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1

Near Earth Objects Program: Orbit Diagrams  

NSDL National Science Digital Library

This page provides access to diagrams of the orbits of a very large number of objects in the asteroid belt as well as comets that cross Earth's orbit. The collection is searchable by object name or designation and users can also browse through an extensive list of potentially hazardous asteroids.

NASA JPL Near Earth Object Program

2

Interactive Molecular Orbitals  

NSDL National Science Digital Library

The majority of Introductory Chemistry texts provide students with an adequate introduction to the visual aspects of the molecular orbital model for homonuclear diatomic molecules. The treatment of heteronuclear diatomic and polyatomic molecules is less uniform. Heteronuclear diatomics, when mentioned, are invariably treated as being derived from homonuclear diatomics. While the atomic orbital energy level differences in heteronuclear diatomics is sometimes pictured, the consequences of those differences for the resultant molecular orbitals are rarely discussed. The discussion of polyatomic molecular orbitals in these texts is limited to showing that parallel p-orbitals produce delocalized pi molecular orbitals. The molecules typically mentioned in this context are benzene, nitrate ion and carbonate ion. However, It is rarely pointed out that the six p-orbitals in benzene would form 6 pi molecular orbitals, and that only one of these orbitals would look like the picture in the text.These interactive modules are designed to clarify this subject.

3

Floating orbital molecular dynamics simulations.  

PubMed

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

Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

2014-04-21

4

Some Observations on Molecular Orbital Theory  

ERIC Educational Resources Information Center

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.

Journal of Chemical Education, 2005

2005-01-01

5

Understanding glycine conformation through molecular orbitals  

NASA Astrophysics Data System (ADS)

The four most stable Cs conformers of glycine have been investigated using a variety of quantum-mechanical methods based on Hartree-Fock theory, density-functional theory (B3LYP and statistical average of orbital potential), and electron propagation (OVGF) treatments. Information obtained from these models were analyzed in coordinate and momentum spaces using dual space analysis to provide insight based on orbitals into the bonding mechanisms of glycine conformers, which are generated by rotation of C-O(H) (II), C-C (III), and C-N (IV) bonds from the global minimum structure (I). Wave functions generated from the B3LYP/TZVP model revealed that each rotation produced a unique set of fingerprint orbitals that correspond to a specific group of outer valence orbitals, generally of a' symmetry. Orbitals 14a', 13a', 12a', and 11a' are identified as the fingerprint orbitals for the C-O(H) (II) rotation, whereas fingerprint orbitals for the C-C (III) bond rotation are located as 16a' [highest occupied molecular orbital (HOMO)], 15a' [next highest molecular occupied molecular orbital (NHOMO)], 14a', and 12a' orbitals. Fingerprint orbitals for IV generated by the combined rotations around the C-C, C-O(H), and C-N bonds are found as 16a', 15a', 14a', 13a', and 11a', as well as in orbitals 2a? and 1a?. Orbital 14a' is identified as the fingerprint orbital for all three conformational processes, as it is the only orbital in the outer valence region which is significantly affected by the conformational processes regardless rotation of which bond. Binding energies, molecular geometries, and other molecular properties such as dipole moments calculated based on the specified treatments agree well with available experimental measurements and with previous theoretical calculation.

Falzon, Chantal T.; Wang, Feng

2005-12-01

6

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

PubMed

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 illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher. PMID:24754304

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

2014-09-16

7

Molecular orbital calculations on transition metal clusters  

Microsoft Academic Search

Transition metal clusters have been subject of experimental and theoretical interest due to their catalytic activity, as well as their unusual physical properties. Semi-empirical extended Hückel molecular orbital calculations are presented for a series of small metal clusters with nuclearity ranging from 3 to 6. Naked and carbonylated clusters of Fe, Ru, and Os are studied. The charge transfer between

M. C. dos Santos; J. Albino O. de Aguiar

1989-01-01

8

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

ERIC Educational Resources Information Center

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…

Orenha, Renato P.; Galembeck, Sérgio E.

2014-01-01

9

Spin–orbit interaction mediated molecular dissociation  

SciTech Connect

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.

Kokkonen, E., E-mail: esko.kokkonen@oulu.fi; Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M. [Department of Physics, University of Oulu, Box 3000, 90014 Oulu (Finland)] [Department of Physics, University of Oulu, Box 3000, 90014 Oulu (Finland); Löytynoja, T. [Department of Physics, University of Oulu, Box 3000, 90014 Oulu (Finland) [Department of Physics, University of Oulu, Box 3000, 90014 Oulu (Finland); Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm (Sweden)

2014-05-14

10

Molecular diagnosis of orbital inflammatory disease.  

PubMed

Orbital inflammatory diseases include thyroid eye disease (TED), granulomatosis with polyangiitis (GPA), sarcoidosis, and nonspecific orbital inflammation (NSOI). Histopathological diagnosis usually relies on the clinical context and is not always definitive. Gene expression profiling provides diagnostic and therapeutic information in several malignancies, but its role in evaluating nonmalignant disease is relatively untested. We hypothesized that gene expression profiling could provide diagnostic information for NSOI. We collected formalin-fixed, paraffin-embedded orbital biopsies from 10 institutions and 83 subjects including 25 with thyroid eye disease, 25 nonspecific orbital inflammation, 20 healthy controls, 6 with granulomatosis with polyangiitis, and 7 with sarcoidosis. Tissues were divided into discovery and validation sets. Gene expression was quantified using Affymetrix U133 Plus 2.0 microarrays. A random forest statistical algorithm based on data from 39 probe sets identified controls, GPA, or TED with an average accuracy of 76% (p=0.02). Random forest analysis indicated that 52% of tissues from patients with nonspecific inflammation were consistent with a diagnosis of GPA. Molecular diagnosis by gene expression profiling will augment clinical data and histopathology in differentiating forms of orbital inflammatory disease. PMID:25595914

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

2015-04-01

11

Molecular-orbital model for metal-sapphire interfacial strength  

NASA Astrophysics Data System (ADS)

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.

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

1982-10-01

12

Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.  

ERIC Educational Resources Information Center

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)

Willis, Christopher J.

1988-01-01

13

Orbits  

NSDL National Science Digital Library

This Topic in Depth explores the Web's offerings on Orbits. The first site is offered by Northwestern University and asks: What is an orbit? (1 ). The site answers questions such as What causes an orbit to happen?, What is a satellite?, What travels in an orbit?, and Are there orbits within orbits?. A great starting site for this subject, visitors should come away with a broad and clear description of the topic. The second site, called Orbit Diagrams (2 ) is provided by the Harvard-Smithsonian Center for Astrophysics. The diagrams are "intended to aid in the visualization of the three-dimensional nature of the orbits and how they are orientated with respect to the orbit of the earth." Next, from the University of Wisconsin-Madison Department of Astronomy comes the Moon Phases (3 ) interactive Web site. Users are able to animate the moon's orbit in various phases and views as well as learn all the names of the phases. The fourth site is another virtual visualization tool provided by NASA's Near Earth Object Program called Orbits (4 ). The site lets users enter the designation or name of any asteroid or comet and then view the three-dimensional orbit of that object. The next site, maintained by the Conservation, Astronomy, Physics and Soaring Page, is called Satellite Orbits - Gravitational Assist from Planets (5 ). The site contains information on Kepler's Laws, which apply to elliptical orbits involving two bodies, hyperbolic orbits, relative motion, and the gravitational sphere of influence. The sixth site is an educational lesson provided by Dr. Richard L. Bowman of Bridgewater College called Planetary Orbit Exercise (6 ). Students are given information on Keplar's Laws of Planetary Motion, a list of definitions, links to outside sites for additional information, and then several questions to answer. The Planetary Physical Data (7 ) page is part of the larger Smithsonian Center for Earth and Planetary Studies Web site. Visitors will find a list of planets along with various information such as their relative sidereal period of orbit, mean orbital velocity, orbital eccentricity, and much more. The last site related to orbits is an educational activity provided by the Physics Classroom called Circular Motion and Planetary Motion (8 ). Four lessons are presented including Motion Characteristics for Circular Motion, Applications of Circular Motion, Universal Gravitation, and Planetary and Satellite Motion. Each contain clear and well written descriptions along with all the necessary information for successful completion.

Brieske, Joel A.

14

Molecular orbital calculations on transition metal dimers containing a linear dinitrogen bridge  

E-print Network

of 23 (Zr{CaHa32 {Ne)) 5o 37a 36a eV 0 -5 -10 5s 4d 3 l 'I 34a 'I 'I / I / 33a / 'I ea ';/+V 28a-33 a iV 1 e ce le" -15 25a-27a V~2 3&o -20 Zr ligands Figure 5. Molecular orbital diagram for the metal fragment (Zr.... The lowest lying MO shown on the diagram is the o bonding combination of the N2 Zo u MO which is stabilized -2 eV by interactions with MO 33a. Nearly equivalent amounts are donated from the N Za MOs in both the Nb u and Zr cases, but significantly more...

Powell, Mary Cynthia

1984-01-01

15

Strong-Field Molecular Ionization from Multiple Orbitals  

SciTech Connect

We demonstrate strong-field ionization from multiple orbitals of excited-state uracil molecules. The molecules are excited to the first bright state by an ultrafast laser pulse in the deep ultraviolet and then ionized with a strong-field laser pulse in the near infrared during ultrafast relaxation back down to the ground state. We measure time- and angle-dependent ion yields for multiple fragments created by strongfield ionization, and interpret the temporally and angularly resolved yields via ab initio electronic structure calculations. We find that the angular distribution for the electron removed from the lowest unoccupied molecular orbital follows the symmetry of the molecular orbital, whereas ionization of the molecule by removing electrons from deeper bound orbitals is more complicated.

Kotur, Marija; Weinacht, Thomas C.; Zhou, Congyi; Matsika, Spiridoula

2011-11-28

16

Orbital tomography of hybridized and dispersing molecular overlayers  

NASA Astrophysics Data System (ADS)

With angle-resolved photoemission experiments and ab initio electronic structure calculations, the pentacene monolayers on Ag(110) and Cu(110) are compared and contrasted, allowing the molecular orientation to be determined and an unambiguous assignment of emissions to specific orbitals to be made. On Ag(110), the orbitals remain essentially isolated-molecule-like, while strong substrate-enhanced dispersion and orbital modification are observed upon adsorption on Cu(110). We show how the photoemission intensity of extended systems can be simulated and that it behaves essentially like that of the isolated molecule modulated by the band dispersion due to intermolecular interactions.

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

2014-10-01

17

SEMIEMPIRICAL MOLECULAR ORBITAL CALCULATIONS OF BAND GAPS OF CONJUGATED POLYMERS  

E-print Network

SEMI­EMPIRICAL MOLECULAR ORBITAL CALCULATIONS OF BAND GAPS OF CONJUGATED POLYMERS Tahir Cagin Research and Development Center, Materials Labarotory, Polymer Branch, Wright Patterson AFB, Ohio 45433 geometries and energy band gaps of conjugated polymers. In this study, we used a modified version of semi

Goddard III, William A.

18

Local reactivity descriptors from degenerate frontier molecular orbitals  

NASA Astrophysics Data System (ADS)

Conceptual Density Functional Theory (DFT) has proposed a set of local descriptors to measure the reactivity on specific sites of a molecule, as an example dual descriptor has been successfully used in analyzing interesting systems to understand their local reactivity, however under the frozen orbital approximation (FOA), it is defined from non-degenerate frontier molecular orbitals (FMOs). In this work, the degeneration is taken into account to propose approximated expressions to obtain the dual descriptor, nucleophilic and electrophilic Fukui functions in closed-shell systems. The proposed expressions have been tested on molecules presenting degenerate FMOs.

Martínez, Jorge

2009-08-01

19

A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets  

ERIC Educational Resources Information Center

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…

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

2014-01-01

20

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

NASA Astrophysics Data System (ADS)

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.

Liu, Shubin; Schauer, Cynthia K.

2015-02-01

21

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

PubMed

To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability. PMID:25662636

Liu, Shubin; Schauer, Cynthia K

2015-02-01

22

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

PubMed

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

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

2014-09-01

23

Phase diagrams of one-dimensional half-filled two-orbital SU (N ) cold fermion systems  

NASA Astrophysics Data System (ADS)

We investigate possible realizations of exotic SU (N ) symmetry-protected topological (SPT) phases with alkaline-earth cold fermionic atoms loaded into one-dimensional optical lattices. A thorough study of two-orbital generalizations of the standard SU (N ) Fermi-Hubbard model, directly relevant to recent experiments, is performed. Using state-of-the-art analytical and numerical techniques, we map out the zero-temperature phase diagrams at half-filling and identify several Mott-insulating phases. While some of them are rather conventional (nondegenerate, charge-density wave, or spin-Peierls-like), we also identify, for even N , two distinct types of SPT phases: an orbital Haldane phase, analogous to a spin-N /2 Haldane phase, and a topological SU (N ) phase, which we fully characterize by its entanglement properties. We also propose sets of nonlocal order parameters that characterize the SU (N ) topological phases found here.

Bois, V.; Capponi, S.; Lecheminant, P.; Moliner, M.; Totsuka, K.

2015-02-01

24

Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln(III) Ions  

NASA Astrophysics Data System (ADS)

Hydration structures of Ln(III) ions were investigated by the fragment molecular orbital-based molecular dynamics simulations. The gadolinium break in changes of coordination numbers from nine to eight was of special interest. No clear "break" at gadolinium was observed in characteristics of both radial and angular distribution functions.

Fujiwara, Takayuki; Mori, Hirotoshi; Komeiji, Yuto; Mochizuki, Yuji

25

A low Earth orbit molecular beam space simulation facility  

NASA Technical Reports Server (NTRS)

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.

Cross, J. B.

1984-01-01

26

Control of substituent ligand over current through molecular devices: An ab initio molecular orbital theory  

Microsoft Academic Search

We explain the order of current curves of the ligand-substituent benzene-derivative devices by an ab initio molecular orbital theory on the basis of the first-principles density functional theory and the nonequilibrium Green function technique. The results of our calculation show the control of the substituent ligand over electronic transport through the molecular device. Contrary to the Hückel tight-binding result, we

H. Chen; J. Q. Lu; J. Wu; H. Mizuseki; Y. Kawazoe

2003-01-01

27

Ab initio molecular simulations with numeric atom-centered orbitals  

NASA Astrophysics Data System (ADS)

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

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

2009-11-01

28

Phase diagram of molecular oxygen adsorption on the (111) platinum surface.  

PubMed

Molecular oxygen adsorption on the Pt(111) surface is studied based on ab initio computations and thermodynamics. An O2 adsorption phase diagram is determined. There are two possible chemisorbed molecular states: one at a bridge site and another one at an fcc hollow site. While some population in the bridge sites persists at all coverages, the states coexist through the intermediate coverage phases. The relative coverage of the two species on the surface is determined by the competition between the Pt lattice distortion energy (that results from O2 adsorption) and the O2 repulsion energy. Our results give a reasonable explanation for the seemingly contradictory findings in previous experimental and theoretical work. PMID:17930841

Wang, Xiao-Gang; Fisher, Galen B

2007-08-10

29

Contribution of Degenerate Molecular Orbitals to Molecular Orbital Angular Momentum in Molecular Magnet Fe(Pc)(CN)2  

Microsoft Academic Search

We measured the static magnetic susceptibility and the electron spin resonance of the Fe(Pc)(CN)2 complexes, and investigated the molecular magnetism of the unit Fe(Pc)(CN)2. The magnetic susceptibility shows a highly anisotropic Curie behavior. Based on the electron spin resonance, we found a highly anisotropic g-value (g1 = 3.62, g2 = 1.11, and g3 = 0.52) in the molecular unit Fe(Pc)(CN)2.

N. Hanasaki; M. Matsuda; H. Tajima; T. Naito; T. Inabe

2003-01-01

30

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

ERIC Educational Resources Information Center

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.

Autschbach, Jochen; Le Guennic, Boris

2007-01-01

31

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

SciTech Connect

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.

Nakata, Hiroya [Tokyo Institute of Technology; Schmidt, Michael W [Ames Laboratory; Fedorov, Dmitri G [National Institute of Advanced Industrial Science and Technology (AIST); Kitaura, Kazuo [Kobe University; Nakamura, Shinichiro [Nakamura Lab; Gordon, Mark S [Ames Laboratory

2014-10-16

32

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

PubMed

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. PMID:25327824

Bâldea, Ioan

2014-11-14

33

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

ERIC Educational Resources Information Center

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…

Cass, Marion E.; Hollingsworth, William E.

2004-01-01

34

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

ERIC Educational Resources Information Center

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…

Johnson, Adam R.

2013-01-01

35

LETTER TO THE EDITOR: Origin of molecular orbital splitting of C60 on Al(110)  

NASA Astrophysics Data System (ADS)

We have investigated the C60 monolayer on Al(110) with angle-dependent photoelectron spectroscopy. We find that orbital components have different angular distributions. Calculations of cross sections of the highest occupied molecular orbital components for free, oriented C60 are found to describe the experimental data quite well. The observed band splitting is attributed to intramolecular electronic correlations, due to the different coupling of the orbital components to the substrate conduction band.

Schiessling, J.; Stener, M.; Balasubramanian, T.; Kjeldgaard, L.; Decleva, P.; Nordgren, J.; Brühwiler, P. A.

2004-09-01

36

Electronic Structures of Molecules XI. Electroaffinity, Molecular Orbitals and Dipole Moments  

Microsoft Academic Search

A convenient criterion for defining equal electronegativity of two atoms is stated in terms of coefficients in LCAO approximate molecular orbitals. Connections between relative electronegativities, coefficients in LCAO orbitals, effective charges on atoms in partially polar molecules, and dipole moments, are then analyzed, and various equations are obtained expressing these connections. The discussion is largely applicable to polyatomic as well

Robert S. Mulliken

1935-01-01

37

Effect of molecular crowding on the temperature-pressure stability diagram of ribonuclease A.  

PubMed

FT-IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure-dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure-induced unfolding of proteins provides insight in protein stability and folding under cell-like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep-sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature-induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high-pressure protein unfolding. The FT-IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure-unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding. PMID:23281099

Zhai, Yong; Winter, Roland

2013-02-01

38

Bounds and phase diagram of efficiency at maximum power for tight-coupling molecular motors  

E-print Network

The efficiency at maximum power (EMP) for tight-coupling molecular motors is investigated based on the constitutive relation between the flux and thermodynamic force. It is found that the EMP is equal to 1/2 when the flux $J$ and thermodynamic force $F$ satisfy $J=J^\\prime F$ where $J^\\prime$ represents the derivative with respect to $F$, and that the EMP is smaller (larger) than 1/2 when $JJ^\\prime F$). The lower and upper bounds of EMP are proved to be $[1-\\mathcal{W}(\\mathrm{e}^{1-\\Delta\\mu})]/\\Delta\\mu$ and $[\\mathcal{W}(\\mathrm{e}^{1+\\Delta\\mu})-1]/\\Delta\\mu$, respectively, where $\\mathcal{W}(.)$ represents the Lambert's W function while $\\Delta \\mu$ is called the reduced chemical potential which is the ratio of the released free energy of fuel in each motor step to the energy scale of thermal motion at the physiological temperature. A phase diagram with phase boundary $\\delta= 2/{\\Delta\\mu}-1/(\\mathrm{e}^{\\Delta\\mu/2}-1)$ is constructed, which shows how $\\Delta \\mu$ and the load distribution factor $\\de...

Tu, Z C

2012-01-01

39

Mechanism of hydrogen activation by frustrated Lewis pairs: A molecular orbital approach  

NASA Astrophysics Data System (ADS)

A detailed molecular orbital treatment of the heterolytic hydrogen splitting by bulky Lewis acid-base pairs is presented. The frontier molecular orbitals of the proposed reactive intermediate are shown to be preorganized but otherwise practically identical to those of the free acid and base molecules. The concerted interaction of the Lewis centers with hydrogen leading to the polarization and, ultimately, to the cleavage of the H=H bond is examined, and the bridge role of hydrogen molecule in the electron transfer is pointed out. The formation of the new covalent bonds is monitored by bond order and natural localized molecular orbital calculations, and found to be synchronous. The stability of the product is interpreted on the basis of favorable orbital interactions. A comparison of various hydrogen activation mechanisms emphasizes the common donation/back-donation motifs and the different ways of making them feasible.

Hamza, Andrea; Stirling, András; András Rokob, Tibor; Pápai, Imre

40

A localized molecular-orbital assembler approach for Hartree-Fock calculations of large molecules  

NASA Astrophysics Data System (ADS)

We describe an alternative fragment-based method, the localized molecular-orbital assembler method, for Hartree-Fock (HF) calculations of macromolecules. In this approach, a large molecule is divided into many small-size fragments, each of which is capped by its local surroundings. Then the conventional HF calculations are preformed on these capped fragments (or subsystems) and the canonical molecular orbitals of these systems are transferred into localized molecular orbitals (LMOs). By assembling the LMOs of these subsystems into a set of LMOs of the target molecule, the total density matrix of the target molecule is constructed and correspondingly the HF energy or other molecular properties can be approximately computed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations with double-zeta and polarized double-zeta basis sets demonstrate that the present approach is able to reproduce the conventional HF energies within a few millihartrees for a broad range of molecules.

Li, Wei; Li, Shuhua

2005-05-01

41

Electron transport through heterocyclic molecule: ab initio molecular orbital theory  

Microsoft Academic Search

We have calculated the electron transport properties of molecule wires by an ab initio molecule orbital theory on the basis of the first-principles density functional theory (DFT) and the non-equilibrium Green function (NEGF) technique. The wires are made of heterocyclic molecule (furan, thiophene, and pyrrole, shown in first figure), in contact with the atomic scale Au electrodes. The results of

W. W. Cheng; Y. X. Liao; H. Chen; H. Mizuseki; Y. Kawazoe

2004-01-01

42

Rigorous non-Born-Oppenheimer theory: Combination of explicitly correlated Gaussian method and nuclear orbital plus molecular orbital theory  

NASA Astrophysics Data System (ADS)

The present study proposes a rigorous non-Born-Oppenheimer theory combining between the explicitly correlated Gaussian (ECG) method and the nuclear orbital plus molecular orbital (NOMO) method. The new method, called ECG-NOMO, adopts the ECG functions between the electronic and nuclear coordinates and, therefore, is capable of describing the nucleus-electron correlation effect accurately. The basic formalism of the ECG-NOMO method is close to the NOMO method, which starts with the Hartree-Fock type equations for NOs and MOs. The present method requires more computational cost than the original NOMO method. However, its cost is significantly smaller than that of the ECG method. The numerical tests was performed for hydrogen-like atoms (H-Ne9+) and dihydrogen cations (H2+, D2+ and T2+), and clarified that the ECG-NOMO method shows the sufficient accuracy.

Hoshino, Minoru; Nishizawa, Hiroaki; Nakai, Hiromi

2011-07-01

43

d Orbital doping into pi charge-ordered molecular insulator.  

PubMed

A quasi-one-dimensional pi-electron charge-ordered insulator, (DI-DCNQI)2Ag, is metallized by Cu doping into the Ag sites. It is found that with doping the charge gap is diminished and then disorder-induced insulating nature comes up, eventually followed by transition or crossover to a pi-d networked metal. The profile of the charge-gap collapse is consistent with the prediction of the theory highlighting the interplay between electron correlation and disorder. The present doping method is regarded as doping of d orbital, which is different from the conventional charge and/or spin doping developed in cuprates and manganites. PMID:12484965

Itou, T; Hiraki, K; Taniguchi, H; Kanoda, K; Takahashi, T

2002-12-01

44

Detection of Molecular Hydrogen Orbiting a ``Naked'' T Tauri Star  

NASA Astrophysics Data System (ADS)

Astronomers have established that for a few million years, newborn stars possess disks of orbiting gas and dust. Such disks, which are likely sites of planet formation, appear to disappear once these stars reach ages of (5-10)×106 yr; yet, >=107 yr is thought necessary for giant planet formation. If disks dissipate in less time than is needed for giant planet formation, such planets may be rare and those known around nearby stars would be anomalies. Here we report the discovery of H2 gas orbiting a weak-lined T Tauri star heretofore presumed nearly devoid of circumstellar material. We estimate that a significant amount of H2 persists in the gas phase, but only a tiny fraction of this mass emits in the near-infrared. We propose that this star possesses an evolved disk that has escaped detection thus far because much of the dust has coagulated into planetesimals. This discovery suggests that the theory that disks are largely absent around such stars should be reconsidered. The widespread presence of such disks would indicate that planetesimals can form quickly and giant planet formation can proceed to completion before the gas in circumstellar disks disperses.

Bary, Jeffrey S.; Weintraub, David A.; Kastner, Joel H.

