features and structural parameters were confronted with the inhibition of the G2 cell cycle checkpoint of mammalian cancer cells. All compounds were submitted to a rigorous conformational analysis using the Tripos 5.2 force field implemented in the Spartan 5.01 program. The electronic density in specific regions of the molecules appears to play a pivotal role towards activity. The molecular planarity creates a broad negative electrostatic potential on the two sides of the active compounds (granulatimide and isogralulatimide) and a positive potential in their central core, while the non-planar compounds (didemnimides A, D, and E, which are inactive) present an asymmetric potential scattered over the molecules. These electrostatic potential features are likely to be the modulator of hydrophobicity or lipophilicity of the compounds, which appear correlated with activity. The hydrogen attached to the N atom of the pyrrole moiety of indole is more positive for active compounds than for the inactive molecules. The theoretical electronic spectra were obtained for all compounds using the configuration interaction method, with the AM1 routine. All transitions present π→π ∗ nature. The theoretical results are in good agreement with experimental values.

  1. Multi-component molecular orbital study on positron attachment to alkali-metal hydride molecules: nature of chemical bonding and dissociation limits of [LiH; e+

    NASA Astrophysics Data System (ADS)

    Oyamada, Takayuki; Tachikawa, Masanori

    2014-08-01

    We have performed multi-component full-configuration interaction calculations to investigate the nature of chemical bonding of [LiH;e+] at the small and large internuclear distance. We discuss the importance of geometrical changes in positronic compounds induced by a positron attachment in terms of the virial theorem, with a comparison of the adiabatic- and vertical-positron affinity (PA). The systematic improvement of the PA values achieved by optimisation of (i) the molecular geometry and (ii) the positronic basis centre is also discussed. The stable dissociation channel of [LiH;e+] is compared with the ionic- and neutral-dissociation channels of its parent molecule LiH through the analysis of the potential energy curve and the electronic and positronic densities. The vertical PA as a function of is also presented, which is the difference between the potential energy curve of the parent molecule (LiH → Li + H) and its positronic compound ([LiH; e+] → Li + [H; e+]). Unlike the preceding study of [M. Mella et al., J. Chem. Phys. 113, 6154 (2000)], it took more than bohr to converge the vertical PA due to the long-range ionic bonding interaction.

  2. Molecular orbital studies on the mechanism of drug-receptor interaction. 2. beta-Adrenergic drugs. An approach to explain the role of the aromatic moiety.

    PubMed

    Petrongolo, C; Macchia, B; Macchia, F; Martinelli, A

    1977-12-01

    The role of the aromatic moiety of beta-adrenergic drugs in the interaction with the receptor was investigated using the quantum mechanical ab initio SCF-MO-LCAO method. The structure-activity relationship was essentially discussed by analyzing the electrostatic molecular potential of three compounds which constitute meaningful portions of isoproterenol, INPEA, and doberol, the first drug having a stimulating activity and the others a blocking one. The results obtained point out the different roles played in the drug-receptor interaction by the various regions of the drugs and they also show that the aromatic moiety influences both the affinity and the intrinsic activity of the drugs. Indeed, the spatial correspondence among zones with negative potentials, which are localized on the phenyl substitutents of isoproterenol and INPEA and on the phenyl ring of doberol, could contribute to the affinity. On the other hand, the intrinsic activity of isoproterenol might be associated both with the proton-donor tendency of one phenolic OH group and with the wide zone of negative potential which spreads on a large part of the aromati moiety. PMID:201757

  3. Depression-Burnout Overlap in Physicians

    PubMed Central

    Wurm, Walter; Vogel, Katrin; Holl, Anna; Ebner, Christoph; Bayer, Dietmar; Mörkl, Sabrina; Szilagyi, Istvan-Szilard; Hotter, Erich; Kapfhammer, Hans-Peter; Hofmann, Peter

    2016-01-01

    Background Whether burnout is a distinct phenomenon rather than a type of depression and whether it is a syndrome, limited to three “core” components (emotional exhaustion, depersonalization and low personal accomplishment) are subjects of current debate. We investigated the depression-burnout overlap, and the pertinence of these three components in a large, representative sample of physicians. Methods In a cross-sectional study, all Austrian physicians were invited to answer a questionnaire that included the Major Depression Inventory (MDI), the Hamburg Burnout Inventory (HBI), as well as demographic and job-related parameters. Of the 40093 physicians who received an invitation, a total of 6351 (15.8%) participated. The data of 5897 participants were suitable for analysis. Results Of the participants, 10.3% were affected by major depression. Our study results suggest that potentially 50.7% of the participants were affected by symptoms of burnout. Compared to physicians unaffected by burnout, the odds ratio of suffering from major depression was 2.99 (95% CI 2.21–4.06) for physicians with mild, 10.14 (95% CI 7.58–13.59) for physicians with moderate, 46.84 (95% CI 35.25–62.24) for physicians with severe burnout and 92.78 (95% CI 62.96–136.74) for the 3% of participants with the highest HBI_sum (sum score of all ten HBI components). The HBI components Emotional Exhaustion, Personal Accomplishment and Detachment (representing depersonalization) tend to correlate more highly with the main symptoms of major depression (sadness, lack of interest and lack of energy) than with each other. A combination of the HBI components Emotional Exhaustion, Helplessness, Inner Void and Tedium (adj.R2 = 0.92) explained more HBI_sum variance than the three “core” components (adj.R2 = 0.85) of burnout combined. Cronbach’s alpha for Emotional Exhaustion, Helplessness, Inner Void and Tedium combined was 0.90 compared to α = 0.54 for the combination of the three

  4. Resonance overlap criterion for H atom ionization by circularly polarized microwave fields

    SciTech Connect

    Sacha, K.; Zakrzewski, J.

