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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. Stability diagrams for a rigid gyrostat in a circular orbit

    NASA Astrophysics Data System (ADS)

    Hughes, P. C.; Golla, D. F.

    1984-05-01

    The dynamics of a rigid gyrostat travelling in a circular orbit are reviewed. The two torques to be balanced are the gyroscopic torque associated with the once per orbit precession of the in plane angular momentum vector, and the gravitational torque that results from the principal inertial axes not being aligned with the orbiting axes. Different methods of balancing these two torques lead to different classes of relative equilibria, viz., the cylindrical case, the conical case, the hyperbolic case, and the general case. The principal contribution is to present a large number of stability diagrams for the many different cases and subcases that arise. A large number of equilbria are, in fact, unstable. However, as shown here, they can usually be stabilized by adding a momentum wheel aligned with the pitch axis.

  4. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

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

  5. Imaging molecular orbitals using photoionization

    NASA Astrophysics Data System (ADS)

    Santra, Robin

    2006-10-01

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

  6. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  7. 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.

  8. 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…

  9. Orbital effect of magnetic field on the Majorana phase diagram

    NASA Astrophysics Data System (ADS)

    Nijholt, Bas; Akhmerov, Anton R.

    2016-06-01

    Studies of Majorana bound states in semiconducting nanowires frequently neglect the orbital effect of a magnetic field. Systematically studying its role leads us to several conclusions for designing Majoranas in this system. Specifically, we show that for experimentally relevant parameter values the orbital effect of a magnetic field has a stronger impact on the dispersion relation than the Zeeman effect. While Majoranas do not require the presence of only one dispersion subband, we observe that the size of the Majoranas becomes unpractically large, and the band gap unpractically small, when more than one subband is filled. Since the orbital effect of a magnetic field breaks several symmetries of the Hamiltonian, it leads to the appearance of large regions in parameter space with no band gap whenever the magnetic field is not aligned with the wire axis. The reflection symmetry of the Hamiltonian with respect to the plane perpendicular to the wire axis guarantees that the wire stays gapped in the topologically nontrivial region as long as the field is aligned with the wire.

  10. Molecular Complexation and Phase Diagrams of Urea/PEG Mixtures

    NASA Astrophysics Data System (ADS)

    Fu, Guoepeng; Kyu, Thein

    2014-03-01

    Polyethylene glycol (PEG) and urea complexation has been known to form a stable crystal due to molecular complexation. The effect of molecular weight of PEG on the phase diagrams of its blends with urea has been explored. In the case of high molecular weight PEG8k/urea, the observed phase diagram is azeotrope, accompanied by eutectoid reactions in the submerged phases such as induced stable ``alpha'' phase crystals and metastable ``beta'' phase crystals. The metastable crystal can transform to stable crystal under a certain thermal annealing condition. However, the phase diagram of PEG1k/urea is of coexistence loop, whereas PEG400/urea exhibits eutectic character. Subsequently, the change of azeotrope to eutectic behavior with PEG molecular weight is analyzed in the context of the combined Flory-Huggins theory of liquid-liquid demixing and phase field theory of crystal solidification. Of particular interest is that only a very small urea amount (2 wt%) is needed to form a stable inclusion crystal via complexation with PEG. Potential application in lithium battery is discussed based on AC impedance spectroscopy and cyclic voltammetry. Supported by NSF-DMR 1161070.

  11. 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.

  12. Argand diagram representation of orbiting resonance in proton-transfer collision

    NASA Astrophysics Data System (ADS)

    Lutrus, C. K.; Suck Salk, S. H.

    1991-05-01

    Dynamic resonance in atom-diatomic molecule collisions has been relatively well studied compared to orbiting resonance. We discuss orbiting resonance on reactive scattering involving proton (charge) transfer. Resonance structure is predicted to exist at forward-scattering angles in both the state-to-state angular distribution and the Argand diagram for the proton-transfer collision system of He+H+2-->HeH++H. The present study demonstrates the possibility of orbiting resonance particularly in proton (charge) -transfer reaction involving atom-diatomic molecule systems.

  13. 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…

  14. 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.)

  15. 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…

  16. Exact phase diagram of multi-orbital spin-fermion model for hole doped cuprates

    NASA Astrophysics Data System (ADS)

    Meetei, Oinam Nganba; Fischer, Mark; Lawler, Michael; Paramekanti, Arun; Kim, Eun-Ah

    2015-03-01

    Recent experiments revealing the ubiquitous presence of spin and charge ordered states in hole-doped cuprates have placed the study of broken symmetry states at the center of high Tc superconductivity research. Here we aim to understand the phase diagram of broken symmetry states using a simple model that captures the essence of hole doped cuprates. The model consists of itinerant quantum holes on oxygen p-orbitals coupled to classical Cu spins. It is amenable to sign problem free Monte-Carlo simulation allowing us to study finite temperature properties as well as unbiased determination of ground state spin and charge configuration. As a function of system parameters, we obtain a rich phase diagram. Our analysis provides a transparent and unifying picture for various charge and spin ordered states as arising from frustration of antiferromagnetic order due to hole doping, through exact finite temperature phase diagram of the model. Supported by the U.S. Department of Energy Grant DE-SC0010313.

  17. 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

  18. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

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

    2014-05-14

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

  19. Phase diagram and collective excitations in an excitonic insulator from an orbital physics viewpoint

    NASA Astrophysics Data System (ADS)

    Nasu, Joji; Watanabe, Tsutomu; Naka, Makoto; Ishihara, Sumio

    2016-05-01

    An excitonic-insulating system is studied from a viewpoint of the orbital physics in strongly correlated electron systems. An effective model Hamiltonian for low-energy electronic states is derived from the two-orbital Hubbard model with a finite-energy difference corresponding to the crystalline-field splitting. The effective model is represented by the spin operators and the pseudospin operators for the spin-state degrees of freedom. The ground-state phase diagram is analyzed by the mean-field approximation. In addition to the low-spin state and high-spin state phases, two kinds of the excitonic-insulating phases emerge as a consequence of the competition between the crystalline-field effect and the Hund coupling. Transitions to the excitonic phases are classified to an Ising-type transition resulted from a spontaneous breaking of the Z2 symmetry. Magnetic structures in the two excitonic-insulating phases are different from each other: an antiferromagnetic order and a spin nematic order. Collective excitations in each phase are examined using the generalized spin-wave approximation. Characteristics in the Goldstone modes in the excitonic-insulating phases are studied through the calculations of the dynamical correlation functions for the spins and pseudospin operators. Both the transverse and longitudinal spin excitation modes are active in the two excitonic-insulating phases in contrast to the low-spin state and high-spin state phases. Relationships of the present results to the perovskite cobalt oxides are discussed.

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

    ERIC Educational Resources Information Center

    Keeports, David

    1986-01-01

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

  1. 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.

  2. 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

  3. Molecular orbitals for properties and spectroscopies

    SciTech Connect

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

    2015-12-31

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

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  5. 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

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

    ERIC Educational Resources Information Center

    Willis, Christopher J.

    1988-01-01

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

  7. 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.

  8. Phase diagram and collective modes in Rashba spin-orbit coupled BEC: Effect of in-plane magnetic field

    NASA Astrophysics Data System (ADS)

    Dong, Dong; Zou, Xu-Bo; Guo, Guang-Can

    2015-07-01

    We studied the system of pure Rashba spin-orbit coupled Bose gas with an in-plane magnetic field. Based on the mean field theory, we obtained the zero temperature phase diagram of the system which exhibits three phases, plane wave (PW) phase, striped wave (SW) phase, and zero momentum (ZM) phase. It was shown that with a growing in-plane field, both SW and ZM phases will eventually turn into the PW phase. Furthermore, we adopted the Bogoliubov theory to study the excitation spectrum as well as the sound speed. Project supported by the National Natural Science Foundation of China (Grant No. 10774088).

  9. 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.

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

    PubMed

    Heßelmann, Andreas

    2016-06-14

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

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

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

    SciTech Connect

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

    1988-01-01

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

  13. 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.

  14. Exploring chemistry with the fragment molecular orbital method.

    PubMed

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

    2012-06-01

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

  15. Coulomb-corrected molecular orbital tomography of nitrogen

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  16. 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

  17. 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

  18. THE FUELING DIAGRAM: LINKING GALAXY MOLECULAR-TO-ATOMIC GAS RATIOS TO INTERACTIONS AND ACCRETION

    SciTech Connect

    Stark, David V.; Kannappan, Sheila J.; Eckert, Kathleen D.; Wei, Lisa H.; Baker, Andrew J.; Leroy, Adam K.; Vogel, Stuart N.

    2013-05-20

    To assess how external factors such as local interactions and fresh gas accretion influence the global interstellar medium of galaxies, we analyze the relationship between recent enhancements of central star formation and total molecular-to-atomic (H{sub 2}/H I) gas ratios, using a broad sample of field galaxies spanning early-to-late type morphologies, stellar masses of 10{sup 7.2}-10{sup 11.2} M{sub Sun }, and diverse stages of evolution. We find that galaxies occupy several loci in a ''fueling diagram'' that plots H{sub 2}/H I ratio versus mass-corrected blue-centeredness, a metric tracing the degree to which galaxies have bluer centers than the average galaxy at their stellar mass. Spiral galaxies of all stellar masses show a positive correlation between H{sub 2}/H I ratio and mass-corrected blue-centeredness. When combined with previous results linking mass-corrected blue-centeredness to external perturbations, this correlation suggests a systematic link between local galaxy interactions and molecular gas inflow/replenishment. Intriguingly, E/S0 galaxies show a more complex picture: some follow the same correlation, some are quenched, and a distinct population of blue-sequence E/S0 galaxies (with masses below key scales associated with transitions in gas richness) defines a separate loop in the fueling diagram. This population appears to be composed of low-mass merger remnants currently in late- or post-starburst states, in which the burst first consumes the H{sub 2} while the galaxy center keeps getting bluer, then exhausts the H{sub 2}, at which point the burst population reddens as it ages. Multiple lines of evidence suggest connected evolutionary sequences in the fueling diagram. In particular, tracking total gas-to-stellar mass ratios within the fueling diagram provides evidence of fresh gas accretion onto low-mass E/S0s emerging from their central starburst episodes. Drawing on a comprehensive literature search, we suggest that virtually all galaxies

  19. Conformation effects on the molecular orbitals of serine

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  20. Communication: Phase diagram of C36 by atomistic molecular dynamics and thermodynamic integration through coexistence regions

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C36. 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 C36, 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 C36 fullerite and of its liquid state, at variance with what previously experienced for C60.

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

    PubMed

    Ferenczy, György G; Adams, William H

    2009-04-01

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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

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

    PubMed

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

    2016-09-13

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

  6. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Autschbach, Jochen; King, Harry F.

    2010-07-01

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

  8. 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.

  9. A low Earth orbit molecular beam space simulation facility

    NASA Technical Reports Server (NTRS)

    Cross, J. B.

    1984-01-01

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

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

    SciTech Connect

    Zwan, Elmar V. van der; Lein, Manfred

    2007-11-29

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

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

    PubMed

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

    2014-09-16

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

  12. 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.

  13. 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

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

    SciTech Connect

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

    1990-11-21

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

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

    PubMed

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

    2006-01-26

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

  16. 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

  17. 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

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

    PubMed

    Mitxelena, Ion; Piris, Mario

    2016-05-28

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

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Mitxelena, Ion; Piris, Mario

    2016-05-01

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

  2. P and N compensation in diamond molecular orbital theory

    NASA Astrophysics Data System (ADS)

    Anderson, Alfred B.; Kostadinov, Lubomir N.

    1997-01-01

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

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

    SciTech Connect

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

    2012-12-28

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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. [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

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

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

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

  10. 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…

  11. 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

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

    PubMed

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

    2004-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Sung; Kim, Taekyeong

    2016-01-01

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

  14. 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.

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

    PubMed

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

    2010-06-11

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

  16. 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…

  17. 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}.

  18. A growth diagram for plasma-assisted molecular beam epitaxy of In-face InN

    SciTech Connect

    Gallinat, C. S.; Koblmueller, G.; Brown, J. S.; Speck, J. S.

    2007-09-15

    We investigated the role of temperature and In/N flux ratios to determine suitable growth windows for the plasma-assisted molecular beam epitaxy of In-face (0001) InN. Under vacuum, InN starts decomposing at 435 deg. C as defined by the release of N{sub 2} from the InN crystal and a buildup of an In adlayer and liquid In droplets on the sample surface. At temperatures greater than 470 deg. C, InN decomposition was characterized by a release of both In vapor and N{sub 2} in the absence of a significant accumulation of an In adlayer. No growth was observed at substrate temperatures above 500 deg. C or at temperatures in which the decomposition rates were higher than the growth rates. A growth diagram was then constructed consisting of two growth regimes: the 'In-droplet regime' characterized by step-flow growth and relatively flat surfaces and the ''N-rich regime'' characterized by rough, three-dimensional surfaces. The growth diagram can then be used to predict the surface structure of films grown at varying substrate temperatures and In fluxes. A 2.5 monolayer In adlayer was observed during In-droplet growth, suggesting that an In wetting layer was necessary for step-flow growth.

