Science.gov

Sample records for molecular orbital diagrams

  1. 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)

  2. ISS EPS Orbital Replacement Unit Block Diagrams

    NASA Technical Reports Server (NTRS)

    Schmitz, Gregory V.

    2001-01-01

    The attached documents are being provided to Switching Power Magazine for information purposes. This magazine is writing a feature article on the International Space Station Electrical Power System, focusing on the switching power processors. These units include the DC-DC Converter Unit (DDCU), the Bi-directional Charge/Discharge Unit (BCDU), and the Sequential Shunt Unit (SSU). These diagrams are high-level schematics/block diagrams depicting the overall functionality of each unit.

  3. Basic primitives for molecular diagram sketching

    PubMed Central

    2010-01-01

    A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates for molecular structures using a bare minimum of input bandwidth. The input requirements for each primitive consist of a small number of discrete choices, which means that these primitives can be used to form the basis of a user interface which does not require an accurate pointing device. This is particularly relevant to software designed for contemporary mobile platforms. The reduction of input bandwidth is accomplished by using algorithmic methods for anticipating probable geometries during the sketching process, and by intelligent use of template grafting. The algorithms and their uses are described in detail. PMID:20923555

  4. 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)

  5. Classification of hyperbolic Dynkin diagrams, root lengths and Weyl group orbits

    NASA Astrophysics Data System (ADS)

    Carbone, Lisa; Chung, Sjuvon; Cobbs, Leigh; McRae, Robert; Nandi, Debajyoti; Naqvi, Yusra; Penta, Diego

    2010-04-01

    We give a criterion for a Dynkin diagram, equivalently a generalized Cartan matrix, to be symmetrizable. This criterion is easily checked on the Dynkin diagram. We obtain a simple proof that the maximal rank of a Dynkin diagram of compact hyperbolic type is 5, while the maximal rank of a symmetrizable Dynkin diagram of compact hyperbolic type is 4. Building on earlier classification results of Kac, Kobayashi-Morita, Li and Saçlio\\skew3\\tildeg lu, we present the 238 hyperbolic Dynkin diagrams in ranks 3-10, 142 of which are symmetrizable. For each symmetrizable hyperbolic generalized Cartan matrix, we give a symmetrization and hence the distinct lengths of real roots in the corresponding root system. For each such hyperbolic root system we determine the disjoint orbits of the action of the Weyl group on real roots. It follows that the maximal number of disjoint Weyl group orbits on real roots in a hyperbolic root system is 4.

  6. How Different Variants of Orbit Diagrams Influence Student Explanations of the Seasons

    ERIC Educational Resources Information Center

    Lee, Victor R.

    2010-01-01

    The cause of the seasons is often associated with a very particular alternative conception: That the earth's orbit around the sun is highly elongated, and the differences in distance result in variations in temperature. It has been suggested that the standard diagrams used to depict the earth's orbit may be in some way responsible for the initial…

  7. 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.

  8. 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.)

  9. Transition Metal d-Orbital Splitting Diagrams: An Updated Educational Resource for Square Planar Transition Metal Complexes

    ERIC Educational Resources Information Center

    Borgel, Jonas; Campbell, Michael G.; Ritter, Tobias

    2016-01-01

    The presentation of d-orbital splitting diagrams for square planar transition metal complexes in textbooks and educational materials is often inconsistent and therefore confusing for students. Here we provide a concise summary of the key features of orbital splitting diagrams for square planar complexes, which we propose may be used as an updated

  10. Transition Metal d-Orbital Splitting Diagrams: An Updated Educational Resource for Square Planar Transition Metal Complexes

    ERIC Educational Resources Information Center

    Bo¨rgel, Jonas; Campbell, Michael G.; Ritter, Tobias

    2016-01-01

    The presentation of d-orbital splitting diagrams for square planar transition metal complexes in textbooks and educational materials is often inconsistent and therefore confusing for students. Here we provide a concise summary of the key features of orbital splitting diagrams for square planar complexes, which we propose may be used as an updated…

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

    ERIC Educational Resources Information Center

    Orenha, Renato P.; Galembeck, Srgio 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

  12. 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…

  13. Simple orbital theory for the molecular electrician.

    PubMed

    Ernzerhof, Matthias

    2011-07-01

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

  14. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

    Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.; Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm

    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.

  15. Phase diagram of strongly attractive p-orbital fermions on optical lattices

    NASA Astrophysics Data System (ADS)

    De Silva, Theja N.

    2015-10-01

    We examine a system of doubly degenerate p-orbital polarized fermions on a two-dimensional square lattice with a strong on-site interaction. We consider the system density at the half filling limit and tackle the strong attractive interaction using a perturbation theory. We treat the four-site square plaquette interaction term generated from the directional tunneling dependence of p-orbitals using the fourth order in perturbation theory. We map the strong coupling particle Hamiltonian into an effective spin-Hamiltonian and then use a variational mean field approach and a linear spin-wave theory to study the phase diagram. Further, we discuss the experimental signatures of these phases within the context of current cold-atom experimental techniques.

  16. 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. PMID:25595914

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  18. Rotation and anisotropic molecular orbital effect in a single H2TPP molecule transistor.

    PubMed

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

    2013-12-13

    Electron transport through a single molecule is determined not only by the intrinsic properties of the molecule but also by the configuration of the molecule with respect to the lead electrodes. Here, we show how electron transport through a single H2TPP molecule is modulated by changes in the configuration. The Coulomb stability diagram of a single H2TPP molecule transistor exhibited a few different patterns in different measurement scans. Furthermore, the sample exhibited negative differential resistance, the magnitude of which changed with the pattern in the Coulomb stability diagram. Such behavior can be explained by the rotation of the molecule with anisotropic molecular orbitals in the gap electrodes induced by electrical stress. Moreover, we find that the energy separations between molecular orbitals are also affected by the rotation, confirming that the metal-molecule interface configuration renormalizes the electronic levels in the molecule. PMID:24483690

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

    PubMed

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

    2016-03-01

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

  20. 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.

  1. 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.

  2. 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. PMID:25969107

  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. Superatomic Molecular Orbitals of C60: First-Principles calculation

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    The molecular structure of buckminsterfullerene or C60 allows for highly delocalized orbitals, but they are not like a planewave, which is completely delocated. Instead they form super atomic molecular orbitals (SAMO). These SAMO are like regular atomic orbitals, but the molecule now acts as a single atom. This implies that SAMO should follow trends similar to that of regular atomic orbitals. Using density functional theory in a real grid mesh, we computed these SAMO of C60. We found that the trend in the orbitals corresponding to these eigenstates can then be compared to the valence electron orbital trends on the periodic table. This information is useful for determining the properties of C60 that are a result the SAMO, and these properties are important in the applying C60 as building blocks in the field of nanoscience.

  5. 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.

  6. Molecular orbital theoretical studies of some organic corrosion inhibitors

    SciTech Connect

    Sastri, V.S.; Perumareddi, J.R.

    1997-08-01

    Molecular orbital theoretical calculations based on the modified neglect of differential overlap (MNDO) method were performed on some substituted methyl pyridines and substituted ethane derivatives in common use as corrosion inhibitors for iron in acid media. New correlations of corrosion rates with the energy of the highest occupied molecular orbital (E{sub HOMO}), the energy gap or difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital (E{sub LUMO}-E{sub HOMO}), and Hammett`s parameter {sigma} were presented. Absolute electronegativity ({chi}) values and the fraction of electrons ({Delta}N) transferred from substituted pyridine and ethane compounds to iron in the bulk metal were calculated and correlated with corrosion rates for the first time.

  7. BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.

    PubMed

    Kim, Jae-Kwan; Cho, Youngsong; Laskowski, Roman A; Ryu, Seong Eon; Sugihara, Kokichi; Kim, Deok-Soo

    2014-09-01

    Molecular external structure is important for molecular function, with voids on the surface and interior being one of the most important features. Hence, recognition of molecular voids and accurate computation of their geometrical properties, such as volume, area and topology, are crucial, yet most popular algorithms are based on the crude use of sampling points and thus are approximations even with a significant amount of computation. In this article, we propose an analytic approach to the problem using the Voronoi diagram of atoms and the beta-complex. The correctness and efficiency of the proposed algorithm is mathematically proved and experimentally verified. The benchmark test clearly shows the superiority of BetaVoid to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the BetaVoid program which is freely available at the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr). PMID:24677176

  8. Ambiguities in the identification of giant molecular cloud complexes from longitude-velocity diagrams

    NASA Technical Reports Server (NTRS)

    Adler, David S.; Roberts, William W., Jr.

    1992-01-01

    Techniques which use longitude-velocity diagrams to identify molecular cloud complexes in the disk of the Galaxy are investigated by means of model Galactic disks generated from N-body cloud-particle simulations. A procedure similar to the method used to reduce the low-level emission in Galactic l-v diagrams is employed to isolate complexes of emission in the model l-v diagram (LVCs) from the 'background'clouds. The LVCs produced in this manner yield a size-line-width relationship with a slope of 0.58 and a mass spectrum with a slope of 1.55, consistent with Galactic observations. It is demonstrated that associations identified as LVCs are often chance superpositions of clouds spread out along the line of sight in the disk of the model system. This indicates that the l-v diagram cannot be used to unambiguously determine the location of molecular cloud complexes in the model Galactic disk. The modeling results also indicate that the existence of a size-line-width relationship is not a reliable indicator of the physical nature of cloud complexes, in particular, whether the complexes are gravitationally bound objects.

  9. A combined reaction class approach with integrated molecular orbital+molecular orbital (IMOMO) methodology: A practical tool for kinetic modeling

    SciTech Connect

    Truong, Thanh N.; Maity, Dilip K.; Truong, Thanh-Thai T.

    2000-01-01

    We present a new practical computational methodology for predicting thermal rate constants of reactions involving large molecules or a large number of elementary reactions in the same class. This methodology combines the integrated molecular orbital+molecular orbital (IMOMO) approach with our recently proposed reaction class models for tunneling. With the new methodology, we show that it is possible to significantly reduce the computational cost by several orders of magnitude while compromising the accuracy in the predicted rate constants by less than 40% over a wide range of temperatures. Another important result is that the computational cost increases only slightly as the system size increases. (c) 2000 American Institute of Physics.

  10. Coulomb-corrected molecular orbital tomography of nitrogen

    PubMed Central

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

    2016-01-01

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

  11. Coulomb-corrected molecular orbital tomography of nitrogen.

    PubMed

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

    2016-01-01

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

  12. Ground-state phase diagram of a spin-orbit-coupled bosonic superfluid in an optical lattice

    NASA Astrophysics Data System (ADS)

    Chen, Zhu; Liang, Zhaoxin

    2016-01-01

    In recent experiments, spin-orbit-coupled (SOC) bosonic gases in an optical lattice have been successfully prepared into any Bloch band [Hamner et al., Phys. Rev. Lett. 114, 070401 (2015), 10.1103/PhysRevLett.114.070401], which promises a viable contender in the competitive field of simulating gauge-related phenomena. However, the ground-state phase diagram of such systems in the superfluid regime is still lacking. Here we present a detailed study of the phase diagram in an optically trapped Bose gas with equal-weight Rashba and Dresselhaus SO coupling. We identify four different quantum phases, which include three normal phases and a mixed phase, by considering the wave vector k1, the longitudinal <σz> , and the transverse <σx> spin polarizations as three order parameters. The ground state of normal phases is a Bloch wave with a single wave vector k1, which can position in arbitrary regions in the Brillouin zone. By contrast, the ground state of the mixed phase is a superposition of two Bloch waves with opposite k1, which, remarkably, may lack periodicity even though the system's Hamiltonian is periodic. This mixed phase in the lattice setting can be seen as the counterpart of the stripe phase associated with the uniform SOC gas. Furthermore, due to the lattice-renormalized SOC, the phase diagram of the model system becomes significantly different from the uniform case when the lattice strength grows. Finally, a scheme for experimentally probing the mixed phase using Bragg spectroscopy is proposed.

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

    SciTech Connect

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

    2015-02-07

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

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

    PubMed

    Liu, Shubin; Schauer, Cynthia K

    2015-02-01

    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. PMID:25662636

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

    NASA Astrophysics Data System (ADS)

    Liu, Shubin; Schauer, Cynthia K.

    2015-02-01

    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.

  16. 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…

  17. 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

  18. 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.

  19. Hydrogen outgassing considerations for an orbiting aluminum molecular shield

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.

    1982-01-01

    A molecular shield and associated hardware made of pure aluminum is shown to have an outgassing rate sufficiently low so that operations in orbit would undergo less density contributions than that present from the upper atmospheric atomic hydrogen contribution. Measurements of the atomic hydrogen outgassing from baked-out 6061 aluminum cylindrical samples 3 mm thick are demonstrated to be less than 1/100 trillion l/sec per sq cm, comparable to that of austenitic stainless steels. Calculations of the density distribution with a hemispherical molecular shield are presented, and the elimination of porosity in the aluminum shells is recommended by means of vacuum melting.

  20. Fragment molecular orbital method: use of approximate electrostatic potential

    NASA Astrophysics Data System (ADS)

    Nakano, Tatsuya; Kaminuma, Tsuguchika; Sato, Toshiyuki; Fukuzawa, Kaori; Akiyama, Yutaka; Uebayasi, Masami; Kitaura, Kazuo

    2002-01-01

    Recently, we have proposed the fragment molecular orbital (FMO) method; an approximate MO method for calculating large molecules such as proteins. The method has been shown to reproduce ab initio total energies and geometries of molecules in good accuracy. The most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation. Numerical calculations on several polypeptides revealed that the approximations brought no significant loss of accuracy in the total energy of molecules and were of practical use.

  1. Molecular orbital analysis of the hydrogen bonded water dimer

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  2. Molecular orbital analysis of the hydrogen bonded water dimer.

    PubMed

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

    2016-01-01

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

  3. Molecular orbital analysis of the hydrogen bonded water dimer

    PubMed Central

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

    2016-01-01

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

  4. 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

  5. Monoclonal origin of localised orbital amyloidosis detected by molecular analysis.

    PubMed Central

    Pasternak, S; White, V A; Gascoyne, R D; Perry, S R; Johnson, R L; Rootman, J

    1996-01-01

    AIMS: Primary localised orbital amyloidosis is a rare disease. The purpose of this study was to describe two cases of primary orbital amyloidosis and emphasise the value of molecular analysis of immunoglobulin gene rearrangement in identifying a monoclonal population of cells responsible for the amyloid production. METHODS: Charts and biopsy specimens of each case were reviewed. Conventional light microscopy, immunohistochemistry, and polymerase chain reaction (PCR) analysis for immunoglobulin gene rearrangement were performed in both cases. RESULTS: An unusual presentation of localised primary amyloidosis with bilateral and extensive enlargement of multiple extraocular muscles was seen in case 1. The presence of amyloid deposits was confirmed by biopsy in both cases. Evidence of a monoclonal population of plasma cells was shown by immunohistochemical analysis in case 2 only. The monoclonal origin of the cells responsible for the amyloid deposition was determined by PCR analysis demonstrating immunoglobulin heavy chain gene rearrangement in both cases. CONCLUSIONS: A monoclonal population of plasma cells responsible for the amyloid deposition was present in these two cases. PCR analysis is extremely helpful in determining monoclonality, a finding that may have important therapeutic and prognostic implications. Images PMID:8976732

  6. 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.

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

    PubMed

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

    2014-08-01

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

  8. 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.

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

    SciTech Connect

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

    2012-12-28

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

  10. 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.

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

    PubMed Central

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

    2015-01-01

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

  12. 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.

  13. 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.

  14. 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.

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

    PubMed

    Ishikawa, Takeshi

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-02-01

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

  17. Visualization of Molecular Orbitals and the Related Electron Densities

    SciTech Connect

    Haranczyk, Maciej; Gutowski, Maciej S.

    2008-02-10

    When plotting different orbitals with consistent contour values, one can create illusions about the relative extension of charge distributions. We suggest that the comparison is not biased when plots reproduce the same fraction of the total charge. We have developed an algorithm and software that facilitate this type of visualization. We propose superimposing molecules and associated orbitals, and creating cross-sections by selecting a particular part of the orbital limited by pre-defined planes.

  18. Construction of Ligand Group Orbitals for Polyatomics and Transition-Metal Complexes Using an Intuitive Symmetry-Based Approach

    ERIC Educational Resources Information Center

    Johnson, Adam R.

    2013-01-01

    A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear

  19. Construction of Ligand Group Orbitals for Polyatomics and Transition-Metal Complexes Using an Intuitive Symmetry-Based Approach

    ERIC Educational Resources Information Center

    Johnson, Adam R.

    2013-01-01

    A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear…

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

    PubMed Central

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

    2013-01-01

    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. PMID:23704835

  1. 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

    2013-01-01

    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. PMID:23704835

  2. 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.

  3. 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…

  4. 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

  5. Core molecular orbital contribution to N2O isomerization as studied using theoretical electron momentum spectroscopy.

    PubMed

    Wang, F; Larkins, F P; Brunger, M J; Michalewicz, M T; Winkler, D A

    2001-01-01

    Core molecular orbital contribution to the electronic structure of N2O isomers has been studied using quantum mechanical density functional theory combined with a plane wave impulse approximation method. Momentum distributions of wave functions for inner shell molecular orbitals of the linear NNO, cyclic and linear NON isomers of N2O are calculated through the (e, 2e) differential cross sections in momentum space. This is possible because this momentum distribution is directly proportional to the modulus squared of the momentum space wave function for the molecular orbital in question. While the momentum distributions of the NNO and cyclic N2O isomers demonstrate strong atomic orbital characteristics in their core space, the outer core molecular orbitals of the linear NON isomer exhibit configuration interactions between them and the valence molecular orbitals. It is suggested that the frozen core approximation breaks down in the prediction of the electronic structure of such an isomer. Core molecular orbital contributions to the electronic structure can alter the order of total energies of the isomers and lead to incorrect conclusions of the stability among the isomers. As a result, full electron calculations should be employed in the study of N2O isomerization. PMID:11209870

  6. Molecular orbital tomography from multi-channel harmonic emission in N2

    NASA Astrophysics Data System (ADS)

    Diveki, Z.; Guichard, R.; Caillat, J.; Camper, A.; Haessler, S.; Auguste, T.; Ruchon, T.; Carré, B.; Maquet, A.; Taïeb, R.; Salières, P.

    2013-03-01

    High-order harmonic generation in aligned molecules can be used as an ultrafast probe of molecular structure and dynamics. By characterizing the emitted signal, one can retrieve information about electronic and nuclear dynamics at the attosecond timescale. In this paper, we discuss the theoretical and experimental aspects of molecular orbital tomography in N2 and investigate the influence of multi-channel ionization on the orbital imaging. By analyzing the harmonics' spectral phase as a function of the driving laser intensity, we address two distinct cases, which in principle allow the orbital reconstruction. First, the contributions from two molecular orbitals could be disentangled in the real and imaginary parts of the measured dipole, allowing to reconstruct both orbitals. Second, by decreasing the driving laser intensity, the transition from a multi-channel to a single-channel ionization regime is shown. The latter approach paves the way towards the generalization of tomography to more complex systems.

  7. Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures.

    PubMed

    Drummond, N D; Monserrat, Bartomeu; Lloyd-Williams, Jonathan H; López Ríos, P; Pickard, Chris J; Needs, R J

    2015-01-01

    Establishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases. PMID:26215251

  8. Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures

    PubMed Central

    Drummond, N. D.; Monserrat, Bartomeu; Lloyd-Williams, Jonathan H.; Ríos, P. López; Pickard, Chris J.; Needs, R. J.

    2015-01-01

    Establishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases. PMID:26215251

  9. A growth diagram for plasma-assisted molecular beam epitaxy of GaN nanocolumns on Si(111)

    SciTech Connect

    Fernandez-Garrido, S.; Grandal, J.; Calleja, E.; Sanchez-Garcia, M. A.; Lopez-Romero, D.

    2009-12-15

    The morphology of GaN samples grown by plasma-assisted molecular beam epitaxy on Si(111) was systematically studied as a function of impinging Ga/N flux ratio and growth temperature (730-850 deg. C). Two different growth regimes were identified: compact and nanocolumnar. A growth diagram was established as a function of growth parameters, exhibiting the transition between growth regimes, and showing under which growth conditions GaN cannot be grown due to thermal decomposition and Ga desorption. Present results indicate that adatoms diffusion length and the actual Ga/N ratio on the growing surface are key factors to achieve nanocolumnar growth.

  10. Molecular orbital study of resonance electron capture by 3-substituted aliphatic acids and their methyl esters

    NASA Astrophysics Data System (ADS)

    Voinov, Valeriy G.; Petrachenko, Nikolay E.; Dorofeyev, Vladimir E.; Nakamatsu, Hirohide; Mukoyama, Takeshi

    1994-10-01

    Molecular orbital calculations by the AM1 and DV-X[alpha] methods were used to study the mechanism of the formation of (M -- H)- ions of saturated and 3-substituted fatty acids and their methyl esters, produced by resonance electron capture ionization. It was found that temporary molecular negative ions are produced for all these substances through the shape resonance mechanism with electron capture into one of the lowest unoccupied molecular orbitals. The molecular negative ions thus formed dissociate into a hydrogen atom and either carboxylate anion for saturated and 3-substituted acids or carbanion in the case of their methyl esters with elimination of the H atom from C(2).

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

    NASA Astrophysics Data System (ADS)

    Bâldea, Ioan

    2014-11-01

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

  12. Effect of molecular architecture on the phase diagram of multi-arm acrylate and nematic liquid crystal mixture

    NASA Astrophysics Data System (ADS)

    Meng, Scott

    2005-03-01

    The effect of molecular architecture on the phase behavior of a binary mixture was investigated by varying the number of functional arms in one component. A new free energy expression was derived from the first principle to account for the entropic correction, when the molecular topology changes from a linear structure to a star shape. In particular, the mixtures of nematic liquid crystal and multi-arm acrylate were selected as our reference systems, owing to their importance in the fabrication of switchable photonic crystals via photolithography. Theoretical phase diagrams have been calculated based on the combination of Flory-Huggins free energy of isotropic mixing, Maier-Saupe free energy of nematic ordering, and the entropy correction term. Good accordance was found between the model predictions and the cloud point curves.

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

    NASA Astrophysics Data System (ADS)

    Lai, Wei; Guo, Chunlei

    2016-04-01

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

  14. Communication: Phase diagram of C{sub 36} by atomistic molecular dynamics and thermodynamic integration through coexistence regions

    SciTech Connect

    Abramo, M. C.; Caccamo, C. Costa, D.; Munaò, G.

    2014-09-07

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C{sub 36}. We first show that free energies obtained via thermodynamic integrations along isotherms displaying “van der Waals loops,” are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C{sub 36}, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400–1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C{sub 36} fullerite and of its liquid state, at variance with what previously experienced for C{sub 60}.

  15. A comprehensive diagram to grow InAlN alloys by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Fernandez-Garrido, S.; Gacevic, Z.; Calleja, E.

    2008-11-10

    Indium incorporation and surface morphology of InAlN layers grown on (0001) GaN by plasma-assisted molecular beam epitaxy were investigated as a function of the impinging In flux and the substrate temperature in the 450-610 deg. C range. In incorporation was found to decrease with substrate temperature due to thermal decomposition of the growing layer, while for a given temperature it increased with the impinging In flux until stoichiometry was reached at the growth front. The InN losses during growth followed an Arrhenius behavior characterized by an activation energy of 2.0 eV. A growth diagram highly instrumental to identify optimum growth conditions was established.

  16. MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.

    PubMed

    Petrek, Martin; Kosinov, Pavlna; Koca, Jaroslav; Otyepka, Michal

    2007-11-01

    We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. This algorithm has been made freely available on the Internet (http://mole.chemi.muni.cz/) and overcomes many of the shortcomings and limitations of the recently developed CAVER software. The core of our MOLE algorithm is a Dijkstra's path search algorithm, which is applied to a Voronoi mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit have demonstrated that the MOLE algorithm performs well. MOLE is thus a powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories in which analysis of a large number of snapshots is required. PMID:17997961

  17. Accurate description of phase diagram of clathrate hydrates at the molecular level

    NASA Astrophysics Data System (ADS)

    Belosludov, Rodion V.; Subbotin, Oleg S.; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki; Belosludov, Vladimir R.

    2009-12-01

    In order to accurately estimate the thermodynamic properties of hydrogen clathrate hydrates, we developed a method based on the solid solution theory of van der Waals and Platteeuw. This model allows one to take into account the influence of guest molecules on the host lattice and guest-guest interactions—especially when more than one guest molecule occupies a cage. The free energies, equations of state, and chemical potentials of hydrogen and mixed propane-hydrogen clathrate hydrates of cubic structure II with different cage fillings have been estimated using this approach. Moreover, the proposed theory has been used for construction p -T phase diagrams of hydrogen hydrate and mixed hydrogen-propane hydrates in a wide range of pressures and temperatures. For the systems with well defined interactions the calculated curves of "guest gas-hydrate-ice Ih" equilibrium agree with the available experimental data. We also believe that the present model allows one not only to calculate the hydrogen storage ability of known hydrogen hydrate but also predict this value for structures that have not yet been realized by experiment.

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

    PubMed

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

    2015-11-01

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

  19. 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.

  20. 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.

  1. Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes

    PubMed Central

    Bonifaci, Núria; Berenguer, Antoni; Díez, Javier; Reina, Oscar; Medina, Ignacio; Dopazo, Joaquín; Moreno, Víctor; Pujana, Miguel Angel

    2008-01-01

    Background Recent advances in whole-genome association studies (WGASs) for human cancer risk are beginning to provide the part lists of low-penetrance susceptibility genes. However, statistical analysis in these studies is complicated by the vast number of genetic variants examined and the weak effects observed, as a result of which constraints must be incorporated into the study design and analytical approach. In this scenario, biological attributes beyond the adjusted statistics generally receive little attention and, more importantly, the fundamental biological characteristics of low-penetrance susceptibility genes have yet to be determined. Methods We applied an integrative approach for identifying candidate low-penetrance breast cancer susceptibility genes, their characteristics and molecular networks through the analysis of diverse sources of biological evidence. Results First, examination of the distribution of Gene Ontology terms in ordered WGAS results identified asymmetrical distribution of Cell Communication and Cell Death processes linked to risk. Second, analysis of 11 different types of molecular or functional relationships in genomic and proteomic data sets defined the "omic" properties of candidate genes: i/ differential expression in tumors relative to normal tissue; ii/ somatic genomic copy number changes correlating with gene expression levels; iii/ differentially expressed across age at diagnosis; and iv/ expression changes after BRCA1 perturbation. Finally, network modeling of the effects of variants on germline gene expression showed higher connectivity than expected by chance between novel candidates and with known susceptibility genes, which supports functional relationships and provides mechanistic hypotheses of risk. Conclusion This study proposes that cell communication and cell death are major biological processes perturbed in risk of breast cancer conferred by low-penetrance variants, and defines the common omic properties, molecular interactions and possible functional effects of candidate genes and proteins. PMID:19094230

  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. PMID:26913837

  3. Facile calculation of Hückel molecular orbital eigenvalues of short (n,0) nanotubes

    NASA Astrophysics Data System (ADS)

    Dias, Jerry Ray

    2016-03-01

    A method for quickly calculating the Hückel molecular orbital eigenvalues and other properties of two series of open-ended single-walled nanotubes is given. Circumscribing generates series of related nanotubes and mirror-plane fragmentation and embedding of larger molecular graphs gives smaller subgraphs resulting in substantial simplification of eigenvalue calculations. Molecular graphs with greater than two-fold symmetry are at least doubly degenerate in about two-thirds of their Hückel molecular orbital eigenvalues and that the right-hand mirror-plane subgraphs only contains one set of these doubly degenerate eigenvalues. Recursion equations derived for the (5,0) nanotube series allow one to obtain eigensolutions for indefinitely large members.

  4. Coupled-Perturbed SCF Approach for Calculating Static Polarizabilities and Hyperpolarizabilities with Nonorthogonal Localized Molecular Orbitals.

    PubMed

    Li, Shaopeng; Hu, Linping; Peng, Liang; Yang, Weitao; Gu, Feng Long

    2015-03-10

    Coupled-perturbed self-consistent-field (CPSCF) approach has been broadly used for polarizabilities and hyperpolarizabilities computation. To extend this application to large systems, we have reformulated the CPSCF equations with nonorthogonal localized molecular orbitals (NOLMOs). NOLMOs are the most localized representation of electronic degrees of freedom. Methods based on NOLMOs are potentially ideal for investigating large systems. In atomic orbital representation, with a static external electric field added, the wave function and SCF operator of unperturbed NOLMO-SCF wave function/orbitals are expanded to different orders of perturbations. We have derived the corresponding equations up to the third order, which are significantly different from those of a conventional CPSCF method because of the release of the orthogonal restrictions on MOs. The solution to these equations has been implemented. Several chemical systems are used to verify our method. This work represents the first step toward efficient calculations of molecular response and excitation properties with NOLMOs. PMID:26579746

  5. 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.

  6. Total π-Electron Energy of Conjugated Molecules with Non-bonding Molecular Orbitals

    NASA Astrophysics Data System (ADS)

    Gutman, Ivan

    2016-02-01

    Lower and upper bounds for the total π-electron energy are obtained, which are applicable to conjugated π-electron systems with non-bonding molecular orbitals (NBMOs). These improve the earlier estimates, in which the number of NBMOs has not been taken into account.

  7. Molecular dynamics of single-particle impacts predicts phase diagrams for large scale pattern formation.

    PubMed

    Norris, Scott A; Samela, Juha; Bukonte, Laura; Backman, Marie; Djurabekova, Flyura; Nordlund, Kai; Madi, Charbel S; Brenner, Michael P; Aziz, Michael J

    2011-01-01

    Energetic particle irradiation can cause surface ultra-smoothening, self-organized nanoscale pattern formation or degradation of the structural integrity of nuclear reactor components. A fundamental understanding of the mechanisms governing the selection among these outcomes has been elusive. Here we predict the mechanism governing the transition from pattern formation to flatness using only parameter-free molecular dynamics simulations of single-ion impacts as input into a multiscale analysis, obtaining good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion: the mechanism dominating both stability and instability is the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. We discuss the potential implications for the formation of a mysterious nanoscale topography, leading to surface degradation, of tungsten plasma-facing fusion reactor walls. Consideration of impact-induced redistribution processes may lead to a new design criterion for stability under irradiation. PMID:21505432

  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. Finite-temperature orbital-free DFT molecular dynamics: Coupling PROFESS and QUANTUM ESPRESSO

    NASA Astrophysics Data System (ADS)

    Karasiev, Valentin V.; Sjostrom, Travis; Trickey, S. B.

    2014-12-01

    Implementation of orbital-free free-energy functionals in the PROFESS code and the coupling of PROFESS with the QUANTUM ESPRESSO code are described. The combination enables orbital-free DFT to drive ab initio molecular dynamics simulations on the same footing (algorithms, thermostats, convergence parameters, etc.) as for Kohn-Sham (KS) DFT. All the non-interacting free-energy functionals implemented are single-point: the local density approximation (LDA; also known as finite-T Thomas-Fermi, ftTF), the second-order gradient approximation (SGA or finite-T gradient-corrected TF), and our recently introduced finite-T generalized gradient approximations (ftGGA). Elimination of the KS orbital bottleneck via orbital-free methodology enables high-T simulations on ordinary computers, whereas those simulations would be costly or even prohibitively time-consuming for KS molecular dynamics (MD) on very high-performance computer systems. Example MD simulations on H over a temperature range 2000 K≤T≤4,000,000 K are reported, with timings on small clusters (16-128 cores) and even laptops. With respect to KS-driven calculations, the orbital-free calculations are between a few times through a few hundreds of times faster.

  10. Roundhouse Diagrams.

    ERIC Educational Resources Information Center

    Ward, Robin E.; Wandersee, James

    2000-01-01

    Students must understand key concepts through reasoning, searching out related concepts, and making connections within multiple systems to learn science. The Roundhouse diagram was developed to be a concise, holistic, graphic representation of a science topic, process, or activity. Includes sample Roundhouse diagrams, a diagram checklist, and…

  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 paper is concluded with a discussion of the assumptions and possible caveats, as well as the position of the model in the Galactic context, highlighting its relation to large-scale gas accretion, the dynamics of the bar, the x2 orbital family, and the origin of the Arches and Quintuplet clusters.

  13. 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.

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

    PubMed Central

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

    2015-01-01

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

  15. Entanglement of molecular-orientation, rotational and orbital degrees of freedom in multiphoton orientational wave packets

    NASA Astrophysics Data System (ADS)

    Mainos, C.; Dutier, G.; Grucker, J.; Perales, F.; Baudon, J.; Ducloy, M.

    2008-02-01

    Multiphoton orientational wave packets induced by short resonant polarized laser pulses in a rotationally-frozen interacting molecule contain relevant information. The entanglement of the orbital, rotational and orientational degrees of freedom shows a strong dependence on the polarization state of the absorbed photons and the space orientation of the interacting molecule and enables one to assign the orbital state of the excited molecular electron, to measure the space orientation of the interacting molecule from the orientational recurrences, to relate the measured temporal widths to the angular momentum photon state and the coherence of the laser pulse, to obtain information on the ground rotational state, or to measure the effective temperature of an isotropic molecular assembly. The space orientation of a small number of independent molecules can be distinguished from their distinct orientational dependence in the formation of the individual orientational wave packets.