    1997-01-01

    The threshold for H atom ionization by circularly polarized microwave fields is discussed within the classical mechanics framework for high microwave frequencies. The Chirikov resonance overlap criterion predictions are compared with estimates obtained adopting the renormalization method. It is shown that the ionization threshold is highly sensitive to the helicity of microwaves. Among all possible initial electronic orbits, those of medium eccentricity are the first to ionize. The results obtained indicate that collisions with the nucleus play a negligible role for the onset of ionization. {copyright} {ital 1997} {ital The American Physical Society}

  5. Molecular geometry, vibrational frequencies, infrared intensities and CN effective bond charges in a series of simple nitrile compounds: HF/6-31+G(d,p) molecular orbital study

    NASA Astrophysics Data System (ADS)

    Dudev, Todor; Bobadova-Parvanova, Petia; Pencheva, Daniela; Galabov, Boris

    1997-12-01

    The structural and vibrational spectroscopic parameters of a series of simple nitrile compounds were evaluated by HF/6-31+G(d,p) ab initio quantum mechanical calculations. The series includes HCN, FCN, CICN, CH 2FCN, CH 2CICN, CH 3CN, CF 3CN, CCl 3CN, HOCN, HSCN and NH 2CN. The theoretical infrared intensities were transformed into quantities associated with the charge distribution and dynamics in the molecules following the formalism of the effective bond charge method. Satisfactory linear relations were found between the effective bond charges and bond lengths, as well as between the bond charges and the molecular electrostatic potential at the nitrogen atom.

  6. Status of the Lunar Reconnaissance Orbiter Geodetic Investigation

    NASA Astrophysics Data System (ADS)

    Mazarico, E.; Rowlands, D. D.; Neumann, G. A.; Smith, D. E.; Torrence, M. H.; Lemoine, F. G.; Zuber, M. T.

    2011-12-01

    We present the status of the Precision Orbit Determination work performed at NASA Goddard Space Flight Center by the Lunar Orbiter Laser Altimeter (LOLA) Science Team. LOLA, the multi-beam laser altimeter instrument onboard the Lunar Reconnaissance Orbiter (LRO), has been operating continuously since July 13, 2009 and has provided more than 4.5 billion measurements as of July 2011. The high precision (10cm) and small footprint (5m) of the altimetric data, as well as the high resolution (25cm per pixel) of the LRO Camera (LROC), require high-accuracy orbits of the LRO spacecraft in order to maximize their scientific value and to enable proper coregistration of the various datasets obtained by LRO. Radiometric tracking data are complemented by altimetric crossover constraints derived from individual LOLA profiles. With a pre-LRO a priori gravity field (GLGM-3), the crossovers helped substantially improve the self-consistency of the reconstructed LRO orbits (assessed through orbit overlaps), from ~70m overlap RMS (radiometric-only) down to ~25m.We also used the LRO tracking and altimetric data to obtain a new solution of the lunar gravity field, specifically designed to provide enhanced orbit accuracy. With this preliminary LRO field (LLGM-1), the radiometric-only orbits achieve ~25m overlap precision. When complemented by the altimetric crossovers, the orbit consistency improves to better than 15m. Results from more than 2 years of radiometric tracking data and LOLA altimetry will be shown, including an updated gravity field solution. Current efforts to use very long integration arcs (4 months at a time) will also be presented, with the goal of combining all the available farside crossover constraints to help refine the short-wavelength farside gravity field.

  7. Realigning the Orbits of Central Office and Schools

    ERIC Educational Resources Information Center

    Larson, Eliot W.

    2007-01-01

    This article discusses why the work of central-office administrators and building administrators seem so disconnected from one another. The fact that central-office administrators and principals seem to travel in orbits with different paths, with seemingly few areas of significant overlap, has a decidedly negative impact on the ability of the…

  8. Translation and integration of numerical atomic orbitals in linear molecules.

    PubMed

    Heinäsmäki, Sami

    2014-02-14

    We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively. PMID:24527905

  9. Translation and integration of numerical atomic orbitals in linear molecules

    NASA Astrophysics Data System (ADS)

    Heinäsmäki, Sami

    2014-02-01

    We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively.

  10. Spectroscopic (FT-IR, FT-Raman and UV) investigation, NLO, NBO, molecular orbital and MESP analysis of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.