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

    PubMed

    Petrek, Martin; Kosinová, Pavlína; 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

  20. 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.

  1. 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.

  2. 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.

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

    PubMed

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

    2009-05-15

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

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

    SciTech Connect

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

    2009-10-15

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

  5. 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

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

  8. 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.

  9. 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.

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

    PubMed

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

    2016-09-01

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

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

    SciTech Connect

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

    2011-10-03

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

  12. The Effects of Presentation Mode and Colour in Teaching the Visualisation of Rotation in Diagrams of Molecular Structures.

    ERIC Educational Resources Information Center

    Seddon, G. M.; Shubber, K. E.

    1984-01-01

    Investigated use of overhead transparencies containing a sequence of diagrams to represent a three-dimensional structure at different stages during a rotation. Significant learning occurred among 120 Bahraini boys (aged 15-16) when the transparencies contained multi-colored diagrams which were exposed simultaneously or individually in a cumulative…

  13. 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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  16. 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.

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

    SciTech Connect

    Feng, Min; Zhao, Jin; Petek, Hrvoje

    2008-04-17

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

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

    SciTech Connect

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

    1992-01-01

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

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

    SciTech Connect

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

    1992-11-01

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

  20. 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

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

    PubMed

    Proppe, Jonny; Herrmann, Carmen

    2015-02-01

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

  2. 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.

  3. 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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Romere, P. O.

    1982-03-01

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

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

    NASA Technical Reports Server (NTRS)

    Romere, P. O.

    1982-01-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1996-05-01

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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2002-10-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed

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

    2013-06-01

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

  14. 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.

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

    PubMed

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

    2016-03-01

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

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Tada, Tomofumi; Aoki, Yuriko; Imamura, Akira

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

  20. Thermodynamic Diagrams

    NASA Astrophysics Data System (ADS)

    Chaston, Scot

    1999-02-01

    Thermodynamic data such as equilibrium constants, standard cell potentials, molar enthalpies of formation, and standard entropies of substances can be a very useful basis for an organized presentation of knowledge in diverse areas of applied chemistry. Thermodynamic data can become particularly useful when incorporated into thermodynamic diagrams that are designed to be easy to recall, to serve as a basis for reconstructing previous knowledge, and to determine whether reactions can occur exergonically or only with the help of an external energy source. Few students in our chemistry-based courses would want to acquire the depth of knowledge or rigor of professional thermodynamicists. But they should nevertheless learn how to make good use of thermodynamic data in their professional occupations that span the chemical, biological, environmental, and medical laboratory fields. This article discusses examples of three thermodynamic diagrams that have been developed for this purpose. They are the thermodynamic energy account (TEA), the total entropy scale, and the thermodynamic scale diagrams. These diagrams help in the teaching and learning of thermodynamics by bringing the imagination into the process of developing a better understanding of abstract thermodynamic functions, and by allowing the reader to keep track of specialist thermodynamic discourses in the literature.

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

    NASA Astrophysics Data System (ADS)

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

    1997-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Fukushima, Kimichika

    1993-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  5. 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.

  6. Liquid/liquid metal extraction: Phase diagram topology resulting from molecular interactions between extractant, ion, oil and water

    NASA Astrophysics Data System (ADS)

    Bauer, C.; Bauduin, P.; Dufrêche, J. F.; Zemb, T.; Diat, O.

    2012-11-01

    We consider the class of surfactants called "extractants" since they specifically interact with some cations and are used in liquid-liquid separation processes. We review here features of water-poor reverse micelles in water/oil/ extractant systems as determined by combined structural studies including small angle scattering techniques on absolute scale. Origins of instabilities, liquid-liquid separation as well as emulsification failure are detected. Phase diagrams contain the same multi-phase domains as classical microemulsions, but special unusual features appear due to the high spontaneous curvature directed towards the polar cores of aggregates as well as rigidity of the film made by extracting molecules.

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

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    SciTech Connect

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

    1986-09-01

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

  10. 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

  11. 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.

  12. 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.

  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. 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

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

    PubMed

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

    2004-11-01

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

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

    PubMed

    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. PMID:25028021

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Kato, Koichiro; Fukuzawa, Kaori; Mochizuki, Yuji

    2015-06-01

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

  19. 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.

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

    PubMed

    Shinagawa, Y

    1992-02-01

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

  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. 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.

  4. 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...

  5. 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.

  6. A Monte Carlo study of the influence of molecular flexibility on the phase diagram of a fused hard sphere model

    NASA Astrophysics Data System (ADS)

    McBride, Carl; Vega, Carlos

    2002-12-01

    A study of a rigid fully flexible fused hard sphere model [C. McBride, C. Vega, and L. G. MacDowell, Phys. Rev. E 64, 011703 (2001)] is extended to the smectic and solid branches of the phase diagram. Computer simulations have been performed for a completely rigid model composed of 15 fused hard spheres (15+0), a model of 15 fused hard spheres of which 2 monomers at one end of the model form a flexible tail (13+2), and a model consisting of 15 fused hard spheres with 5 monomers forming a flexible tail (10+5). For the 15+0 model the phase sequence isotropic-nematic-smectic A-columnar is found on compression, and the sequence solid-smectic A-nematic-isotropic on expansion. For the 13+2 model the phase sequence isotropic-nematic-smectic C is found on compression, and the sequence solid-smectic A-nematic-isotropic on expansion. For the 10+5 model the phase sequence isotropic-glass is found on compression. The expansion runs displayed the phase sequence solid-smectic A-isotropic. The introduction of flexibility was seen to stabilize the smectic A phase at the expense of the nematic phase.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2016-07-28

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

  9. 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.

  10. 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

  11. 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…

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Chakraborty, Debajit; Karasiev, Valentin; Trickey, Samuel

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

  18. 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.

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

    PubMed

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

    2009-01-29

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Gee, Myrlene; Wasylishen, Roderick E.

    2001-06-01

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

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

    SciTech Connect

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

    2015-11-15

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

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

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

    2014-01-24

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

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

    SciTech Connect

    Chen, N.; Yang, R.T.

    1996-11-01

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

  11. 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.

  12. 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.

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

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Taylor, Peter R.

    1990-01-01

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

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

    PubMed

    Saito, N; Fuwa, A

    2000-01-01

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

  15. 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…

  16. 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.

  17. 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.

  18. 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.

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

    PubMed

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

    2014-12-01

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

  4. 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.

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

    NASA Technical Reports Server (NTRS)

    Ehlers, H. K. F.

    1985-01-01

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

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

    PubMed

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

    2015-04-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  8. 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.

  9. 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.

  10. 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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Roemelt, Michael

    2015-07-28

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

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

    NASA Astrophysics Data System (ADS)

    Roemelt, Michael

    2015-07-01

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

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

    PubMed

    Roemelt, Michael

    2015-07-28

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

  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. 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.

  17. 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.

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

    PubMed

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

    2016-07-12

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

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

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  1. 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.

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

    PubMed

    Balachandran, V; Karunakaran, V

    2014-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Kalfaoǧlu, Emel; Karabulut, Bünyamin

    2016-03-01

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

  4. 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.

  5. 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…

  6. 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.

  7. Qualitative extension of the EC' Zone Diagram to a molecular catalyst for a multi-electron, multi-substrate electrochemical reaction.

    PubMed

    Martin, Daniel J; McCarthy, Brian D; Rountree, Eric S; Dempsey, Jillian L

    2016-06-14

    The EC' Zone Diagram, introduced by Savéant and Su over 30 years ago, has been used to classify voltammetric responses for electrocatalytic systems. With a single H2-evolving catalyst, Co(dmgBF2)2(CH3CH)2 (dmgBF2 = difluoroboryl-dimethylglyoxime), and a series of para-substituted anilinium acids, experimental conditions were carefully tuned to access to each region of the classic zone diagram. Close scrutiny revealed the extent to which the kinetic (λ) and excess (γ) factors could be experimentally controlled and used to access a variety of waveforms for this ECEC' catalytic system. It was found that most of the tunable experimental parameters (such as catalyst concentration, scan rate, and substrate concentration) predicted in the EC' Zone Diagram could be extended to a multi-electron system and produced similarly-shaped waveforms with some deviations. Tuning of a single catalyst across every region of the classic zone diagram has previously been prevented due to the seven orders of magnitude that need to be traversed across the kinetic parameter; however, the cobalt catalyst in this study provided unique control of this parameter. By varying the acids used as the proton source, the rate constants for protonation were tuned via a pKa-dependent linear free energy relationship. PMID:26998812

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

    PubMed

    Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi

    2016-01-01

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

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

    SciTech Connect

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

    2009-06-15

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

  10. 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

  11. Mean-Field Theory of Intra-Molecular Charge Ordering in (TTM--TTP)I3

    NASA Astrophysics Data System (ADS)

    Omori, Yukiko; Tsuchiizu, Masahisa; Suzumura, Yoshikazu

    2011-02-01

    We examine an intra-molecular charge-ordered (ICO) state in the multi-orbital molecular compound (TTM--TTP)I3 on the basis of an effective two-orbital model derived from ab initio calculations. Representing the model in terms of the fragment molecular-orbital (MO) picture, the ICO state is described as the charge disproportionation on the left and right fragment MOs. By applying the mean-field theory, the phase diagram of the ground state is obtained as a function of the inter-molecular Coulomb repulsion and the intra-molecular transfer integral. The ICO state is stabilized by large inter-fragment Coulomb interactions, and the small intra-molecular transfer energy between two fragment MOs. Furthermore, we examine the finite-temperature phase diagram. The relevance to the experimental observations in the molecular compound of (TTM--TTP)I3 is also discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  13. 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.

  14. Gravity wave transmission diagram

    NASA Astrophysics Data System (ADS)

    Tomikawa, Yoshihiro

    2016-07-01

    A possibility of gravity wave propagation from a source region to the airglow layer around the mesopause has been discussed based on the gravity wave blocking diagram taking into account the critical level filtering alone. This paper proposes a new gravity wave transmission diagram in which both the critical level filtering and turning level reflection of gravity waves are considered. It shows a significantly different distribution of gravity wave transmissivity from the blocking diagram.

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

    NASA Astrophysics Data System (ADS)

    Itoh, H.; Ertl, G.

    1982-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. 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.

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

    PubMed

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

    2011-06-01

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

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

    SciTech Connect

    Ipatov, A. N.

    2010-02-15

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

  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. 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: ...

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    PubMed

    Nishimoto, Yoshio; Fedorov, Dmitri G

    2016-08-10

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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    PubMed

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

    2015-03-21

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

  9. 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.

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

    PubMed

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

    2016-07-18

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

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

    SciTech Connect

    Thirman, Jonathan Head-Gordon, Martin

    2015-08-28

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

  12. 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.

  13. Dynamical Mean-Field Theory Study of Correlated Electronic Structures and the Phase Diagram of Hydrocarbon Superconductors

    NASA Astrophysics Data System (ADS)

    Kim, Minjae; Choi, Hong Chul; Shim, Ji Hoon; Min, B. I.

    2014-03-01

    We have studied correlated electronic structures and the phase diagram of electron-doped hydrocarbon molecular solids, based on the dynamical mean-field theory. We have determined the phase diagram of hydrocarbon molecular solids as functions of doping and energy parameters including the Coulomb correlation, the Hund coupling, and the molecular-orbital (MO) energy level splitting. We have found that the hydrocarbon superconductors (electron-doped picene and coronene) belong to the multi-band Fermi liquid state, while non-superconducting electron-doped pentacene belongs to the single-band state in the proximity of the metal-insulator transition. The size of the MO energy level splitting plays an important role in deriving the superconductivity of electron-doped hydrocarbon solids. The multi-band nature of hydrocarbon solids from the small MO energy level splitting boosts the superconductivity through the enhanced density of states at the Fermi level.

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

    ERIC Educational Resources Information Center

    Martin, R. Bruce

    1988-01-01

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

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

    PubMed

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

    Conradie, Jeanet; Ghosh, Abhik

    2014-05-19

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  2. 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

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

    PubMed

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

    2013-05-30

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

  4. 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

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

    PubMed

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

    2016-08-17

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

  6. 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.

  7. 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.

  8. 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.

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

    PubMed

    Moncho, Salvador; Autschbach, Jochen

    2010-12-01

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

  10. 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…

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

    PubMed

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

    2013-11-01

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

  12. 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

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

    PubMed

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

    2012-12-14

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

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

    PubMed

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

    2007-11-01

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

  15. 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.

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

    PubMed

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

    2011-08-01

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

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

    PubMed

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

    2015-08-18

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

  18. Quantitative Structure-Cytotoxicity Relationship of Bioactive Heterocycles by the Semi-empirical Molecular Orbital Method with the Concept of Absolute Hardness

    NASA Astrophysics Data System (ADS)

    Ishihara, Mariko; Sakagami, Hiroshi; Kawase, Masami; Motohashi, Noboru

    The relationship between the cytotoxicity of N-heterocycles (13 4-trifluoromethylimidazole, 15 phenoxazine and 12 5-trifluoromethyloxazole derivatives), O-heterocycles (11 3-formylchromone and 20 coumarin derivatives) and seven vitamin K2 derivatives against eight tumor cell lines (HSC-2, HSC-3, HSC-4, T98G, HSG, HepG2, HL-60, MT-4) and a maximum of 15 chemical descriptors was investigated using CAChe Worksystem 4.9 project reader. After determination of the conformation of these compounds and approximation to the molecular form present in vivo (biomimetic) by CONFLEX5, the most stable structure was determined by CAChe Worksystem 4.9 MOPAC (PM3). The present study demonstrates the best relationship between the cytotoxic activity and molecular shape or molecular weight of these compounds. Their biological activities can be estimated by hardness and softness, and by using η-χ activity diagrams.