2002-09-01

45

Synthesis, Structure, and Molecular Orbital Calculations of (Pyrazolato)vanadium(III) Complexes Understanding 2  

E-print Network

FULL PAPER Synthesis, Structure, and Molecular Orbital Calculations of (Pyrazolato)vanadium,[a] Mary Jane Heeg,[a] H. Bernhard Schlegel,[a] and Charles H. Winter*[a] Keywords: Vanadium / Pyrazolato ligands / Ab initio calculations / N ligands / Coordination modes Treatment of trichlorotris(tetrahydrofuran)vanadium

Schlegel, H. Bernhard

46

Thermochemistry of Aluminum Species for Combustion Modeling from Ab Initio Molecular Orbital Calculations  

E-print Network

Thermochemistry of Aluminum Species for Combustion Modeling from Ab Initio Molecular Orbital initio methods for computational thermochemistry have been applied to aluminum compounds expected to be present during combustion of aluminum particles. The computed enthalpies of formation at 298.15 K agree

Swihart, Mark T.

47

Molecular Orbital Studies of Titanium Nitride Chemical Vapor Deposition: Gas Phase Complex Formation,  

E-print Network

Molecular Orbital Studies of Titanium Nitride Chemical Vapor Deposition: Gas Phase Complex Received June 6, 2000 The chemical vapor deposition (CVD) of titanium nitride can be carried out with TiCl4 Titanium nitride thin films have a variety of proper- ties, such as extreme hardness, high chemical

Schlegel, H. Bernhard

48

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

NASA Astrophysics Data System (ADS)

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.

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

2014-04-01

49

Using a Molecular Metaphor to Facilitate Comprehension of 3D Object Diagrams  

E-print Network

provide for round-trip engineering, where a pro- grammer can develop class diagrams and code in tandem stages of the software life-cycle. The approach has already been successful with class di- agrams, which that describes dynamic aspects of the software system, and can be seen as a dynamic manifestation of the class

Malloy, Brian

50

Using a Molecular Metaphor to Facilitate Comprehension of 3D Object Diagrams  

E-print Network

provide for round­trip engineering, where a pro­ grammer can develop class diagrams and code in tandem stages of the software life­cycle. The approach has already been successful with class di­ agrams, which that describes dynamic aspects of the software system, and can be seen as a dynamic manifestation of the class

Malloy, Brian

51

Molecular systems biology: data-flow diagram modeling of process in protein  

Microsoft Academic Search

In this paper, we introduce a new method of modeling tool for a biological process - central dogma. The data-flow diagram is used as a representation of the whole data input and output, which enables us to simulate, analyze, and manipulate (in the future) at our disposal. From DNA to protein via RNA is the one of most well-known biological

J. W. Yeol; I. Barjis; Y. S. Ryu

2005-01-01

52

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

NASA Technical Reports Server (NTRS)

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.

Luther, George W., III

1987-01-01

53

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

SciTech Connect

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

Fernandez-Garrido, S.; Grandal, J.; Calleja, E.; Sanchez-Garcia, M. A.; Lopez-Romero, D. [ISOM and Departamento de Ingenieria Electronica, ETSI Telecomunicacion, Universidad Politecnica de Madrid, 28040 Madrid (Spain)

2009-12-15

54

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

55

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

PubMed

Dicyanovinyl-quinquethiophene (DCV5T-Me2) is a prototype conjugated oligomer for highly efficient organic solar cells. This class of oligothiophenes are built up by an electron-rich donor (D) backbone and terminal electron-deficient acceptor (A) moieties. Here, we investigated its structural and electronic properties when it is adsorbed on a Au(111) surface using low temperature scanning tunneling microscopy/spectroscopy (STM/STS) and atomic force microscopy (AFM). We find that DCV5T-Me2 self-assembles in extended chains, stabilized by intercalated Au atoms. The effect of metal-ligand hybridization with Au adatoms causes an energetic downshift of the DCV5T-Me2 lowest unoccupied molecular orbital (LUMO) with respect to the uncoordinated molecules on the surface. The asymmetric coordination of a gold atom to only one molecular end group leads to an asymmetric localization of the LUMO and LUMO+1 states at opposite sides. Using model density functional theory (DFT) calculations, we explain such orbital reshaping as a consequence of linear combinations of the original LUMO and LUMO+1 orbitals, mixed by the attachment of a bridging Au adatom. Our study shows that the alignment of molecular orbitals and their distribution within individual molecules can be modified by contacting them to metal atoms in specific sites. PMID:25244124

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

2014-10-28

56

Molecular dynamics study of network statistics in lithium disilicate: Qn distribution and the pressure-volume diagram  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations have been performed to study the structures along the pressure-volume diagram of network-glasses and melts exemplified by the lithium disilicate system. Experimentally, densification of the disilicate glass by elevated pressure is known and this feature is reasonably reproduced by the simulations. During the process of densification or decompression of the system, the statistics of Qn (i.e., SiO4 tetrahedron unit with n bridging oxygen linked to the silicon atom where n = 0, 1, 2, 3, or 4) change, and the percentage of the Q3 structures show the maximum value near atmospheric pressure at around Tg. Changes of Qn distribution are driven by the changes of volume (or pressure) and are explained by the different volumes of structural units. Furthermore, some pairs of network structures with equi-volume, but having different distributions of Qn (or different heterogeneity), are found. Therefore, for molecular dynamics simulations of the Qn distributions, it is important to take into account the complex phase behavior including poly-structures with different heterogeneities as well as the position of the system in the P-V-T diagram.

Habasaki, J.; Ngai, K. L.

2013-08-01

57

High-resolution molecular orbital imaging using a p-wave STM tip.  

PubMed

Individual pentacene and naphthalocyanine molecules adsorbed on a bilayer of NaCl grown on Cu(111) were investigated by means of scanning tunneling microscopy using CO-functionalized tips. The images of the frontier molecular orbitals show an increased lateral resolution compared with those of the bare tip and reflect the modulus squared of the lateral gradient of the wave functions. The contrast is explained by tunneling through the p-wave orbitals of the CO molecule. Comparison with calculations using a Tersoff-Hamann approach, including s- and p-wave tip states, demonstrates the significant contribution of p-wave tip states. PMID:21929180

Gross, Leo; Moll, Nikolaj; Mohn, Fabian; Curioni, Alessandro; Meyer, Gerhard; Hanke, Felix; Persson, Mats

2011-08-19

58

Ab initio molecular orbital study of the substituent effect on phosphine borane complexes  

NASA Astrophysics Data System (ADS)

Ab initio molecular orbital calculations have been used to study the substituent effect on H 3BPH nMe 3- n and Me 3- nH nBPH 3 ( n=0-3) phosphine-borane complexes. The ab initio results show that successive methyl substitution on the phosphine favours complex formation, contrary to successive methyl substitution on the borane. The natural bond orbitals partitioning scheme suggests that, in general, there is no correlation between the charge transfer and the complexation energies. It also shows the shortening of the P-H and P-C bond lengths, upon complexation, is due to the increasing `s' character of these bonds.

Anane, Hafid; Jarid, Abdellah; Boutalib, Abderrahim; Nebot-Gil, Ignacio; Tomás, Francisco

1998-11-01

59

Signatures of molecular orbital structure in lateral electron momentum distributions from strong-field ionization.  

PubMed

Strong-field ionization of aligned diatomic and polyatomic molecules such as O_{2}, N_{2}, C_{2}H_{4}, and others in circularly polarized laser fields is investigated theoretically. By calculating the emission-angle-resolved lateral width of the momentum distribution perpendicular to the polarization plane, we show that nodal planes in molecular orbitals are directly imprinted on the angular dependence of the width. We demonstrate that orbital symmetries can be distinguished with the information obtained by observing the lateral width in addition to the angular distributions. PMID:25815929

Petersen, Ingo; Henkel, Jost; Lein, Manfred

2015-03-13

60

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

NASA Astrophysics Data System (ADS)

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

Petersen, Ingo; Henkel, Jost; Lein, Manfred

2015-03-01

61

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

NASA Astrophysics Data System (ADS)

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 (? _red^2=2.0) to the observed position-velocity distribution of dense (n > several 103 cm-3) gas, reproducing all of its key properties. The orbit is also consistent with observational constraints not included in the fitting process, such as the 3D space velocities of Sgr B2 and the Arches and Quintuplet clusters. It differs from previous, parametric models in several respects: (1) the orbit is open rather than closed due to the extended mass distribution in the CMZ, (2) its orbital velocity (100-200 km s-1) is twice as high as in previous models, and (3) Sgr A* coincides with the focus of the (eccentric) orbit rather than being offset. Our orbital solution supports the recently proposed scenario in which the dust ridge between G0.253+0.016 (`the Brick') and Sgr B2 represents an absolute-time sequence of star-forming clouds, of which the condensation was triggered by the tidal compression during their most recent pericentre passage. We position the clouds on a common timeline and find that their pericentre passages occurred 0.30-0.74 Myr ago. Given their short free-fall times (tff ˜ 0.34 Myr), the quiescent cloud G0.253+0.016 and the vigorously star-forming complex Sgr B2 are separated by a single free-fall time of evolution, implying that star formation proceeds rapidly once collapse has been initiated. We provide the complete orbital solution, as well as several quantitative predictions of our model (e.g. proper motions and the positions of star formation `hotspots'). The paper is concluded with a discussion of the assumptions and possible caveats, as well as the position of the model in the Galactic context, highlighting its relation to large-scale gas accretion, the dynamics of the bar, the x2 orbital family, and the origin of the Arches and Quintuplet clusters.

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

2015-02-01

62

Molecular orbital tomography for adsorbed molecules: is a correct description of the final state really unimportant?  

NASA Astrophysics Data System (ADS)

The application of the ‘orbital tomography’ technique to obtain direct images of molecular orbitals of adsorbed molecules from angle-resolved photoemission data, first proposed by Puschnig et al (2009 Science 326 702), is an extremely attractive idea, but is based on the assumption that the photoemission can be described by a plane wave final state. It is well known that this neglect of the spherical-wave nature of the initial emission and of the role of final state scattering both within the molecule and from the substrate can lead to serious errors. Despite this, in the albeit simple systems studied so far the method appears to work reasonably well. Here we provide a detailed critique of this problem, highlight situations in which the orbital tomography approach is likely to lead to major errors, and propose test experiments that could provide clear information on the extent of these problems.

Bradshaw, A. M.; Woodruff, D. P.

2015-01-01

63

A quantum simulator for molecules: Imaging molecular orbitals and electronic dynamics with ultracold atoms  

E-print Network

In the 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 pi electron system with special regard to localization and spin order. The dynamical timescale of ultracold atom simulators are on the order milliseconds which allow for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.

Lühmann, Dirk-Sören; Sengstock, Klaus

2015-01-01

64

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

SciTech Connect

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

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

1985-05-01

65

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

PubMed

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 ? system can make a comparison difficult. PMID:25382464

Proppe, Jonny; Herrmann, Carmen

2015-02-01

66

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method  

NASA Astrophysics Data System (ADS)

We developed a dual basis approach within the fragment molecular orbital formalism enabling efficient and accurate use of large basis sets. The method was tested on water clusters and polypeptides and applied to perform geometry optimization of chignolin (PDB: 1UAO) in solution at the level of DFT/6-31++G??, obtaining a structure in agreement with experiment (RMSD of 0.4526 Å). The polarization in polypeptides is discussed with a comparison of the ?-helix and ?-strand.

Fedorov, Dmitri G.; Kitaura, Kazuo

2014-03-01

67

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

USGS Publications Warehouse

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.

Sherman, D.M.

1986-01-01

68

Spin-orbital entangled molecular jeff states in lacunar spinel compounds  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

69

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

PubMed

The entanglement of the spin and orbital degrees of freedom through the spin-orbit coupling has been actively studied in condensed matter physics. In several iridium oxide systems, the spin-orbital entangled state, identified by the effective angular momentum jeff, can host novel quantum phases. Here we show that a series of lacunar spinel compounds, GaM4X8 (M=Nb, Mo, Ta and W and X=S, Se and Te), gives rise to a molecular jeff state as a new spin-orbital composite on which the low-energy effective Hamiltonian is based. A wide range of electron correlations is accessible by tuning the bandwidth under external and/or chemical pressure, enabling us to investigate the cooperation between spin-orbit coupling and electron correlations. As illustrative examples, a two-dimensional topological insulating phase and an anisotropic spin Hamiltonian are investigated in the weak and strong coupling regimes, respectively. Our finding can provide an ideal platform for exploring jeff physics and the resulting emergent phenomena. PMID:24889209

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

2014-01-01

70

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

SciTech Connect

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.

Gallinat, C. S.; Koblmueller, G.; Brown, J. S.; Speck, J. S. [Materials Department, University of California, Santa Barbara, California 93106-5050 (United States)

2007-09-15

71

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

SciTech Connect

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

Fernandez-Garrido, S.; Gacevic, Z.; Calleja, E. [ISOM and Departamento de Ingenieria Electronica, ETSI Telecomunicacion Universidad Politecnica de Madrid, 28040 Madrid (Spain)

2008-11-10

72

Molecular Orbital Study of the First Excited State of the OLED Material Tris(8-hydroxyquinoline)aluminum(III)  

E-print Network

Molecular Orbital Study of the First Excited State of the OLED Material Tris(8-hydroxyquinoline)aluminum, Michigan 48202 Received February 6, 2001. Revised Manuscript Received May 16, 2001 Tris(8-hydroxyquinoline)aluminum

Schlegel, H. Bernhard

73

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

PubMed

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 I(h)" 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. PMID:20059082

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

2009-12-28

74

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

PubMed

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. PMID:23496628

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

2013-02-01

75

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

SciTech Connect

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.

Kastner, Joel H.; Sacco, G. G. [Center for Imaging Science, Rochester Institute of Technology, 54 Lomb Memorial Drive, Rochester, NY 14623 (United States); Hily-Blant, Pierry; Forveille, Thierry [Laboratoire d'Astrophysique de Grenoble, Universite Joseph Fourier-CNRS, BP 53, 38041 Grenoble Cedex (France); Zuckerman, B., E-mail: jhk@cis.rit.ed [Department of Physics and Astronomy, University of California, Los Angeles 90095, CA (United States)

2010-11-10

76

Stereo Diagrams  

NSDL National Science Digital Library

This exercise is an introduction to stereo diagrams. Students draw stereo diagrams for various models, determine the point group and crystal system of certain crystal shapes, and determine which block models match given stereo diagrams.

Dexter Perkins

77

Envelope molecular-orbital theory of extended systems. I. Electronic states of organic quasilinear nanoheterostructures  

NASA Astrophysics Data System (ADS)

A conceptually appealing and computationally economical course-grained molecular-orbital (MO) theory for extended quasilinear molecular heterostructures is presented. The formalism, which is based on a straightforward adaptation, by including explicitly the vacuum, of the envelope-function approximation widely employed in solid-state physics leads to a mapping of the three-dimensional single-particle eigenvalue equations into simple one-dimensional hole and electron Schrödinger-like equations with piecewise-constant effective potentials and masses. The eigenfunctions of these equations are envelope MO's in which the short-wavelength oscillations present in the full MO's, associated with the atomistic details of the molecular potential, are smoothed out automatically. The approach is illustrated by calculating the envelope MO's of high-lying occupied and low-lying virtual ? states in prototypical nanometric heterostructures constituted by oligomers of polyacetylene and polydiacetylene. Comparison with atomistic electronic-structure calculations reveals that the envelope-MO energies agree very well with the energies of the ? MO's and that the envelope MO's describe precisely the long-wavelength variations of the ? MO's. This envelope MO theory, which is generalizable to extended systems of any dimensionality, is seen to provide a useful tool for the qualitative interpretation and quantitative prediction of the single-particle quantum states in mesoscopic molecular structures and the design of nanometric molecular devices with tailored energy levels and wavefunctions.

Arce, J. C.; Perdomo-Ortiz, A.; Zambrano, M. L.; Mujica-Martínez, C.

2011-03-01

78

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

SciTech Connect

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

Corma, A.; Sastre, G.; Wilson, C. Zicovich (Univ. Politecnica de Valencia (Spain)); Viruela, R. (Univ. de Valencia (Spain))

1992-08-01

79

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

80

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

PubMed

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

Fedorov, Dmitri G; Kitaura, Kazuo

2009-11-01

81

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

ERIC Educational Resources Information Center

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…

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

2012-01-01

82

Unrestricted Hartree-Fock based on the fragment molecular orbital method: energy and its analytic gradient.  

PubMed

A consideration of the surrounding environment is necessary for a meaningful analysis of the reaction activity in large molecular systems. We propose an approach to perform unrestricted Hartree-Fock (UHF) calculations within the framework of the fragment molecular orbital (FMO) method (FMO-UHF) to study large systems with unpaired electrons. Prior to an energy analysis one has to optimize geometry, which requires an accurate analytic energy gradient. We derive the FMO-UHF energy and its analytic gradient and implement them into GAMESS. The performance of FMO-UHF is evaluated for a solvated organic molecule and a solvated metal complex, as well as for the active part of a protein, in terms of energy, gradient, and geometry optimization. PMID:22852600

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

2012-07-28

83

Molecular orbital calculations for modeling acetate-aluminosilicate adsorption and dissolution reactions  

SciTech Connect

Possible molecular configurations of acetic acid and acetate adsorbed onto aluminosilicate minerals are examined. Molecular orbital calculations were performed on molecules and dimers; that are intended to mimic inner sphere and outer sphere adsorption complexes on mineral surfaces. The results predict the structure, energetics, and vibrational spectra of the acetic acid and acetate bonded to alumino-silicate groups. The most likely surface complexes are determined by reaction energetics and comparison of theoretical to experimental vibrational spectra. In addition, a reaction pathway of Si-O-Al cleavage by acetic acid and chemisorption of acetate with tetrahedral Al{sup 3+} is predicted. An activation energy for this reaction is estimated from constrained energy minimizations of the reactants along a reaction pathway. 89 refs., 6 figs., 6 tabs.

Kubicki, J.D.; Apitz, S.E. [Naval Command Control and Surveillance Center, San Diego, CA (United States)] [Naval Command Control and Surveillance Center, San Diego, CA (United States); Blake, G.A. [California Institute of Technology, Pasadena, CA (United States)] [California Institute of Technology, Pasadena, CA (United States)

1997-03-01

84

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.  

PubMed

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts. PMID:24740821

Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

2014-06-14

85

Hybrid treatment combining the translation- and rotation-free nuclear orbital plus molecular orbital theory with generator coordinate method: TRF-NOMO/GCM  

NASA Astrophysics Data System (ADS)

The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed in order to accurately determine the nonadiabatic nuclear and electronic wave functions without Born-Oppenheimer approximation. This study presents a hybrid method combining the TRF-NOMO theory with the generator coordinate method (GCM). The TRF-NOMO/GCM treatment is capable of giving the vibrational excited states with high accuracy, as well as improving the ground-state description by inclusion of the many-body effect. Numerical applications of the TRF-NOMO/GCM calculations to an HF molecule confirm its reliability and usefulness.

Sodeyama, Keitaro; Nishizawa, Hiroaki; Hoshino, Minoru; Kobayashi, Masato; Nakai, Hiromi

2007-01-01

86

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...

87

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

PubMed

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. © 2015 Wiley Periodicals, Inc. PMID:25766721

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

2015-05-01

88

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

SciTech Connect

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.

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

89

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

90

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

PubMed

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

Govindasamy, P; Gunasekaran, S; Srinivasan, S

2014-09-15

91

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

SciTech Connect

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.

Zhou, Xin

1998-11-30

92

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

NASA Astrophysics Data System (ADS)

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.

Safouhi, Hassan; Hoggan, Philip

2003-01-01

93

?-Frontier molecular orbitals in S = 2 ferryl species and elucidation of their contributions to reactivity  

PubMed Central

S = 2 FeIV?O species are key intermediates in the catalysis of most nonheme iron enzymes. This article presents detailed spectroscopic and high-level computational studies on a structurally-defined S = 2 FeIV?O species that define its frontier molecular orbitals, which allow its high reactivity. Importantly, there are both ?- and ?-channels for reaction, and both are highly reactive because they develop dominant oxyl character at the transition state. These ?- and ?-channels have different orientation dependences defining how the same substrate can undergo different reactions (H-atom abstraction vs. electrophilic aromatic attack) with FeIV?O sites in different enzymes, and how different substrates can undergo different reactions (hydroxylation vs. halogenation) with an FeIV?O species in the same enzyme. PMID:22908238

Srnec, Martin; Wong, Shaun D.; England, Jason; Que, Lawrence; Solomon, Edward I.

2012-01-01

94

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

NASA Technical Reports Server (NTRS)

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.

Anderson, A. B.

1985-01-01

95

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

PubMed Central

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

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

2013-01-01

96

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

PubMed

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

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

2013-01-01

97

Design principle for increasing charge mobility of ?-conjugated polymers using regularly localized molecular orbitals  

PubMed Central

The feasibility of using ?-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 ?-conjugated polymers by covering the ?-conjugated chain with macrocycles and regularly localizing ?-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 ?-conjugated polymer chains and that it provides the most effective pathways for inter-site hopping processes. PMID:23575695

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

2013-01-01

98

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

SciTech Connect

In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H{sub 2}, Be{sub 2}, H{sub 2}O, and C{sub 2}H{sub 4}). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory.

Varsano, Daniele, E-mail: daniele.varsano@nano.cnr.it [Dipartimento di Fisica, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185 Roma (Italy)] [Dipartimento di Fisica, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185 Roma (Italy); Barborini, Matteo [Dipartimento di ingegneria e scienze dell'informazione e matematica, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy) [Dipartimento di ingegneria e scienze dell'informazione e matematica, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy)] [Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy)

2014-02-07

99

Orbital-dependent magnetic properties of molecular cluster containing high-spin Co(II) ions  

NASA Astrophysics Data System (ADS)

To shed light on magnetic properties of the magnetic exchange molecular cluster containing the constituent metal ion with unquenched orbital angular momentum, as representative examples two octahedrally coordinated high-spin Co(II)-cluster complexes were synthesized and characterized: complex (1) [Co3(Hbzp)6][ClO4]2· 2CH3OH·H2O (bzp = 2-benzoylpyridine) with a linear core Co(III)-Co(II)-Co(III) and complex (2) [Co4L(N3)4(CH3CN)4](ClO4)4·2H2O (L = Macrocyclic schiff base of tetra-2,6-pyridinedicarboxaldehyde-tetra-ethane-1,2-diamine) comprised by two nearly independent Co(II)-dimers. Following Lines' isotropic exchange approximation the magnetic interaction effective Hamiltonian was introduced, which includes the exchange interactions, the spin-orbit coupling, the low-symmetry crystal field, and the intercluster exchange interaction. On the basis of the irreducible tensor operator approach to solve Hamiltonian we have coded the software, BJMAG package, and performed the best-fit procedure for experimentally temperature variable magnetic susceptibilities for the complexes (1) and (2). The best-fit parameters were obtained as follows: ? = -126 cm-1, ? = 432 cm-1, ? = 0.96, mJ? = 2.7 cm-1 for the complex (1) and ? = -165 cm-1, ? = 960 cm-1, ? = 0.95, J? = 9 cm-1, mJ? = -0.1 cm-1 for the complex (2). To further elucidate the individual role of each interaction in the employed model, the effects of the key factors governing the magnetic properties on temperature variable magnetic susceptibilities were examined in detail. The significance of the intercluster exchange interactions at low temperatures was briefly discussed and a self-consistent molecular field to calculate the thermally average spin of the nearest neighbor in the intercluster interaction was proposed.

Wang, Fan; Zhao, Fei; Wang, Bing-Wu; Wang, Ming-Wei; Zhang, Yuan-Zhu; Wang, Wei; Gao, Song; Chen, Zhi-Da

100

Velocity diagrams  

NASA Technical Reports Server (NTRS)

The selection and design of velocity diagrams for axial flow turbines are considered. Application is treated in two parts which includes: (1) mean-section diagrams, and (2) radial variation of diagrams. In the first part, the velocity diagrams occurring at the mean section are assumed to represent the average conditions encountered by the turbine. The different types of diagrams, their relation to stage efficiency, and their selection when staging is required are discussed. In the second part, it is shown that in certain cases the mean-section diagrams may or may not represent the average flow conditions for the entire blade span. In the case of relatively low hub- to tip-radius ratios, substantial variations in the velocity diagrams are encountered. The radial variations in flow conditions and their effect on the velocity diagrams are considered.

Whitney, W. J.; Stewart, W. L.

1972-01-01

101

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

PubMed

Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the ?-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589nm, respectively. Job(')s method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi-Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded. PMID:25703364

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

2015-05-01

102

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

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, ?=0.808 g/cm(3). PMID:24084483

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

2014-01-24

103

Fragment molecular orbital study on electron tunneling mechanisms in bacterial photosynthetic reaction center.  