    2015-02-01

    In this work, FT-IR and FT-Raman spectra of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid (abbreviated as 2DCPAPAA) have been reported in the regions 4000-450 cm-1 and 4000-50 cm-1, respectively. The molecular structure, geometry optimization, intensities, vibrational frequencies were obtained by the ab initio and DFT levels of theory B3LYP with 6-311++G(d,p) standard basis set and a different scaling of the calculated wave numbers. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using vibrational energy distribution analysis (VEDA 4) program. The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman data. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The thermodynamic properties of the title compound at different temperature reveal the correlations between standard heat capacities (C) standard entropies (S) standard enthalpy changes (ΔH). The important non-linear optical properties such as electric dipole momentum, polarizability and first hyperpolarizability of 2DCPAPAA have been computed using B3LYP/6-311++G(d,p) quantum chemical calculations. The Natural charges, HOMO, LUMO, chemical hardness (η), chemical potential (μ), Electro negativity (χ) and electrophilicity values (ω) are calculated and reported. The oscillator's strength, wave length, and energy calculated by TD-DFT and 2DCPAPAA is approach complement with the experimental findings. The molecular electrostatic potential (MESP) surfaces of the molecule were constructed.

  11. Theory of Secular Chaos and Mercury's Orbit

    NASA Astrophysics Data System (ADS)

    Lithwick, Yoram; Wu, Yanqin

    2011-09-01

    We study the chaotic orbital evolution of planetary systems, focusing on secular (i.e., orbit-averaged) interactions, which dominate on long timescales. We first focus on the evolution of a test particle that is forced by multiple planets. To linear order in eccentricity and inclination, its orbit precesses with constant frequencies. But nonlinearities modify the frequencies, and can shift them into and out of resonance with either the planets' eigenfrequencies (forming eccentricity or inclination secular resonances), or with linear combinations of those frequencies (forming mixed high-order secular resonances). The overlap of these nonlinear secular resonances drives secular chaos. We calculate the locations and widths of nonlinear secular resonances, display them together on a newly developed map (the "map of the mean momenta"), and find good agreement between analytical and numerical results. This map also graphically demonstrates how chaos emerges from overlapping secular resonances. We then apply this newfound understanding to Mercury to elucidate the origin of its orbital chaos. We find that since Mercury's two free precession frequencies (in eccentricity and inclination) lie within ~25% of two other eigenfrequencies in the solar system (those of the Jupiter-dominated eccentricity mode and the Venus-dominated inclination mode), secular resonances involving these four modes overlap and cause Mercury's chaos. We confirm this with N-body integrations by showing that a slew of these resonant angles alternately librate and circulate. Our new analytical understanding allows us to calculate the criterion for Mercury to become chaotic: Jupiter and Venus must have eccentricity and inclination of a few percent. The timescale for Mercury's chaotic diffusion depends sensitively on the forcing. As it is, Mercury appears to be perched on the threshold for chaos, with an instability timescale comparable to the lifetime of the solar system.

  12. Effect of horizontal molecular orientation on triplet-exciton diffusion in amorphous organic films

    NASA Astrophysics Data System (ADS)

    Sawabe, T.; Takasu, I.; Yonehara, T.; Ono, T.; Yoshida, J.; Enomoto, S.; Amemiya, I.; Adachi, C.

    2012-09-01

    Triplet harvesting is a candidate technology for highly efficient and long-life white OLEDs, where green or red phosphorescent emitters are activated by the triplet-excitons diffused from blue fluorescent emitters. We examined two oxadiazole-based electron transport materials with different horizontal molecular orientation as a triplet-exciton diffusion layer (TDL) in triplet-harvesting OLEDs. The device characteristics and the transient electroluminescent analyses of the red phosphorescent emitter showed that the triplet-exciton diffusion was more effective in the highly oriented TDL. The results are ascribed to the strong orbital overlap between the oriented molecules, which provides rapid electron exchange (Dexter energy transfer) in the TDL.

  13. EVOG: a database for evolutionary analysis of overlapping genes.

    PubMed

    Kim, Dae-Soo; Cho, Chi-Young; Huh, Jae-Won; Kim, Heui-Soo; Cho, Hwan-Gue

    2009-01-01

    Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. In this study, we implemented evolutionary visualizer for overlapping genes (EVOG), a Web-based DB with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Using this technique, we collected and analyzed all overlapping genes in human, chimpanzee, orangutan, marmoset, rhesus, cow, dog, mouse, rat, chicken, Xenopus, zebrafish and Drosophila. This integrated database provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG DB components included a number of overlapping genes (10074 in human, 10,009 in chimpanzee, 67,039 in orangutan, 51,001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10,700 in mouse, 7987 in rat, 1439 in chicken, 597 in Xenopus, 2457 in zebrafish and 4115 in Drosophila). The EVOG database is very effective and easy to use for the analysis of the evolutionary process of overlapping genes when comparing different species. Therefore, EVOG could potentially be used as the main tool to investigate the evolution of the human genome in relation to disease by comparing the expression profiles of overlapping genes. EVOG is available at http://neobio.cs.pusan.ac.kr/evog/. PMID:18986995