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

    SciTech Connect

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

    2015-07-07

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

  20. 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.

  1. 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

  2. Upgrading Diagnostic Diagrams

    NASA Astrophysics Data System (ADS)

    Proxauf, B.; Kimeswenger, S.; Öttl, S.

    2014-04-01

    Diagnostic diagrams of forbidden lines have been a useful tool for observers in astrophysics for many decades now. They are used to obtain information on the basic physical properties of thin gaseous nebulae. Moreover they are also the initial tool to derive thermodynamic properties of the plasma from observations to get ionization correction factors and thus to obtain proper abundances of the nebulae. Some diagnostic diagrams are in wavelengths domains which were difficult to take either due to missing wavelength coverage or low resolution of older spectrographs. Thus they were hardly used in the past. An upgrade of this useful tool is necessary because most of the diagrams were calculated using only the species involved as a single atom gas, although several are affected by well-known fluorescence mechanisms as well. Additionally the atomic data have improved up to the present time. The new diagnostic diagrams are calculated by using large grids of parameter space in the photoionization code CLOUDY. For a given basic parameter the input radiation field is varied to find the solutions with cooling-heating-equilibrium. Empirical numerical functions are fitted to provide formulas usable in e.g. data reduction pipelines. The resulting diagrams differ significantly from those used up to now and will improve the thermodynamic calculations.

  3. Trace element indiscrimination diagrams

    NASA Astrophysics Data System (ADS)

    Li, Chusi; Arndt, Nicholas T.; Tang, Qingyan; Ripley, Edward M.

    2015-09-01

    We tested the accuracy of trace element discrimination diagrams for basalts using new datasets from two petrological databases, PetDB and GEOROC. Both binary and ternary diagrams using Zr, Ti, V, Y, Th, Hf, Nb, Ta, Sm, and Sc do a poor job of discriminating between basalts generated in various tectonic environments (continental flood basalt, mid-ocean ridge basalt, ocean island basalt, oceanic plateau basalt, back-arc basin basalt, and various types of arc basalt). The overlaps between the different types of basalt are too large for the confident application of such diagrams when used in the absence of geological and petrological constraints. None of the diagrams we tested can clearly discriminate between back-arc basin basalt and mid-ocean ridge basalt, between continental flood basalt and oceanic plateau basalt, and between different types of arc basalt (intra-oceanic, island and continental arcs). Only ocean island basalt and some mid-ocean ridge basalt are generally distinguishable in the diagrams, and even in this case, mantle-normalized trace element patterns offer a better solution for discriminating between the two types of basalt.

  4. Weyl card diagrams

    SciTech Connect

    Jones, Gregory; Wang, John E.

    2005-06-15

    To capture important physical properties of a spacetime we construct a new diagram, the card diagram, which accurately draws generalized Weyl spacetimes in arbitrary dimensions by encoding their global spacetime structure, singularities, horizons, and some aspects of causal structure including null infinity. Card diagrams draw only nontrivial directions providing a clearer picture of the geometric features of spacetimes as compared to Penrose diagrams, and can change continuously as a function of the geometric parameters. One of our main results is to describe how Weyl rods are traversable horizons and the entirety of the spacetime can be mapped out. We review Weyl techniques and as examples we systematically discuss properties of a variety of solutions including Kerr-Newman black holes, black rings, expanding bubbles, and recent spacelike-brane solutions. Families of solutions will share qualitatively similar cards. In addition we show how card diagrams not only capture information about a geometry but also its analytic continuations by providing a geometric picture of analytic continuation. Weyl techniques are generalized to higher dimensional charged solutions and applied to generate perturbations of bubble and S-brane solutions by Israel-Khan rods.

  5. Weyl card diagrams

    NASA Astrophysics Data System (ADS)

    Jones, Gregory; Wang, John E.

    2005-06-01

    To capture important physical properties of a spacetime we construct a new diagram, the card diagram, which accurately draws generalized Weyl spacetimes in arbitrary dimensions by encoding their global spacetime structure, singularities, horizons, and some aspects of causal structure including null infinity. Card diagrams draw only nontrivial directions providing a clearer picture of the geometric features of spacetimes as compared to Penrose diagrams, and can change continuously as a function of the geometric parameters. One of our main results is to describe how Weyl rods are traversable horizons and the entirety of the spacetime can be mapped out. We review Weyl techniques and as examples we systematically discuss properties of a variety of solutions including Kerr-Newman black holes, black rings, expanding bubbles, and recent spacelike-brane solutions. Families of solutions will share qualitatively similar cards. In addition we show how card diagrams not only capture information about a geometry but also its analytic continuations by providing a geometric picture of analytic continuation. Weyl techniques are generalized to higher dimensional charged solutions and applied to generate perturbations of bubble and S-brane solutions by Israel-Khan rods.

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

    PubMed

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

    2015-03-28

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

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Li, Yanli; Dabo, Ismaila

    2011-10-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-01-01

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

  12. 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

  13. 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.

  14. 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.

  15. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

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

    PubMed

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

    2013-11-01

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

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

    SciTech Connect

    Tachikawa, Masanori

    2015-12-31

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

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  20. Tectonic discrimination diagrams revisited

    NASA Astrophysics Data System (ADS)

    Vermeesch, Pieter

    2006-06-01

    The decision boundaries of most tectonic discrimination diagrams are drawn by eye. Discriminant analysis is a statistically more rigorous way to determine the tectonic affinity of oceanic basalts based on their bulk-rock chemistry. This method was applied to a database of 756 oceanic basalts of known tectonic affinity (ocean island, mid-ocean ridge, or island arc). For each of these training data, up to 45 major, minor, and trace elements were measured. Discriminant analysis assumes multivariate normality. If the same covariance structure is shared by all the classes (i.e., tectonic affinities), the decision boundaries are linear, hence the term linear discriminant analysis (LDA). In contrast with this, quadratic discriminant analysis (QDA) allows the classes to have different covariance structures. To solve the statistical problems associated with the constant-sum constraint of geochemical data, the training data must be transformed to log-ratio space before performing a discriminant analysis. The results can be mapped back to the compositional data space using the inverse log-ratio transformation. An exhaustive exploration of 14,190 possible ternary discrimination diagrams yields the Ti-Si-Sr system as the best linear discrimination diagram and the Na-Nb-Sr system as the best quadratic discrimination diagram. The best linear and quadratic discrimination diagrams using only immobile elements are Ti-V-Sc and Ti-V-Sm, respectively. As little as 5% of the training data are misclassified by these discrimination diagrams. Testing them on a second database of 182 samples that were not part of the training data yields a more reliable estimate of future performance. Although QDA misclassifies fewer training data than LDA, the opposite is generally true for the test data. Therefore LDA is a cruder but more robust classifier than QDA. Another advantage of LDA is that it provides a powerful way to reduce the dimensionality of the multivariate geochemical data in a similar

  1. 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).

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaolei; Zeng, X. C.

    2003-02-01

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

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

    SciTech Connect

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

    1999-04-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Qi, Jianbing

    2016-05-01

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

  11. Wilson Loop Diagrams and Positroids

    NASA Astrophysics Data System (ADS)

    Agarwala, Susama; Marin-Amat, Eloi

    2016-07-01

    In this paper, we study a new application of the positive Grassmannian to Wilson loop diagrams (or MHV diagrams) for scattering amplitudes in N= 4 Super Yang-Mill theory (N = 4 SYM). There has been much interest in studying this theory via the positive Grassmannians using BCFW recursion. This is the first attempt to study MHV diagrams for planar Wilson loop calculations (or planar amplitudes) in terms of positive Grassmannians. We codify Wilson loop diagrams completely in terms of matroids. This allows us to apply the combinatorial tools in matroid theory used to identify positroids (non-negative Grassmannians) to Wilson loop diagrams. In doing so, we find that certain non-planar Wilson loop diagrams define positive Grassmannians. While non-planar diagrams do not have physical meaning, this finding suggests that they may have value as an algebraic tool, and deserve further investigation.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  13. 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.

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

    PubMed

    Ferenczy, György G

    2013-04-01

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

  15. 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.

  16. 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.

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

    PubMed

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

    1995-01-01

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

  18. 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…

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

    NASA Astrophysics Data System (ADS)

    Mazin, Igor; Streltsov, Sergey; Foyevtseva, Kateryna

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  2. 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.

  3. 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.

  4. 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.

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

    SciTech Connect

    Kimura, M.; Lane, N.F.

    1987-01-01

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

  6. 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.

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

    PubMed

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

    2011-10-01

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

  8. Contingency diagrams as teaching tools

    PubMed Central

    Mattaini, Mark A.

    1995-01-01

    Contingency diagrams are particularly effective teaching tools, because they provide a means for students to view the complexities of contingency networks present in natural and laboratory settings while displaying the elementary processes that constitute those networks. This paper sketches recent developments in this visualization technology and illustrates approaches for using contingency diagrams in teaching. ImagesFigure 2Figure 3Figure 4 PMID:22478208

  9. 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)

  10. Intramolecular interactions of L-phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules.

    PubMed

    Ganesan, Aravindhan; Wang, Feng; Falzon, Chantal

    2011-02-01

    Intramolecular interactions between fragments of L-phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L-phenylalanine, benzene and L-alanine are studied using density functional theory methods. While fully resolved experimental PES of L-phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e(1g) and 1a(2u) orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L-phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14-20 eV, rather than outside of this region. This study presents a competent orbital based fragments-in-molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D-PDF technique. PMID:20806261

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

    SciTech Connect

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

    1994-02-01

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

  12. On-Orbit Propulsion OMS/RCS

    NASA Technical Reports Server (NTRS)

    Hurlbert, Eric A.

    2001-01-01

    This slide presentation reviews the Space Shuttle's On-Orbit Propulsion systems: the Orbital Maneuvering System (OMS) and the Reaction Control System (RCS). The functions of each of the systems is described, and the diagrams of the systems are presented. The OMS/RCS thruster is detailed and a trade study comparison of non-toxic propellants is presented.

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

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

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

  14. Concrete and abstract Voronoi diagrams

    SciTech Connect

    Klein, R. )

    1989-01-01

    The Voronoi diagram of a set of sites is a partition of the plane into regions, one to each site, such that the region of each site contains all points of the plane that are closer to this site than to the other ones. Such partitions are of great importance to computer science and many other fields. The challenge is to compute Voronoi diagrams quickly. The problem is that their structure depends on the notion of distance and the sort of site. In this book the author proposes a unifying approach by introducing abstract Voronoi diagrams. These are based on the concept of bisecting curves which are required to have some simple properties that are actually possessed by most bisectors of concrete Voronoi diagrams. Abstract Voronoi diagrams can be computed efficiently and there exists a worst-case efficient algorithm of divide-and-conquer type that applies to all abstract Voronoi diagrams satisfying a certain constraint. The author shows that this constraint is fulfilled by the concrete diagrams based no large classes of metrics in the plane.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

    2013-01-01

    In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

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

    PubMed

    Porchelvi, E Elamurugu; Muthu, S

    2015-01-01

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

  1. Using simple molecular orbital calculations to predict disease: fast DFT methods applied to enzymes implicated in PKU, Parkinson's disease and Obsessive Compulsive Disorder

    NASA Astrophysics Data System (ADS)

    Hofto, Laura; Hofto, Meghan; Cross, Jessica; Cafiero, Mauricio

    2007-09-01

    Many diseases can be traced to point mutations in the DNA coding for specific enzymes. These point mutations result in the change of one amino acid residue in the enzyme. We have developed a model using simple molecular orbital calculations which can be used to quantitatively determine the change in interaction between the enzyme's active site and necessary ligands upon mutation. We have applied this model to three hydroxylase proteins: phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase, and we have obtained excellent correlation between our results and observed disease symptoms. Furthermore, we are able to use this agreement as a baseline to screen other mutations which may also cause onset of disease symptoms. Our focus is on systems where the binding is due largely to dispersion, which is much more difficult to model inexpensively than pure electrostatic interactions. Our calculations are run in parallel on a sixteen processor cluster of 64-bit Athlon processors.

  2. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods. PMID:27308221

  3. Hydration effects on enzyme-substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Ando, Hiroyuki; Shigeta, Yasuteru; Baba, Takeshi; Watanabe, Chiduru; Okiyama, Yoshio; Mochizuki, Yuji; Nakano, Masayoshi

    2015-02-01

    Fragment molecular orbital calculations were successfully applied to a nylon oligomer hydrolase, NylB, to investigate the hydration effects on an enzyme-substrate binding structure. Statistically corrected inter-fragment interaction energy analyses were performed on this system to quantitatively characterise the interactions between the substrate, 6-aminohexanoate linear dimer (ALD), and the amino acid residues, such as Asp181, Ser112, and Ile 345, which are regarded as important for enzyme-substrate complex formation by NylB. We found that the direct interaction between ALD and NylB is weakened by hydration, because water molecules cause charge translation or polarisation of ALD or each amino acid residue. However, including the interaction energy between ALD and water molecules greatly stabilises this complex. These results indicate the importance of the hydration effects in enzyme-substrate complex formation.