  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. Nature of the outer molecular orbitals involved in redox reactions of nitroxyl radicals at electrodes

    SciTech Connect

    Pokhodenko, V.D.; Kuts, V.S.; Platonova, E.P.; Radchenko, N.F.

    1985-05-01

    It was shown by polarography, voltammetry, and EPR that nitroxyl radicals derived from piperidine and alkyl and aromatic amines can undergo reversible one-electron redox reactions at electrodes in aprotic solvents. A correlation could be established between electronic configuration and electrochemical properties of the nitroxyl radicals. It was shown that electron transfer from the electrode (reduction) in the redox reactions occurs to an electron-accepting, half-occupied ..pi..molecular orbital of the radicals, while electron transfer from the radicals to the electrode (oxidation) is accomplished from an electron-donating n-molecular orbital of the radicals. A correlation could be established between quantities ..delta..E/sub 1///sub 2/ = E /sup ox/ /sub 1///sub 2/ - E /sup red/ /sub 1///sub 2/ and the energies of n-..pi..* transitions in the radicals investigated.

  18. 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.

  19. 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.

  20. 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.

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

    PubMed

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

    2014-01-01

    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. PMID:24889209

  2. Keto-enol tautomerism in ?-tricarbonyl compounds: infrared spectroscopy, molecular mechanics and semiempirical (AM1) molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Fabian, Walter M. F.; Trinkel, Martina; Perjssy, Alexander

    1994-01-01

    A combination of experimental (infrared spectroscopy) and theoretical (molecular mechanics, semiempirical) AM1 molecular orbital calculations) methods is used to investigate the ketoenol tautomeric equilibria and the conformational preferences in the ?-tricarbonyls, 2,2-dibenzoyl- N-alkoxycarbonyl acetamides. In CCl 4 only the enol form is present, whereas in CHCl 3 both the triketo and the enol tautomers can be observed. In both solvents enolization of the benzoyl but not the amide carbonyl group occurs. E-enols are found to be more stable than their Z isomers. The AM1 method yields quite reliable tautomerization and conformational energies and is, therefore, a useful complement to experimental studies. In contrast, molecular mechanics calculations using the TRIPOS force field do not give reasonable keto-enol energy differences but are essential in generating a sufficient number of different starting conformations in highly flexible molecules for more advanced computations.

  3. Entropy Diagrams

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.

    1996-08-01

    New displays, called entropy diagrams, show graphically how entropy changes compete in physicochemical processes. Examples of entropy diagrams are given for an equilibrium vaporization, a spontaneous evaporation into a vacuum, a vapor-pressure lowering due to the presence of an involatile solute, a chemical reaction under standard-state conditions and at equilibrium, an osmotic equilibrium, and an electrochemical equilibrium in a galvanic cell. On these diagrams entropy contributions due to standard-state changes, dilutions, and energy exchanges with thermal reservoirs are shown algebraically as well as diagrammatically. Entropy diagrams are useful for illustrating entropy analyses in which all transformations of matter and energy are related to entropy effects.

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

    SciTech Connect

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

    1983-03-30

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

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

    PubMed

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

    2016-02-23

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

  6. 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.

  7. Orbit crowding of molecular gas at a bar-spiral arm transition zone in M83

    NASA Technical Reports Server (NTRS)

    Kenney, Jeffrey D. P.; Lord, Steven D.

    1991-01-01

    The southwestern bar-spiral arm transition zone in M83 is been studied in CO, H-alpha, H I, red light, and the radio continuum. A massive molecular gas complex in the heart of the transition zone is composed or two principal components which have the morphology and kinematics expected from orbit crowding, where gas on highly elliptical orbits form the bar region converges with gas on more circular orbits from the spiral arm region. Three mechanisms for the origin of the orbit crowding are investigated, and it is proposed that the crowding is due primarily to density wave streaming motions caused by the bar and spiral arms. The inner CO component is partially coincident with a region of highly polarized radio continuum emission which precedes the H-alpha spiral arm by 15-25 arcsec, indicating that it lies on or just downstream from a shock front. This suggests that the bar gas approaching the transition zone is shocked and explains the ridge of dense gas seen upstream from the spiral arm.

  8. 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. PMID:25830408

  9. Determination of outer molecular orbitals by collisional ionization experiments and comparison with Hartree-Fock, Kohn-Sham, and Dyson orbitals

    SciTech Connect

    Yamazaki, Masakazu; Horio, Takuya; Kishimoto, Naoki; Ohno, Koichi

    2007-03-15

    Although the outer shapes of molecular orbitals (MO's) are of great importance in many phenomena, they have been difficult to be probed by experiments. Here we show that metastable helium (He{sup *}) atoms can sensitively probe the outer properties of molecules and that an electron spectroscopic technique using velocity-selected He{sup *} atoms in combination with classical trajectory simulations leads to a consistent determination of MO functions and the molecular surface. MO functions composed of linear combinations of atomic orbital functions were fitted to the observed collision energy dependences of partial ionization cross sections (CEDPICS). The obtained CEDPICS MO functions were compared with conventionally available Hartree-Fock, Kohn-Sham, and Dyson orbitals.

  10. 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.

  11. 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.

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

    PubMed

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

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

    2015-05-22

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

  15. Molecular orbital calculation of the soft-hard acidity of zeolites and its catalytic implications

    SciTech Connect

    Corma, A.; Sastre, G.; Wilson, C. Zicovich ); Viruela, R. )

    1992-08-01

    The relative hardness of different compositions of model clusters of acid zeolites and the same clusters containing a metoxy group as alkylating agent were evaluated using the energy of the lowest unoccupied molecular orbital as the index. Different basis sets and pseudopotentials were used in ab initio calculations. Semiempirical MNDO-PM3 calculations were also performed. The results show that the hardness of the zeolite increases when the Si/Al ratio decreases. On the basis of Pearson's HSAB principle, the selectivity obtained during the alkylation of toluene with methanol catalyzed by acid zeolites was interpreted.

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  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. 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.

  19. 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…

  20. 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

  1. Inactivation of [Fe=Fe]-hydrogenase by O2. Thermodynamics and frontier molecular orbitals analyses

    NASA Astrophysics Data System (ADS)

    Dogaru, Daniela; Motiu, Stefan; Gogonea, Valentin

    The oxidation of H-cluster in gas phase, and in aqueous enzyme phase, has been investigated by means of quantum mechanics (QM) and combined quantum mechanics-molecular mechanics (QM/MM). Several potential reaction pathways (in the above-mentioned chemical environments) have been studied, wherein only the aqueous enzyme phase has been found to lead to an inhibited hydroxylated cluster. Specifically, the inhibitory process occurs at the distal iron (Fed) of the catalytic H-cluster (which isalso the atom involved in H2 synthesis). The processes involved in the H-cluster oxidative pathways are O2 binding, e- transfer, protonation, and H2O removal. We found that oxygen binding is nonspontaneous in gas phase, and spontaneous for aqueous enzyme phase where both Fe atoms have oxidation state II; however, it is spontaneous for the partially oxidized and reduced clusters in both phases. Hence, in the protein environment the hydroxylated H-cluster is obtained by means of completely exergonic reaction pathway starting with proton transfer. A unifying endeavor has been carried out for the purpose of understanding the thermodynamic results vis--vis several other performed electronic structural methods, such as frontier molecular orbitals (FMO), natural bond orbital partial charges (NBO), and H-cluster geometrical analysis. An interesting result of the FMO examination (for gas phase) is that an e- is transferred to LUMO? rather than to SOMO?, which is unexpected because SOMO? usually resides in a lower energy rather than LUMO? for open-shell clusters.

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

    PubMed

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

    2015-05-01

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

  3. Diagrams of isoshielding lines of C-N bonds and nitrogen and phosphorus lone pairs

    SciTech Connect

    Aminova, R.M.; Samitov, Yu.Yu.

    1986-01-01

    Diagrams of isoshielding lines in the vicinity of lone pairs of nitrogen and phosphorus atoms, as well as a C-N bond, have been calculated. The magnetic shielding constants of the protons were calculated by the gauge-invariant atomic-orbital method with the use of localized molecular orbitals and expansions of the atomic wave functions in Gaussian functions. The diagrams of the isoshielding lines have been used for the evaluation of chemical shifts in piperidine derivatives for the purpose of accounting for the experimentally observed tendencies in chemical shifts.

  4. 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.

  5. 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.

  6. Molecular geometry, conformational, vibrational spectroscopic, molecular orbital and Mulliken charge analysis of 2-acetoxybenzoic acid

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.; Srinivasan, S.

    2014-09-01

    The Fourier transform infrared (FT-IR) and FT-Raman spectra of 2-acetoxybenzoic acid (2ABA), a painkiller agent were recorded in the region 4000-450 cm-1 and 5000-50 cm-1 respectively. Hartree Fock (HF) and Density functional theory (DFT) methods have been used to determine its optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands of the title molecule. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations were done at HF and DFT/B3LYP level with 6-311++G(d,p) basis set. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) analysis. The Mulliken charges, UV-Visible spectral analysis and HOMO-LUMO energy gap have been calculated and reported. The B3LYP method of calculated parameters is a good complement with the experimental findings. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated and discussed. The electrostatic potential (ESP) contour surface and molecular electrostatic potential (MESP) of the molecule were constructed.

  7. Molecular geometry, conformational, vibrational spectroscopic, molecular orbital and Mulliken charge analysis of 2-acetoxybenzoic acid.

    PubMed

    Govindasamy, P; Gunasekaran, S; Srinivasan, S

    2014-09-15

    The Fourier transform infrared (FT-IR) and FT-Raman spectra of 2-acetoxybenzoic acid (2ABA), a painkiller agent were recorded in the region 4000-450 cm(-1) and 5000-50 cm(-1) respectively. Hartree Fock (HF) and Density functional theory (DFT) methods have been used to determine its optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands of the title molecule. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations were done at HF and DFT/B3LYP level with 6-311++G(d,p) basis set. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) analysis. The Mulliken charges, UV-Visible spectral analysis and HOMO-LUMO energy gap have been calculated and reported. The B3LYP method of calculated parameters is a good complement with the experimental findings. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated and discussed. The electrostatic potential (ESP) contour surface and molecular electrostatic potential (MESP) of the molecule were constructed. PMID:24793483

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

    EPA Science Inventory

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

  9. Orbit Functions

    NASA Astrophysics Data System (ADS)

    Klimyk, Anatoliy; Patera, Jiri

    2006-01-01

    In the paper, properties of orbit functions are reviewed and further developed. Orbit functions on the Euclidean space En are symmetrized exponential functions. The symmetrization is fulfilled by a Weyl group corresponding to a Coxeter-Dynkin diagram. Properties of such functions will be described. An orbit function is the contribution to an irreducible character of a compact semisimple Lie group G of rank n from one of its Weyl group orbits. It is shown that values of orbit functions are repeated on copies of the fundamental domain F of the affine Weyl group (determined by the initial Weyl group) in the entire Euclidean space En. Orbit functions are solutions of the corresponding Laplace equation in En, satisfying the Neumann condition on the boundary of F. Orbit functions determine a symmetrized Fourier transform and a transform on a finite set of points.

  10. 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.

  11. 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.

  12. The convergence of CI calculations for atomic and molecular electronic bound states in a basis of floating Gauss orbitals

    NASA Astrophysics Data System (ADS)

    Klahn, Bruno

    1985-12-01

    The energy convergence of CI calculations for atomic and molecular electronic bound states in a basis set of floating orbitals, which may depend on the number of basis functions used in a calculation, is investigated. Applying a generalization of the Müntz-Szász theorem, a condition for the choice of floating orbital exponents with respect to Gaussians results, which guarantees convergence of energies and wave functions to the right limits in any state, as the number of basis orbitals increases to infinity. This condition is discussed for the special choice of even-tempered Gaussians.

  13. On the room-temperature phase diagram of high pressure hydrogen: An ab initio molecular dynamics perspective and a diffusion Monte Carlo study

    SciTech Connect

    Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

    2014-07-14

    The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhou, Xin

    1998-07-01

    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 s orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5 s 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 c 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 ARPEFS, up to third order multiple scattering is needed to describe fully both the c 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.

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

    PubMed

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

    2011-03-01

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

  17. 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.

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

    PubMed Central

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

    2013-01-01

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

  19. Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities.

    PubMed

    Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

    2014-02-01

    In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory. PMID:24511917

  20. Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities

    NASA Astrophysics Data System (ADS)

    Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

    2014-02-01

    In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory.

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

    PubMed

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

    2016-03-01

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

  2. 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.

  3. 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.

  4. 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.

  5. Fragment molecular orbital calculations on red fluorescent protein (DsRed)

    NASA Astrophysics Data System (ADS)

    Mochizuki, Yuji; Nakano, Tatsuya; Amari, Shinji; Ishikawa, Takeshi; Tanaka, Kiyoshi; Sakurai, Minoru; Tanaka, Shigenori

    2007-01-01

    We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G ∗ level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV.

  6. 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.

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

    PubMed Central

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

    2010-01-01

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

  8. 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.

  9. Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis.

    PubMed

    Tagami, Uno; Takahashi, Kazutoshi; Igarashi, Shunsuke; Ejima, Chieko; Yoshida, Tomomi; Takeshita, Sen; Miyanaga, Wataru; Sugiki, Masayuki; Tokumasu, Munetaka; Hatanaka, Toshihiro; Kashiwagi, Tatsuki; Ishikawa, Kohki; Miyano, Hiroshi; Mizukoshi, Toshimi

    2016-04-14

    X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the K i value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors. PMID:27096055

  10. Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method.

    PubMed

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

    2015-07-14

    The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed. PMID:26575742

  11. Spectroscopic studies and molecular orbital calculations on the charge transfer reaction between DDQ and 2-aminopyridine

    NASA Astrophysics Data System (ADS)

    Al-Ahmary, Khairia M.; El-Kholy, Moustafa M.; Al-Solmy, Iman A.; Habeeb, Moustafa M.

    2013-06-01

    Charge transfer complex formation between 2-aminopyridine (donor, 2AP) with 2,3-dichloro-5,6-dicyano-p-benzoquinone (acceptor, DDQ) has been studied spectrophotometrically in acetonitrile (CH3CN). The newly formed CT-complex has reddish brown color and is characterized by the appearance of new absorption bands in the 375-650 nm regions where acceptor and donor do not have any absorption. Maximum and constant absorbance of the complex was obtained after 10 min at 20 °C with 1 mL 5 × 10-3 M DDQ in CH3CN. Based on photometric titration method, the stoichiometry of the formed CT-complex was found to be 1:1 [(2AP)(DDQ)]. Minimum-maximum absorbances method has been applied to estimate the formation constant of the complex where it recorded large value confirming its high stability. Molecular orbital calculations utilizing GAMESS computations were carried out in order to record changes in the electronic structure and molecular geometry of the formed CT-complex. In addition, the infrared vibrational frequencies of the complex were computed and compared with experimental results.

  12. 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

  13. Molecular Binding in Post-Kohn-Sham Orbital-Free DFT.

    PubMed

    Borgoo, Alex; Green, James A; Tozer, David J

    2014-12-01

    Molecular binding in post-Kohn-Sham orbital-free DFT is investigated, using noninteracting kinetic energy functionals that satisfy the uniform electron gas condition and which are inhomogeneous under density scaling. A parameter is introduced that quantifies binding, and a series of functionals are determined from fits to near-exact effective homogeneities and/or Kohn-Sham noninteracting kinetic energies. These are then used to investigate the relationship between binding and the accuracy of the effective homogeneity and noninteracting kinetic energy at the equilibrium geometry. For a series of 11 molecules, the binding broadly improves as the effective homogeneity improves, although the extent to which it improves is dependent on the accuracy of the noninteracting kinetic energy; optimal binding appears to require both to be accurate simultaneously. The use of a Thomas-Fermi-von Weizsäcker form, augmented with a second gradient correction, goes some way toward achieving this, exhibiting molecular binding on average. The findings are discussed in terms of the noninteracting kinetic potential and the Hellmann-Feynman theorem. The extent to which the functionals can reproduce the system-dependence of the near-exact effective homogeneity is quantified, and potential energy curves are presented for selected molecules. The study provides impetus for including density scaling homogeneity considerations in the design of noninteracting kinetic energy functionals. PMID:26583217

  14. 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

    2015-05-01

    Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 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. PMID:25703364

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  16. 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.

  17. Introduction to Computational Chemistry: Teaching Huckel 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 Schrdinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hckel molecular orbital theory for p bonding in molecules. We present details and results of

  18. 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…

  19. Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes – a new strategy for OLED materials

    PubMed Central

    Ewen, Pascal R; Sanning, Jan; Koch, Tobias; Doltsinis, Nikos L

    2014-01-01

    Summary The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM) and spectroscopy (STS) are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters) with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II) complexes adsorbed on Au(111). The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices. PMID:25551053

  20. Valence photoelectron spectroscopy of N2 and CO: Recoil-induced rotational excitation, relative intensities, and atomic orbital composition of molecular orbitals

    NASA Astrophysics Data System (ADS)

    Thomas, T. D.; Kukk, E.; Ouchi, T.; Yamada, A.; Fukuzawa, H.; Ueda, K.; Püttner, R.; Higuchi, I.; Tamenori, Y.; Asahina, T.; Kuze, N.; Kato, H.; Hoshino, M.; Tanaka, H.; Lindblad, A.; Sæthre, L. J.

    2010-11-01

    Recoil-induced rotational excitation accompanying photoionization has been measured for the X, A, and B states of N2+ and CO+ over a range of photon energies from 60 to 900 eV. The mean recoil excitation increases linearly with the kinetic energy of the photoelectron, with slopes ranging from 0.73×10-5 to 1.40×10-5. These slopes are generally (but not completely) in accord with a simple model that treats the electrons as if they were emitted from isolated atoms. This treatment takes into account the atom from which the electron is emitted, the molecular-frame angular distribution of the electron, and the dependence of the photoelectron cross section on photon energy, on atomic identity, and on the type of atomic orbital from which the electron is ejected. These measurements thus provide a tool for investigating the atomic orbital composition of the molecular orbitals. Additional insight into this composition is obtained from the relative intensities of the various photolines in the spectrum and their variation with photon energy. Although there are some discrepancies between the predictions of the model and the observations, many of these can be understood qualitatively from a comparison of atomic and molecular wavefunctions. A quantum-mechanical treatment of recoil-induced excitation predicts an oscillatory variation with photon energy of the excitation. However, the predicted oscillations are small compared with the uncertainties in the data, and, as a result, the currently available results cannot provide confirmation of the quantum-mechanical theory.

  1. Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

    ERIC Educational Resources Information Center

    Halkides, Christopher J.

    2013-01-01

    In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This

  2. Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

    ERIC Educational Resources Information Center

    Halkides, Christopher J.

    2013-01-01

    In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This…

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  4. 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.

  5. Stable conformation of full-length amyloid-β (1-42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

    NASA Astrophysics Data System (ADS)

    Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki

    2013-07-01

    Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations of solvated Aβ(1-42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1-42) contributing to the stabilization of the monomer are highlighted.

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

    PubMed

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

    2014-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Fedorov, Dmitri G.; Kitaura, Kazuo

    2004-08-01

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

  8. Beyond frontier molecular orbital theory: a systematic electron transfer model (ETM) for polar bimolecular organic reactions.

    PubMed

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

    Polar bimolecular reactions often begin as charge-transfer complexes and may proceed with a high degree of electron transfer character. Frontier molecular orbital (FMO) theory is predicated in part on this concept. We have developed an electron transfer model (ETM) in which we systematically transfer one electron between reactants and then use density functional methods to model the resultant radical or radical ion intermediates. Sites of higher reactivity are revealed by a composite spin density map (SDM) of odd electron character on the electron density surface, assuming that a new two-electron bond would occur preferentially at these sites. ETM correctly predicts regio- and stereoselectivity for a broad array of reactions, including Diels-Alder, dipolar and ketene cycloadditions, Birch reduction, many types of nucleophilic additions, and electrophilic addition to aromatic rings and polyenes. Conformational analysis of radical ions is often necessary to predict reaction stereochemistry. The electronic and geometric changes due to one-electron oxidation or reduction parallel the reaction coordinate for electrophilic or nucleophilic addition, respectively. The effect is more dramatic for one-electron reduction. PMID:23057698

  9. TES buffer-induced phase separation of aqueous solutions of several water-miscible organic solvents at 298.15 K: Phase diagrams and molecular dynamic simulations

    NASA Astrophysics Data System (ADS)

    Taha, Mohamed; Lee, Ming-Jer

    2013-06-01

    Water and the organic solvents tetrahydrofuran, 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone are completely miscible in all proportions at room temperature. Here, we present new buffering-out phase separation systems that the above mentioned organic aqueous solutions can be induced to form two liquid phases in the presence of a biological buffer 2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES). The lower liquid phase is rich in water and buffer, and the upper phase is organic rich. This observation has both practical and mechanistic interests. The phase diagrams of these systems were constructed by experimental measurements at ambient conditions. Molecular dynamic (MD) simulations were performed for TES + water + THF system to understand the interactions between TES, water, and organic solvent at molecular level. Several composition-sets for this system, beyond and inside the liquid-liquid phase-splitting region, have been simulated. Interestingly, the MD simulation for compositions inside the phase separation region showed that THF molecules are forced out from the water network to start forming a new liquid phase. The hydrogen-bonds, hydrogen-bonds lifetimes, hydrogen-bond energies, radial distribution functions, coordination numbers, the electrostatic interactions, and the van der Waals interactions between the different pairs have been calculated. Additionally, MD simulations for TES + water + tert-butanol/acetonitrile/acetone phase separation systems were simulated. The results from MD simulations provide an explanation for the buffering-out phenomena observed in [TES + water + organic solvent] systems by a mechanism controlled by the competitive interactions of the buffer and the organic solvent with water. The molecular mechanism reported here is helpful for designing new benign separation materials.

  10. TES buffer-induced phase separation of aqueous solutions of several water-miscible organic solvents at 298.15 K: phase diagrams and molecular dynamic simulations.

    PubMed

    Taha, Mohamed; Lee, Ming-Jer

    2013-06-28

    Water and the organic solvents tetrahydrofuran, 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone are completely miscible in all proportions at room temperature. Here, we present new buffering-out phase separation systems that the above mentioned organic aqueous solutions can be induced to form two liquid phases in the presence of a biological buffer 2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES). The lower liquid phase is rich in water and buffer, and the upper phase is organic rich. This observation has both practical and mechanistic interests. The phase diagrams of these systems were constructed by experimental measurements at ambient conditions. Molecular dynamic (MD) simulations were performed for TES + water + THF system to understand the interactions between TES, water, and organic solvent at molecular level. Several composition-sets for this system, beyond and inside the liquid-liquid phase-splitting region, have been simulated. Interestingly, the MD simulation for compositions inside the phase separation region showed that THF molecules are forced out from the water network to start forming a new liquid phase. The hydrogen-bonds, hydrogen-bonds lifetimes, hydrogen-bond energies, radial distribution functions, coordination numbers, the electrostatic interactions, and the van der Waals interactions between the different pairs have been calculated. Additionally, MD simulations for TES + water + tert-butanol∕acetonitrile∕acetone phase separation systems were simulated. The results from MD simulations provide an explanation for the buffering-out phenomena observed in [TES + water + organic solvent] systems by a mechanism controlled by the competitive interactions of the buffer and the organic solvent with water. The molecular mechanism reported here is helpful for designing new benign separation materials. PMID:23822250

  11. 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.

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

    PubMed

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

    2016-04-15

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

  13. Kinetic effects on double hysteresis in spin crossover molecular magnets analyzed with first order reversal curve diagram technique

    SciTech Connect

    Stan, Raluca-Maria; Gaina, Roxana; Enachescu, Cristian E-mail: radu.tanasa@uaic.ro; Stancu, Alexandru; Tanasa, Radu E-mail: radu.tanasa@uaic.ro; Bronisz, Robert

    2015-05-07

    In this paper, we analyze two types of hysteresis in spin crossover molecular magnets compounds in the framework of the First Order Reversal Curve (FORC) method. The switching between the two stable states in these compounds is accompanied by hysteresis phenomena if the intermolecular interactions are higher than a threshold. We have measured the static thermal hysteresis (TH) and the kinetic light induced thermal hysteresis (LITH) major loops and FORCs for the polycrystalline Fe(II) spin crossover compound [Fe{sub 1−x}Zn{sub x}(bbtr){sub 3}](ClO{sub 4}){sub 2} (bbtr = 1,4-di(1,2,3-triazol-1-yl)butane), either in a pure state (x = 0) or doped with Zn ions (x = 0.33) considering different sweeping rates. Here, we use this method not only to infer the domains distribution but also to disentangle between kinetic and static components of the LITH and to estimate the changes in the intermolecular interactions introduced by dopants. We also determined the qualitative relationship between FORC distributions measured for TH and LITH.

  14. Kinetic effects on double hysteresis in spin crossover molecular magnets analyzed with first order reversal curve diagram technique

    NASA Astrophysics Data System (ADS)

    Stan, Raluca-Maria; Gaina, Roxana; Enachescu, Cristian; Tanasa, Radu; Stancu, Alexandru; Bronisz, Robert

    2015-05-01

    In this paper, we analyze two types of hysteresis in spin crossover molecular magnets compounds in the framework of the First Order Reversal Curve (FORC) method. The switching between the two stable states in these compounds is accompanied by hysteresis phenomena if the intermolecular interactions are higher than a threshold. We have measured the static thermal hysteresis (TH) and the kinetic light induced thermal hysteresis (LITH) major loops and FORCs for the polycrystalline Fe(II) spin crossover compound [Fe1-xZnx(bbtr)3](ClO4)2 (bbtr = 1,4-di(1,2,3-triazol-1-yl)butane), either in a pure state (x = 0) or doped with Zn ions (x = 0.33) considering different sweeping rates. Here, we use this method not only to infer the domains distribution but also to disentangle between kinetic and static components of the LITH and to estimate the changes in the intermolecular interactions introduced by dopants. We also determined the qualitative relationship between FORC distributions measured for TH and LITH.

  15. 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…

  16. 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

  17. 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.

  18. Molecular high-order harmonic generation with more than one active orbital: Quantum interference effects

    SciTech Connect

    Figueira de Morisson Faria, C.; Augstein, B. B.

    2010-04-15

    We investigate quantum interference effects in high-order harmonic generation in N{sub 2} and N{sub 2}{sup +} beyond the single-active-orbital approximation, with particular emphasis on the role of {sigma} and {pi} orbitals in the overall spectra. In the former case, we consider a simplified multielectron wave function which incorporates the 3{sigma}{sub g} and 1{pi}{sub u} orbitals, and, in the latter, we assume that the optically active electron is in a coherent superposition of the 3{sigma}{sub g} and 1{pi}{sub g}{sup *} one-electron states. If the orbitals are energetically close, such as the 3{sigma}{sub g} and the 1{pi}{sub u} orbitals of N{sub 2}, we show that the quantum interference patterns observed in the high-order harmonic spectra are predominantly determined by the 3{sigma}{sub g} orbital. If, on the other hand, there is a significant difference in their binding energies, such as for the 3{sigma}{sub g} and the 1{pi}{sub g}{sup *} orbitals of N{sub 2}{sup +}, the most loosely bound orbital will determine the shape of the spectra. Due, however, to the different cutoffs encountered, the more deeply bound orbital will leave an imprint on the high-energy harmonics. This holds both for the situation in which the dynamics of the electron is restricted to the plane p{sub x}p{sub z} and for the full three-dimensional case, if the azimuthal angle is integrated over and the degeneracy of the {pi} orbitals is taken into account.

  19. Growth diagram of N-face GaN (0001{sup ¯}) grown at high rate by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Okumura, Hironori McSkimming, Brian M.; Speck, James S.; Huault, Thomas; Chaix, Catherine

    2014-01-06

    N-face GaN was grown on free-standing GaN (0001{sup ¯}) substrates at a growth rate of 1.5 μm/h using plasma-assisted molecular beam epitaxy. Difference in growth rate between (0001{sup ¯}) and (0001) oriented GaN depends on nitrogen plasma power, and the (0001{sup ¯}) oriented GaN had only 70% of the growth rate of the (0001) oriented GaN at 300 W. Unintentional impurity concentrations of silicon, carbon, and oxygen were 2 × 10{sup 15}, 2 × 10{sup 16}, and 7 × 10{sup 16} cm{sup −3}, respectively. A growth diagram was constructed that shows the dependence of the growth modes on the difference in the Ga and active nitrogen flux, Φ{sub Ga} − Φ{sub N*}, and the growth temperature. At high Φ{sub Ga} − Φ{sub N*} (Φ{sub Ga} ≫ Φ{sub N*}), two-dimensional (step-flow and layer-by-layer) growth modes were realized. High growth temperature (780 °C) expanded the growth window of the two-dimensional growth modes, achieving a surface with rms roughness of 0.48 nm without Ga droplets.

  20. 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-Baladrn, M. A.; Martn-Pintado, J.; Mauersberger, R.; Martn, 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

  1. Intercalation of ethidium and analogues with nucleic acids: a molecular orbital study.

    PubMed

    Patterson, S E; Coxon, J M; Strekowski, L

    1997-02-01

    Semiempirical calculations suggest that the intercalation complexes of phenanthridinium cations 1-4 with G-C/C-G and 1 with A-U/U-A are stabilized by frontier orbital interactions between the LUMO of the intercalator and the HOMOs of the adjacent purine bases. The charge on the ring nitrogen of 1-4 appears to be necessary for the orbital interactions, lowering the LUMO, facilitating mixing of this orbital with the HOMOs of the adjacent purine bases to give an extended HOMO stabilizing the complex and resulting in the bathochromic shift in the electron absorption spectrum. Noncationic phenanthridine 5 shows no frontier orbital interactions in the forced intercalation complex with G-C/C-G. The results of the calculations parallel experimental T(m) values. PMID:9061192

  2. Ultrasonic relaxation measurements in aqueous solution and molecular orbital calculation on imipramine.

    PubMed

    Nishikawa, Sadakatsu

    2013-02-14

    Ultrasonic absorption coefficients have been measured in aqueous solution of imipramine {3-(10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine} in the frequency range of 0.8-220 MHz at 25 °C. The frequency dependences of the observed absorption was characterized by a Debye-type relaxational equation with two relaxation frequencies, although only one relaxation had been observed in aqueous solutions of the related molecule amitriptyline. Both of the relaxation frequencies in imipramine solutions were found to be independent of the solute concentration and the amplitudes of the relaxational absorptions increase linearly with increasing solute concentration. It was therefore concluded that these two relaxations are associated with unimolecular reactions, such as a structural change due to rotational motions of the bond in the specified group in the imipramine molecule. To analyze quantitatively the source of the relaxations, semiempirical molecular orbital methods have been applied to determine the standard enthalpy of formation of the imipramine molecule at various dihedral angles around the bonds in the alkylamine side chain. According to the results, only one rotational motion of carbon-carbon bond in the side chain was found to be appropriate and the three minima of the standard enthalpy of formation was obtained as a function of the rotational angle. At the three minimum positions, the values of the standard enthalpy of formation are almost the same. With the assumptions (a) that rotational motion is not accompanied by a volume change of the reaction and (b) that the standard free energy change is close to the difference in the values between the standard enthalpies of formation, the equilibrium constants for the rotational isomerization have been calculated to be near unity. Hence, the forward and backward rate constants of the isomerization reactions are nearly the same. If one assumes that there are two kinds of rotational motions in one bond of the molecule, one proceeds with a rate constant on the order of 10(8) s(-1), whereas the other with a rate constant on the order of 10(6) s(-1). The faster and slower processes are also distinguished by the height of the standard enthalpy of formation. PMID:23339570

  3. 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. PMID:25273421

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

    SciTech Connect

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

    2014-09-28

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

  5. 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.

  6. Calculation of phase diagrams for the FeCl2, PbCl2, and ZnCl2 binary systems by using molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Seo, Won-Gap; Matsuura, Hiroyuki; Tsukihashi, Fumitaka

    2006-04-01

    Recently, molecular dynamics (MD) simulation has been widely employed as a very useful method for the calculation of various physicochemical properties in the molten slags and fluxes. In this study, MD simulation has been applied to calculate the structural, transport, and thermodynamic properties for the FeCl2, PbCl2, and ZnCl2 systems using the Born—Mayer—Huggins type pairwise potential with partial ionic charges. The interatomic potential parameters were determined by fitting the physicochemical properties of iron chloride, lead chloride, and zinc chloride systems with experimentally measured results. The calculated structural, transport, and thermodynamic properties of pure FeCl2, PbCl2, and ZnCl2 showed the same tendency with observed results. Especially, the calculated structural properties of molten ZnCl2 and FeCl2 show the possibility of formation of polymeric network structures based on the ionic complexes of ZnCl{4/2-}, ZnCl{3/-}, FeCl{4/2-}, and FeCl{3/-}, and these calculations have successfully reproduced the measured results. The enthalpy, entropy, and Gibbs energy of mixing for the PbCl2-ZnCl2, FeCl2-PbCl2, and FeCl2-ZnCl2 systems were calculated based on the thermodynamic and structural parameters of each binary system obtained from MD simulation. The phase diagrams of the PbCl2-ZnCl2, FeCl2-PbCl2, and FeCl2-ZnCl2 systems estimated by using the calculated Gibbs energy of mixing reproduced the experimentally measured ones reasonably well.