  14. Effects of overlapping strings in pp collisions

    DOE PAGESBeta

    Bierlich, Christian; Gustafson, Gösta; Lönnblad, Leif; Tarasov, Andrey

    2015-03-26

    In models for hadron collisions based on string hadronization, the strings are usually treated as independent, allowing no interaction between the confined colour fields. In studies of nucleus collisions it has been suggested that strings close in space can fuse to form "colour ropes." Such ropes are expected to give more strange particles and baryons, which also has been suggested as a signal for plasma formation. Overlapping strings can also be expected in pp collisions, where usually no phase transition is expected. In particular at the high LHC energies the expected density of strings is quite high. To investigate possiblemore » effects of rope formation, we present a model in which strings are allowed to combine into higher multiplets, giving rise to increased production of baryons and strangeness, or recombine into singlet structures and vanish. Also a crude model for strings recombining into junction structures is considered, again giving rise to increased baryon production. The models are implemented in the DIPSY MC event generator, using PYTHIA8 for hadronization, and comparison to pp minimum bias data, reveals improvement in the description of identified particle spectra.« less

  15. [Autoimmune hepatitis and overlap syndrome: therapy].

    PubMed

    Löhr, H F

    2002-08-21

    Autoimmune Hepatitis (AIH), primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) represent acute and chronic inflammatory liver diseases in which immune reactions against host antigens are found to be the major pathological mechanism. Only for AIH there is evidence of an autoimmune etiology and humoral and cellular immune reactions are found directed against various liver cell antigens. By diverse autoantibodies several subgroups of autoimmune hepatitis can be distinguished. A very important disease promoting factor seems to be the genetically determined background for autoimmunity characterized by the HLA haplotype A1, B8 and DR3, respectively DR4. Although the histopathology of AIH shows no pathognomonic features distinguishing this type of hepatitis from virus induced chronic hepatitis there are some distinct characteristic morphological lesions. If untreated the prognosis of AIH is unfavourable but the benefit from immunosuppressive therapy with prednisolone and azathioprin is well established. In the last years there was increasing evidence for an overlap syndrome between AIH and PBC and rarely AIH and PSC. These patients are characterized by PBC characteristic bileduct lesions and oftenly antimitochondrial antibodies (AMA). They also show AIH typical inflammatory hepatic lesions in the periportal areas and portal tracts and oftenly the typical genetical background, the HLA haplotype A1, B8, DR3 or DR4. Most of these patients respond probably to a combination therapy containing prednisolon, azathioprine and ursodesoxycholic acid that leads to the reduction of the inflammatory activity. PMID:12233265

  16. Base drive and overlap protection circuit

    DOEpatents

    Gritter, David J.

    1983-01-01

    An inverter (34) which provides power to an A. C. machine (28) is controlled by a circuit (36) employing PWM control strategy whereby A. C. power is supplied to the machine at a preselectable frequency and preselectable voltage. This is accomplished by the technique of waveform notching in which the shapes of the notches are varied to determine the average energy content of the overall waveform. Through this arrangement, the operational efficiency of the A. C. machine is optimized. The control circuit includes a microcomputer and memory element which receive various parametric inputs and calculate optimized machine control data signals therefrom. The control data is asynchronously loaded into the inverter through an intermediate buffer (38). A base drive and overlap protection circuit is included to insure that both transistors of a complimentary pair are not conducting at the same time. In its preferred embodiment, the present invention is incorporated within an electric vehicle (10) employing a 144 VDC battery pack (32) and a three-phase induction motor (18).

  17. Effects of overlapping strings in pp collisions

    SciTech Connect

    Bierlich, Christian; Gustafson, Gösta; Lönnblad, Leif; Tarasov, Andrey

    2015-03-26

    In models for hadron collisions based on string hadronization, the strings are usually treated as independent, allowing no interaction between the confined colour fields. In studies of nucleus collisions it has been suggested that strings close in space can fuse to form "colour ropes." Such ropes are expected to give more strange particles and baryons, which also has been suggested as a signal for plasma formation. Overlapping strings can also be expected in pp collisions, where usually no phase transition is expected. In particular at the high LHC energies the expected density of strings is quite high. To investigate possible effects of rope formation, we present a model in which strings are allowed to combine into higher multiplets, giving rise to increased production of baryons and strangeness, or recombine into singlet structures and vanish. Also a crude model for strings recombining into junction structures is considered, again giving rise to increased baryon production. The models are implemented in the DIPSY MC event generator, using PYTHIA8 for hadronization, and comparison to pp minimum bias data, reveals improvement in the description of identified particle spectra.

  18. Orbit determination and gravity field recovery from tracking data to the Lunar Reconnaissance Orbiter

    NASA Astrophysics Data System (ADS)