PubMed

The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling T(DA) and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (H(L)) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe(2+) and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe(2+) ion, its replacement by Zn(2+), or its removal are found to affect the T(DA) value by factors within 2.2. The calculated T(DA) values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments. PMID:23039745

Kitoh-Nishioka, Hirotaka; Ando, Koji

2012-11-01

104

Nonadiabatic ab initio molecular dynamics including spin-orbit coupling and laser fields.  

PubMed

Nonadiabatic ab initio molecular dynamics (MD) including spin-orbit coupling (SOC) and laser fields is investigated as a general tool for studies of excited-state processes. Up to now, SOCs are not included in standard ab initio MD packages. Therefore, transitions to triplet states cannot be treated in a straightforward way. Nevertheless, triplet states play an important role in a large variety of systems and can now be treated within the given framework. The laser interaction is treated on a non-perturbative level that allows nonlinear effects like strong Stark shifts to be considered. As MD allows for the handling of many atoms, the interplay between triplet and singlet states of large molecular systems will be accessible. In order to test the method, IBr is taken as a model system, where SOC plays a crucial role for the shape of the potential curves and thus the dynamics. Moreover, the influence of the nonresonant dynamic Stark effect is considered. The latter is capable of controlling reaction barriers by electric fields in time-reversible conditions, and thus a control laser using this effect acts like a photonic catalyst. In the IBr molecule, the branching ratio at an avoided crossing, which arises from SOC, can be influenced. PMID:22452086

Marquetand, Philipp; Richter, Martin; González-Vázquez, Jesús; Sola, Ignacio; González, Leticia

2011-01-01

105

A step back: Hydrogen abstraction from methane using a semiempirical molecular orbital method  

SciTech Connect

Several studies have new been completed using semiempirical molecular orbital methods to learn about various aspects of diamond growth. Whole reaction mechanisms for diamond epitaxy have been proposed on the basis of these calculations with supporting evidence from experiment. Attempts have been made to understand the roles of hydrogen atoms, methyl groups, acetylene groups and charged species in diamond film growth from both hot filament and plasmas sources. For the semiempirical method to provide a reasonable description of a diamond film, it is essential that molecular species and configurations to be encountered in the system be included in the parameterization of the method. One way to verify appropriateness of the method is by testing it against simple systems for which detailed experimental measurements and ab initio calculations are available. Unfortunately, the semiempirical methods used in earlier studies have never been tested against simple known systems closely resembling the ones of interest to diamond films. Here we propose to make just such a test, the simplest being the abstraction of hydrogen from methane by a hydrogen atom. Not only is the system simple, but also both experimental and highly accurate theoretical results known for the transition state energy and geometry, key parameters for comparison. The results are reported after a brief review of the computational methods. 10 refs., 3 figs.

Valone, S.M.

1990-01-01

106

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

NASA Technical Reports Server (NTRS)

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.

Almloef, Jan; Taylor, Peter R.

1989-01-01

107

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

PubMed Central

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

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

2014-01-01

108

Open-Shell Hartree—Fock Molecular Orbital Theory of Transition Metal Ion Complexes: KNiF3  

Microsoft Academic Search

In order to investigate the magnetic properties of transition metal salts, we have developed the open shell single determinant Hartree—Fock SCF molecular orbital method for transition metal ion complexes. This cluster approach removes many of the shortcomings of earlier treatments1 and, in principle, provides a framework for obtaining fairly accurate and meaningful results within the single determinant approximation. These wave

D. E. Ellis; A. J. Freeman; P. Ros

1967-01-01

109

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

SciTech Connect

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.

Chen, N.; Yang, R.T. [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemical Engineering] [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemical Engineering

1996-11-01

110

Basis Set Effects on Frontier Molecular Orbital Energies and Energy Gaps: A comparative study between plane waves and localized basis functions in molecular systems  

SciTech Connect

In order to study the KohnSham frontier molecular orbital energies in the complete basis limit, a comparative study between localized functions and plane waves, obtained with the local density approximation exchange-correlation functional is made. The analyzed systems are ethylene and butadiene, since they are theoretical and experimentally well characterized. The localized basis sets used are those developed by Dunning. For the plane-waves method, the pseudopotential approximation is employed. The results obtained by the localized basis sets suggest that it is possible to get an estimation of the orbital energies in the limit of the complete basis set, when the basis set size is large. It is shown that the frontier molecular orbital energies and the energy gaps obtained with plane waves are similar to those obtained with a large localized basis set, when the size of the supercell and the plane-wave expansion have been appropriately calibrated.

Matus, Myrna H.; Garza, Jorge; Galvan, Marcelo

2004-06-08

111

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

SciTech Connect

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

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

1986-01-01

112

Ab initio study of molecular interactions in higher plant and Galdieria partita Rubiscos with the fragment molecular orbital method.  

PubMed

Ribulose bisphosphate carboxylase/oxygenase (Rubisco) from one of the thermophilic red algae Galdieria partita with a high specificity factor shows a characteristic difference from higher plant Rubisco in structural change. We investigate such a difference by evaluating the inter-fragment interaction energy (IFIE) value with fragment molecular orbital (FMO) method in comparison to experimental structural studies. We found some important residues which determine the loop6 stability or which make difference in the structure between higher plant and G. partita Rubiscos. We found that amino acid change of LYS18 to ILE18 is important for the difference in location at which anion binding site is occupied, P1alpha or P1beta, when inorganic anions are bound to the enzyme. Occupation of P2 anion binding site makes the stabilizing interaction between LYS128 and the loop6 stronger. Amino acid change of HIS386 to GLN386 contributed to the difference in the loop6 stability, while amino acid change of MET472 to THR472 did not contribute to it. It is confirmed that the patterns of interactions among THR65, THR67, and THR462 are consistent with previous experimental discussions. However, we found a case that THR65 was not stabilized with anion at P1alpha binding site in a closed-state structure of G. partita Rubisco. PMID:17651697

Watanabe, Hirofumi; Enomoto, Taira; Tanaka, Shigenori

2007-09-21

113

Analyzing molecular properties calculated with two-component relativistic methods using spin-free natural bond orbitals: NMR spin-spin coupling constants  

Microsoft Academic Search

An analysis method for static linear response properties employing two-component (spin-orbit) relativistic density functional theory along with scalar relativistic ``natural localized molecular orbitals'' (NLMOs) and ``natural bond orbitals'' (NBOs) has been developed. The spin-orbit NLMO\\/NBO analysis has been applied to study the indirect spin-spin coupling (J-coupling) constants in Tl-I, PbH4, and a dinuclear Pt-Tl bonded complex with a very large

Jochen Autschbach

2007-01-01

114

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

PubMed

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. PMID:25770496

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

2015-03-14

115

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

116

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)

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.

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

2015-03-01

117

Lucidchart: Diagramming  

NSDL National Science Digital Library

For all those who have wrestled with creating charts and diagrams in word processors, the Google Chrome application Lucidchart may be a long-awaited answer. Users can start using the intuitive drag-and-drop interface right away, although a free signup is required to save diagrams. By sharing a link with coworkers, project collaborators can work on the same diagram at the same time. This application is compatible with all computers running Google Chrome.

2012-08-24

118

Venn Diagrams  

NSDL National Science Digital Library

In this activity, students are given a Venn diagram with certain rules and an element. They must then determine where in the Venn diagram the element belongs. This activity allows students to practice placing elements in Venn diagrams as well as reviewing mathematical terms associated with the different rules. This activity includes supplemental materials, including background information about the topics covered, a description of how to use the application, and exploration questions for use with the java applet.

2011-05-24

119

Magnetic phase diagram of a five-orbital Hubbard model in the real-space Hartree-Fock approximation varying the electronic density  

SciTech Connect

Usingthereal-spaceHartree-Fockapproximation,themagneticphasediagramofa ve-orbitalHubbardmodelfortheiron-basedsuperconductorsisstudiedvaryingtheelectronicdensitynintherangefrom vetosevenelectronspertransitionmetalatom.TheHubbardinteractionUisalsovaried,ata xedHundcouplingJ/U=0.25.Severalqualitativetrendsandavarietyofcompetingmagneticstatesareobserved.Atn=5,arobustG-typeantiferromagneticinsulatorisfound,inagreementwithexperimentalresultsforBaMn2As2.Asnincreasesawayfrom5,magneticstateswithanincreasingnumberofnearest-neighborsferromagneticlinksbecomeenergeticallystable.Thisincludesthewell-knownC-typeantiferromagneticstateatn=6,theE-phaseknowntoexistinFeTe,andalsoavarietyofnovelstatesnotfoundyetexperimentally,someoftheminvolvingblocksofferromagneticallyorientedspins.Regionsofphaseseparation,asinMnoxides,havealsobeendetected.Comparisontoprevioustheoreticalinvestigationsindicatethatthesequalitativetrendsmaybegenericcharacteristicsofphasediagramsofmulti-orbitalHubbardmodels.

Luo, Qinlong [ORNL] [ORNL; Dagotto, Elbio R [ORNL] [ORNL

2014-01-01

120

Cyclopolysilanes: structure, strain, and the form of the singly occupied molecular orbital in their radical anions  

SciTech Connect

The cyclopolysilanes (SiH/sub 2/)/sub n/, n = 3 to 5, have been investigated via ab initio quantum mechanical methods. Strain energies are determined through the use of homodesmotic reactions, and the strain of the three-, four-, and five-membered silicon rings relative to each other and to the corresponding hydrocarbon rings is reasonably explained by consideration of angle strain, torsional strain, and substituent effects. Arguments of sigma-aromaticity, which ascribe the apparent unusual stability of three-membered rings (3MR's) to delocalization of six sigma electrons, fail to account for the observed data, and their fundamental assumption that force constants at one geometry can be used to predict strain energies at a vastly different geometry is seriously called to question. Finally, a model for the singly occupied molecular orbital (SOMO) of cyclopolysilane anion radicals is suggested by their studies which is ..pi..-bonding between the ring atoms and silicon-substituent antibonding. For reasons of symmetry, this ..pi..* model readily explains available evidence from ESR and UV spectroscopy, but cannot easily explain results from recent /sup 29/Si ENDOR studies. On the other hand, a recently developed sigma* model, which appears to account for the ENDOR results, seems at odds with the ESR and UV intensity data.

Grev, R.S.; Schaefer, H.F. III

1987-10-28

121

Venn Diagrams  

NSDL National Science Digital Library

This interactive problem provides an opportunity for children to become familiar with Venn diagrams, while reinforcing knowledge of number properties. Students must place the numbers from 1 to 40 into a Venn diagram of two sets with an intersection. The Teachers' Notes page offers rationale, suggestions for implementation, discussion questions, ideas for extension and support.

122

Venn Diagrams  

NSDL National Science Digital Library

This lesson is designed to introduce students to sorting objects/elements using Venn diagrams. This lesson provides links to discussions and activities related to Venn diagrams as well as suggested ways to integrate them into the lesson. Finally, the lesson provides links to follow-up lessons designed for use in succession with the current one.

2011-05-23

123

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

SciTech Connect

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.

Chen, Ji [International Center for Quantum Materials, Peking University, Beijing 100871 (China); Ren, Xinguo [Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui (China); Li, Xin-Zheng, E-mail: xzli@pku.edu.cn [School of Physics, Peking University, Beijing 100871 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100871 (China); Alfè, Dario, E-mail: d.alfe@ucl.ac.uk [London Centre for Nanotechnology, University College London, London WC1H 0AH (United Kingdom); Department of Physics and Astronomy, University College London, London WC1E6BT (United Kingdom); Department of Earth Sciences, University College London, London WC1E6BT (United Kingdom); Wang, Enge, E-mail: egwang@pku.edu.cn [International Center for Quantum Materials, Peking University, Beijing 100871 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100871 (China)

2014-07-14

124

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)

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.

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-02-01

125

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

ERIC Educational Resources Information Center

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…

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

2013-01-01

126

Inter-Molecular Spin-Orbital Coupling Effects on Magnetoresistance and Spin-Dependent Excited Processes in Organic Semiconductors  

NASA Astrophysics Data System (ADS)

A low magnetic field can change electrical current and electroluminescence in organic semiconductors, leading to magnetoresistance and magnetic field effects due to magnetic field-dependent singlet/triplet ratio involved in charge transport and excited states. In general, an external magnetic field can change singlet and triplet ratios through two major pathways: spin-dependent electron-hole pairing and field-dependent intersystem crossing. We found that tuning inter-molecular spin-orbital coupling leads to a significant change in magnetoresistance, electro-fluorescence, and electro-phosphorescence. These experimental findings indicate that (i) inter-molecular and intra-molecular electron-hole pairs account for magnetoresistance and magnetic field effects, respectively, (ii) spin mixing occurs in inter-molecular excited states, and (iii) spin-mixing is a function of both spin-orbital coupling and singlet-triplet energy difference. This presentation will discuss the effects of magnetic field on both spin-dependent electron-hole pairing and spin mixing in magnetoresistance and magnetic field effects in organic semiconductors.

Yan, Liang; Hu, Bin

2009-03-01

127

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

NASA Astrophysics Data System (ADS)

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

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

2013-01-01

128

Estimation of relationship between structure of newly synthesized dihydroimidazoles determined by a semiempirical molecular-orbital method and their cytotoxicity.  

PubMed

A semiempirical molecular-orbital method (CAChe 4.9, PM5) was applied to delineate the relationship between the cytotoxicity (evaluated by 50% cytotoxic concentration, CC(50)) of twelve dihydroimidazole derivatives, their molecular weight and the eleven chemical parameters (descriptors) determined by CONFLEX/PM5 method. There was no correlation between the CC(50) value and heat of formation, dipole moment, E(HOMO), E(LUMO), absolute hardness (eta), absolute electron negativity (chi), reaction index (omega), length of substituted group in all cell lines tested. However, there was good correlation between the CC(50) and the log P, or molecular size in all cell lines used. Surface and volume calculated by this method are useful in evaluating the cytotoxicity of dihydroimidazole derivatives. PMID:20044611

Takekawa, Fumihiro; Sakagami, Hiroshi; Ishihara, Mariko

2009-12-01

129

Magnetic exchange between metal ions with unquenched orbital angular momenta: basic concepts and relevance to molecular magnetism  

NASA Astrophysics Data System (ADS)

This review article is a first attempt to give a systematic and comprehensive description (in the framework of the unified theoretical approach) of the exchange interactions in polynuclear systems based on orbitally degenerate metal ions in the context of their relevance to the modern molecular magnetism. Interest in these systems is related to the fundamental problems of magnetism and at the same time steered by a number of impressive potential applications of molecular magnets, like high-density memory storage units, nanoscale qubits, spintronics and photoswitchable devices. In the presence of orbital degeneracy, the conventional spin Hamiltonian (Heisenberg-Dirac-van Vleck model) becomes inapplicable even as an approximation. The central component of this review article constitutes the concept of orbitally-dependent exchange interaction between metal ions possessing unquenched orbital angular momenta. We present a rigorous procedure of derivation of the kinetic exchange Hamiltonian for a pair of orbitally degenerate transition metal ions that is expressed in terms of the orbital matrices and spin operators. The microscopic background reveals the interrelations between the parameters of the Hamiltonian and the internal parameters of the system including all relevant transfer integrals and fundamental intracenter interactions. The developed formalism integrated with the irreducible tensor operator (ITO) technique makes it possible to describe the exchange coupling and all relevant interactions (crystal fields, spin-orbit (SO) and Zeeman couplings) in terms of the ITOs of the full spherical group, and in this way to develop anunified and efficient computational tool. The orbitally-dependent exchange was shown to lead to an anomalously strong magnetic anisotropy that can be considered as a main physical manifestation of the unquenched orbital angular momentum in metal clusters of orbitally-degenerate ions. The theoretical background is illustrated by the following applications. The magnetic properties of the binuclear face-shared unit [Ti2Cl9]3- in Cs3Ti2Cl9 are discussed with the emphasis on the observed magnetic anisotropy and on the non-trivial symmetry properties of the exchange Hamiltonian. The major electronic factors controlling the magnetic anisotropy in Co(II) pairs are discussed. The degree of the exchange anisotropy was shown to depend on the strength of the cubic crystal field, on the relative efficiency of the electron transfer pathways between unfilled d-shells and SO coupling. Provided strong SO coupling, the effective Hamiltonian was projected onto the subspace of low-lying Kramers doublets and similarly a pseudo-spin-1/2 Hamiltonian was derived. The described procedure allows to establish the interrelation between idem parameters of the system and the parameters of the pseudo-spin-1/2 Hamiltonian. Pseudo-spin-1/2 approach is illustrated by the study of the inelastic neutron scattering spectra and magnetic susceptibility of polyoxometalates encapsulating Co(II) clusters: Keggin derivative K8[Co2(D2O)(W11O39)] · nD2O, [Co4(H2O)2(PW9O34)2]10- and [Co3W(D2O)2(CoW9O34)2]12- clusters. In the consideration of the cyanide-bridged Mn(III)-CN-Mn(II) pair, it was demonstrated that under certain conditions the orbitally-dependent exchange is able to produce a barrier for the reversal of magnetisation. This seems to be instructive for the controlled design of cyano-based single molecule magnets with high-blocking temperatures.

Palii, Andrei; Tsukerblat, Boris; Clemente-Juan, Juan Modesto; Coronado, Eugenio

130

Exact formulas for multipole moments using Slater-type molecular orbitals  

NASA Technical Reports Server (NTRS)

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

Jones, H. W.

1986-01-01

131

Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: theory and applications to intermolecular interactions involving radicals.  

PubMed

Radical-closed shell and radical-radical intermolecular interactions are less well-understood than those between closed shell species. With the objective of gaining additional insight, this work reports a generalization of the absolutely localized molecular orbital (ALMO) energy decomposition analysis (EDA) to open shell fragments, described by self-consistent field methods, such as standard density functional theory. The ALMO-EDA variationally partitions an intermolecular interaction energy into three separate contributions; frozen orbital interactions, polarization, and charge transfer. The first examples involve comparison of the interactions of alkanes and alkyl radicals (methyl radical, methane, tertiary butyl radical, and isobutane) with sodium, potassium, hydronium, and ammonium cations. A second series of examples involve benzene cation interacting with a series of nucleophiles in both on-top and side-on geometries. The ALMO-EDA yields a variety of interesting insights into the relative roles of its component contributions as the interacting partners and their geometries are changed. PMID:23574220

Horn, Paul R; Sundstrom, Eric Jon; Baker, Thomas A; Head-Gordon, Martin

2013-04-01

132

Venn diagrams  

NSDL National Science Digital Library

These online resources offer varied opportunities to work with Venn diagrams, one of many tools used in logic and reasoning. Their use is especially helpful in learning foundational notions of definition and set theory. One of the five Process Standards promoted by NCTM, Reasoning and Proof requires middle school students to sharpen such skills as they learn to develop mathematical argument.

National Science Digital Library (NSDL) Middle School Portal Staff

2008-03-10

133

Phase Diagrams  

NSDL National Science Digital Library

This handout and problem set is a stand alone tutorial that introduces students to the basics of phase diagrams and the phase rule. It is a rather lengthy exercise, suitable as a homework assignment. It can replace lectures and yields superior learning.

Dexter Perkins

134

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

ERIC Educational Resources Information Center

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…

Halkides, Christopher J.

2013-01-01

135

Variation in emulsion stabilization behavior of hybrid silicone polymers with change in molecular structure: Phase diagram study.  

PubMed

Silicone oils are widely used in cosmetics and personal care applications to improve softness and condition skin and hair. Being insoluble in water and most hydrocarbons, a common mode of delivering them is in the form of emulsions. Currently most applications use polyoxyethylene (non-ionic) modified siloxanes as emulsifiers to stabilize silicone oil emulsions. However, ionically grafted silicone polymers have not received much attention. Ionic silicones have significantly different properties than the non-ionic counterpart. Thus considerable potential exists to formulate emulsions of silicones with different water/silicone oil ratios for novel applications. In order to understand the mechanisms underlying the effects of hydrophilic modifications on the ability of hybrid silicone polymers to stabilize various emulsions, this article focuses on the phase diagram studies for silicone emulsions. The emulsifying ability of functional silicones was seen to depend on a number of factors including hydrophilicity of the polymer, nature of the functional groups, the extent of modification, and the method of emulsification. It was observed that the region of stable emulsion in a phase diagram expanded with increase in shear rate. At a given shear rate, the region of stable emulsion and the nature of emulsion (water-in-oil or oil-in-water) was observed to depend on hydrophilic-hydrophobic balance of the hybrid silicone emulsifier. At a fixed amount of modification, the non-ionically modified silicone stabilized an oil-in-water emulsion, whereas the ionic silicones stabilized inverse water-in-oil emulsions. This was attributed to the greater hydrophilicity of the polyoxyethylene modified silicones than the ionic counterparts. In general, it is postulated that with progressive increase in hydrophilicity of hybrid silicone emulsifiers, their tendency to stabilize water-in-oil emulsion decreases with corresponding increase in oil-in-water emulsion. Further, this behavior is hypothesized to depend on the nature of modifying functional groups. Thus a hybrid silicone polymer can be tailored by selecting the nature and degree of hydrophilicity to obtain a desired silicone emulsion. PMID:19200558

Mehta, Somil C; Somasundaran, P; Kulkarni, Ravi

2009-05-15

136

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

PubMed

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. PMID:19658613

Danel, J-F; Kazandjian, L; Zérah, G

2009-06-01

137

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

PubMed

Excess production of hyaluronan (hyaluronic acid [HA]) in the retro-orbital space is a major component of Graves' ophthalmopathy, and regulation of HA production by orbital cells is a major research area. In most previous studies, HA was measured by ELISAs that used HA-binding proteins for detection and rooster comb HA as standards. We show that the binding efficiency of HA-binding protein in the ELISA is a function of HA polymer size. Using gel electrophoresis, we show that HA secreted from orbital cells is primarily comprised of polymers more than 500 000. We modified a commercially available ELISA by using 1 million molecular weight HA as standard to accurately measure HA of this size. We demonstrated that IL-1?-stimulated HA secretion is at least 2-fold greater than previously reported, and activation of the TSH receptor by an activating antibody M22 from a patient with Graves' disease led to more than 3-fold increase in HA production in both fibroblasts/preadipocytes and adipocytes. These effects were not consistently detected with the commercial ELISA using rooster comb HA as standard and suggest that fibroblasts/preadipocytes may play a more prominent role in HA remodeling in Graves' ophthalmopathy than previously appreciated. PMID:24302624

Krieger, Christine C; Gershengorn, Marvin C

2014-02-01

138

A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals  

NASA Astrophysics Data System (ADS)

We present an ab initio polarizable representation of classical molecular mechanics (MM) atoms by employing an angular momentum-based expansion scheme of the point charges into partial wave orbitals. The charge density represented by these orbitals can be fully polarized, and for hybrid quantum-mechanical-molecular-mechanical (QM/MM) calculations, mutual polarization within the QM/MM Hamiltonian can be obtained. We present the mathematical formulation and the analytical expressions for the energy and forces pertaining to the method. We further develop a variational scheme to appropriately determine the expansion coefficients and then validate the method by considering polarizations of ions by the QM system employing the hybrid GROMACS-CPMD QM/MM program. Finally, we present a simpler prescription for adding isotropic polarizability to MM atoms in a QM/MM simulation. Employing this simpler scheme, we present QM/MM energy minimization results for the classic case of a water dimer and a hydrogen sulfide dimer. Also, we present single-point QM/MM results with and without the polarization to study the change in the ionization potential of tetrahydrobiopterin (BH4) in water and the change in the interaction energy of solvated BH4 (described by MM) with the P450 heme described by QM. The model can be employed for the development of an extensive classical polarizable force-field.

Biswas, P. K.; Gogonea, Valentin

2008-10-01

139

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

NASA Astrophysics Data System (ADS)

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

Buhl, Margaret Linn

140

Variable-energy photoelectron spectroscopy of substituted rhenium and manganese pentacarbonyls: molecular orbital assignments and the interatomic resonant effect.  