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

    NASA Astrophysics Data System (ADS)

    Sand, Andrew M.; Mazziotti, David A.

    2013-06-01

    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)], 10.1103/PhysRevLett.101.253002, 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.

  8. 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. PMID:23822222

  9. Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method.

    PubMed

    Fletcher, Graham D; Fedorov, Dmitri G; Pruitt, Spencer R; Windus, Theresa L; Gordon, Mark S

    2012-01-10

    Benchmark timings are presented for the fragment molecular orbital method on a Blue Gene/P computer. Algorithmic modifications that lead to enhanced performance on the Blue Gene/P architecture include strategies for the storage of fragment density matrices by process subgroups in the global address space. The computation of the atomic forces for a system with more than 3000 atoms and 44 000 basis functions, using second order perturbation theory and an augmented and polarized double-ζ basis set, takes ∼7 min on 131 072 cores. PMID:26592869

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

    ERIC Educational Resources Information Center

    Gillespie, Ronald J.; And Others

    1996-01-01

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

  11. 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.

  12. Analytic energy gradient for second-order Mller-Plesset perturbation theory based on the fragment molecular orbital method.

    PubMed

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

    2011-07-28

    The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order Mller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet. PMID:21806093

  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. PMID:26623658

  14. A Modified ELISA Accurately Measures Secretion of High Molecular Weight Hyaluronan (HA) by Graves' Disease Orbital Cells

    PubMed Central

    Krieger, Christine C.

    2014-01-01

    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. PMID:24302624

  15. 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.

  16. Direct observation of collective modes coupled to molecular orbitaldriven charge transfer

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. 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. PMID:26642258

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

    SciTech Connect

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

    2008-05-20

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

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

    PubMed

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

    2016-04-28

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

  20. Caution: Venn Diagrams Ahead!

    ERIC Educational Resources Information Center

    Kimmins, Dovie L.; Winters, J. Jeremy

    2015-01-01

    Two perspectives of the term "Venn diagram" reflect the typical differences in the uses of Venn diagrams in the subject areas of mathematics and language arts. These differences are subtle; nevertheless, they can potentially be confusing. In language arts, the circles in a Venn diagram typically represent things that can be compared and…

  1. 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.

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

    SciTech Connect

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

    2010-06-11

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

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

    NASA Astrophysics Data System (ADS)

    Park, Young Ran; Kim, Hyeong Jin; Im, Sungjin; Seo, Sunae; Shin, Koo; Choi, Won Kook; Hong, Young Joon

    2016-01-01

    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.

  4. Proposed Alteration of Images of Molecular Orbitals Obtained Using a Scanning Tunneling Microscope as a Probe of Electron Correlation

    NASA Astrophysics Data System (ADS)

    Toroz, Dimitrios; Rontani, Massimo; Corni, Stefano

    2013-01-01

    Scanning tunneling spectroscopy (STS) allows us to image single molecules decoupled from the supporting substrate. The obtained images are routinely interpreted as the square moduli of molecular orbitals, dressed by the mean-field electron-electron interaction. Here we demonstrate that the effect of electron correlation beyond the mean field qualitatively alters the uncorrelated STS images. Our evidence is based on the ab initio many-body calculation of STS images of planar molecules with metal centers. We find that many-body correlations alter significantly the image spectral weight close to the metal center of the molecules. This change is large enough to be accessed experimentally, surviving to molecule-substrate interactions.

  5. 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.

  6. ESR g Factors of Isolated (TMTSF)+ and (TMTSF)2ClO4 Single Crystals: Comparison with Molecular Orbital Calculation

    NASA Astrophysics Data System (ADS)

    Kinoshita, Nobumori; Tokumoto, Madoka; Anzai, Hiroyuki; Ishiguro, Takehiko; Saito, Gunzi; Yamabe, Tokio; Teramae, Hiroyuki

    1984-04-01

    Measurements and comparisons were performed at 4.2 K on the ESR g tensor both of a single crystal of bis-(tetramethyltetraselenafulvalenium) perchlorate, (TMTSF)2ClO4, and its acetone solution in which cations exist in the form of TMTSF+. The results showed that there was no wide difference between the g anisotropy of the single crystal and solution. This fact suggests that the electronic states of (TMTSF)+ can be used as a substitute for (TMTSF)2ClO4 as long as g factors are concerned. The g factors, calculated from molecular orbitals (MO) of a TSF+ cation which were computed using semi-empirical SCF method, were then fitted to those of the single crystal, and π-electron distribution was decided from the highest occupied MO.

  7. Multicomponent Molecular Orbital-Climbing Image-Nudged Elastic Band Method to Analyze Chemical Reactions Including Nuclear Quantum Effect.

    PubMed

    Udagawa, Taro; Suzuki, Kimichi; Tachikawa, Masanori

    2015-10-26

    To analyze the H/D isotope effects on hydrogen transfer reactions in XHCHCHCHY↔XCHCHCHYH (X, Y=O, NH, or CH2 ) including the nuclear quantum effect of proton and deuteron, we propose a multicomponent molecular orbital-climbing image-nudged elastic band (MC_MO-CI-NEB) method. We obtain not only transition state structures but also minimum-energy paths (MEPs) on the MC_MO effective potential energy surface by using MC_MO-CI-NEB method. We find that nuclear quantum effect affects not only stationary-point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate the importance of including nuclear quantum effects for H/D isotope effect on rate constants (kH /kD ). PMID:26295285

  8. 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.

  9. 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).

  10. 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. PMID:26213179

  11. 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.

  12. 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. PMID:26328835

  13. Phase Equilibria Diagrams Database

    National Institute of Standards and Technology Data Gateway

    SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase)   The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  15. Ionization Potential, Electron Affinity, Electronegativity, Hardness, and Electron Excitation Energy: Molecular Properties from Density Functional Theory Orbital Energies

    SciTech Connect

    Zhan, Chang-Guo; Nichols, Jeffrey A.; Dixon, David A.

    2003-05-22

    Representative atomic and molecular systems, including various inorganic and organic molecules with covalent and ionic bonds, have been studied by using density functional theory. The calculations were done with the commonly used exchange-correlation functional B3LYP followed by a comprehensive analysis of the calculated highest-occupied and lowest-unoccupied Kohn-Sham orbital (HOMO and LUMO) energies. The basis set dependence of the DFT results shows that the economical 6-31+G* basis set is generally sufficient for calculating the HOMO and LUMO energies (if the calculated LUMO energies are negative) for use in correlating with molecular properties. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (c), hardness (h), and first electron excitation energy (t) are all in good agreement with the available experimental data. A generally applicable linear correlation relationship exists between the calculated HOMO energies and the experimental/calculated IP's. We have also found satisfactory linear correlation relationships between the calculated LUMO energies and experimental/calculated EA's (for the bound anionic states), between the calculated average HOMO/LUMO energies and c values, between the calculated HOMO-LUMO energy gaps and h values, and between the calculated HOMO-LUMO energy gaps and experimental/calculated first excitation energies. By using these linear correlation relationships, the calculated HOMO and LUMO energies can be employed to semi-quantitatively estimate ionization potential, electron affinity, electronegativity, hardness, and first excitation energy.

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

    PubMed

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

    2016-05-12

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

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

    PubMed

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

    2016-03-15

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

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

    PubMed

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

    2016-04-26

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

  19. 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

  20. 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

    2014-05-01

    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. PMID:24556133

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

    NASA Astrophysics Data System (ADS)

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

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

  2. 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. PMID:25338873

  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. Further evaluation of COMPACT, the molecular orbital approach for the prospective safety evaluation of chemicals.

    PubMed

    Lewis, D F; Ioannides, C; Parke, D V

    1998-01-13

    The molecular dimensions and electronic structures of the first group of 100 US NCI/NTP miscellaneous chemicals, evaluated for potential carcinogenicity by computer-optimized molecular parametric analysis for chemical toxicity (COMPACT) have been re-determined. Using improved criteria for cytochrome P450 (CYP) substrate specificity, re-defined for CYP1 as having a COMPACT radius [square root of (deltaE - 9.5)2 + (a/d(2) - 7.8)2] of < 6.5, and for CYP2E as having a collision diameter of 6.5 angstroms or less and deltaE < 15.5, the likely substrates of CYP1 and CYP2E, which are regarded as potential carcinogens, have been identified. In addition, log P values have been taken into account; those chemicals with log P < 0 are non-lipophilic substrates unlikely to reach the activating cytochrome enzymes, and have been regarded as non-carcinogens. The second group of 100 US NCI/NTP chemicals have also now been categorized by COMPACT into CYP1 and CYP2E substrates, and their potential carcinogenicities evaluated. Of the 203 chemicals in the 2 groups, those positive in the rodent two-species life-span carcinogenicity study (rodent assay) were 53%, those positive in the Ames test (mutagenicity) were 48%, and those positive in the COMPACT programme (carcinogenicity, mutagenicity, cytotoxicity) were 54%. Concordance between the COMPACT prediction of carcinogenicity/cytotoxicity and rodent two species life-span carcinogenicity data for the 203 chemicals is 69%, and correlation of COMPACT with Ames test data is 61%. The sensitivity of COMPACT for predicting rodent carcinogenicity is 72%, whereas the sensitivity of the Ames test for predicting carcinogenicity for the 203 chemicals was only 57%. The degree (severity) of rodent carcinogenicity also showed correlation with the COMPACT predictive evaluations of the chemicals. PMID:9508363

  6. 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

    2015-02-01

    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). PMID:25459510

  7. 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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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. 13C and 1H NMR spectra were recorded and 13C and 1H 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).

  8. 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…

  9. 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

  10. 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.

  11. 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 estimate unknown σ or σ*-values.  . PMID:26121114

  12. 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 , reduces computational costs, while maintaining accuracy in the evaluation of binding energy. PMID:26400829

  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.

    PubMed

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

    2015-07-01

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

  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

    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.

  15. Integrating Diagrams and Text.

    ERIC Educational Resources Information Center

    Wright, Patricia; And Others

    1990-01-01

    Focuses on diagrams giving overviews of complex technical information as facilitators for adult subjects using computers to learn about the business activities of a fictitious family. Finds that features of the author's control over the reader's encounter with the diagram influences whether readers will interrupt their reading to study the…

  16. Hertzsprung-Russell Diagram

    NASA Astrophysics Data System (ADS)

    Chiosi, C.; Murdin, P.

    2000-11-01

    The Hertzsprung-Russell diagram (HR-diagram), pioneered independently by EJNAR HERTZSPRUNG and HENRY NORRIS RUSSELL, is a plot of the star luminosity versus the surface temperature. It stems from the basic relation for an object emitting thermal radiation as a black body: ...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

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

  3. 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 (?) and polarizability (?), anisotropy polarizability (??) and hyperpolarizability (?) of the molecule have been reported. PMID:24853994

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

    NASA Astrophysics Data System (ADS)

    Mahalakshmi, G.; Balachandran, V.

    2014-10-01

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

  5. [Identification of meridian-acupoint diagrams and meridian diagrams].

    PubMed

    Shen, Wei-hong

    2008-08-01

    In acu-moxibustion literature, there are two kinds of diagrams, meridian-acupoint diagrams and meridian diagrams. Because they are very similar in outline, and people now have seldom seen the typical ancient meridian diagrams, meridian-acupoint diagrams have been being incorrectly considered to be the meridian diagrams for a long time. It results in confusion in acu-moxibustion academia. The present paper stresses its importance in academic research and introduces some methods for identifying them correctly. The key points for identification of meridian-acupoint diagrams and meridian diagrams are: the legend of diagrams and the drawing style of the ancient charts. In addition, the author makes a detailed explanation about some acu-moxibustion charts which are easily confused. In order to distinguish meridian-acupoint diagrams and meridian diagrams correctly, he or she shoulnd understand the diagrams' intrinsic information as much as possible and make a comprehensive analysis about them. PMID:18928123

  6. Theoretical phase diagrams for solid H2

    NASA Astrophysics Data System (ADS)

    Surh, Michael P.; Runge, K. J.

    1994-07-01

    Possible phase diagrams for solid molecular para-hydrogen in the 0-200 GPa pressure regime are constructed on the basis of ab initio calculations. Structures for the broken symmetry phase (BSP) and H-A phase have recently been proposed under the assumption that the molecules are centered on sites of a hexagonal close-packed lattice with the ideal c/a ratio, i.e., only molecular orientational and electronic changes are allowed. Symmetry considerations then dictate the simplest phase diagrams consistent with experimental observations, although the possibility of additional transitions cannot be ruled out. A simple model is introduced to describe the BSP and H-A transitions.

  7. 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. PMID:25228040

  8. Analysis of isotope effects in NMR one-bond indirect nuclear spin-spin coupling constants in terms of localized molecular orbitals.

    PubMed

    Provasi, Patricio F; Sauer, Stephan P A

    2009-05-28

    We recently showed, by analyzing contributions from localized molecular orbitals, that the anomalous deuterium isotope effect in the one-bond indirect nuclear spin-spin coupling constant of methane, also called the unexpected differential sensitivity, can be explained by the transfer of s-orbital character from the stretched bond to the other unchanged bonds [ChemPhysChem, 2008, 9, 1259]. We now extend this analysis of isotope effects to the molecules BH(4)(-), NH(4)(+), SiH(4), H(2)O and NH(3) in order to test our conclusions on a wider rage of XH(4) compounds and to investigate whether the lone-pair orbitals are really responsible for the absence of a similar effect in water and ammonia as proposed earlier [J. Chem. Phys., 2000, 113, 3121]. PMID:19440628

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  10. Molecular orbital polarization in Na2Ti2Sb2O : Microscopic route to metal-metal transition without spontaneous symmetry breaking

    NASA Astrophysics Data System (ADS)

    Kim, Heung-Sik; Kee, Hae-Young

    2015-12-01

    Ordered phases such as charge- and spin-density wave state accompany either full or partial gapping of Fermi surface (FS) leading a metal-insulator or metal-metal transition (MMT). However, there are examples of MMT without any signatures of symmetry breaking. One example is Na2Ti2Sb2O , where a partial gapping of FS is observed but a density wave ordering has not been found. Here we propose a microscopic mechanism of such a MMT, which occurs due to a momentum-dependent spin-orbit-coupled molecular orbital polarization. Since a molecular d orbital polarization is present due to a small spin-orbit coupling of Ti, there is no spontaneous symmetry breaking involved. However, a sharp increase of polarization happens above a critical electron interaction which gaps out the d orbtial FS and reduces the density of states significantly, while the rest of FS associated with Sb p orbtials is almost intact across MMT. Experimental implications to test our proposal and applications to other systems are also discussed.

  11. The Gaussian Atomic Orbital Multiplied by a Field-Dependent Gauge Phase for the Hydrogen Molecular Ion in Non-aligned Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Song, Xuanyu; Li, Cun; Wang, Xiaofeng; Qiao, Haoxue

    2016-01-01

    We multiply the anisotropic Gaussian atomic orbital by a field-dependent gauge phase to describe the wave function for the hydrogen molecular ion in non-aligned magnetic fields. With the kind of basis set, the convergence of the total energy at the equilibrium distance for the 1 u state is much improved compared to the same atomic orbital without the gauge phase. For 2.35 × 104 ≤ B ≤ 107 T, better total energies of the 1 u state at the corresponding equilibrium are obtained for the deviations 15°-90° of the magnetic field relative to the molecular axis. The result also shows that, there is a transition of the equilibrium configuration from the vertical orientation to the parallel orientation with increasing field strength.

  12. 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.

  13. Lasing action in a family of perylene derivatives: Singlet absorption and emission spectra, triplet absorption and oxygen quenching constants, and molecular mechanics and semiempirical molecular orbital calcuations

    SciTech Connect

    Sadrai, M.; Hadel, L.; Sauers, R.R.

    1992-10-01

    The authors present experimental and computational determination of the excited-state properties in several perylene dyestuffs that are potential candidates for use as laser dyes. Attention is focused on the following species derived from 3,4,9,10-perylenetetracarboxylic acid dianhydride: the bis ((2,6-dimethylphenyl)imide) (1b, DXP); the bis(methylimide) (1c, DMP); both 1,6,7,12-tetrachloro- (1d, Cl{sub 4}DMP) and 1,2,5,6,7,8,11,12-octachloro- (1e, Cl{sub 8}DMP) derivatives. Soluble derivatives of seven-ringed or larger aromatic systems are produced by the introduction of relatively rigid out-of-plane substituents that prevent intermolecular close packing. Chiral distortions in ring-chlorinated perylene derivatives significantly alter the shape of the absorption bands, a consequence of symmetry breaking. Triplet-triplet absorptions and oxygen-quenching rates are observed under the conditions found in a dye laser cavity. Semiempirical molecular orbital calculations (INDO/S) provide detailed mapping of the singlet and triplet excited state manifolds of DMP, Cl{sub 4}DMP, and Cl{sub 8}DMP. Computed transition energies and intensities are used in the interpretation of the spectral features, in particular the observed T{sub 1} {yields} T{sub n} and potential S{sub 1} {yields} S{sub n} absorptions. The authors conclude the perylene-3,4,9,10-tetracarboxylic acid diimide chromophores may be solubilized and utilized in laser materials exhibiting superior performance in terms of power output, tuning range, and light stability. 42 refs., 5 figs., 7 tabs.

  14. Square Source Type Diagram

    NASA Astrophysics Data System (ADS)

    Aso, N.; Ohta, K.; Ide, S.

    2014-12-01

    Deformation in a small volume of earth interior is expressed by a symmetric moment tensor located on a point source. The tensor contains information of characteristic directions, source amplitude, and source types such as isotropic, double-couple, or compensated-linear-vector-dipole (CLVD). Although we often assume a double couple as the source type of an earthquake, significant non-double-couple component including isotropic component is often reported for induced earthquakes and volcanic earthquakes. For discussions on source types including double-couple and non-double-couple components, it is helpful to display them using some visual diagrams. Since the information of source type has two degrees of freedom, it can be displayed onto a two-dimensional flat plane. Although the diagram developed by Hudson et al. [1989] is popular, the trace corresponding to the mechanism combined by two mechanisms is not always a smooth line. To overcome this problem, Chapman and Leaney [2012] developed a new diagram. This diagram has an advantage that a straight line passing through the center corresponds to the mechanism obtained by a combination of an arbitrary mechanism and a double-couple [Tape and Tape, 2012], but this diagram has some difficulties in use. First, it is slightly difficult to produce the diagram because of its curved shape. Second, it is also difficult to read out the ratios among isotropic, double-couple, and CLVD components, which we want to obtain from the estimated moment tensors, because they do not appear directly on the horizontal or vertical axes. In the present study, we developed another new square diagram that overcomes the difficulties of previous diagrams. This diagram is an orthogonal system of isotropic and deviatoric axes, so it is easy to get the ratios among isotropic, double-couple, and CLVD components. Our diagram has another advantage that the probability density is obtained simply from the area within the diagram if the probability density function of moment tensor's eigenvalues P(λ1, λ2, λ3) depends only on the scalar moment [(λ12+λ22+λ32)/2]0.5. Even if this is not the real case, the easiness of calculating the areal density is useful when we compare the results of analyzing real data with that of analyzing background noise.

  15. Rotational line-integrated photoabsorption cross sections corresponding to the δ(0,0) band of NO:A molecular quantum-defect orbital procedure

    NASA Astrophysics Data System (ADS)

    Mayor, E.; Velasco, A. M.; Martín, I.

    2005-09-01

    The rotational line-integrated photoabsorption cross sections corresponding to the δ(0,0) band of the nitric oxide (NO) molecule at 295 K, calculated with the molecular quantum-defect orbital methodology, are in rather good accord with the experimental measurements available in the literature. The achieved results are of straightforward use in atmospheric chemistry, such as in the assessment of the NO photodissociation rate constant, which is of great relevance for atmospheric modeling.

  16. 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.

  17. E-Orbit Functions

    NASA Astrophysics Data System (ADS)

    Klimyk, Anatoliy U.; Patera, Jiri

    2008-01-01

    We review and further develop the theory of E-orbit functions. They are functions on the Euclidean space En obtained from the multivariate exponential function by symmetrization by means of an even part We of a Weyl group W, corresponding to a Coxeter-Dynkin diagram. Properties of such functions are described. They are closely related to symmetric and antisymmetric orbit functions which are received from exponential functions by symmetrization and antisymmetrization procedure by means of a Weyl group W. The E-orbit functions, determined by integral parameters, are invariant with respect to even part Weaff of the affine Weyl group corresponding to W. The E-orbit functions determine a symmetrized Fourier transform, where these functions serve as a kernel of the transform. They also determine a transform on a finite set of points of the fundamental ! domain Fe of the group Weaff (the discrete E-orbit function transform).

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

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

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

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

    SciTech Connect

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

    1989-09-01

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

  20. Structures and stability of medium silicon clusters. II. Ab initio molecular orbital calculations of Si12-Si20

    NASA Astrophysics Data System (ADS)

    Zhu, X. L.; Zeng, X. C.; Lei, Y. A.; Pan, B.

    2004-05-01

    Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12-20). Selected geometric isomers include those predicted by Ho et al. [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding/genetic algorithm, as well as those found by Rata et al. [Phys. Rev. Lett. 85, 546 (2000)] based on density-functional tight-binding/single-parent evolution algorithm. These geometric isomers are optimized at the Møller-Plesset (MP2) MP2/6-31G(d) level. The single-point energy at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level for several low-lying isomers are further computed. Harmonic vibrational frequency analysis at the MP2/6-31G(d) level of theory is also undertaken to assure that the optimized geometries are stable. For Si12-Si17 and Si19 the isomer with the lowest-energy at the CCSD(T)/6-31G(d) level is the same as that predicted by Ho et al., whereas for Si18 and Si20, the same as predicted by Rata et al. However, for Si14 and Si15, the vibrational frequency analysis indicates that the isomer with the lowest CCSD(T)/6-31G(d) single-point energy gives rise to imaginary frequencies. Small structural perturbation onto the Si14 and Si15 isomers can remove the imaginary frequencies and results in new isomers with slightly lower MP2/6-31G(d) energy; however the new isomers have a higher single-point energy at the CCSD(T)/6-31G(d) level. For most Sin (n=12-18,20) the low-lying isomers are prolate in shape, whereas for Si19 a spherical-like isomer is slightly lower in energy at the CCSD(T)/6-31G(d) level than low-lying prolate isomers.

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

    NASA Astrophysics Data System (ADS)

    Taha, Ali

    2003-04-01

    Solvatochromic mixed ligand complexes of copper(II) with malonate and diamine derivatives, Cu n(RMal)(diam) nXm (where n=1 or 2, m=1-4, RMal, malonic acid (H 2Mal), diethylmalonate (HDEtMal) or diethylethoxyethylenemalonate (DEtEMal), and diam, ethylenediamine (en), 1,3-propylenediamine (1,3-pn), N, N, N'-trimethylethylenediamine (Me 3en), N, N, N'-triethylethylenediamine (Et 3en), N, N, N', N'-tetramethylethylenediamine (Me 4en), N, N, N', N'-tetramethylpropylenediamine (Me 4pn), or N-methyl-1,4-diazacycloheptane (medach); and X=ClO 4- or Cl -), has been synthesized and characterized by spectroscopic, magnetic, molar conductance and electrochemical measurements. The mass spectra along with the analytical data of the complexes show peaks with m/ e corresponding to a bridged binuclear structure for the chloride complexes, while perchlorate complexes showed either mononuclear structure for DEtMal and DEtEMal or bridged binuclear structure for Mal complexes. These results correspond to IR spectral data, which indicated that the modes of ester and carboxylato coordination sites are mono- and/or bidentate. The d-d absorption bands in weak donor solvents suggest square-planar and distorted square pyramidal-trigonal bipyramid geometries for the perchlorate and chloride complexes; respectively. On the other hand, an octahedral structure is identified for complexes in strong donor solvents. Perchlorate complexes show a drastic color change from violet to green as the donation ability of solvent increases, whereas chloride complexes are highly affected by the acceptor properties of the solvent. Cyclic voltammetric measurements on the complexes, proposed a quasi-reversible or irreversible and mainly diffusion controlled reduction process. Such behavior has been explained according to the ECE mechanism. A linear correlation has been found between the Cu(II) reduction potential and the spectral data. Molecular orbital calculations were performed for the ligands on the bases of PM3 level and the results corresponded to the experimental data. The data are discussed in terms of chromotropic concept and its applications as a Lewis acid-base color indicator.

  2. Scrutinizing UML Activity Diagrams

    NASA Astrophysics Data System (ADS)

    Al-Fedaghi, Sabah

    Building an information system involves two processes: conceptual modeling of the “real world domain” and designing the software system. Object-oriented methods and languages (e.g., UML) are typically used for describing the software system. For the system analysis process that produces the conceptual description, object-oriented techniques or semantics extensions are utilized. Specifically, UML activity diagrams are the “flow charts” of object-oriented conceptualization tools. This chapter proposes an alternative to UML activity diagrams through the development of a conceptual modeling methodology based on the notion of flow.

  3. Gravity wave transmission diagram

    NASA Astrophysics Data System (ADS)

    Tomikawa, Y.

    2015-12-01

    A new method of obtaining power spectral distribution of gravity waves as a function of ground-based horizontal phase speed and propagation direction from airglow observations has recently been proposed. To explain gravity wave power spectrum anisotropy, a new gravity wave transmission diagram was developed in this study. Gravity wave transmissivity depends on the existence of critical and turning levels for waves that are determined by background horizontal wind distributions. Gravity wave transmission diagrams for different horizontal wavelengths in simple background horizontal winds with constant vertical shear indicate that the effects of the turning level reflection are significant and strongly dependent on the horizontal wavelength.

  4. Impulse-Momentum Diagrams

    ERIC Educational Resources Information Center

    Rosengrant, David

    2011-01-01

    Multiple representations are a valuable tool to help students learn and understand physics concepts. Furthermore, representations help students learn how to think and act like real scientists. These representations include: pictures, free-body diagrams, energy bar charts, electrical circuits, and, more recently, computer simulations and

  5. Reading Diagrams. Pipefitter.

    ERIC Educational Resources Information Center

    Greater Baton Rouge Chamber of Commerce, LA.

    Developed by the ABCs of Construction National Workplace Literacy Project, these curriculum materials for the occupational area of pipefitting contain a lesson that deals with reading diagrams. The lesson consists of an objective, instruction, and 10 exercises. Three types of problems are provided in each exercise: "try it,""apply it," and "go…

  6. Reading Diagrams. E & I.

    ERIC Educational Resources Information Center

    Greater Baton Rouge Chamber of Commerce, LA.

    Developed by the ABCs of Construction National Workplace Literacy Project, these curriculum materials for the area of electrical and instrumentation contain a lesson that deals with reading diagrams. The lesson consists of an objective, instruction, and 10 exercises. The objective for the lesson is for the student to learn to locate and apply…

  7. Reading Diagrams. Millwright.

    ERIC Educational Resources Information Center

    Greater Baton Rouge Chamber of Commerce, LA.

    Developed by the ABCs of Construction National Workplace Literacy Project, these curriculum materials for the occupational area of millwright contain a lesson that deals with reading diagrams. The lesson consists of an objective, instruction, and 10 exercises. Three types of problems are provided in each exercise: "try it,""apply it," and "go with…

  8. Impulse-Momentum Diagrams

    ERIC Educational Resources Information Center

    Rosengrant, David

    2011-01-01

    Multiple representations are a valuable tool to help students learn and understand physics concepts. Furthermore, representations help students learn how to think and act like real scientists. These representations include: pictures, free-body diagrams, energy bar charts, electrical circuits, and, more recently, computer simulations and…

  9. Understanding Network Diagrams.

    ERIC Educational Resources Information Center

    Waller, Robert

    A survey of a range of introductory university level textbooks in the social sciences found little use of network diagrams (NDs), i.e., graphic representations of processes, organizations, systems, and mechanisms. NDs can be viewed as a text/picture hybrid medium with titles and captions serving to qualify and identify the meaning and status of…

  10. On Argument and Diagrams.

    ERIC Educational Resources Information Center

    Kneupper, Charles W.

    1978-01-01

    Responds to Charles Willard's recommendations (in an article in "Communication Monographs," November 1976) that argument be viewed as an attempt to establish formal relationships among symbolic structures. Demonstrates flaws in this redefinition and shows argument diagrams to be theoretically and practically justifiable. (JMF)

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  12. 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.

  13. Ab initio molecular orbital calculations of molten salt vapor complexes using Gaussian-2 theory: LiAlF[sub 4] and NaAlF[sub 4

    SciTech Connect

    Curtiss, L.A.

    1993-01-01

    The structures and energies of the molten salt vapor complexes LiAlF[sub 4] and NaAlF[sub 4] are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.

  14. Ab initio molecular orbital calculations of molten salt vapor complexes using Gaussian-2 theory: LiAlF{sub 4} and NaAlF{sub 4}

    SciTech Connect

    Curtiss, L.A.

    1993-04-01

    The structures and energies of the molten salt vapor complexes LiAlF{sub 4} and NaAlF{sub 4} are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.

  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; RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 ; Fedorov, Dmitri G.; Yokojima, Satoshi; Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachioji-shi, Tokyo 192-0392 ; 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. Induced spin filtering in electron transmission through chiral molecular layers adsorbed on metals with strong spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Gersten, Joel; Kaasbjerg, Kristen; Nitzan, Abraham

    2013-09-01

    Recent observations of considerable spin polarization in photoemission from metal surfaces through monolayers of chiral molecules were followed by several efforts to rationalize the results as the effect of spin-orbit interaction that accompanies electronic motion on helical, or more generally strongly curved, potential surfaces. In this paper we (a) argue, using simple models, that motion in curved force-fields with the typical energies used and the characteristic geometry of DNA cannot account for such observations; (b) introduce the concept of induced spin filtering, whereupon selectivity in the transmission of the electron orbital angular momentum can induce spin selectivity in the transmission process provided there is strong spin-orbit coupling in the substrate; and (c) show that the spin polarization in the tunneling current as well as the photoemission current from gold covered by helical adsorbates can be of the observed order of magnitude. Our results can account for most of the published observations that involved gold and silver substrates; however, recent results obtained with an aluminum substrate can be rationalized within the present model only if strong spin-orbit coupling is caused by the built-in electric field at the molecule-metal interface.

  17. 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…

  18. Interaction analysis of HIV-1 antibody 2G12 and Man9GlcNAc2 ligand: Theoretical calculations by fragment molecular orbital and MD methods

    NASA Astrophysics Data System (ADS)

    Koyama, Yuka; Ueno-Noto, Kaori; Takano, Keiko

    2013-07-01

    In HIV-1 infection, human antibody 2G12 is capable of recognizing the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. To investigate the ligand binding mechanisms of antibody 2G12 with glycans aiming for the contribution to the medications, we carried out classical molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the antibody 2G12 complex with its high-mannose ligand. We found that Mannose D1 of the ligand had the largest binding affinity with the antibody, which was well consistent with experimental reports. Furthermore, significant roles of Mannose 4 and 4‧ in the ligand binding were theoretically indicated.

  19. Impulse-Momentum Diagrams

    NASA Astrophysics Data System (ADS)

    Rosengrant, David

    2011-01-01

    Multiple representations are a valuable tool to help students learn and understand physics concepts. Furthermore, representations help students learn how to think and act like real scientists.2 These representations include: pictures, free-body diagrams,3 energy bar charts,4 electrical circuits, and, more recently, computer simulations and animations.5 However, instructors have limited choices when they want to help their students understand impulse and momentum. One of the only available options is the impulse-momentum bar chart.6 The bar charts can effectively show the magnitude of the momentum as well as help students understand conservation of momentum, but they do not easily show the actual direction. This paper highlights a new representation instructors can use to help their students with momentum and impulse—the impulse-momentum diagram (IMD).

  20. TEP process flow diagram

    SciTech Connect

    Wilms, R Scott; Carlson, Bryan; Coons, James; Kubic, William

    2008-01-01

    This presentation describes the development of the proposed Process Flow Diagram (PFD) for the Tokamak Exhaust Processing System (TEP) of ITER. A brief review of design efforts leading up to the PFD is followed by a description of the hydrogen-like, air-like, and waterlike processes. Two new design values are described; the mostcommon and most-demanding design values. The proposed PFD is shown to meet specifications under the most-common and mostdemanding design values.

  1. 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.

  2. 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.

  3. Contributions of inner-valence molecular orbitals and multiphoton resonances to high-order-harmonic generation of N2: A time-dependent density-functional-theory study

    NASA Astrophysics Data System (ADS)

    Chu, Xi; Groenenboom, Gerrit C.

    2016-01-01

    Using a time-dependent density-functional-theory (TDDFT) method, we calculated the high-harmonic generation (HHG) spectra of N2 in 800- and 1300-nm intense lasers. The calculations reproduce the experimentally observed minimum near 40 eV and the shift of the minimum due to interference of different molecular orbitals. They also support the proposed shape resonance near 30 eV. The TDDFT method allows us to analyze the involvement of different electronic configurations in the HHG process. We identified a significant role of Rydberg states and autoionizing states in enhancing HHG. This finding is consistent with studies of photoelectron spectra in a similar energy range. Moreover, we discover a significant contribution of the 2 ?g orbital above 40 eV, demonstrating the complexity of electronic structure information contained in molecular HHG. At high energy not only the HOMO and HOMO-1 are important, as suggested by earlier studies, but the HOMO-3 contributes substantially as well.