  4. Theoretical study on the electronic absorption spectra and molecular orbitals of ten novel ruthenium sensitizers derived from N3 and K8.

    PubMed

    Guo, Ping; Ma, Ruimin; Guo, Lianshun; Yang, Linlin; Liu, Jifeng; Zhang, Xianxi; Pan, Xu; Dai, Songyuan

    2010-11-01

    Ten novel sensitizer candidates Ru2, Ru4, Ru5, Ru6, Ru7, Ru8, Ru9, Ru10, Ru11 and Ru12 derived from the sensitizers N3 and K8 were designed and studied using the density functional theory and time-dependent density functional theory calculations. The influences of the C=C double bonds between the carboxyl groups and the bipyridine ring as well as the numbers and positions of the -CN groups adjacent to the carboxyl groups on the properties of the sensitizer candidates were discussed. The energy levels and the spatial distributions of the frontier molecular orbitals as well as the electronic absorption spectra of these complexes were compared with those of N3 and K8. Ru10 and Ru7 were found promising to provide superior photon-to-current conversion efficiency to those of N3 and K8 in ruthenium complex sensitized solar cells. PMID:21036083

  5. Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

    PubMed Central

    Sure, Rebecca; Brandenburg, Jan Gerit

    2015-01-01

    Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221

  6. Phase diagram and dynamics of Yukawa systems

    NASA Astrophysics Data System (ADS)

    Robbins, Mark. O.; Kremer, Kurt; Grest, Gary S.

    1988-03-01

    The phase diagram and dynamical properties of systems of particles interacting through a repulsive screened Coulomb (Yukawa) potential have been calculated using molecular and lattice dynamics techniques. The phase diagram contains both a melting transition and a transition from fcc to bcc crystalline phases. These phase transitions have been studied as a function of potential shape (screening length) and compared to phenomenological criteria for transition temperatures such as those of Lindemann and of Hansen and Verlet. The transition from fcc to bcc with increasing temperature is shown to result from a higher entropy in the bcc phase because of its softer shear modes. Even when the stable solid phase below the melting temperature is fcc, bcc-like local order is found in the liquid phase. This may substantially slow crystallization. The calculated phase diagram and shear modulus are in good agreement with experiments on colloidal suspensions of polystyrene spheres. The single particle dynamics of Yukawa systems show several unusual features. There is a pronounced subdiffusive regime in liquids near and below the melting temperature. This regime reflects the existence of two time scales: a typical phonon period, and the time for a particle to feel a new environment. The second time scale becomes longer as the temperature is lowered or the range of interaction (screening length) increases.

  7. 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. 

  8. 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.

  9. The Hertzsprung-Russell Diagram.

    ERIC Educational Resources Information Center

    Woodrow, Janice

    1991-01-01

    Describes a classroom use of the Hertzsprung-Russell diagram to infer not only the properties of a star but also the star's probable stage in evolution, life span, and age of the cluster in which it is located. (ZWH)

  10. 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.

  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. 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.

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

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

    2016-01-01

    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

  17. Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

    NASA Astrophysics Data System (ADS)

    Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

    From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

  18. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

    PubMed

    Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition. PMID:25791682

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

    PubMed

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

    2016-01-01

    In this paper, the x-ray emissions are measured by the interaction of 1500-3500 keV Xe(q+) (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xe(q+) ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9-1.32 keV over the energy range studied and are proportional to v(1/2) (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field. PMID:27469425

  20. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

    NASA Astrophysics Data System (ADS)

    Zobač, Vladimír; Lewis, James P.; Abad, Enrique; Mendieta-Moreno, Jesús I.; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  1. 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.

  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. Orbit to orbit transportation

    NASA Technical Reports Server (NTRS)

    Bergeron, R. P.

    1980-01-01

    Orbital transfer vehicle propulsion options for SPS include both chemical (COTV) and electrical (EOTV) options. The proposed EOTV construction method is similar to that of the SPS and, by the addition of a transmitting antenna, may serve as a demonstration or precursor satellite option. The results of the studies led to the selection of a single stage COTV for crew and priority cargo transfer. An EOTV concept is favored for cargo transfer because of the more favorable orbital burden factor over chemical systems. The gallium arsenide solar array is favored over the silicon array because of its self annealing characteristics of radiation damage encountered during multiple transitions through the Van Allen radiation belt. Transportation system operations are depicted. A heavy lift launch vehicle (HLLV) delivers cargo and propellants to LEO, which are transferred to a dedicated EOTV by means of an intraorbit transfer vehicle (IOTV) for subsequent transfer to GEO. The space shuttle is used for crew transfer from Earth to LEO. At the LEO base, the crew module is removed from the shuttle cargo bay and mated to a COTV for transfer to GEO. Upon arrival at GEO, the SPS construction cargo is transferred from the EOTV to the SPS construction base by IOTV. Crew consumables and resupply propellants are transported to GEO by the EOTV. Transportation requirements are dominated by the vast quantity of materials to be transported to LEO and GEO.

  4. 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…

  5. Orbital pseudotumor

    MedlinePlus

    ... Names Idiopathic orbital inflammatory syndrome (IOIS) Images Skull anatomy References Goodlick TA, Kay MD, Glaser JS, Tse DT, Chang WJ. Orbital disease and neuro-ophthalmology. In: Tasman W, Jaeger EA, eds. Duane’s ...

  6. Kepler's Orbit

    NASA Video Gallery

    Kepler does not orbit the Earth, rather it orbits the Sun in concert with the Earth, slowly drifting away from Earth. Every 61 Earth years, Kepler and Earth will pass by each other. Throughout the ...

  7. 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 ...

  8. 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.

  9. 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

  10. Pseudohaptic interaction with knot diagrams

    NASA Astrophysics Data System (ADS)

    Weng, Jianguang; Zhang, Hui

    2012-07-01

    To make progress in understanding knot theory, we need to interact with the projected representations of mathematical knots, which are continuous in three dimensions (3-D) but significantly interrupted in the projective images. One way to achieve such a goal is to design an interactive system that allows us to sketch two-dimensional (2-D) knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress in this direction. Pseudohaptics that simulate haptic effects using pure visual feedback can be used to develop such an interactive system. We outline one such pseudohaptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2-D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a physically reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudohaptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of which the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudohaptic four-dimensional (4-D) visualization system that simulates the continuous navigation on 4-D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2-D knot diagrams of 3-D knots and 3-D projective images of 4-D mathematical objects.

  11. 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.

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

    PubMed

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

    2011-11-15

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

  13. 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…

  14. 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.

  15. 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

  16. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method.

    PubMed

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

    2012-05-28

    A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order Møller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 Å for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed. PMID:22667545

  17. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2(+)) Cation.

    PubMed

    Dietrick, Scott M; Iyengar, Srinivasan S

    2012-12-11

    A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted. PMID:26593181

  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. High-T c superconductivity in potassium-doped fullerene, K xC 60, via coupled C 60 (pπ) cluster molecular orbitals and dynamic Jahn-Teller coupling

    NASA Astrophysics Data System (ADS)

    Johnson, K. H.; McHenry, M. E.; Clougherty, D. P.

    1991-11-01

    Recently observed superconductivity at 18 K in potassium-doped fullerene, K xC 60, may be due to Cooper pairing of partially occupied icosahedral C 60 cluster t 1u (pπ) molecular orbitals, induced by cooperative dynamic Jahn-Teller coupling of these orbitals to “soft-mode” vibrations of the C 60 molecules, leading to a BCS-like mechanism. Predicted are a nonvanishing isotope effect and Tc increasing to 30 K or more with optimization of doping, and significant effects with pressure.

  20. Quantum phases of atomic Fermi gases with anisotropic spin-orbit coupling

    SciTech Connect

    Iskin, M.; Subasi, A. L.

    2011-10-15

    We consider a general anisotropic spin-orbit coupling and analyze the phase diagrams of both balanced and imbalanced Fermi gases for the entire BCS-BEC evolution. In the first part, we use the self-consistent mean-field theory at zero temperature, and show that the topological structure of the ground-state phase diagrams is quite robust against the effects of anisotropy. In the second part, we go beyond the mean-field description, and investigate the effects of Gaussian fluctuations near the critical temperature. This allows us to derive the time-dependent Ginzburg-Landau theory, from which we extract the effective mass of the Cooper pairs and their critical condensation temperature in the molecular BEC limit.

  1. 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.).

  2. [Orbital inflammation].

    PubMed

    Mouriaux, F; Coffin-Pichonnet, S; Robert, P-Y; Abad, S; Martin-Silva, N

    2014-12-01

    Orbital inflammation is a generic term encompassing inflammatory pathologies affecting all structures within the orbit : anterior (involvement up to the posterior aspect of the globe), diffuse (involvement of intra- and/or extraconal fat), apical (involvement of the posterior orbit), myositis (involvement of only the extraocular muscles), dacryoadenitis (involvement of the lacrimal gland). We distinguish between specific inflammation and non-specific inflammation, commonly referred to as idiopathic inflammation. Specific orbital inflammation corresponds to a secondary localization of a "generalized" disease (systemic or auto-immune). Idiopathic orbital inflammation corresponds to uniquely orbital inflammation without generalized disease, and thus an unknown etiology. At the top of the differential diagnosis for specific or idiopathic orbital inflammation are malignant tumors, represented most commonly in the adult by lympho-proliferative syndromes and metastases. Treatment of specific orbital inflammation begins with treatment of the underlying disease. For idiopathic orbital inflammation, treatment (most often corticosteroids) is indicated above all in cases of visual loss due to optic neuropathy, in the presence of pain or oculomotor palsy. PMID:25455557

  3. 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.

  4. Hero's journey in bifurcation diagram

    NASA Astrophysics Data System (ADS)

    Monteiro, L. H. A.; Mustaro, P. N.

    2012-06-01

    The hero's journey is a narrative structure identified by several authors in comparative studies on folklore and mythology. This storytelling template presents the stages of inner metamorphosis undergone by the protagonist after being called to an adventure. In a simplified version, this journey is divided into three acts separated by two crucial moments. Here we propose a discrete-time dynamical system for representing the protagonist's evolution. The suffering along the journey is taken as the control parameter of this system. The bifurcation diagram exhibits stationary, periodic and chaotic behaviors. In this diagram, there are transition from fixed point to chaos and transition from limit cycle to fixed point. We found that the values of the control parameter corresponding to these two transitions are in quantitative agreement with the two critical moments of the three-act hero's journey identified in 10 movies appearing in the list of the 200 worldwide highest-grossing films.

  5. Causal diagrams in systems epidemiology

    PubMed Central

    2012-01-01

    Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed. The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties. The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets. Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback. PMID:22429606

  6. Looking inside the butterfly diagram

    NASA Astrophysics Data System (ADS)

    Ternullo, M.

    2007-12-01

    The suitability of Maunder's butterfly diagram to give a realistic picture of the photospheric magnetic flux large scale distribution is discussed. The evolution of the sunspot zone in cycle 20 through 23 is described. To reduce the noise which covers any structure in the diagram, a smoothing algorithm has been applied to the sunspot data. This operation has eliminated any short period fluctuation, and given visibility to long duration phenomena. One of these phenomena is the fact that the equatorward drift of the spot zone center of mass results from the alternation of several prograde (namely, equatorward) segments with other stationary or poleward segments. The long duration of the stationary/retrograde phases as well as the similarities among the spot zone alternating paths in the cycles under examination prevent us from considering these features as meaningless fluctuations, randomly superimposed on the continuous equatorward migration. On the contrary, these features should be considered physically meaningful phenomena, requiring adequate explanations. Moreover, even the smoothed spotted area markedly oscillates. The compared examination of area and spot zone evolution allows us to infer details about the spotted area distribution inside the butterfly diagram. Links between the changing structure of the spot zone and the tachocline rotation rate oscillations are proposed.

  7. Experimental investigation of the EPR parameters and molecular orbital bonding coefficients for VO2+ ion in NaH2PO4·2H2O single crystals

    NASA Astrophysics Data System (ADS)

    Kalfaoğlu, Emel; Karabulut, Bünyamin

    2016-09-01

    Electron paramagnetic resonance (EPR) spectra of VO2+ ions in NaH2PO4·2H2O single crystal have been studied. The spin-Hamiltonian parameters and molecular orbital bonding coefficients were calculated. The angular variation of the EPR spectra shows two different VO2+ complexes. These are located in different chemical environment and each environment contains four magnetically inequivalent VO2+ sites. The crystal field around VO2+ ion is approximately axially symmetric since a strong V=O bond distorts the crystal lattice. Spin Hamiltonian parameters and molecular orbital bonding coefficients were calculated from the EPR data and the nature of bonding in the complex was discussed together.

  8. 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.