PubMed

High-resolution variable-energy photoelectron spectra of M(CO)5X [M = Re, X = Re(CO)5, Cl, Br, and I; and M = Mn, X = Mn(CO)5 and Br] are reported. Tunable synchrotron radiation is used to distinguish the Re 5d and Br 4p orbital based peaks for the controversial Re(CO)5Br. Our results provide firm molecular orbital assignments for all of these molecules. The valence orbital in the ordering of ionization energies for M(CO)5Cl (M = Mn and Re) and Mn(CO)5Br is a 1(M-X) > e(X) > b2(M) > e(M); but for M(CO)5I (M = Mn and Re) and Re(CO)5Br the ordering is a1(M-X) > e(M) > b2(M) > e(X). The crossover of the HOMO in the Re molecules due to the change in the halogen electronegativities occurs at Re(CO)5Br. The metal np-->nd resonance is observed for all of these molecules. For molecules like M2(CO)10 (M = Re and Mn) and Mn(CO)5Br, the observation of this np-->nd resonance is useful in assigning the metal nd based orbitals in their valence level spectra. However, for molecules like Re(CO)5X (X = Br and Cl), a np-->nd type resonance is observed on bands arising from both Re 5d and halogen mp based orbitals. This new resonant effect on the ligand-based orbitals is shown to be mainly due to the interatomic resonant effect. The core and valence level chemical shifts of these compounds are treated using Jolly's approach to confirm the assignments for the valence level spectra of some of these molecules. The high-resolution inner valence and core level spectra of these compounds are reported. Broadening of Re 4f, Br 3d, and I 4d core level spectra is discussed. The Auger peaks are observed in the high-resolution, high-intensity Br 3d of Re(CO)5Br and I 4d of Re(CO)5I spectra. PMID:12526417

Hu, Y F; Bancroft, G M; Tan, K H

2000-03-20

141

Beyond the spin model: exchange coupling in molecular magnets with unquenched orbital angular momenta.  

PubMed

In this critical review we review the problem of exchange interactions in polynuclear metal complexes involving orbitally degenerate metal ions. The key feature of these systems is that, in general, they carry an unquenched orbital angular momentum that manifests itself in all their magnetic properties. Thus, interest in degenerate systems involves fundamental problems related to basic models in magnetism. In particular, the conventional Heisenberg-Dirac-Van Vleck model becomes inapplicable even as an approximation. In the first part we attempt to answer two key questions, namely which theoretical tools are to be used in the case of degeneracy, and how these tools can be employed. We demonstrate that the exchange interaction between orbitally degenerate metal ions can be described by the so-called orbitally-dependent exchange Hamiltonian. This approach has shown to reveal an anomalously strong magnetic anisotropy that can be considered as the main physical manifestation of the unquenched orbital angular momentum in magnetic systems. Along with the exchange coupling, a set of other interactions (such as crystal field effects, spin-orbit and Zeeman coupling), which are specific for the degenerate systems, need to be considered. All these features will be discussed in detail using a pseudo-spin-1/2 Hamiltonian approach. In the second part, the described theoretical background will be used to account for the magnetic properties of several magnetic metal clusters and low-dimensional systems: (i) the dinuclear face-sharing unit [Ti(2)Cl(9)](3-), which exhibits a large magnetic anisotropy; (ii) the rare-earth compounds Cs(3)Yb(2)Cl(9) and Cs(3)Yb(2)Br(9), which, surprisingly, exhibit a full magnetic isotropy; (iii) a zig-zag Co(II) chain exhibiting unusual combination of single-chain magnet behavior and antiferromagnetic exchange coupling; (iv) a trigonal bipyramidal Ni(3)Os(2) complex; (v) various Co(II) clusters encapsulated by polyoxometalate ligands. In the two last examples a pseudospin-1/2 Hamiltonian approach is applied to account for the presence of exchange anisotropy (150 references). PMID:21431145

Palii, Andrei; Tsukerblat, Boris; Klokishner, Sophia; Dunbar, Kim R; Clemente-Juan, Juan M; Coronado, Eugenio

2011-06-01

142

Multipole moments and polarizability of molecular systems with D3h symmetry in orbitally degenerate states  

Microsoft Academic Search

It was proved, by ab initio studies, that the electronic ground states of the molecules MF3 (M dbond V, Cr, Mn), M3 (M dbond Li, Na, K), and C3H3, with D3h symmetry, have orbital degeneracy. It was shown that in the base functions of these degenerate states, the reduced matrix elements of the in-plane E?-type components of the dipole moment,

I. Ya. Ogurtsov; I. Balan; G. Munteanu

2006-01-01

143

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

SciTech Connect

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.

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

2008-05-20

144

The bonding of acetate, methoxy, thiomethoxy and pyridine to Cu surfaces: a molecular orbital study  

NASA Astrophysics Data System (ADS)

The bonding of acetate (CH 3COO), methoxy (CH 3O), thiomethoxy (CH 3S) and pyridine (C 5H 5N) to copper surfaces has been examined employing semi-empirical MO-SCF calculations (INDO/S) and metal clusters of limited size (Cu n, n = 16 or 18 atoms). CH 3COO, CH 3O and CH 3S behave as electron acceptors when adsorbed. For these species, the chemisorption bond is dominated by the interaction between the LUMO of the adsorbate and the Cu(4s, 4p) bands. The relatively weak C?S bond in CH 3S a makes decomposition to form sulfur adatoms and alkanes a very exothermic process (- ?H = 20 to 30 kcal/ mol). In contrast, similar types of decomposition reactions for CH 3O a are almost thermoneutral (as a consequence of a strong C?O bond), and the molecule prefers to decompose forming H 2CO a and H a species. The results of a thermochemical analysis indicate that reactions which involve the cleavage of S?H and/or C?S bonds of alkanethiols are very exothermic on copper. The bonding mechanism of pyridine involves a large charge transfer from the 7a 1, and 2b 1 orbitals of the molecule into the Cu(4s, 4p) orbitals, and a very small electron transfer from the substrate into the C?N antibonding 3b 1 orbital of the adsorbate (?-backbonding). The fact that Cu is poor at ?-backdonation makes the metal inactive for pyridine decomposition. On the basis of these INDO/S results, the possible UPS spectra of CH 3O and CH 3S on Cu(111), and of CH 3COO and C 5H 5N on Cu(110) are discussed and compared with experimental results.

Rodriguez, JoséA.

1992-07-01

145

Estimation of relationship between the structure of 1,2,3,4-tetrahydroisoquinoline derivatives determined by a semiempirical molecular-orbital method and their cytotoxicity.  

PubMed

A semiempirical molecular-orbital method (CAChe 4.9, PM5) was applied to delineate the relationship between the cytotoxicity (evaluated by 50% cytotoxic concentration, CC(50)) of nineteen 1,2,3,4-tetrahydroisoquinoline derivatives, their molecular weight and the sixteen chemical parameters (descriptors) determined by CONFLEX/PM5 method. There was little or no correlation between the CC(50) in HL-60 cells and the heat of formation, stability of hydration (DeltaH), dipole moment, electron affinity, ionization potential, highest occupied molecular orbital energy (E(HOMO)), lowest unoccupied molecular orbital energy (E(LUMO)), absolute hardness (eta, softness and hardness of the molecule) or molecular weight (r(2)<0.312). On the other hand, there was a good correlation between the CC(50) and the hydrophobicity (log P) (r(2)=0.503), and the descriptors for the molecular size such as surface area (r(2)=0.771), volume (r(2)=0.805) and width (r(2)=0.757). Similar, but not so clear-cut correlation was found in HSC-2, HSC-3 and HSC-4 human oral squamous cell carcinoma cell lines. The present study demonstrates that the cytotoxicity of 1,2,3,4-tetrahydroisoquinoline derivatives depends more on the descriptors for molecular size rather than the physicochemical descriptors. PMID:19528491

Ishihara, Mariko; Hatano, Hajime; Kawase, Masami; Sakagami, Hiroshi

2009-06-01

146

Abundances and Energetics for Water Group and Molecular Oxygen Ions in Saturn's Magnetosphere After 24 Cassini Orbits  

NASA Astrophysics Data System (ADS)

We present magnetospheric ion composition results from the Cassini Plasma Spectrometer (CAPS) for the first 24 orbits of Cassini about Saturn. Apoapses of these orbits have local times between 3 and 8 MLT. Data from the Ion Mass Spectrometer (IMS) are summed to achieve better statistics and to bring out features that are otherwise difficult to resolve from an individual orbital pass. We highlight some of our results here. As described previously, water group ions (O+, OH+, H2O+, H3O+; or collectively, W+) dominate over H+ in the inner plasmasphere (Young et al., 2005; Sittler et al., 2005). We find that on average, this dominance persists out to 20 Saturn Radii (RS), and although weakening rapidly, W+ ions are observed out to 25 RS. The density of hydronium, which is the dominant W+ species within 4 RS, peaks at 5 RS and rapidly drops with an radial length scale of 1 RS; hydronium is no longer detectable beyond 14 RS. The W+ plasma has both a core component and a higher-energy tail. The density ratio of the tail to the core increases (length scale of 1.3 RS) out to 10 RS and then flattens out to a constant factor of 0.1. The mean core energy increases by a factor of 20 between 4 and 20 RS, nearly following rigid co-rotation. However, the mean tail energy is flat between 4 and 15 RS, at 3 keV and then increases by a factor of 2 between 15 and 20 RS, indicating a separate dynamic history from the core. Finally, we detect molecular oxygen (O2+) out to 10 RS. At 4.5 RS, the O2+ density is 5% of the W+ density, and the O2+ density drops relative to W+ with a radial length scale of 2 RS.

Martens, Hilary R.; Reisenfeld, D. B.; Williams, J. D.; DiLorenzo, J.; Thomsen, M. F.; Smith, H. T.; Eviatar, A.; Johnson, R. E.; Young, D. T.; Sittler, E. C.; Baragiola, R. A.

2006-09-01

147

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

SciTech Connect

N-face GaN was grown on free-standing GaN (0001{sup ¯}) substrates at a growth rate of 1.5??m/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, ?{sub Ga}????{sub N*}, and the growth temperature. At high ?{sub Ga}????{sub N*} (?{sub Ga}????{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.

Okumura, Hironori, E-mail: okumura@engineering.ucsb.edu; McSkimming, Brian M.; Speck, James S. [Materials Department, University of California, Santa Barbara, California 93106 (United States)] [Materials Department, University of California, Santa Barbara, California 93106 (United States); Huault, Thomas; Chaix, Catherine [RIBER S.A., 3a Rue Casimir Perier, BP 70083, 95873 Bezons Cedex (France)] [RIBER S.A., 3a Rue Casimir Perier, BP 70083, 95873 Bezons Cedex (France)

2014-01-06

148

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

PubMed

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

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

2015-03-01

149

PUBLISHED ONLINE: 26 JUNE 2011 | DOI: 10.1038/NPHYS2029 Generalized molecular orbital tomography  

E-print Network

resolution. Nevertheless, in the following years several experiments demonstrated the role of multielectron that the retrieved XUV emission is negligibly affected by multielectron effects and that it can be exploited.stagira@fisi.polimi.it. Our results show that the dream of imaging complex molecular species through harmonic generation

Loss, Daniel

150

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

NASA Astrophysics Data System (ADS)

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.

Yoshida, Norio

2014-06-01

151

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

NASA Astrophysics Data System (ADS)

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 ?-bonded molecules. The calculated decay constant, ?, 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.

Pati, Ranjit; Karna, Shashi P.

2002-01-01

152

Molecular orbital study of mechanisms of the reactions of alkyl bromides with O(3P) atoms  

NASA Astrophysics Data System (ADS)

Ab initio electronic structure computations have been performed to study the singlet and triplet potential energy surfaces involved in the gas-phase reactions of O(3P) with the alkyl bromides C2H5Br and 1,2-C2H4Br2 to produce spin-allowed OBr and spin-forbidden HOBr products. The computations explore the effects of multiple alkane bromination on the reaction path. Our calculations indicate that high barriers to OBr formation exist on the triplet potential energy surface of alkyl-bromides reacting with O atoms. We compute spin-orbit couplings between the singlet and triplet surfaces at the lowest points where the surfaces intersect. We conclude that OBr products may be observed at sufficiently high collision energies via the triplet path while there is low probability of production of OBr or HOBr from a singlet state.

Stevens, Jonathan E.; Kaufman, Marina S.; Morokuma, Keiji

2003-04-01

153

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

PubMed

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

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

2013-05-30

154

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

E-print Network

photoionization cross sections can now be calculated for small molecules almost quantitatively using ab initio- and energy-resolved photo- electron spectroscopy.10­12 By ionizing optically aligned NO A 2 0 moleculesMolecular-orbital decomposition of the ionization continuum for a diatomic molecule by angle

Zare, Richard N.

155

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

PubMed

Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (?) and hyperpolarizability ?0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP). PMID:25459510

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

2015-02-01

156

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

NASA Astrophysics Data System (ADS)

Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (?) and hyperpolarizability ?0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. 13C and 1H NMR spectra were recorded and 13C and 1H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP).

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

2015-02-01

157

Synthesis, Structure, and Molecular Orbital Studies of Yttrium, Erbium, and Lutetium Complexes Bearing 2-Pyrazolato Ligands: Development of a New Class of Precursors for  

E-print Network

Synthesis, Structure, and Molecular Orbital Studies of Yttrium, Erbium, and Lutetium Complexes, Wisconsin 53706 ReceiVed March 23, 1999 Treatment of yttrium metal with bis(pentafluorophenyl)mercury (1 for 120 h afforded tris(3,5-di-tert-butylpyrazolato)bis- (pyridine)yttrium(III) (33%). In an analogous

Schlegel, H. Bernhard

158

A New Class of Mixed-Valence Systems with Orbitally Degenerate Organic Redox Centers. Examples Based on Hexa-Rhenium Molecular Prisms  

E-print Network

Based on Hexa-Rhenium Molecular Prisms Peter H. Dinolfo,, Veaceslav Coropceanu,§ Jean-Luc Bre.2 Here, we report the MV properties of two supramolecular com- plexes: triangular prisms of the form by direct overlap of donor and acceptor orbitals.3 Surprisingly, the prisms display significant differences

159

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

NASA Astrophysics Data System (ADS)

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.

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

2006-04-01

160

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

PubMed

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 ?max 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

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

2013-11-01

161

Free Body Diagrams  

NSDL National Science Digital Library

This website from the University of Guelph's physics department offers a tutorial on free body diagrams. The tutorial includes an explanation of what free body diagrams are, example problems, a self-test, and a free body diagram java applet.

162

Photoelectron spectra and molecular orbital calculations of dicarbonyl- and dinitrosyl-bridged cobalt, rhodium and iridium cyclopentadienyl dimers and of disulfido- and diselenido-nonacarbonyltriosmium  

E-print Network

-nonacarbonyltriosmium. . (December l987) Greg Lewis Griewe, B. A. , Grinnell College Chairman of Advisory Committee: Dr. Michael B. Hall Gas-phase, ultraviolet photoelectron (PE) spectra and molecular orbital (MO) calculations are reported for Os3(CO)9(s3 X)2 (X=S, Se...). The spectra are similar to that reported for Fe3(CO)9(s3-S)2, but with increased band definition. The HOMO, a 3c-2e (Os-Os-Os) bond, is dominated by the e -like orbitals of the Os(CO)3 fragment and contains most of the net metal-metal overlap population...

Griewe, Greg Lewis

1987-01-01

163

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

PubMed

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

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

2015-03-28

164

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

165

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

NASA Astrophysics Data System (ADS)

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.

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

2015-03-01

166

A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations.  

PubMed

A binding mechanism between human matrix metalloproteinase-12 (MMP-12) and eight arylsulfone analogs having two types of carboxylic and hydroxamic acids as the most representative zinc binding group is investigated using a quantitative structure-activity relationship (QSAR) analysis based on a linear expression by representative energy terms (LERE). The LERE-QSAR analysis quantitatively reveals that the variation in the observed (experimental) inhibitory potency among the arylsulfone analogs is decisively governed by those in the intrinsic binding and dispersion interaction energies. The results show that the LERE-QSAR analysis not only can excellently reproduce the observed overall free-energy change but also can determine the contributions of representative free-energy changes. An inter-fragment interaction energy difference (IFIED) analysis based on the fragment molecular orbital (FMO) method (FMO-IFIED) leads to the identification of key residues governing the variation in the inhibitory potency as well as to the understanding of the difference between the interactions of the carboxylic and hydroxamic acid zinc binding groups. The current results that have led to the optimization of the inhibitory potency of arylsulfone analogs toward MMP-12 to be used in the treatment of chronic obstructive pulmonary disease may be useful for the development of a new potent MMP-12 inhibitor. PMID:25406681

Hitaoka, Seiji; Chuman, Hiroshi; Yoshizawa, Kazunari

2015-01-21

167

Exciton analysis of many-body wave functions: Bridging the gap between the quasiparticle and molecular orbital pictures  

NASA Astrophysics Data System (ADS)

Exciton sizes and electron-hole binding energies, which are central properties of excited states in extended systems and crucial to the design of modern electronic devices, are readily defined within a quasiparticle framework but are quite challenging to understand in the molecular-orbital picture. The intent of this work is to bridge this gap by providing a general way of extracting the exciton wave function out of a many-body wave function obtained by a quantum chemical excited-state computation. This methodology, which is based on the one-particle transition density matrix, is implemented within the ab initio algebraic diagrammatic construction scheme for the polarization propagator and specifically the evaluation of exciton sizes, i.e., dynamic charge separation distances, is considered. A number of examples are presented. For stacked dimers it is shown that the exciton size for charge separated states corresponds to the intermolecular separation, while it only depends on the monomer size for locally excited states or Frenkel excitons. In the case of conjugated organic polymers, the tool is applied to analyze exciton structure and dynamic charge separation. Furthermore, it is discussed how the methodology may be used for the construction of a charge-transfer diagnostic for time-dependent density-functional theory.

Bäppler, Stefanie A.; Plasser, Felix; Wormit, Michael; Dreuw, Andreas

2014-11-01

168

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)

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 ?-? activity diagrams.

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

169

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)

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.

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

2015-02-01

170

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

PubMed

The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists C-H?O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites. PMID:25228040

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

2015-02-25

171

A molecular orbital study of the changing role of d -orbitals in transition metal compounds: ZnS, FeS and CrS  

Microsoft Academic Search

SCF-MO studies as FeS, CrS and ZnS illustrate the changing role ofd-orbitals along a transition series, where they become at first good acceptors playing an important role in the bonding, then\\u000a so stable that their electrons behave essentially as “core” electrons in agreement with the conjecture of Phillips and Williams\\u000a [1].

Alan Hinchliffe; J. Charles Dobson

1975-01-01

172

Analysis of effects of macroscopic propagation and multiple molecular orbitals on the minimum in high-order harmonic generation of aligned CO{sub 2}  

SciTech Connect

We report theoretical calculations of the effect of the multiple-orbital contribution in high-order harmonic generation (HHG) of aligned CO{sub 2} with the inclusion of macroscopic propagation of harmonic fields in the medium. Our results show very good agreement with recent experiments for the dynamics of the minimum in HHG spectra as laser intensity or alignment angle changes. Calculations are carried out to check how the position of the minimum in HHG spectra depends on the degrees of molecular alignment, laser-focusing conditions, and the effects of alignment-dependent ionization rates of the different molecular orbitals. These analyses help to explain why the minima observed in different experiments may vary.

Jin, Cheng; Le, Anh-Thu; Lin, C. D. [J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506-2604 (United States)

2011-05-15

173

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)

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.

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

1988-01-01

174

Ab initio molecular orbital study on three feasible mechanisms for substitution of the vinylic carbon in F 2C=C(OMs)BMe 3?  

Microsoft Academic Search

A substitution on 2,2-difluorovinylic carbon was investigated by using ab initio molecular orbital calculations. Three feasible mechanisms, which are the SN1-like, the SN2-type and the addition-elimination mechanisms, were ex- amined for a model borate, 2,2-difluoro-1-mesyloxyvinyl(trimethyl)borate. Four TSs were obtained depending on the position of Li+ around the vinylborate although activation energies in the gas phase are rather high (ca. 30–40

Kenzi Hori; Shohei Fukuda; Junji Ichikawa

1999-01-01

175

Gravity and Orbits: Orbits  

NSDL National Science Digital Library

This Science Object is the third of three Science Objects in the Gravity and Orbits SciPack. It provides an understanding of how gravitational forces influence the motion of an object in orbit. When a force acts toward a single center, an object's forward motion and its motion toward that center can combine to create a curved path around the center. Gravity governs the motion of all objects in the solar system. The Sun's gravitational pull holds the Earth and other planets in their orbits, just as the planets' gravitational pull keeps their moons in orbit around them. Learning Outcomes:? Describe the conditions that would lead an object into orbital motion in terms of the effects of gravitational force.? Explain how an object orbits a planet in terms of trajectories and free fall.? Identify gravity as the force that keeps the planets in their orbits around the Sun and the moons in their orbits around the planets.

National Science Teachers Association (NSTA)

2006-11-01

176

HD isotope effect of methyl internal rotation for acetaldehyde in ground state as calculated from a multicomponent molecular orbital method.  

PubMed

We have analyzed the differences in the methyl internal rotation induced by the HD isotope effect for acetaldehyde (CH(3)CHO) and deuterated acetaldehyde (CD(3)CDO) in ground state by means of the multicomponent molecular orbital (MC_MO) method, which directly accounts for the quantum effects of protons and deuterons. The rotational constant of CH(3)CHO was in reasonable agreement with experimental one due to the adequate treatment of the protonic quantum effect by the MC_MO method. The C-D bond distances were about 0.007 A shorter than the C-H distances because of the effect of anharmonicity of the potential. The Mulliken population for CD(3) in CD(3)CDO is larger than that for CH(3) in CH(3)CHO because the distribution of wavefunctions for the deuterons was more localized than that for the protons. The barrier height obtained by the MC_MO method for CH(3)CHO was estimated as 401.4 cm(-1), which was in excellent agreement with the experimentally determined barrier height. We predicted the barrier height of CD(3)CDO as 392.5 cm(-1). We suggest that the internal rotation of the CD(3) group was more facile than that of the CH(3) group because the C-D bond distance was observed to be shorter than the C-H distance. Additionally the localized electrons surrounding the CD(3) group in CD(3)CDO caused the extent of hyperconjugation between the CD(3) and CDO groups to be smaller than that in the case of CH(3)CHO, which may have also contributed to the observed differences in methyl internal rotation. The differences in bond distances and electronic populations induced by the H/D isotope effect were controlled by the difference in the distribution of wavefunctions between the protons and deuterons. PMID:18532814

Ishimoto, Takayoshi; Ishihara, Yasuyuki; Teramae, Hiroyuki; Baba, Masaaki; Nagashima, Umpei

2008-05-14

177

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

SciTech Connect

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.

Moreira, Rodrigo A.; Melo, Celso P. de, E-mail: celso@df.ufpe.br [Departamento de Física, Universidade Federal de Pernambuco, Recife-PE 50670-901 (Brazil)

2014-09-28

178

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

PubMed

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. PMID:25273466

Moreira, Rodrigo A; de Melo, Celso P

2014-09-28

179

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

NASA Astrophysics Data System (ADS)

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.

Zhu, Xiaolei; Zeng, X. C.

2003-02-01

180

Aesthetics of Class Diagrams  

Microsoft Academic Search

Visualization of object-oriented programs by class dia- grams is a widely used technique. So far no commonly agreed aesthetic criteria have been recorded in order to standardize and measure the quality of class diagrams. In this paper we focus on UML class diagrams, the standard notation for class diagrams in software engineering. We propose some aesthetic criteria which reflect the

Holger Eichelberger

2002-01-01

181

AFM Diagram Quiz  

NSDL National Science Digital Library

This exercise should be used after you think students know what AFM diagrams are and how they work. This is sort of a quiz - to see if they can properly interpret the diagrams. There is no point moving on to real projects that involve AFM diagrams if the students don't understand the basics.

Dexter Perkins

182

Tree Diagrams and Probability  

NSDL National Science Digital Library

This lesson is designed to develop students' ability to create tree diagrams and figure probabilities of events based on those diagrams. This lesson provides links to discussions and activities related to tree diagrams as well as suggested ways to work them into the lesson. Finally, the lesson provides links to follow-up lessons designed for use in succession with the current one.

2011-01-20

183

From experiment to theory: molecular orbital parameters to interpret the skin sensitization potential of 5-chloro-2-methylisothiazol-3-one and 2-methylisothiazol-3-one.  

PubMed

5-Chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI) are the major constituents of the commercial biocide Kathon CG. These two compounds have both been shown to exhibit skin sensitization potential: MCI is classified as an extreme sensitizer while MI is classified as a moderate sensitizer. The purpose of the present investigation was to provide further insights into the chemistry underlying their skin sensitizing properties. First, a molecular modeling (in silico) study was carried out of the initial reaction pathways of MI and MCI with nucleophiles representative of those involved in the skin sensitization process, and we compared the findings with the reported chemical and allergenic properties of these compounds. These reaction pathways were assessed using molecular orbital calculations. A novel parameter, the activation energy (AE) index, is proposed and is calculated from a knowledge of the energy changes in the frontier molecular orbitals as the electrophile is converted to an anionic intermediate. The AE indices correspond to the reactivity of MCI and MI with nucleophiles and also their skin sensitization potential. Second, the previously unexplained formation of final reaction products from MCI and butylamine is discussed and a reaction mechanism is proposed. A key finding of this analysis is that the reaction produces "positive chlorine" in the form of N-chloro- and/or N,N-dichloro-butylamine, which could contribute to the skin sensitizing properties of MCI. PMID:15720139

Aptula, Aynur O; Roberts, David W; Cronin, Mark T D

2005-02-01

184

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)

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.