  4. [Columbia Sensor Diagrams]. Revised

    NASA Technical Reports Server (NTRS)

    2003-01-01

    A two dimensional graphical event sequence of the time history of relevant sensor information located in the left wing and wheel well areas of the Space Shuttle Columbia Orbiter is presented. Information contained in this graphical event sequence include: 1) Sensor location on orbiter and its associated wire bindle in X-Y plane; 2) Wire bundle routing; 3) Description of each anomalous sensor event; 4) Time annotation by (a) GMT, (b) time relative to LOS, (c) time history bar, and (d) ground track; and 5) Graphical display of temperature rise (based on delta temperature from point it is determined to be anomalous).

  5. 4d-polytopes described by Coxeter diagrams and quaternions

    NASA Astrophysics Data System (ADS)

    Koca, Mehmet

    2011-03-01

    4D-polytopes and their dual polytopes can be described as the orbits of the rank-4 Coxeter-Weyl groups. Their symmetries follow from the quaternionic descriptions of the rank-4 Coxeter-Dynkin diagrams. There exists a one to one correspondence between the finite subgroups of quaternions and the rank-4 Coxeter-Weyl groups.

  6. Imaging momentum orbital densities of conformationally versatile molecules: a benchmark theoretical study of the molecular and electronic structures of dimethoxymethane.

    PubMed

    Huang, Y R; Knippenberg, S; Hajgató, B; François, J-P; Deng, J K; Deleuze, M S

    2007-07-01

    The main purpose of the present work is to predict from benchmark many-body quantum mechanical calculations the results of experimental studies of the valence electronic structure of dimethoxymethane employing electron momentum spectroscopy, and to establish once and for all the guidelines that should systematically be followed in order to reliably interpret the results of such experiments on conformationally versatile molecules. In a first step, accurate calculations of the energy differences between stationary points on the potential energy surface of this molecule are performed using Hartree-Fock (HF) theory and post-HF treatments of improving quality (MP2, MP3, CCSD, CCSD(T), along with basis sets of increasing size. This study focuses on the four conformers of this molecule, namely the trans-trans (TT), trans-gauche (TG), gauche-gauche (G+G+), and gauche-gauche (G+G-) structures, belonging to the C2v, C1, C2, and Cs symmetry point groups, respectively. A focal point analysis supplemented by suited extrapolations to the limit of asymptotically complete basis sets is carried out to determine how the conformational energy differences at 0 K approach the full CI limit. In a second step, statistical thermodynamics accounting for hindered rotations is used to calculate Gibbs free energy corrections to the above energy differences, and to evaluate the abundance of each conformer in the gas phase. It is found that, at room temperature, the G+G+ species accounts for 96% of the conformational mixture characterizing dimethoxymethane. In a third step, the valence one-electron and shake-up ionization spectrum of dimethoxymethane is analyzed according to calculations on the G+G+ conformer alone by means of one-particle Green's function [1p-GF] theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. A complete breakdown of the orbital picture of ionization is noted at electron binding energies above 22 eV. A comparison with available (e,2e) ionization spectra enables us to identify specific fingerprints of through-space orbital interactions associated with the anomeric effect. At last, based on our 1p-GF/ADC(3) assignment of spectral bands, accurate and spherically averaged (e,2e) electron momentum distributions at an electron impact energy of 1200 eV are computed from the related Dyson orbitals. Very significant discrepancies are observed with momentum distributions obtained for several outer-valence levels using standard Kohn-Sham orbitals. PMID:17566995

  7. Diagrams of airplane stability

    NASA Technical Reports Server (NTRS)

    Batemen, H

    1921-01-01

    In this report a study is made of the effect on longitudinal and lateral oscillations of an airplane of simultaneous variations in two resistance derivatives while the remainder of the derivatives are constant. The results are represented by diagrams in which the two variable resistance derivatives are used as coordinates, and curves are plotted along which the modulus of decay of a long oscillation has a constant value. The same type of analysis is also carried out for the stability of the parachute. In discussing the stability of the helicopter it is concluded that the gyroscopic effect on stability will be greater than in the case of the airplane.

  8. 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.

  9. Warped penguin diagrams

    SciTech Connect

    Csaki, Csaba; Grossman, Yuval; Tanedo, Philip; Tsai, Yuhsin

    2011-04-01

    We present an analysis of the loop-induced magnetic dipole operator in the Randall-Sundrum model of a warped extra dimension with anarchic bulk fermions and an IR brane-localized Higgs. These operators are finite at one-loop order and we explicitly calculate the branching ratio for {mu}{yields}e{gamma} using the mixed position/momentum space formalism. The particular bound on the anarchic Yukawa and Kaluza-Klein (KK) scales can depend on the flavor structure of the anarchic matrices. It is possible for a generic model to either be ruled out or unaffected by these bounds without any fine-tuning. We quantify how these models realize this surprising behavior. We also review tree-level lepton flavor bounds in these models and show that these are on the verge of tension with the {mu}{yields}e{gamma} bounds from typical models with a 3 TeV Kaluza-Klein scale. Further, we illuminate the nature of the one-loop finiteness of these diagrams and show how to accurately determine the degree of divergence of a five-dimensional loop diagram using both the five-dimensional and KK formalism. This power counting can be obfuscated in the four-dimensional Kaluza-Klein formalism and we explicitly point out subtleties that ensure that the two formalisms agree. Finally, we remark on the existence of a perturbative regime in which these one-loop results give the dominant contribution.

  10. Impact decision support diagrams

    NASA Astrophysics Data System (ADS)

    Boslough, Mark

    2014-10-01

    One way to frame the job of planetary defense is to find the optimal approach for finding the optimal approach to NEO mitigation. This requires a framework for defining in advance what should be done under various circumstances. The two-dimensional action matrix from the recent NRC report Defending Planet Earth can be generalized to a notional Impact Decision Support Diagram by extending it into a third dimension. The NRC action matrix incorporated two important axes: size and time-to-impact, but probability of impact is also critical (it is part of the definitions of both the Torino and Palermo scales). Uncertainty has been neglected, but is also crucial. It can be incorporated by subsuming it into the NEO size axis by redefining size to be three standard deviations greater than the best estimate, thereby providing a built-in conservative margin. The independent variable is time-to-impact, which is known with high precision. The other two axes are both quantitative assessments of uncertainty and are both time dependent. Thus, the diagram is entirely an expression of uncertainty. The true impact probability is either one or zero, and the true size does not change. The domain contains information about the current uncertainty, which changes with time (as opposed to reality, which does not change).

  11. Pioneer Venus orbiter

    NASA Technical Reports Server (NTRS)

    1974-01-01

    The orbiter mission of the Pioneer Venus probe is discussed. In accordance with the low-cost Pioneer Venus concept, NASA intends to use the same basic spacecraft, known as the bus, for the execution of the two missions. The bus will be equipped with all of the subsystems common to the probe and orbiter missions (for example, thermal control, solar cells and power supply, attitude measurement and control, telemetry and communication electronics, and auxiliary propulsion unit). For the 1977 mission, the bus will be equipped with the large and small probes and a special antenna system. For the orbiter mission, the bus will be equipped with a retro-propulsion motor and a high-gain antenna. A diagram of the system envisaged is shown.

  12. 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

    2015-03-01

    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. PMID:25523048

  13. 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.

  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. PMID:22260560

  15. 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.

  16. Antisymmetric Orbit Functions

    NASA Astrophysics Data System (ADS)

    Klimyk, Anatoliy; Patera, Jiri

    2007-02-01

    In the paper, properties of antisymmetric orbit functions are reviewed and further developed. Antisymmetric orbit functions on the Euclidean space En are antisymmetrized exponential functions. Antisymmetrization is fulfilled by a Weyl group, corresponding to a Coxeter-Dynkin diagram. Properties of such functions are described. These functions are closely related to irreducible characters of a compact semisimple Lie group G of rank n. Up to a sign, values of antisymmetric orbit functions are repeated on copies of the fundamental domain F of the affine Weyl group (determined by the initial Weyl group) in the entire Euclidean space En. Antisymmetric orbit functions are solutions of the corresponding Laplace equation in En, vanishing on the boundary of the fundamental domain F. Antisymmetric orbit functions determine a so-called antisymmetrized Fourier transform which is clo! sely related to expansions of central functions in characters of irreducible representations of the group G. They also determine a transform on a finite set of points of F (the discrete antisymmetric orbit function transform). Symmetric and antisymmetric multivariate exponential, sine and cosine discrete transforms are given.

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

    PubMed

    Prabavathi, N; Nilufer, A; Krishnakumar, V

    2013-10-01

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

  18. 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.

  19. Semiempirical molecular orbital calculations of anisotropic 1H, 13C and 19F hyperfine coupling constants in hydrocarbon and fluorocarbon radicals

    NASA Astrophysics Data System (ADS)

    Barfield, Michael; Babaqi, Abdulla S.; Doddrell, David M.; Gottlieb, Hans P. W.

    The anisotropic hyperfine coupling constants (AHCC) from the electron spin resonance (E.S.R.) spectra of a variety of atoms in organic radicals have been calculated by means of semiempirical molecular orbital wavefunctions in the INDO approximation. Hyperfine tensors involving 1H, 13C and 19F nuclei are obtained for the ĊH, ĊH3, CH3ĊH2, (CH3)3Ċ hydrocarbon radicals, malonic acid radical, ĊH2F, ĊF2H, ĊF3 and CF3ĊH2 radicals. The calculated values are compared with available experimental, non-empirical and semiempirical values for these radicals. All integrals of the operator entering the electronic contributions have been evaluated over Slater type orbitals. The introduction of deorthogonalized wavefunctions gives generally better calculated results. In particular, the tensor components of the 19F AHCC are in good agreement with the experimental results without the necessity of readjusting the effective nuclear charges.

  20. Vibrational spectra, molecular structure, natural bond orbital, first order hyperpolarizability, thermodynamic analysis and normal coordinate analysis of Salicylaldehyde p-methylphenylthiosemicarbazone by density functional method.

    PubMed

    Porchelvi, E Elamurugu; Muthu, S

    2015-01-01

    The thiosemicarbazone compound, Salicylaldehyde p-methylphenylthiosemicarbazone (abbreviated as SMPTSC) was synthesized and characterized by FTIR, FT-Raman and UV. Density functional (DFT) calculations have been carried out for the title compound by performing DFT level of theory using B3LYP/6-31++G(d,p) basis set. The molecular geometry and vibrational frequencies were calculated and compared with the experimental data. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The electronic dipole moment (?D) and the first hyperpolarizability (?tot) values of the investigated molecule were computed using density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. Thearomaticities of the phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Mulliken population analysis on atomic charges is also calculated. The molecule orbital contributions are studied by density of energy states (DOSs). PMID:25033238

  1. Energy stabilization of the s-symmetry superatom molecular orbital by endohedral doping of C82 fullerene with a lanthanum atom

    NASA Astrophysics Data System (ADS)

    Feng, Min; Shi, Yongliang; Lin, Chungwei; Zhao, Jin; Liu, Fupin; Yang, Shangfeng; Petek, Hrvoje

    2013-08-01

    Energy stabilization of the superatom molecular orbitals (SAMOs) in fullerenes is investigated with the goal of involving their nearly free-electron bands in practical charge transport applications. Combining low-temperature scanning tunneling microscopy-based spectroscopic methods and density functional theory calculations on an endohedral metallofullerene La@C82, we confirm that the s-SAMO of C82 fullerene is stabilized by as much as 2 eV with respect to that of C60 by endohedral doping with the La atom. On the copper metal substrate, the s-SAMO energy is further lowered to just 1 eV above the Fermi level, making the applications of s-SAMO state in transport more plausible. We conclude that in an endohedral metallofullerene, the s-SAMO state is stabilized through the hybridization with the s-symmetry valence state of the metal atom and the stabilization energy correlates with the ionization potential of the free atom.

  2. Ionic organoboranes. Part 7. Molecular orbital study of electron distribution in the [7.10 2]hemiousenide ion; explanation for the anomalous 11B NMR spectrum

    NASA Astrophysics Data System (ADS)

    Harmon, K. M.; Nelson, T. E.; Stackowski, B. M.

    2002-02-01

    The 11B NMR spectrum of the [7.10 2]hemiousenide ion (C 7H 6B 10H 9-) demonstrates ground state + T cage to ring electron donation from the region of the two apical borons. The chemically non-equivalent apical borons give an apparent singlet NMR absorption and thus appear to be in very similar electronic environments, even though they are unsymmetrically arranged relative to the cationic ring. Ab initio 3-21G(∗) and semi-empirical PM3 calculations suggest that the π-system of the ring only interacts with cage molecular orbitals that are symmetrical relative to both apical borons in B 10H 102- and that the electron density about the two apical borons is essentially identical in the [7.10 2]hemiousenide ion. Significant ground state electron donation from cage to ring is observed, consonant with conclusions from previous polarographic studies.

  3. 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.

  4. Evaluation of the hydrogen bond energy of base pairs formed between substituted 9-methyladenine derivatives and 1-methyluracil by use of molecular orbital theory.

    PubMed

    Kawahara, S; Taira, K; Sekine, M; Uchimaru, T

    2000-01-01

    Systematic substituent effects on the stability of the hydrogen bonding between substituted 9-methyladenine derivatives (Ax) and 1-methyluracil (U) were studied by ab initio molecular orbital theory. Predicted substituent effects on the hydrogen bond energies of Ax-U base pairs were in good agreement with those observed for experimental binding constants. Ab initio calculation is effective for evaluation of the stability of the hydrogen-bonding pairs of chemically modified nucleic acid base analogues. In contrast to the substitution effect of uracil on hydrogen bond energies of A-Ux base pairs, it is difficult to systematically interpret the substitution effect of adenine derivatives for Ax-U base pairs. PMID:12903356

  5. Argument Diagramming: The Araucaria Project

    NASA Astrophysics Data System (ADS)

    Rowe, Glenn; Reed, Chris

    Formal arguments, such as those used in science, medicine and law to establish a conclusion by providing supporting evidence, are frequently represented by diagrams such as trees and graphs. We describe the software package Araucaria which allows textual arguments to be marked up and represented as standard, Toulmin or Wigmore diagrams. Since each of these diagramming techniques was devised for a particular domain or argumentation, we discuss some of the issues involved in translating between diagrams. The exercise of translating between different diagramming types illustrates that any one diagramming system often cannot capture all of the nuances inherent in an argument. Finally, we describe some areas, such as critical thinking courses in colleges and universities and the analysis of evidence in court cases, where Araucaria has been put to practical use.

  6. Molecular orbital (SCF-X-α-SW) theory of Fe2+-Mn3+, Fe3+-Mn2+, and Fe3+-Mn3+ charge transfer and magnetic exchange in oxides and silicates

    USGS Publications Warehouse

    Sherman, David M.

    1990-01-01

    Metal-metal charge-transfer and magnetic exchange interactions have important effects on the optical spectra, crystal chemistry, and physics of minerals. Previous molecular orbital calculations have provided insight on the nature of Fe2+-Fe3+ and Fe2+-Ti4+ charge-transfer transitions in oxides and silicates. In this work, spin-unrestricted molecular orbital calculations on (FeMnO10) clusters are used to study the nature of magnetic exchange and electron delocalization (charge transfer) associated with Fe3+-Mn2+, Fe3+-Mn3+, and Fe2+-Mn3+ interactions in oxides and silicates. 

  7. Development of a Silicon Carbide Molecular Beam Nozzle for Simulation Planetary Flybys and Low-Earth Orbit

    NASA Technical Reports Server (NTRS)

    Patrick, E. L.; Earle, G. D.; Kasprzak, W. T.; Mahaffy, Paul R.

    2008-01-01

    From commercial origins as a molybdenum molecular beam nozzle, a ceramic nozzle of silicon carbide (SiC) was developed for space environment simulation. The nozzle is mechanically stable under extreme conditions of temperature and pressure. A heated, continuous, supersonically-expanded hydrogen beam with a 1% argon seed produced an argon beam component of nearly 4 km/s, with an argon flux exceeding 1x1014 /cm2.s. This nozzle was part of a molecular beam machine used in the Atmospheric Experiments Branch at NASA Goddard Space Flight Center to characterize the performance of the University of Texas at Dallas Ram Wind Sensor (RWS) aboard the Air Force Communications/Navigation Outage Forecasting System (C/NOFS) launched in the Spring of 2008.

  8. Program Synthesizes UML Sequence Diagrams

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  9. Correlation of molecular valence- and K-shell photoionization resonances with bond lengths

    NASA Technical Reports Server (NTRS)

    Sheehy, J. A.; Gil, T. J.; Winstead, C. L.; Farren, R. E.; Langhoff, P. W.

    1989-01-01

    The relationship between the interatomic distance and the positions of valence-shell and K-shell sigma(asterisk) photoionization resonances is investigated theoretically for the molecules C2, F2, N2, O2, CO, NO, C2H2, C2H4, C2H6, HCN, H2CO, N20, CO2, and C2N2. The results of molecular-orbital computations are presented in three-dimensional diagrams, which are shown to be similar to the wave functions of a particle in a cylindrical well, confirming the validity of free-electron molecular-orbital (FEMO) approximations for modeling the potential along the symmetry axis. FEMO orbital energies and resonance positions are found to be in good agreement with previous theoretical and experimental results. Also included is a Feshbach-Fano analysis of the relevance of virtual-valence orbitals to the appearance of single-channel resonances in molecular photoionization cross sections.

  10. Faceting diagram for sticky steps

    NASA Astrophysics Data System (ADS)

    Akutsu, Noriko

    2016-03-01

    Faceting diagrams for the step-faceting zone, the step droplet zone, and the Gruber-Mullins-Pokrovsky-Talapov (GMPT) zone for a crystal surface are obtained by using the density matrix renormalization group method to calculate the surface tension. The model based on these calculations is the restricted solid-on-solid (RSOS) model with a point-contact-type step-step attraction (p-RSOS model) on a square lattice. The point-contact-type step-step attraction represents the energy gain obtained by forming a bonding state with orbital overlap at the meeting point of the neighboring steps. In the step-faceting zone, disconnectedness in the surface tension leads to the formation of a faceted macrostep on a vicinal surface at equilibrium. The disconnectedness in the surface tension also causes the first-order shape transition for the equilibrium shape of a crystal droplet. The lower zone boundary line (ZBL), which separates the step-faceting zone and the step droplet zone, is obtained by the condition γ 1 = lim n → ∞ γ n / n , where γn is the step tension of the n-th merged step. The upper ZBL, which separates the GMPT zone and the step droplet zone, is obtained by the condition Aq,eff = 0 and Bq,eff = 0, where Aq,eff and Bq,eff represent the coefficients for the | q → | 2 term and the | q → | 3 term, respectively, in the | q → | -expanded form of the surface free energy f eff ( q → ) . Here, q → is the surface gradient relative to the (111) surface. The reason why the vicinal surface inclined in the <101> direction does not exhibit step-faceting is explained in terms of the one-dimensional spinless quasi-impenetrable attractive bosons at absolute zero.

  11. Conformational and Molecular Structures of α,β-Unsaturated Acrylonitrile Derivatives: Photophysical Properties and Their Frontier Orbitals.

    PubMed

    Percino, María Judith; Cerón, Margarita; Rodríguez, Oscar; Soriano-Moro, Guillermo; Castro, María Eugenia; Chapela, Víctor M; Siegler, Maxime A; Pérez-Gutiérrez, Enrique

    2016-01-01

    We report single crystal X-ray diffraction (hereafter, SCXRD) analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylamino)phenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z)-3-(4-(diphenylamino)-phenyl)-2-(pyridin-3-yl)prop-2-enenitrile (I), (2Z)-3-(4-(diphenylamino)phenyl)-2-(pyridin-4-yl)-prop-2-enenitrile (II) and (2Z)-3-(9-ethyl-9H-carbazol-3-yl)-2-(pyridin-2-yl)enenitrile (III). SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z' = 2 and C2/c with Z' = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z' = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z'). It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV). Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide) in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported. PMID:27043499

  12. Ab initio molecular orbital study of substituent effects in vaska type complexes (trans-IrL{sub 2}(CO)X): Electron affinities, ionization potentials, carbonyl stretch frequencies, and the thermodynamics of H{sub 2} dissociative addition

    SciTech Connect

    Abu-Hasanayn, F.; Goldman, A.S.; Krogh-Jespersen, K.

    1994-10-26

    Ab initio electronic structure calculations are used to study substituent effects in Vaska-type complexes, trans-IrL{sub 2}(CO)X (1-X) (X = F, Cl, Br, I, CN, H, CH{sub 3}, SiH{sub 3}, OH, and SH; L = PH{sub 3}). Both the electron affinity and the ionization potential of 1-X are computed to increase upon descending the halogen series of complexes, which indicates, surprisingly, that the complexes with more electronegative halogens are more difficult to reduce and easier to oxidize. The computed electron affinity trend is consistent with the half-wave reduction potential trend known for 1-X (L = PPh{sub 3}; X = F, Cl, Br, and I). Computed carbonyl stretch frequencies for 1-X are greater than experimental values (L = PPh{sub 3}), but observed trends are well reproduced. The redox and spectroscopic trends are discussed in terms of the substituent effects on the electronic structure of 1-X, particularly as revealed in the molecular orbital energy level diagrams of these complexes. The reaction energy for H{sub 2} addition to 1-X, leading to the cis,trans-(H){sub 2}IrL{sub 2}(CO)X (2-X) product, has been computed. After electron correlation effects are included (MP4(SDTQ)), the reaction enthalpy computed for 1-CI is {minus}18.4 kcal/mol (L = PH{sub 3}) as compared to a reported experimental value of {minus}14 kcal/mol (L = PPh{sub 3}). Compared with available experimental data, the electronic effects of L(L = PH{sub 3}, NH{sub 3}, or AsH{sub 3}) and X on the thermodynamics of the H{sub 2} addition reaction are accurately reproduced by the model calculations at all levels of theory (HF and MPn). Formation of the hypothetical products cis,trans- and trans,trans-(H){sub 2}IrL{sub 2}(CO)X(2-X and 3-X) (X = BH{sub 2}, NH{sub 2}, and PH{sub 2}) is used to demonstrate that {pi}-acceptor substituents promote the H{sub 2} addition reaction to 1-X while {pi}-donor substituents disfavor addition.

  13. Space Shuttle Orbiter auxiliary power unit status

    NASA Technical Reports Server (NTRS)

    Reck, M.; Loken, G.; Horton, J.; Lukens, W.; Scott, W.; Baughman, J.; Bauch, T.

    1991-01-01

    An overview of the United States Space Shuttle Orbiter APU, which provides power to the Orbiter vehicle hydraulic system, is presented. Three complete APU systems, each with its own separate fuel system, supply power to three dedicated hydraulic systems. These in turn provide power to all Orbiter vehicle critical flight functions including launch, orbit, reentry, and landing. The basic APU logic diagram is presented. The APU includes a hydrazine-powered turbine that drives a hydraulic pump and various accessories through a high-speed gearbox. The APU also features a sophisticated thermal management system designed to ensure safe and reliable operation in the various launch, orbit, reentry, and landing environments.

  14. Space Shuttle Orbiter auxiliary power unit status

    NASA Astrophysics Data System (ADS)

    Reck, M.; Loken, G.; Horton, J.; Lukens, W.; Scott, W.; Baughman, J.; Bauch, T.

    An overview of the United States Space Shuttle Orbiter APU, which provides power to the Orbiter vehicle hydraulic system, is presented. Three complete APU systems, each with its own separate fuel system, supply power to three dedicated hydraulic systems. These in turn provide power to all Orbiter vehicle critical flight functions including launch, orbit, reentry, and landing. The basic APU logic diagram is presented. The APU includes a hydrazine-powered turbine that drives a hydraulic pump and various accessories through a high-speed gearbox. The APU also features a sophisticated thermal management system designed to ensure safe and reliable operation in the various launch, orbit, reentry, and landing environments.

  15. On-orbit flight control algorithm description

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Algorithms are presented for rotational and translational control of the space shuttle orbiter in the orbital mission phases, which are external tank separation, orbit insertion, on-orbit and de-orbit. The program provides a versatile control system structure while maintaining uniform communications with other programs, sensors, and control effectors by using an executive routine/functional subroutine format. Software functional requirements are described using block diagrams where feasible, and input--output tables, and the software implementation of each function is presented in equations and structured flow charts. Included are a glossary of all symbols used to define the requirements, and an appendix of supportive material.

  16. Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems

    NASA Astrophysics Data System (ADS)

    Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi

    2015-01-01

    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.

  17. 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.

  18. Diagonal Slices of 3D Young Diagrams in the Approach of Maya Diagrams

    NASA Astrophysics Data System (ADS)

    Cai, Li-Qiang; Wang, Li-Fang; Wu, Ke; Yang, Jie

    2014-09-01

    According to the correspondence between 2D Young diagrams and Maya diagrams and the relation between 2D and 3D Young diagrams, we construct 3D Young diagrams in the approach of Maya diagrams. Moreover, we formulate the generating function of 3D Young diagrams, which is the MacMahon function in terms of Maya diagrams.

  19. 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.

  20. Potential-pH Diagrams.

    ERIC Educational Resources Information Center

    Barnum, Dennis W.

    1982-01-01

    Potential-pH diagrams show the domains of redoxpotential and pH in which major species are most stable. Constructing such diagrams provides students with opportunities to decide what species must be considered, search literature for equilibrium constants and free energies of formation, and practice in using the Nernst equation. (Author/JN)

  1. An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework.

    PubMed

    Koyano, Yoshiyuki; Takenaka, Norio; Nakagawa, Yukinori; Nagaoka, Masataka

    2010-11-15

    For the purpose of executing direct dynamic and statistical calculation of chemical reactions in solution, we proposed an optimum strategy using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRPs), that is, the NDDO-SSRP method. It has been further extended to develop the NDDO-MAIS-SSRP method, which is the NDDO-SSRP method reinforced with the method adopted for intermolecular studies (MAIS), to correct the description of the intermolecular core-core repulsion interaction energy. In this strategy, the empirical parameters of the semiempirical MO method are optimized individually for a target chemically reacting molecular system by reference to the ab initio MO calculation data for a lot of instantaneous geometries on the potential energy surface near the reaction path. For demonstration, the NDDO-MAIS-SSRP method was applied, within the QM/MM framework, to a molecular cluster, that is, a couple of a QM solute NH(3)-H(2)O molecule pair and a MM solvent H(2)O molecule. The NDDO-MAIS-SSRP method can reproduce the electrostatic energy in the region R > 4.0 A, though the electrostatic energy shows large difference with those of MP2 level calculations in the region R < 4.0 A in some cases. Both the NDDO-SSRP and the NDDO-MAIS-SSRP methods could promise in the dynamical application to chemical reaction in solution (Takenaka et al., Chem Phys Lett 2010, 485, 119; Koyano et al., Bull Chem Soc Jpn, in press). PMID:20740563

  2. 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.

  3. Yukawa Monte Carlo (YMC) and Orbital Free Molecular Dynamics (OFMD) approaches for the eos of warm dense iron plasma

    NASA Astrophysics Data System (ADS)

    Gilles, Dominique; Lambert, Flavien; Clerouin, Jean

    2008-04-01

    Yukawa Monte Carlo and Molecular Dynamics simulations are powerful techniques extensively used to compute plasma properties such as EOS or transport coefficients, but are limited to applications where the linear electronic screening assumption is valid (1). Recently we have shown that a modified scheme using density functional theory with a Thomas-Fermi kinetic energy functional for the electrons (OFMD) may be well suited to perform MD simulations at high densities and temperature, without any assumption on the electronic screening (2). For selected iron plasma conditions representative of warm and dense matter, we shall compare pressure results calculated using YMC and OFMD codes and QEOS (3) and Sesame EOS models (4) and discuss the influence of keys parameters, like ionization in Yukawa theory. References: [1] D. Gilles, O. Peyrusse, JQSRT 53, 6, 1995. ;Caillol J-M, Gilles D., J. Stat Phys. 100, N5/6, 905-947, 2000; Caillol J-M, Gilles D., J. Phys. A 36, 6243, (2003) ; A. Potekhin, G. Chabrier, Gilles, PRE 65, 036412, 2002. [2] D. Gilles, F. Lambert, J. Cl'erouin, S. Mazevet, Gwena"el Salin, HEDP 3, 95-98, 2007; F. Lambert, J. Cl'erouin, S. Mazevet, D. Gilles, Plama Physics, 47,4-5, 272-280(2007). [3] R.M. More, Lawrence Livermore Laboratory Report, UCRL-84991, (1981). [4] G.I. Kerley, User's Manual for PANDA : A computer Code for calculating Equation of State, Los Alamos National Laboratory, 1981 (LA8833).

  4. Structure investigation of three hydrazones Schiff's bases by spectroscopic, thermal and molecular orbital calculations and their biological activities.

    PubMed

    Belal, Arafa A M; Zayed, M A; El-Desawy, M; Rakha, Sh M A H

    2015-03-01

    Three Schiff's bases AI (2(1-hydrazonoethyl)phenol), AII (2, 4-dibromo 6-(hydrazonomethyl)phenol) and AIII (2(hydrazonomethyl)phenol) were prepared as new hydrazone compounds via condensation reactions with molar ratio (1:1) of reactants. Firstly by reaction of 2-hydroxy acetophenone solution and hydrazine hydrate; it gives AI. Secondly condensation between 3,5-dibromo-salicylaldehyde and hydrazine hydrate gives AII. Thirdly condensation between salicylaldehyde and hydrazine hydrate gives AIII. The structures of AI-AIII were characterized by elemental analysis (EA), mass (MS), FT-IR and (1)H NMR spectra, and thermal analyses (TG, DTG, and DTA). The activation thermodynamic parameters, such as, ΔE(∗), ΔH(∗), ΔS(∗) and ΔG(∗) were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bond responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their anti-microbial potential. PMID:25437844

  5. Orbital cellulitis

    MedlinePlus

    ... Haemophilus influenzae B) vaccine. The bacteria Staphylococcus aureus , Streptococcus pneumoniae , and beta-hemolytic streptococci may also cause orbital cellulitis. Orbital cellulitis infections in children may get worse very quickly and can lead ...

  6. Orbital pseudotumor

    MedlinePlus

    ... called the orbit. The orbit is the hollow space in the skull where the eye sits. The ... of the visual system. In: Goldman L, Schafer AI, eds. Goldman's Cecil Medicine . 24th ed. Philadelphia, PA: ...

  7. Theoretical phase diagrams for solid H{sub 2}

    SciTech Connect

    Surh, M.P.; Runge, K.J.

    1993-07-01

    Possible phase diagrams for solid molecular para-hydrogen in the 0-200 GPa pressure regime are constructed on the basis of ab initio calculations. Structures for the broken symmetry phase (BSP) and H-A phase have recently been proposed under the assumption that the molecules are centered on sites of a hexagonal close-packed lattice with the ideal c/a ratio, i.e., only molecular orientational and electronic changes are allowed. Symmetry considerations then dictate the simplest phase diagrams consistent with experimental observations, although the possibility of additional transitions cannot be ruled out. A simple model is introduced to describe the BSP and H-A transitions.

  8. 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.

  9. Computing operating diagrams of bioreactors.

    PubMed

    Pavlou, S

    1999-05-28

    The operating diagram of a bioreactor is an illustrative way to present the effect that the operating conditions have on its long-term behavior. It can be constructed if a mathematical model of the bioreactor is available. The procedure for constructing the operating diagram consists in analyzing the dynamic behavior of the system of the differential equations of the model. Some methods are described that can be used in computing operating diagrams of bioreactors. They are based on numerical bifurcation techniques for systems of differential equations. Both cases of bioreactors with constant and periodically varying operating conditions are considered. PMID:10483097

  10. 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

    2008-12-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner 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. PMID:19063542

  11. Particles, Feynman Diagrams and All That

    ERIC Educational Resources Information Center

    Daniel, Michael

    2006-01-01

    Quantum fields are introduced in order to give students an accurate qualitative understanding of the origin of Feynman diagrams as representations of particle interactions. Elementary diagrams are combined to produce diagrams representing the main features of the Standard Model.

  12. 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.

  13. 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. PMID:24858354

  14. Atemporal diagrams for quantum circuits

    SciTech Connect

    Griffiths, Robert B.; Wu Shengjun; Yu Li; Cohen, Scott M.

    2006-05-15

    A system of diagrams is introduced that allows the representation of various elements of a quantum circuit, including measurements, in a form which makes no reference to time (hence 'atemporal'). It can be used to relate quantum dynamical properties to those of entangled states (map-state duality), and suggests useful analogies, such as the inverse of an entangled ket. Diagrams clarify the role of channel kets, transition operators, dynamical operators (matrices), and Kraus rank for noisy quantum channels. Positive (semidefinite) operators are represented by diagrams with a symmetry that aids in understanding their connection with completely positive maps. The diagrams are used to analyze standard teleportation and dense coding, and for a careful study of unambiguous (conclusive) teleportation. A simple diagrammatic argument shows that a Kraus rank of 3 is impossible for a one-qubit channel modeled using a one-qubit environment in a mixed state.

