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Sample records for overlap molecular orbital

  1. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    PubMed Central

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

  2. 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…

  3. Calculation of molecular integrals over Slater-type orbitals using recurrence relations for overlap integrals and basic one-center Coulomb integrals.

    PubMed

    Guseinov, Israfil; Mamedov, Bahtiyar; Rzaeva, Afet

    2002-04-01

    The recurrence relations are established for the basic one-center Coulomb integrals over Slater-type orbitals (STOs). These formulae and the recurrence relations for basic overlap integrals are utilized for the calculation of multicenter electron-repulsion integrals. The calculations of multicenter electron-repulsion integrals are performed by the use of translation formulae for STOs obtained from the Lambda and Coulomb Sturmian exponential-type functions (ETFs). It is shown that these integrals show a faster convergence rate in the case of Coulomb Sturmian ETFs. The accuracy of the results is quite high for the quantum numbers of STOs and for the arbitrary values of internuclear distances and screening constants of atomic orbitals.

  4. Finite-Perturbation Intermediate - Neglect - of - Differential - Overlap Molecular Orbital Calculations of Nuclear Magnetic Resonance Spin-Spin Coupling Constants for Polycyclic Aromatic Hydrocarbons and Aromatic Nitrogen Heterocyclics

    NASA Astrophysics Data System (ADS)

    Long, Sheila Ann Thibeault

    The H-H, C-H, and C-C spin-spin coupling constants were calculated by the finite-perturbation, intermediate -neglect-of-differential-overlap method using the Fermi contact interaction for benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations were made using both the actual and the average molecular geometries. For all six of these molecules, the agreements between the calculated and the experimental coupling constants were comparable to those previously reported for other, predominantly smaller, molecules. The actual molecular geometries always gave the correct relative order of values for the H-H coupling constants, whereas the average molecular geometries did not always do so. The magnitudes, but not the signs, of the calculated coupling constants were sensitive to small changes in molecular geometry. The results were the best (next best) for the H-H (C-H) coupling constants. In addition the H-H, C-H, N-H, C-C, and N-C spin -spin coupling constants were calculated in a similar manner for pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, quinoline, quinoxaline, phthalazine, benzo g quinoxaline, and benzo b phenazine. The agreements between the theoretical and the experimental values were comparable to those for the polycyclic aromatic hydrocarbons.

  5. Phonon Overlaps in Molecular Quantum Dot Systems

    NASA Astrophysics Data System (ADS)

    Chang, Connie; Sethna, James

    2004-03-01

    We model the amplitudes and frequencies of the vibrational sidebands for the new molecular quantum dot systems. We calculate the Franck-Condon phonon overlaps in the 3N-dimensional configuration sapce. We solve the general case where the vibrational frequencies and eigenmodes change during the transition. We perform PM3 and DFT calculations for the case of the dumb bell-shaped C140 molecule. We find that the strongest amplitudes are associated with the 11 meV stretch mode, in agreement with experiment. The experimental amplitudes vary from molecule to molecule; indicating that the molecular overlaps are environment dependent. We explore overlaps in the presence of external electric fields from image charges and counter ions.

  6. Analysis of Bonding between Conjugated Organic Molecules and Noble Metal Surfaces Using Orbital Overlap Populations.

    PubMed

    Rangger, Gerold M; Romaner, Lorenz; Hofmann, Oliver T; Heimel, Georg; Ramsey, Michael G; Zojer, Egbert

    2010-11-09

    The electronic structure of metal-organic interfaces is of paramount importance for the properties of organic electronic and single-molecule devices. Here, we use so-called orbital overlap populations derived from slab-type band-structure calculations to analyze the covalent contribution to the bonding between an adsorbate layer and a metal. Using two prototypical molecules, the strong acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) on Ag(111) and the strong donor 1H,1'H-[4,4']bipyridinylidene (HV0) on Au(111), we present overlap populations as particularly versatile tools for describing the metal-organic interaction. Going beyond traditional approaches, in which overlap populations are represented in an atomic orbital basis, we also explore the use of a molecular orbital basis to gain significant additional insight. On the basis of the derived quantities, it is possible to identify the parts of the molecules responsible for the bonding and to analyze which of the molecular orbitals and metal bands most strongly contribute to the interaction and where on the energy scale they interact in bonding or antibonding fashion.

  7. 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.

  8. Diffractive molecular-orbital tomography

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    High-order-harmonic generation in the interaction of femtosecond lasers with atoms and molecules opens the path to molecular-orbital tomography and to probe the electronic dynamics with attosecond-Ångström resolutions. Molecular-orbital tomography requires both the amplitude and phase of the high-order harmonics. Yet the measurement of phases requires sophisticated techniques and represents formidable challenges at present. Here we report a scheme, called diffractive molecular-orbital tomography, to retrieve the molecular orbital solely from the amplitude of high-order harmonics without measuring any phase information. We have applied this method to image the molecular orbitals of N2, CO2, and C2H2 . The retrieved orbital is further improved by taking account the correction of Coulomb potential. The diffractive molecular-orbital tomography scheme, removing the roadblock of phase measurement, significantly simplifies the molecular-orbital tomography procedure and paves an efficient and robust way to the imaging of more complex molecules.

  9. Energy Ordering of Molecular Orbitals

    PubMed Central

    2016-01-01

    Orbitals are invaluable in providing a model of bonding in molecules or between molecules and surfaces. Most present-day methods in computational chemistry begin by calculating the molecular orbitals of the system. To what extent have these mathematical objects analogues in the real world? To shed light on this intriguing question, we employ a photoemission tomography study on monolayers of 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) grown on three Ag surfaces. The characteristic photoelectron angular distribution enables us to assign individual molecular orbitals to the emission features. When comparing the resulting energy positions to density functional calculations, we observe deviations in the energy ordering. By performing complete active space calculations (CASSCF), we can explain the experimentally observed orbital ordering, suggesting the importance of static electron correlation beyond a (semi)local approximation. On the other hand, our results also show reality and robustness of the orbital concept, thereby making molecular orbitals accessible to experimental observations. PMID:27935313

  10. 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)

  11. Simulation of Atomic and Molecular Orbitals

    ERIC Educational Resources Information Center

    Massey, A. G.; Massey S.

    1976-01-01

    Describes the use of magnets to simulate s, p, and d atomic orbitals from which a wide variety of molecular orbitals can be derived. The technique gives students an idea of molecular orbitals' shapes and stresses the importance of symmetry labels. (MLH)

  12. 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.

  13. 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.

  14. Evaluation of overlap integrals with integer and noninteger n Slater-type orbitals using auxiliary functions.

    PubMed

    Guseinov, Israfil; Mamedov, Bahtiyar

    2002-09-01

    The series expansion formulae are derived for the overlap integrals with arbitrary integer n and noninteger n* Slater-type orbitals (ISTOs and NISTOs) in terms of a product of well-known auxiliary functions A(sigma) and B (k). The series becomes an ordinary closed expression when both principal quantum numbers n* and n'* of orbitals are integer n*= n and n'*= n'. These formulae are especially useful for the calculation of overlap integrals for large quantum numbers. Accuracy of the results is satisfactory for values of integer and noninteger quantum numbers up to n= n'=60, n*= n'*<33 and for arbitrary values of screening constants of orbitals and internuclear distances.

  15. 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.

  16. Molecular orbital imaging for partially aligned molecules

    NASA Astrophysics Data System (ADS)

    Qin, Meiyan; Zhu, Xiaosong

    2017-01-01

    We investigate molecular orbital reconstruction using high-order harmonic emissions from partially aligned molecular ensembles. By carrying out the reconstruction procedure using the harmonic sampling with or without the spectral minimum, the roles of the harmonic phase and amplitude modulation due to the partial alignment can be separately studied. It is found that with the prior knowledge of the orbital symmetry, the reconstructed result is very sensitive to the modulation of the harmonic phase for the πg orbital, while in the case of σg orbital, the reconstructed result is mainly determined by the harmonic amplitude. These results can provide an important reference for the future experiment of molecular orbital imaging.

  17. Band formation in a molecular quantum well via 2D superatom orbital interactions.

    PubMed

    Dougherty, Daniel 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 intermolecular orbital overlap in the previously unrecognized superatom character of the σ* orbital of C6F6 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.

  18. 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.)

  19. Molecular Electronic Terms and Molecular Orbital Configurations.

    ERIC Educational Resources Information Center

    Mazo, R. M.

    1990-01-01

    Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)

  20. 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.

  1. 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

  2. Polarized Molecular Orbital Model Chemistry. II. The PMO Method

    PubMed Central

    Zhang, Peng; Fiedler, Luke; Leverentz, Hannah R.; Truhlar, Donald G.; Gao, Jiali

    2012-01-01

    We present a new semiempirical molecular orbital method based on neglect of diatomic differential overlap. This method differs from previous NDDO-based methods in that we include p orbitals on hydrogen atoms to provide a more realistic modeling of polarizability. As in AM1-D and PM3-D, we also include damped dispersion. The formalism is based on the original MNDO one, but in the process of parameterization we make some specific changes to some of the functional forms. The present article is a demonstration of the capability of the new approach, and it presents a successful parametrization for compounds composed only of hydrogen and oxygen atoms, including the important case of water clusters. PMID:23378824

  3. Unitary Optimization of Localized Molecular Orbitals.

    PubMed

    Lehtola, Susi; Jónsson, Hannes

    2013-12-10

    A unified formalism and its implementation is presented for Foster-Boys, fourth moment, Pipek-Mezey, and Edmiston-Ruedenberg type localization schemes of molecular orbitals through unitary optimization of the localizing transform matrix using a recently proposed algorithm [ Abrudan ; et al. Signal Processing 2009 , 89 , 1704 ]. A conjugate gradient algorithm is used with an efficient line search method. The option of using complex valued orbitals is included. Applications to fullerenes from C20 to C100, as well as benzene and arachic acid are presented, showing the capability of the method, which has been implemented in ERKALE, an open source program for electronic structure calculations of atoms and molecules.

  4. 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.

  5. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry.

    PubMed

    Isegawa, Miho; Fiedler, Luke; Leverentz, Hannah R; Wang, Yingjie; Nachimuthu, Santhanamoorthi; Gao, Jiali; Truhlar, Donald G

    2013-01-08

    The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries.

  6. Molecular diagnosis of orbital inflammatory disease.

    PubMed

    Rosenbaum, James T; Choi, Dongseok; Wilson, David J; Grossniklaus, Hans E; Sibley, Cailin H; Harrington, Christina A; Planck, Stephen R

    2015-04-01

    Orbital inflammatory diseases include thyroid eye disease (TED), granulomatosis with polyangiitis (GPA), sarcoidosis, and nonspecific orbital inflammation (NSOI). Histopathological diagnosis usually relies on the clinical context and is not always definitive. Gene expression profiling provides diagnostic and therapeutic information in several malignancies, but its role in evaluating nonmalignant disease is relatively untested. We hypothesized that gene expression profiling could provide diagnostic information for NSOI. We collected formalin-fixed, paraffin-embedded orbital biopsies from 10 institutions and 83 subjects including 25 with thyroid eye disease, 25 nonspecific orbital inflammation, 20 healthy controls, 6 with granulomatosis with polyangiitis, and 7 with sarcoidosis. Tissues were divided into discovery and validation sets. Gene expression was quantified using Affymetrix U133 Plus 2.0 microarrays. A random forest statistical algorithm based on data from 39 probe sets identified controls, GPA, or TED with an average accuracy of 76% (p=0.02). Random forest analysis indicated that 52% of tissues from patients with nonspecific inflammation were consistent with a diagnosis of GPA. Molecular diagnosis by gene expression profiling will augment clinical data and histopathology in differentiating forms of orbital inflammatory disease.

  7. Molecular Orbital Based Design Guidelines for Hypergolic Energetic Ionic Liquids

    DTIC Science & Technology

    2015-01-01

    Journal Article 3. DATES COVERED (From - To) October 2013- December 2013 4. TITLE AND SUBTITLE Molecular Orbital Based Design Guidelines for Hypergolic... orbitals (HOMO) of the anions for a series of ionic liquids and the lowest occupied molecular orbital (LUMO) of HNO3, and variation in the computed...code) 661-525-5657 Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 DOI: 10.1002/prep.201400087 Molecular Orbital Based Design

  8. 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)

  9. Conformational Analysis of Poly-2,5-Benzimidazole (ABPBI), Poly-2,5- Benzoxazole (ABPBO), and Poly-2,6-Benzothiazole (ABPBT) Dimers by the Modified Neglect of Diatomic Overlap (MNDO) and Austin Method 1 (AM1) Semiempirical Molecular Orbital Methods

    DTIC Science & Technology

    1987-07-01

    AFWAL-TR-87-4034 A\\) CONFORMATIONAL ANALYSIS OF POLY-2,5-BENZOIMIDAZOLE (ABPBI), POLY-2,5-BENZOXAZOLE (ABPBO), AND POLY-2,6- BENZOTHIAZOLE (ABPBT... benzothiazole Molecular Orbital 19. ABSTRACT (Continue on reverse if necessar and identif-y by block number) The two repeat unit analogs of three, aromatic...SECURITY CLASSIFICATION OF THIS PAGE 11. TITLE (Cont) Poly-2,5-benzoxazole (ABPBO), and Poly-2,6- benzothiazole (ABPBT) Dimers by the Modified Neglect

  10. Atomic Orbitals, Molecular Orbitals and Related Concepts: Conceptual Difficulties among Chemistry Students.

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    1997-01-01

    Investigates the impact an undergraduate quantum chemistry course has on students' knowledge and understanding of atomic orbitals, molecular orbitals, and related concepts. Analysis reveals that students do not have a clear understanding of these concepts and confuse the various atomic orbital representations. Includes some suggestions and…

  11. Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems.

    PubMed

    Nebgen, Ben; Prezhdo, Oleg V

    2016-09-15

    A method for efficiently simulating nonadiabatic molecular dynamics (NAMD) of nanoscale and condensed phase systems is developed and tested. The electronic structure, including force and nonadiabatic coupling, are obtained with the fragment molecular orbital (FMO) approximation, which provides significant computational savings by splitting the system into fragments and computing electronic properties of each fragment subject to the external field due to other all other fragments. The efficiency of the developed technique is demonstrated by studying the effect of explicit solvent molecules on excited state relaxation in the Fe(CO)4 complex. The relaxation in the gas phase occurs on a 50 fs time scale, which is in excellent agreement with previously recorded femtosecond pump-probe spectroscopy. Adding a solvation shell of ethanol molecules to the simulation results in an increase in the excited state lifetime to 100 fs, in agreement with recent femtosecond X-ray spectroscopy measurements.

  12. Field-dressed orbitals in strong-field molecular ionization

    NASA Astrophysics Data System (ADS)

    Siemering, Robert; Njoya, Oumarou; Weinacht, Thomas; de Vivie-Riedle, Regina

    2015-10-01

    We demonstrate the importance of considering the shape of field-dressed molecular orbitals in interpreting angle-dependent measures of strong-field ionization from excited states. Our calculations of angle-dependent ionization for three homologous polyatomic molecules with very similar valence orbitals show that one has to take into account the shape of the field-dressed orbitals rather than the field-free orbitals in order to rationalize the experimental measurements.

  13. Molecular orbitals for properties and spectroscopies

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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 sp3 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 Fe2+/Fe3+ 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.

  14. 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.

  15. 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.

  16. 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.

  17. Orbital views of molecular conductance perturbed by anchor units.

    PubMed

    Tsuji, Yuta; Staykov, Aleksandar; Yoshizawa, Kazunari

    2011-04-20

    Site-specific electron transport phenomena through benzene and benzenedithiol derivatives are discussed on the basis of a qualitative Hückel molecular orbital analysis for better understanding of the effect of anchoring sulfur atoms. A recent work for the orbital control of electron transport through aromatic hydrocarbons provided an important concept for the design of high-conductance connections of a molecule with anchoring atoms. In this work the origin of the frontier orbitals of benzenedithiol derivatives, the effect of the sulfur atoms on the orbitals and on the electron transport properties, and the applicability of the theoretical concept on aromatic hydrocarbons with the anchoring units are studied. The results demonstrate that the orbital view predictions are applicable to molecules perturbed by the anchoring units. The electron transport properties of benzene are found to be qualitatively consistent with those of benzenedithiol with respect to the site dependence. To verify the result of the Hückel molecular orbital calculations, fragment molecular orbital analyses with the extended Hückel molecular orbital theory and electron transport calculations with density functional theory are performed. Calculated results are in good agreement with the orbital interaction analysis. The phase, amplitude, and spatial distribution of the frontier orbitals play an essential role in the design of the electron transport properties through aromatic hydrocarbons.

  18. Ultrafast molecular orbital imaging based on attosecond photoelectron diffraction.

    PubMed

    Li, Yang; Qin, Meiyan; Zhu, Xiaosong; Zhang, Qingbin; Lan, Pengfei; Lu, Peixiang

    2015-04-20

    We present ab initio numerical study of ultrafast ionization dynamics of H(2)(+) as well as CO(2) and N(2) exposed to linearly polarized attosecond extreme ultraviolet pulses. When the molecules are aligned perpendicular to laser polarization direction, photonionization of these molecules show clear and distinguishing diffraction patterns in molecular attosecond photoelectron momentum distributions. The internuclear distances of the molecules are related to the position of the associated diffraction patterns, which can be determined with high accuracy. Moreover, the relative heights of the diffraction fringes contain fruitful information of the molecular orbital structures. We show that the diffraction spectra can be well produced using the two-center interference model. By adopting a simple inversion algorithm which takes into account the symmetry of the initial molecular orbital, we can retrieve the molecular orbital from which the electron is ionized. Our results offer possibility for imaging of molecular structure and orbitals by performing molecular attosecond photoelectron diffraction.

  19. Correlation between Pi-Orbital Overlap and Conductivity Bis- Phthalocyaninato Lanthanides

    DTIC Science & Technology

    1991-06-10

    Overlap and Conductivity Bis-Phthalo- cyaninato Lanthanides 12. PERSONAL AUTHOR(S) Juan Padilla and William E. Hatfield 13a. TYPE OF REPORT 13b TIME COVERED...phthalocyanine ligands. Conductivity measurements on the iodine-doped bis-phthalocyaninato lanthanides , H[M(Pc)l2 1, show an average increase of four...18. Continued: bis-phthalocyaninato lanthanides mobility model OFFICE OF NAVAL RESERACH Just if o1 Contract N0014-89-J-1734 * R&T Code .135007---05 0

  20. 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.

  1. Low-temperature crystal structures of stibnite implying orbital overlap of Sb 5s2 inert pair electrons

    NASA Astrophysics Data System (ADS)

    Kyono, A.; Kimata, M.; Matsuhisa, M.; Miyashita, Y.; Okamoto, K.

    The crystal structure of stibnite [Sb2S3, Pnma, a=11.314(2), b=3.837(2), c=11.234(3) Å, V= 487.7(3) Å3 at 293 K] was refined in situ at 230, 173, and 128 K. It is a major characteristic of the structure that the Sb-S secondary bonds enclosing Sb 5s2 inert lone-pair electrons at 293 K are significantly shorter than the corresponding sum of the Sb and S van der Waals radii. Concerning the temperature dependence, although both the polyhedral volume and the cation eccentricity of the two SbS7 polyhedra exhibit continuous contractions with decreasing temperature, the sphericity values remain constant, indicating isotropic shrinkage. Consequently, the geometries of Sb 5s2 inert lone-pair electrons and ligand atoms remain unchanged at low temperatures. This is because the crystal structure of stibnite at low temperature induces contraction with attractive interactions, which is called the orbital overlap between Sb 5s2 inert lone-pair electrons and ligand orbitals to maintain the coordination environment. In this case, Sb 5s2 lone-pair electrons are not inert, but active. Such orbital overlaps of inert lone-electron pairs can provide a reasonable explanation for shorter secondary bonds and lower band gap energy of the binary compounds containing heavy elements such as Sb, Te, Pb, and Bi, which are key factors in tracing the origins of color, luster, and semiconductivity of their minerals or compounds.

  2. APOGEE/Kepler Overlap Yields Orbital Solutions for a Variety of Eclipsing Binaries

    NASA Astrophysics Data System (ADS)

    Clark Cunningham, Joni Marie; Windemuth, Diana; Ali, Aleezah; Rawls, Meredith L.; Jackiewicz, Jason

    2017-01-01

    We present orbital solutions, masses, and radii for a set of eclipsing spectroscopic binaries observed by both Kepler and APOGEE. Kepler’s primary mission is to find earth-like planets, but several of the observed stars are instead eclipsing binaries with a range of properties. The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has observed many of these same systems during its near-infrared spectroscopic survey. In this work, we combine Kepler light curves and radial velocities extracted from APOGEE spectra to yield binary orbital solutions, stellar masses, and stellar radii. We select binaries that have at least three good-quality APOGEE visits, are sufficiently bright, are listed in the Kepler Eclipsing Binary Catalog (Kirk et al. 2016), show both a primary and a secondary eclipse, and have well- or semi-detached light curve morphologies. We identify a total of 50 promising targets, and present results for a subset of these. Once radial velocity solutions for both stars in each system are found, we combine them with Kepler light curves to solve for mass and radius. These inferences are especially rare for longer-period binaries, and will contribute to our knowledge of fundamental stellar parameters and binary star statistics. This work is supported the SDSS Faculty and Student (FAST) initiative.

  3. 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)

  4. 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.

  5. The rotational barrier in ethane: a molecular orbital study.

    PubMed

    Quijano-Quiñones, Ramiro F; Quesadas-Rojas, Mariana; Cuevas, Gabriel; Mena-Rejón, Gonzalo J

    2012-04-20

    The energy change on each Occupied Molecular Orbital as a function of rotation about the C-C bond in ethane was studied using the B3LYP, mPWB95 functional and MP2 methods with different basis sets. Also, the effect of the ZPE on rotational barrier was analyzed. We have found that σ and π energies contribution stabilize a staggered conformation. The σ(s) molecular orbital stabilizes the staggered conformation while the stabilizes the eclipsed conformation and destabilize the staggered conformation. The π(z) and molecular orbitals stabilize both the eclipsed and staggered conformations, which are destabilized by the π(v) and molecular orbitals. The results show that the method of calculation has the effect of changing the behavior of the energy change in each Occupied Molecular Orbital energy as a function of the angle of rotation about the C-C bond in ethane. Finally, we found that if the molecular orbital energy contribution is deleted from the rotational energy, an inversion in conformational preference occurs.

  6. 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.

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

    SciTech Connect

    Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; Bock, Nicolas; Wall, Michael E.; Niklasson, Anders Mauritz

    2016-06-06

    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 re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement 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 e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the 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 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.

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

    DOE PAGES

    Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

    2016-06-06

    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 re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the 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 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

  9. 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.

  10. Molecular design of electron transport with orbital rule: toward conductance-decay free molecular junctions.

    PubMed

    Tada, Tomofumi; Yoshizawa, Kazunari

    2015-12-28

    In this study, we report our viewpoint of single molecular conductance in terms of frontier orbitals. The orbital rule derived from orbital phase and amplitude is a powerful guideline for the qualitative understanding of molecular conductance in both theoretical and experimental studies. The essence of the orbital rule is the phase-related quantum interference, and on the basis of this rule a constructive or destructive pathway for electron transport is easily predicted. We have worked on the construction of the orbital rule for more than ten years and recently found from its application that π-stacked molecular junctions fabricated experimentally are in line with the concept for conductance-decay free junctions. We explain the orbital rule using benzene molecular junctions with the para-, meta- and ortho-connections and discuss linear π-conjugated chains and π-stacked molecular junctions with respect to their small decay factors in this manuscript.

  11. Imaging the Temporal Evolution of Molecular Orbitals during Ultrafast Dissociation

    NASA Astrophysics Data System (ADS)

    Sann, H.; Havermeier, T.; Müller, C.; Kim, H.-K.; Trinter, F.; Waitz, M.; Voigtsberger, J.; Sturm, F.; Bauer, T.; Wallauer, R.; Schneider, D.; Weller, M.; Goihl, C.; Tross, J.; Cole, K.; Wu, J.; Schöffler, M. S.; Schmidt-Böcking, H.; Jahnke, T.; Simon, M.; Dörner, R.

    2016-12-01

    We investigate the temporal evolution of molecular frame angular distributions of Auger electrons emitted during ultrafast dissociation of HCl following a resonant single-photon excitation. The electron emission pattern changes its shape from that of a molecular σ orbital to that of an atomic p state as the system evolves from a molecule into two separated atoms.

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

    SciTech Connect

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

    2016-01-21

    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.

  13. 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…

  14. Developmental AB Initio Molecular Orbital Theory

    NASA Astrophysics Data System (ADS)

    Blurock, Edward (Ned) Samuel

    The frozen core approximation (FCA) was applied to the main group elements of the first four rows of the periodic table (i.e., through Iodine). For hydride bond lengths, the results of the FCA calculation were consistently closer to experiment. The FCA calculation assumes that the core space is complete and restricts its further optimization. The standard calculation does not have this restriction and further completion of the core space (during the optimization procedure) by valence orbitals on neighboring atoms produced shorter (compared to FCA and experiment) hydride bond lengths. A new set of two-electron integrals was developed combining the use of Rys quadrature and the axis-switch algorithm. The combined algorithm was found to be advantageous only under higher contraction. Also, it was determined that extension of the algorithm to higher angular momentum functions would yield improvement in only selected cases. The SYMGEN program, a symbolic algebra program written by the author, was used to generate and globally optimize the newly developed code. The SYMGEN program is a general program with potential uses in a variety of other coding and global optimization problems.

  15. Overlap of PIV syndrome, VACTERL and Pallister-Hall syndrome: clinical and molecular analysis.

    PubMed

    Killoran, C E; Abbott, M; McKusick, V A; Biesecker, L G

    2000-07-01

    The polydactyly, imperforate anus, vertebral anomalies syndrome (PIV, OMIM 174100) was determined as a distinct syndrome by Say and Gerald in 1968 (Say B, Gerald PS. Lancet 1968: 2: 688). We noted that the features of PIV overlap with the VATER association and Pallister-Hall syndrome (PHS, OMIM 146510), which includes polydactyly, (central or postaxial), shortened fingers, hypoplastic nails, renal anomalies, imperforate anus, and hypothalamic hamartoma. Truncation mutations in GL13, a zinc finger transcription factor gene, have been shown to cause PHS. We performed a molecular evaluation on a patient diagnosed with PIV, whose mother, grandfather, and maternal aunt had similar malformations. We sequenced the GLI3 gene in the patient to determine if she had a mutation. The patient was found to have a deletion in nucleotides 2188-2207 causing a frameshift mutation that predicts a truncated protein product of the gene. Later clinical studies demonstrated that the patient also has a hypothalamic hamartoma, a finding in PHS. We concluded that this family had atypical PHS and not PIV. This result has prompted us to re-evaluate the PIV literature to see if PIV is a valid entity. Based on these data and our examination of the literature, we conclude that PIV is not a valid diagnostic entity. We conclude that patients diagnosed with PIV should be reclassified as having VACTERL, or PHS, or another syndrome with overlapping malformations.

  16. 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.

  17. 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

    2016-03-22

    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.

  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. Molecular and Genetic Characterization of Depression: Overlap with other Psychiatric Disorders and Aging.

    PubMed

    Ding, Ying; Chang, Lun-Ching; Wang, Xingbin; Guilloux, Jean-Philippe; Parrish, Jenna; Oh, Hyunjung; French, Beverly J; Lewis, David A; Tseng, George C; Sibille, Etienne

    2015-05-01

    Genome-wide expression and genotyping technologies have uncovered the genetic bases of complex diseases at unprecedented rates; However despite its heavy burden and high prevalence, the molecular characterization of major depressive disorder (MDD) has lagged behind. Transcriptome studies report multiple brain disturbances but are limited by small sample sizes. Genome-wide association studies (GWAS) report weak results but suggest overlapping genetic risk with other neuropsychiatric disorders. We performed systematic molecular characterization of altered brain function in MDD, using meta-analysis of differential expression in eight gene array studies in three corticolimbic brain regions in 101 subjects. The identified "metaA-MDD" genes suggest altered neurotrophic support, brain plasticity and neuronal signaling in MDD. Notably, metaA-MDD genes display low connectivity and hubness in coexpression networks, and uniform genomic distribution, consistent with diffuse polygenic mechanisms. We next integrated these findings with results from over 1800 published GWAS and show that genetic variations nearby metaA-MDD genes predict greater risk for neuropsychiatric disorders and notably for age-related phenotypes, but not for other medical illnesses, including those frequently co-morbid with depression, or body characteristics. Collectively, the intersection of unbiased investigations of gene function (transcriptome) and structure (GWAS) provides novel leads to investigate molecular mechanisms of MDD and suggest common biological pathways between depression, other neuropsychiatric diseases, and brain aging.

  20. 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).

  1. Frontier orbital control of molecular conductance and its switching.

    PubMed

    Tsuji, Yuta; Hoffmann, Roald

    2014-04-14

    For transmission of electrons through a π system, when the Landauer theory of molecular conductance is viewed from a molecular orbital (MO) perspective, there obtains a simple perturbation theoretic dependence, due to Yoshizawa and Tada, on a) the product of the orbital coefficients at the sites of electrode attachment, and b) the MO energies. The frontier orbitals consistently and simply indicate high or low transmission, even if other orbitals may contribute. This formalism, with its consequent reinforcement and/or interference of conductance, accounts for the (previously explained) difference in direct vs. cross conjugated transmission across an ethylene, as well as the comparative ON/OFF ratios in the experimentally investigated dimethyldihydropyrene and dithienylethene-type single-molecule switches. A strong dependence of the conductance on the site of attachment of the electrodes in a π system is an immediate extrapolation; the theory then predicts that for some specified sites the switching behavior will be inverted; i.e. the "open" molecular form of the switch will be more conductive.