    Maier, Andrea; Baur, Oliver

    2015-04-01

    The Lunar Reconnaissance Orbiter (LRO), launched in 2009, is well suited for the estimation of the long wavelengths of the lunar gravity field due to its low altitude of 50 km. Further, the orbit of LRO was polar for two years providing global coverage. The satellite has been primarily tracked via S-band (mainly two-way Doppler range-rates and two-way radiometric ranges) from the dedicated station in White Sands and from the Universal Space Network (USN). Due to the onboard altimeter the orbital precision requirement in the radial direction was rigorously defined as 1m. Because simulation studies before LRO's launch showed that this precision could not be reached with S-band observations alone, it was decided to additionally track LRO via optical laser ranges. It is worthwhile to point out that LRO is the first spacecraft in interplanetary space routinely tracked with optical one-way laser ranges. Gravity field recovery from orbit perturbations is intrinsically related to precise orbit determination. This is why considerable effort was made to find the optimum settings for orbit modeling. For a time span of three months we conducted a series of orbit overlapping tests based on Doppler observations to find the optimum arc length and the optimum set of empirical parameters. The analysis of observation residuals and orbit overlap differences showed that the estimated orbits are most precise when subdividing the time span into 2.5 days and estimating one constant empirical acceleration in along track direction. These settings were then used to analyze 13 months of Doppler data to LRO. The processing of the optical one-way laser was difficult due to the involvement of two non-synchronous clocks in one measurement (one clock at the ground station and one clock onboard LRO). The NASA software GEODYN, which was used for orbit determination and parameter estimation, models the LRO clock using a drift rate (first-order term) and an aging rate (second-order term). It seems

  19. Lunar Reconnaissance Orbiter Orbit Determination Accuracy Analysis

    NASA Technical Reports Server (NTRS)

    Slojkowski, Steven E.

    2014-01-01

    Results from operational OD produced by the NASA Goddard Flight Dynamics Facility for the LRO nominal and extended mission are presented. During the LRO nominal mission, when LRO flew in a low circular orbit, orbit determination requirements were met nearly 100% of the time. When the extended mission began, LRO returned to a more elliptical frozen orbit where gravity and other modeling errors caused numerous violations of mission accuracy requirements. Prediction accuracy is particularly challenged during periods when LRO is in full-Sun. A series of improvements to LRO orbit determination are presented, including implementation of new lunar gravity models, improved spacecraft solar radiation pressure modeling using a dynamic multi-plate area model, a shorter orbit determination arc length, and a constrained plane method for estimation. The analysis presented in this paper shows that updated lunar gravity models improved accuracy in the frozen orbit, and a multiplate dynamic area model improves prediction accuracy during full-Sun orbit periods. Implementation of a 36-hour tracking data arc and plane constraints during edge-on orbit geometry also provide benefits. A comparison of the operational solutions to precision orbit determination solutions shows agreement on a 100- to 250-meter level in definitive accuracy.

  20. A Detailed Derivation of Gaussian Orbital-Based Matrix Elements in Electron Structure Calculations

    ERIC Educational Resources Information Center

    Petersson, T.; Hellsing, B.

    2010-01-01

    A detailed derivation of analytic solutions is presented for overlap, kinetic, nuclear attraction and electron repulsion integrals involving Cartesian Gaussian-type orbitals. It is demonstrated how s-type orbitals can be used to evaluate integrals with higher angular momentum via the properties of Hermite polynomials and differentiation with…

  1. A Lower Bound for Quantifying Overlap Effects: An Empirical Approach

    SciTech Connect

    Bassetti, Federico

    1997-12-31

    Among the many features that are implemented in today`s microprocessors there are some that have the capability of reducing the execution time via overlapping of different operations. Overlapping of instructions with other instructions, and overlapping of computation with memory activities are the main way in which execution time is reduced. In this paper we will introduce a notion of overlap and its definition, and a few different ways to capture its effects. We will characterize some of the DOE Accelerated Strategic Computing Initiative (ASCI) benchmarks using the overlap and some other quantities related to it. Also, we will present a characterization of the overlap effects using a lower bound derived empirically from measured data. We will conclude by using the lower bound to estimate other components of the overall execution time.

  2. Effect of Molecular Stacking on Exciton Diffusion in Crystalline Organic Semiconductors.

    PubMed

    Pinto, Rui M; Maçôas, Ermelinda M S; Neves, Ana I S; Raja, Sebastian; Baleizão, Carlos; Santos, Isabel C; Alves, Helena

    2015-06-10

    Exciton diffusion is at the heart of most organic optoelectronic devices' operation, and it is currently the most limiting factor to their achieving high efficiency. It is deeply related to molecular organization, as it depends on intermolecular distances and orbital overlap. However, there is no clear guideline for how to improve exciton diffusion with regard to molecular design and structure. Here, we use single-crystal charge-transfer interfaces to probe favorable exciton diffusion. Photoresponse measurements on interfaces between perylenediimides and rubrene show a higher photocurrent yield (+50%) and extended spectral coverage (+100 nm) when there is increased dimensionality of the percolation network and stronger orbital overlap. This is achieved by very short interstack distances in different directional axes, which favors exciton diffusion by a Dexter mechanism. Even if the core of the molecule shows strong deviation from planarity, the similar electrical resistance of the different systems, planar and nonplanar, shows that electronic transport is not compromised. These results highlight the impact of molecular organization in device performance and the necessity of optimizing it to take full advantage of the materials' properties. PMID:25990135

  3. Evaluation of Improved Spacecraft Models for GLONASS Orbit Determination

    NASA Astrophysics Data System (ADS)

    Weiss, J. P.; Sibthorpe, A.; Harvey, N.; Bar-Sever, Y.; Kuang, D.