  15. Structures, molecular orbitals and UV-vis spectra investigations on methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate: A computational study

    NASA Astrophysics Data System (ADS)

    Wang, Tsang-Hsiu; Chu, Hsing-Yu; Wang, I.-Teng

    2014-10-01

    The methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate (C11H11N3O2) has been studied by theoretically methods. The structure of this compound is optimized by density functional theory (DFT), the second-order Møller-Plesset perturbation theory (MP2) and G3 theory (G3(MP2)) levels. Our calculation results are in very good agreement with experimental values. Compared to a perfect pentagonal structure, the geometrical structures of C11H11N3O2 show a little distortion of 1,2,3-triazole ring due to the highly electronegativity of substitution groups. In addition, dipole moment and frontier molecular orbitals (FMOs) of the C11H11N3O2 are calculated as well. Because of solvent effect, the HOMO-LUMO energy gap in methanol is predicted to be smaller than in gas phase by 0.367 eV. The simulated UV-vis spectra are investigated by time-dependent density functional theory (TD-DFT), and two obviously absorption features have been predicted. These two absorption features are located between 170 nm and 210 nm, which is in ultraviolet C range. Moreover, the UV absorption features in methanol are predicted to be more intense than in gas phase; besides, the red shift is predicted in methanol as well.

  16. Design of donors with broad absorption regions and suitable frontier molecular orbitals to match typical acceptors via substitution on oligo(thienylenevinylene) toward solar cells.

    PubMed

    Tang, Shanshan; Zhang, Jingping

    2012-06-01

    A series of oligo(thienylenevinylene) derivatives with or without thieno[3,2-b]thiophene analogs as cores and three types substituent has been investigated at the PBE0/6-31G(d) and the TD-PBE0/6-31+G(d,p) levels to design materials with high performance such as suitable frontier molecular orbital (FMO) energies to match those of [6,6]-phenyl-C(61)-butyric acid methyl ester (PCBM) and its derivatives, broad absorption spectra, higher and balance transfer property, and better stability. The results reveal that fused cores have slight effects on photophysical properties of investigated derivatives. The electron-withdrawing or push-pull substituents result in red shifts of absorption spectra and better stabilities for investigated derivatives. The calculated reorganization energies of designed derivatives suggest them to be good potential ambipolar transport materials under the proper operating conditions. The promising donors for PCBM, bisPCBM, PC70BM, and indene-C(60) bisadduct (ICBA) as acceptors are recommended theoretically for solar cells based on the proper match for FMOs between donors and acceptors. Moreover, we have also predicted the mobility of designed molecule with better performance. PMID:22488353

  17. A molecular orbital study on the conformational properties of dopamine [1,2-benzenediol-4(2-aminoethyl)]and dopamine cation

    NASA Astrophysics Data System (ADS)

    Fausto, Rui; Ribeiro, Maria João S.; de Lima, João J. Pedroso

    1999-06-01

    The results of a series of ab initio (3-21G) and semiempirical (PM3) molecular orbital (MO) calculations on neutral, zwitterionic and cationic forms of dopamine [1,2-benzenediol-4(2-aminoethyl)] are reported. In particular, optimised geometries, relative stabilities, dipole moments and electron charge distributions for the relevant conformational states of the studied molecules are presented and the conformational dependence of some relevant structural parameters is used to characterise the most important intramolecular interactions present in the studied conformers. It is shown that all the studied molecules have a considerably high degree of conformational flexibility, and may exist as a mixture of several conformers of similar energies differing by the relative orientation of the aromatic ring with respect to the alkylamine chain or of the hydroxyl groups. For both neutral dopamine and dopamine cation, the conformational ground state corresponds to a form where the meta-hydroxy group has its hydrogen atom directed towards the para-hydroxy group, the aromatic ring and the alkylamine axis are nearly perpendicular and the C-C-C-N axis assumes a gauche geometry, with the amine group in the same side of the meta-hydroxy group. In turn, the zwitterionic form of dopamine is predicted not to correspond to a minimum in the potential energy surface (PES) for the isolated molecule situation. However, in the zwitterion dimmer, the conformation assumed by the individual molecules is predicted to be similar to that previously observed in crystalline dopamine hydrochloride.

  18. Structure, electronic and magnetic properties of hexagonal boron nitride sheets doped by 5d transition metal atoms: First-principles calculations and molecular orbital analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Zhaofu; Geng, Zhaohui; Cai, Danyun; Pan, Tongxi; Chen, Yixin; Dong, Liyuan; Zhou, Tiege

    2015-01-01

    A first-principles calculation based on density functional theory is carried out to reveal the geometry, electronic structures and magnetic properties of hexagonal boron nitride sheets (h-BNSs) doped by 5d transitional mental atoms (Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au and Hg) at boron-site (B5d) and nitrogen-site (N5d). Results of pure h-BNS, h-BNS with B vacancy (VB) and N vacancy (VN) are also given for comparison. It is shown that all the h-BNSs doped with 5d atoms possess a C3v local symmetry except for NLu and NHg which have a clear deviation. For the same 5d dopant, the binding energy of B5d is larger than that of N5d, which indicates the substitution of a 5d atom for B is preferred. The total densities of states are presented, where impurity energy levels exist. Besides, the total magnetic moments (TMMs) change regularly with the increment of the 5d atomic number. Theoretical analyses by molecular orbital under C3v symmetry explain the impurity energy levels and TMMs.

  19. A Localized Molecular Orbital Study of the Halogen Substitution Effect on (103)Rh NMR Shielding in [Cp*RhX2]2, Where X = Cl, Br, or I.

    PubMed

    Mirzaeva, Irina V; Mainichev, Dmitry A; Kozlova, Svetlana G

    2016-03-24

    (103)Rh NMR parameters and the bonding structure of three complexes of [Cp*RhX2]2, where X = Cl, Br, or I, have been studied with the help of natural bond orbitals (NBOs) and natural localized molecular orbitals (NLMOs). The complexes of [Cp*RhX2]2, where X = Cl, Br, or I, have similar bonding structures, with the major difference being in the degree of covalency of the Rh-X bonds. The decomposition of (103)Rh NMR shielding into diamagnetic, paramagnetic, and spin-orbit terms shows that normal halogen dependence (NHD) of the (103)Rh NMR shift is defined mostly by the paramagnetic term, with the spin-orbit term being significantly smaller. The decomposition of (103)Rh shielding into spin-free NBO and NLMO contributions shows that (103)Rh shielding is dominated by Rh d-orbital deshielding contributions. We explain the NHD of the (103)Rh NMR shift with the increase in the energies of the virtual antibonding Rh-X orbitals along the X = Cl, Br, and I series. PMID:26927955

  20. Phase diagrams of decomposing nanoalloys

    NASA Astrophysics Data System (ADS)

    Shirinyan, A. S.; Gusak, A. M.

    2004-02-01

    The thermodynamics of nucleation and decomposition in small isolated particles are considered. There exist three possibilities: phase separation, prohibition of decomposition and a metastable state. We investigate the peculiarities of phase diagrams related to depletion of the nanosize parent phase even at the nucleation stage. For small particles the equilibrium diagram becomes split (and shifted and size dependent). Concentration, size and temperature hystereses take place. Size-dependent 'critical supersaturation', increasing with decreasing size, has been analysed.

  1. Quantum mechanical calculations and spectroscopic (FT-IR, FT-Raman and UV) investigations, molecular orbital, NLO, NBO, NLMO and MESP analysis of 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl] benzene-1-sulfonamide

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.

    2015-02-01

    The molecular structural parameters and vibrational frequencies of the fundamental modes of 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl] benzene-1-sulfonamide(abbreviated as 4MPTFM1HPB1SA) have been obtained using Density functional theory (DFT) technique in the B3LYP approximation with 6-311G(d,p) and 6-311++G(d,p) basis sets. Detailed vibrational assignments of the observed FT-IR and FT-Raman bands have been proposed on the basis of potential energy distribution (PED). The difference between the observed and the calculated wavenumbers values are very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. The molecular electrostatic potential has been mapped primarily for predicting sites and relative reactivities toward electrophilic and nucleophilic attack. The intramolecular contacts have been interpreted using Natural Bond Orbital (NBO) and Natural Localized Molecular Orbital (NLMO) analysis. Important non-linear properties such as electric dipolemoment and first hyperpolarizability of 4MPTFM1HPB1SA have been computed using B3LYP quantum chemical calculation. The absorption wavelength, energy and oscillator's strength are calculated by TD-DFT and 4MPTFM1HPB1SA is approach complement with the experimental findings. The temperature dependence of thermodynamic properties has been analyzed. The Natural charges, Frontier molecular orbitals (FMOs), chemical hardness (η), chemical potential (μ), Electro negativity (χ) and electrophilicity values (ω) are calculated and reported.

  2. Energy Tracking Diagrams

    NASA Astrophysics Data System (ADS)

    Scherr, Rachel E.; Harrer, Benedikt W.; Close, Hunter G.; Daane, Abigail R.; DeWater, Lezlie S.; Robertson, Amy D.; Seeley, Lane; Vokos, Stamatis

    2016-02-01

    Energy is a crosscutting concept in science and features prominently in national science education documents. In the Next Generation Science Standards, the primary conceptual learning goal is for learners to conserve energy as they track the transfers and transformations of energy within, into, or out of the system of interest in complex physical processes. As part of tracking energy transfers among objects, learners should (i) distinguish energy from matter, including recognizing that energy flow does not uniformly align with the movement of matter, and should (ii) identify specific mechanisms by which energy is transferred among objects, such as mechanical work and thermal conduction. As part of tracking energy transformations within objects, learners should (iii) associate specific forms with specific models and indicators (e.g., kinetic energy with speed and/or coordinated motion of molecules, thermal energy with random molecular motion and/or temperature) and (iv) identify specific mechanisms by which energy is converted from one form to another, such as incandescence and metabolism. Eventually, we may hope for learners to be able to optimize systems to maximize some energy transfers and transformations and minimize others, subject to constraints based in both imputed mechanism (e.g., objects must have motion energy in order for gravitational energy to change) and the second law of thermodynamics (e.g., heating is irreversible). We hypothesize that a subsequent goal of energy learning—innovating to meet socially relevant needs—depends crucially on the extent to which these goals have been met.

  3. Global quantum Hall phase diagram from visibility diagrams

    NASA Astrophysics Data System (ADS)

    Chandelier, F.; Georgelin, Y.; Masson, T.; Wallet, J.-C.

    2002-09-01

    Starting from a framework encoding rather simple symmetry principle based on modular subgroups, we construct a zero temperature global phase diagram for the QHE. This phase diagram is found to involve two insulating phases. One noticeable prediction is the possibility to have direct transitions from an insulting phase to any integer ν as well as ν=1/(2 k+1) ( k∈ N) fractional quantum Hall liquid phases which seems to agree with some recent experimental observations. We also propose selection rules for the possible plateau-plateau (and plateau-insulator) transitions which may constitute testable predictions.

  4. The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n-butane conformation and SN2 reaction: RCl+Cl -

    NASA Astrophysics Data System (ADS)

    Humbel, Stéphane; Sieber, Stefan; Morokuma, Keiji

    1996-08-01

    A new theoretical method, called IMOMO (integrated MO (molecular orbital)+MO), for integration of two different levels of MO approximation is presented. Only the active or more difficult part of a molecule is treated at a higher level of approximation and the rest of the molecule at a lower level of approximation. The integrated total energy and energy derivatives are defined from three different calculations, and the structure of transition state as well as the equilibrium structure can be optimized using the integrated energy. Any combination of any molecular orbital approximations (ab initio, density functional to semi-empirical) can be used. Test calculations in the IMOMO method have been performed and compared with normal MO calculations for the conformation energy of ethane and n-butane and the SN2 reaction of ethyl, propyl, isobutyl, and neopentyl chloride with Cl-. The results indicate that these methods have a tremendous potential for theoretical study of larger molecules, in particular for transition states.

  5. Automatically Assessing Graph-Based Diagrams

    ERIC Educational Resources Information Center

    Thomas, Pete; Smith, Neil; Waugh, Kevin

    2008-01-01

    To date there has been very little work on the machine understanding of imprecise diagrams, such as diagrams drawn by students in response to assessment questions. Imprecise diagrams exhibit faults such as missing, extraneous and incorrectly formed elements. The semantics of imprecise diagrams are difficult to determine. While there have been…

  6. 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. PMID:26580761

  7. Role of O/sup -/ surface radicals for methane CH bond activation and subsequent reactions on MoO/sub 3/: molecular orbital theory

    SciTech Connect

    Mehandru, S.P.; Anderson, A.B.; Brazdil, J.F.; Grasselli, R.K.

    1987-05-21

    A molecular orbital study is made of the reaction of methane with O/sup -/ hole centers on the surface of MoO/sub 3/. The following predictions are made. When the O/sup -/ is created by a UV O 2p ..cap alpha.. Mo 4d charge-transfer excitation, heterolytic products, OH/sup -/ and Mo/sub V/ x CH/sub 3/, form readily at the edges of the crystals where unsaturated molybdenum sites are present. Deexcitation to OH/sup -/ and Mo/sup VI/:CH/sub 3//sup -/ is expected to proceed rapidly and a side reaction to slightly less stale homolytic products, OH/sup -/, 2Mo/sup V/, and OCH/sub 3//sup -/, may also take place, preventing deexcitation so that Mo/sup V/ is not oxidized to Mo/sup VI/, so that the excitation energy may be said to be chemically stored. The CH bond activation barrier is calculated to be 0.7 eV. Activation is a consequence of a stabilizing 3-centered CH-O/sup -/ sigma-donation interaction, the antibonding counterpart of which takes the hole and is occupied by only one electron in the transition state. If a second electron-hole pair is formed, the methyl radical can shift to the O/sup -/ center with a slight loss in stability, and the surface is reduced by two electrons. The methyl cation which is formed can be viewed as a methyl radical which has promoted an electron to a nearby Mo/sup VI/. Once the methyl radical moves to a basal plane of the crystal, which is covered entirely by oxygen anions, it diffuses with a low approx.0.4-eV barrier.

  8. Matched designs and causal diagrams

    PubMed Central

    Mansournia, Mohammad A; Hernán, Miguel A; Greenland, Sander

    2013-01-01

    We use causal diagrams to illustrate the consequences of matching and the appropriate handling of matched variables in cohort and case-control studies. The matching process generally forces certain variables to be independent despite their being connected in the causal diagram, a phenomenon known as unfaithfulness. We show how causal diagrams can be used to visualize many previous results about matched studies. Cohort matching can prevent confounding by the matched variables, but censoring or other missing data and further adjustment may necessitate control of matching variables. Case-control matching generally does not prevent confounding by the matched variables, and control of matching variables may be necessary even if those were not confounders initially. Matching on variables that are affected by the exposure and the outcome, or intermediates between the exposure and the outcome, will ordinarily produce irremediable bias. PMID:23918854

  9. Phase diagrams and crystal growth

    NASA Astrophysics Data System (ADS)

    Venkrbec, Jan

    1980-04-01

    Phase diagrams are briefly treated as generalized property-composition relationships, with respect to crystal technology optimization. The treatment is based on mutual interaction of three systems related to semiconductors: (a) the semiconducting material systems, (b0 the data bank, (c) the system of crystallization methods. A model is proposed enabling optimatization on the path from application requirements to the desired material. Further, several examples of the selection as to the composition of LED and laser diode material are given. Some of molten-solution-zone methods are being successfully introduced for this purpose. Common features of these methods, the application of phase diagrams, and their pecularities compared with other crystallization methods are illustrated by schematic diagrams and by examples. LPE methods, particularly the steady-state LPE methods such as Woodall's ISM and Nishizawa's TDM-CVP, and the CAM-S (Crystallization Method Providing Composition Autocontrol in Situ) have been chosen as examples. Another approach of exploiting phase diagrams for optimal material selection and for determination of growth condition before experimentation through a simple calculation is presented on InP-GaP solid solutions. Ternary phase diagrams are visualized in space through calculation and constructions based on the corresponding thermodynamic models and anaglyphs. These make it easy to observe and qualitatively analyze the crystallization of every composition. Phase diagrams can be also used as a powerful tool for the deduction of new crystallization methods. Eutectic crystallization is an example of such an approach where a modified molten-solution-zone method can give a sandwich structure with an abrupt concentration change. The concentration of a component can range from 0 to 100% in the different solid phases.

  10. Orbiter Autoland reliability analysis

    NASA Technical Reports Server (NTRS)

    Welch, D. Phillip

    1993-01-01

    The Space Shuttle Orbiter is the only space reentry vehicle in which the crew is seated upright. This position presents some physiological effects requiring countermeasures to prevent a crewmember from becoming incapacitated. This also introduces a potential need for automated vehicle landing capability. Autoland is a primary procedure that was identified as a requirement for landing following and extended duration orbiter mission. This report documents the results of the reliability analysis performed on the hardware required for an automated landing. A reliability block diagram was used to evaluate system reliability. The analysis considers the manual and automated landing modes currently available on the Orbiter. (Autoland is presently a backup system only.) Results of this study indicate a +/- 36 percent probability of successfully extending a nominal mission to 30 days. Enough variations were evaluated to verify that the reliability could be altered with missions planning and procedures. If the crew is modeled as being fully capable after 30 days, the probability of a successful manual landing is comparable to that of Autoland because much of the hardware is used for both manual and automated landing modes. The analysis indicates that the reliability for the manual mode is limited by the hardware and depends greatly on crew capability. Crew capability for a successful landing after 30 days has not been determined yet.

  11. The Hot Orbit: Orbital Cellulitis

    PubMed Central

    Chaudhry, Imtiaz A.; Al-Rashed, Waleed; Arat, Yonca O.

    2012-01-01

    Orbital cellulitis is an uncommon condition previously associated with severe complications. If untreated, orbital cellulitis can be potentially sight and life threatening. It can affect both adults and children but has a greater tendency to occur in the pediatric age group. The infection most commonly originates from sinuses, eyelids or face, retained foreign bodies, or distant soources by hematogenous spread. It is characterized by eyelid edema, erythema, chemosis, proptosis, blurred vision, fever, headache, and double vision. A history of upper respiratory tract infection prior to the onset is very common especially in children. In the era prior to antibiotics, vision loss from orbital cellulitis was a dreaded complication. Currently, imaging studies for detection of orbital abcess, the use of antibiotics and early drainage have mitigated visual morbidity significantly. The purpose of this review is to describe current investigative strategies and management options in the treatment of orbital cellulitis, establish their effectiveness and possible complications due to late intervention. PMID:22346113

  12. Voronoi Diagrams and Spring Rain

    ERIC Educational Resources Information Center

    Perham, Arnold E.; Perham, Faustine L.

    2011-01-01

    The goal of this geometry project is to use Voronoi diagrams, a powerful modeling tool across disciplines, and the integration of technology to analyze spring rainfall from rain gauge data over a region. In their investigation, students use familiar equipment from their mathematical toolbox: triangles and other polygons, circumcenters and…

  13. The Butterfly Diagram internal structure .

    NASA Astrophysics Data System (ADS)

    Ternullo, M.

    A new graphic representation of the spotgroup distribution with respect to time and latitude is presented. At variance with Maunder's Butterfly Diagram, which registers the mere presence of spotgroups, the diagram presented here accounts for the spotgroup area. It shows that spotgroups aggregate in a few small, heavenly spotted portions (``knots'') of the diagram. Each knot is the signature of a photospheric region tightly limited in latitude, active for a short time. The butterfly diagram is but a cluster of knots and the spot zone is the latitude range inside which knots activate. The cycle is a sequence of knots activations and extinctions. Even though knots show the overall tendency to appear at lower and lower latitudes as the cycle goes on, a knot may appear at either lower or higher latitudes than previous ones. The examination of the knot distribution inside the ``butterfly wings'' suggests that - at any cycle and at any hemisphere - two ``activity waves" drift equatorward at a rate roughly twice the drift rate of the spot zone as a whole.

  14. 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.

  15. The tetrahedral framework in glasses and melts — inferences from molecular orbital calculations and implications for structure, thermodynamics, and physical properties

    NASA Astrophysics Data System (ADS)

    Navrotsky, A.; Geisinger, K. L.; McMillan, P.; Gibbs, G. V.

    1985-01-01

    Results of ab initio molecular orbital (MO) calculations provide a basis for the interpretation of structural and thermodynamic properties of crystals, glasses, and melts containing tetrahedrally coordinated Si, Al, and B. Calculated and experimental tetrahedral atom-oxygen ( TO) bond lengths are in good agreement and the observed average SiO and AlO bond lengths remain relatively constant in crystalline, glassy, and molten materials. The TO T framework geometry, which determines the major structural features, is governed largely by the local constraints of the strong TO bonds and its major features are modeled well by ab initio calculations on small clusters. Observed bond lengths for non-framework cations are not always in agreement with calculated values, and reasons for this are discussed in the text. The flexibility of SiOSi, SiOAl, and AlOAl angles is in accord with easy glass formation in silicates and aluminosilicates. The stronger constraints on tetrahedral BOB and BOSi angles, as evidenced by much deeper and steeper calculated potential energy versus angle curves, suggest much greater difficulty in substituting tetrahedral B than Al for Si. This is supported by the pattern of immiscibility in borosilicate glasses, although the occurrence of boron in trigonal coordination is an added complication. The limitations on glass formation in oxysulfide and oxynitride systems may be related to the angular requirements of SiSSi and Si(NH)Si groups. Although the SiO and AlO bonds are the strongest ones in silicates and aluminosilicates, they are perturbed by other cations. Increasing perturbation and weakening of the framework occurs with increasing ability of the other atom to compete with Si or Al for bonding to oxygen, that is, with increasing cation field strength. The perturbation of TO T groups, as evidenced by TO bond lengthening predicted by MO calculations and observed in ordered crystalline aluminosilicates, increases in the series Ca, Mg and K, Na, Li. This perturbation correlates strongly with thermochemical mixing properties of glasses in the systems SiO2- M {1/ n/ n+}AlO2 and SiO2- M n+O n/2 ( M=Li, Na, K, Rb, Cs, and Mg, Ca, Sr, Ba, Pb), with tendencies toward immiscibility in these systems, and with systematics in vibrational spectra. Trends in physical properties, including viscosity at atmospheric and high pressure, can also be correlated.

  16. Molecular orbital calculations on the vibrational spectra of Q 3 T-(OH) species and the hydrolysis of a three-membered aluminosilicate ring

    NASA Astrophysics Data System (ADS)

    Kubicki, J. D.; Sykes, Dan

    1995-12-01

    Force constant analyses of the molecules [(H 3SiO) 3Al-(OH)] 1-, Na +[(H 3SiO) 3Al-(OH)] 1-, [((OH) 3SiO) 3Al-(OH)] 1- [(H 3SiO) 3Si-(OH)],[((OH) 3SiO) 3Si-(OH)],[((OH) 3SiO) 2((OH) 3A10)Si(OH)] 1- and Na + [(H 3SiO ) 2 (H 3Al0) Si- (OH)] 1- have been performed with ab initio molecular orbital calculations to determine the frequencies and H-D shifts of T- (OH) vibrations in Q 3 T- (OH) species where T is a So 4+ or Al 3+. Calculated Q 3 Si-(OH) vibrations are close to the observed value in H 2O-bearing Si0 2 glass. The theoretical Al-(OH) stretching frequency in Na +[ (H 3SiO) 3A1-(OH)] 1- matches the 880 cm - shoulder in the vibrational spectra of hydrous albitic glasses within experimental error. Isotopic substitution of deuterium for hydrogen in the T-(OH) bond results in frequency shifts of less than 25 cm -1 in all cases consistent with the small H-D frequency shifts observed in silica (Mysen and Virgo, 1986) and Na-aluminosilicate glasses (McMillan et al., 1993). Hydrolysis of a three-membered aluminosilicate ring into a trimeric chain (i.e., [H 6SiAl 20 9] 2- + H 2O → [H 8SiAl 20 10] 2-) was also calculated. Hydrolysis occurs through a pentavalent Al 3+ transition state complex. Calculated energies of the reactants and product in the above reaction predict that the chain configuration is in a marginally lower potential energy state (-36 kJ/mol) than the H 2O-ring dimer. An activation energy of + 171 kJ/mol is predicted between the two species for hydrolysis and +207 kJ/mol for the reverse reaction.

  17. A study of gas-phase reactions of radical cations of mono- and dihaloethenes with alcohols by FT-ICR spectrometry and molecular orbital calculations: substitution versus oxidation.

    PubMed

    Nixdorf, A; Grützmacher, H F

    2001-03-16

    The ion-molecule reactions of the radical cations of vinyl chloride (1), vinyl bromide (2), 1,2-dichloroethene (3), 1,2-dibromoethene (4), 1,1-dichloroethene (5), and 1,1-dibromoethene (6) with methanol (MeOH) and ethanol (EtOH) have been studied by FT-ICR spectrometry. In the case of EtOH as reactant the oxidation of the alcohol to protonated acetaldehyde by a formal hydride transfer to the haloethene radical cation is the main process if not only reaction observed with the exception of the 1,2-dibromoethene radical cation which exhibits slow substitution. In secondary reactions the protonated acetaldehyde transfers the proton to EtOH which subsequently undergoes a well known condensation reaction of EtOH to form protonated diethyl ether. With MeOH as reactant, the 1,2-dihaloethene radical cations of 3.+ and 4.+ exhibit no reaction, while the other haloethene radical cations undergo the analogous reaction sequence of oxidation yielding protonated formaldehyde. Generally, bromo derivatives of haloethene radical cations react predominantly by substitution and chloro derivatives by oxidation. This selectivity can be understood by the thermochemistry of the competing processes which favors substitution of Br while the effect of the halogen substituent on the formal hydride transfer is small. However, the bimolecular rate constants and reaction efficiencies of the total reactions of the haloethene radical cations with both alcohols exhibit distinct differences, which do not follow the exothermicity of the reactions. It is suggested that the substitution reaction as well as the oxidation by formal hydride transfer proceeds by mechanisms which include fast and reversible addition of the alcohol to the ionized double bond of the haloethene radical cation which generates a beta-distonic oxonium ion as the crucial intermediate. This intermediate is energetically excited by the exothermic addition and fragments either directly by elimination of a halogen substituent to complete the substitution process or rearranges by hydrogen migration before dissociation into the protonated aldehyde and a beta-haloethyl radical. Reversible addition and hydrogen migrations within a long lived intermediate is proven experimentally by H/D exchange accompanying the reaction of the radical cations of vinyl chloride (1) and 1,1-dichloroethene (5) with CD3OH. The suggested mechanisms are substantiated by ab initio molecular orbital calculations. PMID:11322551

  18. The Phase Diagram of Superionic Ice

    NASA Astrophysics Data System (ADS)

    Sun, Jiming; Clark, Bryan; Car, Roberto

    2014-03-01

    Using the variable cell Car-Parrinello molecular dynamics method, we study the phase diagram of superionic ice from 200GPa to 2.5TPa. We present evidence that at very high pressure the FCC structure of the oxygen sublattice may become unstable allowing for a new superionic ice phase, in which the oxygen sublattice takes the P21 structure found in zero-temperature total energy calculations. We also report on how the melting temperature of the hydrogen sublattice is affected by this new crystalline structure of the oxygen sublattice. This work was supported by the NSF under grant DMS-1065894(J.S. and R.C.) and PHY11-25915(B.C.).

  19. Spectral Determinants on Mandelstam Diagrams

    NASA Astrophysics Data System (ADS)

    Hillairet, Luc; Kalvin, Victor; Kokotov, Alexey

    2015-11-01

    We study the regularized determinant of the Laplacian as a functional on the space of Mandelstam diagrams (noncompact translation surfaces glued from finite and semi-infinite cylinders). A Mandelstam diagram can be considered as a compact Riemann surface equipped with a conformal flat singular metric {|?|^2} , where {?} is a meromorphic one-form with simple poles such that all its periods are pure imaginary and all its residues are real. The main result is an explicit formula for the determinant of the Laplacian in terms of the basic objects on the underlying Riemann surface (the prime form, theta-functions, the canonical meromorphic bidifferential) and the divisor of the meromorphic form {?} . As an important intermediate result we prove a decomposition formula of the type of Burghelea-Friedlander-Kappeler for the determinant of the Laplacian for flat surfaces with cylindrical ends and conical singularities.

  20. Unveiling the butterfly diagram structure

    NASA Astrophysics Data System (ADS)

    Ternullo, Maurizio

    2011-06-01

    A Butterfly Diagram showing the spotted area distribution is presented. The diagram reveals that most of the spotted area is concentrated in few, small portions (``knots'') of the butterfly wings. A knot may appear at either lower or higher latitudes than previous ones, in a seemingly random way; accordingly, the spot mean latitude abruptly drifts equatorward or even poleward at any knot activation, in spite of any smoothing procedure. The description, assuming that spots scatter around the ``spot mean latitude'' steadily drifting equatorward, is questioned. In a relevant number of cases, knots appear to be arranged in two roughly parallel, oblique streams, the ``spot mean latitude'' being located in the underspotted band lying between these streams.

  1. The Butterfly Diagram Internal Structure

    NASA Astrophysics Data System (ADS)

    Ternullo, Maurizio

    2013-06-01

    A time-latitude diagram, where the spotgroup area is taken into account, is presented for cycles 12 through 23. The results show that the spotted area is concentrated in few, small portions ("knots") of the Butterfly Diagram (BD). The BD may be described as a cluster of knots. Knots are distributed in the butterfly wings in a seemingly randomly way. A knot may appear at either lower or higher latitudes than previous ones, in spite of the prevalent tendency to appear at lower and lower latitudes. Accordingly, the spotted area centroid, far from continuously drifting equatorward, drifts poleward or remains stationary in any hemisphere for significant fractions (≈ 1/3) of the cycle total duration. In a relevant number of semicycles, knots seem to form two roughly parallel, oblique "chains", separated by an underspotted band. This picture suggests that two (or more) "activity streams" approach the equator at a rate higher than the spot zone as a whole.

  2. Spectral Determinants on Mandelstam Diagrams

    NASA Astrophysics Data System (ADS)

    Hillairet, Luc; Kalvin, Victor; Kokotov, Alexey

    2016-04-01

    We study the regularized determinant of the Laplacian as a functional on the space of Mandelstam diagrams (noncompact translation surfaces glued from finite and semi-infinite cylinders). A Mandelstam diagram can be considered as a compact Riemann surface equipped with a conformal flat singular metric {|ω|^2}, where {ω} is a meromorphic one-form with simple poles such that all its periods are pure imaginary and all its residues are real. The main result is an explicit formula for the determinant of the Laplacian in terms of the basic objects on the underlying Riemann surface (the prime form, theta-functions, the canonical meromorphic bidifferential) and the divisor of the meromorphic form {ω}. As an important intermediate result we prove a decomposition formula of the type of Burghelea-Friedlander-Kappeler for the determinant of the Laplacian for flat surfaces with cylindrical ends and conical singularities.

  3. INCONEL 718: A solidification diagram

    NASA Astrophysics Data System (ADS)

    Knorovsky, G. A.; Cieslak, M. J.; Headley, T. J.; Romig, A. D.; Hammetter, W. F.

    1989-10-01

    As part of a program studying weldability of Ni-base superalloys, results of an integrated analytical approach are used to generate a constitution diagram for INCONEL 718* in the temperature range associated with solidification. Differential thermal analysis of wrought material and optical and scanning electron microscopy, electron probe microanalysis, and analytical electron microscopy of gas tungsten arc welds are used in conjunction with solidification theory to generate data points for this diagram. The important features of the diagram are an austenite (γ)/Laves phase eutectic which occurs at ≈19.1 wt pct Nb between austenite containing ≈9.3 wt pct Nb and a Laves phase which contains ≈22.4 wt pct Nb. The distribution coefficient for Nb was found to be ≈0.5. The solidification sequence of INCONEL 718 was found to be (1) proeutectic γ, followed by (2) a γ/NbC eutectic at ≈1250°C, followed by (3) continued γ solidification, followed by (4) a γ/Laves phase eutectic at ≈1200°C. An estimate of the volume fraction eutectic is made using the Scheil solidification model, and the fraction of each phase in the eutectic is calculated via the lever rule. These are compared with experimentally determined values and found to be in good agreement.

  4. 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. PMID:25266873

  5. 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.

  6. Arrows in Comprehending and Producing Mechanical Diagrams

    ERIC Educational Resources Information Center

    Heiser, Julie; Tversky, Barbara

    2006-01-01

    Mechanical systems have structural organizations--parts, and their relations--and functional organizations--temporal, dynamic, and causal processes--which can be explained using text or diagrams. Two experiments illustrate the role of arrows in diagrams of mechanical systems. In Experiment 1, people described diagrams with or without arrows,…

  7. 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.

  8. 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.

  9. Understanding machines from text and diagrams

    NASA Astrophysics Data System (ADS)

    Hegarty, Mary; Just, Marcel A.

    1987-12-01

    Instructional materials typically use both text and diagrams to explain how machines work. In this paper we give an account of what information is involved in understanding a mechanical device and the role that diagrams might play in communicating this information. We propose a model of how people read a text and inspect an accompanying diagram which states that people inspect diagrams for three reasons: (1) to form a representation of information read in the text, (2) to reactivate information that has already been represented, and (3) to encode information that is absent from the text. Using data from subjects' eye fixations while they read a text and inspected an accompanying diagram, we find that low-ability subjects need to inspect diagrams more often than high-ability text. The data also suggest that knowledge of what is relevant in a diagram might be a prerequisite for encoding new information from a diagram. Instructional materials typically use both text and diagrams to explain how machines work. In this paper we give an account of what information is involved in understanding a mechanical device and the role that diagrams might play in communicating this information. We propose a model of how people read a text and inspect an accompanying diagram which states that people inspect diagrams for three reasons: (1) to form a representation of information read in the text; (2) to reactivate information that was alsready represented, and *3) to encode information that is absent from the text. Uinsg data from subjects' eye fixations while they read a text and inspected an accompanying diagram, we find that low-ability subjects need to inspect diagrmas more often than high-ability tesxt. The data also suggest that knowledge of what is relevant in a diagram might be a prerequisite and encoding information on a diagram.