  2. Analytical evaluation of molecular electronic integrals using Poisson's equation: Exponential-type orbitals and atom pairs

    NASA Astrophysics Data System (ADS)

    Absi, Noureddine; Hoggan, Philip

    The integral bottleneck in evaluating molecular energies arises from the two-electron contributions. These are difficult and time-consuming to evaluate, especially over exponential type orbitals, used here to ensure the correct behavior of atomic orbitals. The two-center two-electron integrals are essential to describe atom pairs in molecules and distinguish those that are bound. In this work on analytical integration, it is shown that the two-center Coulomb integrals involved can be expressed as one-electron kinetic energy-like integrals. This is accomplished using the fact that the Coulomb operator is a Green's function of the Laplacian. The ensuing integrals may be further simplified by defining spectral forms for the one-electron potential satisfying Poisson's equation therein. A sum of overlap integrals with the atomic orbital energy eigenvalue as a factor is then obtained to give the Coulomb energy. This is most easily evaluated by direct integration. The orbitals involved in three and four center integrals are translated to two centers. This is discussed very briefly. The evaluation of exchange energy is a straightforward extension of this work. The summation coefficients in spectral forms are evaluated analytically from Gaunt coefficients. The Poisson method may be used to calculate Coulomb energy integrals efficiently. For a single processor, gains of CPU time for a given chemical accuracy exceed a factor of 4. This method lends itself to efficient evaluation on a parallel computer.

  3. 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

  4. 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…

  5. Orbit-orbit relativistic correction calculated with all-electron molecular explicitly correlated Gaussians

    NASA Astrophysics Data System (ADS)

    Stanke, Monika; Palikot, Ewa; KÈ©dziera, Dariusz; Adamowicz, Ludwik

    2016-12-01

    An algorithm for calculating the first-order electronic orbit-orbit magnetic interaction correction for an electronic wave function expanded in terms of all-electron explicitly correlated molecular Gaussian (ECG) functions with shifted centers is derived and implemented. The algorithm is tested in calculations concerning the H2 molecule. It is also applied in calculations for LiH and H3+ molecular systems. The implementation completes our work on the leading relativistic correction for ECGs and paves the way for very accurate ECG calculations of ground and excited potential energy surfaces (PESs) of small molecules with two and more nuclei and two and more electrons, such as HeH-, H3+, HeH2, and LiH2+. The PESs will be used to determine rovibrational spectra of the systems.

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

    PubMed

    Liu, Shubin; Schauer, Cynthia K

    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. 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.

  8. 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.

  9. Molecular orbital theory of ballistic electron transport through molecules

    NASA Astrophysics Data System (ADS)

    Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

    2009-03-01

    Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on molecular electronic devices (MEDs). To model these phenomena, we use a non-Hermitian model Hamiltonian [1] for the description of open systems that exchange current density with their environment. We derive qualitative, molecular-orbital-based rules relating molecular structure and conductance. We show how side groups attached to molecular conductors [2] can completely suppress the conductance. We discuss interference effects in aromatic molecules [3] that can also inhibit electron transport. Rules are developed [1] for the prediction of Fano resonances. All these phenomena are explained with a molecular orbital theory [1,4] for molecules attached to macroscopic reservoirs. [1] F. Goyer, M. Ernzerhof, and M. Zhuang, JCP 126, 144104 (2007); M. Ernzerhof, JCP 127, 204709 (2007). [2] M. Ernzerhof, M. Zhuang, and P. Rocheleau, JCP 123, 134704 (2005); G. C. Solomon, D Q. Andrews, R P. Van Duyne, and M A. Ratner, JACS 130, 7788 (2008). [3] M. Ernzerhof, H. Bahmann, F. Goyer, M. Zhuang, and P. Rocheleau, JCTC 2, 1291 (2006); G. C. Solomon, D. Q. Andrews, R. P. Van Duyne, and M. A. Ratner, JCP 129, 054701 (2008). [4] B.T. Pickup, P.W. Fowler, CPL 459, 198 (2008); P. Rocheleau and M. Ernzerhof, JCP, submitted.

  10. 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

    2015-05-05

    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.

  11. Analytic Gradients for the Effective Fragment Molecular Orbital Method.

    PubMed

    Bertoni, Colleen; Gordon, Mark S

    2016-10-11

    The analytic gradient for the Coulomb, polarization, exchange-repulsion, and dispersion terms of the fully integrated effective fragment molecular orbital (EFMO) method is derived and the implementation is discussed. The derivation of the EFMO analytic gradient is more complicated than that for the effective fragment potential (EFP) gradient, because the geometry of each EFP fragment is flexible (not rigid) in the EFMO approach. The accuracy of the gradient is demonstrated by comparing the EFMO analytic gradient with the numeric gradient for several systems, and by assessing the energy conservation during an EFMO NVE ensemble molecular dynamics simulation of water molecules. In addition to facilitating accurate EFMO geometry optimizations, this allows calculations with flexible EFP fragments to be performed.

  12. Comparison of overlap-based models for approximating the exchange-repulsion energy.

    PubMed

    Söderhjelm, Pär; Karlström, Gunnar; Ryde, Ulf

    2006-06-28

    Different ways of approximating the exchange-repulsion energy with a classical potential function have been investigated by fitting various expressions to the exact exchange-repulsion energy for a large set of molecular dimers. The expressions involve either the orbital overlap or the electron-density overlap. For comparison, the parameter-free exchange-repulsion model of the effective fragment potential (EFP) is also evaluated. The results show that exchange-repulsion energy is nearly proportional to both the orbital overlap and the density overlap. For accurate results, a distance-dependent correction is needed in both cases. If few parameters are desired, orbital overlap is superior to density overlap, but the fit to density overlap can be significantly improved by introducing more parameters. The EFP performs well, except for delocalized pi systems. However, an overlap expression with a few parameters seems to be slightly more accurate and considerably easier to approximate.

  13. Assessment of delocalized and localized molecular orbitals through electron momentum spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Cheung, Ling-Fung; Ning, Chuan-Gang

    2014-06-01

    Recently, there was a hot controversy about the concept of localized orbitals, which was triggered by Grushow's work titled “Is it time to retire the hybrid atomic orbital?” [J. Chem. Educ. 88, 860 (2011)]. To clarify the issue, we assess the delocalized and localized molecular orbitals from an experimental view using electron momentum spectroscopy. The delocalized and localized molecular orbitals based on various theoretical models for CH4, NH3, and H2O are compared with the experimental momentum distributions. Our results show that the delocalized molecular orbitals rather than the localized ones can give a direct interpretation of the experimental (e, 2e) results.

  14. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

    NASA Astrophysics Data System (ADS)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

    We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

  15. 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

  16. 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.

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

    PubMed

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

    2014-08-07

    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.

  18. 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.

  19. 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.

  20. Computation of overlap integrals over STOs with mathematica

    NASA Astrophysics Data System (ADS)

    Yükçü, S. A.; Yükçü, N.

    2017-02-01

    Overlap integrals which encountered in molecular structure calculations are the most basic of molecular integrals. Also, other molecular integrals can be expressed in terms of these integrals. Overlap integrals can be calculated by using Slater Type Orbitals (STOs). In this work, we develop algorithms for two-center overlap integrals which are calculated over the STOs in ellipsoidal coordinates and some auxiliary functions by S. M. Mekelleche's group. During the computation of this paper, Mathematica programming language has been used to produce algorithms. Numerical results for some quantum numbers are presented in the tables. Finally, our numerical results and others are compared, then some details of evaluation method are discussed.

  1. Spectroscopic signatures of molecular orbitals in transition metal oxides with a honeycomb lattice

    NASA Astrophysics Data System (ADS)

    Pchelkina, Z. V.; Streltsov, S. V.; Mazin, I. I.

    2016-11-01

    A tendency to form benzenelike molecular orbitals has recently been shown to be a common feature of the 4 d and 5 d transition metal oxides with a honeycomb lattice. This tendency competes with other interactions such as the spin-orbit coupling and Hubbard correlations and can be partially or completely suppressed. In the calculations, SrRu2O6 presents the cleanest case of well-formed molecular orbitals so far; however, direct experimental evidence for or against this proposition has been missing. In this paper, we show that combined photoemission and optical studies can be used to identify molecular orbitals in SrRu2O6 . Symmetry-driven election selection rules suppress optical transitions between certain molecular orbitals, while photoemission and inverse photoemission measurements are insensitive to them. Comparing the photoemission and optical conductivity spectra, one should be able to observe clear signatures of molecular orbitals.

  2. Ab initio molecular simulations with numeric atom-centered orbitals

    NASA Astrophysics Data System (ADS)

    Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

    2009-11-01

    We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

  3. Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations.

    PubMed

    van Meer, R; Gritsenko, O V; Baerends, E J

    2014-10-14

    In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent density functional theory (TDDFT) calculations of excitation energies have been performed. The tested functionals do not approximate exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of molecular excitations. Benchmark calculations are performed for the statistical average of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential does not only perform satisfactorily for calculated vertical excitation energies of both valence and Rydberg transitions but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calculated with local density, generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in molecules: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).

  4. Imprints of the molecular-orbital geometry on the high-harmonic ellipticity.

    PubMed

    Qin, Meiyan; Zhu, Xiaosong; Liu, Kunlong; Zhang, Qingbin; Lu, Peixiang

    2012-08-27

    The influence of the orbital symmetry on the ellipticity of the high-order harmonics is investigated. It is found that the ellipticity maps have distinct shapes for the molecular orbitals with different symmetry. Our analysis shows that the feature of the harmonic ellipticity map is essentially determined by the nodal structure of the nonsymmetric orbital. The results indicate that the molecular-orbital geometry is imprinted on the ellipticity of the high-order harmonics, which invites the use of ellipticity measurements as a probe of the orbital structure for polar molecules.

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

    PubMed

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

    2015-10-01

    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.

  6. 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.

  7. Overview of Molecular Line Parameters for the Orbiting Carbon Observatory

    NASA Astrophysics Data System (ADS)

    Brown, L.; Crisp, D.; Miller, C.; Martin-Torres, J.; Toth, R.

    2009-04-01

    The Orbiting Carbon Observatory, scheduled to launch early in 2009, will make spatially resolved measurements of the column averaged CO2 dry air mole fraction, XCO2, with precisions of 1 ppm to distinguish their spatial and temporal gradients of CO2. Achieving this goal requires implementation of non-Voigt line shape models, line mixing and improved molecular line parameters for near infrared absorption bands of O2 (near 760 nm), and CO2 (near 1600 and 2060 nm) . The first interval is dominated by the absorptions of the O2 A-band while the others contain strong CO2 features, as well as weak transitions of water and methane. The OCO linelist is composed of results from numerous new laboratory studies undertaken to improve experimental precisions and to characterize line mixing effects. The sources and accuracies of the new linelist for the three OCO channels1 will be described. The research described in this paper was performed at the Jet Propulsion Laboratory, California Institute of Technology, under contract with The National Aeronautics and Space Administration.

  8. Orbital-Free Molecular Dynamics Simulations at Extreme Conditions

    NASA Astrophysics Data System (ADS)

    Kress, J. D.; Collins, L. A.; Ticknor, C.

    2015-06-01

    Large-scale molecular dynamics (MD) simulations in an orbital-free (OF) density-functional theory (DFT) formulation have been performed for pure and mixed species over a broad range of temperatures (T) and densities (ρ) that includes the warm, dense matter and high-energy density physics regimes. A finite-temperature Thomas-Fermi-Dirac form with a local-density exchange-correlation potential and a regularized electron-ion interaction represents the quantum nature of the electrons. In particular, we examine the efficacy of the OFMD approach as an effective bridge between Kohn-Sham DFT MD at low temperatures and simple, fully-ionized plasma models at high temperatures. Comparisons against intermediate-range constructions such as the Yukawa and one-component plasmas are also made. We examine the mass transport (diffusion, viscosity) properties of various systems, ranging from light to heavy elements, including lithium hydride (LiH), mixtures of LiH with uranium, mixtures of deuterium-tritium (DT) with plutonium and mixtures of DT with plastic (CH). The OFMD mass transport results have been fitted to simple functions of ρ and T suitable for use in hydrodynamics simulation codes.

  9. 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.

  10. [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).

  11. Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals

    SciTech Connect

    Khaliullin, Rustam Z.; Head-Gordon, Martin; Bell, Alexis T.

    2008-05-14

    A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

  12. Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Bell, Alexis T; Head-Gordon, Martin

    2008-05-14

    A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

  13. Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals

    NASA Astrophysics Data System (ADS)

    Khaliullin, Rustam Z.; Bell, Alexis T.; Head-Gordon, Martin

    2008-05-01

    A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

  14. 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.

  15. Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method.

    PubMed

    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.

  16. Molecular definition of the shortest region of deletion overlap in the Langer-Giedion syndrome

    PubMed Central

    Lüdecke, Hermann-Josef; Johnson, Carey; Wagner, Michael J.; Wells, Dan E.; Turleau, Catherine; Tommerup, Niels; Latos-Bielenska, Anna; Sandig, Klaus-Rainer; Meinecke, Peter; Zabel, Bernhard; Horsthemke, Bernhard

    1991-01-01

    The Langer-Giedion syndrome (LGS), which is characterized by craniofacial dysmorphism and skeletal abnormalities, is caused by a genetic defect in 8q24.1. We have used 13 anonymous DNA markers from an 8q24.1-specific microdissection library, as well as c-myc and thyroglobulin gene probes, to map the deletion breakpoints in 16 patients with LGS. Twelve patients had a cytogenetically visible deletion, two patients had an apparently balanced translocation, and two patients had an apparently normal karyotype. In all cases except one translocation patient, loss of genetic material was detected. The DNA markers fall into 10 deletion intervals. Clone L48 (D8S51) defines the shortest region of deletion overlap (SRO), which is estimated to be less than 2 Mbp. Three clones–pl7-2.3EE (D8S43), L24 (D8S45), and L40 (D8S49)–which flank the SRO recognize evolutionarily conserved sequences. ImagesFigure 1Figure 3Figure 4 PMID:1836105

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

    NASA Astrophysics Data System (ADS)

    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 phenyl

  18. Resolving Multiple Molecular Orbitals Using Two-Dimensional High-Harmonic Spectroscopy

    NASA Astrophysics Data System (ADS)

    Yun, Hyeok; Lee, Kyung-Min; Sung, Jae Hee; Kim, Kyung Taec; Kim, Hyung Taek; Nam, Chang Hee

    2015-04-01

    High-harmonic radiation emitted from molecules in a strong laser field contains information on molecular structure and dynamics. When multiple molecular orbitals participate in high-harmonic generation, resolving the contribution of each orbital is crucial for understanding molecular dynamics and for extending high-harmonic spectroscopy to more complicated molecules. We show that two-dimensional high-harmonic spectroscopy can resolve high-harmonic radiation emitted from the two highest-occupied molecular orbitals, HOMO and HOMO-1, of aligned molecules. By the application of an orthogonally polarized two-color laser field that consists of the fundamental and its second-harmonic fields to aligned CO2 molecules, the characteristics attributed to the two orbitals are found to be separately imprinted in odd and even harmonics. Two-dimensional high-harmonic spectroscopy may open a new route to investigate ultrafast molecular dynamics during chemical processes.

  19. Resolving multiple molecular orbitals using two-dimensional high-harmonic spectroscopy.

    PubMed

    Yun, Hyeok; Lee, Kyung-Min; Sung, Jae Hee; Kim, Kyung Taec; Kim, Hyung Taek; Nam, Chang Hee

    2015-04-17

    High-harmonic radiation emitted from molecules in a strong laser field contains information on molecular structure and dynamics. When multiple molecular orbitals participate in high-harmonic generation, resolving the contribution of each orbital is crucial for understanding molecular dynamics and for extending high-harmonic spectroscopy to more complicated molecules. We show that two-dimensional high-harmonic spectroscopy can resolve high-harmonic radiation emitted from the two highest-occupied molecular orbitals, HOMO and HOMO-1, of aligned molecules. By the application of an orthogonally polarized two-color laser field that consists of the fundamental and its second-harmonic fields to aligned CO2 molecules, the characteristics attributed to the two orbitals are found to be separately imprinted in odd and even harmonics. Two-dimensional high-harmonic spectroscopy may open a new route to investigate ultrafast molecular dynamics during chemical processes.

  20. A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2001-11-01

    We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.

  1. 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…

  2. Destructive quantum interference in electron transport: A reconciliation of the molecular orbital and the atomic orbital perspective

    NASA Astrophysics Data System (ADS)

    Zhao, Xin; Geskin, Victor; Stadler, Robert

    2017-03-01

    Destructive quantum interference (DQI) in single molecule electronics is a purely quantum mechanical effect and is entirely defined by the inherent properties of the molecule in the junction such as its structure and symmetry. This definition of DQI by molecular properties alone suggests its relation to other more general concepts in chemistry as well as the possibility of deriving simple models for its understanding and molecular device design. Recently, two such models have gained a wide spread attention, where one was a graphical scheme based on visually inspecting the connectivity of the carbon sites in conjugated π systems in an atomic orbital (AO) basis and the other one puts the emphasis on the amplitudes and signs of the frontier molecular orbitals (MOs). There have been discussions on the range of applicability for these schemes, but ultimately conclusions from topological molecular Hamiltonians should not depend on whether they are drawn from an AO or a MO representation, as long as all the orbitals are taken into account. In this article, we clarify the relation between both models in terms of the zeroth order Green's function and compare their predictions for a variety of systems. From this comparison, we conclude that for a correct description of DQI from a MO perspective, it is necessary to include the contributions from all MOs rather than just those from the frontier orbitals. The cases where DQI effects can be successfully predicted within a frontier orbital approximation we show them to be limited to alternant even-membered hydrocarbons, as a direct consequence of the Coulson-Rushbrooke pairing theorem in quantum chemistry.

  3. Ab initio molecular orbital calculation considering the quantum mechanical effect of nuclei by path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2000-12-01

    We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.

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

    SciTech Connect

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

    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 Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. 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.

  5. End-group Influence on the Frontier Molecular Orbital Reorganization in Molecular Junctions -- Effect on Thermopower

    NASA Astrophysics Data System (ADS)

    Balachandran, Janakiraman; Reddy, Pramod; Dunietz, Barry; Gavini, Vikram

    2014-03-01

    The frontier molecular orbital (FMO) reorganization and in turn on the thermopower of the aromatic molecules trapped between metal electrodes (aka molecular junctions) depends on two effects namely (1) the stabilization effect - due to the physical presence of the metal electrode atoms and (2) change in e-e interactions - due to end-group mediated charge transfer. The stabilization effect always reduces the FMO energies. The charge transfer effect increases the FMO energies in charge-gaining molecules, which in turn opposes the stabilization effect resulting in a small overall shift. However, the charge transfer effect decreases the FMO energies in charge-losing molecules, which in turn complements the stabilization effect resulting in a large overall downward shift. This hypothesis is validated by delineating the shifts due to stabilization and charge-transfer effects independently. Further we also demonstrate the generality of the hypothesis by applying it on a wide range of aromatic molecules with different length and end-groups. Finally, we also present computationally efficient strategies, based on the proposed mechanism, to quantitatively compute the FMO reorganization which in turn has potential for high throughput analysis of molecular junctions.

  6. Efficient Geometry Optimization of Large Molecular Systems in Solution Using the Fragment Molecular Orbital Method.

    PubMed

    Nakata, Hiroya; Fedorov, Dmitri G

    2016-12-15

    The analytic gradient is derived for the frozen domain formulation of the fragment molecular orbital (FMO) method combined with the polarizable continuum model. The accuracy is tested in comparison to full FMO calculations for a representative set of systems in terms of the gradient accuracy, protein-ligand binding energies, and optimized structures. The frozen domain method reproduced geometries optimized with full FMO within 0.03-0.09 Å in terms of reduced mean square deviations, whereas a single-point gradient calculation is accelerated by the factor of 38 (Trp-cage protein in explicit solvent, PDB: 1L2Y ) and 12 (crambin, PDB: 1CRN ). The method is applied to a geometry optimization of the K-Ras protein-ligand complex (4Q03) using two domain definitions, and the optimized structures are consistent with experiment. Pair interaction analysis is used to identify residues important in binding the ligand.

  7. Spin–orbit coupled molecular quantum magnetism realized in inorganic solid

    PubMed Central

    Park, Sang-Youn; Do, S.-H.; Choi, K.-Y.; Kang, J.-H.; Jang, Dongjin; Schmidt, B.; Brando, Manuel; Kim, B.-H.; Kim, D.-H.; Butch, N. P.; Lee, Seongsu; Park, J.-H.; Ji, Sungdae

    2016-01-01

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal–organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin–orbit coupled pseudospin-½ Yb3+ ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky–Moriya interaction originating from strong spin–orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky–Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets. PMID:27650796

  8. Spin-orbit coupled molecular quantum magnetism realized in inorganic solid.

    PubMed

    Park, Sang-Youn; Do, S-H; Choi, K-Y; Kang, J-H; Jang, Dongjin; Schmidt, B; Brando, Manuel; Kim, B-H; Kim, D-H; Butch, N P; Lee, Seongsu; Park, J-H; Ji, Sungdae

    2016-09-21

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-½ Yb(3+) ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets.

  9. Orbital

    NASA Astrophysics Data System (ADS)

    Hanson, Robert M.

    2003-06-01

    ORBITAL requires the following software, which is available for free download from the Internet: Netscape Navigator, version 4.75 or higher, or Microsoft Internet Explorer, version 5.0 or higher; Chime Plug-in, version compatible with your OS and browser (available from MDL).

  10. 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.

  11. 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.

  12. Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals.

    PubMed

    Cui, Ganglong; Fang, Weihai; Yang, Weitao

    2010-01-14

    Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-orthogonal localized molecular orbitals (NOLMOs). NOLMO is the most localized representation of electronic degrees of freedom and has been used in ground state calculations. In atomic orbital (AO) representation, the sparsity of NOLMO is transferred to the coefficient matrix of molecular orbitals (MOs). Its novel use in TDDFT here leads to a very simple form of time propagation equations which can be solved with linear-scaling effort. We have tested the method for several long-chain saturated and conjugated molecular systems within the self-consistent charge density-functional tight-binding method (SCC-DFTB) and demonstrated its accuracy. This opens up pathways for TDDFT applications to large bio- and nano-systems.

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

    PubMed

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

    2015-01-01

    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.

  14. 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

    2016-09-07

    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.

  15. O( N) tight-binding molecular dynamics on massively parallel computers: an orbital decomposition approach

    NASA Astrophysics Data System (ADS)

    Canning, A.; Galli, G.; Mauri, F.; De Vita, A.; Car, R.

    1996-04-01

    The implementation of an O( N) tight-binding molecular dynamics code on the Cray T3D parallel computer is discussed. The O( N) energy functional depends on non-orthogonal, localised orbitals and a chemical potential parameter which determines the number of electrons in the system. The localisation introduces a sparse nature to the orbital data and Hamiltonian matrix, greatly changing the coding on parallel machines compared to non-localised systems. The data distribution, communication routines and dynamic load-balancing scheme of the program are presented in detail together with the speed and scaling of the code on various homogeneous and inhomogeneous physical systems. Performance results will be presented for systems of 2048 to 32768 atoms on 32 to 512 processors. We discuss the relevance to quantum molecular dynamics simulations with localised orbitals, of techniques used for programming short-range classical molecular dynamics simulations on parallel machines. The absence of global communications and the localised nature of the orbitals makes these algorithms extremely scalable in terms of memory and speed on parallel systems with fast communications. The main aim of this article is to present in detail all the new concepts and programming techniques that localisation of the orbitals introduces which scientists, coming from a background in non-localised quantum molecular dynamics simulations, may be unfamiliar with.

  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. 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.

  18. Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Roskop, Luke; Fedorov, Dmitri G.; Gordon, Mark S.

    2013-07-01

    The fragment molecular orbital (FMO) method is used to model truncated portions of mesoporous silica nanoparticle (MSN) pores. The application of the FMO/RHF (restricted Hartree-Fock) method to MCM-41 type MSNs is discussed and an error analysis is given. The FMO/RHF method is shown to reliably approximate the RHF energy (error ∼0.2 kcal/mol), dipole moment (error ∼0.2 debye) and energy gradient (root mean square [RMS] error ∼0.2 × 10-3 a.u./bohr). Several FMO fragmentation schemes are employed to provide guidance for future applications to MSN models. An MSN pore model is functionalised with (phenyl)propyl substituents and the diffusion barrier for benzene passing through the pore is computed by the FMO/RHF-D method with the Grimme dispersion correction (RHF-D). For the reaction coordinates examined here, the maximum FMO/RHF-D interaction energies range from -0.3 to -5.8 kcal/mol.

  19. Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

    2004-03-01

    Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the “Wannier gauge.” An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches.

  20. A Molecular Orbital Study of Atmospherically Important Species.

    DTIC Science & Technology

    1983-06-01

    from the OH to the H2 0 upon formation of the hydrogen bond. The electron density is transferred to the oxygen and terminal hydrogen of the water ...Method," J. Chem. Phys., 52, 3362-3368, 1970. • -o . ..-.. . -34- 48. Chipman, D.M. "Effect of Molecular Geometry on the Electron Affinity of Water ...34 J. Phvs. Chem., 82, 1080-1083, 1978. 49. Benedict, W.S., N. Gailar, and E.K. Plvler, "Rotation-Vibration Spectra of Deuteriated Water Vapor," J. Chem

  1. Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation

    NASA Astrophysics Data System (ADS)

    Wu, Di; Kofke, David A.

    2005-08-01

    We consider ways to quantify the overlap of the parts of phase space important to two systems, labeled A and B. Of interest is how much of the A-important phase space lies in that important to B, and how much of B lies in A. Two measures are proposed. The first considers four total-energy distributions, formed from all combinations made by tabulating either the A-system or the B-system energy when sampling either the A or B system. Measures for A in B and B in A are given by two overlap integrals defined on pairs of these distributions. The second measure is based on information theory, and defines two relative entropies which are conveniently expressed in terms of the dissipated work for free-energy perturbation (FEP) calculations in the A →B and B →A directions, respectively. Phase-space overlap is an important consideration in the performance of free-energy calculations. To demonstrate this connection, we examine bias in FEP calculations applied to a system of independent particles in a harmonic potential. Systems are selected to represent a range of overlap situations, including extreme subset, subset, partial overlap, and nonoverlap. The magnitude and symmetry of the bias (A →B vs B →A) are shown to correlate well with the overlap, and consequently with the overlap measures. The relative entropies are used to scale the amount of sampling to obtain a universal bias curve. This result leads to develop a simple heuristic that can be applied to determine whether a work-based free-energy measurement is free of bias. The heuristic is based in part on the measured free energy, but we argue that it is fail-safe inasmuch as any bias in the measurement will not promote a false indication of accuracy.

  2. 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.

  3. 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.

  4. In pursuit of negative Fukui functions: examples where the highest occupied molecular orbital fails to dominate the chemical reactivity.

    PubMed

    Echegaray, Eleonora; Cárdenas, Carlos; Rabi, Sandra; Rabi, Nataly; Lee, Sungmin; Zadeh, Farnaz Heidar; Toro-Labbe, Alejandro; Anderson, James S M; Ayers, Paul W

    2013-07-01

    In our quest to explore molecules with chemically significant regions where the Fukui function is negative, we explored reactions where the frontier orbital that indicates the sites for electrophilic attack is not the highest occupied molecular orbital. The highest occupied molecular orbital (HOMO) controls the location of the regions where the Fukui function is negative, supporting the postulate that negative values of the Fukui function are associated with orbital relaxation effects and nodal surfaces of the frontier orbitals. Significant negative values for the condensed Fukui function, however, were not observed.

  5. High resolution NEXAFS of perylene and PTCDI: a surface science approach to molecular orbital analysis.

    PubMed

    Fratesi, Guido; Lanzilotto, Valeria; Stranges, Stefano; Alagia, Michele; Brivio, Gian Paolo; Floreano, Luca

    2014-07-28

    We made use of synchrotron radiation to perform near edge X-ray absorption fine structure spectroscopy, NEXAFS, at the carbon K-edge of perylene and perylene-tetracarboxylic-diimide, PTCDI. Reference spectra measured for isolated molecules in the gas phase are compared with polarization dependent NEXAFS spectra measured on highly oriented thin films in order to study the symmetry of the molecular orbitals. The molecular overlayers are grown onto the rutile TiO2(110) surface for which the large anisotropic corrugation effectively drives the molecular orientation, while its dielectric nature prevents the rehybridization of the molecular orbitals. We employed density functional theory, DFT, calculations to disentangle the contribution of specific carbon atoms to the molecular density of states. Numerical simulations correctly predict the observed NEXAFS azimuthal dichroism of the σ* resonances above the ionization threshold, from which we determine the full geometric orientation of the overlayer molecules. A discrepancy observed for the spectral contribution of the imide carbon atom to the calculated unoccupied molecular orbitals has been explained in terms of initial state effects, as determined by Hartree-Fock corrections and in full agreement with the corresponding shift of the C 1s core level measured by X-ray photoelectron spectroscopy, XPS.

  6. Electronic and Redox Properties of Stacked-Ring Silicon Phthalocyanines from Molecular Orbital Theory.

    DTIC Science & Technology

    1984-10-19

    a molecular orbital approximation to the electron delocalization energy.1 8 The ASED theory is derived from the Hellmann- Feynman formula for...34 . . 4.•" " ., .7% . r .- - - . , .-. - . . _ .-.- :.- .- . v ._ . _ . " - . ’ " _ _ 12. Wheeler , B. L.; Nagasubramanian, G.; Bard, A. J

  7. 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…

  8. 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.

  9. 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…

  10. Orbital redistribution in molecular nanostructures mediated by metal-organic bonds.

    PubMed

    Yang, Zechao; Corso, Martina; Robles, Roberto; Lotze, Christian; Fitzner, Roland; Mena-Osteritz, Elena; Bäuerle, Peter; Franke, Katharina J; Pascual, Jose I

    2014-10-28

    Dicyanovinyl-quinquethiophene (DCV5T-Me2) is a prototype conjugated oligomer for highly efficient organic solar cells. This class of oligothiophenes are built up by an electron-rich donor (D) backbone and terminal electron-deficient acceptor (A) moieties. Here, we investigated its structural and electronic properties when it is adsorbed on a Au(111) surface using low temperature scanning tunneling microscopy/spectroscopy (STM/STS) and atomic force microscopy (AFM). We find that DCV5T-Me2 self-assembles in extended chains, stabilized by intercalated Au atoms. The effect of metal-ligand hybridization with Au adatoms causes an energetic downshift of the DCV5T-Me2 lowest unoccupied molecular orbital (LUMO) with respect to the uncoordinated molecules on the surface. The asymmetric coordination of a gold atom to only one molecular end group leads to an asymmetric localization of the LUMO and LUMO+1 states at opposite sides. Using model density functional theory (DFT) calculations, we explain such orbital reshaping as a consequence of linear combinations of the original LUMO and LUMO+1 orbitals, mixed by the attachment of a bridging Au adatom. Our study shows that the alignment of molecular orbitals and their distribution within individual molecules can be modified by contacting them to metal atoms in specific sites.