    2010-12-01

    High-fidelity spacecraft models become more important as orbit determination strategies achieve greater levels of precision and accuracy. In this presentation, we assess the impacts of new solar radiation pressure and attitude models on precise orbit determination (POD) for GLONASS spacecraft within JPLs GIPSY-OASIS software. A new solar radiation pressure model is developed by empirically fitting a Fourier expansion to solar pressure forces acting on the spacecraft X, Y, Z components using one year of recent orbit data. Compared to a basic “box-wing” solar pressure model, the median 24-hour orbit prediction accuracy for one month of independent test data improves by 43%. We additionally implement an updated yaw attitude model during eclipse periods. We evaluate the impacts of both models on post-processed POD solutions spanning 6-months. We consider a number of metrics such as internal orbit and clock overlaps as well as comparisons to independent solutions. Improved yaw attitude modeling reduces the dependence of these metrics on the “solar elevation” angle. The updated solar pressure model improves orbit overlap statistics by several mm in the median sense and centimeters in the max sense (1D). Orbit differences relative to the IGS combined solution are at or below the 5 cm level (1D RMS).

  4. Solving Fluid Flow Problems on Moving and Adaptive Overlapping Grids

    SciTech Connect

    Henshaw, W

    2005-07-28

    Solution of fluid dynamics problems on overlapping grids will be discussed. An overlapping grid consists of a set of structured component grids that cover a domain and overlap where they meet. Overlapping grids provide an effective approach for developing efficient and accurate approximations for complex, possibly moving geometry. Topics to be addressed include the reactive Euler equations, the incompressible Navier-Stokes equations and elliptic equations solved with a multigrid algorithm. Recent developments coupling moving grids and adaptive mesh refinement and preliminary parallel results will also be presented.

  5. How molecular is the chemisorptive bond?

    PubMed

    van Santen, R A; Tranca, I

    2016-08-01

    Trends in adsorption energies as a function of transition metal differ for adsorbates that are attached atop a surface atom or are adsorbed onto a high coordination site. When adsorption onto early and late transition metals is compared variation in relative bond energies of adsorbates attached to different sites is large. A theoretical understanding is provided based on the analysis of the electronic structure of the respective chemical bonds. The electronic structure analysis is based on partial density of states (PDOS) and bond order overlap population densities from crystal orbital Hamiltonian population (COHP) calculations available from DFT electronic structure computations. This is complemented by calculations of Bader charge densities and electron density topology properties. Variation of the respective bond energies depends on the symmetry of the molecular orbitals that form the chemical bond. The key electronic structure parameters are the position of the Fermi level in the bonding or antibonding molecular orbital partial density of states region of the chemical bond and chemical bond polarity. These are very different for adsorbates adsorbed onto the same transition metal surface, but which have different coordination with surface metal atoms. The adsorption energies and the respective electronic structures of adatoms H, C and O and molecular fragments CHx (x = 1-3) are compared with those of the analogous molecules that contain a single transition metal atom. When adsorbed atop, trends in bond energies are remarkably similar to those of the corresponding molecules. The difference in bond energies of adsorbates and transition metal molecules, i.e. the embedding energy, is shown to consist of three contributions: quenching of the sometimes high molecular spin states, weakening of the adsorbate-surface interaction energy and weakening of the metal-metal atom bond energies next to the adsorbate. Conventional scaling rules of the interaction energies of

  6. Artist concept of Magellan spacecraft in elliptical orbit around Venus

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Magellan spacecraft is shown in elliptical orbit around Venus, collecting data (radar mapping), and then transmitting data back to Earth in this artist concept. When the spacecraft orbit is close to Venus the synthetic aperature radar (SAR) will image a swath between 9 and 15 nautical miles (10 and 17 statute miles), beginning at or near the north pole and continuing to the southern hemisphere. Subsequent swaths will slightly overlap and, during its primary mission, the spacecraft will map most of the planet. When the spacecraft moves into the part of its elliptical orbit farthest from Venus, the spacecraft high-gain antenna will be turned toward Earth and will send the data collected during the imaging to Earth. Magellan, named after the 16th century Portuguese explorer, will orbit Venus about once every three hours, acquiring radar data for 37 minutes of each orbit. Magellan is managed by the Jet Propulsion Laboratory (JPL); Martin Marietta is developing the spacecraft and Hughes Air

  7. Artist concept of Magellan spacecraft in elliptical orbit around Venus

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Magellan spacecraft is shown in elliptical orbit around Venus, collecting data (radar mapping), and then transmitting data back to Earth in this artist concept. When the spacecraft orbit is close to Venus the synthetic aperature radar (SAR) will image a swath between 9 and 15 nautical miles (10 and 17 statute miles) (highlighted in image), beginning at or near the north pole and continuing to the southern hemisphere. Subsequent swaths will slightly overlap and, during its primary mission, the spacecraft will map most of the planet. When the spacecraft moves into the part of its elliptical orbit farthest from Venus, the spacecraft high-gain antenna will be turned toward Earth and will send the data collected during the imaging to Earth. Magellan, named after the 16th century Portuguese explorer, will orbit Venus about once every three hours, acquiring radar data for 37 minutes of each orbit. Magellan is managed by the Jet Propulsion Laboratory (JPL); Martin Marietta is developing the sp