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

2015-01-01

185

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.

186

A Diagramming Software for UML Class Diagrams  

Microsoft Academic Search

\\u000a UML diagrams have become increasingly important in the engineering and reengineering processes for software systems. Of particular\\u000a interest are UML class diagrams whose purpose is to display class hierarchies (generalizations), associations, aggregations,\\u000a and compositions in one picture. The combination of hierarchical and non-hierarchical relations poses a special challenge\\u000a to a graph layout tool.

Carsten Gutwengerl; Michael Jünger; Karsten Kleinl; Joachim Kupkel; Sebastian Leipert; Petra Mutzel

187

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

188

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

SciTech Connect

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

Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan) [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Fedorov, Dmitri G. [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan)] [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Yokojima, Satoshi [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan) [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachioji-shi, Tokyo 192-0392 (Japan); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan)] [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Sakurai, Minoru [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan)] [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)] [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

2014-04-14

189

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

NASA Astrophysics Data System (ADS)

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.

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

2013-07-01

190

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

SciTech Connect

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.

Burakovsky, Leonid [Los Alamos National Laboratory; Kress, Joel D. [Los Alamos National Laboratory; Collins, Lee A. [Los Alamos National Laboratory

2012-05-31

191

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

PubMed

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 (?0), related properties (?, ?0 and ??) 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 ?* and ?* 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

Prabavathi, N; Nilufer, A; Krishnakumar, V

2013-10-01

192

Induced spin filtering in electron transmission through chiral molecular layers adsorbed on metals with strong spin-orbit coupling  

NASA Astrophysics Data System (ADS)

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

Gersten, Joel; Kaasbjerg, Kristen; Nitzan, Abraham

2013-09-01

193

Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; part II: influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions.  

PubMed

The ab initio fragment molecular orbital (FMO) calculations were performed for retinoid X receptor (RXR) complexes with its ligand 9-cis retinoic acid (9cRA) and steroid receptor coactivator-1 (SRC1) to examine the influence of mutations in transcriptional activation function 2 activating domain core (AF2C) of RXR on molecular interactions between 9cRA liganded RXR and SRC1 coactivator. The RXR-SRC1 interactions in three types of RXR-9cRA-SRC1 complexes, namely, a wild type (WT), a mutant whose Glu453 of AF2C was substituted by Lys (E453K), and another mutant whose Glu456 of AF2C was substituted by Lys (E456K), were compared. Through the comparison of WT, E453K, and E456K, possible causes for a marked decrease in the transcriptional activity of RXR by the mutation of Glu453, which is known as a highly conserved charged residue of AF2C, were discussed. It was quantitatively demonstrated that the strength of the RXR-SRC1 interaction correlates with the degree of the transcriptional activation (WT > E456K > E453K). In E453K, the RXR-SRC1 interaction was substantially reduced by the AF2C-SRC1 repulsive interaction, and the charge transfer (CT) from RXR to SRC1 was also inhibited by the decreased electron donation from AF2C to SRC1. Our findings suggest that the inhibitions of the local RXR-SRC1 interaction via AF2C and of the local CT from RXR to SRC1 via AF2C would be the possible causes for the marked decrease in the transcriptional activity of RXR. PMID:18020317

Ito, Mika; Fukuzawa, Kaori; Mochizuki, Yuji; Nakano, Tatsuya; Tanaka, Shigenori

2008-03-13

194

1,1,2,2-tetrachlorodisilane (Cl 2HSi-SiHCl 2): molecular structure, conformation and torsional potential as determined by gas-phase electron diffraction, vibrational spectroscopic data and ab initio molecular orbital calculations  

NASA Astrophysics Data System (ADS)

The molecular structure, conformational composition and torsional potential of 1,1,2,2-tetrachlorodisilane (TCDS), Cl 2HSi-SiHCl 2, were studied using gas phase electron diffraction (GED) data at 23°C, together with earlier recorded spectroscopic data and normal coordinate- and ab initio molecular orbital calculations. The title compound exists in the gas phase at room temperature as a mixture of two conformers, anti, with a torsion angle ?(HSiSiH)=180°, and gauche, with a torsion angle ?(HSiSiH)?60°. The gauche conformer predominates, occupying approximately 80% of the gas composition at 23°C. Some structural parameter values obtained from the GED refinements, using results from the earlier spectroscopic work and ab initio molecular orbital calculations as constraints, are as follows ( gauche conformer with estimated 2 ? uncertainties): bond lengths ( rg): r(Si-Si)=2.310(8) Å, r<(Si-Cl)>=2.039(2) Å (average value), r(Si-H)=1.511 Å (assumed value). Bond angles (? ?): ?=108.9(4)° (average value), ?ClSiCl=109.7(3)°, ?SiSiH=111.5° (assumed value).

Johansen, Tore H.; Hagen, Kolbjørn; Stølevik, Reidar

1999-08-01

195

Venn Diagram Shape Sorter  

NSDL National Science Digital Library

In this activity, students practice placing big and small shapes into Venn diagrams depending on the rules of the diagram. Students can either specify these rules or have the applet assign the rules so they can try to figure them out by placing shapes in the diagram. This activity allows students to explore Venn diagrams and the terms associated with set theory. This activity includes supplemental materials, including background information about the topics covered, a description of how to use the application, and exploration questions for use with the java applet.

2010-01-01

196

Molecular identification of Rhizomucor pusillus as a cause of sinus-orbital zygomycosis in a patient with acute myelogenous leukemia.  

PubMed

Sinus-orbital zygomycosis caused by Rhizomucor pusillus in a patient with acute myelogenous leukemia is described. Identification was achieved by sequencing of the internal transcribed spacer (ITS) regions of the rRNA gene and by expression of zygospores in mating. This report highlights the value of ITS sequencing as a diagnostic tool for the identification of R. pusillus and expands the understanding of infection types caused by this zygomycete. PMID:16272531

Iwen, Peter C; Freifeld, Alison G; Sigler, Lynne; Tarantolo, Stefano R

2005-11-01

197

Molecular Identification of Rhizomucor pusillus as a Cause of Sinus-Orbital Zygomycosis in a Patient with Acute Myelogenous Leukemia  

PubMed Central

Sinus-orbital zygomycosis caused by Rhizomucor pusillus in a patient with acute myelogenous leukemia is described. Identification was achieved by sequencing of the internal transcribed spacer (ITS) regions of the rRNA gene and by expression of zygospores in mating. This report highlights the value of ITS sequencing as a diagnostic tool for the identification of R. pusillus and expands the understanding of infection types caused by this zygomycete. PMID:16272531

Iwen, Peter C.; Freifeld, Alison G.; Sigler, Lynne; Tarantolo, Stefano R.

2005-01-01

198

Natural bond orbital analysis of molecular interactions Theoretical studies of binary complexes of HF, H2O, NH3, O2, F2, CO, and CO2 with HF, H2O, and NH3  

Microsoft Academic Search

Ab initio molecular orbital theory and natural bond orbital analysis were applied to the binary complexes of HF, H2O, NH3, N2, O2, F2, CO and CO2 with HF, H2O and NH3. Both hydrogen-bonded and nonhydrogen-bonded structures were found for complexes involving N2, O2, F2, CO, and CO2; these structures were defined by NBO analysis of charge transfer, which is generally

A. E. Reed; F. Weinhold; L. A. Curtiss; D. J. Pochatko

1986-01-01

199

Natural bond orbital analysis of molecular interactions: Theoretical studies of binary complexes of HF, H2O, NH3, N2, O2, F2, CO, and CO2 with HF, H2O, and NH3  

Microsoft Academic Search

The binary complexes of HF, H2O, NH3, N2, O2, F2, CO, and CO2 with HF, H2O, and NH3 have been studied by abinitio molecular orbital theory and natural bond orbital (NBO) analysis. Most of the complexes involving N2, O2, F2, CO, and CO2 are found to have both hydrogen-bonded and non-hydrogen-bonded structures. The NBO analysis provides a consistent picture of

Alan E. Reed; Frank Weinhold; Larry A. Curtiss; David J. Pochatko

1986-01-01

200

PHASE DIAGRAMS Phase Rule  

E-print Network

diagram demarcates regions of existence of various phases. This is similar to a map which demarcates regions based on political, geographical, ecological etc. criteria. Phase diagrams are maps* Thorough) are extensively used in materials science and will be considered in detail in this chapter. Also, we shall

Subramaniam, Anandh

201

Xilinx State Diagram  

E-print Network

Xilinx State Diagram Tutorial Department of Electrical and Computer Engineering State University of New York ­ New Paltz © Fall 2006 Baback Izadi #12;Start a new Project Next. #12;This opens the New Project Dialog box. Click on New Source. Select State Diagram and give

Izadi, Baback

202

Orbital pseudotumor  

MedlinePLUS

Orbital pseudotumor is a swelling of the tissues behind the eye in an area called the orbit. The ... and tissue that surround it. Unlike cancerous tumors, orbital pseudotumor does not spread to other tissues or places ...

203

Molecular orbital (SCF-X??-SW) theory of Fe2+-Mn3+, Fe 3+-Mn 2+, and Fe3+-Mn3+ charge transfer and magnetic exchange in oxides and silicates  

USGS Publications Warehouse

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. -from Author

Sherman, D.M.

1990-01-01

204

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

NASA Technical Reports Server (NTRS)

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.

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

1989-01-01

205

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

SciTech Connect

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.

Jaume, J.C.; Portolano, S.; Prummel, M.F.; McLachlan, S.M.; Rapoport, B. [Univ. of California, San Francisco, CA (United States)] [Univ. of California, San Francisco, CA (United States)

1994-02-01

206

Interactions of Metal Ions with Water: Ab Initio Molecular Orbital Studies of Structure, Bonding Enthalpies, Vibrational Frequencies and Charge Distributions. 1. Monohydrates.  

PubMed

The formation and properties of a wide range of metal ion monohydrates, M(n)()(+)-OH(2), where n = 1 and 2, have been studied by ab initio molecular orbital calculations at the MP2(FULL)/6-311++G//MP2(FULL)/6-311++G and CCSD(T)(FULL)/6-311++G//MP2(FULL)/6-311++G computational levels. The ions M are from groups 1A, 2A, 3A, and 4A in the second, third, and fourth periods of the periodic table and the first transition series. Structural parameters, vibrational frequencies, bonding enthalpies, orbital occupancies and energies, and atomic charge distributions are reported. Trends in these properties are correlated with the progressive occupancy of the s, p, and d orbitals. Except for K(+)-OH(2) and Ca(2+)-OH(2), the O-H bond lengths and HOH angles are greater in the hydrates than in unbound water. The M-O bond lengths decrease proceeding from group 1A --> 4A but become larger in proceeding from the second --> fourth period. The bonding enthalpies, are found to be inversely linearly dependent on the M-O bond length M(n)()(+) according to equations of the form = A + B(1/M-O) for n = 1 and n = 2. Within each monohydrate the distribution of atomic charge reveals a small but definite transfer of charge from water to the metal ion. Compared to unbound water there is, in a metal-ion-bound water complex, an increase in the electronic (negative) charge on the oxygen atom, accompanied by a (significantly) larger decrease in the electronic charge on the hydrogen atoms. The bonding of the water molecule, although electrostatic in origin, is thus more complex than a simple interaction between a point charge on the metal ion, and the water dipole. PMID:11670579

Trachtman, Mendel; Markham, George D.; Glusker, Jenny P.; George, Philip; Bock, Charles W.

1998-08-24

207

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)

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.

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

2007-09-01

208

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

PubMed

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

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

2010-11-01

209

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

NASA Astrophysics Data System (ADS)

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

Porchelvi, E. Elamurugu; Muthu, S.

2015-01-01

210

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)

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 ?* and ?* 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.

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

2013-01-01

211

Huckel Molecular Orbital Theory for Buckminsterfullerene 1. Number the carbons after inspection of the molecular structure and fill in data needed below.  

E-print Network

that C60 has a high electron affinity and forms ionic compounds with alkali metals such as potassium of the molecular structure and fill in data needed below. Natoms 60 The number of carbon atoms and -electrons. Nocc structure. The LUMO is three-fold degenerate and not far away in energy. This is consistent with the fact

Rioux, Frank

212

The geometry of polynomial diagrams  

E-print Network

In this paper we introduce the concept of polynomial diagrams and its area for special polynomials.We study the properties of polynomial area diagrams. The formula for the area of an arbitrary polynomial diagram.

Maksim Alennikov

2015-02-18

213

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

SciTech Connect

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

Kobayashi, Masato, E-mail: kobayashi@suou.waseda.jp [Waseda Institute for Advanced Study, Waseda University, Tokyo 169-8050 (Japan)] [Waseda Institute for Advanced Study, Waseda University, Tokyo 169-8050 (Japan)

2014-02-28

214

Molecular Orbital Imaging of the Acetone S2 Excited State Using Time-Resolved (e , 2 e ) Electron Momentum Spectroscopy  

NASA Astrophysics Data System (ADS)

We report a time-resolved (e , 2 e ) experiment on the deuterated acetone molecule in the S2 Rydberg state with a lifetime of 13.5 ps. The acetone S2 state was prepared by a 195 nm pump laser and probed with electron momentum spectroscopy using a 1.2 keV incident electron beam of 1 ps temporal width. In spite of the low data statistics as well as of the limited time resolution (±35 ps ) due to velocity mismatch, the experimental results clearly demonstrate that electron momentum spectroscopy measurements of short-lived transient species are feasible, opening the door to time-resolved orbital imaging in momentum space.

Yamazaki, Masakazu; Oishi, Keiya; Nakazawa, Hiroyuki; Zhu, Chaoyuan; Takahashi, Masahiko

2015-03-01

215

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

NASA Technical Reports Server (NTRS)

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.

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

2008-01-01

216

Diagram of Computer Keyboard  

NSDL National Science Digital Library

This is a line drawing of a Windows PC keyboard complete with labels for each key. This diagram is used on tests where students are asked to circle the keys that would be used to perform various functions.

Dr. Charles Ward

217

Satellite Venn Diagram  

NSDL National Science Digital Library

In this activity, students will use the background information they have read to organize a list of sources and objects, putting each item given in the appropriate part of the Venn diagram, depending on which instrument will study that item. Students will demonstrate their understanding of spectra, astronomical observations, and have read the background material on Chandra, Astro-E and the microcalorimeter, and the Constellation X-ray Observatory. They will write a five minute summary of the capabilities of the three observatories, based on their Venn diagram. Students' understanding of the background material will be evaluated based on the accuracy of their Venn diagrams and the interpretation of the information on the Venn diagrams from their closure paper.

218

Phase Diagrams in Vivo  

NSDL National Science Digital Library

This activity uses three experiments for students to construct a phase diagram; the experiments have been videotaped and can be seen online. The purpose of this laboratory as designed is to gain familiarity with simple phase diagrams, their construction, and their applications to the understanding of geological and environmental problems. Subsidiary objectives include development of strategies for data processing including evaluation of assumptions and sources of errors, as well as honing of computer, spreadsheet, presentation (tabular and graphical), and report writing skills.

219

Weyl Card Diagrams  

E-print Network

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 non-trivial 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. This paper is a condensed and simplified presentation of the card diagrams in hep-th/0409070.

Gregory C. Jones; John E. Wang

2005-06-02

220

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

PubMed

The FT-IR and FT-Raman spectra of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene (musk ambrette) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The total energy calculations of musk ambrette were tried for the possible conformers. The molecular structure, geometry optimization, vibrational frequencies were obtained by the density functional theory (DFT) using B3LYP and LSDA method with 6-311G(d,p) basis set for the most stable conformer "C1". The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated and the scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugate interactions and the charge delocalization has been analyzed using bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The dipole moment (?), polarizability (?), anisotropy polarizability (??) and first hyperpolarizability (?tot) of the molecule have been reported. The thermodynamic functions (heat capacity, entropy and enthalpy) were obtained for the range of temperature 100-1000 K. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP). PMID:24508884

Saravanan, S; Balachandran, V; Vishwanathan, K

2014-04-24

221

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

NASA Astrophysics Data System (ADS)

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 (?) of asymmetric ?-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 ?(t) and system polarization p(t) are calculated by the QME approach. Dynamic ? in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(?). Spatial contributions of electrons to ? are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2?. We apply the present method to the calculation of the dynamic ? 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.

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

2015-01-01

222

Diffusion-controlled detection of trinitrotoluene: interior nanoporous structure and low highest occupied molecular orbital level of building blocks enhance selectivity and sensitivity.  

PubMed

Development of simple, cost-effective, and sensitive fluorescence-based sensors for explosives implies broad applications in homeland security, military operations, and environmental and industrial safety control. However, the reported fluorescence sensory materials (e.g., polymers) usually respond to a class of analytes (e.g., nitroaromatics), rather than a single specific target. Hence, the selective detection of trace amounts of trinitrotoluene (TNT) still remains a big challenge for fluorescence-based sensors. Here we report the selective detection of TNT vapor using the nanoporous fibers fabricated by self-assembly of carbazole-based macrocyclic molecules. The nanoporosity allows for time-dependent diffusion of TNT molecules inside the material, resulting in further fluorescence quenching of the material after removal from the TNT vapor source. Under the same testing conditions, other common nitroaromatic explosives and oxidizing reagents did not demonstrate this postexposure fluorescence quenching; rather, a recovery of fluorescence was observed. The postexposure fluorescence quenching as well as the sensitivity is further enhanced by lowering the highest occupied molecular orbital (HOMO) level of the nanofiber building blocks. This in turn reduces the affinity for oxygen, thus allocating more interaction sites for TNT. Our results present a simple and novel way to achieve detection selectivity for TNT by creating nanoporosity and tuning molecular electronic structure, which when combined may be applied to other fluorescence sensor materials for selective detection of vapor analytes. PMID:22339204

Che, Yanke; Gross, Dustin E; Huang, Helin; Yang, Dongjiang; Yang, Xiaomei; Discekici, Emre; Xue, Zheng; Zhao, Huijun; Moore, Jeffrey S; Zang, Ling

2012-03-14

223

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

PubMed

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

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

2015-05-01

224

The electronic structure of arene tricarbonyl complexes of group 6 metals: ultraviolet photoelectron spectra and molecular orbital calculations, and the low-temperature X-ray crystal structure of hexamethylbenzene chromium tricarbonyl  

E-print Network

diagram for (Hmb)Mo(CO)s. 23 Table IV. Orbital energies and percent character of the valence orbitals of M(CO)s fragments. a) Cr(CO)s Metal Carbonyl Orb Eng d s 2 3 e -0 95 2 e -6 73 25. 21 2a1 -6 86 le -14 00 4 62 lar -15. 92 18. 75 18. 75 25.... 21 8. 20 8. 20 62. 40 4. 62 9. 67 9. 67 6. 22 p 4 o 17. 69 5. 02 36. 88 31. 38 34. 77 5. 82 2. 72 63. 05 7. 98 82, 03 b) Mo(CO)s 3 e -0. 74 -- -- 13. 88 13 88 2 e -7. 60 23. 96 23. 96 8. 90 8. 90 2a& -7. 68 -- -- -- -- 62. 84 le -15, 06 4...

Byers, Brien Patrick

1986-01-01

225

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)

From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (? = 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.

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

226

Reconstruction of frozen-core all-electron orbitals from pseudo-orbitals  

Microsoft Academic Search

We investigate the numerical feasibility of reconstructing frozen-core all-electron molecular orbitals from corresponding pseudo-orbitals. We perform density-functional calculations on simple atomic and molecular model systems using ultrasoft pseudopotentials to represent the atomic cores. We apply a transformation due to Blo¨chl [Phys. Rev. B 50, 17953 (1994)] to each calculated pseudo-orbital to obtain a corresponding frozen-core all-electron molecular orbital. Our model

Bala´zs Hete´nyi; Filippo De Angelis; Paolo Giannozzi; Roberto Car

2001-01-01

227

Reconstruction of frozen-core all-electron orbitals from pseudo-orbitals  

Microsoft Academic Search

We investigate the numerical feasibility of reconstructing frozen-core all-electron molecular orbitals from corresponding pseudo-orbitals. We perform density-functional calculations on simple atomic and molecular model systems using ultrasoft pseudopotentials to represent the atomic cores. We apply a transformation due to Blöchl [Phys. Rev. B 50, 17953 (1994)] to each calculated pseudo-orbital to obtain a corresponding frozen-core all-electron molecular orbital. Our model

Balázs Hetényi; Filippo de Angelis; Paolo Giannozzi; Roberto Car

2001-01-01

228

On-orbit flight control algorithm description  

NASA Technical Reports Server (NTRS)

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.

1975-01-01

229

The Orbital Acceleration Research Experiment  

NASA Technical Reports Server (NTRS)

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

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

1986-01-01

230

Weyl card diagrams  

SciTech Connect

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.

Jones, Gregory [Department of Physics, Harvard University, Cambridge, Massachusetts 02138 (United States); Wang, John E. [Department of Physics, Harvard University, Cambridge, Massachusetts 02138 (United States); Department of Physics, National Taiwan University, Taipei 106, Taiwan (China); National Center for Theoretical Sciences, Taiwan, National Taiwan University, Taipei 10617, Taiwan (China)

2005-06-15

231

Computational study and molecular orbital analysis of NMR shielding, spin-spin coupling, and electric field gradients of azido platinum complexes.  

PubMed

(195)Pt, (14)N, and (15)N NMR data for five azido (N(3)(-)) complexes are studied using relativistic density functional theory (DFT). Good agreement with experiment is obtained for Pt and N chemical shifts as well as Pt-N J-coupling constants. Calculated (14)N electric field gradients (EFGs) reflect experimentally observed trends for the line broadening of azido (14)N NMR signals. A localized molecular orbital analysis of the nitrogen EFGs and chemical shifts is performed to explain some interesting trends seen experimentally and in the first-principles calculations: (i) (14)N NMR signals for the Pt-coordinating (N(?)) nuclei in the azido ligands are much broader than for the central (N(?)) or terminal (N(?)) atoms. The N(?) signals are particularly narrow; (ii) compared to N(?), the N(?) nuclei are particularly strongly shielded; (iii) N(?) nuclei have much larger chemical shifts than N(?) and N(?) ; and (iv) The Pt-N(?) J-coupling constants are small in magnitude when considering the formal sp hybridization of N(?). It is found that for N(?) a significant shielding reduction due to formation of the dative N(?)-Pt bond is counterbalanced by an increased shielding from spin-orbit (SO) coupling originating at Pt. Upon coordination, the strongly delocalized ? system of free azide localizes somewhat on N(?) and N(?). This effect, along with rehybridization at N(?) upon bond formation with Pt, is shown to cause a deshielding of N(?) relative to N(?) and a strong increase of the EFG at N(?). The large 2p character of the azide ? bonds is responsible for the particularly high N(?) chemical shifts. The nitrogen s-character of the Pt-N(?) bond is low, which is the reason for the small J-coupling. Similar bonding situations are likely to be found in azide complexes with other transition metals. PMID:22794134

Sutter, Kiplangat; Autschbach, Jochen

2012-08-15

232

Orbital Decompression  

MedlinePLUS

INTRODUCTION Orbital decompression is a surgical procedure which has been in existence for well over 100 years to treat a variety ... optic nerve) and fat). The goal of orbital decompression is to remove some of the bony walls ...

233

Scrutinizing UML Activity Diagrams  

NASA Astrophysics Data System (ADS)

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

Al-Fedaghi, Sabah

234

Diblock copolymer phase diagram  

NSDL National Science Digital Library

Adaptation of the Matsen and Bates BCP phase diagram predicted using Mean-field Theory. * Matsen MW, Bates FS, ''http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ma951138i Unifying weak- and strong-segregation block copolymer theories. Diblock copolymer phase diagram as calculated using Mean-field Theory by Matsen and Bates, where fA is the Block fraction, ? is the Flory-Huggins Chi Parameter, and N is the length of the block.

Iacovella, Christopher R.

2006-11-20

235

Orbits in the H2O molecule  

E-print Network

We study the forms of the orbits in a symmetric configuration of a realistic model of the H2O molecule with particular emphasis on the periodic orbits. We use an appropriate Poincar\\'e surface of section (PSS) and study the distribution of the orbits on this PSS for various energies. We find both ordered and chaotic orbits. The proportion of ordered orbits is almost 100% for small energies, but decreases abruptly beyond a critical energy. When the energy exceeds the escape energy there are still non-escaping orbits around stable periodic orbits. We study in detail the forms of the various periodic orbits, and their connections, by providing appropriate stability and bifurcation diagrams.

K. Efstathiou; G. Contopoulos

2001-02-07

236

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

NASA Astrophysics Data System (ADS)

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, ?E?, ?H?, ?S? and ?G? 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.