  11. Signatures of Molecular Orbital Structure in Lateral Electron Momentum Distributions from Strong-Field Ionization

    NASA Astrophysics Data System (ADS)

    Petersen, Ingo; Henkel, Jost; Lein, Manfred

    2015-03-01

    Strong-field ionization of aligned diatomic and polyatomic molecules such as O2, N2, C2H4, and others in circularly polarized laser fields is investigated theoretically. By calculating the emission-angle-resolved lateral width of the momentum distribution perpendicular to the polarization plane, we show that nodal planes in molecular orbitals are directly imprinted on the angular dependence of the width. We demonstrate that orbital symmetries can be distinguished with the information obtained by observing the lateral width in addition to the angular distributions.

  12. 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

  13. The divide-and-conquer second-order proton propagator method based on nuclear orbital plus molecular orbital theory for the efficient computation of proton binding energies.

    PubMed

    Tsukamoto, Yusuke; Ikabata, Yasuhiro; Romero, Jonathan; Reyes, Andrés; Nakai, Hiromi

    2016-10-05

    An efficient computational method to evaluate the binding energies of many protons in large systems was developed. Proton binding energy is calculated as a corrected nuclear orbital energy using the second-order proton propagator method, which is based on nuclear orbital plus molecular orbital theory. In the present scheme, the divide-and-conquer technique was applied to utilize local molecular orbitals. This use relies on the locality of electronic relaxation after deprotonation and the electron-nucleus correlation. Numerical assessment showed reduction in computational cost without the loss of accuracy. An initial application to model a protein resulted in reasonable binding energies that were in accordance with the electrostatic environment and solvent effects.

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

    PubMed

    Proppe, Jonny; Herrmann, Carmen

    2015-02-05

    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.

  15. Molecular orbital studies of enzyme activity: I: Charge relay system and tetrahedral intermediate in acylation of serine proteinases.

    PubMed Central

    Scheiner, S; Kleier, D A; Lipscomb, W N

    1975-01-01

    The charge relay ststem and its role in the acylation of serine proteinases is studied using the partial retention of diatomic differential overlap (PRDDO) technique to perform approximate ab initio molecular orbital calculations on a model of the enzyme-substrate complex. The aspartate in the charge relay system is seen to act as the ultimate proton acceptor during the charging of the serine nucleophile. A projection of the potential energy surface is obtained in a subspace corresponding to this charge transfer and to the coupled motions of active site residues and the substrate. These results together with extended basis set results for cruder models suggest that a concerted transfer of protons from Ser-195 to His-57 and from His-57 to Asp-102 occurs with an energy barrier of 20-25 kcal/mole (84-105 kJ/mole). The subsequent nucleophilic attack on the scissile peptide linkage by the charged serine is then seen to proceed energetically downhill to the tetrahedral intermediate. The formation of the tetrahedral intermediate from the Michaelis complex is calculated to be nearly thermoneutral. PMID:1058476

  16. 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.

  17. 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.

  18. Visualizing the Role of Molecular Orbitals in Charge Transport through Individual Diarylethene Isomers

    PubMed Central

    2016-01-01

    Diarylethene molecules are prototype molecular switches with their two isomeric forms exhibiting strikingly different conductance, while maintaining similar length. We employed low-temperature scanning tunneling microscopy (STM) to resolve the energy and the spatial extend of the molecular orbitals of the open and closed isomers when lying on a Au(111) surface. We find an intriguing difference in the extension of the respective HOMOs and a peculiar energy splitting of the formerly degenerate LUMO of the open isomer. We then lift the two isomers with the tip of the STM and measure the current through the individual molecules. By a simple analytical model of the transport, we show that the previously determined orbital characteristics are essential ingredients for the complete understanding of the transport properties. We also succeeded in switching the suspended molecules by the current, while switching the ones which are in direct contact to the surface occurs nonlocally with the help of the electric field of the tip. PMID:27775886

  19. 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.

  20. Spin-orbital entangled molecular jeff states in lacunar spinel compounds.

    PubMed

    Kim, Heung-Sik; Im, Jino; Han, Myung Joon; Jin, Hosub

    2014-06-03

    The entanglement of the spin and orbital degrees of freedom through the spin-orbit coupling has been actively studied in condensed matter physics. In several iridium oxide systems, the spin-orbital entangled state, identified by the effective angular momentum jeff, can host novel quantum phases. Here we show that a series of lacunar spinel compounds, GaM4X8 (M=Nb, Mo, Ta and W and X=S, Se and Te), gives rise to a molecular jeff state as a new spin-orbital composite on which the low-energy effective Hamiltonian is based. A wide range of electron correlations is accessible by tuning the bandwidth under external and/or chemical pressure, enabling us to investigate the cooperation between spin-orbit coupling and electron correlations. As illustrative examples, a two-dimensional topological insulating phase and an anisotropic spin Hamiltonian are investigated in the weak and strong coupling regimes, respectively. Our finding can provide an ideal platform for exploring jeff physics and the resulting emergent phenomena.

  1. Molecular orbital view of the electronic coupling between two metal nanoparticles

    SciTech Connect

    Troparevsky, Claudia; Zhao, Ke; Xiao, Di; Eguiluz, Adolfo G; Zhang, Zhenyu

    2010-01-01

    The electronic coupling between metal nanoparticles is responsible for intriguing new phenomena observed when the particles are near touching contact, which is exemplified by recent investigations of nanoparticle dimers. However, little is known about the role of the molecular orbitals of the nanoparticle dimers. The expectation is that the physics and chemistry of the system must be reflected in the orbitals that control the bonding at touching contact. This expectation is borne out in the present investigation in which we present a comprehensive theoretical study based on density-functional theory of the electronic coupling between two silver nanoparticles. We explain our findings by studying the molecular orbitals of the dimers as a function of the separation and relative orientation between the nanoparticles. We show that as the nanoparticles approach each other a bond-forming step takes place, and that the strength of the hybridization is a key element to determine various properties of the system. We find that the relative orientation between the nanoparticles plays an important role in determining the strength of the coupling which can be visualized by the spatial distribution of the highest occupied molecular orbitals. Moreover, the strength of the coupling will in turn determine the ease of their transition to the nonlinear dielectric-response regime. This effect allows for the tunability of the electronic coupling and magnetic moment of the dimer. Our findings are essential for understanding and tailoring desired physical and chemical properties of closely aggregated nanoparticles relevant for applications such as surface-enhanced Raman scattering and quantum transport in molecular devices.

  2. 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.

  3. 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.

  4. 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.

  5. Molecular orbital calculations on atomic structures of Si-based covalent amorphous ceramics

    SciTech Connect

    Matsunaga, K.; Matsubara, H.

    1999-07-01

    The authors have performed ab-initio Hartree-Fock molecular orbital calculations of local atomic structures and chemical bonding states in Si-N covalent amorphous ceramics. Solute elements such as boron, carbon and oxygen were considered in the Si-N network, and the bonding characteristics around the solute elements were analyzed. When a nitrogen atom is substituted by a carbon atom, it was found that Si-C bonds reinforce the Si-N network due to strong covalency.

  6. A molecular orbital rationalization of ligand effects in N2 activation.

    PubMed

    Ariafard, Alireza; Brookes, Nigel J; Stranger, Robert; Yates, Brian F

    2008-01-01

    Molecular orbital theory has been used to study a series of [(micro-N2){ML3}2] complexes as models for dinitrogen activation, with M=Mo, Ta, W, Re and L=NH2, PH2, AsH2, SbH2 and N(BH2)2. The main aims of this study have been to provide a thorough electronic analysis of the complexes and to extend previous work involving molecular orbital analyses. Molecular orbital diagrams have been used to rationalize why for L=NH2 ligand rotation is important for the singlet state but not the triplet, to confirm the effect of ligand pi donation, and to rationalize the importance of the metal d-electron configuration. The outcomes of this study will assist with a more in-depth understanding of the electronic basis for N2 activation and allow clearer predictions to be made about the structure and multiplicity of systems involved in transition-metal catalysis.

  7. Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.

    PubMed

    Simoncini, David; Nakata, Hiroya; Ogata, Koji; Nakamura, Shinichiro; Zhang, Kam Yj

    2015-02-01

    Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

  8. Molecular Genetic Evidence for Genetic Overlap between General Cognitive Ability and Risk for Schizophrenia: A Report from the Cognitive Genomics Consortium (COGENT)

    PubMed Central

    Lencz, Todd; Knowles, Emma; Davies, Gail; Guha, Saurav; Liewald, David C; Starr, John M; Djurovic, Srdjan; Melle, Ingrid; Sundet, Kjetil; Christoforou, Andrea; Reinvang, Ivar; Mukherjee, Semanti; Lundervold, Astri; Steen, Vidar M.; John, Majnu; Espeseth, Thomas; Räikkönen, Katri; Widen, Elisabeth; Palotie, Aarno; Eriksson, Johan G; Giegling, Ina; Konte, Bettina; Ikeda, Masashi; Roussos, Panos; Giakoumaki, Stella; Burdick, Katherine E.; Payton, Antony; Ollier, William; Horan, Mike; Donohoe, Gary; Morris, Derek; Corvin, Aiden; Gill, Michael; Pendleton, Neil; Iwata, Nakao; Darvasi, Ariel; Bitsios, Panos; Rujescu, Dan; Lahti, Jari; Hellard, Stephanie Le; Keller, Matthew C.; Andreassen, Ole A.; Deary, Ian J; Glahn, David C.; Malhotra, Anil K.

    2014-01-01

    It has long been recognized that generalized deficits in cognitive ability represent a core component of schizophrenia, evident prior to full illness onset and independent of medication. The possibility of genetic overlap between risk for schizophrenia and cognitive phenotypes has been suggested by the presence of cognitive deficits in first-degree relatives of patients with schizophrenia; however, until recently, molecular genetic approaches to test this overlap have been lacking. Within the last few years, large-scale genome-wide association studies (GWAS) of schizophrenia have demonstrated that a substantial proportion of the heritability of the disorder is explained by a polygenic component consisting of many common SNPs of extremely small effect. Similar results have been reported in GWAS of general cognitive ability. The primary aim of the present study is to provide the first molecular genetic test of the classic endophenotype hypothesis, which states that alleles associated with reduced cognitive ability should also serve to increase risk for schizophrenia. We tested the endophenotype hypothesis by applying polygenic SNP scores derived from a large-scale cognitive GWAS meta-analysis (~5000 individuals from 9 non-clinical cohorts comprising the COGENT consortium) to four schizophrenia case-control cohorts. As predicted, cases had significantly lower cognitive polygenic scores compared to controls. In parallel, polygenic risk scores for schizophrenia were associated with lower general cognitive ability. Additionally, using our large cognitive meta-analytic dataset, we identified nominally significant cognitive associations for several SNPs that have previously been robustly associated with schizophrenia susceptibility. Results provide molecular confirmation of the genetic overlap between schizophrenia and general cognitive ability, and may provide additional insight into pathophysiology of the disorder. PMID:24342994

  9. Terazulene: a high-performance n-type organic field-effect transistor based on molecular orbital distribution control.

    PubMed

    Yamaguchi, Yuji; Ogawa, Keisuke; Nakayama, Ken-Ichi; Ohba, Yoshihiro; Katagiri, Hiroshi

    2013-12-26

    We present herein a linear expanded π-conjugation system comprising azulene units: 2,6':2',6″-terazulene. This simple hydrocarbon exhibits excellent n-type transistor performance with an electron mobility of up to 0.29 cm(2) V(-1) s(-1). The lowest unoccupied molecular orbital (LUMO) is well distributed over the entire molecule, whereas the highest occupied molecular orbital (HOMO) is localized at one end. These findings indicate a disadvantage of hole carrier transport and an advantage of n-type-specific transport behavior. This system presents an unconventional concept: polarity control of OFET by molecular orbital distribution control.

  10. Batch processing of overlapping molecular spectra as a tool for spatio-temporal diagnostics of power modulated microwave plasma jet

    NASA Astrophysics Data System (ADS)

    Voráč, Jan; Synek, Petr; Potočňáková, Lucia; Hnilica, Jaroslav; Kudrle, Vít

    2017-02-01

    Power modulated microwave plasma jet operating in argon at atmospheric pressure was studied by spatio-temporally resolved optical emission spectroscopy (OES) in order to clarify the influence of modulation on plasma parameters. OES was carried out in OH, NH, N2 and {{{N}}}2+ spectral regions using a spectrometer with intensified CCD detector synchronised with 101–103 Hz sine modulating signal. A special software, able to fit even the overlapping spectra, was developed to batch process the massive datasets produced by this spatio-temporal study. Results show that studied species with the exception of {{{N}}}2+ have balanced rotational and vibrational temperatures across the modulation frequencies. Significant influence of modulation can be clearly observed on temperature spatial gradients. Whereas for low modulation frequencies where the temperatures reach sharp maxima upon discharge tip, the high frequency modulation produces thermally homogeneous plasma.

  11. 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.

  12. Study on Electric Charge Trapping in Cross-linking Polyethylene and Byproducts by using Molecular Orbital Calculation

    NASA Astrophysics Data System (ADS)

    Takada, Tatsuo; Hayase, Yuji; Miyake, Hiroaki; Tanaka, Yasuhiro; Yoshida, Masafumi

    This paper reports an examination of hetero-space charge trapping site in cross linked polyethylene (XLPE) using Molecular Orbital calculation. We chose a simple model for polyethylene (C24H50) with one molecular of acetophenone (one of cross linking byproducts), for the examination of XLPE sample. Molecular Orbital calculation can give the microscopic information of electron energy levels, electron density distributions and electro-static potential maps for the simple molecular mode of XLPE. It is presumed that the negative hetero-space charge (electron) and positive hetero-space charge (hole) were trapped at the permanent dipole of acetophenone, and the hole carrier could move in the polyethylene chain.

  13. In vitro and in vivo imaging of ultra-high-molecular-weight polyethylene orbital implants.

    PubMed

    Olszycki, Marek; Kozakiewicz, Marcin; Elgalal, Marcin; Majos, Agata; Stefanczyk, Ludomir

    2015-01-01

    The aim of this study is to compare magnetic resonance imaging (MRI) with computed tomography (CT) for visualization of an orbital alloplastic prosthesis made of ultra-high-molecular-weight polyethylene (UHMW-PE) both in vitro and in vivo. A study of 15 test implants from UHMW-PE visualized in vitro in CT and MRI and an in vivo visualization in a patient who suffered from orbital injury and underwent reconstructive surgery is presented. The postsurgery MRI showed the UHMW-PE material clearly, with no significant artifacts. The surrounding tissues could be satisfactorily evaluated. The CT scans did not present the graft material. Both techniques were sufficient tools for in vitro evaluation of the shape and measurement of the prosthesis.

  14. 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.

  15. 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.

  16. Molecular Orbital Rule for Quantum Interference in Weakly Coupled Dimers: Low-Energy Giant Conductivity Switching Induced by Orbital Level Crossing.

    PubMed

    Nozaki, Daijiro; Lücke, Andreas; Schmidt, Wolf Gero

    2017-02-16

    Destructive quantum interference (QI) in molecular junctions has attracted much attention in recent years. It can tune the conductance of molecular devices dramatically, which implies numerous potential applications in thermoelectric and switching applications. There are several schemes that address and rationalize QI in single molecular devices. Dimers play a particular role in this respect because the QI signal may disappear, depending on the dislocation of monomers. We derive a simple rule that governs the occurrence of QI in weakly coupled dimer stacks of both alternant and nonalternant polyaromatic hydrocarbons (PAHs) and extends the Tada-Yoshizawa scheme. Starting from the Green's function formalism combined with the molecular orbital expansion approach, it is shown that QI-induced antiresonances and their energies can be predicted from the amplitudes of the respective monomer terminal molecular orbitals. The condition is illustrated for a toy model consisting of two hydrogen molecules and applied within density functional calculations to alternant dimers of oligo(phenylene-ethynylene) and nonalternant PAHs. Minimal dimer structure modifications that require only a few millielectronvolts and lead to an energy crossing of the essentially preserved monomer orbitals are shown to result in giant conductance switching ratios.

  17. 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.

  18. Efficient vibrational analysis for unrestricted Hartree-Fock based on the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nakata, Hiroya; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

    2014-05-01

    We developed the analytic second derivative of the energy for unrestricted Hartree-Fock based on the fragment molecular orbital (FMO) method. We formulated the second order derivative for the separated dimer approximation in both restricted and unrestricted methods, which accelerated the calculations by the factor of 9 for a radical system containing 704 atoms. The accuracy was evaluated for organic radicals in explicit solvent, in comparison to full ab initio results. The method was applied to study the change of IR absorption spectra in the tyrosine oxidation reaction for a polypeptide representing the active part of the photosynthetic reaction center.

  19. 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.

  20. Development of minimized mixing molecular orbital method for designing organic ferromagnets.

    PubMed

    Zhu, Xun; Aoki, Yuriko

    2015-06-15

    Predicting the high spin stability of organic radicals correctly for designing organic ferromagnets remains a significant challenge. We have developed a method with an index (L(min)) for predicting the high spin stability of conjugated organic radicals at the restricted open-shell Hartree-Fock level. Unitary transformations were performed for localizing the coefficients of nonbonding molecular orbitals, and subsequently the localized coefficients were used to calculate L(min) that indicates the high spin stability of conjugated organic radicals. This method can be combined with the elongation method to treat huge high spin open-shell systems. Thus, this method is useful for designing organic ferromagnets.

  1. 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.

  2. Localization of open-shell molecular orbitals via least change from fragments to molecule

    NASA Astrophysics Data System (ADS)

    Li, Hongyang; Liu, Wenjian; Suo, Bingbing

    2017-03-01

    Both top-down and bottom-up localization schemes are proposed for constructing localized molecular orbitals (LMOs) of open-shell systems, via least change from fragments to molecule. The success of both schemes stems from (1) the primitive fragment LMOs that are local not only in space but also in energy and (2) the "conquer step" that allows arbitrary assignment of the unpaired electrons to fragments. Moreover, integral occupations are retained, so as to facilitate subsequent treatment of electron correlation and excitation.

  3. Path Integral Molecular Dynamics for Hydrogen with Orbital-Free Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Runge, Keith; Karasiev, Valentin; Deymier, Pierre

    2014-03-01

    The computational bottleneck for performing path-integral molecular dynamics (PIMD) for nuclei on a first principles electronic potential energy surface has been the speed with which forces from the electrons can be generated. Recent advances in orbital-free density functional theory (OF-DFT) not only allow for faster generation of first principles forces but also include the effects of temperature on the electron density. We will present results of calculations on hydrogen in warm dense matter conditions where the protons are described by PIMD and the electrons by OF-DFT. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.

  4. Molecular orbital predictions of the vibrational frequencies of some molecular ions

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    The initial detections of IR vibration-rotation bands in polyatomic molecular ions by recent spectroscopic advances were guided by ab initio prediction of vibrational frequencies. The present calculations predict the vibrational frequencies of additional ions which are candidates for laboratory analysis. Neutral molecule vibrational frequencies were computed at three levels of theory and then compared with experimental data; the effect of scaling was also investigated, in order to determine how accurately vibrational frequencies could be predicted. For 92 percent of the frequencies examined, the relatively simple HF/6-31G theory's vibrational frequencies were within 100/cm of experimental values, with a mean absolute error of 49/cm. On this basis, the frequencies of 30 molecular ions (many possessing astrophysical significance) were computed.

  5. Validity boundary of orbital-free molecular dynamics method corresponding to thermal ionization of shell structure

    NASA Astrophysics Data System (ADS)

    Gao, Chang; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping; He, X. T.

    2016-11-01

    With 6LiD as an example, we show that the applicable region of the orbital-free molecular dynamics (OFMD) method in a large temperature range is determined by the thermal ionization process of bound electrons in shell structures. The validity boundary of the OFMD method is defined roughly by the balance point of the average thermal energy of an electron and the ionization energy of the lowest localized electronic state. This theoretical proposition is based on the observation that the deviation of the OFMD method originates from its less accurate description to the charge density in partially ionized shells, as compared with the results of the extended first-principles molecular dynamics method, which well reproduces the charge density of shell structures.

  6. 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.

  7. Spin-orbit force, recoil corrections, and possible BB¯* and DD¯* molecular states

    NASA Astrophysics Data System (ADS)

    Zhao, Lu; Ma, Li; Zhu, Shi-Lin

    2014-05-01

    In the framework of the one-boson exchange model, we have calculated the effective potentials between two heavy mesons BB¯* and DD¯* from the t- and u-channel π-, η-, ρ-, ω-, and σ-meson exchanges with four kinds of quantum number: I=0, JPC=1++; I =0, JPC=1+-; I =1, JPC=1++; I =1, JPC=1+-. We keep the recoil corrections to the BB¯* and DD¯* systems up to O(1/M2). The spin-orbit force appears at O(/1M), which turns out to be important for the very loosely bound molecular states. Our numerical results show that the momentum-related corrections are unfavorable to the formation of the molecular states in the I =0, JPC=1++ and I =1, JPC=1+- channels in the DD¯* system.

  8. 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…

  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.

  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. MORATE: a program for direct dynamics calculations of chemical reaction rates by semiempirical molecular orbital theory

    NASA Astrophysics Data System (ADS)

    Truong, Thanh N.; Lu, Da-hong; Lynch, Gillian C.; Liu, Yi-Ping; Melissas, Vasilios S.; Stewart, James J. P.; Steckler, Rozeanne; Garrett, Bruce C.; Isaacson, Alan D.; Gonzalez-Lafont, Angels; Rai, Sachchida N.; Hancock, Gene C.; Joseph, Tomi; Truhlar, Donald G.

    1993-04-01

    We present a computer program, MORATE (Molecular Orbital RATE calculations), for direct dynamics calculations of unimolecular and bimolecular rate constants of gas-phase chemical reactions involving atoms, diatoms, or polyatomic species. The potential energies, gradients, and higher derivatives of the potential are calculated whenever needed by semiempirical molecular orbital theory without the intermediary of a global or semiglobal fit. The dynamical methods used are conventional or variational transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. The computer program is conveniently interfaced package consisting of the POLYRATE program, version 4.5.1, for dynamical rate calculations, and the MOPAC program, version 5.03, for semiempirical electronic structure computations. All semiempirical methods available in MOPAC, in particular MINDO/3, MNDO, AM1, and PM3, can be called on to calculate the potential and gradient. Higher derivatives of the potential are obtained by numerical derivatives of the gradient. Variational transition states are found by a one-dimensional search of generalized-transition-state dividing surfaces perpendicular to the minimum-energy path, and tunneling probabilities are evaluated by numerical quadrature.

  12. Quantum Monte Carlo Method for Heavy Atomic and Molecular Systems with Spin-Orbit Interactions

    NASA Astrophysics Data System (ADS)

    Melton, Cody; Mitas, Lubos

    We present a new quantum Monte Carlo (QMC) method that can treat spin-orbit and other types of spin-depentent interactions explicitly. It is based on generalization of the fixed-phase and projection of the nonlocal operators with spinor trial wave functions. For testing the method we calculate several atomic and molecular systems such as Bi, W, Pb, PbH and PbO, some of them with both large- and small-core pseudopotentials. We validate the quality of the results against other correlated methods such as configuration interaction in two-component formalism. We find excellent agreement with extrapolated values for the total energies and we are able to reliably reproduce experimental values of excitation energies, electron affinity and molecular binding. We show that in order to obtain the agreement with experimental values the explicit inclusion of the spin-orbit interactions is crucial. U.S. D.O.E. grant de-sc0012314 and NERSC Contract No. DE-AC02-05CH11231.

  13. Molecular orbital studies of gas-phase interactions between complex molecules.

    PubMed

    Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M

    2006-03-16

    Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  15. 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.

  16. 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.

  17. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  18. Nanoscale orbital excitations and the infrared spectrum of a molecular Mott insulator: A15-Cs3C60.

    PubMed

    Naghavi, S S; Fabrizio, M; Qin, T; Tosatti, E

    2016-10-14

    The quantum physics of ions and electrons behind low-energy spectra of strongly correlated molecular conductors, superconductors and Mott insulators is poorly known, yet fascinating especially in orbitally degenerate cases. The fulleride insulator Cs3C60 (A15), one such system, exhibits infrared (IR) spectra with low temperature peak features and splittings suggestive of static Jahn-Teller distortions with a breakdown of orbital symmetry in the molecular site. That is puzzling, since there is no detectable static distortion, and because the features and splittings disappear upon modest heating, which they should not. Taking advantage of the Mott-induced collapse of electronic wavefunctions from lattice-extended to nanoscale localized inside a caged molecular site, we show that the unbroken spin and orbital symmetry of the ion multiplets explains the IR spectrum without adjustable parameters. This demonstrates the importance of a fully quantum treatment of nuclear positions and orbital momenta in the Mott insulator sites, dynamically but not statically distorted. The observed demise of these features with temperature is explained by the thermal population of a multiplet term whose nuclear positions are essentially undistorted, but whose energy is very low-lying. That term is in fact a scaled-down orbital excitation analogous to that of other Mott insulators, with the same spin 1/2 as the ground state, but with a larger orbital momentum of two instead of one.

  19. 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

    2015-12-24

    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.

  20. IMAGING THE MOLECULAR DISK ORBITING THE TWIN YOUNG SUNS OF V4046 Sgr

    SciTech Connect

    Rodriguez, David R.; Kastner, Joel H.; Wilner, David; Qi, Chunhua E-mail: jhk@cis.rit.ed E-mail: cqi@cfa.harvard.ed

    2010-09-10

    We have imaged the disk surrounding the nearby (D {approx} 73 pc), {approx}12 Myr, classical T Tauri binary system V4046 Sgr with the Submillimeter Array (SMA) at an angular resolution of {approx}2''. We detect a rotating disk in {sup 12}CO(2-1) and {sup 13}CO(2-1) emission and resolve the continuum emission at 1.3 mm. We infer disk gas and dust masses of {approx}110 and {approx}40 Earth masses, respectively. Fits to a power-law disk model indicate that the molecular disk extends to {approx}370 AU and is viewed at an inclination of between {approx}33{sup 0} and {approx}39{sup 0} for dynamical stellar masses ranging from 1.8 M {sub sun} down to 1.5 M {sub sun} (the range of the total mass previously determined for the central, 2.4 day spectroscopic binary). This range of disk inclination is consistent with that assumed in deducing the central binary mass (i.e., 35{sup 0}), suggesting that the V4046 Sgr binary system and its circumbinary, molecular disk are coplanar. In light of the system's age and binarity, the presence of an extensive molecular disk orbiting V4046 Sgr provides constraints on the timescales of processes related to Jovian planet formation and demonstrates that circumbinary Jovian planets potentially could form around close binary systems.

  1. 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.

  2. 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.

  3. Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method.

    PubMed

    Pruitt, Spencer R; Steinmann, Casper

    2017-03-02

    The Claisen rearrangement of chorismate to prephenate is mapped across the entire reaction pathway using the fragment molecular orbital (FMO) method. Three basis sets (6-31G(d), cc-pVDZ, and pcseg-1) are studied to provide guidance toward obtaining high accuracy with the FMO method on such systems. Using a fragmentation scheme of one residue per fragment, the FMO method using the 6-31G(d) basis set and second-order Møller-Plesset perturbation theory (MP2) with the hybrid orbital projection fragmentation scheme provides the most reliable results across the entire reaction pathway. Calculations using the multilayer FMO method are performed and shown to be in agreement with single-layer calculations in all cases with differences of less than one kilocalorie per mole for all tested basis set combinations along the entire reaction path. The use of restricted Hartree-Fock for the lower-level layer and MP2 for the higher-level layer gives the most consistent results when using the same basis set for both layers. Pair interaction energy decomposition analysis calculations confirm that electrostatic interactions are the predominant force between three key arginine residues and chorismate and that dispersion and charge transfer interactions in the binding pocket also play a role in the local chemistry of the reaction.

  4. Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus

    PubMed Central

    Tubert-Brohman, Ivan; Guimarães, Cristiano Ruch Werneck; Jorgensen, William L.

    2008-01-01

    The PDDG/PM3 semiempirical molecular orbital method has been parameterized for molecules, ions, and complexes containing sulfur; the mean absolute error (MAE) for heats of formation, ΔHf, of 6.4 kcal/mol is 35 − 40 % smaller than for PM3, AM1, and MNDO/d. For completeness, parameterization was also carried out for silicon and phosphorous. For 144 silicon-containing molecules, the ΔHf MAE for PDDG/PM3, PM3, and AM1 is 11 − 12 kcal/mol, while MNDO/d yields 9.4 kcal/mol. For the limited set of 43 phosphorus-containing molecules, MNDO/d also yields the best results followed by PDDG/PM3, AM1, and PM3. The benefits of the d-orbitals in MNDO/d for hypervalent compounds are apparent for silicon and phosphorous, while they are masked in the larger dataset for sulfur by large errors for branched compounds. Overall, for 1480 molecules, ions, and complexes containing the elements H, C, N, O, F, Si, P, S, Cl, Br, and I, the MAEs in kcal/mol for ΔHf are 6.5 (PDDG/PM3), 8.7 (PM3), 10.3 (MNDO/d), 10.8 (AM1), and 19.8 (MNDO). PMID:19011692

  5. 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.

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

    PubMed

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

    2016-03-09

    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.

  7. Analytic second derivatives of the energy in the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

    2013-04-01

    We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm-1 in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.

  8. Orbital-free molecular dynamics simulations of transport properties in dense-plasma uranium

    NASA Astrophysics Data System (ADS)

    Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.

    2011-09-01

    We have calculated the self-diffusion coefficients and shear viscosity of dense-plasma uranium using orbital-free molecular dynamics (OFMD) at the Thomas-Fermi-Dirac level. The transport properties of uranium in this regime have not previously been investigated experimentally or theoretically. The OFMD calculations were performed for temperatures from 50 to 5000 eV and densities from ambient to 10 times compressed. The results are compared with the one-component-plasma (OCP) model, using effective charges given by the average-atom code INFERNO and by the regularization procedure from the OFMD method. The latter generally showed better agreement with the OFMD for viscosity and the former for diffusion. A Stokes-Einstein relationship of the OFMD viscosities and diffusion coefficients is found to hold fairly well with a constant of 0.075 ± 0.10, while the OCP/INFERNO model yields 0.13 ± 0.10.