  8. Lunar orbiting prospector

    NASA Technical Reports Server (NTRS)

    1988-01-01

    One of the prime reasons for establishing a manned lunar presence is the possibility of using the potential lunar resources. The Lunar Orbital Prospector (LOP) is a lunar orbiting platform whose mission is to prospect and explore the Moon from orbit in support of early lunar colonization and exploitation efforts. The LOP mission is divided into three primary phases: transport from Earth to low lunar orbit (LLO), operation in lunar orbit, and platform servicing in lunar orbit. The platform alters its orbit to obtain the desired surface viewing, and the orbit can be changed periodically as needed. After completion of the inital remote sensing mission, more ambitious and/or complicated prospecting and exploration missions can be contemplated. A refueled propulsion module, updated instruments, or additional remote sensing packages can be flown up from the lunar base to the platform.

  9. Synthesis, spectroscopic, molecular orbital calculation, cytotoxic, molecular docking of DNA binding and DNA cleavage studies of transition metal complexes with N-benzylidene-N'-salicylidene-1,1-diaminopropane

    NASA Astrophysics Data System (ADS)

    Al-Mogren, Muneerah M.; Alaghaz, Abdel-Nasser M. A.; Elbohy, Salwa A. H.

    2013-10-01

    Eight mononuclear chromium(III), manganese(II), iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of Schiff's base ligand were synthesized and determined by different physical techniques. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the eight metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff base is found to act as tridentate ligand using N2O donor set of atoms leading to an octahedral geometry for the complexes around all the metal ions. Quantum chemical calculations were performed with semi-empirical method to find the optimum geometry of the ligand and its complexes. Additionally in silico, the docking studies and the calculated pharmacokinetic parameters show promising futures for application of the ligand and complexes as high potency agents for DNA binding activity. The interaction of the complexes with calf thymus DNA (CT-DNA) has been investigated by UV absorption method, and the mode of CT-DNA binding to the complexes has been explored. Furthermore, the DNA cleavage activity by the complexes was performed. The Schiff base and their complexes have been screened for their antibacterial activity against bacterial strains [Staphylococcus aureus (RCMB010027), Staphylococcus epidermidis (RCMB010024), Bacillis subtilis (RCMB010063), Proteous vulgaris (RCMB 010085), Klebsiella pneumonia (RCMB 010093) and Shigella flexneri (RCMB 0100542)] and fungi [(Aspergillus fumigates (RCMB 02564), Aspergillus clavatus (RCMB 02593) and Candida albicans (RCMB05035)] by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligand.

  10. Preliminary orbital parallax catalog

    NASA Technical Reports Server (NTRS)

    Halliwell, M.

    1981-01-01

    The study is undertaken to calibrate the more reliable parallaxes derived from a comparison of visual and spectroscopic orbits and to encourage observational studies of other promising binaries. The methodological techniques used in computing orbital parallaxes are analyzed. Tables summarizing orbital data and derived system properties are then given. Also given is a series of detailed discussions of the 71 individual systems included in the tables. Data are listed for 57 other systems which are considered promising candidates for eventual orbital parallax determination.

  11. Spectroscopic Line Shapes of Vibrational Quanta in the Presence of Molecular Resonances.

    PubMed

    Meierott, Stefan; Néel, Nicolas; Kröger, Jörg

    2016-07-01

    Line shapes of molecular vibrational quanta in inelastic electron tunneling spectroscopy may indicate the strength of electron-vibration coupling, the hybridization of the molecule with its environment, and the degree of vibrational damping by electron-hole pair excitation. Bare as well as C60-terminated Pb tips of a scanning tunneling microscope and clean as well as C60-covered Pb(111) surfaces were used in low-temperature experiments. Depending on the overlap of orbital and vibrational spectral ranges different spectroscopic line shapes of molecular vibrational quanta were observed. The energy range covered by the molecular resonance was altered by modifying the adsorption configuration of the molecule terminating the tip apex. Concomitantly, the line shapes of different vibrational modes were affected. The reported observations represent an experimental proof to theoretical predictions on the contribution from resonant processes to inelastic electron tunneling. PMID:27280313

  12. A reexamination of the small overlap frontal crash.

    PubMed

    Scullion, Paul; Morgan, Richard M; Mohan, Pradeep; Kan, Cing-Dao; Shanks, Kurt; Jin, Wook; Tangirala, Ravi

    2010-01-01

    The objective of this study was to examine and rank the Small Overlap Frontal Crash as one of the eight-group taxonomy proposed by Ford. The Ford taxonomy classifies real-world frontal-impact crashes based on the National Automotive Sampling System (NASS). Frontally-impacted vehicles were identified for 1985 - 2008 model year passenger vehicles with Collision Deformation Classification (CDC) data from the 1995 - 2008 years of NASS. Small overlap frontal cases were identified where there was no engagement of the vehicle frame rails, and the direct damage was located entirely outside of the vehicle frame rails. The results are that full engagement and offset (offset category means the direct damage overlaps the vehicle frame rail, with the center of direct damage between the frame rails) were the most frequent crashes contributing 35% each. The frequency of the small overlap frontal was 6%. The risks of injury (AIS ≥ 2) for the full engagement, offset, and small overlap were 8%, 6%, and 3% respectively. For this study, the number of small overlap vehicles was 1,118 and the number of injured nearside occupants was 100. This study-following the Ford approach and reasonably identifying the location of the longitudinal rails based on CDC-suggests that the small overlap is at worst a moderately dangerous crash in the overall scheme of frontal crashes. The implications of this study are that the safety community should reexamine the significance of the small overlap frontal crash against an overall taxonomy of crashes. PMID:21050598

  13. An Exposition of Fischer's Model of Overlapping Contracts.

    ERIC Educational Resources Information Center

    Fields, T. Windsor; Hart, William R.