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

2015-03-01

237

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

PubMed

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, ?E(?), ?H(?), ?S(?) and ?G(?) 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

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

2015-03-01

238

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)

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 (?) and the first order hyper polarizability (?) 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.

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

2014-11-01

239

Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid.  

PubMed

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 (?) and the first order hyper polarizability (?) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. PMID:24858354

Suresh, S; Gunasekaran, S; Srinivasan, S

2014-11-11

240

Carbon Cycle Diagram  

NSDL National Science Digital Library

This diagram illustrates some of the most abundant stores of carbon and identifies some of the pathways in the carbon cycle along which carbon is transferred from one form to another. Long-term sinks of carbon are labelled in black; shorter-term fluxes are labelled in purple. Amounts are in billions of tons.

241

Venn Diagrams and Logic  

NSDL National Science Digital Library

This math lesson from Illuminations uses Venn diagrams to illustrate direct, indirect and transitive reasoning. Students will learn the definitions of direct, indirect and transitive reasoning and give examples of each. Several student activity sheets are included. The material is intended for grades 9-12 and should require 2 and a half class periods to complete.

2011-01-04

242

Plagioclase Phase Diagram  

NSDL National Science Digital Library

This is a short exercise aimed at evaluating whether students understand how to interpret the Ab-An phase diagram. If students know what is going on, it takes about 10 minutes to complete. This active learning exercise makes a good break from lecture. It is best done as a group activity.

Dexter Perkins

243

Understanding Network Diagrams.  

ERIC Educational Resources Information Center

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

Waller, Robert

244

Impulse-Momentum Diagrams  

ERIC Educational Resources Information Center

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…

Rosengrant, David

2011-01-01

245

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

NASA Astrophysics Data System (ADS)

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

Govindasamy, P.; Gunasekaran, S.

2015-02-01

246

Bound states of positron with simple carbonyl and aldehyde species with configuration interaction multi-component molecular orbital and local vibrational approaches  

NASA Astrophysics Data System (ADS)

Characteristic features of the positron-binding structure of some carbonyl and aldehyde species such as formaldehyde, acetaldehyde, acetone and propionaldehyde are discussed with the configuration interaction scheme of multi-component molecular orbital (MC_MO) calculations. This method can take the electron-positron correlation contribution into account through single electronic-single positronic excitation configurations. Our vertical positron affinity (PA) values of acetaldehyde and acetone with electronic 6-31 + +G(2df,2pd) and positronic [15s15p3d2f1g] basis sets are as 52 and 92 meV, which can be compared to the recent experimental values of 90 and 173 meV by Danielson et al (2010 Phys. Rev. Lett. 104 233201). For formaldehyde we have also found that the PA values are enhanced by including the local C= \\!\\! =O vibrational contribution from the vertical PA value of 15 meV to 17, 21 and 25 meV after averaging over the zeroth, first and second vibrational states, respectively, due to the anharmonicity of the potential.

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

2012-03-01

247

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

PubMed

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 A? for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed. PMID:22667545

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

2012-05-28

248

Q-Band single-crystal EPR study and molecular orbital calculations of [(C 6H 5) 4As][Re VINCl 4/Re VOCl 4  

NASA Astrophysics Data System (ADS)

A Q-band single-crystal EPR study of tetraphenylarsoniumtetrachloro-nitridorhenate(VI), [(C 6H 5) 4As][Re VINCl 4], diamagnetically diluted by the isoelectronic oxorhenate(V) complex is reported. The EPR spectra are typical of an ion with 5d 1 ( S=1/2) configuration and are influenced by large rhenium hyperfine coupling constants and nuclear quadrupole interactions. They are characterized by well-resolved 185,187Re hyperfine patterns with almost equal spacings and the occurrence of "forbidden" transitions ( ?mI=±1, ?mI=±2). The 185,187Re hyperfine parameters as well as the data obtained from density functional theory (DFT) and the extended Hückel theory (EHT) molecular orbital calculations are used to analyze the spin density distribution in the system under study. Thereby, the negative sign found for the spin density at the nitrogen from DFT is mainly determined by spin polarization. In addition, both MO methods are used to calculate the electric field gradient being responsible for the 185,187Re nuclear quadrupole coupling.

Voigt, A.; Abram, U.; Böttcher, R.; Richter, U.; Reinhold, J.; Kirmse, R.

2000-03-01

249

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)

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.

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

2015-01-01

250

Interactions of metal ions with water: ab initio molecular orbital studies of structure, vibrational frequencies, charge distributions, bonding enthalpies, and deprotonation enthalpies. 2. Monohydroxides.  

PubMed

The formation and properties of a wide range of metal ion monohydroxides, M(n)(+)[OH(-)], where n = 1 and 2, have been studied by ab initio molecular orbital calculations at the MP2(FULL)/6-311++G**//MP2(FULL)/6-311++G** and CCSD(T)(FULL)/6-311++G**//MP2(FULL)/6-311++G** computational levels. The ions M(n)()(+) are from groups 1A, 2A, 3A, and 4A in the second, third, and fourth periods of the Periodic Table and from the first transition series. Geometrical parameters, vibrational frequencies, atomic charge distributions, orbital occupancies, and bonding enthalpies are reported. The M(n)(+)-O distances are shorter in the hydroxides than in the corresponding hydrates (published previously as Part 1, Inorg. Chem. 1998, 37, 4421-4431) due to a greater electrostatic interaction in the hydroxides. The natural bond orbitals for most of the first-row transition metal ion hydroxides do not contain a formal metal-oxygen bonding orbital; nevertheless the atomic charge distributions show that for both n = 1 and 2 a significant amount of electron density is consistently transferred from the hydroxide ion to the bound metal ion. Deprotonation enthalpies for the hydrates have been evaluated according to the simple dissociation process, M(n)(+)[OH(2)] --> M(n)(+)[OH(-)] + H(+), and also via proton transfer to another water molecule, M(n)(+)[OH(2)] + H(2)O --> M(n)(+)[OH(-)] + H(3)O(+). The drastic reduction in these deprotonation enthalpies as H(2)O molecules are sequentially bonded in the first coordination shell of the metal ion (amounting to 71, 64, 85, and 91 kcal/mol for the bonding of six water molecules to Mg(2+), Ca(2+), Mn(2+), and Zn(2+), respectively) is found to be due to the greater decrease in the bonding enthalpies for the hydroxides relative to the hydrates. Proton transfer to bases other than water, for example side chain groups of certain amino acids, could more than offset the decrease in deprotonation energy due to the filling of the first coordination shell. Linear relationships have been found between the pK(a) values for ionization of the Mg(2+), Ca(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+) aquo ions, and Delta for the bonding of the first water molecule, for the bonding of the hydroxide ion, and for proton dissociation from the monohydrate. Similar relationships have also been found between the pK(a) values and the reciprocal of the M-O bond lengths in both the monohydrates and hydroxides. Thus the ionization of metal hydrates in water echoes the properties of the monomeric species M(n)(+)[OH(2)]. PMID:11487327

Trachtman, M; Markham, G D; Glusker, J P; George, P; Bock, C W

2001-08-13

251

Electronic spectrum and orbital filling in a single-molecule junction  

NASA Astrophysics Data System (ADS)

We study single-electron tunneling in three-terminal devices in which a single molecule bridges the gap between source and drain electrode. The molecular devices are made by electromigration and at low temperatures excitations appear in the stability diagram. For the OPV-5 molecule more than fifteen different excitations are visible, of which twelve match RAMAN spectra and the remaining ones are due to vibratrions of the molecule attached to gold electrodes at energies below 10 meV. Similar to carbon nanotubes, the observation of a singlet-triplet transition allow us to determine the orbital filling and spin configuration of the molecule.

Osorio, Edgar A.; O'Neill, Kevin; Wegewijs, Maarten; Stuhr-Hansen, Nicolai; Paaske, Jens; Bjornholm, Thomas; van der Zant, Herre

2008-03-01

252

Molecular orbital (SCF-X??-SW) theory of metal-metal charge transfer processes in minerals - I. application to Fe2+???Fe3+ charge transfer and "electron delocalization" in mixed-valence iron oxides and silicates  

USGS Publications Warehouse

A number of mixed valence iron oxides and silicates (e.g., magnetite, ilvaite) exhibit thermally induced electron delocalization between adjacent Fe2+ and Fe3+ ions and optically induced electronic transitions which are assigned to Fe2+???Fe3+ intervalence charge transfer. In this paper, the mechanism of electron delocalization (i.e., polarons versus itinerant electrons) and the nature of optically induced intervalence charge-transfer in minerals are investigated using molecular orbital theory. SCF-X??-SW molecular orbital calculations were done for several mixed-valence (Fe2O10)15- clusters corresponding to edgesharing Fe2+ and Fe3+ coordination polyhedra. A spinunrestricted formalism was used so that the effect of ferromagnetic versus antiferromagnetic coupling of adjacent Fe2+ and Fe3+ cations could be determined. The molecular orbital results can be related to the polaron theory of solid state physics and the perturbation theory formalism used by Robin and Day (1967) and others to describe electron transfer in mixed valence compounds. Intervalence charge-transfer results from the overlap of Fe(3d) orbitals across the shared edges of adjacent FeO6 polyhedra to give weak Fe-Fe bonds. Electron delocalization, however, requires that adjacent Fe cations be ferromagnetically coupled. Antiferromagnetic coupling results in distinguishable Fe2+ and Fe3+ cations. 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. ?? 1987 Springer-Verlag.

Sherman, D.M.

1987-01-01

253

An Introduction to Tree Diagrams  

NSDL National Science Digital Library

This brief article describes the use of tree diagrams in calculating probabilities. The author provides examples of how tree diagrams are used to calculate specific probabilities and why the language chosen relates to the operations used to find the probability.

Stu Cork

2014-01-01

254

Linking diagrams for free  

E-print Network

Linking diagrams with path composition are ubiquitous, for example: Temperley-Lieb and Brauer monoids, Kelly-Laplaza graphs for compact closed categories, and Girard's multiplicative proof nets. We construct the category Link=Span(iRel), where iRel is the category of injective relations (reversed partial functions) and show that the aforementioned linkings, as well as Jones-Martin partition monoids, reside inside Link. Path composition, including collection of loops, is by pullback. Link contains the free compact closed category on a self-dual object (hence also the looped Brauer and Temperly-Lieb monoids), and generalises partition monoids with partiality (vertices in no partition) and empty- and infinite partitions. Thus we obtain conventional linking/partition diagrams and their composition "for free", from iRel.

Dominic J. D. Hughes

2008-05-11

255

[Orbital inflammation].  

PubMed

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

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

2014-12-01

256

Hertzsprung-Russell Diagram  

NSDL National Science Digital Library

Authored by Martin Hackworth of Idaho State University, This lab asks students to construct two Hertzsprung-Russell diagrams, one for the Pleiades Cluster and the other for the Trapezium Cluster. Students should then to be able to recognize the evolution process of all stars depending on their mass. The page features objectives, equipment, discussion, procedure, and exercises. The lesson plan is outlined in an understandable format for translation into almost any curriculum. The resource is available in a pdf format.

Hackworth, Martin

257

UML class diagram metrics tool  

Microsoft Academic Search

Many of the object-oriented (OO) metrics that have been proposed over the last decade can be applied to measure internal quality attributes of class diagrams. This paper describes a tool that automates the computation of the important metrics that are applicable to the UML class diagrams. The tool collects information by parsing the XMI format of the class diagram to

Moheb R. Girgis; T. M. Mahmoud; Rehab R. Nour

2009-01-01

258

On web diagrams Jun Murakami  

E-print Network

On web diagrams Jun Murakami Department of Mathematics, Graduate School of Science, Osaka­ tive invariant is defined in the space of web diagrams, and it includes the Casson­ Walker invariant of the mapping class groups. (cf. [9], [10]) 2. Web space 2.1. Web diagram. To explain the universal perturbative

259

Modeling process flow using diagrams  

Microsoft Academic Search

In the practice of process improvement, tools such as the flowchart, the value-stream map (VSM), and a variety of ad hoc variants of such diagrams are commonly used. The purpose of this paper is to present a clear, precise, and consistent framework for the use of such flow diagrams in process improvement projects. The paper finds that traditional diagrams, such

Benjamin Kemper; Jeroen de Mast; Michel Mandjes

2010-01-01

260

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

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

Song, Lingchun; Mo, Yirong; Gao, Jiali

2009-01-01

261

Extension of the Fenske-Hall Molecular Orbital Approach to Tight-Binding Band Structure Calculations: Bulk and Surface Electronic Structure of MoS(2).  

PubMed

A new tight-binding band structure calculation method is described. This method, which is based on the Fenske-Hall molecular orbital technique, should be extremely useful in the study of the bulk and surface electronic structure of inorganic materials. The approximations used in the Fenske-Hall method are reviewed, and the extension of this approach to periodic band structure calculations is outlined. Results of calculations for bulk MoS(2) are in good agreement with previous experimental and theoretical results. Results of calculations for two-dimensional MoS(2) slabs exposing (100) edge planes provide a description of coordinatively unsaturated Mo and S atoms on these edges. Coordinative unsaturation at the Mo atoms introduces new surface states near the Fermi level. Coordinative unsaturation at the S atoms leads to high-energy occupied bands that can be attributed to S lone pair electrons. Surface bonds between Mo atoms and terminal S atoms are stronger than bulk Mo-S bonds, suggesting that terminal S atoms may be more difficult to remove from the edges of MoS(2) than bridging S atoms. Bonding in a single two-dimensional layer of MoS(2) is found to be more ionic than the bonding in the full three-dimensional structure. This effect is also observed in one-dimensional MoS(2) ribbons that expose (100) edge planes. The simplified one-dimensional ribbons will be used for further studies of the electronic structure of the edge planes of MoS(2). PMID:11670376

Tan, Agnes; Harris, Suzanne

1998-05-01

262

Extension of the Fenske-Hall molecular orbital approach to tight-binding band structure calculations: Bulk and surface electronic structure of MoS{sub 2}  

SciTech Connect

A new tight-binding band structure calculation method is described. This method, which is based on the Fenske-Hall molecular orbital technique, should be extremely useful in the study of the bulk and surface electronic structure of inorganic materials. The approximations used in the Fenske-Hall method are reviewed, and the extension of this approach to periodic band structure calculations is outlined. Results of calculations for bulk MoS{sub 2} are in good agreement with previous experimental and theoretical results. Results of calculations for two-dimensional MoS{sub 2} slabs exposing (100) edge planes provide a description of coordinatively unsaturated Mo and S atoms on these edges. Coordinative unsaturation at the Mo atoms introduces new surface states near the Fermi level. Coordinative unsaturation at the S atoms leads to high-energy occupied bands that can be attributed to S line pair electrons. Surface bonds between Mo atoms and terminal S atoms are strong than bulk Mo-S bonds, suggesting that terminal S atoms may be more difficult to remove from the edges of MoS{sub 2} than bridging S atoms. Bonding in a single two-dimensional layer of MoS{sub 2} is found to be more ionic than the bonding in the full three-dimensional structure. This effect is also observed in one-dimensional MoS{sub 2} ribbons that expose (100) edge planes. The simplified one-dimensional ribbons will be used for further studies of the electronic structure of the edge planes of MoS{sub 2}.

Tan, A.; Harris, S. [Univ. of Wyoming, Laramie, WY (United States). Dept. of Chemistry] [Univ. of Wyoming, Laramie, WY (United States). Dept. of Chemistry

1998-05-04

263

Molecular orbital study of the primary electron donor P700 of photosystem I based on a recent X-ray single crystal structure analysis  

NASA Astrophysics Data System (ADS)

The X-ray structure analysis of photosystem (PS) I single crystals showed that the primary electron donor P700 is a heterodimer formed by one chlorophyll (Chl) a and one Chl a' [Nature 411 (2001) 909]. The electronic structure of the cation radical P700 + rad of the primary donor, which is created in the charge separation process, has been probed by semiempirical molecular orbital calculations including spin polarization effects (RHF-INDO/SP). The calculations, which were based on the X-ray structure, clearly show that P700 is a supermolecule formed by two chlorophyll species. They furthermore predict an asymmetrical charge and spin density distribution in favor of the monomeric Chl a half of this dimer in accordance with results from earlier EPR and ENDOR studies [J. Phys. Chem. B 105 (2000) 1225]. The stepwise inclusion of various electrostatic interactions of the dimer with its nearest surrounding (one threonine forming a hydrogen bond to the keto group of Chl a' and two histidines liganding the Mg atoms of the two chlorophylls) leads to a systematic enhancement of this electronic asymmetry yielding a spin density ratio of almost 5:1 as also found experimentally. A large part of this value is caused by spin polarization effects. This result is only weakly affected by the electrostatic field of more remote amino acid residues and other pigment molecules ('accessory' Chl a molecules) present in PS I. A separate group of calculations involving local geometry optimizations by energy minimization techniques yields a further enhancement of the spin density asymmetry. A particularly strong effect is obtained by allowing for variations of the geometry of the vinyl groups on both chlorophylls of the P700 dimer. Theoretical results for individual isotropic proton and nitrogen hyperfine coupling constants, showing a satisfactory agreement with experimental findings, are also presented.

Plato, Martin; Krauß, Norbert; Fromme, Petra; Lubitz, Wolfgang

2003-11-01

264

Elliptical Orbits  

NSDL National Science Digital Library

This resource provides a textual explanation as well as animated illustration of elliptical orbits with different eccentricities. It also shows how the Sun is at the focus of an ellipse, and some of the math behind elliptical orbits. Beginner, intermediate and advanced versions of the content are available.

Roberta Johnson

2000-07-01

265

Natural bond orbital analysis of steric interactions  

Microsoft Academic Search

We describe an ab initio procedure for extracting the Pauli exchange antisymmetry (“steric”) contributions to molecular potential energy in the framework of self-consistent-field molecular orbital (SCFMO) theory. This “natural steric analysis” method is based on natural bond orbital (NBO) representation of the SCFMO wave function, which allows the steric exchange energy to be approximated as an energy difference between “preorthogonal”

J. K. Badenhoop; F. Weinhold

1997-01-01

266

The Hot Orbit: Orbital Cellulitis  

PubMed Central

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

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

2012-01-01

267

Orbiter Autoland reliability analysis  

NASA Technical Reports Server (NTRS)

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.

Welch, D. Phillip

1993-01-01

268

Warped penguin diagrams  

SciTech Connect

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.

Csaki, Csaba; Grossman, Yuval; Tanedo, Philip; Tsai, Yuhsin [Institute for High Energy Phenomenology, Newman Laboratory of Elementary Particle Physics, Cornell University, Ithaca, New York 14853 (United States)

2011-04-01

269

Impact decision support diagrams  

NASA Astrophysics Data System (ADS)

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

Boslough, Mark

2014-10-01

270

Orbital Myiasis  

PubMed Central

Purpose To present a case of massive orbital myiasis. Case Report An 87-year-old debilitated woman suffering from left ocular pain of four days’ duration presented with a severely necrotized left orbit and several attached live larvae. The upper and lower eyelids and the eyeball were completely destroyed. She had history of eyelid surgery in the same eye due to a skin lesion, apparently some type of skin cancer, 15 years before. The larvae were identified as Chrysomya bezziana (Diptera: Calliphoridae) or old world screwworm fly. Conclusion Infestation of ocular and orbital tissues by fly larvae (ophthalmomyiasis) progresses rapidly and can completely destroy orbital tissues within days, especially in patients with poor general health. Treatment consists of removal of the larvae and surgical debridement. PMID:22454736

Khataminia, Gholamreza; Aghajanzadeh, Roja; Vazirianzadeh, Babak; Rahdar, Mahmoud

2011-01-01

271

Argument Diagramming: The Araucaria Project  

NASA Astrophysics Data System (ADS)

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.

Rowe, Glenn; Reed, Chris

272

Orbital resonances in exoplanetary systems  

NASA Astrophysics Data System (ADS)

At present, more than 700 exoplanetary systems are known to have been discovered. They incorporate more than 130 multiplanet systems, i.e. those hosting two or more planets. The orbital resonance and near-resonance phenomena are ubiquitous in them. We present a statistical and dynamical analysis of the resonance structure of the multiplanet systems and planetary systems of binary stars. We have built distributions of the orbital period ratios, separately considering the cases of inner and outer location of the massive perturber. The histograms reveal apparent peaks close to the first order orbital resonances 2/1 and 3/2 in both cases; this confirms previous findings. We have performed analytical modelling of the histograms, and obtained exact positions of the peaks. Moreover, we have built the "period ratio – eccentricity" diagrams, with collision curves superimposed, so that to find anomalous systems.

Popova, E. A.; Shevchenko, I. I.

2014-12-01

273

Generating function for web diagrams  

E-print Network

We present the description of the exponentiated diagrams in terms of generating function within the universal diagrammatic technique. In particular, we show the exponentiation of the gauge theory amplitudes involving products of an arbitrary number of Wilson lines of arbitrary shapes, which generalizes the concept of web diagrams. The presented method gives a new viewpoint on the web diagrams and proves the non-Abelian exponentiation theorem.

A. A. Vladimirov

2014-09-06

274

Program Synthesizes UML Sequence Diagrams  

NASA Technical Reports Server (NTRS)

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.

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

275

Natural bond orbital analysis of molecular interactions Theoretical studies of binary complexes of HF, H2O, NH3, O2, F2, CO, and CO2 with HF, H2O, and NH3  

NASA Astrophysics Data System (ADS)

Ab initio molecular orbital theory and natural bond orbital analysis were applied to the binary complexes of HF, H2O, NH3, N2, O2, F2, CO and CO2 with HF, H2O and NH3. Both hydrogen-bonded and nonhydrogen-bonded structures were found for complexes involving N2, O2, F2, CO, and CO2; these structures were defined by NBO analysis of charge transfer, which is generally stronger in H-bonded than in non-H-bonded complexes. The internal rotation barrier (1 kcal/mol) of the H2O-CO2 complex was found to be primarily of electrostatic origin with only a small charge transfer contribution. The role of electrostatic interactions, effect of electron correlation, and comparison of theory with experiment are also discussed.

Reed, A. E.; Weinhold, F.; Curtiss, L. A.; Pochatko, D. J.

1986-05-01

276

Molecular orbital (SCF-X??-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

A molecular orbital description, based on X??-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(t2 g) and Ti(t2 g) 3 d orbitals. ?? 1987 Springer-Verlag.

Sherman, D.M.

1987-01-01

277

Lunar Reconnaissance Orbiter FlatSat  

NASA Technical Reports Server (NTRS)

This viewgraph presentation reviews the use of FlatSat as a platform for use during flight integration and testing (I&T) of the Lunar Reconnaissance Orbiter (LRO). Included in the presentations are requirements for the facility, a diagram of the LRO FlatSat lab, and discussion of the operational documentation, facility scheduling, and issues and lessons learned.

Wright, Michael

2008-01-01

278

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

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 ?-? 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

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

2015-06-01

279

Scale Models and Diagrams  

NSDL National Science Digital Library

This is a set of three, one-page problems about the scale of objects in images returned by spacecraft. Learners will measure scaled drawings using high-resolution images of the lunar and martian surfaces. Options are presented so that students may learn about the Lunar Reconnaissance Orbiter (LRO) mission through a NASA press release or by viewing a NASA eClips video [4 min.]. This activity is part of the Space Math multi-media modules that integrate NASA press releases, NASA archival video, and mathematics problems targeted at specific math standards commonly encountered in middle school.

2014-03-19

280

Physiology Flow-Diagram Models  

NSDL National Science Digital Library

A set of physiology flow-diagrams for the cardiovascular system, cardiac auto-rhythmic cell, cardiac contractile cell, respiratory system, coagulation/hemostasis, digestive system, excretion, and autonomic nervous system. These flow-diagrams show cause-and-effect markup and have accompanying tutorials.

PhD Sandra J Bruner (Polk Community College Biology)

2005-10-04

281

Perturbations to the Hubble diagram  

E-print Network

We compute the linear responses of the Hubble diagram to small scalar perturbations in the Robertson-Walker metric and to small peculiar velocities of emitter and receiver. We discuss the monotonicity constraint of the Hubble diagram in the light of these responses.

Thomas Schucker; Ilhem ZouZou

2005-11-17

282

Summarization of Diagrams in Documents  

Microsoft Academic Search

Documents are composed of text and graphics. There is substantial work on automated text summarization but almost none on the automated summarization of graphics. Four examples of diagrams from the scientific literature are used to indicate the problems and possible solutions: a table of images, a flow chart, a set of x,y data plots, and a block diagram. Manual summaries

Robert P. Futrelle

1999-01-01

283

Sets and the Venn Diagram  

NSDL National Science Digital Library

This lesson is designed to introduce students to sets, terms used with sets, and Venn diagrams. This lesson provides links to discussions and activities related to sets and Venn diagrams as well as suggested ways to integrate them into the lesson. Finally, the lesson provides links to follow-up lessons designed for use in succession with the current one.