  9. Ab initio molecular orbital calculations of DNA radical ions. 5. Scaling of calculated electron affinities and ionization potentials to experimental values

    SciTech Connect

    Sevilla, M.D.; Colson, A.O. ); Besler, B. )

    1995-01-19

    Ab initio molecular orbital calculations of the electron affinities (EAs) and ionization potentials (IPs) of the DNA bases are presented in this work. Comparisons of calculated and experimental values are made for a series of compounds of size and/or structure similar to the DNA bases. Excellent correlations between calculated and experimental values are found for both Koopmans EAs at the 6-31G[sup *] and D95v levels and calculated vertical EAs of the model compounds. Several basis sets are considered: 6-31G[sup *], 6-31+G(d), and D95v. Calculations at 6-31G[sup *] and 6-31+G(d) using both ROHF and ROMP2 theories show a consistent difference between calculated vertical and adiabatic EAs. This allows for a good estimate of DNA base adiabatic EAs. i.e., -0.7, -0.3, 0.2, 0.3, and 0.4 eV; from the vertical EAs -1.23, -0.74, -0.40, -0.32, and -0.19 eV for G, A, C, T, and U respectively. While EAs must be scaled, we find that Koopmans IPs calculated at the simple 3-21G level predict vertical IPs of the DNA bases with only a 0.15 eV average absolute deviation from the experimentally reported values and calculations at MP2/6-31+G(d)//6-31G[sup *] for the adiabatic ionization potentials of the DNA bases are all within 0.1 eV of experiment. 41 refs., 2 figs., 5 tabs.

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

    PubMed Central

    Song, Lingchun; Mo, Yirong; Gao, Jiali

    2009-01-01

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

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

    PubMed

    Song, Lingchun; Mo, Yirong; Gao, Jiali

    2009-01-01

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

  12. Twistor Diagrams and Quantum Field Theory.

    NASA Astrophysics Data System (ADS)

    O'Donald, Lewis

    Available from UMI in association with The British Library. Requires signed TDF. This thesis uses twistor diagram theory, as developed by Penrose (1975) and Hodges (1990c), to try to approach some of the difficulties inherent in the standard quantum field theoretic description of particle interactions. The resolution of these issues is the eventual goal of the twistor diagram program. First twistor diagram theory is introduced from a physical view-point, with the aim of studying larger diagrams than have been typically explored. Methods are evolved to tackle the double box and triple box diagrams. These lead to three methods of constructing an amplitude for the double box, and two ways for the triple box. Next this theory is applied to translate the channels of a Yukawa Feynman diagram, which has more than four external states, into various twistor diagrams. This provides a test of the skeleton hypothesis (of Hodges, 1990c) in these cases, and also shows that conformal breaking must enter into twistor diagrams before the translation of loop level Feynman diagrams. The issue of divergent Feynman diagrams is then considered. By using a twistor equivalent of the sum-over -states idea of quantum field theory, twistor translations of loop diagrams are conjectured. The various massless propagator corrections and vacuum diagrams calculated give results consistent with Feynman theory. Two diagrams are also found that give agreement with the finite parts of the Feynman "fish" diagrams of phi^4 -theory. However it is found that a more rigorous translation for the time-like fish requires new boundaries to be added to the twistor sum-over-states. The twistor diagram obtained is found to give the finite part of the relevant Feynman diagram.

  13. 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,…

  14. Differential Effectiveness of Two Science Diagram Types.

    ERIC Educational Resources Information Center

    Holliday, William G.

    Reported is an Aptitude Treatment Instruction (ATI) Study designed to evaluate the aptitude of verbal comprehension in terms of two unitary complex science diagram types: a single complex block word diagram and a single complex picture word diagram.. ATI theory and research indicate that different effective instructional treatments tend to help…

  15. 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.

  16. 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.

  17. 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…

  18. The Lenz Vector and Orbital Analog Computers

    ERIC Educational Resources Information Center

    Harter, W. G.

    1976-01-01

    Describes a single geometrical diagram based on the Lenz vector which shows the qualitative and quantitative features of all three types of Coulomb orbits. Explains the use of a simple analog computer with an overhead projector to demonstrate many of these effects. (Author/CP)

  19. 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.

  20. Optical generation of Voronoi diagram.

    PubMed

    Giavazzi, F; Cerbino, R; Mazzoni, S; Giglio, M; Vailati, A

    2008-03-31

    We present results of experiments of diffraction by an amplitude screen, made of randomly distributed circular holes. By careful selection of the experimental parameters we obtain an intensity pattern strongly connected to the Voronoi diagram (VD) generated by the centers of the apertures. With the help of simulations we give a description of the observed phenomenon and elucidate the optimal parameters for its observation. Finally, we also suggest how it can be used for a fast, all-optical generation of VDs. PMID:18542580

  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. Phase Diagrams of Nuclear Pasta

    NASA Astrophysics Data System (ADS)

    Caplan, Matthew; Horowitz, Chuck; Berry, Don; da Silva Schneider, Andre

    2016-03-01

    In the inner crust of neutrons stars, where matter is near the saturation density, protons and neutrons arrange themselves into complex structures called nuclear pasta. Early theoretical work predicted a simple graduated hierarchy of pasta phases, consisting of spheres, cylinders, slabs, and uniform matter with voids. Previous work has simulated these phases with a simple classical model and has shown that the formation of these structures is dependent on the temperature, density, and proton fraction. However, previous work only studied a limited range of these parameters due to computational limitations. Thanks to recent advances in computing it is now possible to survey the structure of nuclear pasta for a larger range of parameters. By simulating nuclear pasta with constant temperature and proton fraction in an expanding simulation volume we are able to study the phase transitions in nuclear pasta, and thus produce a set of phase diagrams. We report on these phase diagrams as well as newly identified phases of nuclear pasta and discuss their implications for neutron star observables.

  3. 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.

  4. Ab initio base fragment molecular orbital studies of influenza viral hemagglutinin HA1 full-domains in complex with sialoside receptors

    PubMed Central

    Sawada, Toshihiko; Hashimoto, Tomohiro; Tokiwa, Hiroaki; Suzuki, Tohru; Nakano, Hirofumi; Ishida, Hideharu; Kiso, Makoto; Suzuki, Yasuo

    2009-01-01

    Mutations in avian influenza A viral hemagglutinin HA1 domain may alter the binding specificity of HA for α-sialosaccharide receptors, shifting the virus's host range from birds to humans. The amino acid mutations can occur at the sialoside binding site, as well as the antigenic site, far from the binding site. Thus, a theoretical study involving the in silico prediction of HA-sialosaccharide binding may require quantum chemical analysis of HA1 full domain complexed with sialosides, balancing a computational cost with model size of HA1-sialoside complex. In addition, there is no insight to relationship between the model size of HA1-sialoside complex and its binding energy. In this study, H3 subtype HA1 full domains complexed with avian- and human-type Neu5Acα(2-3 and 2-6)Gal receptor analogs was investigated by ab initio based fragment molecular orbital (FMO) method at the level of second-order Møller–Plesset perturbation (MP2)/6-31G. Using this approach, we found avian H3 HA1 to bind to avian α2-3 receptor more strongly than to human α2-6 receptor in gas phase, by a value of 15.3-16.5 kcal/mol. This binding benefit was larger than that in the small model complex. Analysis of the interfragment interaction energies (IFIEs) between Neu5Ac-Gal receptor and amino acid residues on the full domain of H3 HA1 also confirmed the higher avian H3-avian α2-3 binding specificity. It was particularly important to evaluate the IFIEs of amino acid residues in a 13Å radius around Neu5Ac-Gal to take account of long-range electrostatic interactions in the larger HA1-sialoside complex model. These results suggest suitable size of HA1-sialoside complex is significant to estimate HA1-sialoside binding energy and IFIE analysis with FMO method. PMID:19565017

  5. Molecular orbital calculation and spectroscopic study of the photochemical generation of Bis(2,2{prime}-bipyridine)rhodium(I) from Bis(2,2{prime}-bipyridine)(oxalato)rhodium(III)

    SciTech Connect

    Shinozaki, Kazuteru; Takahashi, Naoto

    1996-06-19

    A planar complex, [Rh(bpy){sub 2}]{sup +} (bpy=2,2{sup {prime}}-bipyridine), was obtained from [Rh(ox)(bpy){sub 2}]{sup +} (ox=oxalato) by photoirradiation. A rate constant k for the photoreaction was evaluated as 1 x 10{sup 8} s{sup {minus}1} in simple first-order kinetics, whereas a ligand dissociation, a reorganization of the coordinated bpy, and a two-electron transfer were involved in the reaction. The process of the Rh(I) complex generation was investigated in terms of a discrete variational(DV)-X{alpha} molecular orbital calculation on [Rh(ox)(HN=CHCH=NH){sub 2}]{sup +} instead of [Rh(ox)(bpy){sub 2}]{sup +}. From the calculation, using the transition-state method, it was predicted that a transition of the ox {pi}{sup *} orbital to the metal 4d{sub z}{sup 2} orbital caused the ligand dissociation and the reorganization of the coordinated bpy occurred in the ox {pi} to Rh 4d{sub x{sup 2}-y{sup 2}} excited state stabilized by the ox elimination. Upon release of the ligand and a change from octahedral to square-planar geometry, the electron density on the metal increased and the Rh 4d orbital acquired a d{sup 8} electronic configuration.

  6. 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

  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. Phase diagram of ammonium nitrate

    NASA Astrophysics Data System (ADS)

    Dunuwille, M.; Yoo, C. S.

    2014-05-01

    Ammonium Nitrate (AN) has often 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 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 17 GPa2 and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400 °C.

  9. Phase diagrams for the blue phases of highly chiral liquid crystals

    NASA Astrophysics Data System (ADS)

    Bowling, Miriam B.; Collings, Peter J.; Booth, Christopher J.; Goodby, John W.

    1993-11-01

    Polarizing microscopy and optical-activity measurements are used to determine the phase diagram for the blue phases of chiral-racemic mixtures of terephthaloyloxy-bis-4-(2'-methylbutyl) benzoate. Contrary to an earlier report, it is the second blue phase (BP II) rather than the first blue phase (BP I) that is not stable relative to the other blue phases at high chirality. With this development, all phase diagrams for the blue phases reported to date have the same topology. Using similar data for two other highly chiral systems, it is found that a simple scaling of the temperature and chiral-fraction axes produces phase diagrams in quantitative agreement with the present results. Thus, in spite of differences in molecular structure, the number of chiral centers, and phase-transition temperatures, these three systems possess remarkably similar phase diagrams and lend evidence for a universal phase diagram for the blue phases.

  10. 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.

  11. The neptunium-iron phase diagram

    NASA Astrophysics Data System (ADS)

    Gibson, J. K.; Haire, R. G.; Beahm, E. C.; Gensini, M. M.; Maeda, A.; Ogawa, T.

    1994-08-01

    The phase relations in the Np-Fe alloy system have been elucidated using differential thermal analysis. A phase diagram for this system is postulated based upon the experimental results, regular-solution model calculations, and an expected correspondence to the U-Fe and Pu-Fe diagrams. The postulated Np-Fe diagram is characterized by limited terminal solid solubilities, two intermetallic solid phases, NpFe 2 and Np 6Fe, and two eutectics.

  12. 4,5-Dicyano-3,6-diethylbenzo-1,2-diselenete, a highly stable 1,2-diselenete: its preparation, structural characterization, calculated molecular orbitals, and complexation with tetrakis(triphenylphosphine)palladium.

    PubMed

    Kimura, Takeshi; Nakahodo, Tsukasa; Fujihara, Hisashi; Suzuki, Eiichi

    2014-05-01

    The first isolable benzo-1,2-diselenete, 4,5-dicyano-3,6-diethylbenzo-1,2-diselenete (4), was prepared by the reaction of 4,5-(o-xylylenediseleno)-3,6-diethylphthalonitrile (3) with aluminum chloride in toluene. X-ray crystallographic analysis demonstrated that 4 contains a trapezoidal diselenide ring rather than a benzo-1,2-diselenone structure. In crystal form, 4 undergoes self-assembly and generates structures based on layered molecular sheets since the unit cell contains only one molecule. While the cyclic voltammogram of 4 exhibited only one irreversible peak (Ep = 1.59 V) during oxidation and two quasireversible couples during reduction, three peaks were observed in the differential pulse voltammogram of the reduction couples (E1/2 = -1.19, -0.75, and -0.69 V). Although a THF solution of 4 in the presence of sodium metal was EPR silent, various signals were readily observed in its (1)H, (13)C, and (77)Se NMR spectra. Molecular orbital calculations for 4 demonstrated that the HOMO orbital is primarily localized at the two selenium atoms and four of the benzene carbon atoms while the LUMO orbital is situated solely on the diselenete ring. It appears that the HOMO and LUMO orbitals of 4 receive significant stabilization from the nitrile groups compared to the level of stabilization in the unsubstituted benzo-1,2-diselenete (BDS). The reaction of 4 with tetrakis(triphenylphosphine)palladium in benzene was found to produce a dinuclear palladium complex (8), and the structure of this complex was determined by X-ray crystallographic analysis. The central four membered ring of 8 consists of the Pd1, Se2, Pd2, and Se3 atoms and is not planar but rather adopts a folded arrangement. PMID:24724937

  13. Temperature-field phase diagram of extreme magnetoresistance.

    PubMed

    Fallah Tafti, Fazel; Gibson, Quinn; Kushwaha, Satya; Krizan, Jason W; Haldolaarachchige, Neel; Cava, Robert Joseph

    2016-06-21

    The recent discovery of extreme magnetoresistance (XMR) in LaSb introduced lanthanum monopnictides as a new platform to study this effect in the absence of broken inversion symmetry or protected linear band crossing. In this work, we report XMR in LaBi. Through a comparative study of magnetotransport effects in LaBi and LaSb, we construct a temperature-field phase diagram with triangular shape that illustrates how a magnetic field tunes the electronic behavior in these materials. We show that the triangular phase diagram can be generalized to other topological semimetals with different crystal structures and different chemical compositions. By comparing our experimental results to band structure calculations, we suggest that XMR in LaBi and LaSb originates from a combination of compensated electron-hole pockets and a particular orbital texture on the electron pocket. Such orbital texture is likely to be a generic feature of various topological semimetals, giving rise to their small residual resistivity at zero field and subject to strong scattering induced by a magnetic field. PMID:27274081

  14. Ion potential diagrams for electrochromic devices

    SciTech Connect

    Varsano, F. |; Cahen, D.; Decker, F.; Guillemoles, J.F. |; Masetti, E.