  9. Molecular orbital study of the bond-valence sum rule using Lewis-electron pair theory.

    PubMed

    Mohri, Fumihito

    2003-04-01

    The bond-valence sum rule has been examined by molecular-orbital methods related to spin-coupling matrix theory [Okada & Fueno (1976). Bull. Chem. Soc. Jpn, 49, 1524-1530], to give a new formulation of the Lewis-electron pair concept. It is shown that the 'pair-coupling population' between atoms M and X exhibits the same behaviour as the bond valence between them. A quantum chemical definition for bond valence is proposed and successfully applied to Al(2)Cl(6), Te(4)Cl(16) and Al(2)Be(3)(SiO(3))(6) (beryl). Using an alternative bond-valence definition it is shown that for oxides the bond valence can possibly be taken as the double pair-coupling population.

  10. Spin-orbit coupling effects on the molecular structure of Thallium(I)formiate

    NASA Astrophysics Data System (ADS)

    Berger, Raphael J. F.

    2017-03-01

    While scalar relativistic effects on molecular structures have been described for ample compounds both experimentally and theoretically, not much is known about the influence of non-scalar relativistic effects like spin-orbit-coupling (SOC) on geometric structure parameters of free molecules. 'Fully-relativistic' optimizations based on four-component DFT calculations on thallium(I)hydride (TlH) and thallium(I)formiate (Tl[O2CH]) are presented. In TlH at 4c-PBE0/VTZ level of theory SOC shortens re(Tl-H) by 0.008 Å (from 1.882 Å to 1.874 Å (exp.: 1.872 Å)). In Tl[O2CH] (C2v symmetry) SOC shortens re(Tl⋯O) by 0.006 Å (from 2.446 Å to 2.440 Å).

  11. 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.

  12. 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.

  13. 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.

  14. Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.

    PubMed

    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 [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.

  15. Analytic second derivatives of the energy in the fragment molecular orbital method.

    PubMed

    Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

    2013-04-28

    We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm(-1) in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.

  16. The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

    PubMed Central

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

    2012-01-01

    We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. PMID:22844433

  17. Molecular orbital studies of enzyme activity: catalytic mechanism of serine proteinases.

    PubMed Central

    Scheiner, S; Lipscomb, W N

    1976-01-01

    The catalytic activity of the serine proteinases is studied using molecular orbital methods on a model of the enzyme-substrate complex. A mechanism is employed in which Ser-195, upon donating a proton to the His-57-Asp-102 dyad, attacks the substrate to form the tetrahedral intermediate. As His-57 then donates a proton to the leaving group, the intermediate decomposes to the acyl enzyme. An analogous process takes place during deacylation, as a water molecule takes the place of Ser-195 as the nucleophile. The motility of the histidine is found to be an important factor in both steps. An attempt is made to include the effects of those atoms not explicitly included in the calculations and to compare the reaction rate of the proposed mechanism with that of the uncatalyzed hydrolysis. This mechanism is found to be in good agreement with structural and kinetic data. PMID:1061145

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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).

  3. 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.

  4. 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

  5. Properties of hot dense plasmas by Orbital-Free Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Clerouin, Jean

    2011-10-01

    During the last decade DFT calculations have been successfully applied to the WDM regime. To overcome the limitations of DFT in temperature and density we propose to return to the very basis of DFT by using an ``only on the density'' formulation of the electronic kinetic energy, essentially captured by the finite temperature formulation of the Thomas-Fermi theory. High temperatures (up to few KeV) and high densities (up to 10 ×ρ0) systems can be addressed by orbital free molecular dynamics simulations (OFMD) at the expense of a fine description of atomic properties such as binding properties. Thanks to an efficient numerical scheme, up to thousands of particles can be propagated giving accurate static and dynamical properties without any assumptions on the ionization state or on the screening of interactions. Simulations of hydrogen and iron up to 5 keV and boron up to 10 times the normal density were performed. Very dissymmetrical mixtures can be also treated without difficulties. More recently, this method has been applied to hydrogen at high density (up to 160 g/cc) and high temperature (up to 1 KeV) to generate long trajectories for a later computation of the thermal conductivity with classical DFT. This method bridges the gap between quantum and classical molecular dynamics in the field of hot-dense plasmas and could be also used as a platform to include more physics such as nuclear reactions or interaction with a radiative field.

  6. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Cobar, Erika A; Lochan, Rohini C; Bell, Alexis T; Head-Gordon, Martin

    2007-09-13

    An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

  7. CaH Rydberg series, oscillator strengths and photoionization cross sections from Molecular Quantum Defect and Dyson Orbital theories

    NASA Astrophysics Data System (ADS)

    Velasco, A. M.; Lavín, C.; Díaz-Tinoco, Manuel; Ortiz, J. V.

    2017-01-01

    In this work, electron-propagator methods are applied to the calculation of the ionization potential and vertical excitation energies for several Rydberg series of the CaH molecule. The present calculations cover more highly excited states than those previously reported. In particular, excitation energies for ns (n>5), np (n>5), nd (n>4) and nf Rydberg states are given. Oscillator strengths for electronic transitions involving Rydberg states of CaH, as well as photoionization cross sections for Rydberg channels, also have been determined by using the Molecular Quantum Defect Orbital approach. Good agreement has been found with the scarce comparative data that are available for oscillator strengths. To our knowledge, predictions of photoionization cross sections from the outermost orbital of CaH are made here for the first time. A Cooper minimum and mixed atomic orbital character in some of the Dyson orbitals are among the novel features of these present calculations.

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

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

    2015-05-05

    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 589nm, 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.

  12. 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…

  13. Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique.

    PubMed

    Li, Junjie; Iyengar, Srinivasan S

    2015-09-08

    Here, we demonstrate the application of fragment-based electronic structure calculations in (a) ab initio molecular dynamics (AIMD) and (b) reduced dimensional potential calculations, for medium- and large-sized protonated water clusters. The specific fragmentation algorithm used here is derived from ONIOM, but includes multiple, overlapping “model” systems. The interaction between the various overlapping model systems is (a) approximated by invoking the principle of inclusion-exclusion at the chosen higher level of theory and (b) within a real calculation performed at the chosen lower level of theory. The fragmentation algorithm itself is written using bit-manipulation arithmetic, which will prove to be advantageous, since the number of fragments in such methods has the propensity to grow exponentially with system size. Benchmark calculations are performed for three different protonated water clusters: H₉O₄⁺, H₁₃O₆⁺ and H(H₂O)₂₁⁺. For potential energy surface benchmarks, we sample the normal coordinates and compare our surface energies with full MP2 and CCSD(T) calculations. The mean absolute error for the fragment-based algorithm is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07 kcal/mol, when compared with CCSD(T) calculations over 693 different geometries for the H₉O₄⁺ system. For the larger H(H₂O)₂₁⁺ water cluster, the mean absolute error is on the order of a 0.1 kcal/mol, when compared with full MP2 calculations for 84 different geometries, at a fraction of the computational cost. Ab initio dynamics calculations were performed for H₉O₄⁺ and H₁₃O₆⁺, and the energy conservation was found to be of the order of 0.01 kcal/mol for short trajectories (on the order of a picosecond). The trajectories were kept short because our algorithm does not currently include dynamical fragmentation, which will be considered in future publications. Nevertheless, the velocity autocorrelation functions and their

  14. Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nakata, Hiroya; Nishimoto, Yoshio; Fedorov, Dmitri G.

    2016-07-01

    The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well.

  15. Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method.

    PubMed

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

    2016-07-28

    The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well.

  16. 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.

  17. 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.

  18. Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method.

    PubMed

    Tokuda, Kana; Watanabe, Chiduru; Okiyama, Yoshio; Mochizuki, Yuji; Fukuzawa, Kaori; Komeiji, Yuto

    2016-09-01

    The fragment molecular orbital (FMO) method was applied to quantum chemical calculations of neuramic acid, the natural substrate of the influenza virus neuraminidase, and two of its competitive inhibitors, Oseltamivir (Tamiful(®)) and Zanamivir (Relenza(®)), to investigate their hydrated structures and energetics. Each of the three ligands was immersed in an explicit water solvent, geometry-optimized by classical MM and QM/MM methods, and subjected to FMO calculations with 2-, 3-, and 4-body corrections under several fragmentation options. The important findings were that QM/MM optimization was preferable to obtain reliable hydrated structures of the ligands, that the 3-body correction was important for quantitative evaluation of the solvation energy, and that the dehydration effect was most remarkable near the hydrophobic sections of the ligands. In addition, the hydration energy calculated by the explicit solvent was compared with the hydration free energy calculated by the implicit solvent via the Poisson-Boltzmann equation, and the two showed a fairly good correlation. These findings will serve as useful information for rapid drug design.

  19. 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.

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

    PubMed

    Plasser, Felix; Ruckenbauer, Matthias; Mai, Sebastian; Oppel, Markus; Marquetand, Philipp; González, Leticia

    2016-03-08

    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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. Reduced explicitly correlated Hartree-Fock approach within the nuclear-electronic orbital framework: applications to positronic molecular systems.

    PubMed

    Sirjoosingh, Andrew; Pak, Michael V; Swalina, Chet; Hammes-Schiffer, Sharon

    2013-07-21

    In the application of the nuclear-electronic orbital (NEO) method to positronic systems, all electrons and the positron are treated quantum mechanically on the same level. Explicit electron-positron correlation can be included using Gaussian-type geminal functions within the variational self-consistent-field procedure. In this paper, we apply the recently developed reduced explicitly correlated Hartree-Fock (RXCHF) approach to positronic molecular systems. In the application of RXCHF to positronic systems, only a single electronic orbital is explicitly correlated to the positronic orbital. We apply NEO-RXCHF to three systems: positron-lithium, lithium positride, and positron-lithium hydride. For all three of these systems, the RXCHF approach provides accurate two-photon annihilation rates, average contact densities, electronic and positronic single-particle densities, and electron-positron contact densities. Moreover, the RXCHF approach is significantly more accurate than the original XCHF approach, in which all electronic orbitals are explicitly correlated to the positronic orbital in the same manner, because the RXCHF wavefunction is optimized to produce a highly accurate description of the short-ranged electron-positron interaction that dictates the annihilation rates and other local properties. Furthermore, RXCHF methods that neglect or approximate the electronic exchange interactions between the geminal-coupled electronic orbital and the regular electronic orbitals lead to virtually identical annihilation rates and densities as the fully antisymmetric RXCHF method but offer substantial advantages in computational tractability. Thus, NEO-RXCHF is a promising, computationally practical approach for studying larger positron-containing systems.

  6. 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…

  7. 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.

  8. Light-Controlled Reversible Modulation of Frontier Molecular Orbital Energy Levels in Trifluoromethylated Diarylethenes.

    PubMed

    Herder, Martin; Eisenreich, Fabian; Bonasera, Aurelio; Grafl, Anna; Grubert, Lutz; Pätzel, Michael; Schwarz, Jutta; Hecht, Stefan

    2017-01-17

    Among bistable photochromic molecules, diarylethenes (DAEs) possess the distinct feature that upon photoisomerization they undergo a large modulation of their π-electronic system, accompanied by a marked shift of the HOMO/LUMO energies and hence oxidation/reduction potentials. The electronic modulation can be utilized to remote-control charge- as well as energy-transfer processes and it can be transduced to functional entities adjacent to the DAE core, thereby regulating their properties. In order to exploit such photoswitchable systems it is important to precisely adjust the absolute position of their HOMO and LUMO levels and to maximize the extent of the photoinduced shifts of these energy levels. Here, we present a comprehensive study detailing how variation of the substitution pattern of DAE compounds, in particular using strongly electron-accepting and chemically stable trifluoromethyl groups either in the periphery or at the reactive carbon atoms, allows for the precise tuning of frontier molecular orbital levels over a broad energy range and the generation of photoinduced shifts of more than 1 eV. Furthermore, the effect of different DAE architectures on the transduction of these shifts to an adjacent functional group is discussed. Whereas substitution in the periphery of the DAE motif has only minor implications on the photochemistry, trifluoromethylation at the reactive carbon atoms strongly disturbs the isomerization efficiency. However, this can be overcome by using a nonsymmetrical substitution pattern or by combination with donor groups, rendering the resulting photoswitches attractive candidates for the construction of remote-controlled functional systems.

  9. 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.

  10. 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.

  11. Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding.

    PubMed

    Nishimoto, Yoshio; Fedorov, Dmitri G

    2017-03-15

    The three-body fragment molecular orbital (FMO3) method is formulated for density-functional tight-binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for polarizable continuum model. The accuracy of FMO3-DFTB is evaluated for five proteins, sodium cation in explicit solvent, and three isomers of polyalanine. It is shown that FMO3-DFTB is considerably more accurate than FMO2-DFTB. Molecular dynamics simulations for sodium cation in water are performed for 100 ps, yielding radial distribution functions and coordination numbers. © 2017 Wiley Periodicals, Inc.

  12. Analytic energy gradients with frozen molecular orbitals in coupled-cluster and many-body perturbation theory methods: Systematic study of the magnitude and trends of the effects of frozen molecular orbitals

    NASA Astrophysics Data System (ADS)

    Baeck, Kyoung K.; Watts, John D.; Bartlett, Rodney J.

    1997-09-01

    Analytic coupled-cluster (CC) and many-body perturbation theory (MBPT) energy gradient methods with restricted Hartree-Fock (RHF), unrestricted Hartree-Fock (UHF), restricted open-shell Hartree-Fock (ROHF), and quasi-RHF(QRHF) reference functions are extended to permit dopping core and excited orbitals. By using the canonical property of the semicanonical ROHF orbitals and the RHF orbitals from which the QRHF reference function is constructed, it is shown that a general procedure can be established not only for RHF and UHF, but also for ROHF and QRHF reference functions. The basic theory and implementation are reported. To provide a systematic study of the trends and magnitudes of the effects of dropped molecular orbitals (MOs) on the structures, harmonic frequencies, and ir intensities, we study HCN, C2H2, CO2, HO2, and C2H4 at increasing levels of correlation and basis sets. The effects of the dropped MOs with the largest basis sets are about 0.003 Å and 0.1° in structures and about 1% on harmonic frequencies and ir intensities. The magnitude and the direction of the drop-MO effect tend to be almost constant from MBPT(2) to CCSD(T) methods. The two isomers of S3 are studied by the drop-MO-method, yielding very accurate results.

  13. 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.

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

    PubMed

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-05

    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 ((1)H and (13)C) 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.

  15. Exact formulas for multipole moments using Slater-type molecular orbitals

    NASA Technical Reports Server (NTRS)

    Jones, H. W.

    1986-01-01

    A triple infinite sum of formulas expressed as an expansion in Legendre polynomials is generated by use of computer algebra to represent the potential from the midpoint of two Slater-type orbitals; the charge density that determines the potential is given as the product of the two orbitals. An example using 1s orbitals shows that only a few terms are needed to obtain four-figure accuracy. Exact formulas are obtained for multipole moments by means of a careful study of expanded formulas, allowing an 'extrapolation to infinity'. This Loewdin alpha-function approach augmented by using a C matrix to characterize Slater-type orbitals can be readily generalized to all cases.

  16. Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals

    SciTech Connect

    Hay, P.J.; Wadt, W.R.

    1985-01-01

    Ab initio effective core potentials (ECP's) have been generated to replace the innermost core electron for third-row (K--Au), fourth-row (Rb--Ag), and fifth-row (Cs--Au) atoms. The outermost core orbitals: corresponding to the ns/sup 2/np/sup 6/ configuration for the three rows here: are not replaced by the ECP but are treated on an equal footing with the nd, (n+1)s and (n+1)p valence orbitals. These ECP's have been derived for use in molecular calculations where these outer core orbitals need to be treated explicitly rather than to be replaced by an ECP. The ECP's for the forth and fifth rows also incorporate the mass--velocity and Darwin relativistic effects into the potentials. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3s, 3p, 3d, 4s, 4p), (4s, 4p, 4d, 5s, 5p), and (5s, 5p, 5d, 6s, 6p) ortibals of the three respective rows.

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

    PubMed

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

    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(5)) model systems with well-known electronic structure, viz., atomic Fe(3+), high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)6](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.

  18. Negative differential resistance in a hybrid silicon-molecular system: resonance between the intrinsic surface-states and the molecular orbital.

    PubMed

    Wang, Weihua; Ji, Yongfei; Zhang, Hui; Zhao, Aidi; Wang, Bing; Yang, Jinlong; Hou, J G

    2012-08-28

    It has been a long-term desire to fabricate hybrid silicon-molecular devices by taking advantages of organic molecules and the existing silicon-based technology. However, one of the challenging tasks is to design applicable functions on the basis of the intrinsic properties of the molecules, as well as the silicon substrates. Here we demonstrate a silicon-molecular system that produces negative differential resistance (NDR) by making use of the well-defined intrinsic surface-states of the Si (111)-√3 × √3-Ag (R3-Ag/Si) surface and the molecular orbital of cobalt(II)-phthalocyanine (CoPc) molecules. From our experimental results obtained using scanning tunneling microscopy/spectroscopy, we find that NDR robustly appears at the Co(2+) ion centers of the CoPc molecules, independent of the adsorption configuration of the CoPc molecules and irrespective of doping type and doping concentration of the silicon substrates. Joint with first principle calculations, we conclude that NDR is originated from the resonance between the intrinsic surface-state band S(1) of the R3-Ag/Si surface and the localized unoccupied Co(2+)d(z(2)) orbital of the adsorbed CoPc molecules. We expect that such a mechanism can be generally used in other silicon-molecular systems.

  19. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions.

    PubMed

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

    2016-01-25

    Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.

  20. 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.

  1. Control over the Emission Properties of [5]Helicenes Based on the Symmetry and Energy Levels of Their Molecular Orbitals.

    PubMed

    Kubo, Hiromu; Hirose, Takashi; Matsuda, Kenji

    2017-03-30

    The effect of different substituents on the fluorescence properties of [5]helicene derivatives was investigated in terms of molecular orbital symmetry. Unsubstituted [5]helicene is nonemissive due to the symmetry-forbidden S1 → S0 transition. However, the fluorescence emission rate constant (kf) of [5]helicenes is efficiently increased by removing the orbital degeneracy involved in the S1 → S0 transition. As a result, we achieved a [5]helicene derivative exhibiting a high fluorescence quantum yield (Φf = 0.23) and short emission lifetime (⟨τf⟩ = 1.5 ns), which is in marked contrast to unsubstituted [5]helicene (Φf = 0.04 and ⟨τf⟩ = 26 ns).

  2. 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.

  3. 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.

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

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-09

    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.

  5. Molecular orbital assistance in the design of intramolecular and photoinduced electron transfer systems

    NASA Astrophysics Data System (ADS)

    Petsalakis, Ioannis D.; Theodorakopoulos, Giannoula

    2012-02-01

    A theoretical approach is described for the design of donor-acceptor intramolecular charge transfer (ICT) systems and for photoinduced electron transfer (PET) hybrids of fullerene, based on orbital level diagrams of the separate donor and acceptor moieties. Minimization of the HOMO-LUMO (highest occupied-lowest unoccupied orbital) gap in ICT systems, translates to a requirement for near degeneracy of the HOMO of the donor and LUMO of the acceptor, determined separately for the two moieties by density functional theory calculations. Similarly, near degeneracy of the LUMO of the donor and LUMO of the acceptor moieties would indicate the possibility of PET in the combined hybrid.

  6. Effect of molecular-orbital rotations on ground-state energies in the parametric two-electron reduced density matrix method.

    PubMed

    Sand, Andrew M; Mazziotti, David A

    2013-06-28

    Different sets of molecular orbitals and the rotations connecting them are of great significance in molecular electronic structure. Most electron correlation methods depend on a reference wave function that separates the orbitals into occupied and unoccupied spaces. Energies and properties from these methods depend upon rotations between the spaces. Some electronic structure methods, such as modified coupled electron pair approximations and the recently developed parametric two-electron reduced density matrix (2-RDM) methods [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], also depend upon rotations between occupied orbitals and rotations between unoccupied orbitals. In this paper, we explore the sensitivity of the ground-state energies from the parametric 2-RDM method to rotations within the occupied space and within the unoccupied space. We discuss the theoretical origin of the rotational dependence and provide computational examples at both equilibrium and non-equilibrium geometries. We also study the effect of these rotations on the size extensivity of the parametric 2-RDM method. Computations show that the orbital rotations have a small effect upon the parametric 2-RDM energies in comparison to the energy differences observed between methodologies such as coupled cluster and parametric 2-RDM. Furthermore, while the 2-RDM method is rigorously size extensive in a local molecular orbital basis set, calculations reveal negligible deviations in nonlocal molecular orbital basis sets such as those from canonical Hartree-Fock calculations.

  7. 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.

  8. A modified ELISA accurately measures secretion of high molecular weight hyaluronan (HA) by Graves' disease orbital cells.

    PubMed

    Krieger, Christine C; Gershengorn, Marvin C

    2014-02-01

    Excess production of hyaluronan (hyaluronic acid [HA]) in the retro-orbital space is a major component of Graves' ophthalmopathy, and regulation of HA production by orbital cells is a major research area. In most previous studies, HA was measured by ELISAs that used HA-binding proteins for detection and rooster comb HA as standards. We show that the binding efficiency of HA-binding protein in the ELISA is a function of HA polymer size. Using gel electrophoresis, we show that HA secreted from orbital cells is primarily comprised of polymers more than 500 000. We modified a commercially available ELISA by using 1 million molecular weight HA as standard to accurately measure HA of this size. We demonstrated that IL-1β-stimulated HA secretion is at least 2-fold greater than previously reported, and activation of the TSH receptor by an activating antibody M22 from a patient with Graves' disease led to more than 3-fold increase in HA production in both fibroblasts/preadipocytes and adipocytes. These effects were not consistently detected with the commercial ELISA using rooster comb HA as standard and suggest that fibroblasts/preadipocytes may play a more prominent role in HA remodeling in Graves' ophthalmopathy than previously appreciated.

  9. Analysis of electron correlation effects and contributions of NMR J-couplings from occupied localized molecular orbitals.

    PubMed

    Zarycz, Natalia; Aucar, Gustavo A

    2012-02-02

    NMR J-coupling calculations at the second-order of polarization propagator approach, SOPPA, are among the most reliable. They include a high percentage of the total electron correlation effects in saturated and unsaturated molecular systems. Furthermore, J-couplings are quite sensitive to the whole electronic molecular framework. We present in this article the first study of all three response mechanisms, Fermi contact, FC, spin-dipolar, SD and paramagnetic spin-orbital, PSO, for J-couplings with occupied localized molecular orbitals at the SOPPA level of approach. Even though SOPPA results are not invariant under unitary transformations, the difference between results obtained with canonical and localized molecular orbitals, LMOs, are small enough to permit its application with confidence. The following small-size saturated and unsaturated compounds were analyzed: CH(4), CH(3)F, C(2)H(6), NH(3), C(2)H(4), CH(2)NH, H(2)C═CHF, and FHC═CHF. The local character of the FC mechanism that appears in J-couplings of these molecular models is shown through the analysis of contributions from LMOs. The importance of including the electron correlation on the engaged bonding orbitals for one-bond couplings is emphasized. Almost all electron correlation effects are included in such orbitals. Interesting findings were the large contributions by s-type LMOs to the C-H and C-C J-couplings; they are responsible for the variation of (1)J(C-C) when going from ethane to ethene and to 1,2-difluoroethene. The previously proposed hyperconjugative transfer mechanism has been tested. Among other tests we found the difference anti-syn of one-bond (1)J(C-H) in imine as due to both the corresponding σ(C-H) and the lone-pair, LP, contribution. Geminal and vicinal J-couplings were also analyzed. Our findings are in accord with a previous work by Pople and Bothner-by, who considered results taken from calculations or empirical data. For all geminal couplings the pattern of J-couplings, like

  10. 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.

  11. 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.

  12. Steganalysis of overlapping images

    NASA Astrophysics Data System (ADS)

    Whitaker, James M.; Ker, Andrew D.

    2015-03-01

    We examine whether steganographic images can be detected more reliably when there exist other images, taken with the same camera under the same conditions, of the same scene. We argue that such a circumstance is realistic and likely in practice. In `laboratory conditions' mimicking circumstances favourable to the analyst, and with a custom set of digital images which capture the same scenes with controlled amounts of overlap, we use an overlapping reference image to calibrate steganographic features of the image under analysis. Experimental results show that the analysed image can be classified as cover or stego with much greater reliability than traditional steganalysis not exploiting overlapping content, and the improvement in reliability depends on the amount of overlap. These results are curious because two different photographs of exactly the same scene, taken only a few seconds apart with a fixed camera and settings, typically have steganographic features that differ by considerably more than a cover and stego image.

  13. 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.

  14. a Moessbauer Effect and Fenske-Hall Molecular Orbital Study of the Electronic Properties of Organoiron Clusters.

    NASA Astrophysics Data System (ADS)

    Buhl, Margaret Linn

    The electronic properties of trinuclear iron, tetranuclear iron butterfly, iron-cobalt, and iron-copper clusters have been studied experimentally at 78K by the Mossbauer effect and theoretically by Fenske-Hall molecular orbital calculations. The Mossbauer effect isomer shift is very sensitive to the differences in the iron s-electron densities in these clusters and, as expected, decreases as the sum of the iron 4s Mulliken population and the Clementi and Raimondi effective nuclear charge increases. The molecular orbital wave functions and the Mulliken atomic charges are used to calculate the electric field gradient at the metal nuclei and the iron Mossbauer effect quadrupole splittings. The valence contribution was found to be the major component of the electric field gradient in all the clusters studied. In general the calculated value of Delta E_ {Q} is larger than the observed value, as a result of neglect of the valence Sternheimer factor, R. The metal charge depends upon its electronegativity and upon the nature of its Lewis base ligands. The carbonyl ligand carbon charge becomes more positive as the metal electronegativity increases. The oxygen charge becomes more negative as the anionic cluster charge increases, and in so doing, yields the maximum anionic charge separation. The electronic properties of the terminal carbonyl ligands are similar to those of carbon monoxide, whereas the electronic properties of the bridging carbonyl ligands are similar to those of the carbonyl group found in aldehydes and ketones.

  15. Understanding the On-Off Switching Mechanism in Cationic Tetravalent Group-V-Based Fluoride Molecular Sensors Using Orbital Analysis.

    PubMed

    Usui, Kosuke; Ando, Mikinori; Yokogawa, Daisuke; Irle, Stephan

    2015-12-24

    The precise control of on-off switching is essential to the design of ideal molecular sensors. To understand the switching mechanism theoretically, we selected as representative example a 9-anthryltriphenylstibonium cation, which was reported as a fluoride ion sensor. In this molecule, the first excited singlet state exhibits two minimum geometries, where one of them is emissive and the other one dark. The excited state at the geometry with bright emission is of π-π* character, whereas it is of π-σ* character at the "dark" geometry. Geometry changes in the excited state were identified by geometry optimization and partial potential energy surface (PES) mapping. We also studied Group V homologues of this molecule. A barrierless relaxation pathway after vertical excitation to the "dark" geometry was found for the Sb-containing compound on the excited-states PES, whereas barriers appear in the case of P and As. Molecular orbital analysis suggests that the σ* orbital of the antimony compound is stabilized along such relaxation and that the excited state changes its nature correspondingly. Our results indicate that the size of the central atom is crucial for the design of fluoride sensors with this ligand framework.

  16. Primary orbital synovial sarcoma: A clinicopathologic review with a differential diagnosis and discussion of molecular genetics.

    PubMed

    Stagner, Anna M; Jakobiec, Frederick A; Fay, Aaron

    Synovial sarcoma is a soft-tissue sarcoma of the extremities developing in young adults that has rarely been reported in the orbit. Synovial sarcoma is associated with a unique translocation, resulting in an SYT-SSX fusion gene. We analyze 7 published periocular cases, together with the current one, to gain a better appreciation of the features of the tumor in this location and to compare the findings with those derived from nonophthalmic studies. An inferior orbital mass developed in a 31-year-old woman after experiencing periorbital and hemifacial pain for more than a decade. Radiographically, the mass was circumscribed and displayed coarse internal calcifications. A large but subtotal excision with histopathologic examination disclosed a primitive tumor composed of spindled and ovoid cells. Immunohistochemistry demonstrated positivity for nuclear transducin-like enhancer of split 1 and membranous CD99, typical for synovial sarcoma. Fluorescence in situ hybridization identified a (X,18) translocation in the tumor cells. The patient underwent postoperative adjuvant proton beam radiotherapy with a good response that has been maintained during 1 year of follow-up. Orbital soft-tissue tumors of all types are increasingly identified by their distinctive genetic signatures that offer more specificity than standard immunohistochemical tests.

  17. Spin-orbit coupling manipulating composite topological spin textures in atomic-molecular Bose-Einstein condensates

    NASA Astrophysics Data System (ADS)

    Liu, Chao-Fei; Juzeliūnas, Gediminas; Liu, W. M.

    2017-02-01

    Atomic-molecular Bose-Einstein condensates (BECs) offer brand new opportunities to revolutionize quantum gases and probe the variation of fundamental constants with unprecedented sensitivity. The recent realization of spin-orbit coupling (SOC) in BECs provides a new platform for exploring completely new phenomena unrealizable elsewhere. In this study, we find a way of creating a Rashba-Dresselhaus SOC in atomic-molecular BECs by combining the spin-dependent photoassociation and Raman coupling, which can control the formation and distribution of a different type of topological excitation—carbon-dioxide-like skyrmion. This skyrmion is formed by two half-skyrmions of molecular BECs coupling with one skyrmion of atomic BECs, where the two half-skyrmions locate at both sides of one skyrmion. Carbon-dioxide-like skyrmion can be detected by measuring the vortices structures using the time-of-flight absorption imaging technique in real experiments. Furthermore, we find that SOC can effectively change the occurrence of the Chern number in k space, which causes the creation of topological spin textures from some separated carbon-dioxide-like monomers each with topological charge -2 to a polymer chain of the skyrmions. This work helps in creating dual SOC atomic-molecular BECs and opens avenues to manipulate topological excitations.

  18. 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.

  19. 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.

  20. Molecular-Orbital Basis for Superconductivity in High- and Low-Dimensional Metals.

    DTIC Science & Technology

    1982-09-24

    between 150A and 50A, respectively. [5,6] Similar increases of Tc with decreasing grain size have be-n measured for evaporated aluminum thin films . [69,70...momentum h/F F = h/2d (2) and kinetic energy (the Fermi energy) 2m 2 2 F /2m = h2/8md2 (3) On the other hand, within each layer-orbital component of...potential can be written in the form (30), which Weisskopf views as being contained in a "long thin tube" of length z and diameter d while acting only

  1. A Spectroscopic Search for Molecular Emission due to the Planets Orbiting 51 Peg and UPS And

    NASA Astrophysics Data System (ADS)

    Deming, D.; Bjoraker, G.; Wiedemann, G.