  10. Diagram, a Learning Environment for Initiation to Object-Oriented Modeling with UML Class Diagrams

    ERIC Educational Resources Information Center

    Py, Dominique; Auxepaules, Ludovic; Alonso, Mathilde

    2013-01-01

    This paper presents Diagram, a learning environment for object-oriented modelling (OOM) with UML class diagrams. Diagram an open environment, in which the teacher can add new exercises without constraints on the vocabulary or the size of the diagram. The interface includes methodological help, encourages self-correcting and self-monitoring, and…

  11. Mapping the topological phase diagram of multiband semiconductors with supercurrents

    NASA Astrophysics Data System (ADS)

    Prada, Elsa; San-Jose, Pablo; Aguado, Ramon

    2014-03-01

    We show that Josephson junctions made of multiband semiconductors with strong spin-orbit coupling carry a critical supercurrent Ic that contains information about the non-trivial topology of the system. In particular, we find that the emergence and annihilation of Majorana bound states in the junction is reflected in strong even-odd effects in Ic under specific conditions. This effect allows for a mapping between Ic and the topological phase diagram of the junction, thus providing a dc measurement of its topology. European Research Council, Spanish Ministry of Economy and Innovation and the Ramón y Cajal Program.

  12. Handling the handbag diagram in Compton scattering on the proton

    NASA Astrophysics Data System (ADS)

    Miller, Gerald A.

    2004-05-01

    Poincaré invariance, gauge invariance, conservation of parity, and time reversal invariance are respected in an impulse approximation evaluation of the handbag diagram. Proton wave functions, previously constrained by comparison with measured form factors, that incorporate the influence of quark transverse and orbital angular momentum (and the corresponding violation of proton helicity conservation) are used. Computed cross sections are found to be in reasonably good agreement with early measurements. The helicity correlation between the incident photon and outgoing proton, KLL , is both large and positive at back angles. For photon laboratory energies of ⩽6 GeV , we find that KLL ≠ ALL , and DLL ≠1 .

  13. Orbital Mechanics.

    ERIC Educational Resources Information Center

    Dalton, Joel B.

    Three computer programs are presented that allow the high school student to explore and understand the physical forces involved in orbital flight at a greater depth than is usually possible. For each program, introductory material is given including the physics and mathematics involved. This is followed by the computer program in BASIC language.…

  14. Orbit analysis

    SciTech Connect

    Michelotti, L.

    1995-09-01

    We take an overview of recently developed methods for studying single particle orbits in accelerators and discuss some physics underlying those which involve Lie operators. It will be further argued that object-oriented programming provides the appropriate computing strategy in which to model accelerators and to implement these techniques.

  15. Origin and use of crystallization phase diagrams.

    PubMed

    Rupp, Bernhard

    2015-03-01

    Crystallization phase diagrams are frequently used to conceptualize the phase relations and also the processes taking place during the crystallization of macromolecules. While a great deal of freedom is given in crystallization phase diagrams owing to a lack of specific knowledge about the actual phase boundaries and phase equilibria, crucial fundamental features of phase diagrams can be derived from thermodynamic first principles. Consequently, there are limits to what can be reasonably displayed in a phase diagram, and imagination may start to conflict with thermodynamic realities. Here, the commonly used `crystallization phase diagrams' are derived from thermodynamic excess properties and their limitations and appropriate use is discussed. PMID:25760697

  16. 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.

  17. The butterfly diagram internal structure

    NASA Astrophysics Data System (ADS)

    Ternullo, M.

    2010-07-01

    This work originates from the need of getting a picture of the spot zone that is sharp enough to efficiently help us place tighter and more realistic constraints than we would usually do on dynamo models, in order to improve their predictive performance. This paper questions the confidence in Maunder’s Butterfly Diagram (BD) as the fundamental tool for describing the magnetic flux large-scale distribution and presents a new version of the time-latitude diagram for cycles 21 through 23, where spot groups are given proportional relevance to their area. The diagram presented here confirms the active regions’ well-known tendency to repeatedly appear in a few photospheric regions (“ activity nests”) tightly limited in latitude, active for a short time. Activity nests leave their signature in the BD, in the form of small portions (“ knots”) characterized by the spotted area high density. The BD may be described as a cluster of knots. A knot may appear at either lower or higher latitudes than previous ones; accordingly, the spot mean latitude abruptly drifts equatorward or even poleward, even though the knot’s prevalent tendency is to appear at lower and lower latitudes. A careful inspection of the BD suggests that its intricate fine structure may be (partially) disentangled by recognizing that, in any hemisphere, the activity is split into two or more distinct “activity waves” (out of phase compared to each other), drifting equatorward at a rate higher than the spot zone as a whole. Preliminary computations confirm this suggestion.

  18. A Hubble Diagram for Quasars

    NASA Astrophysics Data System (ADS)

    Risaliti, Guido; Lusso, Elisabeta

    2015-09-01

    We present a new method to test the cosmological model at high z, and measure the cosmological parameters, based on the non-linear correlation between UV and X-ray luminosity in quasars. While the method can be successfully tested with the data available today, a deep X-ray survey matching the future LSST and Euclid quasar catalogs is needed to achieve a high precision. Athena could provide a Hubble diagram for quasar analogous to that available today for supernovae, but extending up to z>6.

  19. Voronoi Diagrams Without Bounding Boxes

    NASA Astrophysics Data System (ADS)

    Sang, E. T. K.

    2015-10-01

    We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010) and Nerbonne et al (2011).

  20. Magnetized effective QCD phase diagram

    NASA Astrophysics Data System (ADS)

    Ayala, Alejandro; Dominguez, C. A.; Hernández, L. A.; Loewe, M.; Zamora, R.

    2015-11-01

    The QCD phase diagram in the temperature vs quark chemical potential plane is studied in the presence of a magnetic field, using the linear sigma model coupled to quarks. It is shown that the decrease of the couplings with increasing field strength obtained in this model leads to the critical temperature for the phase transition to decrease with increasing field intensity (inverse magnetic catalysis). This happens provided that plasma screening is properly accounted for. It is also found that with increasing field strength the location of the critical end point in the phase diagram moves toward lower values of the critical quark chemical potential and larger values of the critical temperature. In addition, the critical end point approaches the temperature axis for large values of the magnetic field. We argue that a similar behavior is to be expected in QCD, since the physical impact of the magnetic field, regardless of strength, is to produce a spatial dimension reduction, whereby virtual quark-antiquark pairs are closer on average and thus the strength of their interaction decreases due to asymptotic freedom.

  1. Cell flipping in permutation diagrams

    NASA Astrophysics Data System (ADS)

    Golumbic, Martin Charles; Kaplang, Haim

    Permutation diagrams have been used in circuit design to model a set of single point nets crossing a channel, where the minimum number of layers needed to realize the diagram equals the clique number ω(G) of its permutation graph, the value of which can be calculated in O(n log n) time. We consider a generalization of this model motivated by "standard cell" technology in which the numbers on each side of the channel are partitioned into consecutive subsequences, or cells, each of which can be left unchanged or flipped (i.e., reversed). We ask, for what choice of fiippings will the resulting clique number be minimum or maximum. We show that when one side of the channel is fixed (no flipping), an optimal flipping for the other side can be found in O(n log n) time for the maximum clique number. We prove that the general problem is NP-complete for the minimum clique number and O(n 2) for the maximum clique number. Moreover, since the complement of a permutation graph is also a permutation graph, the same complexity results hold for the independence number.

  2. The phase diagram and transport properties for hydrogen-helium fluid planets

    NASA Technical Reports Server (NTRS)

    Stevenson, D. J.; Salpeter, E. E.

    1977-01-01

    The properties of pure hydrogen and helium are examined, taking into account metallic hydrogen, molecular hydrogen, and the molecular-metallic transition. Metallic hydrogen-helium mixtures are considered along with molecular hydrogen-helium mixtures, the total phase diagram, and minor constituents, including deuterium. The transport properties of the metallic and the molecular phase are also discussed, giving attention to electrical conductivity, thermal conductivity, viscosity, self-diffusion, interdiffusion, radiative opacity, and second-order transport coefficients.

  3. Structure-retention diagrams of ceramides established for their identification.

    PubMed

    Gaudin, Karen; Chaminade, Pierre; Baillet, Arlette

    2002-10-11

    Molecular species analysis of ceramides was carried out using porous graphitic carbon with gradient elution: chloroform-methanol from 45:55 to 85:15 with a slope at 2.7%/min. These conditions gave a linear relationship between retention data and structure of ceramides. It was demonstrated that linearity occurred when a high slope value of linear gradient elution was used. Thereby the linear diagram was evolved by plotting the adjusted retention time against the total number of carbon atoms of ceramide molecules. Each line represents one ceramide class. Such a Structure-Retention Diagram describes ceramide retention and thus constitutes an identification method using only retention data. This Structure-Retention Diagram was assessed and compared to another obtained from octadesyl-grafted silica in terms of their reproducibility, precision and ability to provide ceramide identification. Better identification was obtained using the results from both Structure-Retention Diagrams. This approach with a two-dimensional separation system allowed to take advantage of the specificity of both identification models. PMID:12437165

  4. 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 ...

  5. Bifurcation Diagrams and Heteroclinic Networks of Octagonal H-Planforms

    NASA Astrophysics Data System (ADS)

    Faye, Grégory; Chossat, Pascal

    2012-06-01

    This paper completes the classification of bifurcation diagrams for H-planforms in the Poincaré disc {D} whose fundamental domain is a regular octagon. An H-planform is a steady solution of a PDE or integro-differential equation in {D}, which is invariant under the action of a lattice subgroup Γ of U(1,1), the group of isometries of {{D}}. In our case Γ generates a tiling of {D} with regular octagons. This problem was introduced as an example of spontaneous pattern formation in a model of image feature detection by the visual cortex where the features are assumed to be represented in the space of structure tensors. Under `generic' assumptions the bifurcation problem reduces to an ODE which is invariant by an irreducible representation of the group of automorphisms {G} of the compact Riemann surface {D}/\\varGamma . The irreducible representations of {G} have dimensions one, two, three and four. The bifurcation diagrams for the representations of dimensions less than four have already been described and correspond to well-known group actions. In the present work we compute the bifurcation diagrams for the remaining three irreducible representations of dimension four, thus completing the classification. In one of these cases, there is generic bifurcation of a heteroclinic network connecting equilibria with two different orbit types.

  6. Mathematical review on source-type diagrams

    NASA Astrophysics Data System (ADS)

    Aso, Naofumi; Ohta, Kazuaki; Ide, Satoshi

    2016-03-01

    A source-type diagram is a visualization tool used to display earthquake sources, including double-couples, compensated linear vector dipoles, and isotropic deformation. Together with recent observations of non-double-couple events in a variety of tectonic settings, it is important to be able to recognize the source type intuitively from a representative diagram. Since previous works have proposed diagrams created using a range of projections, we review these diagrams in the framework of the moment tensor eigenvalue space. For further applications, we also provide complete formulas for conversion between moment tensor representation and the coordinate system of each diagram style. Using both a global catalog and synthetic data, we discuss differences between types of diagrams and the relative effectiveness of each.

  7. Hubble's diagram and cosmic expansion

    PubMed Central

    Kirshner, Robert P.

    2004-01-01

    Edwin Hubble's classic article on the expanding universe appeared in PNAS in 1929 [Hubble, E. P. (1929) Proc. Natl. Acad. Sci. USA 15, 168–173]. The chief result, that a galaxy's distance is proportional to its redshift, is so well known and so deeply embedded into the language of astronomy through the Hubble diagram, the Hubble constant, Hubble's Law, and the Hubble time, that the article itself is rarely referenced. Even though Hubble's distances have a large systematic error, Hubble's velocities come chiefly from Vesto Melvin Slipher, and the interpretation in terms of the de Sitter effect is out of the mainstream of modern cosmology, this article opened the way to investigation of the expanding, evolving, and accelerating universe that engages today's burgeoning field of cosmology. PMID:14695886

  8. Hubble's diagram and cosmic expansion

    NASA Astrophysics Data System (ADS)

    Kirshner, Robert P.

    2004-01-01

    Edwin Hubble's classic article on the expanding universe appeared in PNAS in 1929 [Hubble, E. P. (1929) Proc. Natl. Acad. Sci. USA 15, 168-173]. The chief result, that a galaxy's distance is proportional to its redshift, is so well known and so deeply embedded into the language of astronomy through the Hubble diagram, the Hubble constant, Hubble's Law, and the Hubble time, that the article itself is rarely referenced. Even though Hubble's distances have a large systematic error, Hubble's velocities come chiefly from Vesto Melvin Slipher, and the interpretation in terms of the de Sitter effect is out of the mainstream of modern cosmology, this article opened the way to investigation of the expanding, evolving, and accelerating universe that engages today's burgeoning field of cosmology.

  9. Phase diagram of ammonium nitrate.

    PubMed

    Dunuwille, Mihindra; Yoo, Choong-Shik

    2013-12-01

    Ammonium Nitrate (AN) is a fertilizer, yet becomes an explosive upon a small addition of chemical impurities. The origin of enhanced chemical sensitivity in impure AN (or AN mixtures) is not well understood, posing significant safety issues in using AN even today. To remedy the situation, we have carried out an extensive study to investigate the phase stability of AN and its mixtures with hexane (ANFO-AN mixed with fuel oil) and Aluminum (Ammonal) at high pressures and temperatures, using diamond anvil cells (DAC) and micro-Raman spectroscopy. The results indicate that pure AN decomposes to N2, N2O, and H2O at the onset of the melt, whereas the mixtures, ANFO and Ammonal, decompose at substantially lower temperatures. The present results also confirm the recently proposed phase IV-IV' transition above 17 GPa and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400°C. PMID:24320387

  10. A Regime Diagram for Subduction

    NASA Astrophysics Data System (ADS)

    Stegman, D. R.; Farrington, R.; Capitanio, F. A.; Schellart, W. P.

    2009-12-01

    Regime diagrams and associated scaling relations have profoundly influenced our understanding of planetary dynamics. Previous regime diagrams characterized the regimes of stagnant-lid, small viscosity contrast, transitional, and no-convection for temperature-dependent (Moresi and Solomatov, 1995), and non-linear power law rheologies (Solomatov and Moresi, 1997) as well as stagnant-lid, sluggish-lid, and mobile-lid regimes once the finite strength of rock was considered (Moresi and Solomatov, 1998). Scalings derived from such models have been the cornerstone for parameterized models of thermal evolution of rocky planets and icy moons for the past decade. While such a theory can predict the tectonic state of a planetary body, it is still rather incomplete in regards to predicting tectonics. For example, the mobile-lid regime is unspecific as to how continuous lithospheric recycling should occur on a terrestrial planet. Towards this goal, Gerya et al., (2008) advanced a new regime diagram aiming to characterize when subduction would manifest itself as a one-sided or two-sided downwelling and either symmetric or asymmetric. Here, we present a regime diagram for the case of a single-sided, asymmetric type of subduction (most Earth-like type). Using a 3-D numerical model of a free subduction, we describe a total of 5 different styles of subduction that can possibly occur. Each style is distinguished by its upper mantle slab morphology resulting from the sinking kinematics. We provide movies to illustrate the different styles and their progressive time-evolution. In each regime, subduction is accommodated by a combination of plate advance and slab rollback, with associated motions of forward plate velocity and trench retreat, respectively. We demonstrate that the preferred subduction mode depends upon two essential controlling factors: 1) buoyancy of the downgoing plate and 2) strength of plate in resisting bending at the hinge. We propose that a variety of subduction regimes are generated primarily as a product of two mechanisms. The first mechanism is that of the competition between the weight of the slab and the strength of the plate, which can be understood in terms of the applied bending moment, and this competition results in a particular radius of curvature (for which we provide a simple scaling theory). The second mechanism is the interaction between the slab and the more viscous lower mantle, which produces each regime's distinct slab morphology. Thus, the emergence of five distinct styles of subduction is a direct consequence of the presence of the modest barrier to flow into the lower mantle. Although only 2 of these styles presently operate on Earth, the possibility exists that other modes may have been the predominant mode in the past. Based on these models, we propose that the lithosphere is the primary factor in describing key elements of the plate tectonics system over time, rather than the convecting mantle. We discuss the various factors that may have influenced secular changes in Earth's tectonic behavior, some of which may have interesting consequences for the geochemical evolution of the Earth.

  11. Risk Mitigation for Managing On-Orbit Anomalies

    NASA Technical Reports Server (NTRS)

    La, Jim

    2010-01-01

    This slide presentation reviews strategies for managing risk mitigation that occur with anomalies in on-orbit spacecraft. It reviews the risks associated with mission operations, a diagram of the method used to manage undesirable events that occur which is a closed loop fault analysis and until corrective action is successful. It also reviews the fish bone diagram which is used if greater detail is required and aids in eliminating possible failure factors.

  12. Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N'-hydroxy-pyrimidine-2-carboximidamide by DFT approach.

    PubMed

    Jasmine, N Jeeva; Muthiah, P Thomas; Arunagiri, C; Subashini, A

    2015-06-01

    The FT-IR, FT-Raman, (1)H, (13)C NMR and UV-Visible spectral measurements of N'-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure. PMID:25756689

  13. Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N‧-hydroxy-pyrimidine-2-carboximidamide by DFT approach

    NASA Astrophysics Data System (ADS)

    Jeeva Jasmine, N.; Thomas Muthiah, P.; Arunagiri, C.; Subashini, A.

    2015-06-01

    The FT-IR, FT-Raman, 1H, 13C NMR and UV-Visible spectral measurements of N‧-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure.

  14. 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.

  15. Satake diagrams of affine Kac Moody algebras

    NASA Astrophysics Data System (ADS)

    Tripathy, L. K.; Pati, K. C.

    2006-02-01

    Satake diagrams of affine Kac-Moody algebras (untwisted and twisted) are obtained from their Dynkin diagrams. These diagrams give a classification of restricted root systems associated with these algebras. In the case of simple Lie algebras, these root systems and Satake diagrams correspond to symmetric spaces which have recently found many physical applications in quantum integrable systems, quantum transport problems, random matrix theories etc. We hope these types of root systems may have similar applications in theoretical physics in future and may correspond to symmetric spaces analogue of affine Kac-Moody algebras if they exist.

  16. High-Resolution Soft X-Ray Spectral Analysis in the CK Region of Titanium Carbide (TiC) using the DV-X alpha Molecular Orbital Method

    SciTech Connect

    Shimomura, Kenta; Muramatsu, Yasuji; Denlinger, Jonathan D.; Gullikson, Eric M.

    2008-10-31

    We used the DV-X alpha method to analyze the high-resolution soft X-ray emission and absorption spectra in the CK region of titanium carbide (TiC). The spectral profiles of the X-ray emission and absorption can be ssuscfucelly reproduced by the occupied and unoccupied density of states (DOS ), respectively, in the C2p orbitals of the center carbon atoms in a Ti62C63 cluster model, suggesting that the center carbon atom in a large cluster model expanded to the cubic-structured 53 (= 125) atoms provides sufficient DOS for the X-ray spectral analysis of rock-salt structured metal carbides.

  17. 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.

  18. Space shuttle on-orbit flight control software requirements, preliminary version

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Software modules associated with various flight control functions for the space shuttle orbiter are described. Data flow, interface requirements, initialization requirements and module sequencing requirements are considered. Block diagrams and tables are included.

  19. Precision orbit determination at the NASA Goddard Space Flight Center

    NASA Technical Reports Server (NTRS)

    Putney, B.; Kolenkiewicz, R.; Smith, D.; Dunn, P.; Torrence, M. H.

    1990-01-01

    This paper describes the GEODYN computer program developed by the Geodynamics Branch at the NASA Goddard Space Flight Center and outlines the procedure for accurate satellite orbit and tracking-data analyses. The capabilities of the program allow the development of gravity fields as large as 90 by 90, and a complete modeling of tidal parameters. It is also feasible to numerically integrate a continuous orbit of a satellite such as Lageos for up to 12 years. The evolution of the orbit can be studied, and, by comparison with locally determined orbits, force model improvements can be made. The GEODYN flow diagrams are presented.

  20. Orbital order of spinless fermions near an optical Feshbach resonance

    SciTech Connect

    Hauke, Philipp; Zhao, Erhai; Goyal, Krittika; Deutsch, Ivan H.; Liu, W. Vincent; Lewenstein, Maciej

    2011-11-15

    We study the quantum phases of a three-color Hubbard model that arises in the dynamics of the p-band orbitals of spinless fermions in an optical lattice. Strong, color-dependent interactions are induced by an optical Feshbach resonance. Starting from the microscopic scattering properties of ultracold atoms, we derive the orbital exchange constants at 1/3 filling on the cubic optical lattice. Using this, we compute the phase diagram in a Gutzwiller ansatz. We find phases with ''axial orbital order'' in which p{sub z} and p{sub x}+ip{sub y} (or p{sub x}-ip{sub y}) orbitals alternate.

  1. Vesicle deformation by microtubules: A phase diagram

    NASA Astrophysics Data System (ADS)

    Emsellem, Virginie; Cardoso, Olivier; Tabeling, Patrick

    1998-10-01

    The experimental investigation of vesicles deformed by the growth of encapsulated microtubules shows that the axisymmetric morphologies can be classified into ovals, lemons, φ, cherries, dumbbells, and pearls. A geometrical phase diagram is established. Numerical minimization of the elastic energy of the membrane reproduces satisfactorily well the observed morphologies and the corresponding phase diagram.

  2. 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.

  3. Phase Diagram of Ammonium Nitrate

    NASA Astrophysics Data System (ADS)

    Dunuwille, Mihindra; Yoo, Choong-Shik

    2013-06-01

    Ammonium Nitrate (AN) has often been subjected to uses in improvised explosive devices, due to its wide availability as a fertilizer and its capability of becoming explosive with slight additions of organic and inorganic compounds. Yet, the origin of enhanced energetic properties of impure AN (or AN mixtures) is neither chemically unique nor well understood - resulting in rather catastrophic disasters in the past1 and thereby a significant burden on safety, in using ammonium nitrates even today. To remedy this situation, we have carried out an extensive study to investigate the phase stability of AN, in different chemical environments, at high pressure and temperature, using diamond anvil cells and micro-Raman spectroscopy. The present results confirm the recently proposed phase IV-to-IV' transition above 15 GPa2 and provide new constraints for the melting and phase diagram of AN to 40 GPa and 673 K. The present study has been supported by the U.S. DHS under Award Number 2008-ST-061-ED0001.

  4. Phase diagram of ammonium nitrate

    SciTech Connect

    Dunuwille, Mihindra; Yoo, Choong-Shik

    2013-12-07

    Ammonium Nitrate (AN) is a fertilizer, yet becomes an explosive upon a small addition of chemical impurities. The origin of enhanced chemical sensitivity in impure AN (or AN mixtures) is not well understood, posing significant safety issues in using AN even today. To remedy the situation, we have carried out an extensive study to investigate the phase stability of AN and its mixtures with hexane (ANFO–AN mixed with fuel oil) and Aluminum (Ammonal) at high pressures and temperatures, using diamond anvil cells (DAC) and micro-Raman spectroscopy. The results indicate that pure AN decomposes to N{sub 2}, N{sub 2}O, and H{sub 2}O at the onset of the melt, whereas the mixtures, ANFO and Ammonal, decompose at substantially lower temperatures. The present results also confirm the recently proposed phase IV-IV{sup ′} transition above 17 GPa and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400°C.

  5. Operations space diagram for ECRH and ECCD

    NASA Astrophysics Data System (ADS)

    Bindslev, Henrik

    2004-07-01

    A Clemmov-Mullaly-Allis (CMA) type diagram, the ECW-CMA diagram, for representing the operational possibilities of electron cyclotron heating and current drive (ECRH/ECCD) systems for fusion plasmas is presented. In this diagram, with normalized density and normalized magnetic field coordinates, the parameter range in which it is possible to achieve a given task (e.g. O-mode current drive for stabilizing a neoclassical tearing mode) appears as a region. With also the Greenwald density limit shown, this diagram condenses the information on operational possibilities, facilitating the overview required at the design phase. At the operations phase it may also prove useful in setting up experimental scenarios by showing operational possibilities, avoiding the need for survey type ray-tracing at the initial planning stages. The diagram may also serve the purpose of communicating operational possibilities to non-experts. JET and ITER like plasmas are used, but the method is generic.

  6. Energy stabilization of the s -symmetry superatom molecular orbital by endohedral doping of C 82 fullerene with a lanthanum atom

    SciTech Connect

    Feng, Min; Shi, Yongliang; Lin, Chungwei; Zhao, Jin; Liu, Fupin; Yang, Shangfeng; Petek, Hrvoje

    2013-08-01

    Energy stabilization of the superatom molecular orbitals (SAMOs) in fullerenes is investigated with the goal of involving their nearly free-electron bands in practical charge transport applications. Combining low-temperature scanning tunneling microscopy-based spectroscopic methods and density functional theory calculations on an endohedral metallofullerene La@C82, we confirm that the s-SAMO of C82 fullerene is stabilized by as much as 2 eV with respect to that of C60 by endohedral doping with the La atom. On the copper metal substrate, the s-SAMO energy is further lowered to just 1 eV above the Fermi level, making the applications of s-SAMO state in transport more plausible. We conclude that in an endohedral metallofullerene, the s-SAMO state is stabilized through the hybridization with the s-symmetry valence state of the metal atom and the stabilization energy correlates with the ionization potential of the free atom.

  7. Analysis of Bonding Patterns in the Valence Isoelectronic series O3, S3, SO2 and OS2 in Terms of Oriented Quasi-Atomic Molecular Orbitals

    SciTech Connect

    Glezakou, Vassiliki Alexandra; Elbert, Stephen T; Xantheas, Sotiris S; Ruedenberg, Klaus

    2010-08-26

    A novel analysis of the chemical bonding pattern in the valence isoelectronic series of triatomic molecules O3, S3, SO2 and OS2 is reported. The analysis is based on examining the bond order matrix elements between the Oriented Localized Molecular Orbitals (OLMOs) that are localized on the three individual left (L), center (C) and right (R) atoms. The analysis indicates that there is a (L-C) and (C-R) π-bonding interaction and a (L-R) π-antibonding interaction. This finding supports the previously proposed "partial biradical" interpretation of these triatomic systems, which had recently been challenged.

  8. Spin and orbital magnetic moments of molecular beam epitaxy {gamma}{sup '}-Fe{sub 4}N films on LaAlO{sub 3}(001) and MgO(001) substrates by x-ray magnetic circular dichroism

    SciTech Connect

    Ito, K.; Lee, G. H.; Harada, K.; Suzuno, M.; Suemasu, T.; Takeda, Y.; Saitoh, Y.; Ye, M.; Kimura, A.; Akinaga, H.

    2011-03-07

    10-nm-thick {gamma}{sup '}-Fe{sub 4}N films were grown epitaxially on LaAlO{sub 3}(001) and MgO(001) substrates by molecular beam epitaxy using solid Fe and a radio-frequency NH{sub 3} plasma. The lattice mismatch of these substrates to {gamma}{sup '}-Fe{sub 4}N is 0% and 11%, respectively. Spin and orbital magnetic moments of these {gamma}{sup '}-Fe{sub 4}N epitaxial films were deduced by x-ray magnetic circular dichroism measurements at 300 K. The total magnetic moments are almost the same for the two substrates, that is, 2.44{+-}0.06 {mu}{sub B} and 2.47{+-}0.06 {mu}{sub B}, respectively. These values are very close to those predicted theoretically, and distinctively larger than that for {alpha}-Fe.

  9. Majorana states and magnetic orbital motion in planar hybrid nanowires

    NASA Astrophysics Data System (ADS)

    Osca, Javier; Serra, Llorenç

    2015-06-01

    The Majorana phase boundaries in planar 2D hybrid (semiconductor-superconductor) nanowires are modified by orbital effects due to off plane magnetic components. We show that Majorana zero modes survive sizable vertical field tiltings, uncovering a remarkable phase diagram. Analytical expressions of the phase boundaries are given for the strong orbital limit. These phase boundaries can be fulfilled with attainable setups, such as an InAs nanowire of 150 nm in transverse width.

  10. Small orbits

    NASA Astrophysics Data System (ADS)

    Borsten, L.; Duff, M. J.; Ferrara, S.; Marrani, A.; Rubens, W.

    2012-04-01

    We study both the large and small U-duality charge orbits of extremal black holes appearing in D=5 and D=4 Maxwell-Einstein supergravity theories with symmetric scalar manifolds. We exploit a formalism based on cubic Jordan algebras and their associated Freudenthal triple systems, in order to derive the minimal charge representatives, their stabilizers and the associated “moduli spaces.” After recalling N=8 maximal supergravity, we consider N=2 and N=4 theories coupled to an arbitrary number of vector multiplets, as well as N=2 magic, STU, ST2 and T3 models. While the STU model may be considered as part of the general N=2 sequence, albeit with an additional triality symmetry, the ST2 and T3 models demand a separate treatment, since their representative Jordan algebras are Euclidean or only admit nonzero elements of rank 3, respectively. Finally, we also consider minimally coupled N=2, matter-coupled N=3, and pure N=5 theories.

  11. Orbital ordering in RVO3 (R=Y,Tb) controlled by hydrostatic pressure

    NASA Astrophysics Data System (ADS)

    Bizen, D.; Nakatsuka, K.; Murata, T.; Nakao, H.; Murakami, Y.; Miyasaka, S.; Tokura, Y.

    2008-12-01

    Orbital ordered states of YVO3 have been systematically investigated using the low-temperature and high-pressure x-ray diffraction technique. The pressure-temperature phase diagram for the orbital state is determined from the lattice constants and the reflection conditions. The phase diagram shows that the C -type orbital ordering (C-OO) is significantly stabilized relative to the G -type orbital ordering (G-OO) by application of hydrostatic pressure. Based on the result, we could achieve the 3d -orbital state switching in TbVO3 from the G-OO to the C-OO by applying pressure. The pressure effect on the orbital ordering is discussed from the viewpoint of the covalency among the R -ion d , the oxygen 2p , and the vanadium 3d orbitals.

  12. Possible phase diagrams for reversibly interpenetrating polymer networks

    NASA Astrophysics Data System (ADS)

    Tanaka, Fumihiko

    1992-05-01

    We present possible equilibrium phase diagrams on the temperature-concentration plane for binary interpenetrating polymer networks (IPN) in which network junctions are formed by reversible cross-linking. It is shown that, in most parts of the phase plane, the formed networks of both species are mutually exclusive so that the system demixes into small domains of heterophases, but that there is a small region just above the top of the miscibility gap in which a molecularly mixed IPN can stay in a stable phase. The condition for the existence of a stable IPN is examined. Competition between network formation and two-phase demixing is studied.

  13. How to Draw Energy Level Diagrams in Excitonic Solar Cells.

    PubMed

    Zhu, X-Y

    2014-07-01

    Emerging photovoltaic devices based on molecular and nanomaterials are mostly excitonic in nature. The initial absorption of a photon in these materials creates an exciton that can subsequently dissociate in each material or at their interfaces to give charge carriers. Any attempt at mechanistic understanding of excitonic solar cells must start with drawing energy level diagrams. This seemingly elementary exercise, which is described in textbooks for inorganic solar cells, has turned out to be a difficult subject in the literature. The problem stems from conceptual confusion of single-particle energy with quasi-particle energy and the misleading practice of mixing the two on the same energy level diagram. Here, I discuss how to draw physically accurate energy diagrams in excitonic solar cells using only single-particle energies (ionization potentials and electron affinities) of both ground and optically excited states. I will briefly discuss current understanding on the electronic energy landscape responsible for efficient charge separation in excitonic solar cells. PMID:26279547

  14. Algorithmic Identification for Wings in Butterfly Diagrams.

    NASA Astrophysics Data System (ADS)

    Illarionov, E. A.; Sokolov, D. D.

    2012-12-01

    We investigate to what extent the wings of solar butterfly diagrams can be separated without an explicit usage of Hale's polarity law as well as the location of the solar equator. Two algorithms of cluster analysis, namely DBSCAN and C-means, have demonstrated their ability to separate the wings of contemporary butterfly diagrams based on the sunspot group density in the diagram only. Here we generalize the method for continuous tracers, give results concerning the migration velocities and presented clusters for 12 - 20 cycles.

  15. A Hubble Diagram for Quasars

    NASA Astrophysics Data System (ADS)

    Risaliti, G.; Lusso, E.