    1998-12-01

    Ion potential diagrams can facilitate the description of systems in which ionic species are mobile. They depict qualitatively the spatial dependence of the potential energy for mobile ions, somewhat akin to band diagrams for electrons. The authors construct ion potential diagrams for the mixed conducting (oxide), optically active electrodes of five-layer electrochromic devices, based on reversible Li{sup +} intercalation. These serve to analyze stability problems that arise in these systems. The authors then use them as building blocks to arrive at ion diagrams for complete devices. This allows analyses of (dis)coloration kinetics.

  15. Orbital cellulitis.

    PubMed Central

    Martin-Hirsch, D P; Habashi, S; Hinton, A H; Kotecha, B

    1992-01-01

    Orbital cellulitis is an emergency. It may cause blindness and progress to life-threatening sequelae such as brain abscess, meningitis and cavernous sinus thrombosis. Successful management is dependent upon urgent referral and immediate treatment. Although isolated eyelid erythema and swelling usually indicate primary infection anterior to the orbital septum, they may also be the first signs of an underlying frontal or ethmoidal sinusitis. The condition always requires emergency referral to both an ophthalmologist and otorhinolaryngologist. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:1388488

  16. 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.

  17. 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.

  18. 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.

  19. Charge transport in organic crystals: Critical role of correlated fluctuations unveiled by analysis of Feynman diagrams

    SciTech Connect

    Packwood, Daniel M.; Oniwa, Kazuaki; Jin, Tienan; Asao, Naoki

    2015-04-14

    Organic crystals have unique charge transport properties that lie somewhere between delocalised band-type transport and localised hopping transport. In this paper, we use a stochastic tight-binding model to explore how dynamical disorder in organic crystals affects charge transport. By analysing the model in terms of Feynman diagrams (virtual processes), we expose the crucial role of correlated dynamical disorder to the charge transport dynamics in the model at short times in the order of a few hundred femtoseconds. Under correlated dynamical disorder, the random motions of molecules in the crystal allow for low-energy “bonding”-type interactions between neighboring molecular orbitals can persist over long periods of time. On the other hand, the dependence of charge transport on correlated dynamical disorder also tends to localize the charge, as correlated disorder cannot persist far in space. This concept of correlation may be the “missing link” for describing the intermediate regime between band transport and hopping transport that occurs in organic crystals.

  20. 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.

  1. 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.

  2. Reading fitness landscape diagrams through HSAB concepts

    NASA Astrophysics Data System (ADS)

    Vigneresse, Jean-Louis

    2014-10-01

    Fitness landscapes are conceived as range of mountains, with local peaks and valleys. In terms of potential, such topographic variations indicate places of local instability or stability. The chemical potential, or electronegativity, its value changed of sign, carries similar information. In addition to chemical descriptors defined through hard-soft acid-base (HSAB) concepts and computed through density functional theory (DFT), the principles that rule chemical reactions allow the design of such landscape diagrams. The simplest diagram uses electrophilicity and hardness as coordinates. It allows examining the influence of maximum hardness or minimum electrophilicity principles. A third dimension is introduced within such a diagram by mapping the topography of electronegativity, polarizability or charge exchange. Introducing charge exchange during chemical reactions, or mapping a third parameter (f.i. polarizability) reinforces the information carried by a simple binary diagram. Examples of such diagrams are provided, using data from Earth Sciences, simple oxides or ligands.

  3. Dynamic phase diagrams and compensation behaviors in molecular-based ferrimagnet A F eΙΙ F eΙΙΙ(C2O4)3 under an oscillating magnetic field

    NASA Astrophysics Data System (ADS)

    Shi, Xiaoling; Wang, Li; Zhao, Jie; Xu, Xingguang

    2016-07-01

    Within the effective-field theory (EFT), the compensation behaviors in molecular-based ferrimagnet A F eΙΙ F e Ι Ι Ι(C2O4)3 which is described by a mixed spin-2 (FeΙΙ) and spin-5/2 (FeΙΙΙ) ferrimagnetic Ising model on a honeycomb lattice are studied. The Glauber-type stochastic dynamic is used to describe the time evolution of the system under an oscillating magnetic field. A magnetic field dependence of the compensation temperature and a temperature dependence of compensating magnetic field are calculated and both curves agree qualitatively with experimental data. In particular, a two-compensation-points phenomenon which has been reported in the experimental work is also observed in this compound. Dynamic phase boundaries containing the compensation points are calculated. The dynamic tricritical point and critical end point exist on the phase transition lines. Comparing with previous theoretical results obtained by the mean-field theory (MFT), the effective-field theory results show a reasonable improvement over the MFT results.

  4. Theoretical investigation of the molecular structures and excitation spectra of triphenylamine and its derivatives.

    PubMed

    Sumimoto, Michinori; Yokogawa, Daisuke; Komeda, Masahiro; Yamamoto, Hidetoshi; Hori, Kenji; Fujimoto, Hitoshi

    2011-10-15

    The molecular geometries, electronic structures, and excitation energies of NPh(3), NPh(2)Me, NPhMe(2), and NMe(3), were investigated using DFT and post-Hartree Fock methods. When the structural stabilities of these compounds were compared to results obtained by using MP4(SDQ) method, it was confirmed that the optimized geometries by using MP2 method were sufficiently reliable. The excited states with large oscillator strengths consisted of transition components from the HOMO. It should be noted that the orbitals of the nitrogen atom mix with the π-orbital of the phenyl group in an anti-bonding way in the HOMO, and the orbital energy increases with this mixing. The unoccupied orbitals are generated from bonding and anti-bonding type interactions between the π-orbitals of the phenyl groups; therefore, the number of phenyl groups strongly affects the energy diagram of the compounds studied. The differences in the energy diagram cause a spectral change in these compounds in the ultraviolet region. PMID:21795108

  5. Theoretical investigation of the molecular structures and excitation spectra of triphenylamine and its derivatives

    NASA Astrophysics Data System (ADS)

    Sumimoto, Michinori; Yokogawa, Daisuke; Komeda, Masahiro; Yamamoto, Hidetoshi; Hori, Kenji; Fujimoto, Hitoshi

    2011-10-01

    The molecular geometries, electronic structures, and excitation energies of NPh 3, NPh 2Me, NPhMe 2, and NMe 3, were investigated using DFT and post-Hartree Fock methods. When the structural stabilities of these compounds were compared to results obtained by using MP4(SDQ) method, it was confirmed that the optimized geometries by using MP2 method were sufficiently reliable. The excited states with large oscillator strengths consisted of transition components from the HOMO. It should be noted that the orbitals of the nitrogen atom mix with the π-orbital of the phenyl group in an anti-bonding way in the HOMO, and the orbital energy increases with this mixing. The unoccupied orbitals are generated from bonding and anti-bonding type interactions between the π-orbitals of the phenyl groups; therefore, the number of phenyl groups strongly affects the energy diagram of the compounds studied. The differences in the energy diagram cause a spectral change in these compounds in the ultraviolet region.

  6. Global petrologic variations of the Moon: A ternary-diagram approach

    NASA Technical Reports Server (NTRS)

    Davis, Philip A.; Spudis, Paul D.

    1987-01-01

    A ternary-diagram approach is used to show on a single map as much detailed geochemical information concerning petrologic variations within the lunar crust as is possible. The classification map shows the global spatial distributions of end-member compositions, the transitional spatial relations between end-member compositions, and quantitative estimates of relative proportions of each end member at each pixel location within the orbital groundtracks. The use of elemental ratios in this analysis, instead of the commonly used elemental bivariate diagrams, shows geologic information that is otherwise hidden in individual elemental databases.

  7. Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis of 4-4'-(1H-1,2,4-triazol-1-yl methylene) dibenzonitrile based on abinitio and DFT methods.

    PubMed

    Sheela, N R; Muthu, S; Sampathkrishnan, S

    2014-01-01

    The Fourier transform infrared (FTIR) and FT Raman (FTR) of 4-4'-(1H-1, 2, 4-triazol-1-yl methylene) dibenzonitrile (4-HTMDBN) have been recorded and analyzed. The equilibrium geometry harmonic vibrational frequencies have been investigated with the help of standard HF and DFT methods with 6-31G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). Theoretical simulations of the FTIR and FTR spectra of the title compound have been calculated. The (1)H and (13)C Nuclear Magnetic Resonance (NMR) chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. The stability of the molecule has been analyzed using natural bond orbital (NBO) analysis. The linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using HF/DFT/6-31G(d,p) methods on the finite field approach. UV-Vis spectrum of the compound is recorded and the electronic properties such as HOMO and LUMO energies, are performed. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), electrophilicity index (ω), hardness (η) and chemical potential (ρ) are all correlated with the HOMO and LUMO energies with their molecular properties. Mulliken population analysis on atomic charges, molecular electrostatic potential maps (MEP) and thermodynamical properties of title compound at different temperature have been calculated. PMID:24184626

  8. 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 ...

  9. 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.

  10. Payload/orbiter contamination control requirement study

    NASA Technical Reports Server (NTRS)

    Bareiss, L. E.; Rantanen, R. O.; Ress, E. B.

    1974-01-01

    A study was conducted to determine and quantify the expected particulate and molecular on-orbit contaminant environment for selected space shuttle payloads as a result of major shuttle orbiter contamination sources. Individual payload susceptibilities to contamination are reviewed. The risk of payload degradation is identified and preliminary recommendations are provided concerning the limiting factors which may depend on operational activities associated with the payload/orbiter interface or upon independent payload functional activities. A basic computer model of the space shuttle orbiter which includes a representative payload configuration is developed. The major orbiter contamination sources, locations, and flux characteristics based upon available data have been defined and modeled.

  11. 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.

  12. 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.

  13. 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.

  14. Phase diagram of a reentrant gel of patchy particles

    SciTech Connect

    Roldán-Vargas, Sándalo; Smallenburg, Frank; Sciortino, Francesco; Kob, Walter

    2013-12-28

    We study the phase diagram of a binary mixture of patchy particles which has been designed to form a reversible gel. For this we perform Monte Carlo and molecular dynamics simulations to investigate the thermodynamics of such a system and compare our numerical results with predictions based on the analytical parameter-free Wertheim theory. We explore a wide range of the temperature-density-composition space that defines the three-dimensional phase diagram of the system. As a result, we delimit the region of thermodynamic stability of the fluid. We find that for a large region of the phase diagram the Wertheim theory is able to give a quantitative description of the system. For higher densities, our simulations show that the system is crystallizing into a BCC structure. Finally, we study the relaxation dynamics of the system by means of the density and temperature dependences of the diffusion coefficient. We show that there exists a density range where the system passes reversibly from a gel to a fluid upon both heating and cooling, encountering neither demixing nor phase separation.

  15. Equations of state and phase diagrams of hydrogen isotopes

    SciTech Connect

    Urlin, V. D.

    2013-11-15

    A new form of the semiempirical equation of state proposed for the liquid phase of hydrogen isotopes is based on the assumption that its structure is formed by cells some of which contain hydrogen molecules and others contain hydrogen atoms. The values of parameters in the equations of state of the solid (molecular and atomic) phases as well as of the liquid phase of hydrogen isotopes (protium and deuterium) are determined. Phase diagrams, shock adiabats, isentropes, isotherms, and the electrical conductivity of compressed hydrogen are calculated. Comparison of the results of calculations with available experimental data in a wide pressure range demonstrates satisfactory coincidence.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Mass-imbalanced Fermi gases with spin-orbit coupling

    SciTech Connect

    Iskin, M.; Subasi, A. L.

    2011-10-15

    We use the mean-field theory to analyze the ground-state phase diagrams of spin-orbit-coupled mass-imbalanced Fermi gases throughout the BCS-BEC evolution, including both the population-balanced and -imbalanced systems. Our calculations show that the competition between the mass and population imbalance and the Rashba-type spin-orbit coupling gives rise to very rich phase diagrams, involving normal, superfluid, and phase-separated regions. In addition, we find quantum phase transitions between the topologically trivial gapped superfluid and the nontrivial gapless superfluid phases, opening the way for the experimental observation of exotic phenomena with cold atom systems.