    1997-12-01

    We have calculated synthetic infrared (2-5 micron) spectra for the planets orbiting 51 Pegasus and Upsilon Andromeda. Our calculations assume these are gas-giant planets, wherein planetary methane absorbs stellar near-infrared flux, forming a hot planetary stratosphere. The planetary spectrum consists of emission in methane and carbon monoxide lines, which may be detectable superposed on the spectrum of the parent star. We describe the results of preliminary observations designed to detect these very weak features in the stellar spectra.

  2. 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.

  3. 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.

  4. 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)

  5. Analytic formulation of derivative coupling vectors for complete active space configuration interaction wavefunctions with floating occupation molecular orbitals

    NASA Astrophysics Data System (ADS)

    Hohenstein, Edward G.

    2016-11-01

    The floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is quite promising for the study of nonadiabatic processes. Use of this method directly in nonadiabatic dynamics simulations has been limited by the lack of available first-order nonadiabatic coupling vectors. Here, an analytic formulation of these derivative coupling vectors is presented for FOMO-CASCI wavefunctions using a simple Lagrangian-based approach. The derivative coupling vectors are applied in the optimization of minimum energy conical intersections of an aqueously solvated model compound for the chromophore of the green fluorescent protein (including 100 water molecules). The computational cost of the FOMO-CASCI derivative coupling vector is shown to scale quadratically, O ( N 2 ) , with system size and is applied to systems with up to 1000 atoms.

  6. Tailoring the highest occupied molecular orbital level of poly(N-vinylcarbazole) hole transport layers in organic multilayer heterojunctions

    SciTech Connect

    Park, Young Ran; Kim, Hyeong Jin; Hong, Young Joon E-mail: yjhong@sejong.ac.kr; Im, Sungjin; Shin, Koo E-mail: yjhong@sejong.ac.kr; Seo, Sunae; Choi, Won Kook

    2016-01-11

    We report the tailoring of the electronic structure of poly(N-vinylcarbazole) (PVK) using a mixture layer of polyaniline:poly(p-styrenesulfonic acid) (PANI:PSS) in organic multilayer PVK/PANI:PSS/poly(3,4-ethylenedioxythiophene):PSS heterojunctions. The overall electronic structure of the PVK overlayer was systematically down-shifted while the work function of PANI:PSS increased as a function of the PSS-to-PANI weight ratio for the ratio range from 1 to 11 in the PANI:PSS film. The down-shift in the highest occupied molecular orbital of PVK markedly reduced the hole injection barrier from PVK to quantum-dot (QD) layers in QD-light emitting diode (QD-LED) structures, resulting in superior electrical and electroluminescent characteristics for QD-LEDs. The influences of PANI:PSS thickness on the electronic structure of PVK and the performance of QD-LEDs are also discussed.

  7. Analytic formulation of derivative coupling vectors for complete active space configuration interaction wavefunctions with floating occupation molecular orbitals.

    PubMed

    Hohenstein, Edward G

    2016-11-07

    The floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is quite promising for the study of nonadiabatic processes. Use of this method directly in nonadiabatic dynamics simulations has been limited by the lack of available first-order nonadiabatic coupling vectors. Here, an analytic formulation of these derivative coupling vectors is presented for FOMO-CASCI wavefunctions using a simple Lagrangian-based approach. The derivative coupling vectors are applied in the optimization of minimum energy conical intersections of an aqueously solvated model compound for the chromophore of the green fluorescent protein (including 100 water molecules). The computational cost of the FOMO-CASCI derivative coupling vector is shown to scale quadratically, O(N(2)), with system size and is applied to systems with up to 1000 atoms.

  8. Theoretical investigation of EPR and molecular orbital coefficient parameters for [Cu(hsm) 2(sac) 2] complex

    NASA Astrophysics Data System (ADS)

    Kalfaoğlu, Emel; Karabulut, Bünyamin

    2011-03-01

    In this study, the molecular orbital coefficients and the spin Hamiltonian parameters of bis(histamine-saccharinate) copper(II) complex, [Cu(hsm) 2(sac) 2], are calculated theoretically. Two d- d transition spectra and four EPR parameters g∥,g⊥,A∥,A⊥ for the Cu(II) complex are calculated by using crystal-field theory. The calculated values are in good agreement with the experimental values. The g and A parameters have indicated that the paramagnetic centre is axially symmetric. Having the relations of g∥>g⊥>ge and A∥>A⊥ for Cu 2+ ions, it can be concluded that Cu 2+ ions are located in distorted octahedral sites (D 4h) elongated along the z-axis and that the ground state of the paramagnetic electron is d ( 2B1g state).

  9. Lower Rydberg series of methane: a combined coupled cluster linear response and molecular quantum defect orbital calculation.

    PubMed

    Velasco, A M; Pitarch-Ruiz, J; Sánchez de Merás, Alfredo M J; Sánchez-Marín, J; Martin, I

    2006-03-28

    Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator strengths in the molecular-adapted quantum defect orbital formalism from a distorted Cs geometry selected on the basis of outer valence green function calculations. The present work provides a wide range of data of excitation energies and absolute oscillator strengths which correspond to the Rydberg series converging to the three lower ionization potential values of the distorted methane molecule, in energy regions for which experimentally measured data appear to be unavailable.

  10. 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.

  11. 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.

  12. An ab initio molecular orbital study of the reaction NH 2+NO → H 2+N 2O

    NASA Astrophysics Data System (ADS)

    Baker, Lane A.; Su, Shujun

    1998-03-01

    Potential energy surface of the reaction NH 2+NO → H 2+N 2O has been studied at several high levels of ab initio molecular orbital theory. The reaction pathway involves initially the formation without a barrier of a twisted non-planar H 2N-NO nitrosamine intermediate, and a C s symmetry transition state, followed by a dihydrogen H 2 elimination to form the products. The reaction path bifurcates before the transition state. At MP4(SDTQ)/6-311G(2d,p)//CASSCF/6-31G(d,p) level of theory, the reaction barrier for this path is found to be +33.7 kcal/mol.

  13. Bound states of the positron with nitrile species with a configuration interaction multi-component molecular orbital approach.

    PubMed

    Tachikawa, Masanori; Kita, Yukiumi; Buenker, Robert J

    2011-02-21

    Characteristic features of the positron binding structure of some nitrile (-CN functional group) species such as acetonitrile, cyanoacetylene, acrylonitrile, and propionitrile are discussed with the configuration interaction scheme of multi-component molecular orbital calculations. This method can take the electron-positron correlation contribution into account through single electronic-single positronic excitation configurations. Our PA value of acetonitrile with the electronic 6-31++G(2df,2pd) and positronic [15s15p3d2f1g] basis set is calculated as 4.96 mhartree, which agrees to within 25% with the recent experimental value of 6.6 mhartree by Danielson et al. [Phys. Rev. Lett., 2010, 104, 233201]. Our PA values of acrylonitrile and propionitrile (5.70 and 6.04 mhartree) are the largest among these species, which is consistent with the relatively large dipole moments of the latter two systems.

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

    PubMed

    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.

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Thirman, Jonathan; Head-Gordon, Martin

    2015-08-01

    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. Distal tibiofibular radiological overlap

    PubMed Central

    Sowman, B.; Radic, R.; Kuster, M.; Yates, P.; Breidiel, B.; Karamfilef, S.

    2012-01-01

    Objectives Overlap between the distal tibia and fibula has always been quoted to be positive. If the value is not positive then an injury to the syndesmosis is thought to exist. Our null hypothesis is that it is a normal variant in the adult population. Methods We looked at axial CT scans of the ankle in 325 patients for the presence of overlap between the distal tibia and fibula. Where we thought this was possible we reconstructed the images to represent a plain film radiograph which we were able to rotate and view in multiple planes to confirm the assessment. Results The scans were taken for reasons other than pathology of the ankle. We found there was no overlap in four patients. These patients were then questioned about previous injury, trauma, surgery or pain, in order to exclude underlying pathology. Conclusion We concluded that no overlap between the tibia and fibula may exist in the population, albeit in a very small proportion. PMID:23610666

  19. 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)

  20. 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.

  1. Molecular Structures of Isomeric Ortho, Meta, and Para Bromo-Substituted α-Methylsulfonyl-α-diethoxyphosphoryl Acetophenones by X-ray and DFT Molecular Orbital Calculations.

    PubMed

    Rodrigues, Alessandro; Olivato, Paulo R; Zukerman-Schpector, Julio; Maganhi, Stella H; Reis, Adriana K C A; Tiekink, Edward R T

    2015-08-13

    The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.

  2. 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.

  3. 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.

  4. 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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. 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.

  5. 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.

    PubMed

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

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(N-H) coupling constant in NH3. 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.

  6. Urea's effect on the ribonuclease A catalytic efficiency: a kinetic, 1H NMR and molecular orbital study.

    PubMed

    Almarza, Jorge; Rincón, Luis; Bahsas, Alí; Pinto, María Angela; Brito, Francisco

    2013-02-01

    Understanding of protein-urea interactions is one of the greatest challenges to modern structural protein chemistry. Based in enzyme kinetics experiments and (1)H NMR spectroscopic analysis we proposed that urea, at low concentrations, directly interacts with the protonated histidines of the active center of RNase A, following a simple model of competitive inhibition. These results were supported by theoretical analysis based on the frontier molecular orbital theory and suggest that urea might establish a favorable interaction with the cationic amino acids. Our experimental evidence and theoretical analysis indicate that the initials steps of the molecular mechanism of Urea-RNase A interaction passes through the establishment of a three center four electron adduct. Also, our results would explain the observed disruption of the (1)H NMR signals corresponding to H12 and H119 (involved in catalysis) of the RNase A studied in the presence of urea. Our interaction model of urea-amino acids (cationic) can be extended to explain the inactivation of other enzymes with cationic amino acids at the active site.

  7. 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

  8. 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.

  9. 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

  10. The Plate Overlap Technique.

    DTIC Science & Technology

    1978-07-31

    INTRODUCTION 1 II. NOTATION 2 III. THE GNOMONIC PROJECTION 4 IV . THE PLATE OVERLAP TECHNIQUE 6 A. MOTIVATION 6 B. FORNULATION 9 C. ON STATISTICAL RIGOR 14 D...and new hardware. Since this aim was clearly recognized long ago, wherever possible in earlier documents or software development flexibility was...reader should see 1, 2, and 3. The procedures one should use to update stellar positions are discussed in 4 with applica- tions to the SAOC in 5. Non

  11. Studies of the molecular geometry, vibrational spectra, frontier molecular orbital, nonlinear optical and thermodynamics properties of aceclofenac by quantum chemical calculations.

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-05-05

    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.

  12. Molecular structure, vibrational spectra, natural bond orbital and thermodynamic analysis of 3,6-dichloro-4-methylpyridazine and 3,6-dichloropyridazine-4-carboxylic acid by dft approach.

    PubMed

    Prabavathi, N; Senthil Nayaki, N; Venkatram Reddy, B

    2015-02-05

    Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (μ) and hyperpolarizability β0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP).

  13. 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…

  14. Nodular Fasciitis of the Orbit: A Case Report Confirmed by Molecular Cytogenetic Analysis.

    PubMed

    Anzeljc, Andrew J; Oliveira, Andre M; Grossniklaus, Hans E; Kim, Hee Joon; Hayek, Brent

    2016-02-12

    Nodular fasciitis is a benign fibroblastic proliferation typically found in the subcutaneous tissue or superficial fascia of the extremities that is often confused for malignancy. These lesions rarely occur on the eyelids and ocular adnexa and are seldom analyzed by ophthalmic pathologists. USP6 gene rearrangement has been recently demonstrated in nodular fasciitis and this rearrangement may lead to the formation of a fusion gene MYH9-USP6 in some cases. Herein, the authors describe a 38-year-old woman with a 6-month history of a progressively enlarging mass beneath her right medial upper eyelid. Histopathologic analysis of the excisional biopsy confirmed classic features of nodular fasciitis. Molecular cytogenetic analysis revealed a rearrangement of the USP6 locus, confirming the diagnosis of benign nodular fasciitis.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-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.

  16. 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.

  17. 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

  18. 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.

  19. Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method.

    PubMed

    Otsuka, Takao; Okimoto, Noriaki; Taiji, Makoto

    2015-11-15

    In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics-based force fields, although they cannot fully describe protein-ligand interactions. A noteworthy computational method in development involves large-scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large-scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange-correlation functionals, and solvation effects) on the binding energies of the FK506-binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2-MP2/6-31G(d), is suitable for evaluating the protein-ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure-activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein-ligand interaction distance. Our acceleration scheme, which uses FMO2-HF/STO-3G:MP2/6-31G(d) at R(int) = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy.

  20. 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.

  1. Molecular-orbital decomposition of the ionization continuum for a diatomic molecule by angle- and energy-resolved photoelectron spectroscopy. I. Formalism

    NASA Astrophysics Data System (ADS)

    Park, Hongkun; Zare, Richard N.

    1996-03-01

    A theoretical formalism is developed for the quantum-state-specific photoelectron angular distributions (PADs) from the direct photoionization of a diatomic molecule in which both the ionizing state and the state of the ion follow Hund's case (b) coupling. The formalism is based on the molecular-orbital decomposition of the ionization continuum and therefore fully incorporates the molecular nature of the photoelectron-ion scattering within the independent electron approximation. The resulting expression for the quantum-state-specific PADs is dependent on two distinct types of dynamical quantities, one that pertains only to the ionization continuum and the other that depends both on the ionizing state and the ionization continuum. Specifically, the electronic dipole-moment matrix element rlλ exp(iηlλ) for the ejection of a photoelectron with orbital angular momentum quantum number l making a projection λ on the internuclear axis is expressed as ΣαλŪlαλλ exp (iπτ¯αλλ) Mαλλ, where Ūλ is the electronic transformation matrix, τ¯αλλ is the scattering phase shift associated with the αλth continuum molecular orbital, and Mαλλ is the real electronic dipole-moment matrix element that connects the ionizing orbital to the αλth continuum molecular orbital. Because Ūλ and τ¯αλλ depend only on the dynamics in the ionization continuum, this formalism allows maximal exploitation of the commonality between photoionization processes from different ionizing states. It also makes possible the direct experimental investigation of scattering matrices for the photoelectron-ion scattering and thus the dynamics in the ionization continuum by studying the quantum-state-specific PADs, as illustrated in the companion article on the photoionization of NO.

  2. 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.

  3. 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.

  4. Comparative Binding Analysis of Dipeptidyl Peptidase IV (DPP-4) with Antidiabetic Drugs – An Ab Initio Fragment Molecular Orbital Study

    PubMed Central

    Arulmozhiraja, Sundaram; Matsuo, Naoya; Ishitsubo, Erika; Okazaki, Seiji; Shimano, Hitoshi

    2016-01-01

    Dipeptidyl peptidase IV (DPP-4) enzyme is responsible for the degradation of incretins that stimulates insulin secretion and hence inhibition of DPP-4 becomes an established approach for the treatment of type 2 diabetics. We studied the interaction between DPP-4 and its inhibitor drugs (sitagliptin 1, linagliptin 2, alogliptin 3, and teneligliptin 4) quantitatively by using fragment molecular orbital calculations at the RI-MP2/cc-pVDZ level to analyze the inhibitory activities of the drugs. Apart from having common interactions with key residues, inhibitors encompassing the DPP-4 active site extensively interact widely with the hydrophobic pocket by their hydrophobic inhibitor moieties. The cumulative hydrophobic interaction becomes stronger for these inhibitors and hence linagliptin and teneligliptin have larger interaction energies, and consequently higher inhibitory activities, than their alogliptin and sitagliptin counterparts. Though effective interaction for both 2 and 3 is at S2' subsite, 2 has a stronger binding to this subsite interacting with Trp629 and Tyr547 than 3 does. The presence of triazolopiperazine and piperazine moiety in 1 and 4, respectively, provides the interaction to the S2 extensive subsite; however, the latter’s superior inhibitory activity is not only due to a relatively tighter binding to the S2 extensive subsite, but also due to the interactions to the S1 subsite. The calculated hydrophobic interfragment interaction energies correlate well with the experimental binding affinities (KD) and inhibitory activities (IC50) of the DPP-4 inhibitors. PMID:27832184

  5. 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.

  6. 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.

  7. 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.

  8. Calculation of positron binding energies of amino acids with the any-particle molecular-orbital approach

    NASA Astrophysics Data System (ADS)

    Charry, J.; Romero, J.; Varella, M. T. do N.; Reyes, A.

    2014-05-01

    We report positron binding energies (PBEs) for the 20 standard amino acids in the global minimum, hydrogen-bonded, and zwitterionic forms. The calculations are performed at the any-particle molecular-orbital (APMO) Hartree-Fock (HF), Koopmans' theorem (KT), second-order Möller-Plesset (MP2), and second-order propagator (P2) levels of theory. Our study reveals that the APMO KT and APMO P2 methods generally provide higher PBEs than the APMO HF and APMO MP2 methods, respectively, with only a fraction of the computational costs of the latter. We also discuss the impact of the choice of the positronic center on the PBEs and propose a simple and inexpensive procedure, based on the condensed Fukui functions of the parent molecules, to select the most suitable expansion center. The results reported so far indicate that APMO KT and APMO P2 methods are convenient options for a qualitative or semiquantitative analysis of positron binding in medium to large polyatomic systems.

  9. 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

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

    PubMed

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

    2016-05-13

    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.

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

    PubMed

    Mahalakshmi, G; Balachandran, V

    2014-10-15

    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 200-400nm 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.

  12. Energetics and structure in solvent: A dielectric continuum model of solvation combined with molecular mechanics, Ab Initio, and Semi-empirical molecular orbital treatments of the solute

    SciTech Connect

    Tawa, G.J.; Pratt, L.R.; Martin, R.L.

    1996-12-31

    We present a method for computing the electrostatic component of the solvation free energy, {Delta}G{sup el}, of a solute molecule in the presence of solvent modeled as a dielectric continuum. The method is based on an integral form of Poisson`s equation which is solved to obtain a distribution of induced polarization charge at the solute-solvent dielectric interface. The solution of Poisson`s equation is obtained by application of a boundary element procedure. The method is tested by comparing its predictions of {Delta}G{sup el} to exact values for several model problems. The method is then used in a variety of contexts to assess its qualitative prediction ability. It is first combined with a molecular mechanics treatment of the solute to evaluate the effects of aqueous solvent on the conformational equilibria of several small molecules of interest-these are N-methyl acetamide and alanine dipeptide. For both molecules dielectric continuum solvation predicts torsional free energies of solvation that are in accord with other more complete treatments of solvation. The method is then combined with ab initio and semi-empirical molecular orbital theory for the solute. Self consistent reaction field calculations (SCRF) are performed to evaluate the correlation is in general very good. Relative agreement with experiment is best for ions where electrostatics predominate and worst for non-polar neutral molecules were electrostatics are minor. Semi-empirical configuration interaction SCRF calculations are also performed in the presence of solvent in order to determine ground-to-excited state absorption energy shifts for formaldehyde and indole mine ground-to-excited state absorption energy shifts for formaldehyde and indole when placed in water. We find a rough correlation between transition energy shifts and the dipole moments of the initial and final states involved in the transition.

  13. 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.

  14. 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

    2015-07-07

    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 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.

  15. 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.

  16. Determination of the optimal cell-penetrating peptide sequence for intestinal insulin delivery based on molecular orbital analysis with self-organizing maps.

    PubMed

    Kamei, Noriyasu; Kikuchi, Shingo; Takeda-Morishita, Mariko; Terasawa, Yoshiaki; Yasuda, Akihito; Yamamoto, Shuichi; Ida, Nobuo; Nishio, Reiji; Takayama, Kozo

    2013-02-01

    Our recent work has shown that the intestinal absorption of insulin can be improved significantly by coadministration of cell-penetrating peptides (CPPs), especially penetratin. However, a relatively high dose of penetratin is required to adequately stimulate the intestinal absorption of insulin. Therefore, in this study, we sought to determine the CPP that most effectively enhanced intestinal insulin absorption. An in situ loop absorption study using 26 penetratin analogues suggested that the chain length, hydrophobicity, and amphipathicity of the CPPs, as well as their basicity, contribute to their absorption-enhancing efficiency. Moreover, a molecular orbital method with self-organizing maps (SOMs) classification suggested that multiple factors, including the molecular weight, basicity, the lowest unoccupied molecular orbital energy, absolute hardness, and chemical potential of CPPs, are associated with their effects on intestinal insulin absorption. Furthermore, the new CPPs proposed by SOM clustering had a marked capacity to interact with insulin, and their ability to enhance insulin absorption was much stronger than that of the original penetratin. Therefore, the peptide sequence that optimally enhances intestinal insulin absorption could be defined by SOM with the molecular orbital method, and our present work emphasizes the utility of such methodologies in the development of effective drug delivery systems.

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

    PubMed

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

    2015-02-25

    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 C-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.

  18. Proof by EPR spectroscopy that the unpaired electron in an Os(2)(7+) species is in a delta* metal-based molecular orbital.

    PubMed

    Cotton, F Albert; Chiarella, Gina M; Dalal, Naresh S; Murillo, Carlos A; Wang, Zhenxing; Young, Mark D

    2010-01-04

    Variable temperature structural and EPR studies are reported on the paddlewheel compound [Os(2)(hpp)(4)Cl(2)]PF(6), 1, (hpp = the anion of the bicyclic guanidine 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) that contains a rare M(2)(7+) species, with the goal of determining whether the unpaired electron resides in a metal- or ligand-based molecular orbital. Crystallographic studies show that the Os-Os distance in 1 remains essentially unchanged from 213 to 30 K, which is consistent with no changes in electronic structure in this range of temperature. It is noteworthy that the metal-metal distance in 1 is about 0.05 A shorter than that in the precursor Os(2)(hpp)(4)Cl(2), which is consistent with the loss of an electron in a delta* orbital. EPR spectra of 1 were measured in dilute frozen solution, powder, and single crystals. The spectra were observable only below about 50 K, with an exceptionally large line width, approximately 3,750 gauss, for a powdered sample, due to dipolar interactions and to short relaxation times. There is a very small average g value of approximately 0.750 and a cylindrical symmetry about the Os-Os bond. These data are consistent with the unpaired electron orbital having a large L value, such as that of a delta* orbital. The combination of X-ray structural data, the short relaxation time, and the magnetic data provide strong evidence that the unpaired electron in this nine-electron Os(2)(7+) species is localized in a metal-based orbital with this electron residing predominantly in a delta* orbital rather than in a pi* orbital and, thus, having an electronic configuration of sigma(2)pi(4)delta(2)delta*.

  19. 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.

  20. Molecular Orbitals and Superconductivity.

    DTIC Science & Technology

    1979-12-31

    Slater and K. H. Johnson, Physics Today 27, 34 (1974). -34- 17. J. C. Slater, in Advances in Quantum Chemistry , Vol. 6, edited by P.-O. Ldwdln...18. K. H. Johnson, J. Chem. Phys. 45, 3085 (1966); in Advances in Quantum Chemistry , Vol. 7, edited by P.-O. LOwdin (Academic, New York, 1973), p

  1. 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

  2. Diabatic Molecular Orbitals, Potential Energies, and Potential Energy Surface Couplings by the 4-fold Way for Photodissociation of Phenol.

    PubMed

    Xu, Xuefei; Yang, Ke R; Truhlar, Donald G

    2013-08-13

    Complete-active-space self-consistent-field (CASSCF) calculations provide useful reference wave functions for configuration interaction or perturbation theory calculations of excited-state potential energy surfaces including dynamical electron correlation. However, the canonical molecular orbitals (MOs) of CASSCF calculations usually have mixed character in regions of strong interaction of two or more electronic states; therefore, they are unsuitable for diabatization using the configurational uniformity approach. Here, CASSCF diabatic MOs for phenol have been obtained by the 4-fold way, and comparison to the CASSCF canonical MOs shows that they are much smoother. Using these smooth CASSCF diabatic MOs, we performed direct diabatization calculations for the three low-lying states ((1)ππ, (1)ππ*, and (1)πσ*) and their diabatic (scalar) couplings at the dynamically correlated multiconfiguration quasidegenerate perturbation theory (MC-QDPT) level. We present calculations along the O-H stretching and C-C-O-H torsion coordinates for the nonadiabatic photodissociation of phenol to the phenoxyl radical and hydrogen atom. The seams of (1)ππ*/(1)πσ* and (1)ππ/(1)πσ* diabatic crossings are plotted as functions of these coordinates. We also present diabatization calculations for displacements along the out-of-plane ring distortion modes 16a and 16b of the phenyl group. The dominant coupling modes of the two conical intersections ((1)ππ*/(1)πσ* and (1)ππ/(1)πσ*) are discussed. The present diabatization method is confirmed to be valid even for significantly distorted ring structures by diabatization calculations along a reaction path connecting the planar equilibrium geometry of phenol to its strongly distorted prefulvenic form. The present work provides insight into the mode specificity of phenol photodissociation and shows that diabatization at the MC-QDPT level employing CASSCF diabatic MOs can be a good starting point for multidimensional dynamics

  3. Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Re, Suyong; Sugita, Yuji; Ten-no, Seiichiro

    2013-01-01

    The nudged elastic band (NEB) and string methods are widely used to obtain the reaction path of chemical reactions and phase transitions. In these methods, however, it is difficult to define an accurate Lagrangian to generate the conservative forces. On the other hand, the constrained optimization with locally updated planes (CO-LUP) scheme defines target function properly and suitable for micro-iteration optimizations in quantum mechanical/molecular mechanical (QM/MM) systems, which uses the efficient second order QM optimization. However, the method does have problems of inaccurate estimation of reactions and inappropriate accumulation of images around the energy minimum. We introduce three modifications into the CO-LUP scheme to overcome these problems: (1) An improved tangent estimation of the reaction path, which is used in the NEB method, (2) redistribution of images using an energy-weighted interpolation before updating local tangents, and (3) reduction of the number of constraints, in particular translation/rotation constraints, for improved convergence. First, we test the method on the isomerization of alanine dipeptide without QM/MM calculation, showing that the method is comparable to the string method both in accuracy and efficiency. Next, we apply the method for defining the reaction paths of the rearrangement reaction catalyzed by chorismate mutase (CM) and of the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA) using generalized hybrid orbital QM/MM calculations. The reaction energy barrier of CM is in high agreement with the experimental value. The path of PKA reveals that the enzyme reaction is associative and there is a late transfer of the substrate proton to Asp 166, which is in agreement with the recently published result using the NEB method.

  4. 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.

  5. 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.

  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. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    PubMed

    Ferenczy, György G

    2013-04-05

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.

  9. 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

    2013-04-05

    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.

  10. 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.

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

    PubMed

    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 C(2)H(3) 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 C(2)H(3) 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.

  12. Specific interactions between amyloid-β peptides in an amyloid-β hexamer with three-fold symmetry: Ab initio fragment molecular orbital calculations in water

    NASA Astrophysics Data System (ADS)

    Ishimura, Hiromi; Tomioka, Shogo; Kadoya, Ryushi; Shimamura, Kanako; Okamoto, Akisumi; Shulga, Sergiy; Kurita, Noriyuki

    2017-03-01

    The accumulation of amyloid-beta (Aβ) aggregates in brain contributes to the onset of Alzheimer's disease (AD). Recent structural analysis for the tissue obtained from AD patients revealed that Aβ aggregates have a single structure with three-fold symmetry. To explain why this structure possesses significant stability, we here investigated the specific interactions between Aβ peptides in the aggregate, using ab initio fragment molecular orbital calculations. The results indicate that the interactions between the Aβ peptides of the stacked Aβ pair are stronger than those between the Aβ peptides of the trimer with three-fold symmetry and that the charged amino-acids are important.

  13. 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.

  14. A Star-Shaped Molecule with Low-Lying Lowest Unoccupied Molecular Orbital Level, n-Type Panchromatic Electrochromism, and Long-Term Stability.

    PubMed

    Yao, Bin; Zhou, Yue; Ye, Xichong; Wang, Rong; Zhang, Jie; Wan, Xinhua

    2017-04-03

    An electron-deficient star-shaped molecule based on anthraquinone imide was synthesized and characterized. It showed high electron accommodating capacity and strong electron-withdrawing ability with a low-lying lowest unoccupied molecular orbital (LUMO) of -4.10 eV. In addition, it exhibited panchromatic electrochromism attributed to the simultaneous presence of π*-π* transitions and intervalence charge transfer (IV-CT) upon one-electron reduction, and revealed long-term stability in electron gain and loss due to the proper LUMO energy level and ordered intermolecular assembly.

  15. Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems

    SciTech Connect

    Nakata, Hiroya; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Sakurai, Minoru; Nakamura, Shinichiro

    2014-04-14

    We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.

  16. Sclerosing Orbital Inflammation Caused by Leishmania braziliensis.

    PubMed

    Cruz, Antonio Augusto V; Alves-Ferreira, Eliza V C; Milbratz-Moré, Gherusa; Chahud, Fernando; Ruy, Patricia C; Duarte, Maria Irma Seixas; Cruz, Angela Kaysel

    2017-01-11

    Orbital biopsy of nonspecific orbital inflammation, commonly referred to as "orbital pseudotumor," typically shows a combination of polyclonal lymphocytes, plasmocytes, leukocytes, macrophages, and variable degrees of collagen deposition. Herein, we report a patient with a positive history of mucocutaneous leishmaniasis who presented with an orbital mass with a histological profile of idiopathic orbital inflammation. Immunohistochemical and molecular analysis of the orbital specimens demonstrated that the orbital inflammation was associated with the presence of antigens of Leishmania braziliensis and DNA from the parasite.