2011-05-23

284

Architecture flow diagrams under Teamwork  

Microsoft Academic Search

The Teamwork CASE tool allows data flow diagrams (DFDs) to be maintained for structured analysis. Fermilab has extended Teamwork under UNIX to permit Hatley and Pirbhai architecture flow diagrams (AFDs) to be associated with DFDs and subsequently maintained. This extension, called TWKAFD, allows a user to open an AFD, graphically edit it, and replace it into a TWKAFD maintained library.

Tom Nicinski

1992-01-01

285

Time-Based Voronoi Diagram  

Microsoft Academic Search

We consider a variation of Voronoi diagram, or time-based Voronoi diagram, for a set S of points in the presence of transportation lines or highways in the plane. A shortest time-distance path from a query point to any given point in S is a path that takes the least travelling time. The travelling speeds and hence travelling times of the

D. T. Lee; Chung-Shou Liao; Wei-Bung Wang

286

Orbital Debris  

NASA Technical Reports Server (NTRS)

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.

Kessler, D. J. (compiler); Su, S. Y. (compiler)

1985-01-01

287

Transformations of triangle ladder diagrams  

E-print Network

It is shown how dual space diagrammatic representation of momentum integrals corresponding to triangle ladder diagrams with an arbitrary number of rungs can be transformed to half-diamonds. In paper arXiv:0803.3420 [hep-th] the half-diamonds were related by conformal integral substitution to the diamonds which represent the dual space image of four-point ladder integrals in the four-dimensional momentum space. Acting in the way described in the present paper we do not need to use the known result for diamond (four-point) diagrams as an external input in deriving relations of arXiv:0803.3420 [hep-th], however, that result for the diamond diagram arises in the present proof as an intermediate consequence in a step-by-step diagrammatic transformation from the triangle ladder diagram to the half-diamond diagrams.

Igor Kondrashuk; Alvaro Vergara

2010-02-13

288

Molecular Menagerie  

NSDL National Science Digital Library

In this activity, learners use molecular model kits to construct familiar molecules like lactose, caffeine, and Aspirin. This activity helps learners understand how scientists use models to study molecules as well as how advances in 3-D graphics have made the use of computer models much easier. This activity guide includes chemical formulas and 3-D structural diagrams of various natural and artificial molecules. Note: the cost of molecular model kits is included in the estimated cost of materials.

Howard Hughes Medical Institute

2002-01-01

289

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)

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.

Greene, E. F.; Hall, R. B.; Mason, E. A.

1975-01-01

290

The Extent of Disorder among Charge-balancing Cations in Silicate Glasses and Melts: Spectroscopic Analysis and ab initio Molecular Orbital Calculations  

NASA Astrophysics Data System (ADS)

Aluminosilicate melts are one of the dominant components in upper mantle and crust. Essential to the thermodynamic and transport properties of these systems is the full understanding on the atomic arrangements and the extent of disorder. Recent quantification of the extent of disorder among 'framework cations' in silicate melts using NMR provided improved prospects on the atomic structure of the glasses and melt and their corresponding properties and allowed the degree of randomness to be evaluated in terms of the degree of Al-avoidance (Q) and degree of phase separations (P) (Lee and Stebbins, J. Phys. Chem. B 104, 4091; Lee and Stebbins, GCA in press). Quantitative estimation of the extent of disorder among 'charge-balancing cations' including Na in aluminosilicate glasses, however, has remained an unsolved problem and these cations have often been assumed to be randomly distributed. Here, we explore the intermediate range order around Na in charge-balanced aluminosilicate glasses using Na-23 NMR and Near-edge X-ray absorption fine structure (NEXAFS) with full multiple scattering (FMS) simulations combined with ab initio molecular orbital calculations. We also quantify the extent of disorder in charge balancing cations as a function of Na-O bond length (d(Na-O)) distribution with composition and present a structural model favoring ordered Na distributions. Peak position in Na-23 magic angle spinning (MAS) spectra of aluminosilicate glasses with varying R (Si/Al) at 14.1 T varies from -10.28 ppm (R = 0.7) to -19.98 ppm (R = 6). These results suggest that average d(Na-O) increases with increasing R, which is confirmed by Na-23 multiple quantum MAS spectra where the chemical shift moves toward lower frequency with increasing Si and shows the individual Gaussian components of Na-O distributions such as Na-(Al-O-Al), Na-(Si-O-Al) and Na-(Si-O-Si). Calculated d(Na-(Al-O-Al)) of 2.57 Å is shorter than d(Na-(Si-O-Si)) of 2.88 Å. Strong compositional dependence is further manifested in Na K-edge NEXAFS spectra for aluminosilicate glasses that are characterized by two main peaks at about 1057 ev (A) and 1062 ev (B). The intensity ratio between peak A and B increases with increasing R, which is consistent with our FMS simulations of model clusters with R and implies that the Na has rather well ordered oxygen coordination and Na-O distribution depends on the types of nearby framework cations. The potential energy surfaces for model six-member rings (NaAl2Si4O6(OH)12, with and without Al-O-Al) were calculated using ab initio calculations at the HF/6-311G(d) level in order to investigate the equilibrium atomic configurations around Na. The results manifest the varying bonding preference of Na to different framework oxygens. Na is located at single deep and narrow basin in potential energy surfaces. The motion of Na is therefore restricted to near equilibrium position even at higher temperature contrary to conventional random distribution model with moderate Na mobility, demonstrating that dynamics of Na should be associated with the collective motions of framework cations and oxygens. In this study, we provide new insights into the nature of disorder in charge-balancing cations in silicate glasses using spectroscopy combined with simulations, highlighting more complete, atomic-level understanding on the dynamic processes in silicate magmas.

Lee, S.; Doyle, C. S.; Stebbins, J. F.

2001-12-01

291

Compound orbits break-up in constituents: an algorithm  

E-print Network

In this paper decomposition of periodic orbits in bifurcation diagrams are derived in unidimensional dynamics system $x_{n+1}=f(x_{n};r)$, being $f$ an unimodal function. We proof a theorem which states the necessary and sufficient conditions for the break-up of compound orbits in their simpler constituents. A corollary to this theorem provides an algorithm for the computation of those orbits. This process closes the theoretical framework initiated in (Physica D, 239:1135--1146, 2010).

Jesús San Martín; A. González Gómez; Ma José Moscoso; Daniel Rodríguez-Pérez

2014-02-24

292

Elliptical Orbits  

NSDL National Science Digital Library

Although not inquiry, this activity is important for students to understand what an ellipse is and what a focus is, and to break misconceptions about Earth's orbit being highly elliptical. This is the perfect place to check to see if students have the mis

Michael Horton

2009-05-30

293

Orbital Surgery  

MedlinePLUS

The orbit is the boney socket in your skull that contains and houses the eye and all the associated structures that support the function of the eye ... variety of problems can occur in the eye socket that effect the function of the eye. These ...

294

Orbital Elements  

NSDL National Science Digital Library

Coordinates for tracking the International Space Station and the Mir Space Station are available here from NASA's Johnson Space Center Flight Design and Dynamics Division. The Orbital Elements page offers real-time data for use in ground track plotting programs. The site cautions the data are for ground track plotting programs only and "should not be used for precise applications or analysis!"

295

Continuous phase diagrams of complex material systems  

NASA Astrophysics Data System (ADS)

High throughput and systematic study of complex material systems is described. Initial efforts using thin film discrete material chips are briefly reviewed in perspective of material discovery and optimization. We then focus our discussion to the experimental technique of epitaxial thin film growth "continuous phase diagram" (CPD) and mapping its physical properties in two different material systems; perovskite manganese oxides and Ni1-xFe x metal alloy. In the former, we discuss the results of mapping optical, electrical, and magnetic properties of manganese oxides as functions of doping concentration, ionic radius, etc. We discuss the surprising evidences that suggest various electronic phase transitions, such as orbital orderings and smectic phase formation, in this highly correlated electronic system. In Ni 1-xFex metal alloy, we discuss a different application of CPD to describe the structure-property relation of a traditional materials science.

Yoo, Young-Kook K.

296

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

NASA Astrophysics Data System (ADS)

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

Muthu, S.; Renuga, S.

2014-01-01

297

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

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 (?) and the first order hyperpolarizability (?) 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 (?), electrophilicity index (?), hardness (?) and chemical potential (?) 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

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

2014-01-01

298

Eye and orbit ultrasound  

MedlinePLUS

Echography - eye orbit; Ultrasound - eye orbit; Ocular ultrasonography; Orbital ultrasonography ... eye is numbed with medicine (anesthetic drops). The ultrasound wand (transducer) is placed against the front surface ...

299

Orbiting Hotel  

NSDL National Science Digital Library

It is the year 2025 and a large company, Z-Tech, wants to put a hotel in space having it orbit around one of the planets in our solar system. Our 9th grade class has been given a very important job. We have to search for the perfect location for the hotel. Our job is to report back to the company with the planet that is the best place for an orbiting hotel. The Task: You are to write a report recommending which planet should be chosen. Your report should include pictures of the planet you recommended. Here are the questions you should answer in order to report back to Z-Tech with your recommendation. * Which planet will be the ...

Mrs. Hicken

2009-10-19

300

Achieving Orbit  

NSDL National Science Digital Library

In this Engineering Design Challenge activity, participants use balloons to investigate how a two-stage rocket, like that used in the IBEX mission, can propel a satellite to a specific orbit. Participants will construct a two-stage balloon that will be required to reach a particular location on the balloon track, simulating the proper orbit to be reached by the IBEX satellite. This activity is adapted from the NASA Rockets Educators Guide (EG-2003-01-108-HQ) and the NASA Glenn Research Center’s online Learning Technologies Project for facilitation with an informal museum audience. Each short activity/product helps to build awareness and engagement in the science and engineering aspects of the mission that is reinforced as visitors choose to participate in more activities, including viewing the planetarium show and mission Web site.

Michelle Nichols

2008-01-15

301

The Hertzsprung-Russell Diagram.  

ERIC Educational Resources Information Center

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)

Woodrow, Janice

1991-01-01

302

Formulae and Flow-Diagrams  

ERIC Educational Resources Information Center

The author recommends the use of flow charting to help students understand the manipulation of algebraic formulae. He identifies some problems with flow charts and suggests an alternative method of constructing flow diagrams. (SD)

Willson, William Wynne

1977-01-01

303

Bringing class diagrams to life  

Microsoft Academic Search

Research in formal methods emphasizes a fundamental interconnection between modeling, calculation and prototyping, made possible\\u000a by a common unambiguous, mathematical semantics. This paper, building on a broader research agenda on coalgebraic semantics\\u000a for Unified Modeling Language diagrams, concentrates on class diagrams and discusses how such a coalgebraic perspective can\\u000a be of use not only for formalizing their specification, but also

Luís Soares Barbosa; Sun Meng

2010-01-01

304

Interpreting T-X Diagrams  

NSDL National Science Digital Library

This short problem set works well as a group activity that can be completed in class. The purpose of the exercise is for students to begin to think about T-X phase diagrams and how they are interpreted. Along the way, students learn that text book authors sometimes make mistakes. The figure in the handout is from Winter's Petrology. But, Winter goofed and left some reactions off of the phase diagram.

Dexter Perkins

305

Changing Perceptions of Animated Diagrams  

Microsoft Academic Search

\\u000a While the educational effectiveness of static diagrams is underpinned by a long heritage of manipulating visuospatial characteristics\\u000a of the depicted content to improve explanatory power, no corresponding evolution has occurred regarding temporal manipulation\\u000a of animated diagrams. When complex dynamic subject matter is presented using animations that depict temporal information in\\u000a a behaviorally realistic manner, the perceptual properties of the display

Richard Lowe

2006-01-01

306

Inflammation of the Orbit  

MedlinePLUS

... Socket Disorders 4 Inflammation of the Orbit (Inflammatory Orbital Pseudotumor) Any or all of the structures within the ... entire orbit and its contents is called inflammatory orbital pseudotumor (which is not really a tumor and is ...

307

Orbit analysis  

SciTech Connect

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.

Michelotti, L.

1995-01-01

308

Everything in OrbitEverything in Orbit Orbital VelocityOrbital Velocity  

E-print Network

is the speed at which a planetary body moves in Orbital velocity is the speed at which a planetary body moves Escape velocity = "speed required to project a body completely Escape velocity = "speed requiredEverything in OrbitEverything in Orbit #12;Orbital VelocityOrbital Velocity Orbital velocity

Herrick, Robert R.

309

Rock-Around Orbits  

E-print Network

; !). Using these parameters, one can create an orbit that will surround the target orbit allowing the satellite in the Rock-Around Orbit (RAO) orbit to have a 360 degree view of RSOs in the target orbit. The RAO orbit can be applied to any circular...

Bourgeois, Scott K.

2010-07-14

310

A. Syntax Diagrams A-1 Appendix A  

E-print Network

A. Syntax Diagrams A-1 Appendix A: Syntax Diagrams References: · Kathleen Jensen/Niklaus Wirth A is a short introduction to syntax diagrams. · Don Chamberlin: A Complete Guide to DB2 Universal Database. Morgan Kaufmann, 1998. Section 1.1.2 is a very quick introduction to syntax diagrams. Stefan Brass

Brass, Stefan

311

Automatically Assessing Graph-Based Diagrams  

ERIC Educational Resources Information Center

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…

Thomas, Pete; Smith, Neil; Waugh, Kevin

2008-01-01

312

CONTEXTEXPLOITING SHAPES FOR DIAGRAM TRANSFORMATION Frank Drewes  

E-print Network

with editors for control flow diagrams, Nassi­Shneiderman diagrams, message sequence charts, state charts primitives, and reduces them to dia­ gram symbols, like assignments and branches in a control flow diagramCONTEXT­EXPLOITING SHAPES FOR DIAGRAM TRANSFORMATION Frank Drewes Institutionen fË?or Datavetenskap

Drewes, Frank

313

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

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.

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

2008-10-31

314

Precision orbit determination at the NASA Goddard Space Flight Center  

NASA Technical Reports Server (NTRS)

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.

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

1990-01-01

315

Orbital order of spinless fermions near an optical Feshbach resonance  

SciTech Connect

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.

Hauke, Philipp [ICFO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, E-08860 Castelldefels (Spain); Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 (United States); Zhao, Erhai [Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 (United States); Department of Physics and Astronomy, George Mason University, Fairfax, Virginia 22030 (United States); Goyal, Krittika; Deutsch, Ivan H. [Center for Quantum Information and Control (CQuIC), and Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Liu, W. Vincent [Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 (United States); Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (United States); Lewenstein, Maciej [ICFO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, E-08860 Castelldefels (Spain); Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 (United States); ICREA-Institucio Catalana de Recerca i Estudis Avancats, Lluis Companys 23, E-08010 Barcelona (Spain)

2011-11-15

316

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

NASA Astrophysics Data System (ADS)

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

Carter, Melvin Keith

2007-04-01

317

NAAP HR Diagram Explorer 1/9 HR Diagram Student Guide  

E-print Network

Name: NAAP ­ HR Diagram Explorer 1/9 HR Diagram ­ Student Guide Background Information Work through Orionis O9 Radius (R) Temperature (T) Luminosity (L) 1 1 1 2 1 9 1 1/2 #12;NAAP ­ HR Diagram Explorer 2 Diagram Explorer Open the HR Diagram Explorer. Begin by familiarizing yourself with the capabilities

Farritor, Shane

318

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

NASA Technical Reports Server (NTRS)

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.

1975-01-01

319

Analysis of the electronic structure of liquid rubidium by the methods of ab initio molecular dynamics, linear muffin-tin orbitals and recursion.  

PubMed

It is well known that liquid rubidium shows some unusual properties at low densities. The ab initio SIESTA package and the supercell technique within the linear muffin-tin orbital method were used to investigate this phenomenon. Electronic structures of liquid rubidium at different temperatures from the melting point up to the critical point were obtained. The atomic structure for the supercell technique was simulated for a cluster of 4000 atoms by the Schommers method on the basis of experimental structure factors of Rb obtained by Tamura and co-workers at different temperatures (from 373 up to 1973 K). The Kubo-Greenwood formula was applied for the calculations of the melt conductivity. The results obtained indicate that the metal-nonmetal transition in liquid rubidium is not connected to the gap at the Fermi energy in the density of electronic states, but, more likely, with electron localization on some kind of atomic cluster. PMID:21694197

Mirzoev, A A; Mirzoev, A A; Sobolev, A N; Gelchinski, B R

2008-03-19

320

Shapes of d Orbitals  

NSDL National Science Digital Library

Shapes of d Orbitals shows the d orbitals in an axis set. Running the mouse over an orbital reveals the "name" of that orbital. This is good practice for helping students link the name of an orbital to the orientation.Shapes of d Orbitals has a link to D Orbitals in an Octahedral Ligand Field. Here the user may click on the name of any one of the d orbitals to obtain a larger 3-dimensional image. The images are rotatable and scalable. Orbital phase is shown by the different colors.

321

Dynamic programming and influence diagrams  

Microsoft Academic Search

The concept of a super value node is developed to extend the theory of influence diagrams to allow dynamic programming to be performed within this graphical modeling framework. The operations necessary to exploit the presence of these nodes and efficiently analyze the models are developed. The key result is that by representing value function separability in the structure of the

JOSEPH A. TATMAN; ROSS D. SHACHTER

1990-01-01

322

ccsd00000445, Making diagrams speak,  

E-print Network

raised by the presence of diagrams in a VIIth century Sanskrit mathematical com- mentary. Exploring di- agrammes dans un commentaire math#19;ematique en langue sanskrite datant du VII#18;eme si#18;ecle: A. Keller is a French CNRS researcher working on medieval sanskrit mathematics but also

323

Causal diagrams for empirical research  

Microsoft Academic Search

The primary aim of this paper is to show how graphical models can be used as a mathematical language for integrating statistical and subject-matter information. In particular, the paper develops a principled, nonparametric framework for causal inference, in which diagrams are queried to determine if the assumptions available are sufficient for identifying causal effects from nonexperimental data. If so the

JUDEA PEARL

1995-01-01

324

Phase Diagrams for Sonoluminescing Bubbles  

Microsoft Academic Search

Sound driven gas bubbles in water can emit light pulses. This phenomenon is called sonoluminescence (SL). Two different phases of single bubble SL have been proposed: diffusively stable and diffusively unstable SL. We present phase diagrams in the gas concentration vs forcing pressure state space and also in the ambient radius vs gas concentration and vs forcing pressure state spaces.

Sascha Hilgenfeldt; Detlef Lohse; Michael P. Brenner

1996-01-01

325

Precipitation and the Sounding Diagram  

NSDL National Science Digital Library

This undergraduate meteorology tutorial deals with the interplay between the vertical temperature structure of the atmosphere and the temperature of the ascending air in the formation of precipitation. Students learn about the dry and moist adiabatic lapse rates, reading and interpreting sounding diagrams, and determining the change in temperature as air parcels rise or sink.

John Nielsen-Gammon

1996-01-01

326

Using influence diagrams for PERT  

Microsoft Academic Search

Summary form only given. We describe a new method for explicit modeling of decisions that bear on activity times in a project. This method extends the PERT belief network (PBN) model to include decisions variables. The resulting network is called PERT Influence Diagram (PID). A PID is a PBN that includes decision variables, where arrows into decision nodes mean that

A. Jenzarli

1997-01-01

327

Voronoi Diagrams and Spring Rain  

ERIC Educational Resources Information Center

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…

Perham, Arnold E.; Perham, Faustine L.

2011-01-01

328

Index of Animated Phase Diagrams  

NSDL National Science Digital Library

This is a collection of animated phase diagrams by Kenneth Windom at Iowa State University. These short Power Point animations can be used to illustrate equilibrium crystallization concepts. There are slide shows for plagioclase feldspars (albite and anorthite); forsterite, diopside and anorthite; forsterite, enstatite and silica; and diopside and anorthite.

Kenneth E Windom

329

Concrete and Abstract Voronoi Diagrams  

Microsoft Academic Search

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

Rolf Klein

1989-01-01

330

Telesynergy V3 Wiring Diagram  

Cancer.gov

Extron 8 port Video/Audio Switch WAVE Camera Telesynergy v3 Wiring Diagram ISDN T1/PRI Module CTRLR 0 Legend: S-Video Audio VGA DVI USB RS-232 Serial Microphone Ethernet Planar C5i AMD Exam Cam Canon Document Camera Olympus BX51 Sony DVD Recorder JVC

331

Policy Specification Using Sequence Diagrams  

E-print Network

of Information Science and Media Studies and at the Faculty of Social Sciences at the Uni- versity of BergenPolicy Specification Using Sequence Diagrams Applied to Trust Management Bjørnar Solhaug which was funded by the Research Council of Norway. The ENFORCE project was a joint initiative between

Stølen, Ketil

332

State diagrams of linear sequential machines  

E-print Network

14 37 38 LIST OF FIGURFS FIGURE Page 1. State Diagram M . 2. Diagram of Example l. 3. Diagram of Example 2. 4. Diagram of Example 3. 5. State Diagram of a Linear Sequential Machine. 6. State Diagram of a Sequential Machine . 24 26 35 36.... A sequential machine N is a five-tuple &S, I, s, 6, x& where S is a set of states, I is a set of input symbols, A is a set of output symbols, s is the transition function, and ~ is the output function. A particular three-state machine h1=&S, I, a...

English, Linda Sue

1977-01-01

333

Triton clustering in neutron rich nuclei and Ikeda - like diagrams  

E-print Network

It is shown here that new experiments confirm author's recent prediction of a strong tendency for triton clustering in light neutron rich nuclei. As such the neutron halo phenomena is naturally explained here. Prediction of exotic molecular states rich in tritonic clusters is made here through new Ikeda-like diagram configurations for the nuclei ${^{3Z}_Z} A_{2Z}$ . Hence this model is well confirmed experimentally and makes several new predictions which can be tested experimentally.

Afsar Abbas

2003-07-14

334

Orbit design concepts for Jupiter orbiter missions  

NASA Technical Reports Server (NTRS)

Advanced mission and orbit planning efforts are currently in progress for a Mariner-class Jupiter orbiter. Baseline spacecraft and orbit design criteria are the goals of a NASA effort to define such a mission. Orbit design concepts that have been discovered during the early stages of mission planning are both challenging and exciting. A description is given of several such concepts that may greatly increase the flexibility and scientific return of orbiters designed for close study of the Galilean satellites and exploration of the Jovian system. Some new jargon is introduced in discussions to describe the exploitation of gravity-assist trajectories using the giant satellites for orbit control. Orbit 'pumping' and 'cranking' and 'resonance hopping' are defined and shown to be dynamically feasible means of controlling the orbit and, thus, the scientific return. A candidate encounter sequence is presented for an equatorial tour of the Galilean moons.

Uphoff, C.; Roberts, P. H.; Friedman, L. D.

1974-01-01

335

Generation of powder compaction response diagrams  

SciTech Connect

The effect of elastic compliances in the testing system is shown to have a considerable influence on the compaction diagram generated via an automatic procedure. Proper accounting of this effect allows rapid and accurate diagrams to be made.

Matsumoto, R.L.K.

1986-10-01

336

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding.  

PubMed

One hundred complexes have been investigated exhibiting D-X···A interactions, where X = H, Cl or Li and DX is the 'X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized 'Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the XA bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X···A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared- and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X···A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding. PMID:25127185

Shahi, Abhishek; Arunan, Elangannan

2014-11-14

337

The Butterfly Diagram Internal Structure  

NASA Astrophysics Data System (ADS)

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

Ternullo, Maurizio

2013-06-01

338

Reasoning on UML class diagrams  

Microsoft Academic Search

UML is the de-facto standard formalism for software design and analysis. To sup- port the design of large-scale industrial applications, sophisticated CASE tools are available on the market, that provide a user-friendly environment for editing, stor- ing, and accessing multiple UML diagrams. It would be highly desirable to equip such CASE tools with automated reasoning capabilities, such as those studied

Daniela Berardi; Diego Calvanese; Giuseppe De Giacomo

2005-01-01

339

Reasoning on UML Class Diagrams  

Microsoft Academic Search

UML is the de-facto standard formalism for software design and analysis. To support the design of large-scale industrial applications, sophisticated CASE tools are available on the market, that provide a user-friendly environment for editing, storing, and accessing multiple UML diagrams. It would be highly desirable to equip such CASE tools with automated reasoning capabilities in order to detect relevant formal

Daniela Berardi; Andrea Cal; Diego Calvanese; Giuseppe De Giacomo

2003-01-01

340

T-X Phase Diagrams  

NSDL National Science Digital Library

This is a 15 page tutorial and problem set designed to get students familiar with T-X diagrams, their implications, and uses. Students start by reading but, after 10-15 minutes, the room becomes noisy as they work their way through the questions at the end. Often there are "Eureka" moments as they all of a sudden grasp some fundamental principles. It is also interesting to hear them try to explain these insights to others.