    2015-12-01

    We present a new method to test the ΛCDM cosmological model and to estimate cosmological parameters based on the nonlinear relation between the ultraviolet and X-ray luminosities of quasars. We built a data set of 1138 quasars by merging several samples from the literature with X-ray measurements at 2 keV and SDSS photometry, which was used to estimate the extinction-corrected 2500 Å flux. We obtained three main results: (1) we checked the nonlinear relation between X-ray and UV luminosities in small redshift bins up to z˜ 6, confirming that the relation holds at all redshifts with the same slope; (2) we built a Hubble diagram for quasars up to z˜ 6, which is well matched to that of supernovae in the common z = 0-1.4 redshift interval and extends the test of the cosmological model up to z˜ 6; and (3) we showed that this nonlinear relation is a powerful tool for estimating cosmological parameters. Using the present data and assuming a ΛCDM model, we obtain {{{Ω }}}M = 0.22{}-0.08+0.10 and {{{Ω }}}{{Λ }} = 0.92{}-0.30+0.18 ({{{Ω }}}M = 0.28 ± 0.04 and {{{Ω }}}{{Λ }} = 0.73 +/- 0.08 from a joint quasar-SNe fit). Much more precise measurements will be achieved with future surveys. A few thousand SDSS quasars already have serendipitous X-ray observations from Chandra or XMM-Newton, and at least 100,000 quasars with UV and X-ray data will be made available by the extended ROentgen Survey with an Imaging Telescope Array all-sky survey in a few years. The Euclid, Large Synoptic Survey Telescope, and Advanced Telescope for High ENergy Astrophysics surveys will further increase the sample size to at least several hundred thousand. Our simulations show that these samples will provide tight constraints on the cosmological parameters and will allow us to test for possible deviations from the standard model with higher precision than is possible today.

  16. Handling the Handbag Diagram in Compton Scattering on the Proton

    SciTech Connect

    Miller, Gerald A.

    2004-02-25

    Poincare invariance, gauge invariance, conservation of parity and time reversal invariance are respected in an impulse approximation evaluation of the handbag diagram. Proton wave functions, previously constrained by comparison with measured form factors, that incorporate the influence of quark transverse and orbital angular momentum (and the corresponding violation of proton helicity conservation) are used. Computed cross sections are found to be in reasonably good agreement with early measurements. The helicity correlation between the incident photon and outgoing proton, K{sub LL}, is both large and positive at back angles. For photon laboratory energies of {le} 6 GeV, we find that K{sub LL} {ne} A{sub LL}, D{sub LL} {ne} 1, and that the polarization P can be large.

  17. A Smart Thermal Block Diagram Tool

    NASA Technical Reports Server (NTRS)

    Tsuyuki, Glenn; Miyake, Robert; Dodge, Kyle

    2008-01-01

    The presentation describes a Smart Thermal Block Diagram Tool. It is used by JPL's Team X in studying missions during the Pre-Phase A. It helps generate cost and mass estimates using proprietary data bases.

  18. Veitch diagram plotter simplifies Boolean functions

    NASA Technical Reports Server (NTRS)

    Rubin, D. K.

    1964-01-01

    This device for simplifying the plotting of a Veitch diagram consists of several overlays for blocking out the unwanted squares. This method of plotting the various input combinations to a computer is used in conjunction with the Boolean functions.

  19. An Improved Mnemonic Diagram for Thermodynamic Relationships.

    ERIC Educational Resources Information Center

    Rodriguez, Joaquin; Brainard, Alan J.

    1989-01-01

    Considers pressure, volume, entropy, temperature, Helmholtz free energy, Gibbs free energy, enthalpy, and internal energy. Suggests the mnemonic diagram is for use with simple systems that are defined as macroscopically homogeneous, isotropic, uncharged, and chemically inert. (MVL)

  20. A Phase Diagram for Solar Flares

    NASA Astrophysics Data System (ADS)

    Balasubramaniam, K. S.; Winter, Lisa; Pernak, Rick

    2015-04-01

    Using the data from the NOAA/GOES X-ray observations of ~50,000 flares, we develop a Phase Diagram for solar flares. Such a Solar Flare Phase Diagram helps to trace the underlying energy structure of solar flares, and provides a prediction framework. The temperature (maximum ratio of short (0.5 - 4 A) to long band (1-8 A) band) and background solar x-ray radiation (at 1-8 A band) forms the basis of the phase diagram. Using the phase diagram and relevant statistical analysis, we derive insights into the eruptive nature of flares during the solar-cycle ramp (ramp up to and ramp down from solar maximum) phases and peak phase of the solar cycle.

  1. Architecture flow diagrams under teamwork reg sign

    SciTech Connect

    Nicinski, T.

    1992-02-01

    The Teamwork CASE tool allows Data Flow Diagrams (DFDs) to be maintained for structured analysis. Fermilab has extended teamwork under UNIX{trademark} to permit Hatley and Pirbhai Architecture Flow Diagrams (AFDs) to be associated with DFDs and subsequently maintained. This extension, called TWKAFD, allows a user to open an AFD, graphically edit it, and replace it into a TWKAFD maintained library. Other aspects of Hatley and Pirbhai's methodology are supported. This paper presents a quick tutorial on Architecture Diagrams. It then describes the user's view of TWKAFD, the experience incorporating it into teamwork, and the successes with using the Architecture Diagram methodology along with the shortcomings of using the teamwork/TWKAFD tool. 8 refs.

  2. Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in Cu(A) Sites of Cytochrome c Oxidase.

    PubMed

    Zitare, Ulises; Alvarez-Paggi, Damián; Morgada, Marcos N; Abriata, Luciano A; Vila, Alejandro J; Murgida, Daniel H

    2015-08-10

    The Cu(A) site of cytochrome c oxidase is a redox hub that participates in rapid electron transfer at low driving forces with two redox cofactors in nearly perpendicular orientations. Spectroscopic and electrochemical characterizations performed on first and second-sphere mutants have allowed us to experimentally detect the reversible switching between two alternative electronic states that confer different directionalities to the redox reaction. Specifically, the M160H variant of a native Cu(A) shows a reversible pH transition that allows to functionally probe both states in the same protein species. Alternation between states exerts a dramatic impact on the kinetic redox parameters, thereby suggesting this effect as the mechanism underlying the efficiency and directionality of Cu(A) electron transfer in vivo. These findings may also prove useful for the development of molecular electronics. PMID:26118421

  3. 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.

  4. A universal structured-design diagramer

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Program (FLOWCHARTER) generates standardized flowcharts and concordances for development and debugging of programs in any language. User describes programming-language grammar, providing syntax rules in Backus-Naur form (BNF), list of semantic rules, and set of concordance rules. Once grammar is described, user supplies only source code of program to be diagrammed. FLOWCHARTER automatically produces flow diagram and concordance. Source code for program is written for PASCAL Release 2 compiler, as distributed by University of Minnesota.

  5. Reliability computation from reliability block diagrams

    NASA Technical Reports Server (NTRS)

    Chelson, P. O.; Eckstein, R. E.

    1971-01-01

    A method and a computer program are presented to calculate probability of system success from an arbitrary reliability block diagram. The class of reliability block diagrams that can be handled include any active/standby combination of redundancy, and the computations include the effects of dormancy and switching in any standby redundancy. The mechanics of the program are based on an extension of the probability tree method of computing system probabilities.

  6. Lattice and Phase Diagram in QCD

    SciTech Connect

    Lombardo, Maria Paola

    2008-10-13

    Model calculations have produced a number of very interesting expectations for the QCD Phase Diagram, and the task of a lattice calculations is to put these studies on a quantitative grounds. I will give an overview of the current status of the lattice analysis of the QCD phase diagram, from the quantitative results of mature calculations at zero and small baryochemical potential, to the exploratory studies of the colder, denser phase.

  7. Elementary diagrams in nuclear and neutron matter

    SciTech Connect

    Wiringa, R.B.

    1995-08-01

    Variational calculations of nuclear and neutron matter are currently performed using a diagrammatic cluster expansion with the aid of nonlinear integral equations for evaluating expectation values. These are the Fermi hypernetted chain (FHNC) and single-operator chain (SOC) equations, which are a way of doing partial diagram summations to infinite order. A more complete summation can be made by adding elementary diagrams to the procedure. The simplest elementary diagrams appear at the four-body cluster level; there is one such E{sub 4} diagram in Bose systems, but 35 diagrams in Fermi systems, which gives a level of approximation called FHNC/4. We developed a novel technique for evaluating these diagrams, by computing and storing 6 three-point functions, S{sub xyz}(r{sub 12}, r{sub 13}, r{sub 23}), where xyz (= ccd, cce, ddd, dde, dee, or eee) denotes the exchange character at the vertices 1, 2, and 3. All 35 Fermi E{sub 4} diagrams can be constructed from these 6 functions and other two-point functions that are already calculated. The elementary diagrams are known to be important in some systems like liquid {sup 3}He. We expect them to be small in nuclear matter at normal density, but they might become significant at higher densities appropriate for neutron star calculations. This year we programmed the FHNC/4 contributions to the energy and tested them in a number of simple model cases, including liquid {sup 3}He and Bethe`s homework problem. We get reasonable, but not exact agreement with earlier published work. In nuclear and neutron matter with the Argonne v{sub 14} interaction these contributions are indeed small corrections at normal density and grow to only 5-10 MeV/nucleon at 5 times normal density.

  8. Shuttle Orbiter Uplink Text and Graphics System

    NASA Technical Reports Server (NTRS)

    Hoover, A. A.; Land, C. K.; Lipoma, P. C.

    1978-01-01

    This paper presents the definition of requirements for and current design of the Shuttle Orbiter Uplink Text and Graphics System (UT&GS). Beginning in early 1981, the UT&GS will support Shuttle flights by providing the capability of transmitting single-frame imagery from the ground to the orbiting Shuttle vehicle. Such imagery is in the form of maps, text, diagrams, or photographs, and is outputted on the Orbiter as a paper hard copy. Four modes of operation will be provided to minimize the time required to transmit less than full-resolution imagery. This paper discusses the considerations and complications leading to the four modes and associated resolution requirements. The paper also presents the design of the CCD array ground scanner and airborne CRT hardcopier.

  9. Effectiveness of Using Computer-Assisted Instruction in Teaching the Shapes of Atomic Orbitals.

    ERIC Educational Resources Information Center

    Shubbar, Khalil E.

    2003-01-01

    Investigates the effect of computer-assisted instruction (CAI) when used as a supplement to classroom instruction to improve secondary school students' understanding of orbital shapes. Results indicate that the CAI approach enhanced student learning and helped them figure out cues portrayed in diagrams of atomic orbitals. (Contains 22 references.)

  10. Effectiveness of Using Computer-Assisted Instruction in Teaching the Shapes of Atomic Orbitals.

    ERIC Educational Resources Information Center

    Shubbar, Khalil E.

    2003-01-01

    Investigates the effect of computer-assisted instruction (CAI) when used as a supplement to classroom instruction to improve secondary school students' understanding of orbital shapes. Results indicate that the CAI approach enhanced student learning and helped them figure out cues portrayed in diagrams of atomic orbitals. (Contains 22 references.)…

  11. Molecular orbital calculations, experimental and theoretical UV spectra of granulatimides and didemnimides, biologically active polycyclic heteroaromatic alkaloids from the ascidian Didemnum granulatum

    NASA Astrophysics Data System (ADS)

    Camargo, A. J.; Oliveira, J. H. H. L.; Trsic, M.; Berlinck, R. G. S.

    2001-01-01

    A detailed computational study was performed for compounds granulatimide, isogranulatimide, and didemnimides A, D, and E, using the semiempirical Austin model 1 quantum chemical method. The electronic features and structural parameters were confronted with the inhibition of the G2 cell cycle checkpoint of mammalian cancer cells. All compounds were submitted to a rigorous conformational analysis using the Tripos 5.2 force field implemented in the Spartan 5.01 program. The electronic density in specific regions of the molecules appears to play a pivotal role towards activity. The molecular planarity creates a broad negative electrostatic potential on the two sides of the active compounds (granulatimide and isogralulatimide) and a positive potential in their central core, while the non-planar compounds (didemnimides A, D, and E, which are inactive) present an asymmetric potential scattered over the molecules. These electrostatic potential features are likely to be the modulator of hydrophobicity or lipophilicity of the compounds, which appear correlated with activity. The hydrogen attached to the N atom of the pyrrole moiety of indole is more positive for active compounds than for the inactive molecules. The theoretical electronic spectra were obtained for all compounds using the configuration interaction method, with the AM1 routine. All transitions present π→π ∗ nature. The theoretical results are in good agreement with experimental values.

  12. 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.

  13. Molecular geometry, vibrational frequencies, infrared intensities and CN effective bond charges in a series of simple nitrile compounds: HF/6-31+G(d,p) molecular orbital study

    NASA Astrophysics Data System (ADS)

    Dudev, Todor; Bobadova-Parvanova, Petia; Pencheva, Daniela; Galabov, Boris

    1997-12-01

    The structural and vibrational spectroscopic parameters of a series of simple nitrile compounds were evaluated by HF/6-31+G(d,p) ab initio quantum mechanical calculations. The series includes HCN, FCN, CICN, CH 2FCN, CH 2CICN, CH 3CN, CF 3CN, CCl 3CN, HOCN, HSCN and NH 2CN. The theoretical infrared intensities were transformed into quantities associated with the charge distribution and dynamics in the molecules following the formalism of the effective bond charge method. Satisfactory linear relations were found between the effective bond charges and bond lengths, as well as between the bond charges and the molecular electrostatic potential at the nitrogen atom.

  14. Non-planar on-shell diagrams

    NASA Astrophysics Data System (ADS)

    Franco, Sebastián; Galloni, Daniele; Penante, Brenda; Wen, Congkao

    2015-06-01

    We initiate a systematic study of non-planar on-shell diagrams in SYM and develop powerful technology for doing so. We introduce canonical variables generalizing face variables, which make the d log form of the on-shell form explicit. We make significant progress towards a general classification of arbitrary on-shell diagrams by means of two classes of combinatorial objects: generalized matching and matroid polytopes. We propose a boundary measurement that connects general on-shell diagrams to the Grassmannian. Our proposal exhibits two important and non-trivial properties: positivity in the planar case and it matches the combinatorial description of the diagrams in terms of generalized matroid polytopes. Interestingly, non-planar diagrams exhibit novel phenomena, such as the emergence of constraints on Plücker coordinates beyond Plücker relations when deleting edges, which are neatly captured by the generalized matching and matroid polytopes. This behavior is tied to the existence of a new type of poles in the on-shell form at which combinations of Plücker coordinates vanish. Finally, we introduce a prescription, applicable beyond the MHV case, for writing the on-shell form as a function of minors directly from the graph.

  15. Spectroscopic (FT-IR, FT-Raman and UV) investigation, NLO, NBO, molecular orbital and MESP analysis of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.

    2015-02-01

    In this work, FT-IR and FT-Raman spectra of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid (abbreviated as 2DCPAPAA) have been reported in the regions 4000-450 cm-1 and 4000-50 cm-1, respectively. The molecular structure, geometry optimization, intensities, vibrational frequencies were obtained by the ab initio and DFT levels of theory B3LYP with 6-311++G(d,p) standard basis set and a different scaling of the calculated wave numbers. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using vibrational energy distribution analysis (VEDA 4) program. The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman data. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The thermodynamic properties of the title compound at different temperature reveal the correlations between standard heat capacities (C) standard entropies (S) standard enthalpy changes (ΔH). The important non-linear optical properties such as electric dipole momentum, polarizability and first hyperpolarizability of 2DCPAPAA have been computed using B3LYP/6-311++G(d,p) quantum chemical calculations. The Natural charges, HOMO, LUMO, chemical hardness (η), chemical potential (μ), Electro negativity (χ) and electrophilicity values (ω) are calculated and reported. The oscillator's strength, wave length, and energy calculated by TD-DFT and 2DCPAPAA is approach complement with the experimental findings. The molecular electrostatic potential (MESP) surfaces of the molecule were constructed.

  16. Students' Understanding of Diagrams for Solving Word Problems: A Framework for Assessing Diagram Proficiency

    ERIC Educational Resources Information Center

    Poch, Apryl L.; van Garderen, Delinda; Scheuermann, Amy M.

    2015-01-01

    A visual representation, such as a diagram, can be a powerful strategy for solving mathematical word problems. However, using a representation to solve mathematical word problems is not as simple as it seems! Many students with learning disabilities struggle to use a diagram effectively and efficiently. This article provides a framework for…

  17. Students' Understanding of Diagrams for Solving Word Problems: A Framework for Assessing Diagram Proficiency

    ERIC Educational Resources Information Center

    Poch, Apryl L.; van Garderen, Delinda; Scheuermann, Amy M.

    2015-01-01

    A visual representation, such as a diagram, can be a powerful strategy for solving mathematical word problems. However, using a representation to solve mathematical word problems is not as simple as it seems! Many students with learning disabilities struggle to use a diagram effectively and efficiently. This article provides a framework for

  18. The Semiotic Structure of Geometry Diagrams: How Textbook Diagrams Convey Meaning

    ERIC Educational Resources Information Center

    Dimmel, Justin K.; Herbst, Patricio G.

    2015-01-01

    Geometry diagrams use the visual features of specific drawn objects to convey meaning about generic mathematical entities. We examine the semiotic structure of these visual features in two parts. One, we conduct a semiotic inquiry to conceptualize geometry diagrams as mathematical texts that comprise choices from different semiotic systems. Two,…

  19. The Semiotic Structure of Geometry Diagrams: How Textbook Diagrams Convey Meaning

    ERIC Educational Resources Information Center

    Dimmel, Justin K.; Herbst, Patricio G.

    2015-01-01

    Geometry diagrams use the visual features of specific drawn objects to convey meaning about generic mathematical entities. We examine the semiotic structure of these visual features in two parts. One, we conduct a semiotic inquiry to conceptualize geometry diagrams as mathematical texts that comprise choices from different semiotic systems. Two,

  20. The phase diagram of solid hydrogen at high pressure: A challenge for first principles calculations

    NASA Astrophysics Data System (ADS)

    Azadi, Sam; Foulkes, Matthew

    2015-03-01

    We present comprehensive results for the high-pressure phase diagram of solid hydrogen. We focus on the energetically most favorable molecular and atomic crystal structures. To obtain the ground-state static enthalpy and phase diagram, we use semi-local and hybrid density functional theory (DFT) as well as diffusion quantum Monte Carlo (DMC) methods. The closure of the band gap with increasing pressure is investigated utilizing quasi-particle many-body calculations within the GW approximation. The dynamical phase diagram is calculated by adding proton zero-point energies (ZPE) to static enthalpies. Density functional perturbation theory is employed to calculate the proton ZPE and the infra-red and Raman spectra. Our results clearly demonstrate the failure of DFT-based methods to provide an accurate static phase diagram, especially when comparing insulating and metallic phases. Our dynamical phase diagram obtained using fully many-body DMC calculations shows that the molecular-to-atomic phase transition happens at the experimentally accessible pressure of 374 GPa. We claim that going beyond mean-field schemes to obtain derivatives of the total energy and optimize crystal structures at the many-body level is crucial. This work was supported by the UK engineering and physics science research council under Grant EP/I030190/1, and made use of computing facilities provided by HECTOR, and by the Imperial College London high performance computing centre.

  1. Fishbone Diagrams: Organize Reading Content with a "Bare Bones" Strategy

    ERIC Educational Resources Information Center

    Clary, Renee; Wandersee, James

    2010-01-01

    Fishbone diagrams, also known as Ishikawa diagrams or cause-and-effect diagrams, are one of the many problem-solving tools created by Dr. Kaoru Ishikawa, a University of Tokyo professor. Part of the brilliance of Ishikawa's idea resides in the simplicity and practicality of the diagram's basic model--a fish's skeleton. This article describes how…

  2. The Use of Computational Diagrams and Nomograms in Higher Education.

    ERIC Educational Resources Information Center

    Brandenburg, Richard K.; Simpson, William A.

    1984-01-01

    The use of computational diagrams and nomographs for the calculations that frequently occur in college administration is examined. Steps in constructing a nomograph and a four-dimensional computational diagram are detailed, and uses of three- and four-dimensional diagrams are covered. Diagrams and nomographs are useful in the following cases: (1)…

  3. Fishbone Diagrams: Organize Reading Content with a "Bare Bones" Strategy

    ERIC Educational Resources Information Center

    Clary, Renee; Wandersee, James

    2010-01-01

    Fishbone diagrams, also known as Ishikawa diagrams or cause-and-effect diagrams, are one of the many problem-solving tools created by Dr. Kaoru Ishikawa, a University of Tokyo professor. Part of the brilliance of Ishikawa's idea resides in the simplicity and practicality of the diagram's basic model--a fish's skeleton. This article describes how

  4. Science Visual Literacy: Learners' Perceptions and Knowledge of Diagrams

    ERIC Educational Resources Information Center

    McTigue, Erin M.; Flowers, Amanda C.

    2011-01-01

    Constructing meaning from science texts relies not only on comprehending the words but also the diagrams and other graphics. The goal of this study was to explore elementary students' perceptions of science diagrams and their skills related to diagram interpretation. 30 students, ranging from second grade through middle school, completed a diagram

  5. 49 CFR 1152.10 - System diagram map.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 8 2010-10-01 2010-10-01 false System diagram map. 1152.10 Section 1152.10... TRANSPORTATION UNDER 49 U.S.C. 10903 System Diagram § 1152.10 System diagram map. (a) Each carrier shall prepare a diagram of its rail system on a map, designating all lines in its system by the...

  6. Complete inhibition of rhTSH-, Graves' disease IgG-, and M22-induced cAMP production in differentiated orbital fibroblasts by a low-molecular-weight TSHR antagonist.

    PubMed

    van Zeijl, Clementine J J; van Koppen, Chris J; Surovtseva, Olga V; de Gooyer, Marcel E; Plate, Ralf; Conti, Paolo; Karstens, Willem-Jan; Timmers, Marco; Saeed, Peerooz; Wiersinga, Wilmar M; Miltenburg, André M M; Fliers, Eric; Boelen, Anita

    2012-05-01

    The TSH receptor (TSHR) on orbital fibroblasts (OF) is a proposed target of the autoimmune attack in Graves' ophthalmopathy. In the present study, we tested whether the novel low-molecular-weight (LMW) TSHR antagonist Org-274179-0 inhibits cAMP production induced by rhTSH, Graves' disease IgG (GD-IgG), or M22 (a potent human monoclonal TSHR stimulating antibody) in cultured and differentiated OF from Graves' ophthalmopathy patients. cAMP production significantly increased after incubation either with 10 mU/ml rhTSH (3-fold; P ≤ 0.05), 1 mg/ml GD-IgG (2-fold; P ≤ 0.05), or 500 ng/ml M22 (5-fold; P ≤ 0.05). Incubation with the LMW TSHR antagonist dose dependently inhibited rhTSH, GD-IgG as well as the M22-induced cAMP production at nanomolar concentrations; complete blockade was affected at 10(-6) M. Our results suggest that GD-IgG- and M22-induced cAMP production in differentiated OF is exclusively mediated via the TSHR because it can be completely blocked by the LMW TSHR antagonist, Org 274179-0. PMID:22419705

  7. Sunset Science. II. A useful diagram

    NASA Astrophysics Data System (ADS)

    Young, Andrew T.; Kattawar, George W.

    1998-06-01

    We present diagrams that show how layers in atmospheric thermal structure are related to the altitudes at which they are seen tangentially. These dip diagrams show that the inferior mirage greatly magnifies the apparent angular size of the lowest few centimeters of atmosphere. Conversely, inversion layers below eye level are compressed even to zero apparent thickness, in ducts. The diagrams show that, even when distant objects are miraged, the ray crossings occur beyond the lowest point on each ray where the line of sight is tangent to a horizontal surface in the atmosphere. Therefore the apparent altitudes of these tangent points are a monotonic function of their actual heights in the atmosphere. This monotonicity explains an apparent paradox in low-Sun images.

  8. The Butterfly diagram leopard skin pattern

    NASA Astrophysics Data System (ADS)

    Ternullo, Maurizio

    2011-08-01

    A time-latitude diagram where spotgroups are given proportional relevance to their area is presented. The diagram reveals that the spotted area distribution is higly dishomogeneous, most of it being concentrated in few, small portions (``knots'') of the Butterfly Diagram; because of this structure, the BD may be properly described as a cluster of knots. The description, assuming that spots scatter around the ``spot mean latitude'' steadily drifting equatorward, is challenged. Indeed, spots cluster around at as many latitudes as knots; a knot may appear at either lower or higher latitudes than previous ones, in a seemingly random way; accordingly, the spot mean latitude abruptly drifts equatorward or even poleward at any knot activation, in spite of any smoothing procedure. Preliminary analyses suggest that the activity splits, in any hemisphere, into two or more distinct ``activity waves'', drifting equatorward at a rate higher than the spot zone as a whole.

  9. 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.

  10. Transfer orbit determination accuracy for orbit maneuvers

    NASA Astrophysics Data System (ADS)

    Pinheiro, Mery Passos

    This work intends to show the accuracy of the orbital elements determined during transfer orbit as a function of data span, as well as the feasibility of performance maneuvers. The orbit estimator used is a weighted least squares algorithm. The observation vector is composed of angle data (azimuth and elevation) and range data and are from the Astra IC mission. The state vector is either propagated by Brower model or numerical integration (for small eccentricities and inclination). The complete software to determine the orbit has been developed by Hughes Aircraft and been used for all Hughes satellite mission.

  11. Minkowski diagram in relativity and holography.

    PubMed

    Abramson, N

    1988-05-01

    Now that ultrashort laser pulses can be used in holography, the temporal and spatial resolution approach the same order of magnitude. In that case the limited speed of light sometimes causes large measuring errors if correction methods are not introduced. Therefore, we want to revive the Minkowski diagram, which was invented in 1908 to visualize relativistic relations between time and space. We show how this diagram in a modified form can be used to derive both the static holodiagram, used for conventional holography, including ultrahigh-speed recordings of wavefronts, and a dynamic holodiagram used for studying the apparent distortions of objects recorded at relativistic speeds. PMID:20531662

  12. B-Fe-U Phase Diagram

    NASA Astrophysics Data System (ADS)

    Dias, Marta; Carvalho, Patrícia Almeida; Mardolcar, Umesh Vinaica; Tougait, Olivier; Noël, Henri; Gonçalves, António Pereira

    2014-04-01

    The liquidus projection of the U-rich corner of the B-Fe-U phase diagram is proposed based on X-ray powder diffraction measurements, differential thermal analysis, and scanning electron microscopy observations complemented with energy- and wavelength-dispersive X-ray spectroscopies. Two ternary reactions in this U-rich region were observed and their approximate temperatures were established. In addition, an overview of the complete phase diagram is given, including the liquidus projection; isothermal sections at 1053 K, 1223 K, and 1373 K (780 °C, 950 °C, and 1100 °C); and a U:(Fe,B) = 1:5 isopleth.

  13. Pilot-wave hydrodynamics in a rotating frame: Exotic orbits

    SciTech Connect

    Oza, Anand U.; Harris, Daniel M.; Rosales, Rodolfo R.; Bush, John W. M.; Wind-Willassen, Øistein

    2014-08-15

    We present the results of a numerical investigation of droplets walking on a rotating vibrating fluid bath. The drop's trajectory is described by an integro-differential equation, which is simulated numerically in various parameter regimes. As the forcing acceleration is progressively increased, stable circular orbits give way to wobbling orbits, which are succeeded in turn by instabilities of the orbital center characterized by steady drifting then discrete leaping. In the limit of large vibrational forcing, the walker's trajectory becomes chaotic, but its statistical behavior reflects the influence of the unstable orbital solutions. The study results in a complete regime diagram that summarizes the dependence of the walker's behavior on the system parameters. Our predictions compare favorably to the experimental observations of Harris and Bush [“Droplets walking in a rotating frame: from quantized orbits to multimodal statistics,” J. Fluid Mech. 739, 444–464 (2014)].

  14. Network legos: building blocks of cellular wiring diagrams.

    PubMed

    Murali, T M; Rivera, Corban G

    2008-09-01

    Publicly available datasets provide detailed and large-scale information on multiple types of molecular interaction networks in a number of model organisms. The wiring diagrams composed of these interaction networks capture a static view of cellular state. An important challenge in systems biology is obtaining a dynamic perspective on these networks by integrating them with gene expression measurements taken under multiple conditions. We present a top-down computational approach to identify building blocks of molecular interaction networks by: (i) integrating gene expression measurements for a particular disease state (e.g., leukemia) or experimental condition (e.g., treatment with growth serum) with molecular interactions to reveal an active network, which is the network of interactions active in the cell in that disease state or condition; and (ii) systematically combining active networks computed for different experimental conditions using set-theoretic formulae to reveal network legos, which are modules of coherently interacting genes and gene products in the wiring diagram. We propose efficient methods to compute active networks, systematically mine candidate legos, assess the statistical significance of these candidates, arrange them in a directed acyclic graph (DAG), and exploit the structure of the DAG to identify true network legos. We describe methods to assess the stability of our computations to changes in the input and to recover active networks by composing network legos. We analyze two human datasets using our method. A comparison of three leukemias demonstrates how a biologist can use our system to identify specific differences between these diseases. A larger-scale analysis of 13 distinct stresses illustrates our ability to compute the building blocks of the interaction networks activated in response to these stresses. Source code implementing our algorithms is available under version 2 of the GNU General Public License at http://bioinformatics.cs.vt.edu/ murali/software/network-lego. PMID:18707557

  15. Phase diagram of carbon-oxygen plasma mixtures in white dwarf stars

    NASA Astrophysics Data System (ADS)

    Schneider, A. S.; Horowitz, C. J.; Hughto, J.; Berry, D. K.

    2012-12-01

    The liquid-solid phase-diagram of dense carbon-oxygen plasma mixtures found in white dwarf stars interiors is determined from molecular dynamics (MD) simulations. Our MD simulations consist of boxes with 55296 ions with different carbon to oxygen ratios. Finite size effects are estimated comparing the new MD simulations results to previous smaller simulations. We use bond angle metric to identify whether an ion is in the solid, liquid or interface and study non-equilibrium effects by obtaining the diffusion coefficients in the different phases. Our phase diagram agrees with predictions from Medin and Cumming obtained by an independent method.

  16. Manned Venus Orbiting Mission

    NASA Technical Reports Server (NTRS)

    Willis, E. A., Jr.

    1967-01-01

    Manned orbiting stopover round trips to Venus are studied for departure dates between 1975 and 1986 over a range of trip times and stay times. The use of highly elliptic parking orbits at Venus leads to low initial weights in Earth orbit compared with circular orbits. For the elliptic parking orbit, the effect of constraints on the low altitude observation time on the initial weight is shown. The mission can be accomplished with the Apollo level of chemical propulsion, but advanced chemical or nuclear propulsion can give large weight reductions. The Venus orbiting mission weights than the corresponding Mars mission.

  17. Orbital Models Made of Plastic Soda Bottles

    NASA Astrophysics Data System (ADS)

    Samoshin, Vyacheslav V.

    1998-08-01

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

  18. The Binary Temperature-Composition Phase Diagram

    ERIC Educational Resources Information Center

    Sanders, Philip C.; Reeves, James H.; Messina, Michael

    2006-01-01

    The equations for the liquid and gas lines in the binary temperature-composition phase diagram are derived by approximating that delta(H)[subscript vap] of the two liquids are equal. It is shown that within this approximation, the resulting equations are not too difficult to present in an undergraduate physical chemistry lecture.

  19. Drawing conformal diagrams for a fractal landscape

    SciTech Connect

    Winitzki, Sergei

    2005-06-15

    Generic models of cosmological inflation and the recently proposed scenarios of a recycling universe and the string theory landscape predict spacetimes whose global geometry is a stochastic, self-similar fractal. To visualize the complicated causal structure of such a universe, one usually draws a conformal (Carter-Penrose) diagram. I develop a new method for drawing conformal diagrams, applicable to arbitrary 1+1-dimensional spacetimes. This method is based on a qualitative analysis of intersecting lightrays and thus avoids the need for explicit transformations of the spacetime metric. To demonstrate the power and simplicity of this method, I present derivations of diagrams for spacetimes of varying complication. I then apply the lightray method to three different models of an eternally inflating universe (scalar-field inflation, recycling universe, and string theory landscape) involving the nucleation of nested asymptotically flat, de Sitter and/or anti-de Sitter bubbles. I show that the resulting diagrams contain a characteristic fractal arrangement of lines.

  20. Enhanced Pomeron diagrams: Resummation of unitarity cuts

    SciTech Connect

    Ostapchenko, S.

    2008-02-01

    Unitarity cuts of enhanced Pomeron diagrams are analyzed in the framework of the Reggeon field theory. Assuming the validity of the Abramovskii-Gribov-Kancheli cutting rules, we derive a complete set of cut nonloop enhanced graphs and observe important cancellations between certain subclasses of the latter. We demonstrate also how the present method can be generalized to take into consideration Pomeron loop contributions.

  1. Constructing Causal Diagrams to Learn Deliberation

    ERIC Educational Resources Information Center

    Easterday, Matthew W.; Aleven, Vincent; Scheines, Richard; Carver, Sharon M.

    2009-01-01

    Policy problems like "What should we do about global warming?" are ill-defined in large part because we do not agree on a system to represent them the way we agree Algebra problems should be represented by equations. As a first step toward building a policy deliberation tutor, we investigated: (a) whether causal diagrams help students learn to…

  2. Computer-Generated Diagrams for the Classroom.

    ERIC Educational Resources Information Center

    Carle, Mark A.; Greenslade, Thomas B., Jr.