  3. 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.

  4. The Art of Free-Body Diagrams.

    ERIC Educational Resources Information Center

    Puri, Avinash

    1996-01-01

    Discusses the difficulty of drawing free-body diagrams which only show forces exerted on a body from its neighbors. Presents three ways a body may be modeled: a particle, rigid extended, and nonrigid extended. (MKR)

  5. Phase diagram for passive electromagnetic scatterers.

    PubMed

    Lee, Jeng Yi; Lee, Ray-Kuang

    2016-03-21

    With the conservation of power, a phase diagram defined by amplitude square and phase of scattering coefficients for each spherical harmonic channel is introduced as a universal map for any passive electromagnetic scatterers. Physically allowable solutions for scattering coefficients in this diagram clearly show power competitions among scattering and absorption. It also illustrates a variety of exotic scattering or absorption phenomena, from resonant scattering, invisible cloaking, to coherent perfect absorber. With electrically small core-shell scatterers as an example, we demonstrate a systematic method to design field-controllable structures based on the allowed trajectories in this diagram. The proposed phase diagram and inverse design can provide tools to design functional electromagnetic devices. PMID:27136839

  6. 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)

  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. 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.

  9. 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.

  10. Fluctuations and the QCD phase diagram

    SciTech Connect

    Schaefer, B.-J.

    2012-06-15

    In this contribution the role of quantum fluctuations for the QCD phase diagram is discussed. This concerns in particular the importance of the matter back-reaction to the gluonic sector. The impact of these fluctuations on the location of the confinement/deconfinement and the chiral transition lines as well as their interrelation are investigated. Consequences of our findings for the size of a possible quarkyonic phase and location of a critical endpoint in the phase diagram are drawn.

  11. 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.

  12. 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.

  13. Class diagram based evaluation of software performance

    NASA Astrophysics Data System (ADS)

    Pham, Huong V.; Nguyen, Binh N.

    2013-03-01

    The evaluation of software performance in the early stages of the software life cycle is important and it has been widely studied. In the software model specification, class diagram is the important object-oriented software specification model. The measures based on a class diagram have been widely studied to evaluate quality of software such as complexity, maintainability, reuse capability, etc. However the software performance evaluation based on Class model has not been widely studied, especially for object-oriented design of embedded software. Therefore, in this paper we propose a new approach to directly evaluate the software performance based on class diagrams. From a class diagram, we determine the parameters which are used to evaluate and build formula of the measures such as Size of Class Variables, Size of Class Methods, Size of Instance Variables, Size of Instance Methods, etc. Then, we do analysis of the dependence of performance on these measures and build the performance evaluation function from class diagram. Thereby we can choose the best class diagram based on this evaluation function.

  14. Pressure-enthalpy diagrams for alternative refrigerants

    SciTech Connect

    Chen, J.; Kruse, H.

    1996-10-01

    Thermodynamic diagrams, particularly log(p)-h diagrams, have become very convenient tools for refrigeration and air-conditioning industries. To promote alternative refrigerants-related development and application, it is urgently required to provide the industries with reliable engineering diagrams for the most promising candidate refrigerants. A computer program has been developed for automatically producing log(p)-h diagrams for alternative refrigerants. The Lee Kesler Ploecker (LKP) equation of state has been used to calculate thermodynamic data. Some modifications have been made to the LKP to improve the calculation convergency. In this paper three sample diagrams for R134a, a binary R410A and a ternary R407B which have been enclosed and analyzed. To investigate the LKP calculation accuracy details, an extensive deviation analysis has been made for R134a. For mixed refrigerants, good calculation accuracy was achieved by optimizing the binary interactive parameters. The system can produce log(p)-h diagrams with reliable accuracy, high quality, and flexibility to meet any size and color requirements.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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…

  20. 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,…

  1. 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)…

  2. 49 CFR 1152.10 - System diagram map.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 8 2012-10-01 2012-10-01 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...

  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. 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...

  5. 49 CFR 1152.10 - System diagram map.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 8 2014-10-01 2014-10-01 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. 49 CFR 1152.10 - System diagram map.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 8 2011-10-01 2011-10-01 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...

  7. 49 CFR 1152.10 - System diagram map.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 8 2013-10-01 2013-10-01 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...

  8. Computationally useful bridge diagram series. II. Diagrams in h-bonds

    NASA Astrophysics Data System (ADS)

    Perkyns, John S.; Dyer, Kippi M.; Pettitt, B. Montgomery

    2002-06-01

    Equations for calculating accurate 4-point and 5-point bridge diagrams in terms of h-bonds have been presented and solved for various phase points of the Lennard-Jones fluid. A method of finding a self-consistent solution for the bridge function and the radial distribution function is demonstrated. The significance of this result over bridge diagrams expressed as f-bonds, in terms of its applicability to charged and dipolar models is discussed. Two very simple phenomenological bridge diagram forms for the bridge function for this model are examined and found to give results almost as accurate and in some cases more accurate than previous forms in the literature. This work represents the first use of directly calculated 5-point bridge diagrams in terms of h-bonds, and the many extra orders of f-bond diagrams which they include, in an integral equation result.

  9. Computationally Useful Bridge Diagram Series. II. Diagrams in H-Bonds

    SciTech Connect

    Perkyns, John S.; Dyer, Kippi M.; Pettitt, Bernard M.

    2002-06-01

    Equations for calculating accurate 4-point and 5-point bridge diagrams in terms of h-bonds have been presented and solved for various phase points of the Lennard-Jones fluid. A method of finding a self-consistent solution for the bridge function and the radial distribution function is demonstrated. The significance of this result over bridge diagrams expressed as f-bonds, in terms of its applicability to charged and dipolar models is discussed. Two very simple phenomenological bridge diagram forms for the bridge function for this model are examined and found to give results almost as accurate and in some cases more accurate than previous forms in the literature. This work represents the first use of directly calculated 5-point bridge diagrams in terms of h-bonds, and the many extra orders of f-bond diagrams which they include, in an integral equation result.

  10. A new method for diagramming pacemaker electrocardiograms.

    PubMed

    Hesselson, A B; Parsonnet, V

    1994-08-01

    Advancements in technology have made paced ECG interpretation increasingly difficult. A new method for depicting the complex pacemaker/heart interactions that eliminates the extensive use of symbols and repetitious use of refractory period and rate limit information of previous methods has been devised. The method uses a framework of parallel horizontal lines drawn on grid paper underneath the ECG. The lines are spaced apart by the actual programmed values (lower rate, AV, VA intervals) of the pacemaker in question. This framework allows the simultaneous use of the horizontal and vertical directions for the diagram of pacemaker timing intervals. Also, a single representation of refractory periods, upper rate intervals, and other variables can be labeled vertically and extrapolated horizontally across the entire diagram. Single chamber, dual chamber, and rate-modulated ECGs are readily represented. The diagram is easily plotted on standard ECG paper and flexible enough to represent complex ECGs. PMID:7526348

  11. The renormalon diagram in gauge theories on

    NASA Astrophysics Data System (ADS)

    Anber, Mohamed M.; Sulejmanpasic, Tin

    2015-01-01

    We analyze the renormalon diagram of gauge theories on . In particular, we perform exact one loop calculations for the vacuum polarization in QCD with adjoint matter and observe that all infrared logarithms, as functions of the external momentum, cancel between the vacuum part and finite volume part, which eliminates the IR renormalon problem. We argue that the singularities in the Borel plane, arising from the topological neutral bions, are not associated with the renormalon diagram, but with the proliferation of the Feynman diagrams. As a byproduct, we obtain, for the first time, an exact one-loop result of the vacuum polarization which can be adapted to the case of thermal compactification of QCD.

  12. 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.

  13. Phase diagram of a truncated tetrahedral model.

    PubMed

    Krcmar, Roman; Gendiar, Andrej; Nishino, Tomotoshi

    2016-08-01

    Phase diagram of a discrete counterpart of the classical Heisenberg model, the truncated tetrahedral model, is analyzed on the square lattice, when the interaction is ferromagnetic. Each spin is represented by a unit vector that can point to one of the 12 vertices of the truncated tetrahedron, which is a continuous interpolation between the tetrahedron and the octahedron. Phase diagram of the model is determined by means of the statistical analog of the entanglement entropy, which is numerically calculated by the corner transfer matrix renormalization group method. The obtained phase diagram consists of four different phases, which are separated by five transition lines. In the parameter region, where the octahedral anisotropy is dominant, a weak first-order phase transition is observed. PMID:27627273

  14. A pseudo-haptic knot diagram interface

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Weng, Jianguang; Hanson, Andrew J.

    2011-01-01

    To make progress in understanding knot theory, we will need to interact with the projected representations of mathematical knots which are of course continuous in 3D but significantly interrupted in the projective images. One way to achieve such a goal would be to design an interactive system that allows us to sketch 2D knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress to be made in this direction. Pseudo-haptics that simulates haptic effects using pure visual feedback can be used to develop such an interactive system. This paper outlines one such pseudo-haptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a "physically" reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudo-haptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of whom the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudo-haptic 4D visualization system that simulates the continuous navigation on 4D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2D knot diagrams of 3D knots and 3D projective images of 4D mathematical objects.

  15. 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

  16. 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.

  17. 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.

  18. Orbital selective directional conductor in the two-orbital Hubbard model

    SciTech Connect

    Mukherjee, Anamitra; Patel, Niravkumar D.; Moreo, Adriana; Dagotto, Elbio R

    2016-01-01

    Employing a recently developed many-body technique that allows for the incorporation of thermal effects, the rich phase diagram of a two-dimensional two-orbital (degenerate dxz and dyz) Hubbard model is presented varying temperature and the repulsion U. Our main result is the finding at intermediate U of an antiferromagnetic orbital selective state where an effective dimensional reduction renders one direction insulating and the other metallic. Possible realizations of this state are discussed. In addition, we also study nematicity above the N eel temperature. After a careful finite-size scaling analysis, the nematicity temperature window appears to survive in the bulk limit, although it is very narrow.

  19. 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.

  20. Preparation, optical and electrochemical properties, and molecular orbital calculations of tetraazaporphyrinato ruthenium (II) bis(4-methylpyridine) fused with one to four diphenylthiophene units.

    PubMed

    Kimura, Takeshi; Murakami, Naoko; Suzuki, Eiichi; Furuyama, Taniyuki; Nakahodo, Tsukasa; Fujihara, Hisashi; Kobayashi, Nagao

    2016-05-01

    2,5-Diphenyl-3,4-dicyanothiophene (1) and phthalonitrile (2) were mixed and treated with ruthenium (III) trichloride, 4-methylpyridine, and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in 2-ethoxyethanol at 135°C, to produce low-symmetrical tetraazaporphyrins (TAPs) (3), (4), (5), and (6) with one to three thiophene rings. Two thiophene-annelated tetraazaporphyrins were isolated as opposite and adjacent isomers 4 and 5. The structure of 3 was determined by X-ray crystallography, showing that the thiophene ring linked at the 3,4-positions on the tetraazaporphyrin scaffold deviates from the mean plane of the four central pyrrole nitrogen atoms (N1-N3-N5-N7). Optical and electrochemical properties of the products were examined by UV-vis and magnetic circular dichroism (MCD) spectroscopy, together with cyclic voltammetry. In the (1)H NMR spectra, the signals of 4-methylpyridine coordinating to the central ruthenium atom appeared at a higher magnetic field than those of uncoordinated 4-methylpyridine itself due to the shielding effect of the TAP ring. Increasing the number of fused thiophene rings resulted in 1) lower magnetic field shifts of the signals of axially coordinated 4-methylpyridine in the (1)H NMR spectra, 2) lower energy shifts of the Q band absorption in the UV-vis spectra, and 3) decreasing (cathodic shift) of the first oxidation potentials. The structures of simplified model compounds were optimized using the DFT method with the Gaussian 09 program at the B3LYP/LANL2DZ level for the Ru atom and the B3LYP/6-31G (d, p) level for the C, H, N, and S atoms. The optimized structures were utilized to calculate the NMR shielding constants, the HOMO and LUMO orbital energies, and the electronic absorption spectra. PMID:26876817

  1. 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.

  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. NFHS Court and Field Diagram Guide.

    ERIC Educational Resources Information Center

    Gillis, John, Ed.

    This guide contains a comprehensive collection of diagrams and specifications of playing fields and courts used in interscholastic and recreational sports, along with information on how to set up various formats of tournament drawings, how to compute golf handicaps, and how to convert metric-to-English distances. Lists are provided of national…

  4. Journeys on the H-R diagram

    SciTech Connect

    Kaler, J.B.

    1988-05-01

    The evolution of various types of stars along the H-R diagram is discussed. Star birth and youth is addressed, and the events that occur due to core contraction, shell burning, and double-shell burning are described. The evolutionary courses of planetary nebulae, white dwarfs, and supernovas are examined.

  5. On phase diagrams of magnetic reconnection

    SciTech Connect

    Cassak, P. A.; Drake, J. F.