    1992-01-01

    Suggests how the classic model of overlapping contracts can be incorporated into the contract wage model of aggregate supply. Illustrates dynamics of macroeconomic adjustment following a shock to aggregate demand. Concludes that overlapping contracts do not prolong the adjustment process; rather, the longest remaining contract determines the time…

  14. Overlaps and Accumulation in the Use of Rehabilitation Services

    ERIC Educational Resources Information Center

    Pulkki, Jutta M.; Rissanen, Pekka; Raitanen, Jani A.; Viitanen, Elina A.

    2011-01-01

    The Finnish rehabilitation system is considered fragmented and multisectoral, and thus it may produce "multiclients" receiving inefficient and overlapping services. This paper addresses the overlaps and accumulation in the delivery of rehabilitation services in Finnish rehabilitation subsystems. Data were drawn from several administrative…

  15. Identifying Cluster Overlap with NORMIX Population Membership Probabilities.

    ERIC Educational Resources Information Center

    Price, Lydia J.

    1993-01-01

    The ability of the NORMIX algorithm to recover overlapping population structures was compared to the OVERCLUS procedure and another clustering procedure in a Monte Carlo study. NORMIX is found to be more accurate than other procedures in recovering overlapping population structure when appropriate implementation options are specified. (SLD)

  16. "Listenership" in Japanese: An Examination of Overlapping Listener Response

    ERIC Educational Resources Information Center

    Ikeda, Keiko

    2004-01-01

    This study focuses on a particular listening pattern in Japanese which occurs by overlapping with the current speaker's incrementing utterance. Applying the Conversational Analysis approach to conversational data, the study delineates how native speakers utilize overlapping listener responses to indicate their strong alignment, and why learners of…

  17. AREA OVERLAP METHOD FOR DETERMINING ADEQUATE CHROMATOGRAPHIC RESOLUTION

    EPA Science Inventory

    The Area Overlap method for evaluating analytical chromatograms is evaluated and compared with the Depth-of-the-Valley, IUPAC and Purnell criteria. The method is a resolution criterion based on the fraction of area contributed by an adjacent, overlapping peak. It accounts for bot...

  18. Overlap loss of manually and automatically guided mowers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Overlap loss in harvesting machinery has been observed as a necessary inefficiency for many years. Each time a non-row-crop machine makes a pass in the field, it is favorable for the operator to overlap slightly into the previous pass (where the crop has already been cut), as opposed to undercutting...

  19. Spousal Network Overlap as a Basis for Spousal Support

    ERIC Educational Resources Information Center

    Cornwell, Benjamin

    2012-01-01

    The role social network structure plays in facilitating flows of support between spouses is often overlooked. This study examined whether levels of support between spouses depended on the degree of overlap between spouses' networks. Network overlap may enhance spouses' support capacities by increasing their understanding of each other's support…

  20. Overlapping and Non-overlapping Functions of Condensins I and II in Neural Stem Cell Divisions

    PubMed Central

    Nishide, Kenji; Hirano, Tatsuya

    2014-01-01

    During development of the cerebral cortex, neural stem cells (NSCs) divide symmetrically to proliferate and asymmetrically to generate neurons. Although faithful segregation of mitotic chromosomes is critical for NSC divisions, its fundamental mechanism remains unclear. A class of evolutionarily conserved protein complexes, known as condensins, is thought to be central to chromosome assembly and segregation among eukaryotes. Here we report the first comprehensive genetic study of mammalian condensins, demonstrating that two different types of condensin complexes (condensins I and II) are both essential for NSC divisions and survival in mice. Simultaneous depletion of both condensins leads to severe defects in chromosome assembly and segregation, which in turn cause DNA damage and trigger p53-induced apoptosis. Individual depletions of condensins I and II lead to slower loss of NSCs compared to simultaneous depletion, but they display distinct mitotic defects: chromosome missegregation was observed more prominently in NSCs depleted of condensin II, whereas mitotic delays were detectable only in condensin I-depleted NSCs. Remarkably, NSCs depleted of condensin II display hyperclustering of pericentric heterochromatin and nucleoli, indicating that condensin II, but not condensin I, plays a critical role in establishing interphase nuclear architecture. Intriguingly, these defects are taken over to postmitotic neurons. Our results demonstrate that condensins I and II have overlapping and non-overlapping functions in NSCs, and also provide evolutionary insight into intricate balancing acts of the two condensin complexes. PMID:25474630