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

    PubMed Central

    Pogni, Rebecca; Basosi, Riccardo; Donati, Alessandro; Rossi, Claudio; Sabadini, Luciano; Rollo, Libertario; Lorenzini, Sauro; Gelli, Renata; Marcolongo, Roberto

    1995-01-01

    The oxygen radical scavenger activity (ORSA) of [CuII(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 [CuII(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 (1.02·10−4M) and [CuII(Pir)2(DMF)2] (1.08·10−5M)/HPir (8.01·10−−5M) systems was higher than 12 (not stimulated) [excess of piroxicam was added (Cu/Pir molar ratio ≈1:10) in order to have most of the metal complexed as bischelate]. In contrast, the ratio of residual radicals for the CuCl2 (1.00·10−5M) and [CuII(Pir)2(DMF)2] (1.08·10−5M)/Hpir (8.01·10−5M)system was 5. The [CuII(Pir)2] compound is therefore a stronger radical scavenger than either HPir or CuCl2. A molecular mechanics (MM) analysis of the gas phase structures of neutral HPir, its zwitterionic (HPir+-) and anionic (Pir-) forms, and some CuII-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 CuII (and CdII 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 [CuII(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 [CuII(Pir)2(DMF)2] in acetone a brown microcystalline solid with the Cu(Pir)2·0.5DMF stoichiometry was in fact prepared. 13C spin-lattice relaxation

  18. Resonance Overlap Is Responsible for Ejecting Planets in Binary Systems

    NASA Astrophysics Data System (ADS)

    Mudryk, Lawrence R.; Wu, Yanqin

    2006-03-01

    A planet orbiting around a star in a binary system experiences both secular and resonant perturbations from the companion star. It may be dislodged from its host star if it is simultaneously affected by two or more resonances. We find that overlap between subresonances lying within mean-motion resonances (mostly of the j:1 type) can account for the boundary of orbital stability within binary systems first observed in numerical studies (e.g., Holman & Wiegert). Strong secular forcing from the companion displaces the centroids of different subresonances, producing large regions of resonance overlap. Planets lying within these overlapping regions experience chaotic diffusion, which in most cases leads to their eventual ejection. The overlap region extends to shorter period orbits as either the companion's mass or its eccentricity increase, with boundaries largely agreeing with those obtained by Holman & Wiegert. Furthermore, we find the following two results: First, at a given binary mass ratio, the instability boundary as a function of eccentricity appears jagged, with jutting peninsulas and deep inlets corresponding to islands of instability and stability, respectively; as a result, the largest stable orbit could be reduced from the Holman & Wiegert values by as much as 20%. Second, very high-order resonances (e.g., 50:3) do not significantly modify the instability boundary; these weak resonances, while producing slow chaotic diffusion that may be missed by finite-duration numerical integrations, do not contribute markedly to planet instability. We present some numerical evidence for the first result. More extensive experiments are called for to confirm these conclusions. For the special case of circular binaries, we are intrigued to find that the Hill criterion (based on the critical Jacobi integral) yields an instability boundary that is very similar to that obtained by resonance overlap arguments, making the former both a necessary and a sufficient condition for

  19. Successive hydrogen-elimination reactions with low activation energies in the a-Si:H formation process: An ab initio molecular-orbital study

    NASA Astrophysics Data System (ADS)

    Sato, Kota; Sugiyama, Yoko; Uchiyama, Akihiko; Iwabuchi, Susumu; Hirano, Tsuneo; Koinuma, Hideomi

    1992-07-01

    Successive hydrogen elimination reactions with low activation energies during the formation of a-Si:H by silane plasma chemical vapor deposition are proposed on the basis of an ab initio molecular-orbital method. The activation energy of the first step, the reaction of a dangling-bond site with an adjacent tetrahedrally coordinated silicon atom, was found to be 25.2 kcal/mol at 0 K when the zero-point vibrational energy was taken into account. The subsequent step was an exothermic process with a lower activation energy. The total process was thermodynamically much more favorable than the molecular processes by which a hydrogen atom or molecule is eliminated.

  20. Orbital cellulitis

    MedlinePlus

    ... hemolytic streptococci may also cause orbital cellulitis. Orbital cellulitis infections in children may get worse very quickly and ... in the space around the eye. An orbital cellulitis infection can get worse very quickly. A person with ...

  1. A Guide to Using STITCHER for Overlapping Assembly PCR Applications.

    PubMed

    O'Halloran, Damien M

    2017-01-01

    Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online.

  2. 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.

  3. Role of molecular orbital symmetry on the alignment dependence of high-order harmonic generation with molecules

    SciTech Connect

    Zhou Xiaoxin; Tong, X.M.; Zhao, Z.X.; Lin, C.D.

    2005-06-15

    It is shown that the alignment dependence of the yields of high-order harmonic generation (HHG) from molecules by intense lasers is governed by the orbital symmetry of the outermost electron(s). For N{sub 2}, with its outermost {sigma}{sub g} electron, the HHG yield is maximal when the molecules are aligned with the laser polarization direction, in agreement with the recent experiment of Itatani et al. [Nature 432, 867 (2004)]. For O{sub 2}, with its outermost {pi}{sub g} electron, the HHG yield peaks when the molecules are aligned at about 45 deg. from the polarization axis. We emphasize that the alignment dependence is determined mostly by the orbital symmetry and weakly on the laser parameters or the species.

  4. 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.

  5. Charge-transfer mechanism for electrophilic aromatic nitration and nitrosation via the convergence of (ab initio) molecular-orbital and Marcus-Hush theories with experiments.

    PubMed

    Gwaltney, Steven R; Rosokha, Sergiy V; Head-Gordon, Martin; Kochi, Jay K

    2003-03-19

    The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.

  6. Nickel(II) in chelate N2O2 environment. DFT approach and in-depth molecular orbital and configurational analysis.

    PubMed

    Trifunović, Srećko R; Miletić, Vesna D; Jevtić, Verica V; Meetsma, Auke; Matović, Zoran D

    2013-10-07

    The O-N-N-O-type tetradentate ligands H2S,S-eddp (H2S,S-eddp stands for S,S-ethylenediamine-N,N'-di-2-propionic acid) and H2edap (H2edap stands for ethylenediamine-N-acetic-N'-3-propionic acid) and the corresponding novel octahedral nickel(II) complexes have been prepared and characterized. N2O2 ligands coordinate to the nickel(II) ion via four donor atoms (two deprotonated carboxylate atoms and two amine nitrogens) affording octahedral geometry in the case of all investigated Ni(II) complexes. A six coordinate, octahedral geometry has been verified crystallographically for the s-cis-[Ni(S,S-eddp)(H2O)2] complex. Structural data correlating similarly chelated Ni(II) complexes have been used to carry out an extensive configuration analysis. Molecular mechanics and Density Functional Theory (DFT) have been used to model the most stable geometric isomer, yielding, at the same time, significant structural and spectroscopic (TDDFT) data. The results from density functional studies have been compared to X-ray data. Natural Bond Orbital (NBO) and Natural Energetic Decomposition Analysis (NEDA) have been done for the [Ni(edda-type)(H2O)(2-n)] and nH2O fragments. Molecular orbital analysis (MPA) is given as well. The infra-red and electronic absorption spectra of the complexes are discussed in comparison to the related complexes of known geometries.

  7. FIRST-ORDER RESONANCE OVERLAP AND THE STABILITY OF CLOSE TWO-PLANET SYSTEMS

    SciTech Connect

    Deck, Katherine M.; Payne, Matthew; Holman, Matthew J.

    2013-09-10

    Motivated by the population of observed multi-planet systems with orbital period ratios 1 < P{sub 2}/P{sub 1} {approx}< 2, we study the long-term stability of packed two-planet systems. The Hamiltonian for two massive planets on nearly circular and nearly coplanar orbits near a first-order mean motion resonance can be reduced to a one-degree-of-freedom problem. Using this analytically tractable Hamiltonian, we apply the resonance overlap criterion to predict the onset of large-scale chaotic motion in close two-planet systems. The reduced Hamiltonian has only a weak dependence on the planetary mass ratio m{sub 1}/m{sub 2}, and hence the overlap criterion is independent of the planetary mass ratio at lowest order. Numerical integrations confirm that the planetary mass ratio has little effect on the structure of the chaotic phase space for close orbits in the low-eccentricity (e {approx}< 0.1) regime. We show numerically that orbits in the chaotic web produced primarily by first-order resonance overlap eventually experience large-scale erratic variation in semimajor axes and are therefore Lagrange unstable. This is also true of the orbits in this overlap region which satisfy the Hill criterion. As a result, we can use the first-order resonance overlap criterion as an effective stability criterion for pairs of observed planets. We show that for low-mass ({approx}< 10 M{sub Circled-Plus }) planetary systems with initially circular orbits the period ratio at which complete overlap occurs and widespread chaos results lies in a region of parameter space which is Hill stable. Our work indicates that a resonance overlap criterion which would apply for initially eccentric orbits likely needs to take into account second-order resonances. Finally, we address the connection found in previous work between the Hill stability criterion and numerically determined Lagrange instability boundaries in the context of resonance overlap.

  8. 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

  9. Kinetic temperatures toward X1/X2 orbit interceptions regions and giant molecular loops in the Galactic center region

    NASA Astrophysics Data System (ADS)

    Riquelme, D.; Amo-Baladrón, M. A.; Martín-Pintado, J.; Mauersberger, R.; Martín, S.; Bronfman, L.

    2013-01-01

    Context. It is well known that the kinetic temperatures, Tkin, of the molecular clouds in the Galactic center region are higher than in typical disk clouds. However, the Tkin of the molecular complexes found at higher latitudes towards the giant molecular loops in the central region of the Galaxy is so far unknown. The gas of these high-latitude molecular clouds (hereafter referred to as "halo clouds") is located in a region where the gas in the disk may interact with the gas in the halo in the Galactic center region. Aims: To derive Tkin in the molecular clouds at high latitude and understand the physical process responsible for the heating of the molecular gas both in the central molecular zone (the concentration of molecular gas in the inner ~500 pc) and in the giant molecular loops. Methods: We measured the metastable inversion transitions of NH3 from (J,K) = (1,1) to (6,6) toward six positions selected throughout the Galactic central disk and halo. We used rotational diagrams and large velocity gradient (LVG) modeling to estimate the kinetic temperatures toward all the sources. We also observed other molecules like SiO, HNCO, CS, C34S, C18O, and 13CO, to derive the densities and to trace different physical processes (shocks, photodissociation, dense gas) expected to dominate the heating of the molecular gas. Results: We derive for the first time Tkin of the high-latitude clouds interacting with the disk in the Galactic center region. We find high rotational temperatures in all the observed positions. We derive two kinetic temperature components (~150 K and ~40 K) for the positions in the central molecular zone, and only the warm kinetic temperature component for the clouds toward the giant molecular loops. The fractional abundances derived from the different molecules suggest that shocks provide the main heating mechanism throughout the Galactic center, also at high latitudes. Appendices A and B are available in electronic form at http://www.aanda.org

  10. 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.

  11. 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.

  12. Evaluation of the ultraviolet/ozone technique for on-orbit removal of photolyzed molecular contamination from optical surfaces

    NASA Astrophysics Data System (ADS)

    Frink, Mark E.; Folkman, Mark A.; Darnton, Lane A.

    1992-12-01

    Molecular species outgassed from spacecraft materials adhere tenaciously to and darken spacecraft surfaces when exposed to solar ultraviolet (UV) radiation. Such deposits severely degrade the performance of optical systems operating at UV and visible wavelengths. Data is presented which demonstrates the feasibility of a UV/Ozone cleaning technique in removing such deposits in a space-compatible configuration without damage to the optical surface. The technique involves the UV irradiation of the optical surface in the presence of low pressure molecular oxygen, resulting in the photolytic formation of ozone (O3) and subsequent photochemical removal of the contamination.

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

    PubMed

    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(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.

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

    NASA Astrophysics Data System (ADS)

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-01

    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 Cs-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.

  16. Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods.

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2015-03-05

    The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100cm(-1) respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  17. Gradient of molecular Hartree-Fock-Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions

    NASA Astrophysics Data System (ADS)

    Kobayashi, Masato

    2014-02-01

    The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.

  18. Gradient of molecular Hartree-Fock-Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions.

    PubMed

    Kobayashi, Masato

    2014-02-28

    The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.

  19. Gradient of molecular Hartree–Fock–Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions

    SciTech Connect

    Kobayashi, Masato

    2014-02-28

    The analytical gradient for the atomic-orbital-based Hartree–Fock–Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree–Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.

  20. 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.

  1. Study of Electron Delocalization in 1,2-, 1,3-, and 1,4-Azaborines Based on the Canonical Molecular Orbital Contributions to the Induced Magnetic Field and Polyelectron Population Analysis.

    PubMed

    Papadopoulos, Anastasios G; Charistos, Nickolas D; Kyriakidou, Katerina; Sigalas, Michael P

    2015-10-01

    The electron delocalization in 1,2-azaborine, 1,3-azaborine, and 1,4-azaborine is studied using canonical molecular orbital contributions to the induced magnetic field (CMO-IMF) method and polyelectron population analysis (PEPA). Contour maps of the out-of-plane component of the induced magnetic field (Bz(ind)) of the π system show that the three azaborines, in contrast with borazine, sustain much of benzene's π-aromatic character. Among them, 1,3-azaborine exhibits the strongest π delocalization, while 1,4-azaborine is the weakest. Contour maps of Bz(ind) for individual π orbitals reveal that the differentiation of the magnetic response among the three isomers originates from the π-HOMO orbitals, whose magnetic response is governed by rotational allowed transitions to unoccupied orbitals. The low symmetry of azaborines enables a paratropic response from HOMO to unoccupied orbitals excitations, with their magnitude depending on the shape of interacting orbitals. 1,3-Azaborine presents negligible paratropic contributions to Bz(ind) from HOMO to unoccupied orbitals transitions, where 1,2- and 1,4-azaborine present substantial paratropic contributions, which lead to reduced diatropic response. Natural bond orbital (NBO) analysis employing PEPA shows that only the 1,3-azaborine contains π-electron fully delocalized resonance structures.

  2. Influence of electron correlation and degeneracy on the Fukui matrix and extension of frontier molecular orbital theory to correlated quantum chemical methods.

    PubMed

    Bultinck, Patrick; Van Neck, Dimitri; Acke, Guillaume; Ayers, Paul W

    2012-02-21

    The Fukui function is considered as the diagonal element of the Fukui matrix in position space, where the Fukui matrix is the derivative of the one particle density matrix (1DM) with respect to the number of electrons. Diagonalization of the Fukui matrix, expressed in an orthogonal orbital basis, explains why regions in space with negative Fukui functions exist. Using a test set of molecules, electron correlation is found to have a remarkable effect on the eigenvalues of the Fukui matrix. The Fukui matrices at the independent electron model level are mathematically proven to always have an eigenvalue equal to exactly unity while the rest of the eigenvalues possibly differ from zero but sum to zero. The loss of idempotency of the 1DM at correlated levels of theory causes the loss of these properties. The influence of electron correlation is examined in detail and the frontier molecular orbital concept is extended to correlated levels of theory by defining it as the eigenvector of the Fukui matrix with the largest eigenvalue. The effect of degeneracy on the Fukui matrix is examined in detail, revealing that this is another way by which the unity eigenvalue and perfect pairing of eigenvalues can disappear.

  3. 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.

  4. Examination of the hydrogen-bonding networks in small water clusters (n = 2-5, 13, 17) using absolutely localized molecular orbital energy decomposition analysis.

    PubMed

    Cobar, Erika A; Horn, Paul R; Bergman, Robert G; Head-Gordon, Martin

    2012-11-28

    Using the ωB97X-D and B3LYP density functionals, the absolutely localized molecular orbital energy decomposition method (ALMO-EDA) is applied to the water dimer through pentamer, 13-mer and 17-mer clusters. Two-body, three-body, and total interaction energies are decomposed into their component energy terms: frozen density interaction energy, polarization energy, and charge transfer energy. Charge transfer, polarization, and frozen orbital interaction energies are all found to be significant contributors to the two-body and total interaction energies; the three-body interaction energies are dominated by polarization. Each component energy term for the two-body interactions is highly dependent on the associated hydrogen bond distance. The favorability of the three-body terms associated with the 13- and 17-mer structures depends on the hydrogen-donor or hydrogen-acceptor roles played by each of the three component waters. Only small errors arise from neglect of three-body interactions without two adjacent water molecules, or beyond three-body interactions. Interesting linear correlations are identified between the contributions of charge-transfer and polarization terms to the two and three-body interactions, which permits elimination of explicit calculation of charge transfer to a good approximation.

  5. 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

    2015-01-05

    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).

  6. 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.

  7. Analysis of solute-solvent interactions in the fragment molecular orbital method interfaced with effective fragment potentials: theory and application to a solvated griffithsin-carbohydrate complex.

    PubMed

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

    2012-09-13

    Based on the proposed new expression of the polarization energy for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFPs), we develop an analysis of the solute(FMO)-solvent(EFP) interactions by defining individual fragment contributions for both solute and solvent. The obtained components are compared to all-electron calculations where water is treated as FMO fragments in the pair interaction energy decomposition analysis. The new energy expression is shown to be accurate, and the developed energy analysis is applied to the solvated griffithsin-carbohydrate complex. The details of the ligand recognition are revealed in the context with their interplay with the solvent effects. Tyr residue fragments are shown to reduce the desolvation penalty for Asp, which strongly binds the ligand.

  8. 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

  9. 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.

  10. Orbital-free ab initio molecular dynamics study of the free liquid surface of Sn. From pseudopotential generation to structural and dynamic properties

    NASA Astrophysics Data System (ADS)

    Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique

    We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface of Sn at 1000 K. A key ingredient in the OF-AIMD method is the local ionic pseudopotential describing the ions-valence electrons interaction. We have developed a force-matching method to derive a local ionic pseudopotential suitable to account for a rapidly varying density system, such as in a free liquid surface. We obtain very good results for several structural properties. We have also studied the evolution of some dynamical properties when going from the central region (where the system behaves like the bulk liquid) towards the free liquid surface. We aknowledge the spanish MSI (Project FIS2012-33126) and the University of Valladolid for the provision of a PhD grant.

  11. 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. 

  12. A new approach to molecular dynamics with non-adiabatic and spin-orbit effects with applications to QM/MM simulations of thiophene and selenophene

    NASA Astrophysics Data System (ADS)

    Pederzoli, Marek; Pittner, Jiří

    2017-03-01

    We present surface hopping dynamics on potential energy surfaces resulting from the spin-orbit splitting, i.e., surfaces corresponding to the eigenstates of the total electronic Hamiltonian including the spin-orbit coupling. In this approach, difficulties arise because of random phases of degenerate eigenvectors and possibility of crossings of the resulting mixed states. Our implementation solves these problems and allows propagation of the coefficients both in the representation of the spin free Hamiltonian and directly in the "diagonal representation" of the mixed states. We also provide a detailed discussion of the state crossing and point out several peculiarities that were not mentioned in the previous literature. We also incorporate the effect of the environment via the quantum mechanics/molecular mechanics approach. As a test case, we apply our methodology to deactivation of thiophene and selenophene in the gas phase, ethanol solution, and bulk liquid phase. First, 100 trajectories without spin-orbit coupling have been calculated for thiophene starting both in S1 and S2 states. A subset of 32 initial conditions starting in the S2 state was then used for gas phase simulations with spin-orbit coupling utilizing the 3-step integrator of SHARC, our implementation of the 3-step propagator in Newton-X and two new "one-step" approaches. Subsequently, we carried out simulations in ethanol solution and bulk liquid phase for both thiophene and selenophene. For both molecules, the deactivation of the S2 state proceeds via the ring opening pathway. The total population of triplet states reaches around 15% and 40% after 80 fs for thiophene and selenophene, respectively. However, it only begins growing after the ring opening is initiated; hence, the triplet states do not directly contribute to the deactivation mechanism. For thiophene, the resulting deactivation lifetime of the S2 state was 68 fs in the gas phase, 76 fs in ethanol solution, and 78 fs in the liquid phase

  13. 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.

  14. 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 ...

  15. 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.

  16. 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

    2016-03-28

    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.

  17. The Orbital Acceleration Research Experiment

    NASA Technical Reports Server (NTRS)

    Blanchard, R. C.; Hendrix, M. K.; Fox, J. C.; Thomas, D. J.; Nicholson, J.

    1986-01-01

    The hardware and software of NASA's proposed Orbital Acceleration Research Experiment (OARE) are described. The OARE is to provide aerodynamic acceleration measurements along the Orbiter's principal axis in the free-molecular flow-flight regime at orbital attitude and in the transition regime during reentry. Models considering the effects of electromagnetic effects, solar radiation pressure, orbiter mass attraction, gravity gradient, orbital centripetal acceleration, out-of-orbital-plane effects, orbiter angular velocity, structural noise, mass expulsion signal sources, crew motion, and bias on acceleration are examined. The experiment contains an electrostatically balanced cylindrical proofmass accelerometer sensor with three orthogonal sensing axis outputs. The components and functions of the experimental calibration system and signal processor and control subsystem are analyzed. The development of the OARE software is discussed. The experimental equipment will be enclosed in a cover assembly that will be mounted in the Orbiter close to the center of gravity.

  18. 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.

  19. Conformational stability, molecular orbital studies (chemical hardness and potential), vibrational investigation and theoretical NBO analysis of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene.

    PubMed

    Saravanan, S; Balachandran, V; Vishwanathan, K

    2014-04-24

    The FT-IR and FT-Raman spectra of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene (musk ambrette) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The total energy calculations of musk ambrette were tried for the possible conformers. The molecular structure, geometry optimization, vibrational frequencies were obtained by the density functional theory (DFT) using B3LYP and LSDA method with 6-311G(d,p) basis set for the most stable conformer "C1". The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated and the scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugate interactions and the charge delocalization has been analyzed using bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The dipole moment (μ), polarizability (α), anisotropy polarizability (Δα) and first hyperpolarizability (βtot) of the molecule have been reported. The thermodynamic functions (heat capacity, entropy and enthalpy) were obtained for the range of temperature 100-1000 K. 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 molecular electrostatic potential (MEP).

  20. 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.

  1. 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

    2015-05-08

    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.

  2. The use of methods involving semi-empirical molecular orbital theory to study the structure and reactivity of transition metal complexes.

    PubMed

    Mohr, Matthias; McNamara, Jonathan P; Wang, Hong; Rajeev, Surendran A; Ge, Jun; Morgado, Claudio A; Hillier, Ian H

    2003-01-01

    The electronic structure of molecular systems containing transition metal atoms is traditionally studied using methods based on density functional theory (DFT). Although such an approach has been quite successful, the treatment of large systems, be they transition metal complexes, bioinorganic molecules or the solid state, is still extremely computationally demanding at this level, and may not be practical for many systems of interest. In this paper we describe how semi-empirical MO methods can be used to overcome these computational bottlenecks, yet still provide predictions of the necessary accuracy. We describe strategies to achieve this by focussing on: (i) obtaining appropriate parameters for transition metal atoms via a genetic algorithm, to be used within a parallelised implementation of neglect of differential diatomic overlap (NDDO) methods, and (ii) the use of multilevel treatments which involve DFT and semi-empirical methods to describe different regions of the molecule. Here we show by reference to histidine and porphyrin complexes, the importance of a correct partitioning of the organic substrate. We illustrate the potential of such a dual level approach by reporting preliminary results showing the catalytic role of the enzyme, dimethyl sulfoxide reductase.

  3. Understanding field variation, quantum chemical modeling and molecular orbital analyses of trans-3-(trans-4-imidazolyl) acrylic acid

    NASA Astrophysics Data System (ADS)

    Gayathri, R.; Arivazhagan, M.

    2017-02-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab-initio) study on the structure and the vibrations of Trans-3-(trans-4-imidazolyl) acrylic acid (TTIAA) are compared and analyzed. The assignment of each normal mode has been made using the observed and calculated frequencies. The optimized geometries, harmonic vibrational wavenumbers and intensities of vibrational bands of trans-3-(trans-4-imidazolyl) acrylic acid (TTIAA) have been carried out using the HF/B3LYP method using the standard 6311++G(d,p) basis set calculations in this investigation. The result describes the variation in electrostatic and transport properties for zero and various external applied field. The variation in MPA charges are small due to the application of EFs: however, in most cases it is found to be systematic and almost uniform. When the field increases from 0.00 to 0.02 VÅ-1, the hybridization of molecular levels broadens the DOS and decreases the HLG from 3.6609 to 1.2325 eV; the decrease of band gap at the high field indicates that this molecule exhibit considerable electrical conductivity. Fukui indices to determine the local reactive site for the molecular systems during electrophilic, nucleophilic, radical and dual descriptor attacks. The results clearly show the superiority of MPA scheme. This study may be useful to design new molecules with more electrical conductivity.

  4. 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.

  5. The molecular structure and conformational characteristics of some specific benzodiazepine receptor ligands: A molecular orbital study of C3-substituted betacarboline derivatives

    SciTech Connect

    Konschin, H.; Tylli, H. ); Gynther, J. ); Rouvinen, J. )

    1989-01-01

    The molecular structures of the benzodiazepine receptor ligands {beta}-carboline-3-carboxylic acid (BCCA), its methyl, ethyl, and propyl esters (BCCM, BCCE, and BCCP, respectively), and 3-CN-{beta}-carboline (BC-3-CN) have been investigated on a minimal basis STO-3G level of accuracy. For BCCM, BCCE, and BCCP semiempirical AM 1 calculations have also been performed. Fully optimized molecular geometries are reported. Comparisons with available experimental structures indicate that minimal basis results may have a useful predictive value. For the mobile ester side chains, a study of chosen points on the conformational surface was made. Both the STO-3G and the AM 1 results give the planar conformers is the most stable structures with small barriers to internal rotation, provided the ester side chain remains extended. The calculated STO-3G rotational barriers are higher than are the corresponding AM 1 barriers. Partial optimization, i.e., of side-chain structure parameters only, seems sufficient to map the conformational characteristics of these compounds. The orientation of the dipole moment vector and its magnitude may have consequences for possible interaction with a receptor. On the basis of the sidechain internal dynamics, the intramolecular flexibility tends to be confined to certain regions of conformational space.

  6. Specific interactions between vitamin-D receptor and its ligands: Ab initio molecular orbital calculations in water.

    PubMed

    Takeda, Ryosuke; Kobayashi, Ittetsu; Shimamura, Kanako; Ishimura, Hiromi; Kadoya, Ryushi; Kawai, Kentaro; Kittaka, Atsushi; Takimoto-Kamimura, Midori; Kurita, Noriyuki

    2017-02-27

    Vitamin D is recognized to play important roles not only in the bone metabolism and the regulation of Ca amount in the blood but also in the onset of immunological diseases. These physiological actions caused by vitamin D are triggered by the specific interaction between vitamin D receptor (VDR) and vitamin D. In the present study, we investigated the interactions between VDR and vitamin D derivatives using ab initio molecular simulation, in order to elucidate the reason for the significant difference in their effects on VDR activity. Based on the results simulated, we elucidated which parts of the derivatives and which residues of VDR mainly contribute to the specific binding between VDR and the derivatives at an electronic level. This finding will be helpful for proposing new vitamin D derivatives as a potent modulator or inhibitor against VDR.

  7. 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

  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

    2015-03-05

    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.

  9. 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.

  10. 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.

  11. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

    PubMed

    Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A

    2008-12-07

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  12. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

    PubMed Central

    Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

    2008-01-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner , J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT’s inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G*, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal∕mol [obtained with B3LYP∕6-311++G(3df,3pd)] to 0.8 kcal∕mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies. PMID:19063542

  13. Hydrogen bonding: part 78. Ab initio molecular orbital study of intra- and intermolecular hydrogen bonding in choline and betaine and their compounds with HF and H 2O

    NASA Astrophysics Data System (ADS)

    Harmon, K. M.; Avci, G. F.; Madeira, S. L.; Mounts, P. A.; Thiel, A. C.

    2001-10-01

    We previously prepared several compounds of the zwitterions [(CH 3) 3NCH 2CH 2O] 0 (deprotonated choline, herein named cholaine) and [(CH 3) 3NCH 2CO 2] 0 (betaine) and proposed structures based on infrared spectroscopy. We now examine these compounds with use of ab initio molecular orbital methods to further elucidate possible structure. These calculations demonstrate that: (1) cholaine and betaine both have internal CHO hydrogen bonds, and these are retained in some form in all other compounds. (2) Cholaine hydrate and hydrofluoride and betaine hydrofluoride monomers have covalent three-center hydrogen bonds between H 2O or HF and negative zwitterion oxygen, and additional CHX hydrogen bonds to H 2O oxygen or HF fluorine. (3) Cholaine monohydrate and cholaine hydrofluoride monohydrate form dimers of Ci symmetry which contain planar C2 h (H 2O·O) 2 and (HOH·F) 2 clusters. (4) Cholaine hydrofluoride forms head-to-tail dimers bound by intermolecular CHX hydrogen bonds; this arrangement could lead to extended linear structures in the solid state. (5) Betaine hydrofluoride, in contrast, forms a tightly bound discrete dimeric unit in which two molecules join in a head-to-head manner held together by five intermolecular hydrogen bonds and by the mutual proximities of negative fluorides to positive nitrogens.

  14. Ab initio molecular orbital study of Fe{sub 2}C1{sub 6} and FeA1C1{sub 6}.

    SciTech Connect

    Scholz, G.; Curtiss, L. A.; Humboldt Univ. zu Berlin

    2000-07-24

    Ab initio molecular orbital theory was used to determine the equilibrium structure and vibrational frequencies of Fe{sub 2}Cl{sub 6} and FeAlCl{sub 6}. The equilibrium structure the Fe{sub 2}Cl{sub 6} dimer has D{sub 2h} symmetry with a planar arrangement of the four membered {l_brace}FeCl{sub br}FeCl{sub br}{r_brace} ring, similar to the Al{sub 2}Cl{sub 6} dimer. The calculated bond distances and vibrational frequencies are in good agreement with experiment. The potential energy surface for the puckering of the {l_brace}FeCl{sub br}FeCl{sub br}{r_brace} ring is extremely flat. This prevents an unambiguous assignment of either D{sub 2h} or C{sub 2v} symmetry to the Fe{sub 2}Cl{sub 6}structure in electron diffraction measurements. The FeAlCl{sub 6} molecule is found to have a C{sub 2v} structure similar to Fe{sub 2}Cl{sub 6} with vibrational frequencies in good agreement with experiment.

  15. Fragment molecular orbital study of the cAMP-dependent protein kinase catalyzed phosphoryl transfer: a comparison with the differential transition state stabilization method.

    PubMed

    Öberg, H; Brinck, T

    2016-06-01

    The importance of key residues to the activity of the cAMP-dependent protein kinase catalyzed phosphoryl transfer and to the stabilization of the transition state of the reaction has been investigated by means of the fragment molecular orbital (FMO) method. To evaluate the accuracy of the method and its capability of fragmenting covalent bonds, we have compared stabilization energies due to the interactions between individual residues and the reaction center to results obtained with the differential transition state stabilization method (Szarek, et al., J. Phys. Chem. B, 2008, 112, 11819-11826) and observe, despite a size difference in the fragment describing the reaction center, near-quantitative agreement. We have also computed deletion energies to investigate the effect of virtual deletion of key residues on the activation energy. These results are consistent with the stabilization energies and yield additional information as they clearly capture the effect of secondary interactions, i.e. interactions in the second coordination layer of the reaction center. We find that using FMO to calculate deletion energies is a powerful and time efficient approach to analyze the importance of key residues to the activity of an enzyme catalyzed reaction.