    2013-06-15

    Recently, “phase diagrams” of magnetic reconnection were developed to graphically organize the present knowledge of what type, or phase, of reconnection is dominant in systems with given characteristic plasma parameters. Here, a number of considerations that require caution in using the diagrams are pointed out. First, two known properties of reconnection are omitted from the diagrams: the history dependence of reconnection and the absence of reconnection for small Lundquist number. Second, the phase diagrams mask a number of features. For one, the predicted transition to Hall reconnection should be thought of as an upper bound on the Lundquist number, and it may happen for considerably smaller values. Second, reconnection is never “slow,” it is always “fast” in the sense that the normalized reconnection rate is always at least 0.01. This has important implications for reconnection onset models. Finally, the definition of the relevant Lundquist number is nuanced and may differ greatly from the value based on characteristic scales. These considerations are important for applications of the phase diagrams. This is demonstrated by example for solar flares, where it is argued that it is unlikely that collisional reconnection can occur in the corona.

  6. 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…

  7. 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.

  8. 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,…

  9. 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)

  10. 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.

  11. 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)

  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. Fine structure of the butterfly diagram revisited

    NASA Astrophysics Data System (ADS)

    Major, Balázs

    The latitudinal time distribution of sunspots (butterfly diagram) was studied by Becker (1959) and Antalová & Gnevyshev (1985). Our goal is to revisit these studies. In the first case we check whether there is a poleward migration in sunspot activity. In the second case we confirm the results, and make more quantitative statements concerning their significance and the position of the activity peaks.

  14. Phase diagram of spiking neural networks

    PubMed Central

    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

  15. 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…

  16. 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

  17. 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.

  18. Students' different understandings of class diagrams

    NASA Astrophysics Data System (ADS)

    Boustedt, Jonas

    2012-03-01

    The software industry needs well-trained software designers and one important aspect of software design is the ability to model software designs visually and understand what visual models represent. However, previous research indicates that software design is a difficult task to many students. This article reports empirical findings from a phenomenographic investigation on how students understand class diagrams, Unified Modeling Language (UML) symbols, and relations to object-oriented (OO) concepts. The informants were 20 Computer Science students from four different universities in Sweden. The results show qualitatively different ways to understand and describe UML class diagrams and the "diamond symbols" representing aggregation and composition. The purpose of class diagrams was understood in a varied way, from describing it as a documentation to a more advanced view related to communication. The descriptions of class diagrams varied from seeing them as a specification of classes to a more advanced view, where they were described to show hierarchic structures of classes and relations. The diamond symbols were seen as "relations" and a more advanced way was seeing the white and the black diamonds as different symbols for aggregation and composition. As a consequence of the results, it is recommended that UML should be adopted in courses. It is briefly indicated how the phenomenographic results in combination with variation theory can be used by teachers to enhance students' possibilities to reach advanced understanding of phenomena related to UML class diagrams. Moreover, it is recommended that teachers should put more effort in assessing skills in proper usage of the basic symbols and models and students should be provided with opportunities to practise collaborative design, e.g. using whiteboards.

  19. SB9: The ninth catalogue of spectroscopic binary orbits

    NASA Astrophysics Data System (ADS)

    Pourbaix, D.; Tokovinin, A. A.; Batten, A. H.; Fekel, F. C.; Hartkopf, W. I.; Levato, H.; Morrell, N. I.; Torres, G.; Udry, S.

    2004-09-01

    The Ninth Catalogue of Spectroscopic Binary Orbits (http://sb9.astro.ulb.ac.be) continues the series of compilations of spectroscopic orbits carried out over the past 35 years by Batten and collaborators. As of 2004 May 1st, the new Catalogue holds orbits for 2386 systems. Some essential differences between this catalogue and its predecessors are outlined and three straightforward applications are presented: (1) completeness assessment: period distribution of SB1s and SB2s; (2) shortest periods across the H-R diagram; (3) period-eccentricity relation.

  20. 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.

  1. First-principles pressure-temperature phase diagrams in metals

    SciTech Connect

    Moriarty, J.A.

    1993-07-01

    Using interatomic potentials derived from first-principles generalized pseudopotential theory, finite-temperature phase transitions in both simple and transition metals can be studied through a combination of analytic statistical methods and molecular-dynamics simulation. In the prototype simple metal-Mg, where volume and pair forces adequately describe the energetics, a complete and accurate phase diagram has thereby been obtained to 60 GPa. A rapidly temperature-dependent hcp-bcc phase line is predicted which ends in a triple point on the melting curve near 4 GPa. In central transition metals such as Mo or Fe, on the other hand, the energetics are complicated by d-state interactions which give rise to both many-body angular forces and enhanced electron-thermal contributions. We have made a detailed study of these phenomena and their impact on melting in the prototype case of Mo and a full melting curve to 2 Mbar has been obtained. In the case of Fe, we are examining the high-pressure phase diagram and the question of whether or not there exists a high-pressure, high-temperature solid bcc phase, as has been speculated. To date, we have shown that the bcc structure is both thermodynamically and mechanically unstable at high pressure and zero temperature, with a large and increasing bcc-hcp energy difference under compression.

  2. 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.

  3. Multi-component molecular orbital study on positron attachment to alkali-metal hydride molecules: nature of chemical bonding and dissociation limits of [LiH; e+

    NASA Astrophysics Data System (ADS)

    Oyamada, Takayuki; Tachikawa, Masanori

    2014-08-01

    We have performed multi-component full-configuration interaction calculations to investigate the nature of chemical bonding of [LiH;e+] at the small and large internuclear distance. We discuss the importance of geometrical changes in positronic compounds induced by a positron attachment in terms of the virial theorem, with a comparison of the adiabatic- and vertical-positron affinity (PA). The systematic improvement of the PA values achieved by optimisation of (i) the molecular geometry and (ii) the positronic basis centre is also discussed. The stable dissociation channel of [LiH;e+] is compared with the ionic- and neutral-dissociation channels of its parent molecule LiH through the analysis of the potential energy curve and the electronic and positronic densities. The vertical PA as a function of is also presented, which is the difference between the potential energy curve of the parent molecule (LiH → Li + H) and its positronic compound ([LiH; e+] → Li + [H; e+]). Unlike the preceding study of [M. Mella et al., J. Chem. Phys. 113, 6154 (2000)], it took more than bohr to converge the vertical PA due to the long-range ionic bonding interaction.

  4. Molecular orbital studies on the mechanism of drug-receptor interaction. 2. beta-Adrenergic drugs. An approach to explain the role of the aromatic moiety.

    PubMed

    Petrongolo, C; Macchia, B; Macchia, F; Martinelli, A

    1977-12-01

    The role of the aromatic moiety of beta-adrenergic drugs in the interaction with the receptor was investigated using the quantum mechanical ab initio SCF-MO-LCAO method. The structure-activity relationship was essentially discussed by analyzing the electrostatic molecular potential of three compounds which constitute meaningful portions of isoproterenol, INPEA, and doberol, the first drug having a stimulating activity and the others a blocking one. The results obtained point out the different roles played in the drug-receptor interaction by the various regions of the drugs and they also show that the aromatic moiety influences both the affinity and the intrinsic activity of the drugs. Indeed, the spatial correspondence among zones with negative potentials, which are localized on the phenyl substitutents of isoproterenol and INPEA and on the phenyl ring of doberol, could contribute to the affinity. On the other hand, the intrinsic activity of isoproterenol might be associated both with the proton-donor tendency of one phenolic OH group and with the wide zone of negative potential which spreads on a large part of the aromati moiety. PMID:201757

  5. 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.

  6. 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

  7. 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

  8. The weighted-volume derivative of a space-filling diagram

    PubMed Central

    Edelsbrunner, Herbert; Koehl, Patrice

    2003-01-01

    Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The formula is given in terms of the weights, radii, and distances between the centers as well as the sizes of the facets of the power diagram restricted to the space-filling diagram. Special attention is given to the detection and treatment of singularities as well as discontinuities of the derivative. PMID:12601153

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.

    2015-02-01

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

  11. 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.

  12. 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.

  13. 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.

  14. Direct Measurement of the Fluid Phase Diagram.

    PubMed

    Bao, Bo; Riordon, Jason; Xu, Yi; Li, Huawei; Sinton, David

    2016-07-19

    The thermodynamic phase of a fluid (liquid, vapor or supercritical) is fundamental to all chemical processes, and the critical point is particularly important for supercritical chemical extraction. Conventional phase measurement methods require hours to obtain a single datum on the pressure and temperature diagram. Here, we present the direct measurement of the full pressure-temperature phase diagram, with 10 000 microwells. Orthogonal, linear, pressure and temperature gradients are obtained with 100 parallel microchannels (spanning the pressure range), each with 100 microwells (spanning the temperature range). The phase-mapping approach is demonstrated with both a pure substance (CO2) and a mixture (95% CO2 + 5% N2). Liquid, vapor, and supercritical regions are clearly differentiated, and the critical pressure is measured at 1.2% error with respect to the NIST standard. This approach provides over 100-fold improvement in measurement speed over conventional methods. PMID:27331613

  15. 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.

  16. MHV diagrams in momentum twistor space

    NASA Astrophysics Data System (ADS)

    Bullimore, Mathew; Mason, Lionel; Skinner, David

    2010-12-01

    We show that there are remarkable simplifications when the MHV diagram formalism for mathcal{N} = 4 super Yang-Mills is reformulated in momentum twistor space. The vertices are replaced by unity while each propagator becomes a dual superconformal `R-invariant' whose arguments may be read off from the diagram, and include an arbitrarily chosen reference twistor. The momentum twistor MHV rules generate a formula for the full, all-loop planar integrand for the super Yang-Mills S-matrix that is manifestly dual superconformally invariant up to the choice of a reference twistor. We give a general proof of this reformulation and illustrate its use by computing the momentum twistor NMHV and N2MHV tree amplitudes and the integrands of the MHV and NMHV 1-loop and the MHV 2-loop planar amplitudes.

  17. Band diagram of strained graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Prabhakar, Sanjay; Melnik, Roderick; Bonilla, Luis

    2016-04-01

    The influence of ripple waves on the band diagram of zigzag strained graphene nanoribbons (GNRs) is analyzed by utilizing the finite element method. Such waves have their origin in electromechanical effects. With a novel model, we demonstrate that electron-hole band diagrams of GNRs are highly influenced (i.e. level crossing of the bands are possible) by two combined effects: pseudo-magnetic fields originating from electroelasticity theory and external magnetic fields. In particular, we show that the level crossing point can be observed at large external magnetic fields (B ≈ 100T ) in strained GNRs, when the externally applied tensile edge stress is on the order of -100 eV/nm and the amplitude of the out-of-plane ripple waves is on the order of 1nm.

  18. Ring-Diagram Analysis: Status and Perspectives

    NASA Astrophysics Data System (ADS)

    Hill, F.

    Ring diagram analysis is now more than a decade old. While the details of the technique are still evolving, the application of the method to MDI, TON, Mt. Wilson, HLH, and GONG data is providing intriguing results. Thanks to the work of many people, it is now becoming possible to observationally infer the complicated dynamics in the outer 15 Mm of the solar convection zone, investigate the depth dependence of meridional flow, and get a closer look at zonal jet-stream structures in the mid-latitudes. We may soon be able to similarly investigate the spatio-temporal distribution of scalar fields. As ring diagrams and other local helioseismology methods such as time-distance and acoustic imaging continue to mature, the comparison of results from different techniques on common data sets will provide a useful reality check.

  19. Persistence diagrams of cortical surface data.

    PubMed

    Chung, Moo K; Bubenik, Peter; Kim, Peter T

    2009-01-01

    We present a novel framework for characterizing signals in images using techniques from computational algebraic topology. This technique is general enough for dealing with noisy multivariate data including geometric noise. The main tool is persistent homology which can be encoded in persistence diagrams. These diagrams visually show how the number of connected components of the sublevel sets of the signal changes. The use of local critical values of a function differs from the usual statistical parametric mapping framework, which mainly uses the mean signal in quantifying imaging data. Our proposed method uses all the local critical values in characterizing the signal and by doing so offers a completely new data reduction and analysis framework for quantifying the signal. As an illustration, we apply this method to a 1D simulated signal and 2D cortical thickness data. In case of the latter, extra homological structures are evident in an control group over the autistic group. PMID:19694279

  20. Extracting parameters from colour-magnitude diagrams

    NASA Astrophysics Data System (ADS)

    Bonatto, C.; Campos, F.; Kepler, S. O.; Bica, E.

    2015-07-01

    We present a simple approach for obtaining robust values of astrophysical parameters from the observed colour-magnitude diagrams (CMDs) of star clusters. The basic inputs are the Hess diagram built with the photometric measurements of a star cluster and a set of isochrones covering wide ranges of age and metallicity. In short, each isochrone is shifted in apparent distance modulus and colour excess until it crosses over the maximum possible Hess density. Repeating this step for all available isochrones leads to the construction of the solution map, in which the optimum values of age and metallicity - as well as foreground/background reddening and distance from the Sun - can be searched for. Controlled tests with simulated CMDs show that the approach is efficient in recovering the input values. We apply the approach to the open clusters M 67, NGC 6791 and NGC 2635, which are characterized by different ages, metallicities and distances from the Sun.