    1986-01-01

    Describes 10 computer programs used to draw diagrams usually drawn on chalkboards, such as addition of three vectors, vector components, range of a projectile, lissajous figures, beats, isotherms, Snell's law, waves passing through a lens, magnetic field due to Helmholtz coils, and three curves. Several programming tips are included. (JN)

  3. Spin wave Feynman diagram vertex computation package

    NASA Astrophysics Data System (ADS)

    Price, Alexander; Javernick, Philip; Datta, Trinanjan

    Spin wave theory is a well-established theoretical technique that can correctly predict the physical behavior of ordered magnetic states. However, computing the effects of an interacting spin wave theory incorporating magnons involve a laborious by hand derivation of Feynman diagram vertices. The process is tedious and time consuming. Hence, to improve productivity and have another means to check the analytical calculations, we have devised a Feynman Diagram Vertex Computation package. In this talk, we will describe our research group's effort to implement a Mathematica based symbolic Feynman diagram vertex computation package that computes spin wave vertices. Utilizing the non-commutative algebra package NCAlgebra as an add-on to Mathematica, symbolic expressions for the Feynman diagram vertices of a Heisenberg quantum antiferromagnet are obtained. Our existing code reproduces the well-known expressions of a nearest neighbor square lattice Heisenberg model. We also discuss the case of a triangular lattice Heisenberg model where non collinear terms contribute to the vertex interactions.

  4. Construction of Lax operators from weight diagrams

    SciTech Connect

    Carbon, S.L.; Piard, E.J.

    1991-05-01

    We show that cyclic weight diagrams corresponding to representations of affine Lie algebras allow one to read-off the associated Lax operator. The resultant Lax pair generates the modified KdV equations, and have been shown in some cases to produce acceptable solutions of the string equation of matrix models.

  5. Fog Machines, Vapors, and Phase Diagrams

    ERIC Educational Resources Information Center

    Vitz, Ed

    2008-01-01

    A series of demonstrations is described that elucidate the operation of commercial fog machines by using common laboratory equipment and supplies. The formation of fogs, or "mixing clouds", is discussed in terms of the phase diagram for water and other chemical principles. The demonstrations can be adapted for presentation suitable for elementary…

  6. Image Attributes: A Study of Scientific Diagrams.

    ERIC Educational Resources Information Center

    Brunskill, Jeff; Jorgensen, Corinne

    2002-01-01

    Discusses advancements in imaging technology and increased user access to digital images, as well as efforts to develop adequate indexing and retrieval methods for image databases. Describes preliminary results of a study of undergraduates that explored the attributes naive subjects use to describe scientific diagrams. (Author/LRW)

  7. Complexities of One-Component Phase Diagrams

    ERIC Educational Resources Information Center

    Ciccioli, Andrea; Glasser, Leslie

    2011-01-01

    For most materials, the solid at and near the triple-point temperature is denser than the liquid with which it is in equilibrium. However, for water and certain other materials, the densities of the phases are reversed, with the solid being less dense. The profound consequences for the appearance of the "pVT" diagram of one-component materials…

  8. Complexities of One-Component Phase Diagrams

    ERIC Educational Resources Information Center

    Ciccioli, Andrea; Glasser, Leslie

    2011-01-01

    For most materials, the solid at and near the triple-point temperature is denser than the liquid with which it is in equilibrium. However, for water and certain other materials, the densities of the phases are reversed, with the solid being less dense. The profound consequences for the appearance of the "pVT" diagram of one-component materials

  9. Dynamic Tactile Diagram Simplification on Refreshable Displays

    ERIC Educational Resources Information Center

    Rastogi, Ravi; Pawluk, Dianne T. V.

    2013-01-01

    The increasing use of visual diagrams in educational and work environments, and even our daily lives, has created obstacles for individuals who are blind or visually impaired to "independently" access the information they represent. Although physical tactile pictures can be created to convey the visual information, it is typically a slow,…

  10. Dynamic Tactile Diagram Simplification on Refreshable Displays

    ERIC Educational Resources Information Center

    Rastogi, Ravi; Pawluk, Dianne T. V.

    2013-01-01

    The increasing use of visual diagrams in educational and work environments, and even our daily lives, has created obstacles for individuals who are blind or visually impaired to "independently" access the information they represent. Although physical tactile pictures can be created to convey the visual information, it is typically a slow,

  11. Phase diagram of spiking neural networks.

    PubMed

    Seyed-Allaei, Hamed

    2015-01-01

    In computer simulations of spiking neural networks, often it is assumed that every two neurons of the network are connected by a probability of 2%, 20% of neurons are inhibitory and 80% are excitatory. These common values are based on experiments, observations, and trials and errors, but here, I take a different perspective, inspired by evolution, I systematically simulate many networks, each with a different set of parameters, and then I try to figure out what makes the common values desirable. I stimulate networks with pulses and then measure their: dynamic range, dominant frequency of population activities, total duration of activities, maximum rate of population and the occurrence time of maximum rate. The results are organized in phase diagram. This phase diagram gives an insight into the space of parameters - excitatory to inhibitory ratio, sparseness of connections and synaptic weights. This phase diagram can be used to decide the parameters of a model. The phase diagrams show that networks which are configured according to the common values, have a good dynamic range in response to an impulse and their dynamic range is robust in respect to synaptic weights, and for some synaptic weights they oscillates in α or β frequencies, independent of external stimuli. PMID:25788885

  12. Constructing Causal Diagrams to Learn Deliberation

    ERIC Educational Resources Information Center

    Easterday, Matthew W.; Aleven, Vincent; Scheines, Richard; Carver, Sharon M.

    2009-01-01

    Policy problems like "What should we do about global warming?" are ill-defined in large part because we do not agree on a system to represent them the way we agree Algebra problems should be represented by equations. As a first step toward building a policy deliberation tutor, we investigated: (a) whether causal diagrams help students learn to

  13. Weight diagram construction of Lax operators

    SciTech Connect

    Carbon, S.L.; Piard, E.J.

    1991-10-01

    We review and expand methods introduced in our previous paper. It is proved that cyclic weight diagrams corresponding to representations of affine Lie algebras allow one to construct the associated Lax operator. The resultant Lax operator is in the Miura-like form and generates the modified KdV equations. The algorithm is extended to the super-symmetric case.

  14. Impersonal parameters from Hertzsprung-Russell diagrams

    NASA Astrophysics Data System (ADS)

    Wilson, R. E.; Hurley, Jarrod R.

    2003-10-01

    An objective process for estimation of star cluster parameters from Hertzsprung-Russell (HR) diagrams is introduced, with direct inclusion of multiple stars, a least-squares fitting criterion, and standard error estimates. No role is played by conventional isochrones. Instead the quantity compared between observation and theory is the density of points (areal ) as it varies over the diagram. With as the effective observable quantity, standard parameter adjustment theory can be brought to bear on HR diagram analysis. Here we use the method of differential corrections with a least-squares fitting criterion, but any of the many known fitting methods should be applicable to comparison of observed and theoretical distributions. Diverse numerical schemes were developed to make the overall algorithm workable, including two that improve differentiability of by rendering point distributions effectively equivalent to continuous distributions in certain respects. Statistics of distributions are handled not via Monte Carlo methods but by the Functional Statistics Algorithm (hereafter FSA), a statistical algorithm that has been developed for HR diagram fitting but should serve as an alternative to Monte Carlo in many other applications. FSA accomplishes the aims of Monte Carlo with orders of magnitude less computation. Analysis of luminosity functions is included within the HR diagram algorithm as a special case. Areal density analysis of HR diagrams is acceptably fast because we handle stellar evolution via approximation functions, whose output also is more precisely differentiable than that of a full stellar evolution program. Evolution by approximation functions is roughly a million times as fast as full evolution and has virtually no numerical noise. The algorithmic ideas that lead to objective solutions can be applied to many kinds of HR diagram analysis that are now done subjectively. The present solution program is limited by speed considerations to use of one evolution program and exploration of variations in evolutionary physics is left for future versions. The program has miscellaneous refinements, such as allowing for distributions of chemical composition and interstellar extinction, as well as inclusion of binary star evolution, but so far not all have been tried in solutions. An algorithm is described for dealing with field stars directly in terms of , but has not yet been actively implemented. A synthetic globular cluster with known properties is analysed to demonstrate parameter convergence, solution consistency and comparison with known answers.

  15. Phase diagram and entanglement of two interacting topological Kitaev chains

    NASA Astrophysics Data System (ADS)

    Herviou, Loïc; Mora, Christophe; Le Hur, Karyn

    2016-04-01

    A superconducting wire described by a p -wave pairing and a Kitaev Hamiltonian exhibits Majorana fermions at its edges and is topologically protected by symmetry. We consider two Kitaev wires (chains) coupled by a Coulomb-type interaction and study the complete phase diagram using analytical and numerical techniques. A topological superconducting phase with four Majorana fermions occurs until moderate interactions between chains. For large interactions, both repulsive and attractive, by analogy with the Hubbard model, we identify Mott phases with Ising-type magnetic order. For repulsive interactions, the Ising antiferromagnetic order favors the occurrence of orbital currents spontaneously breaking time-reversal symmetry. By strongly varying the chemical potentials of the two chains, quantum phase transitions towards fully polarized (empty or full) fermionic chains occur. In the Kitaev model, the quantum critical point separating the topological superconducting phase and the polarized phase belongs to the universality class of the critical Ising model in two dimensions. When increasing the Coulomb interaction between chains, then we identify an additional phase corresponding to two critical Ising theories (or two chains of Majorana fermions). We confirm the existence of such a phase from exact mappings and from the concept of bipartite fluctuations. We show the existence of negative logarithmic corrections in the bipartite fluctuations, as a reminiscence of the quantum critical point in the Kitaev model. Other entanglement probes such as bipartite entropy and entanglement spectrum are also used to characterize the phase diagram. The limit of large interactions can be reached in an equivalent setup of ultracold atoms and Josephson junctions.

  16. Synthesis, spectroscopic, molecular orbital calculation, cytotoxic, molecular docking of DNA binding and DNA cleavage studies of transition metal complexes with N-benzylidene-N'-salicylidene-1,1-diaminopropane.

    TOXLINE Toxicology Bibliographic Information

    Al-Mogren MM; Alaghaz AN; Ebrahem EA

    2013-10-01

    Eight mononuclear chromium(III), manganese(II), iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of Schiff's base ligand were synthesized and determined by different physical techniques. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the eight metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff base is found to act as tridentate ligand using N2O donor set of atoms leading to an octahedral geometry for the complexes around all the metal ions. Quantum chemical calculations were performed with semi-empirical method to find the optimum geometry of the ligand and its complexes. Additionally in silico, the docking studies and the calculated pharmacokinetic parameters show promising futures for application of the ligand and complexes as high potency agents for DNA binding activity. The interaction of the complexes with calf thymus DNA (CT-DNA) has been investigated by UV absorption method, and the mode of CT-DNA binding to the complexes has been explored. Furthermore, the DNA cleavage activity by the complexes was performed. The Schiff base and their complexes have been screened for their antibacterial activity against bacterial strains [Staphylococcus aureus (RCMB010027), Staphylococcus epidermidis (RCMB010024), Bacillis subtilis (RCMB010063), Proteous vulgaris (RCMB 010085), Klebsiella pneumonia (RCMB 010093) and Shigella flexneri (RCMB 0100542)] and fungi [(Aspergillus fumigates (RCMB 02564), Aspergillus clavatus (RCMB 02593) and Candida albicans (RCMB05035)] by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligand.

  17. Synthesis, spectroscopic, molecular orbital calculation, cytotoxic, molecular docking of DNA binding and DNA cleavage studies of transition metal complexes with N-benzylidene-N'-salicylidene-1,1-diaminopropane.

    PubMed

    Al-Mogren, Muneerah M; Alaghaz, Abdel-Nasser M A; Ebrahem, Ebrahem A

    2013-10-01

    Eight mononuclear chromium(III), manganese(II), iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of Schiff's base ligand were synthesized and determined by different physical techniques. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the eight metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff base is found to act as tridentate ligand using N2O donor set of atoms leading to an octahedral geometry for the complexes around all the metal ions. Quantum chemical calculations were performed with semi-empirical method to find the optimum geometry of the ligand and its complexes. Additionally in silico, the docking studies and the calculated pharmacokinetic parameters show promising futures for application of the ligand and complexes as high potency agents for DNA binding activity. The interaction of the complexes with calf thymus DNA (CT-DNA) has been investigated by UV absorption method, and the mode of CT-DNA binding to the complexes has been explored. Furthermore, the DNA cleavage activity by the complexes was performed. The Schiff base and their complexes have been screened for their antibacterial activity against bacterial strains [Staphylococcus aureus (RCMB010027), Staphylococcus epidermidis (RCMB010024), Bacillis subtilis (RCMB010063), Proteous vulgaris (RCMB 010085), Klebsiella pneumonia (RCMB 010093) and Shigella flexneri (RCMB 0100542)] and fungi [(Aspergillus fumigates (RCMB 02564), Aspergillus clavatus (RCMB 02593) and Candida albicans (RCMB05035)] by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligand. PMID:23831943

  18. Synthesis, spectroscopic, molecular orbital calculation, cytotoxic, molecular docking of DNA binding and DNA cleavage studies of transition metal complexes with N-benzylidene-N'-salicylidene-1,1-diaminopropane

    NASA Astrophysics Data System (ADS)

    Al-Mogren, Muneerah M.; Alaghaz, Abdel-Nasser M. A.; Elbohy, Salwa A. H.

    2013-10-01

    Eight mononuclear chromium(III), manganese(II), iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of Schiff's base ligand were synthesized and determined by different physical techniques. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the eight metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff base is found to act as tridentate ligand using N2O donor set of atoms leading to an octahedral geometry for the complexes around all the metal ions. Quantum chemical calculations were performed with semi-empirical method to find the optimum geometry of the ligand and its complexes. Additionally in silico, the docking studies and the calculated pharmacokinetic parameters show promising futures for application of the ligand and complexes as high potency agents for DNA binding activity. The interaction of the complexes with calf thymus DNA (CT-DNA) has been investigated by UV absorption method, and the mode of CT-DNA binding to the complexes has been explored. Furthermore, the DNA cleavage activity by the complexes was performed. The Schiff base and their complexes have been screened for their antibacterial activity against bacterial strains [Staphylococcus aureus (RCMB010027), Staphylococcus epidermidis (RCMB010024), Bacillis subtilis (RCMB010063), Proteous vulgaris (RCMB 010085), Klebsiella pneumonia (RCMB 010093) and Shigella flexneri (RCMB 0100542)] and fungi [(Aspergillus fumigates (RCMB 02564), Aspergillus clavatus (RCMB 02593) and Candida albicans (RCMB05035)] by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligand.

  19. Lunar orbiting prospector

    NASA Technical Reports Server (NTRS)

    1988-01-01

    One of the prime reasons for establishing a manned lunar presence is the possibility of using the potential lunar resources. The Lunar Orbital Prospector (LOP) is a lunar orbiting platform whose mission is to prospect and explore the Moon from orbit in support of early lunar colonization and exploitation efforts. The LOP mission is divided into three primary phases: transport from Earth to low lunar orbit (LLO), operation in lunar orbit, and platform servicing in lunar orbit. The platform alters its orbit to obtain the desired surface viewing, and the orbit can be changed periodically as needed. After completion of the inital remote sensing mission, more ambitious and/or complicated prospecting and exploration missions can be contemplated. A refueled propulsion module, updated instruments, or additional remote sensing packages can be flown up from the lunar base to the platform.

  20. Orbital signatures of methyl in L-alanine.

    PubMed

    Falzon, Chantal T; Wang, Feng; Pang, Wenning

    2006-05-18

    Molecular orbital signatures of the methyl substituent in L-alanine have been identified with respect to those of glycine from information obtained in coordinate and momentum space, using dual space analysis. Electronic structural information in coordinate space is obtained using ab initio (MP2/TZVP) and density functional theory (B3LYP/TZVP) methods, from which the Dyson orbitals are simulated based on the plane wave impulse approximation into momentum space. In comparison to glycine, relaxation in geometry and valence orbitals in L-alanine is found as a result of the attachment of the methyl group. Five orbitals rather than four orbitals are identified as methyl signatures. That is, orbital 6a in the core shell, orbitals 11a and 12a in the inner valence shell, and orbitals 19a and 20a in the outer valence shell. In the inner valence shell, the attachment of methyl to glycine causes a splitting of its orbital 10a' into orbitals 11a and 12a of L-alanine, whereas in the outer valence shell the methyl group results in an insertion of an additional orbital pair of 19a and 20a. The frontier molecular orbitals, 24a and 23a, are found without any significant role in the methylation of glycine. PMID:16686523

  1. Preliminary orbital parallax catalog

    NASA Technical Reports Server (NTRS)

    Halliwell, M.

    1981-01-01

    The study is undertaken to calibrate the more reliable parallaxes derived from a comparison of visual and spectroscopic orbits and to encourage observational studies of other promising binaries. The methodological techniques used in computing orbital parallaxes are analyzed. Tables summarizing orbital data and derived system properties are then given. Also given is a series of detailed discussions of the 71 individual systems included in the tables. Data are listed for 57 other systems which are considered promising candidates for eventual orbital parallax determination.

  2. Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges

    NASA Astrophysics Data System (ADS)

    Karp, Peter D.; Latendresse, Mario; Paley, Suzanne

    2011-03-01

    Cellular networks are graphs of molecular interactions within the cell. Thanks to the confluence of genome sequencing and bioinformatics, scientists are now able to reconstruct cellular network models for more than 1,000 organisms. A variety of bioinformatics tools have been developed to support the visualization and navigation of cellular network data. Another important application is the use of cellular network diagrams to visualize and interpret large-scale datasets, such as gene-expression data. We present the Cellular Overview, a network visualization tool developed at SRI International (SRI) to support visualization, navigation, and interpretation of large-scale datasets on metabolic networks. Different variations of the diagram have been generated algorithmically for more than 1,000 organisms. We discuss the graphical design of the diagram and its interactive capabilities.

  3. Glass and liquid phase diagram of a polyamorphic monatomic system.

    PubMed

    Reisman, Shaina; Giovambattista, Nicolas

    2013-02-14

    We perform out-of-equilibrium molecular dynamics (MD) simulations of a monatomic system with Fermi-Jagla (FJ) pair potential interactions. This model system exhibits polyamorphism both in the liquid and glass state. The two liquids, low-density (LDL) and high-density liquid (HDL), are accessible in equilibrium MD simulations and can form two glasses, low-density (LDA) and high-density amorphous (HDA) solid, upon isobaric cooling. The FJ model exhibits many of the anomalous properties observed in water and other polyamorphic liquids and thus, it is an excellent model system to explore qualitatively the thermodynamic properties of such substances. The liquid phase behavior of the FJ model system has been previously characterized. In this work, we focus on the glass behavior of the FJ system. Specifically, we perform systematic isothermal compression and decompression simulations of LDA and HDA at different temperatures and determine "phase diagrams" for the glass state; these phase diagrams varying with the compression/decompression rate used. We obtain the LDA-to-HDA and HDA-to-LDA transition pressure loci, P(LDA-HDA)(T) and P(HDA-LDA)(T), respectively. In addition, the compression-induced amorphization line, at which the low-pressure crystal (LPC) transforms to HDA, P(LPC-HDA)(T), is determined. As originally proposed by Poole et al. [Phys. Rev. E 48, 4605 (1993)] simulations suggest that the P(LDA-HDA)(T) and P(HDA-LDA)(T) loci are extensions of the LDL-to-HDL and HDL-to-LDL spinodal lines into the glass domain. Interestingly, our simulations indicate that the P(LPC-HDA)(T) locus is an extension, into the glass domain, of the LPC metastability limit relative to the liquid. We discuss the effects of compression/decompression rates on the behavior of the P(LDA-HDA)(T), P(HDA-LDA)(T), P(LPC-HDA)(T) loci. The competition between glass polyamorphism and crystallization is also addressed. At our "fast rate," crystallization can be partially suppressed and the glass phase diagram can be related directly with the liquid phase diagram. However, at our "slow rate," crystallization cannot be prevented at intermediate temperatures, within the glass region. In these cases, multiple crystal-crystal transformations are found upon compression/decompression (polymorphism). PMID:23425481

  4. Glass and liquid phase diagram of a polyamorphic monatomic system

    NASA Astrophysics Data System (ADS)

    Reisman, Shaina; Giovambattista, Nicolas

    2013-02-01

    We perform out-of-equilibrium molecular dynamics (MD) simulations of a monatomic system with Fermi-Jagla (FJ) pair potential interactions. This model system exhibits polyamorphism both in the liquid and glass state. The two liquids, low-density (LDL) and high-density liquid (HDL), are accessible in equilibrium MD simulations and can form two glasses, low-density (LDA) and high-density amorphous (HDA) solid, upon isobaric cooling. The FJ model exhibits many of the anomalous properties observed in water and other polyamorphic liquids and thus, it is an excellent model system to explore qualitatively the thermodynamic properties of such substances. The liquid phase behavior of the FJ model system has been previously characterized. In this work, we focus on the glass behavior of the FJ system. Specifically, we perform systematic isothermal compression and decompression simulations of LDA and HDA at different temperatures and determine "phase diagrams" for the glass state; these phase diagrams varying with the compression/decompression rate used. We obtain the LDA-to-HDA and HDA-to-LDA transition pressure loci, PLDA-HDA(T) and PHDA-LDA(T), respectively. In addition, the compression-induced amorphization line, at which the low-pressure crystal (LPC) transforms to HDA, PLPC-HDA(T), is determined. As originally proposed by Poole et al. [Phys. Rev. E 48, 4605 (1993)], 10.1103/PhysRevE.48.4605 simulations suggest that the PLDA-HDA(T) and PHDA-LDA(T) loci are extensions of the LDL-to-HDL and HDL-to-LDL spinodal lines into the glass domain. Interestingly, our simulations indicate that the PLPC-HDA(T) locus is an extension, into the glass domain, of the LPC metastability limit relative to the liquid. We discuss the effects of compression/decompression rates on the behavior of the PLDA-HDA(T), PHDA-LDA(T), PLPC-HDA(T) loci. The competition between glass polyamorphism and crystallization is also addressed. At our "fast rate," crystallization can be partially suppressed and the glass phase diagram can be related directly with the liquid phase diagram. However, at our "slow rate," crystallization cannot be prevented at intermediate temperatures, within the glass region. In these cases, multiple crystal-crystal transformations are found upon compression/decompression (polymorphism).

  5. Introducing Earth's Orbital Eccentricity

    ERIC Educational Resources Information Center

    Oostra, Benjamin

    2015-01-01

    Most students know that planetary orbits, including Earth's, are elliptical; that is Kepler's first law, and it is found in many science textbooks. But quite a few are mistaken about the details, thinking that the orbit is very eccentric, or that this effect is somehow responsible for the seasons. In fact, the Earth's orbital eccentricity is…

  6. Introducing Earth's Orbital Eccentricity

    ERIC Educational Resources Information Center

    Oostra, Benjamin

    2015-01-01

    Most students know that planetary orbits, including Earth's, are elliptical; that is Kepler's first law, and it is found in many science textbooks. But quite a few are mistaken about the details, thinking that the orbit is very eccentric, or that this effect is somehow responsible for the seasons. In fact, the Earth's orbital eccentricity is

  7. Orbital-Lifetime Program

    NASA Technical Reports Server (NTRS)

    Orr, L. H.

    1986-01-01

    Orbital Lifetime Program (OL) analyzes long-term motion of Earthorbiting spacecraft at altitudes of up to 2,500 km. Models perturbations to orbit caused by solar-radiation pressure, atmospheric drag, and gravitational effects of Sun, Moon, and oblate Earth. Used to predict orbital lifetime and decay rate of satellites. OL written in FORTRAN 77.

  8. A Diagram Editor for Efficient Biomedical Knowledge Capture and Integration

    PubMed Central

    Yu, Bohua; Jakupovic, Elvis; Wilson, Justin; Dai, Manhong; Xuan, Weijian; Mirel, Barbara; Athey, Brian; Watson, Stanley; Meng, Fan

    2008-01-01

    Understanding the molecular mechanisms underlying complex disorders requires the integration of data and knowledge from different sources including free text literature and various biomedical databases. To facilitate this process, we created the Biomedical Concept Diagram Editor (BCDE) to help researchers distill knowledge from data and literature and aid the process of hypothesis development. A key feature of BCDE is the ability to capture information with a simple drag-and-drop. This is a vast improvement over manual methods of knowledge and data recording and greatly increases the efficiency of the biomedical researcher. BCDE also provides a unique concept matching function to enforce consistent terminology, which enables conceptual relationships deposited by different researchers in the BCDE database to be mined and integrated for intelligible and useful results. We hope BCDE will promote the sharing and integration of knowledge from different researchers for effective hypothesis development. PMID:21347131

  9. A Simple Approach for Boundary Improvement of Euler Diagrams.

    PubMed

    Simonetto, Paolo; Archambault, Daniel; Scheidegger, Carlos

    2016-01-01

    General methods for drawing Euler diagrams tend to generate irregular polygons. Yet, empirical evidence indicates that smoother contours make these diagrams easier to read. In this paper, we present a simple method to smooth the boundaries of any Euler diagram drawing. When refining the diagram, the method must ensure that set elements remain inside their appropriate boundaries and that no region is removed or created in the diagram. Our approach uses a force system that improves the diagram while at the same time ensuring its topological structure does not change. We demonstrate the effectiveness of the approach through case studies and quantitative evaluations. PMID:26529723

  10. Experimental evidence for the role of the {pi}{sub CO}* orbital in electron transfer to gas phase acetic acid CH{sub 3}CO{sub 2}H: Effects of molecular orientation

    SciTech Connect

    Brooks, Philip R.

    2009-04-21

    Electron transfer from K atoms to oriented acetic acid molecules produces acetate ions (and K{sup +}) when the CO{sub 2}H end of the molecule is attacked. The electron enters the {pi}{sub CO}* orbital and the donor atom distorts the molecule to allow migration to the {sigma}{sub OH}{sup *} orbital, thereby breaking the bond.

  11. Orbit Software Suite

    NASA Technical Reports Server (NTRS)

    Osgood, Cathy; Williams, Kevin; Gentry, Philip; Brownfield, Dana; Hallstrom, John; Stuit, Tim

    2012-01-01

    Orbit Software Suite is used to support a variety of NASA/DM (Dependable Multiprocessor) mission planning and analysis activities on the IPS (Intrusion Prevention System) platform. The suite of Orbit software tools (Orbit Design and Orbit Dynamics) resides on IPS/Linux workstations, and is used to perform mission design and analysis tasks corresponding to trajectory/ launch window, rendezvous, and proximity operations flight segments. A list of tools in Orbit Software Suite represents tool versions established during/after the Equipment Rehost-3 Project.

  12. Lunar Reconnaissance Orbiter Orbit Determination Accuracy Analysis

    NASA Technical Reports Server (NTRS)

    Slojkowski, Steven E.

    2014-01-01

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

  13. Orbit correction in an orbit separated cyclotron

    NASA Astrophysics Data System (ADS)

    Plostinar, C.; Rees, G. H.

    2014-04-01

    The orbit separated proton cyclotron (OSC) described in [1] differs in concept from that of a separated orbit cyclotron (SOC) [2]. Synchronous acceleration in an OSC is based on harmonic number jumps and orbit length adjustments via reverse bending. Four-turn acceleration in the OSC enables it to have four times fewer cryogenic-cavity systems than in a superconducting linac of the same high beam power and energy range. Initial OSC studies identified a progressive distortion of the spiral beam orbits by the off-axis, transverse deflecting fields in its accelerating cavities. Compensation of the effects of these fields involves the repeated use of a cavity field map, in a 3-D linac tracking code, to determine the modified arc bends required for the OSC ring. Subsequent tracking studies confirm the compensation scheme and show low emittance growth in acceleration.

  14. Pions in the quark matter phase diagram

    SciTech Connect

    Zablocki, D.; Blaschke, D.; Anglani, R.

    2008-08-29

    The relationship between mesonic correlations and quantum condensates in the quark matter phase diagram is explored within a quantum field theoretical approach of the Nambu and Jona-Lasinio (NJL) type. Mean-field values in the scalar meson and diquark channels are order parameters signaling the occurrence of quark condensates, entailing chiral symmetry breaking ({chi}SB) and color superconductivity (2SC) in quark matter. We investigate the spectral properties of scalar and pseudoscalar meson excitations in the phase diagram in Gaussian approximation and show that outside the {chi}SB region where the pion is a zero-width bound state, there are two regions where it can be considered as a quasi-bound state with a lifetime exceeding that of a typical heavy-ion collision fireball: (A) the high-temperature {chi}SB crossover region at low densities and (B) the high-density color superconducting phase at temperatures below 100 MeV.

  15. Prediction of boron carbon nitrogen phase diagram

    NASA Astrophysics Data System (ADS)

    Yao, Sanxi; Zhang, Hantao; Widom, Michael

    We studied the phase diagram of boron, carbon and nitrogen, including the boron-carbon and boron-nitrogen binaries and the boron-carbon-nitrogen ternary. Based on the idea of electron counting and using a technique of mixing similar primitive cells, we constructed many ''electron precise'' structures. First principles calculation is performed on these structures, with either zero or high pressures. For the BN binary, our calculation confirms that a rhmobohedral phase can be stablized at high pressure, consistent with some experimental results. For the BCN ternary, a new ground state structure is discovered and an Ising-like phase transition is suggested. Moreover, we modeled BCN ternary phase diagram and show continuous solubility from boron carbide to the boron subnitride phase.

  16. Modeling the Round Earth through Diagrams

    NASA Astrophysics Data System (ADS)

    Padalkar, Shamin; Ramadas, Jayashree

    Earlier studies have found that students, including adults, have problems understanding the scientifically accepted model of the Sun-Earth-Moon system and explaining day-to-day astronomical phenomena based on it. We have been examining such problems in the context of recent research on visual-spatial reasoning. Working with middle school students in India, we have developed a pedagogical sequence to build the mental model of the Earth and tried it in three schools for socially and educationally disadvantaged students. This pedagogy was developed on the basis of (1) a reading of current research in imagery and visual-spatial reasoning and (2) students' difficulties identified during the course of pretests and interviews. Visual-spatial tools such as concrete (physical) models, gestures, and diagrams are used extensively in the teaching sequence. The building of a mental model is continually integrated with drawing inferences to understand and explain everyday phenomena. The focus of this article is inferences drawn with diagrams.

  17. Phase diagram of a single lane roundabout

    NASA Astrophysics Data System (ADS)

    Echab, H.; Lakouari, N.; Ez-Zahraouy, H.; Benyoussef, A.

    2016-03-01

    Using the cellular automata model, we numerically study the traffic dynamic in a single lane roundabout system of four entry/exit points. The boundaries are controlled by the injecting rates α1, α2 and the extracting rate β. Both the system with and without Splitter Islands of width Lsp are considered. The phase diagram in the (α1 , β) space and its variation with the roundabout size, Pagg (i.e. the probability of aggressive entry), and Pexit (i.e. the probability of preferential exit) are constructed. The results show that the phase diagram in both cases consists of three phases: free flow, congested and jammed. However, as Lsp increases the free flow phase enlarges while the congested and jammed ones shrink. On the other hand, the short sized roundabout shows better performance in the free flow phase while the large one is more optimal in the congested phase. The density profiles are also investigated.

  18. Phase Coexistence in a Dynamic Phase Diagram.

    PubMed

    Gentile, Luigi; Coppola, Luigi; Balog, Sandor; Mortensen, Kell; Ranieri, Giuseppe A; Olsson, Ulf

    2015-08-01

    Metastability and phase coexistence are important concepts in colloidal science. Typically, the phase diagram of colloidal systems is considered at the equilibrium without the presence of an external field. However, several studies have reported phase transition under mechanical deformation. The reason behind phase coexistence under shear flow is not fully understood. Here, multilamellar vesicle (MLV)-to-sponge (L3 ) and MLV-to-Lα transitions upon increasing temperature are detected using flow small-angle neutron scattering techniques. Coexistence of Lα and MLV phases at 40 °C under shear flow is detected by using flow NMR spectroscopy. The unusual rheological behavior observed by studying the lamellar phase of a non-ionic surfactant is explained using (2) H NMR and diffusion flow NMR spectroscopy with the coexistence of planar lamellar-multilamellar vesicles. Moreover, a dynamic phase diagram over a wide range of temperatures is proposed. PMID:26083451

  19. Krajewski diagrams and the standard model

    SciTech Connect

    Stephan, Christoph A.

    2009-04-15

    This paper provides a complete list of Krajewski diagrams representing the standard model of particle physics. We will give the possible representations of the algebra and the anomaly free lifts which provide the representation of the standard model gauge group on the fermionic Hilbert space. The algebra representations following from the Krajewski diagrams are not complete in the sense that the corresponding spectral triples do not necessarily obey to the axiom of Poincare duality. This defect may be repaired by adding new particles to the model, i.e., by building models beyond the standard model. The aim of this list of finite spectral triples (up to Poincare duality) is therefore to provide a basis for model building beyond the standard model.

  20. Penguin diagrams for improved staggered fermions

    SciTech Connect

    Lee, Weonjong

    2005-01-01

    We calculate, at the one-loop level, penguin diagrams for improved staggered fermion operators constructed using various fat links. The main result is that diagonal mixing coefficients with penguin operators are identical between the unimproved operators and the improved operators using such fat links as Fat7, Fat7+Lepage, Fat7, HYP (I) and HYP (II). In addition, it turns out that the off-diagonal mixing vanishes for those constructed using fat links of Fat7, Fat7 and HYP (II). This is a consequence of the fact that the improvement by various fat links changes only the mixing with higher dimension operators and off-diagonal operators. The results of this paper, combined with those for current-current diagrams, provide complete matching at the one-loop level with all corrections of O(g{sup 2}) included.