  16. Monte Carlo simulations on atropisomerism of thienotriazolodiazepines applicable to slow transition phenomena using potential energy surfaces by ab initio molecular orbital calculations.

    PubMed

    Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru

    2014-01-01

    Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.

  17. Organometallic Computational Exercise: Semiempirical Molecular Orbital Calculations on (C6H6)Cr(CO)3 and (B3N3H6Cr(CO)3

    NASA Astrophysics Data System (ADS)

    O'Brien, James F.; Haworth, Daniel T.

    2001-01-01

    A student exercise employing semiempirical molecular orbital calculations in the area of organometallic chemistry is presented. PM3 level calculations are applied to the ground-state structures of C6H6)Cr(CO)3 and (B3N3H6)Cr(CO)3. The calculations are generally successful in computing the known features of the ground-state structures. Comparison of the geometries computed for free and complexed C6H6 and B3N3H6 allow discussion of the reasons for the changes observed. The structures of the transition states for rotation of the rings with respect to Cr(CO)3 are also computed. These results permit calculation of the activation energies for the ring rotations. The activation energies computed at the PM3 level are 0.4 and 18.3 kcal/mol for (C6H6)Cr(CO)3 and (B3N3H6)Cr(CO)3, respectively. These results highlight the differences between the two molecules. Students are encouraged to comment on structural changes in the rings, on the phenomenon of ring rotation in these systems and others such as ferrocene, on the question of the aromaticity of the borazine ring, and on the effect of p back-bonding on the positions of the carbonyl stretching bands in the both complexes.

  18. Addition theorems for Slater-type orbitals and their application to multicenter multielectron integrals of central and noncentral interaction potentials.

    PubMed

    Guseinov, Israfil

    2003-06-01

    By the use of complete orthonormal sets of psi(alpha)-ETOs (alpha=1, 0, m1, m2,...) introduced by the author, new addition theorems are derived for STOs and arbitrary central and noncentral interaction potentials (CIPs and NCIPs). The expansion coefficients in these addition theorems are expressed through the Gaunt and Gegenbauer coefficients. Using the addition theorems obtained for STOs and potentials, general formulae in terms of three-center overlap integrals are established for the multicenter t-electron integrals of CIPs and NCIPs that arise in the solution of the N-electron atomic and molecular problem (2hthN) when a Hylleraas approximation in Hartree-Fock-Roothaan theory is employed. With the help of expansion formulae for translation of STOs, the three-center overlap integrals are expressed through the two-center overlap integrals. The formulae obtained are valid for arbitrary quantum numbers, screening constants and location of orbitals.

  19. 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.

  20. 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.

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-11-11

    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.

  1. Heuristic overlap-exchange model of noble gas chemical shifts

    NASA Astrophysics Data System (ADS)

    Adrian, Frank J.

    2004-05-01

    It is now generally recognized that overlap-exchange interactions are the primary cause of the medium-dependent magnetic shielding (chemical shift) in all noble gases except helium, although the attractive electrostatic-dispersion (van der Waals) interactions play an indirect role in determining the penetration of the interacting species into the repulsive overlap-exchange region. The short-range nature of these overlap-exchange interactions, combined with the fact that they often can be approximated by simple functions of the overlap of the wave functions of the interacting species, suggests a useful semiempirical model of these chemical shifts. In it the total shielding is the sum of shieldings due to pairwise interactions of the noble gas atom with the individual atoms of the medium, with the "atomic" shielding terms either estimated by simple functions of the atomic overlap integrals averaged over their Boltzmann-weighted separations, or determined by fits to experimental data in systems whose complexity makes the former procedure impractical. Results for 129Xe chemical shifts in the noble gases and in a variety of molecular and condensed systems, including families of n-alkanes, straight-chain alcohols, and the endohedral compounds Xe@C60 and Xe@C70 are encouraging for the applicability of the model to systems of technical and biomedical interest.

  2. Overlapping structures in sensory-motor mappings.

    PubMed

    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.

  3. 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

  4. Molecular characterization of an autoantigen of PM-Scl in the polymyositis/scleroderma overlap syndrome: a unique and complete human cDNA encoding an apparent 75-kD acidic protein of the nucleolar complex

    PubMed Central

    1991-01-01

    About 50% of patients with the polymyositis/scleroderma (PM-Scl) overlap syndrome are reported to have autoantibodies to a nuclear/nucleolar particle termed PM-Scl. The particle is composed of several polypeptides of which two have been identified as autoantigens. In this report, human cDNA clone coding for the entire 75-kD autoantigen of the PM-Scl particle (PM-Scl 75) was isolated from a MOLT- 4 lambda gt-11 library. The deduced amino acid sequence of the cDNA clone represented a protein of 355 amino acids and 39.2 kD; the in vitro translation product of this cDNA migrated in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) at approximately 70 kD. The aberrant migration of the polypeptide in SDS-PAGE was shown to be related to the COOH half that was rich in acidic residues. Authenticity of the cDNA coding for PM-Scl 75 was shown by immunoreactivity of PM-Scl sera with in vitro translation products and recombinant fusion proteins encoded by the cDNA. In addition, rabbit antibodies raised to recombinant fusion protein reacted in immunofluorescence, immunoblotting, and immunoprecipitation with the characteristic features displayed by human anti-PM-Scl sera. PMID:2007859

  5. Molecular (SNP) Analyses of Overlapping Hemizygous Deletions of 10q25.3 to 10qter in Four Patients: Evidence for HMX2 and HMX3 as Candidate Genes in Hearing and Vestibular Function

    PubMed Central

    Miller, Nathaniel D.; Nance, Melonie A.; Wohler, Elizabeth S.; Hoover-Fong, Julie E.; Lisi, Emily; Thomas, George H.; Pevsner, Jonathan

    2009-01-01

    We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single nucleotide polymorphism (SNP) studies (Illumina 550 K) established that these deletions resulted in the hemizygous loss of ∼6.1, ∼6.1, ∼12.5, and ∼7.0 Mb respectively. Additionally, these data establish that Patients 1, 2, and 3 share common, distal, hemizygous deleted regions of 6.09 Mb containing 37 RefSeq genes. Patients 3 and 4 share a 2.52 Mb deleted region corresponding to the proximal deleted region of Patient 3 and the distal deleted region of Patient 4. This common, hemizygous region contains 20 RefSeq genes including two H6 family homeobox genes (HMX2 and HMX3). Based on previous reports that Hmx2/Hmx3 knockout mice have vestibular anomalies, we propose that hemizygous deletions of HMX2 and HMX3 are responsible for the inner ear malformations observed from CT images, vestibular dysfunction, and congenital sensorineural hearing loss found in Patients 3 and 4. PMID:19253379

  6. Quantifying entanglement of overlapping indistinguishable particles

    NASA Astrophysics Data System (ADS)

    Gittings, Joseph R.

    This thesis develops the quantitative study of quantum entanglement in systems of identical particles. Understanding this topic is essential for the construction of quantum information processing devices involving identical particles. A brief overview of necessary concepts and methods, such as the density matrix, the entanglement in pure and mixed states of distinguishable particles, and some common applications of entanglement is given in the introduction. Some competing methods of calculating the entanglement in bipartite pure states of indistinguishable particles are examined. It is shown that only the 'site entropy' measure introduced by Zanardi satisfies all the criteria for a correct entanglement measure. A teleportation protocol which utilizes all the entanglement carried (in both the spin and space degrees of freedom) in a doubly- occupied molecular bonding orbital is presented. The output from an interferometer in a thought experiment described by Omar et al. is studied as an example to see whether entanglement can be separated into space-only, spin-only, and space-spin components. A similar exercise is performed for a doubly-occupied molecular bonding orbital. The relationship between these results and the application of superselection rules (SSRs) to the quantification of useful entanglement is discussed. A numerical method for estimating the entanglement of formation of a mixed state of arbitrary dimension by a conjugate gradient algorithm is described. The results of applying an implementation of the algorithm to both random and isotropic states of 2 qutrits (i.e. two three-dimensional systems) is described. Existing work on calculating entanglement between two sites in various spin systems is outlined. New methods for calculating the entanglement between two sites in various types of degenerate quantum gas - a Fermi gas, a Bose condensate, and a BCS superconductor - are described. The results of numerical studies of the entanglement in a normal metal

  7. Charge-Shift Bonding Emerges as a Distinct Electron-Pair Bonding Family from Both Valence Bond and Molecular Orbital Theories.

    PubMed

    Zhang, Huaiyu; Danovich, David; Wu, Wei; Braïda, Benoît; Hiberty, Philippe C; Shaik, Sason

    2014-06-10

    The charge-shift bonding (CSB) concept was originally discovered through valence bond (VB) calculations. Later, CSB was found to have signatures in atoms-in-molecules and electron-localization-function and in experimental electron density measurements. However, the CSB concept has never been derived from a molecular orbital (MO)-based theory. We now provide a proof of principle that an MO-based approach enables one to derive the CSB family alongside the distinctly different classical family of covalent bonds. In this bridging energy decomposition analysis, the covalent-ionic resonance energy, RECS, of a bond is extracted by cloning an MO-based purely covalent reference state, which is a constrained two-configuration wave function. The energy gap between this reference state and the variational TCSCF ground state yields numerical values for RECS, which correlate with the values obtained at the VBSCF level. This simple MO-based method, which only takes care of static electron correlation, is already sufficient for distinguishing the classical covalent or polar-covalent bonds from charge-shift bonds. The equivalence of the VB and MO-based methods is further demonstrated when both methods are augmented by dynamic correlation. Thus, it is shown from both MO and VB perspectives that the bonding in the CSB family does not arise from electron correlation. Considering that the existence of the CSB family is associated also with quite a few experimental observations that we already reviewed ( Shaik , S. , Danovich , D. , Wu , W. , and Hiberty , P. C. Nat. Chem. , 2009 , 1 , 443 - 449 ), the new bonding concept has passed by now two stringent tests. This derivation, on the one hand, supports the new concept and on the other, it creates bridges between the two main theories of electronic structure.

  8. Valence Band Density of States of Cu3Si Studied by Soft X-Ray Emission Spectroscopy and a First-Principle Molecular Orbital Calculation

    NASA Astrophysics Data System (ADS)

    An, Zhenlian; Kamezawa, Chihiro; Hirai, Masaaki; Kusaka, Masahiko; Iwami, Motohiro

    2002-12-01

    A systematic study of the valence band structure of Cu3Si has been performed by soft X-ray emission spectroscopy and a first-principle molecular orbital calculation using the discrete-variational (DV)-Xα cluster model. The existence of Cu 4s, 4p states in the valence band and their important contributions to the valence band as that of Cu 3d are indicated together with previously reported ones. The high-binding energy peak in the Si L2,3 emission spectrum is considered to originate mainly from the Si-Si 3s bonding state but also have a certain contribution of Si 3s bonding state with Cu 4s, 4p. On the other hand, the low-binding energy peaks in the Si L2,3 emission band are attributed to both the antibonding states of Si 3s and the bonding states of Si 3d with Cu 4s, 4p and Cu 3d. The bonding states of Si 3s with Cu 4s, 4p and Cu 3d are expected to exist in the lower part of the valence band for η\\prime-Cu3Si on the basis of the theoretical calculations. As for Si p states, the high-binding energy peak and the low-binding energy peak in the Si Kβ emission spectrum should be attributed to the Si 3p bonding state and antibonding state with Cu 3d and Cu 4s, 4p, respectively, according to the theoretical calculations. A comparison is made between experimental spectra and theoretical density of states.

  9. Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design.

    PubMed

    Watanabe, Chiduru; Fukuzawa, Kaori; Okiyama, Yoshio; Tsukamoto, Takayuki; Kato, Akifumi; Tanaka, Shigenori; Mochizuki, Yuji; Nakano, Tatsuya

    2013-04-01

    We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.

  10. 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.

  11. 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.

  12. Finding overlapping communities using seed set

    NASA Astrophysics Data System (ADS)

    Yang, Jin-Xuan; Zhang, Xiao-Dong

    2017-02-01

    The local optimization algorithm using seed set to find overlapping communities has become more and more a significant method, but it is a great challenge how to choose a good seed set. In this paper, a new method is proposed to achieve the choice of candidate seed sets, and yields a new algorithm to find overlapping communities in complex networks. By testing in real world networks and synthetic networks, this method can successfully detect overlapping communities and outperform other state-of-the-art overlapping community detection methods.

  13. Overlap syndromes among autoimmune liver diseases.

    PubMed

    Rust, Christian; Beuers, Ulrich

    2008-06-07

    The three major immune disorders of the liver are autoimmune hepatitis (AIH), primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC). Variant forms of these diseases are generally called overlap syndromes, although there has been no standardised definition. Patients with overlap syndromes present with both hepatitic and cholestatic serum liver tests and have histological features of AIH and PBC or PSC. The AIH-PBC overlap syndrome is the most common form, affecting almost 10% of adults with AIH or PBC. Single cases of AIH and autoimmune cholangitis (AMA-negative PBC) overlap syndrome have also been reported. The AIH-PSC overlap syndrome is predominantly found in children, adolescents and young adults with AIH or PSC. Interestingly, transitions from one autoimmune to another have also been reported in a minority of patients, especially transitions from PBC to AIH-PBC overlap syndrome. Overlap syndromes show a progressive course towards liver cirrhosis and liver failure without treatment. Therapy for overlap syndromes is empiric, since controlled trials are not available in these rare disorders. Anticholestatic therapy with ursodeoxycholic acid is usually combined with immunosuppressive therapy with corticosteroids and/or azathioprine in both AIH-PBC and AIH-PSC overlap syndromes. In end-stage disease, liver transplantation is the treatment of choice.

  14. 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)

  15. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... operation would involve overlap of signal strength contours with any other station licensed by the... separation Contour of proposed station Contour of other station Co-channel 0.1mV/m (40 dBu)1 mV/m (60 dBu) 1... if the proposed operation would involve overlap of signal strength contours with any other station...

  16. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... operation would involve overlap of signal strength contours with any other station licensed by the... separation Contour of proposed station Contour of other station Co-channel 0.1mV/m (40 dBu)1 mV/m (60 dBu) 1... if the proposed operation would involve overlap of signal strength contours with any other station...

  17. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... operation would involve overlap of signal strength contours with any other station licensed by the... separation Contour of proposed station Contour of other station Co-channel 0.1mV/m (40 dBu)1 mV/m (60 dBu) 1... if the proposed operation would involve overlap of signal strength contours with any other station...

  18. 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.

  19. 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.

  20. Disorder and the extent of polymerization in calcium silicate and aluminosilicate glasses: O-17 NMR results and quantum chemical molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Lee, Sung Keun; Stebbins, Jonathan F.

    2006-08-01

    Estimation of the framework connectivity and the atomic structure of depolymerized silicate melts and glasses (NBO/T > 0) remains a difficult question in high-temperature geochemistry relevant to magmatic processes and glass science. Here, we explore the extent of disorder and the nature of polymerization in binary Ca-silicate and ternary Ca-aluminosilicate glasses with varying NBO/T (from 0 to 2.67) using O-17 NMR at two different magnetic fields of 9.4 and 14.1 T in conjunction with quantum chemical calculations. Non-random distributions among framework cations (Si and Al) are demonstrated in the variation of relative populations of oxygen sites with NBO/T. The proportion of non-bridging oxygen (NBO, Ca-O-Si) in the binary and ternary aluminosilicate glasses increases with NBO/T. While the trend is consistent with predictions from composition, the detailed fractions apparently deviate from the predicted values, suggesting further complications in the nature of polymerization. The proportion of each bridging oxygen in the glasses also varies with NBO/T. The fractions of Al-O-Si and Al-O-Al increase with increasing polymerization as CaO is replaced with Al 2O 3, while that of Si-O-Si seems to decrease, implying that activity of silica may decrease from calcium silicate to polymerized aluminosilicates (X=constant). Quantum chemical molecular orbital calculations based on density functional theory show that a silicate chain with Al-NBO (Ca-O-Al) has an energy penalty (calculated cluster energy difference) of about 108 kJ/mol compared with the cluster with Ca-O-Si, consistent with preferential depolymerization of Si-networks, reported in an earlier O-17 NMR study [Allwardt, J., Lee, S.K., Stebbins, J.F., 2003. Bonding preferences of non-bridging oxygens in calcium aluminosilicate glass: Evidence from O-17 MAS and 3QMAS NMR on calcium aluminate glass. Am. Mineral.88, 949-954]. These prominent types of non-randomness in the distributions suggest significant chemical

  1. Conjugated polymers based on benzo[2,1-b:3,4-b']dithiophene with low-lying highest occupied molecular orbital energy levels for organic photovoltaics.

    PubMed

    Xiao, Shengqiang; Stuart, Andrew C; Liu, Shubin; You, Wei

    2009-07-01

    Fusing bithiophene units with a benzo moiety, benzo[2,1-b:3,4-b']dithiophene (BDT), was projected by theoretical calculations to lower the highest occupied molecular orbital (HOMO) energy level of the resulting polymers compared with that of the bithiophene unit, which would enhance the open circuit voltage of bulk heterojunction photovoltaic cells fabricated from BDT-based polymers blended with PCBM. The homopolymer of BDT (HMPBDT) and alternating copolymer of BDT with 2,1,3-benzothiadiazole (PBDT-BT) were therefore synthesized and fully characterized. Both the homopolymer (HMPBDT) and the copolymer (PBDT-BT) were experimentally confirmed to have low HOMO energy levels (-5.70 eV for HMPBDT and -5.34 eV for PBDT-BT). Introducing the acceptor moiety (2,1,3-benzothiadiazole) successfully lowered the optical band gap of the copolymer from 2.31 eV (HMPBDT) to 1.78 eV (PBDT-BT). Bulk heterojunction photovoltaic devices were fabricated from blends of these structurally related polymers with PBCM to investigate the photovoltaic performances. The optimized device of HMPBDT:PCBM (1:3, 180 nm) exhibited an improved open circuit voltage (V(oc)) of 0.76 V, a short circuit current (J(sc)) of 0.34 mA/cm(2), and a fill factor (FF) of 0.40, offering an overall efficiency of 0.10%. The observed large phase separation of the thin film by AFM and the large band gap were accountable for the small current. The optimized device of PBDT-BT:PCBM (1:3, 55 nm) demonstrated a better efficiency of 0.6%, with V(oc) = 0.72 V, J(sc) = 2.06 mA/cm(2), and FF = 0.42. The much improved current was attributed to the lower bandgap and better film morphology. However, the low hole mobility limited the thickness of the PBDT-BT:PCBM film, making inaccessible the thicker film which would utilize more light and enhance the current. Further improvements are expected if the mobility and film morphology can be improved by the new materials design, together with low band gap and low HOMO energy level.

  2. Nuclear orbiting

    SciTech Connect

    Shapira, D.

    1988-01-01

    Nuclear orbiting following collisions between sd and p shell nuclei is discussed. The dependence of this process on the real and imaginary parts of the nucleus-nucleus potential is discussed, as well as the evolution of the dinucleus toward a fully equilibrated fused system. 26 refs., 15 figs.

  3. 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

  4. 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

  5. Investigation of the resonance-assisted hydrogen bond in model β-diketones through localized molecular orbital analysis of the spin-spin coupling constants related to the O-H···O hydrogen bond.

    PubMed

    Zarycz, M Natalia C; Provasi, Patricio F

    2015-02-01

    The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons.

  6. [Asthma and chronic obstructive pulmonary disease overlap].

    PubMed

    Müller, Veronika; Gálffy, Gabriella; Tamási, Lilla

    2011-01-16

    Asthma bronchiale and chronic obstructive pulmonary disease are the most prevalent lung diseases characterized by inflammation of the airways. International and Hungarian guidelines provide proper definitions for clinical symptoms, diagnostics and therapy of both diseases. However, in everyday clinical practice, overlap of asthma and chronic obstructive pulmonary disease has become more frequent. As guidelines are mainly based on large, multicenter, randomized, controlled trials that exclude overlap patients, there is a lack of diagnostic and especially therapeutic strategies for these patients. This review summarizes clinical characteristics of asthma and chronic obstructive pulmonary disease overlap, and provides daily practical examples for its management.

  7. A minimal basis bond-orbital investigation of the linear water dimer

    NASA Astrophysics Data System (ADS)

    Magnasco, Valerio; Musso, Gian Franco; Costa, Camilla; Figari, Giuseppe

    The perturbative configuration interaction approach based on non-orthogonal bond-orbitals previously used for dealing with rotational barriers is applied to the study of the hydrogen bonding in the linear water dimer. First and second-order interaction energies are obtained in terms of static and transition charge distributions fully accounting for intermolecular overlap. Neglecting electron correlation, the second-order calculations include all single excitations from bonding to antibonding orbitals accounting for induction including exchange and giving results close to the corresponding supermolecular SCF-MOs in the same basis. Ab initio calculations using different gaussian minimal bases show that Clementi's GTO basis MEDIUM is the most suitable for describing molecular interactions. Detailed component analysis of the energy up to second order is possible and reveals the main features of the intermolecular hydrogen bonding occurring between the water molecules.

  8. 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.

  9. 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

    2015-06-05

    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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Datta, Dipayan; Kossmann, Simone; Neese, Frank

    2016-09-01

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

  12. Molecular design of photoactive acenes for organic photovoltaics

    NASA Astrophysics Data System (ADS)

    Huang, Liping; Rocca, Dario; Baroni, Stefano; Gubbins, Keith E.; Nardelli, Marco Buongiorno

    2009-05-01

    Absorption spectra of n-acenes (n from 2 to 6, for naphthalene, anthracene, tetracene, pentacene, and hexacene, respectively) have been calculated using a newly developed code based on time-dependent density-functional theory. Our calculations show that absorption spectra and charge carrier mobility of acenes not only depend on the molecular identity but also on the molecular packing. By designing the interaction between metal substrates and the first layer of acene molecules, they can be packed in a face-to-face fashion instead of the conventional herringbone (face-to-edge) arrangement. Acenes in the cofacial packing would increase the π-orbital overlap and thus enhance the charge mobility by maximizing electronic coupling between adjacent molecules. Absorption spectra of cofacially packed acenes have a better overlap with the solar spectrum, which allows harvesting more of the solar energy from red photons.

  13. 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.

  14. 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 ...

  15. Infrared lidar overlap function: an experimental determination.

    PubMed

    Guerrero-Rascado, Juan Luis; Costa, Maria João; Bortoli, Daniele; Silva, Ana Maria; Lyamani, Hassan; Alados-Arboledas, Lucas

    2010-09-13

    The most recent works demonstrate that the lidar overlap function, which describes the overlap between the laser beam and the receiver field of view, can be determined experimentally for the 355 and 532 nm channels using Raman signals. Nevertheless, the Raman channels cannot be used to determine the lidar overlap for the infrared channel (1064 nm) because of their low intensity. In addition, many Raman lidar systems only provide inelastic signals with reasonable signal-to-noise ratio at nighttime. In view of this fact, this work presents a modification of that method, based on the comparison of attenuated backscatter profiles derived from lidar and ceilometer, to retrieve the overlap function for the lidar infrared channel. Similarly to the Raman overlap method, the approach presented here allows to derive the overlap correction without an explicit knowledge of all system parameters. The application of the proposed methodology will improve the potential of Raman lidars to investigate the aerosol microphysical properties in the planetary boundary layer, extending the information of 1064 nm backscatter profiles to the ground and allowing the retrieval of microphysical properties practically close to the surface.

  16. Overlapping Antisense Transcription in the Human Genome

    PubMed Central

    Fahey, M. E.; Moore, T. F.

    2002-01-01

    Accumulating evidence indicates an important role for non-coding RNA molecules in eukaryotic cell regulation. A small number of coding and non-coding overlapping antisense transcripts (OATs) in eukaryotes have been reported, some of which regulate expression of the corresponding sense transcript. The prevalence of this phenomenon is unknown, but there may be an enrichment of such transcripts at imprinted gene loci. Taking a bioinformatics approach, we systematically searched a human mRNA database (RefSeq) for complementary regions that might facilitate pairing with other transcripts. We report 56 pairs of overlapping transcripts, in which each member of the pair is transcribed from the same locus. This allows us to make an estimate of 1000 for the minimum number of such transcript pairs in the entire human genome. This is a surprisingly large number of overlapping gene pairs and, clearly, some of the overlaps may not be functionally significant. Nonetheless, this may indicate an important general role for overlapping antisense control in gene regulation. EST databases were also investigated in order to address the prevalence of cases of imprinted genes with associated non-coding overlapping, antisense transcripts. However, EST databases were found to be completely inappropriate for this purpose. PMID:18628857

  17. 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.

  18. Adaptive braking by Ase1 prevents overlapping microtubules from sliding completely apart.

    PubMed

    Braun, Marcus; Lansky, Zdenek; Fink, Gero; Ruhnow, Felix; Diez, Stefan; Janson, Marcel E

    2011-09-04

    Short regions of overlap between ends of antiparallel microtubules are central elements within bipolar microtubule arrays. Although their formation requires motors, recent in vitro studies demonstrated that stable overlaps cannot be generated by molecular motors alone. Motors either slide microtubules along each other until complete separation or, in the presence of opposing motors, generate oscillatory movements. Here, we show that Ase1, a member of the conserved MAP65/PRC1 family of microtubule-bundling proteins, enables the formation of stable antiparallel overlaps through adaptive braking of Kinesin-14-driven microtubule-microtubule sliding. As overlapping microtubules start to slide apart, Ase1 molecules become compacted in the shrinking overlap and the sliding velocity gradually decreases in a dose-dependent manner. Compaction is driven by moving microtubule ends that act as barriers to Ase1 diffusion. Quantitative modelling showed that the molecular off-rate of Ase1 is sufficiently low to enable persistent overlap stabilization over tens of minutes. The finding of adaptive braking demonstrates that sliding can be slowed down locally to stabilize overlaps at the centre of bipolar arrays, whereas sliding proceeds elsewhere to enable network self-organization.

  19. Ab initio electron propagator theory of molecular wires. I. Formalism.

    PubMed

    Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V

    2005-11-08

    Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.

  20. Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case.

    PubMed

    Seligmann, Hervé

    2012-12-01

    Mitochondrial genes code for additional proteins after +2 frameshifts by reassigning stops to code for amino acids, which defines overlapping genetic codes for overlapping genes. Turtles recode stops UAR → Trp and AGR → Lys (AGR → Gly in the marine Olive Ridley turtle, Lepidochelys olivacea). In Lepidochelys the +2 frameshifted mitochondrial Cytb gene lacks stops, open reading frames from other genes code for unknown proteins, and for regular mitochondrial proteins after frameshifts according to the overlapping genetic code. Lepidochelys' inversion between proteins coded by regular and overlapping genetic codes substantiates the existence of overlap coding. ND4 differs among Lepidochelys mitochondrial genomes: it is regular in DQ486893; in NC_011516, the open reading frame codes for another protein, the regular ND4 protein is coded by the frameshifted sequence reassigning stops as in other turtles. These systematic patterns are incompatible with Genbank/sequencing errors and DNA decay. Random mixing of synonymous codons, conserving main frame coding properties, shows optimization of natural sequences for overlap coding; Ka/Ks analyses show high positive (directional) selection on overlapping genes. Tests based on circular genetic codes confirm programmed frameshifts in ND3 and ND4l genes, and predicted frameshift sites for overlap coding in Lepidochelys. Chelonian mitochondria adapt for overlapping gene expression: cloverleaf formation by antisense tRNAs with predicted anticodons matching stops coevolves with overlap coding; antisense tRNAs with predicted expanded anticodons (frameshift suppressor tRNAs) associate with frameshift-coding in ND3 and ND4l, a potential regulation of frameshifted overlap coding. Anaeroby perhaps switched between regular and overlap coding genes in Lepidochelys.

  1. 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.

  2. 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

  3. Investigation of the encapsulation of metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) by the dipeptide Phe-Phe using natural bond orbital theory and molecular dynamics simulation.

    PubMed

    Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K

    2017-03-01

    Complexes of the dipeptide phenylalanine-phenylalanine (Phe-Phe) with divalent metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) were studied at the B3LYP and MP2 levels of theory with the basis sets 6-311++G(d,p) and 6-31 + G(d) in the gas phase. The relative energies of these complexes indicated that cation-π bidentate/tridentate conformations are more favourable than other conformations with uncoordinated rings. These findings were confirmed by the calculated values of thermodynamic parameters such as the Gibbs free energy. Natural bond orbital (NBO) analysis was carried out to explore the metal-ligand coordination in Phe-Phe-Cu(2+)/Zn(2+) complexes. Possible orbital transitions, types of orbitals and their occupancies were determined for a range of Phe-Phe-Cu(2+)/Zn(2+) complexes. The charge transfer involved in various orbital transitions was explored by considering the second-order perturbation energy. NBO analysis revealed that the change transfer is stronger when the metal cation uses both the 4s + 4p subshells rather than just its 4p subshell. We also performed molecular dynamics (MD) simulations to check the stability and consistency of the most favourable binding motifs of Cu(2+), Zn(2+), Ca(2+) and Ba(2+) with Phe-Phe over time. The structures of the Phe-Phe-Cu(2+)/Zn(2+)/Ca(2+)/Ba(2+) complexes obtained using MD simulation were found to be in good agreement with those obtained in the DFT-based calculations. Graphical Abstract Conformational search on encapsulation of divalent metal cations (Ca(2+), Zn(2+), Ca(2+), Ba(2+)) by the Phe-Phe dipeptide.

  4. 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.

  5. Dyson orbitals for ionization from the ground and electronically excited states within equation-of-motion coupled-cluster formalism: theory, implementation, and examples.

    PubMed

    Oana, C Melania; Krylov, Anna I

    2007-12-21

    Implementation of Dyson orbitals for coupled-cluster and equation-of-motion coupled-cluster wave functions with single and double substitutions is described and demonstrated by examples. Both ionizations from the ground and electronically excited states are considered. Dyson orbitals are necessary for calculating electronic factors of angular distributions of photoelectrons, Compton profiles, electron momentum spectra, etc, and can be interpreted as states of the leaving electron. Formally, Dyson orbitals represent the overlap between an initial N-electron wave function and the N-1 electron wave function of the corresponding ionized system. For the ground state ionization, Dyson orbitals are often similar to the corresponding Hartree-Fock molecular orbitals (MOs); however, for ionization from electronically excited states Dyson orbitals include contributions from several MOs and their shapes are more complex. The theory is applied to calculating the Dyson orbitals for ionization of formaldehyde from the ground and electronically excited states. Partial-wave analysis is employed to compute the probabilities to find the ejected electron in different angular momentum states using the freestanding and Coulomb wave representations of the ionized electron. Rydberg states are shown to yield higher angular momentum electrons, as compared to valence states of the same symmetry. Likewise, faster photoelectrons are most likely to have higher angular momentum.

  6. 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.

  7. Probing genetic overlap among complex human phenotypes.

    PubMed

    Rzhetsky, Andrey; Wajngurt, David; Park, Naeun; Zheng, Tian

    2007-07-10

    Geneticists and epidemiologists often observe that certain hereditary disorders cooccur in individual patients significantly more (or significantly less) frequently than expected, suggesting there is a genetic variation that predisposes its bearer to multiple disorders, or that protects against some disorders while predisposing to others. We suggest that, by using a large number of phenotypic observations about multiple disorders and an appropriate statistical model, we can infer genetic overlaps between phenotypes. Our proof-of-concept analysis of 1.5 million patient records and 161 disorders indicates that disease phenotypes form a highly connected network of strong pairwise correlations. Our modeling approach, under appropriate assumptions, allows us to estimate from these correlations the size of putative genetic overlaps. For example, we suggest that autism, bipolar disorder, and schizophrenia share significant genetic overlaps. Our disease network hypothesis can be immediately exploited in the design of genetic mapping approaches that involve joint linkage or association analyses of multiple seemingly disparate phenotypes.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Triple differential cross section measurements for the outer valence molecular orbitals (1t2) of a methane molecule at 250 eV electron impact

    NASA Astrophysics Data System (ADS)

    Işık, N.; Doğan, M.; Bahçeli, S.

    2016-03-01

    In this study, detailed experimental research of triple differential cross section (TDCS) measurements is performed to investigate single ionization dynamics for the 1t2 orbital of methane molecule by 250 eV electron impact. In our experiments, the outgoing electrons are simultaneously measured in coincidence in a coplanar asymmetric geometry with the scattering angles of 10° and 20°. Therefore, TDCS measurements are performed for two different values of momentum transfer (K ≈ 0.9 au and 1.5 au). A detailed analysis of the dependence of the TDCS versus the momentum transfer is reported here.

  13. Australian University Libraries: Collections Overlap Study

    ERIC Educational Resources Information Center

    Missingham, Roxanne; Walls, Robert

    2003-01-01

    In 2002, the Department of Education, Science and Training (DEST), Higher Education Information Infrastructure Advisory Committee commissioned the National Library of Australia to analyse the uniqueness and overlap of Australian university library collections, comparing library collections in each state, using the National Bibliographic Database…

  14. 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.

  15. Stochastic Cooling with Schottky Band Overlap

    NASA Astrophysics Data System (ADS)

    Lebedev, Valeri

    2006-03-01

    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.

  16. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 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 other than a Class D (secondary) station will not be accepted if the...

  17. 47 CFR 73.509 - Prohibited overlap.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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 other than a Class D (secondary) station will not be accepted if the...

  18. 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…

  19. The overlap syndromes of autoimmune hepatitis.

    PubMed

    Czaja, Albert J

    2013-02-01

    Autoimmune hepatitis has two major variant phenotypes in which the features of classical disease are co-mingled with those of primary biliary cirrhosis or primary sclerosing cholangitis. These overlap syndromes lack codified diagnostic criteria, established pathogenic mechanisms, and confident management strategies. Their clinical importance relates mainly to the identification of patients who respond poorly to conventional corticosteroid treatment. Scoring systems that lack discriminative power have been used in their definition, and a clinical phenotype based on pre-defined laboratory and histological findings has not been promulgated. The frequency of overlap with primary biliary cirrhosis is 7-13 %, and the frequency of overlap with primary sclerosing cholangitis is 8-17 %. Patients with autoimmune hepatitis and features of cholestatic disease must be distinguished from patients with cholestatic disease and features of autoimmune hepatitis. Variants of the overlap syndromes include patients with small duct primary sclerosing cholangitis, antimitochondrial antibody-negative primary biliary cirrhosis, autoimmune sclerosing cholangitis, and immunoglobulin G4-associated disease. Conventional corticosteroid therapy alone or in conjunction with ursodeoxycholic acid (13-15 mg/kg daily) has been variably effective, and cyclosporine, mycophenolate mofetil, and budesonide have been beneficial in selected patients. The key cholestatic features that influence the prognosis of autoimmune hepatitis must be defined and incorporated into the definition of the syndrome rather than rely on designations that imply the co-mingling of different diseases with manifestations of variable clinical relevance. The overlap syndromes in autoimmune hepatitis are imprecise, heterogeneous, and unfounded, but they constitute a clinical reality that must be accepted, diagnosed, refined, treated, and studied.

  20. 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.

  1. Molecular orbital studies (hardness, chemical potential, electronegativity and electrophilicity), vibrational spectroscopic investigation and normal coordinate analysis of 5-{1-hydroxy-2-[(propan-2-yl)amino]ethyl}benzene-1,3-diol.

    PubMed

    Muthu, S; Renuga, S

    2014-01-24

    FT-IR and FT-Raman spectra of 5-{1-hydroxy-2-[(propan-2-yl) amino] ethyl} benzene-1,3-diol (abbrevi- 54 ated as HPAEBD) were recorded in the region 4000-450 cm(-1) and 4000-100 cm(-1) respectively. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (B3LYP) and HF method with 6-31 G(d,p) as basis set. The theoretical wave numbers were scaled and compared with experimental 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). Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ antibonding orbitals and E (2) energies confirm the occurrence of intra molecular charge transfer (ICT) within the molecule. The molecule orbital contributions were studied by using the total (TDOS), sum of α and β electron (αβDOS) density of States. Mulliken population analysis of atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in this compound. On the basis of vibrational analyses, the thermodynamic properties of title compound at different temperatures have been calculated.

  2. 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.

  3. Study of the molecular structure, ionization spectrum, and electronic wave function of 1,3-butadiene using electron momentum spectroscopy and benchmark Dyson orbital theories

    NASA Astrophysics Data System (ADS)

    Deleuze, M. S.; Knippenberg, S.

    2006-09-01

    The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within ˜0.2eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense π-2 π*+1 satellite at ˜13.1eV in the ionization spectrum of the s-trans conformer.

  4. Correlation of electronic transitions and redox potentials measured for pyrocatechol, resorcinol, hydroquinone, pyrogallol, and gallic acid with results of semi-empirical molecular orbital computations A useful interpretation tool

    NASA Astrophysics Data System (ADS)

    Carter, Melvin Keith

    2007-04-01

    Cyclic voltammogram (CV) electrochemical measurements for pyrocatechol, resorcinol, hydroquinone, pyrogallol, and gallic acid in strong alkaline solution produced observable oxidation-reduction potentials for each hydroxy group present except for resorcinol. UV absorption spectra were also observed for the diluted solutions. Semi-empirical molecular orbital computations were conducted for these molecules of C2 v point group symmetry to determine the character and energies to aid interpretation of the experimental results. CV oxidation removed a π-electron by a radiationless π-π* transition followed by an electron shift from a negative oxygen to the positive aromatic π-system indicated by an observable σ-π* transition. Simple semi-empirical computations correlated with measured excited electronic states during electron transfer.

  5. Ab initio molecular-orbital study on successive hydrogen-elimination reactions with low activation energies in the a-Si:H formation process: Cluster-size dependence of activation energies

    NASA Astrophysics Data System (ADS)

    Sato, Kota; Honna, Hiroshi; Iwabuchi, Susumu; Hirano, Tsuneo; Koinuma, Hideomi

    1994-07-01

    Successive hydrogen-elimination reactions with low activation energies during the formation of a-Si:H by silane plasma chemical-vapor deposition proposed by us were studied by using a larger cluster model on the basis of an ab initio molecular-orbital method. The activation energy of the first step, the reaction of a dangling-bond site with an adjacent tetrahedrally coordinated silicon, was found to be 18.2 kcal/mol (0.79 eV) by employing a larger cluster model. The total process was also shown to be thermodynamically more favorable by using larger cluster models. Thus, the successive process is considered to play an important role in a-Si:H formation processes.

  6. Imaging of autoimmune hepatitis and overlap syndromes.

    PubMed

    Malik, Neera; Venkatesh, Sudhakar K

    2017-01-01

    Autoimmune hepatitis (AIH) is an uncommon, chronic inflammatory, and relapsing liver disease of unknown origin that may lead to liver cirrhosis, hepatocellular carcinoma, liver transplantation, or death. AIH occurs in all age groups and races but can frequently manifest as acute fulminant hepatitis. Clinical presentation of AIH can have features similar to primary sclerosing cholangitis (PSC) and primary biliary cirrhosis (PBC), and these diseases may coexist leading to overlap syndromes. Although histological diagnosis is necessary, imaging features often can demonstrate characteristics that may be helpful to distinguish these diseases. Imaging features of AIH are those of chronic liver disease, and imaging plays important role in detection of complications and ruling out other possible causes of chronic liver disease. Emerging techniques such as elastography provide non-invasive options for diagnosis of significant fibrosis and cirrhosis during clinical follow-up as well as assessment of response to treatment. In this study, we will describe imaging findings in AIH and overlap syndromes.

  7. "Overlapped" rhinitis: a real trap for rhinoallergologists.

    PubMed

    Gelardi, M

    2014-11-01

    Under the broad heading of "vasomotor" rhinitis two big groups can be distinguished: allergic rhinitis (IgE-mediated), and nonallergic rhinitis. Since they are two separate nosological entities, they can co-exist in the same patient, classifying themselves in the group of "overlapped" rhinitis (OR). Although not absolutely rare (indeed it is estimated a 15-20% incidence among all vasomotor rhinopathies), this condition is not investigated and diagnosed, with significant implications in the clinical-diagnostic and therapeutic field.

  8. Overlap of fibromyalgia with other medical conditions.

    PubMed

    Martínez-Lavín, M

    2001-08-01

    Fibromyalgia is a multisystem illness. One of its defining features, generalized pain, may also be present in other rheumatic entities. The diagnosis of fibromyalgia is not easy by any means, it requires a profound knowledge of internal medicine. This article discusses the different rheumatic and nonrheumatic diseases that overlap or are prone to be confused with fibromyalgia. It emphasizes the key points in the differential diagnosis.

  9. 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.

  10. A computational study on the N-heterocyclic carbene-catalyzed Csp(2)-Csp(3) bond activation/[4+2] cycloaddition cascade reaction of cyclobutenones with imines: a new application of the conservation principle of molecular orbital symmetry.

    PubMed

    Wang, Yang; Wu, Bohua; Zhang, Haoyang; Wei, Donghui; Tang, Mingsheng

    2016-07-20

    A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction.

  11. Overlaps between Frailty and Sarcopenia Definitions.

    PubMed

    Cederholm, Tommy

    2015-01-01

    Aging is characterized by the catabolism of muscles leading to sarcopenia and frailty. These are two geriatric syndromes with partly overlapping phenotypes. Primary sarcopenia, i.e. loss of muscle mass and function related to aging alone, usually precedes frailty. Thus, robustness passes from sarcopenia over frailty to disability leading eventually to a mortal outcome. Frailty (defined according to the phenotype model) encompasses states as exhaustion, weakness, and slowness, whereas sarcopenia, combining mass and function, is more strictly focused on muscles. Frailty is age related, whereas sarcopenia is also related to disease, starvation, and disuse. In general, the criteria for the two conditions overlap, but frailty requires weight loss, whereas sarcopenia requires muscle loss. Both gait speed and hand grip strength are suggested to be used as diagnostic measures for the two conditions since muscle function is crucial for any of the two syndromes. It is suggested that frailty screening should be part of the geriatric comprehensive assessment starting with measuring walking capacity and complemented by taking a history of fatigue and low activity. For younger adults (i.e. <70 years), sarcopenia screening could first register gait speed or hand grip strength and then body composition measurements. Simple questionnaires are feasible clinical alternatives. Treatment of frailty and sarcopenia overlaps, i.e. provide adequate protein and vitamin D supplementation, and encourage resistance exercise.

  12. 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.

  13. Vertical overlap of probability density functions of cloud and precipitation hydrometeors: CLOUD AND PRECIPITATION PDF OVERLAP

    SciTech Connect

    Ovchinnikov, Mikhail; Lim, Kyo-Sun Sunny; Larson, Vincent E.; Wong, May; Thayer-Calder, Katherine; Ghan, Steven J.

    2016-11-05

    Coarse-resolution climate models increasingly rely on probability density functions (PDFs) to represent subgrid-scale variability of prognostic variables. While PDFs characterize the horizontal variability, a separate treatment is needed to account for the vertical structure of clouds and precipitation. When sub-columns are drawn from these PDFs for microphysics or radiation parameterizations, appropriate vertical correlations must be enforced via PDF overlap specifications. This study evaluates the representation of PDF overlap in the Subgrid Importance Latin Hypercube Sampler (SILHS) employed in the assumed PDF turbulence and cloud scheme called the Cloud Layers Unified By Binormals (CLUBB). PDF overlap in CLUBB-SILHS simulations of continental and tropical oceanic deep convection is compared with overlap of PDF of various microphysics variables in cloud-resolving model (CRM) simulations of the same cases that explicitly predict the 3D structure of cloud and precipitation fields. CRM results show that PDF overlap varies significantly between different hydrometeor types, as well as between PDFs of mass and number mixing ratios for each species, - a distinction that the current SILHS implementation does not make. In CRM simulations that explicitly resolve cloud and precipitation structures, faster falling species, such as rain and graupel, exhibit significantly higher coherence in their vertical distributions than slow falling cloud liquid and ice. These results suggest that to improve the overlap treatment in the sub-column generator, the PDF correlations need to depend on hydrometeor properties, such as fall speeds, in addition to the currently implemented dependency on the turbulent convective length scale.

  14. 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

  15. Unique human orbital morphology compared with that of apes.

    PubMed

    Denion, Eric; Hitier, Martin; Guyader, Vincent; Dugué, Audrey-Emmanuelle; Mouriaux, Frédéric

    2015-06-25

    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.

  16. Multichannel molecular state and rectified short-range boundary condition for spin-orbit-coupled ultracold fermions near p -wave resonances

    NASA Astrophysics Data System (ADS)

    Cui, Xiaoling

    2017-03-01

    We study the interplay of spin-orbit coupling (SOC) and strong p -wave interactions to the scattering property of spin-1/2 ultracold Fermi gases. Based on a two-channel square-well potential generating p -wave resonance, we show that the presence of an isotropic SOC, even for its length being much longer than the potential range, can greatly modify the p -wave short-range boundary condition (BC). As a result, the conventional p -wave BC cannot predict the induced molecules near p -wave resonances, which can be fully destroyed due to strong interference between the s - and p -wave channels. By analyzing the intrinsic reasons for the breakdown of the conventional BC, we propose a p -wave BC that can excellently reproduce the exact molecule solutions and also equally apply for a wide class of single-particle potentials besides SOC. This work reveals the significant effect of SOC on both the short- and long-range properties of fermions near p -wave resonances, paving the way for future explorations of interesting few- and many-body physics in such systems.

  17. Origin of gene overlap: the case of TCP1 and ACAT2.

    PubMed Central

    Shintani, S; O'hUigin, C; Toyosawa, S; Michalová, V; Klein, J

    1999-01-01

    The human acetyl-CoA acetyltransferase 2 gene, ACAT2, codes for a thiolase, an enzyme involved in lipid metabolism. The human T-complex protein 1 gene, TCP1, encodes a molecular chaperone of the chaperonin family. The two genes overlap by their 3'-untranslated regions, their coding sequences being located on opposite DNA strands in a tail-to-tail orientation. To find out how the overlap might have arisen in evolution, the homologous genes of the zebrafish, the African toad, caiman, platypus, opossum, and wallaby were identified. In each species, standard or long polymerase chain reactions were used to determine whether the ACAT2 and TCP1 homologs are closely linked and, if so, whether they overlap. The results reveal that the overlap apparently arose during the transition from therapsid reptiles to mammals and has been retained for >200 million years. Part of the overlapping untranslated region shows remarkable sequence conservation. The overlap presumably arose during the chromosomal rearrangement that brought the two unrelated and previously separated genes together. One or both of the transposed genes found by chance signals that are necessary for the processing of their transcripts to be present on the noncoding strand of the partner gene. PMID:10353914

  18. Projected seniority-two orbital optimization of the antisymmetric product of one-reference orbital geminal.

    PubMed

    Boguslawski, Katharina; Tecmer, Paweł; Limacher, Peter A; Johnson, Paul A; Ayers, Paul W; Bultinck, Patrick; De Baerdemacker, Stijn; Van Neck, Dimitri

    2014-06-07

    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.

  19. 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.

  20. 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

  1. 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.

  2. Overextended sarcomeres regain filament overlap following stretch.

    PubMed

    Panchangam, Appaji; Herzog, Walter

    2012-09-21

    Sarcomere overextension has been widely implicated in stretch-induced muscle injury. Yet, sarcomere overextensions are typically inferred based on indirect evidence obtained in muscle and fibre preparations, where individual sarcomeres cannot be observed during dynamic contractions. Therefore, it remains unclear whether sarcomere overextensions are permanent following injury-inducing stretch-shortening cycles, and thus, if they can explain stretch-induced force loss. We tested the hypothesis that overextended sarcomeres can regain filament overlap in isolated myofibrils from rabbit psoas muscles. Maximally activated myofibrils (n=13) were stretched from an average sarcomere length of 2.6±0.04μm by 0.9μm sarcomere(-1) at a speed of 0.1μm sarcomere(-1)s(-1) and immediately returned to the starting lengths at the same speed (sarcomere strain=34.1±2.3%). Myofibrils were then allowed to contract isometrically at the starting lengths (2.6μm) for ∼30s before relaxing. Force and individual sarcomere lengths were measured continuously. Out of the 182 sarcomeres, 35 sarcomeres were overextended at the peak of stretch, out of which 26 regained filament overlap in the shortening phase while 9 (∼5%) remained overextended. About 35% of the sarcomeres with initial lengths on the descending limb of the force-length relationship and ∼2% of the sarcomeres with shorter initial lengths were overextended. These findings provide first ever direct evidence that overextended sarcomeres can regain filament overlap in the shortening phase following stretch, and that the likelihood of overextension is higher for sarcomeres residing initially on the descending limb.

  3. 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.

  4. Orbital dystopia due to orbital roof defect.

    PubMed

    Rha, Eun Young; Joo, Hong Sil; Byeon, Jun Hee

    2013-01-01

    We performed a retrospective review of patients who presented with delayed dystopia as a consequence of an orbital roof defect due to fractures and nontraumatic causes to search for a correlation between orbital roof defect size and surgical indications for the treatment thereof. Retrospective analyses were performed in 7 patients, all of whom presented with delayed dystopia due to orbital roof defects, between January 2001 and June 2011. The causes of orbital roof defects were displaced orbital roof fractures (5 cases), tumor (1 case), and congenital sphenoid dysplasia (1 case). All 7 patients had initially been treated conservatively and later presented with significant dystopia. The sizes of the defects were calculated on computed tomographic scans. Among the 7 patients, aspiration of cerebrospinal fluid, which caused ocular symptoms, in 1 patient with minimal displaced orbital roof and reconstruction with calvarial bone, titanium micromesh, or Medpor in 6 other patients were performed. The minimal size of the orbital roof in patients who underwent orbital roof reconstruction was 1.2 cm (defect height) x 1.0 cm (defect length), 0.94 cm(2). For all patients with orbital dystopia, displacement of the globe was corrected without any complications, regardless of whether the patient was evaluated grossly or by radiology. In this retrospective study, continuous monitoring of clinical signs and active surgical management should be considered for cases in which an orbital roof defect is detected, even if no definite symptoms are noted, to prevent delayed sequelae.

  5. Sclerosing idiopathic orbital inflammation.

    PubMed

    Brannan, Paul A; Kersten, Robert C; Kulwin, Dwight R

    2006-01-01

    A 5-year-old girl referred for orbital cellulitis was found to have a right orbital mass. Computed tomography revealed a mass occupying the inferotemporal orbit, extending into the maxillary sinus. Biopsy yielded a diagnosis of sclerosing idiopathic orbital inflammation. She was successfully treated with prednisone.

  6. 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.

  7. Direct Pathway to Molecular Photodissociation on Metal Surfaces Using Visible Light.

    PubMed

    Kazuma, Emiko; Jung, Jaehoon; Ueba, Hiromu; Trenary, Michael; Kim, Yousoo

    2017-03-01

    We demonstrate molecular photodissociation on single-crystalline metal substrates, driven by visible-light irradiation. The visible-light-induced photodissociation on metal substrates has long been thought to never occur, either because visible-light energy is much smaller than the optical energy gap between the frontier electronic states of the molecule or because the molecular excited states have short lifetimes due to the strong hybridization between the adsorbate molecular orbitals (MOs) and metal substrate. The S-S bond in dimethyl disulfide adsorbed on both Cu(111) and Ag(111) surfaces was dissociated through direct electronic excitation from the HOMO-derived MO (the nonbonding lone-pair type orbitals on the S atoms (nS)) to the LUMO-derived MO (the antibonding orbital localized on the S-S bond (σ*SS)) by irradiation with visible light. A combination of scanning tunneling microscopy and density functional theory calculations revealed that visible-light-induced photodissociation becomes possible due to the interfacial electronic structures constructed by the hybridization between molecular orbitals and the metal substrate states. The molecule-metal hybridization decreases the gap between the HOMO- and LUMO-derived MOs into the visible-light energy region and forms LUMO-derived MOs that have less overlap with the metal substrate, which results in longer excited-state lifetimes.

  8. Orbital fractures: a review

    PubMed Central

    Joseph, Jeffrey M; Glavas, Ioannis P

    2011-01-01

    This review of orbital fractures has three goals: 1) to understand the clinically relevant orbital anatomy with regard to periorbital trauma and orbital fractures, 2) to explain how to assess and examine a patient after periorbital trauma, and 3) to understand the medical and surgical management of orbital fractures. The article aims to summarize the evaluation and management of commonly encountered orbital fractures from the ophthalmologic perspective and to provide an overview for all practicing ophthalmologists and ophthalmologists in training. PMID:21339801

  9. 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.

  10. 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.

  11. Activation of words with phonological overlap

    PubMed Central

    Friedrich, Claudia K.; Felder, Verena; Lahiri, Aditi; Eulitz, Carsten

    2013-01-01

    Multiple lexical representations overlapping with the input (cohort neighbors) are temporarily activated in the listener's mental lexicon when speech unfolds in time. Activation for cohort neighbors appears to rapidly decline as soon as there is mismatch with the input. However, it is a matter of debate whether or not they are completely excluded from further processing. We recorded behavioral data and event-related brain potentials (ERPs) in auditory-visual word onset priming during a lexical decision task. As primes we used the first two syllables of spoken German words. In a carrier word condition, the primes were extracted from spoken versions of the target words (ano-ANORAK “anorak”). In a cohort neighbor condition, the primes were taken from words that overlap with the target word up to the second nucleus (ana—taken from ANANAS “pineapple”). Relative to a control condition, where primes and targets were unrelated, lexical decision responses for cohort neighbors were delayed. This reveals that cohort neighbors are disfavored by the decision processes at the behavioral front end. In contrast, left-anterior ERPs reflected long-lasting facilitated processing of cohort neighbors. We interpret these results as evidence for extended parallel processing of cohort neighbors. That is, in parallel to the preparation and elicitation of delayed lexical decision responses to cohort neighbors, aspects of the processing system appear to keep track of those less efficient word candidates. PMID:24009593

  12. The Hippocampus and Disambiguation of Overlapping Sequences

    PubMed Central

    Agster, Kara L.; Fortin, Norbert J.; Eichenbaum, Howard

    2010-01-01

    Recent models of hippocampal function emphasize its potential role in disambiguating sequences of events that compose distinct episodic memories. In this study, rats were trained to distinguish two overlapping sequences of odor choices. The capacity to disambiguate the sequences was measured by the critical odor choice after the overlapping elements of the sequences. When the sequences were presented in rapid alternation, damage to the hippocampus, produced either by infusions of the neurotoxin ibotenic acid or by radiofrequency current, produced a severe deficit, although animals with radiofrequency lesions relearned the task. When the sequences were presented spaced apart and in random order, animals with radiofrequency hippocampal lesions could perform the task. However, they failed when a memory delay was imposed before the critical choice. These findings support the hypothesis that the hippocampus is involved in representing sequences of nonspatial events, particularly when interference between the sequences is high or when animals must remember across a substantial delay preceding items in a current sequence. PMID:12097529

  13. Visualizing fuzzy overlapping communities in networks.

    PubMed

    Vehlow, Corinna; Reinhardt, Thomas; Weiskopf, Daniel

    2013-12-01

    An important feature of networks for many application domains is their community structure. This is because objects within the same community usually have at least one property in common. The investigation of community structure can therefore support the understanding of object attributes from the network topology alone. In real-world systems, objects may belong to several communities at the same time, i.e., communities can overlap. Analyzing fuzzy community memberships is essential to understand to what extent objects contribute to different communities and whether some communities are highly interconnected. We developed a visualization approach that is based on node-link diagrams and supports the investigation of fuzzy communities in weighted undirected graphs at different levels of detail. Starting with the network of communities, the user can continuously drill down to the network of individual nodes and finally analyze the membership distribution of nodes of interest. Our approach uses layout strategies and further visual mappings to graphically encode the fuzzy community memberships. The usefulness of our approach is illustrated by two case studies analyzing networks of different domains: social networking and biological interactions. The case studies showed that our layout and visualization approach helps investigate fuzzy overlapping communities. Fuzzy vertices as well as the different communities to which they belong can be easily identified based on node color and position.

  14. 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.

  15. Octave illusion elicited by overlapping narrowband noises.

    PubMed

    Jonas Brännström, K; Nilsson, Patrik

    2011-05-01

    The octave or Deutsch illusion occurs when two tones, separated by about one octave, are presented simultaneously but alternating between ears, such that when the low tone is presented to the left ear the high tone is presented to the right ear and vice versa. Most subjects hear a single tone that alternates both between ears and in pitch; i.e., they hear a low pitched tone in one ear alternating with a high pitched tone in the other ear. The present study examined whether the illusion can be elicited by aperiodic signals consisting of low-frequency band-pass filtered noises with overlapping spectra. The amount of spectral overlap was held constant, but the high- and low-frequency content of the signals was systematically varied. The majority of subjects perceived an auditory illusion in terms of a dominant ear for pitch and lateralization by frequency, as proposed by Deutsch [(1975a) Sci. Am. 233, 92-104]. Furthermore, the salience of the illusion increased as the high frequency of the content in the signal increased. Since no harmonics were present in the stimuli, it is highly unlikely that this illusion is perceived on the basis of binaural diplacusis or harmonic binaural fusion.

  16. Heterogeneity of asthma–COPD overlap syndrome

    PubMed Central

    Joo, Hyonsoo; Han, Deokjae; Lee, Jae Ha; Rhee, Chin Kook

    2017-01-01

    Many patients suffering from asthma or COPD have overlapping features of both diseases. However, a phenotypical approach for evaluating asthma–COPD overlap syndrome (ACOS) has not been established. In this report, we examined the phenotypes in patients with ACOS. Patients diagnosed with ACOS between 2011 and 2015 were identified and classified into four phenotype groups. Group A was composed of patients who smoked <10 pack years and had blood eosinophil counts ≥300. Group B was composed of patients who smoked <10 pack years and had blood eosinophil counts <300. Group C was composed of patients who smoked ≥10 pack years and had blood eosinophil counts ≥300. Group D was composed of patients who smoked <10 pack years and had blood eosinophil counts <300. Clinical characteristics were analyzed and compared among groups. Comparisons were made among 103 ACOS patients. Patients in group D were oldest, while patients in group A were youngest. There were relatively more female patients in groups A and B; the majority of patients in groups C and D were male. The degree of airflow obstruction was most severe in group C. The rate of being free of severe exacerbation was significantly lower in group C than in the other groups. In this study, each ACOS phenotype showed different characteristics. The proportion of patients free of severe exacerbation differed significantly among groups. At this time, further studies on the phenotypes of ACOS are required. PMID:28260876

  17. Adaptive overlapped sub-blocks contrast enhancement

    NASA Astrophysics Data System (ADS)

    Chen, Anqiu; Yuan, Fei; Liu, Jing; Liu, Siqi; Li, An; Zheng, Zhenrong

    2016-09-01

    In this paper, an overlapped sub-block gray-level average method for contrast enhancement is presented. The digital image correction of uneven illumination under microscope transmittance is a problem in image processing, also sometimes the image in the dark place need to correct the uneven problem. A new correction method was proposed based on the mask method and sub-blocks gray-level average method because Traditional mask method and background fitting method are restricted due to application scenarios, and the corrected image brightness is low by using background fitting method, so it has some limitations of the application. In this paper, we introduce a new method called AOSCE for image contrast enhancement. The image is divided into many sub-blocks which are overlapped, calculate the average gray-level of the whole image as M and the calculate the average gray-level of each one as mi, next for each block it can get d = mi - m, each block minus d to get a new image, and then get the minimum gray-level of each block into a matrix DD to get the background, and use bilinearity to get the same scale of the image. over fitting the image in matlab in order to get smoother image, then minus the background to get the contrast enhancement image.

  18. 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.

  19. THEORY OF SECULAR CHAOS AND MERCURY'S ORBIT

    SciTech Connect

    Lithwick, Yoram; Wu Yanqin

    2011-09-20

    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 {approx}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.

  20. π-π orbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

    NASA Astrophysics Data System (ADS)

    Maciá, Enrique

    2009-09-01

    The presence of synchronized, collective twist motions of the Watson-Crick base pairs in DNA duplexes (helicoidal standing waves) can efficiently enhance the π-π orbital overlapping between nonconsecutive base pairs via a long-range, phonon-correlated tunneling effect. The resulting structural patterns are described within the framework of dynamical phyllotaxis, providing a realistic treatment which takes into account both the intrinsic three-dimensional, helicoidal geometry of DNA, and the coupling between the electronic degrees of freedom and double-helix DNA molecular dynamics at low frequencies. The main features of the resulting electronic band structures are discussed for several resonance frequencies of interest, highlighting the possible biophysical implications of the obtained results.