Dexter Perkins

341

Phase Diagrams and Chemographic Projections  

NSDL National Science Digital Library

This exercise is a good way to get students thinking about the phase rule, metastable and stable reactions and phase diagrams. The exercise contains a lot of reading, and is suitable for in-class work or for homework. The idea is that students can do this on their own with little help from their instructor. The students only answer a few questions making this is more of a tutorial than a worksheet.

Dexter Perkins

342

Online Diagnosis Using Influence Diagrams  

Microsoft Academic Search

\\u000a This paper presents the utilization of influence diagrams in the diagnosis of industrial processes. The diagnosis in this\\u000a context signifies the early detection of abnormal behavior, and the selection of the best recommendation for the operator\\u000a in order to correct the problem or minimize the effects. A software architecture is presented, based on the Elvira package, including the connection with

Baldramino Morales Sánchez; Pablo H. Ibargüengoytia

2004-01-01

343

Algorithm Discovery with Venn Diagrams  

NSDL National Science Digital Library

This lesson is designed to develop students' abilities to create algorithms or a set of directions to solve a problem. In this lesson, the problem is to determine the rules in a Venn diagram. This lesson provides links to discussions and activities related to the topic as well as suggested ways to integrate them into the lesson. Finally, the lesson provides links to follow-up lessons designed for use in succession with the current one.

2011-05-23

344

INCONEL 718: A solidification diagram  

NASA Astrophysics Data System (ADS)

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

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

1989-10-01

345

2IW05 Software Specification Class Diagrams  

E-print Network

2IW05 ­ Software Specification Class Diagrams Mohammad Mousavi Formal Systems Analysis (FSA) Model-Driven Software Engineering Department of Computer Science TU/Eindhoven September 7, 2012 #12;News 1 Send me specification: 1 Class diagram: data types, their operations and dependencies (extended ERDs) 2 Package diagram

Mousavi, Mohammad

346

On Class Diagrams, Crossings and Metrics  

Microsoft Academic Search

UML class diagrams, internationally specified and widely used in software engineering, are a great challenge in automatic drawing of graphs. Due to the complex nature of UML class diagrams and the requirements of software engineers, who need to read these diagrams, layout rules and algo- rithms for general graphs can not be applied without adaptions, extensions and modifications. In this

Holger Eichelberger

2005-01-01

347

Diagrams in Biology1 Laura Perini  

E-print Network

, as biologists plan experiments with flow charts, and draw models to represent hypotheses for consideration representational features of diagrams. Analysis of the relation between the forms and contents of diagrams1 Diagrams in Biology1 Laura Perini Department of Philosophy Pomona College Abstract Biologists

McBurney, Peter

348

Semantics of the Domain of Flow Diagrams  

Microsoft Academic Search

A domain of flow diagrams similar to that proposed by Scott, a domain of linear flow diagrams proposed by Goguen et al , a domain of decision table diagrams involving mfimtary branching, and a domain of processes based on the ideas of Milner and Beklc are each provided with a direct semantics, closely related to partial-function semantics, and a continuation

John C. Reynolds

1977-01-01

349

A Layout Algorithm for Data Flow Diagrams  

Microsoft Academic Search

A layout algorithm is presented that allows the automatic drawing of data flow diagrams, a diagrammatic representation widely used in the functional analysis of information systems. A grid standard is defined for such diagrams, and aesthetics for a good readability are identified. The layout algorithm receives as input an abstract graph, specifying connectivity relations between the elements of the diagram,

Carlo Batini; Enrico Nardelli; Roberto Tamassia

1986-01-01

350

A Formal Semantics of Data Flow Diagrams  

Microsoft Academic Search

This document presents a full version of the formal semantics of data ow diagrams reported in [Larsen&93]. Data Flow Diagrams are used in Structured Analysis and are based on an abstract model for data flow transformations. The semantics consists of a collection of VDM functions, transforming an abstract syntax representation of a data flow diagram into an abstract syntax representation

Peter Gorm Larsen; Nico Plat; Hans Toetenel

1994-01-01

351

Retrieving Information from Data Flow Diagrams  

Microsoft Academic Search

For reverse engineering, we need tools that can extract information from documents written before routine digital storage was feasible. Documents contain both text and diagrams; data flow diagrams play a prominent role in software documents. Using current techniques, it is possible to recover the information in a data flow diagram by scanning the printed document and processing the data obtained.

Gregory Butler; Peter Grogono; Rajjan Shinghal; Indra A. Tjandra

1995-01-01

352

Shuttle Orbiter Uplink Text and Graphics System  

NASA Technical Reports Server (NTRS)

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.

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

1978-01-01

353

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

ERIC Educational Resources Information Center

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…

Py, Dominique; Auxepaules, Ludovic; Alonso, Mathilde

2013-01-01

354

Frontier molecular orbital analysis of dual fluorescent dyes: predicting two-color emission in N-aryl-1,8-naphthalimides.  

PubMed

A 3 x 3 matrix of disubstituted N-aryl-1,8-naphthalimides was synthesized for the evaluation and discovery of dual fluorescence (DF). The matrix elements included for this study were based on a predictive model that is proposed as a seesaw balanced photophysical model. This model serves as a guide to optimize the dual fluorescence emission from N-phenyl-1,8-naphthalimides by appropriate placement of substituent groups at both the 4-position of the N-arene as well as the 4'-position of the naphthalene ring. Steady-state fluorescence studies under a variety of solvents indicate that four of the nine dyes in the matrix are dual fluorescent. To provide a more quantitative description of the model, cyclic voltammetry experiments were used to calculate HOMO/LUMO energies of the aromatic components that comprise these DF dyes and give evidence in support for potential mixing of S1 and S2 excited states. Given the difficulties in predicting excited state properties such as molecular fluorescence, this ratio of four out of nine "hits" for discovering DF signifies proof of principle for this proposed model and should provide a rational basis for the synthesis of future DF 1,8-naphthalimide systems. PMID:20626080

Nandhikonda, Premchendar; Begaye, Michael P; Cao, Zhi; Heagy, Michael D

2010-07-21

355

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)

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.

Oyamada, Takayuki; Tachikawa, Masanori

2014-08-01

356

Origin and use of crystallization phase diagrams.  

PubMed

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

Rupp, Bernhard

2015-03-01

357

PROTOTYPING LHC ORBIT CONTROL  

Microsoft Academic Search

Orbit correction consists in varying the strengths of the corrector magnets to make the measured beam position match a predefined reference. In the two LHC rings, this involves around 1000 beam position monitors and over 500 orbit correctors in each plane. The orbit control loop of the LHC must be able to compensate orbit drifts at frequencies between 10?2 and

J. Wenninger; T. Wijnands; B. Srinivasan

2002-01-01

358

Orbital dystopia due to orbital roof defect.  

PubMed

We performed a retrospective review of patients who presented with delayed dystopia as a consequence of an orbital roof defect due to fractures and nontraumatic causes to search for a correlation between orbital roof defect size and surgical indications for the treatment thereof. Retrospective analyses were performed in 7 patients, all of whom presented with delayed dystopia due to orbital roof defects, between January 2001 and June 2011. The causes of orbital roof defects were displaced orbital roof fractures (5 cases), tumor (1 case), and congenital sphenoid dysplasia (1 case). All 7 patients had initially been treated conservatively and later presented with significant dystopia. The sizes of the defects were calculated on computed tomographic scans. Among the 7 patients, aspiration of cerebrospinal fluid, which caused ocular symptoms, in 1 patient with minimal displaced orbital roof and reconstruction with calvarial bone, titanium micromesh, or Medpor in 6 other patients were performed. The minimal size of the orbital roof in patients who underwent orbital roof reconstruction was 1.2 cm (defect height) x 1.0 cm (defect length), 0.94 cm(2). For all patients with orbital dystopia, displacement of the globe was corrected without any complications, regardless of whether the patient was evaluated grossly or by radiology. In this retrospective study, continuous monitoring of clinical signs and active surgical management should be considered for cases in which an orbital roof defect is detected, even if no definite symptoms are noted, to prevent delayed sequelae. PMID:24163861

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

2013-01-01

359

Working With Orbits  

NSDL National Science Digital Library

This site offers two programs to illustrate how orbits work. The Orbital Elements calculator contains animations to see how the appearance of an orbit depends on the values of the orbital elements which include distance from the Sun, eccentricity, pericenter location and anomaly. This is available in two or three dimensions. The Solar System allows users to watch several planets in our Solar System simultaneously orbit the Sun. An additional object (asteroid or comet) is present and users change the orbital parameters to see what types of orbits are possible for this object.

Douglas Hamilton

360

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)

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 (?H). 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 (?), chemical potential (?), Electro negativity (?) and electrophilicity values (?) 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.

Govindasamy, P.; Gunasekaran, S.

2015-02-01

361

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.  

PubMed

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 4000-450cm(-1) and 4000-50cm(-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 (?H). 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 (?), chemical potential (?), Electro negativity (?) and electrophilicity values (?) 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. PMID:25459716

Govindasamy, P; Gunasekaran, S

2014-10-24

362

Orbital fractures: a review  

PubMed Central

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

Joseph, Jeffrey M; Glavas, Ioannis P

2011-01-01

363

Quantum Monte Carlo and high-level ab initio molecular orbital investigation of dissociation channels of the positronic alkali-metal hydrides, [XH;e+] (X = Li, Na, and K)  

NASA Astrophysics Data System (ADS)

Energy thresholds for dissociation channels of positronic alkali-metal hydrides, [XH;e+] (X = Li, Na, and K), to XH + e+(positron dissociation), XH+ + Ps (positronium dissociation), and X+ + [H-;e+] (positronic hydride ion dissociation) have been calculated using quantum Monte Carlo and high-level ab initio molecular orbital methods, and including quantum zero-point vibrational energy of all of the particles. As the atomic number of X increases from Li to K, the dissociation energy to XH + e+ increases because the dipole moment of XH increases with the atomic number of X, while the dissociation energy to XH+ + Ps decreases. The energy threshold for the ionic dissociation to X+ + [H-;e+] is also reduced, and we obtain 0.975 (3) eV, 0.573 (12) eV, and 0.472 (19) eV for [LiH;e+], [NaH;e+], and [KH;e+], respectively, for this channel. Our results strongly support the conclusion that, among these three channels, the lowest energy dissociation for [XH;e+] is the pathway to X+ + [H-;e+], where X = Li, Na, and K.

Yamada, Yurika; Kita, Yukiumi; Tachikawa, Masanori; Towler, Mike D.; Needs, Richard J.

2014-03-01

364

Lunar Reconnaissance Orbiter Orbit Determination Accuracy Analysis  

NASA Technical Reports Server (NTRS)

Results from operational OD produced by the NASA Goddard Flight Dynamics Facility for the LRO nominal and extended mission are presented. During the LRO nominal mission, when LRO flew in a low circular orbit, orbit determination requirements were met nearly 100% of the time. When the extended mission began, LRO returned to a more elliptical frozen orbit where gravity and other modeling errors caused numerous violations of mission accuracy requirements. Prediction accuracy is particularly challenged during periods when LRO is in full-Sun. A series of improvements to LRO orbit determination are presented, including implementation of new lunar gravity models, improved spacecraft solar radiation pressure modeling using a dynamic multi-plate area model, a shorter orbit determination arc length, and a constrained plane method for estimation. The analysis presented in this paper shows that updated lunar gravity models improved accuracy in the frozen orbit, and a multiplate dynamic area model improves prediction accuracy during full-Sun orbit periods. Implementation of a 36-hour tracking data arc and plane constraints during edge-on orbit geometry also provide benefits. A comparison of the operational solutions to precision orbit determination solutions shows agreement on a 100- to 250-meter level in definitive accuracy.

Slojkowski, Steven E.

2014-01-01

365

Spectroscopic (FT-IR, FT-Raman, and UV-visible) and quantum chemical studies on molecular geometry, Frontier molecular orbitals, NBO, NLO and thermodynamic properties of 1-acetylindole  

NASA Astrophysics Data System (ADS)

Quantum chemical calculations of ground state energy, geometrical structure and vibrational wavenumbers of 1-acetylindole were carried out using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. The FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational wavenumbers were calculated and a good correlation between experimental and scaled calculated wavenumbers has been accomplished. Electric dipole moment, polarizability and first static hyperpolarizability values of 1-acetylindole have been calculated at the same level of theory and basis set. The results show that the 1-acetylindole molecule possesses nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-Visible spectrum of the molecule was recorded in the region 200-500 nm and the electronic properties like HOMO and LUMO energies and composition were obtained using TD-DFT method. The calculated energies and oscillator strengths are in good correspondence with the experimental data. The thermodynamic properties of the compound under investigation were calculated at different temperatures.

Shukla, Vikas K.; Al-Abdullah, Ebtehal S.; El-Emam, Ali A.; Sachan, Alok K.; Pathak, Shilendra K.; Kumar, Amarendra; Prasad, Onkar; Bishnoi, Abha; Sinha, Leena

2014-12-01

366

Pilot-wave hydrodynamics in a rotating frame: Exotic orbits  

SciTech Connect

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

Oza, Anand U.; Harris, Daniel M.; Rosales, Rodolfo R.; Bush, John W. M., E-mail: bush@math.mit.edu [Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Wind-Willassen, Øistein [Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby (Denmark)

2014-08-15

367

W-reps, nilp orbits, orbit method  

E-print Network

W reps nilp orbits W reps Explaining the arrows Remembrance of things past Weyl group Institute of Technology Lie groups: structure, actions and representations In honor of Joe Wolf, on his 75th of things past Outline What is representation theory about? Nilpotent orbits from G reps W reps from G reps

Vogan, David

368

Efficient orbit integration by orbital longitude methods  

NASA Astrophysics Data System (ADS)

Recently we developed a new formulation of numerical integration of orbital motion named manifold correction methods. The main trick is to keep rigorously the consistency of some physical relations such as that of the orbital energy, of the orbital angular momentum, or of the Laplace integral of a binary subsystem. This maintenance is done by applying a sort of correction to the integrated variables at every integration step. Typical methods of correction are certain geometric transformation such as the spatial scaling and the spatial rotation, which are commonly used in the comparison of reference frames, or mathematically-reasonable operations such as the modularization of angle variables into the standard domain [-?, ?). The finally-evolved form of the manifold correction methods is the orbital longitude methods, which enable us to conduct an extremely precise integration of orbital motions. In the unperturbed orbits, the integration errors are suppressed at the machine epsilon level for an infinitely long period. In the perturbed cases, on the other hand, the errors initially grow in proportion to the square root of time and then increase more rapidly, the onset time of which depends on the type and the magnitude of perturbations. This feature is also realized for highly eccentric orbits by applying the same idea to the KS-regularization. Expecially the introduction of time element greatly enhances the performance of numerical integration of KS-regularized orbits whether the scaling is applied or not.

Fukushima, Toshio

369

A layout algorithm for data flow diagrams  

SciTech Connect

A layout algorithm is presented that allows the automatic drawing of data flow diagrams, a diagrammatic representation widely used in the functional analysis of information systems. A grid standard is defined for such diagrams, and aesthetics for a good readability are identified. The layout algorithm receives as input an abstract graph, specifying connectivity relations between the elements of the diagram, and produces as output a corresponding diagram according to the aesthetics. The basic strategy is to build incrementally the layout; first, a good topology is constructed with few crossings between edges; subsequently, the shape of the diagram is determined in terms of angles appearing along edges; and finally, dimensions are given to the graph, obtaining a grid skeleton for the diagram.

Batini, C.; Nardelli, E.; Tamassia, R.

1986-04-01

370

Nonverbal Poetry: Family Life-Space Diagrams  

Microsoft Academic Search

The purpose of this article is to examine life-space diagrams as a form of nonverbal poetry. Family life-space diagrams, by their very nature, are a nonverbal blend of lyrical, narrative, and dramatic poetry. The life-space diagram taps personal feelings, tells a story, and characterizes a particular life situation. The human memory process, with its multilevel consciousness, provides the basis for

Donald R. Bardill

2001-01-01

371

Variable stars across the observational HR diagram  

Microsoft Academic Search

An overview of pulsating variable stars across the observational Hertzprung-Russel (HR) diagram is presented, together with a summary of their global properties. The HR diagram is presented with a third colour-coded dimension, visualizing the fraction of variable, the amplitude of variability or the period of variability. The distribution of variable stars in the other observational diagrams, such as the Period-Amplitude

Laurent Eyer; Nami Mowlavi

2008-01-01

372

Object Flow Definition for Refined Activity Diagrams  

Microsoft Academic Search

Activity diagrams are a well-known means to model the control flow of system behavior. Their expressiveness can be enhanced\\u000a by using their object flow notation. In addition, we refine activities by pairs of pre- and post-conditions formulated by\\u000a interrelated object diagrams. To define a clear semantics for refined activity diagrams with object flow, we use a graph transformation\\u000a approach. Control

Stefan Jurack; Leen Lambers; Katharina Mehner; Gabriele Taentzer; Gerd Wierse

2009-01-01

373

Variable stars across the observational HR diagram  

E-print Network

An overview of pulsating variable stars across the observational Hertzprung-Russel (HR) diagram is presented, together with a summary of their global properties. The HR diagram is presented with a third colour-coded dimension, visualizing the fraction of variable, the amplitude of variability or the period of variability. The distribution of variable stars in the other observational diagrams, such as the Period-Amplitude diagram, is also presented. Some of the progresses performed in the field of variable stars during the last decade are briefly summarized, and future projects that will improve our knowledge of variable stars are mentioned.

Laurent Eyer; Nami Mowlavi

2007-12-21

374

Hofstadter Butterfly Diagram in Noncommutative Space  

E-print Network

We study an energy spectrum of electron moving under the constant magnetic field in two dimensional noncommutative space. It take place with the gauge invariant way. The Hofstadter butterfly diagram of the noncommutative space is calculated in terms of the lattice model which is derived by the Bopp's shift for space and by the Peierls substitution for external magnetic field. We also find the fractal structure in new diagram. Although the global features of the new diagram are similar to the diagram of the commutative space, the detail structure is different from it.

Hidenori Takahashi; Masanori Yamanaka

2006-06-23

375

Atomic Orbital Shapes  

NSDL National Science Digital Library

This applet shows 3-dimensional representations of hydrogenic orbital surfaces. Orbital phase is shown by the different colors. The images are rotatable and scalable. This applet will run very slowly on older, slower machines.

376

Lunar orbiting prospector  

NASA Technical Reports Server (NTRS)

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

1988-01-01

377

Phase diagram of ammonium nitrate  

NASA Astrophysics Data System (ADS)

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

Dunuwille, Mihindra; Yoo, Choong-Shik

2013-12-01

378

Hubble's diagram and cosmic expansion  

NASA Astrophysics Data System (ADS)

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.

Kirshner, Robert P.

2004-01-01

379

THE RHIC ORBIT CONTROL  

Microsoft Academic Search

The paper describes the methods used at RHIC collider for both global orbit correction over the whole ring and lo- cal orbit control in particular regions. Most routinely used tools of the local orbit control include the beam separa- tion, to avoid beam-beam effects at the acceleration, and the beam steering for collisions. The correction on the ramp uses feed-forward

V. Ptitsyn; T. Satogata

380

Mars Reconnaissance Orbiter  

NSDL National Science Digital Library

This is the mission web site for the Mars Reconnaissance Orbiter, which went into orbit around Mars on March 10, 2006. The site provides links to updates and information about the project. The site features links to Mars Reconnaissance Orbiter images, animations, and datasets. Science operations commence in November, 2006.

Jet Propulsion Laboratory

381

Five Equivalent d Orbitals  

ERIC Educational Resources Information Center

Amplifies and clarifies a previous paper on pyramidal d orbitals. Discusses two sets of pyramid d orbitals with respect to their maximum bond strength and their symmetry. Authors described the oblate and prolate pentagonal antiprisms arising from the two sets of five equivalent d orbitals. (RR)

Pauling, Linus; McClure, Vance

1970-01-01

382

Orbital-Lifetime Program  

NASA Technical Reports Server (NTRS)

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

Orr, L. H.

1986-01-01

383

SEASAT B orbit synthesis  

NASA Technical Reports Server (NTRS)

Addition were made to Battelle's Interactive Graphics Orbit Selection (IGOS) program; IGOS was exercised via telephone lines from JPL, and candidate SEASAT orbits were analyzed by Battelle. The additions to the program enable clear understanding of the implications of a specific orbit to the diverse desires of the SEASAT user community.

Rea, F. G.; Warmke, J. M.

1976-01-01

384

A tutorial on flow diagrams: A tool for developing the structure of multicomponent phase diagrams  

Microsoft Academic Search

The tabular form of multiphase equilibria in temperature- or pressure-ordered sequence, often referred to as flow diagrams,\\u000a shows the interrelations that exist among the various types or classes of equilibria in a system. These interrelations establish\\u000a the structures of the various forms of phase diagrams. Flow diagrams have been used to simplify the presentation of complex\\u000a ternary phase diagrams. However,

R. G. Connell

1994-01-01

385

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

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

386

Equations of state and phase diagrams of hydrogen isotopes  

SciTech Connect

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.

Urlin, V. D., E-mail: urlin@vniief.ru [Russian Federal Nuclear Center All-Russia Research Institute of Experimental Physics (Russian Federation)

2013-11-15

387

Phase diagram and excitations of a Shiba molecule  

NASA Astrophysics Data System (ADS)

We analyze the phase diagram associated with a pair of magnetic impurities trapped in a superconducting host. The natural interplay between Kondo screening, superconductivity, and exchange interactions leads to a rich array of competing phases, whose transitions are characterized by discontinuous changes of the total spin. Our analysis is based on a combination of numerical renormalization group techniques as well as semiclassical analytics. In addition to the expected screened and unscreened phases, we observe a new molecular doublet phase where the impurity spins are only partially screened by a single extended quasiparticle. Direct signatures of the various Shiba molecule states can be observed via radio-frequency spectroscopy.

Yao, N. Y.; Moca, C. P.; Weymann, I.; Sau, J. D.; Lukin, M. D.; Demler, E. A.; Zaránd, G.

2014-12-01

388

Measuring the Jamming Phase Diagram for Repulsive Liquids  

NASA Astrophysics Data System (ADS)

We perform constant shear-rate and constant stress nonequilibrium molecular dynamics simulations on liquids and glasses with purely repulsive interactions in both 2D and 3D. Sheared glasses jam and become disordered solids when the applied shear stress is decreased below the yield stress. We measure the yield stress as a function of temperature and packing fraction for this model repulsive system, and thus construct its jamming phase diagram. We also discuss whether the measurements of the yield stress using the constant shear-rate and constant stress ensembles give consistent results.

Xu, Ning; O'Hern, Corey

2003-03-01

389

Orbit Software Suite  

NASA Technical Reports Server (NTRS)

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

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

2012-01-01

390

OTV orbital tanking systems  

NASA Technical Reports Server (NTRS)

Orbital transfer of cryogenic propellants could benefit spacecraft and Orbital Transfer Vehicle (OTV) missions in the 1980s by supplying main propulsion, attitude control, or other fluid systems. The Space Shuttle can operate as a tanker when equipped with cryogenic propellant storage and orbital transfer systems. The key technologies are multilayer insulation, capillary propellant acquisition, zero-g gaging, orbital chilldown, and possibly large flight weight dewars. The technologies and operations could be realistically demonstrated using a Centaur that has been integrated with the Shuttle. Orbital refueling capability can enhance the usefulness of the whole Shuttle program

Heald, D. A.; Merino, F.

1979-01-01

391

Environmental dynamics at orbital altitudes  

NASA Technical Reports Server (NTRS)

The work reported involved the improvement of aerodynamic theory for free molecular and transition flow regimes. The improved theory was applied to interpretation of the dynamic response of objects traveling through the atmosphere. Satellite drag analysis includes analysis methods, atmospheric super rotation effects, and satellite lift effects on orbital dynamics. Transition flow regimes were studied with falling sphere data and errors resulting in inferred atmospheric parameters from falling sphere techniques. Improved drag coefficients reveal considerable error in previous falling sphere data. The drag coefficient has been studied for the entire spectrum of Knudsen Number and speed ratio, with particular emphasis on the theory of the very low-speed ratio regime.

Karr, G. R.

1976-01-01

392

Hybridization of Rydberg electron orbitals by molecule formation  

E-print Network

The formation of ultralong-range Rydberg molecules is a result of the attractive interaction between Rydberg electron and polarizable ground state atom in an ultracold gas. In the nondegenerate case the backaction of the polarizable atom on the electronic orbital is minimal. Here we demonstrate, how controlled degeneracy of the respective electronic orbitals maximizes this backaction and leads to stronger binding energies and lower symmetry of the bound dimers. Consequently, the Rydberg orbitals hybridize due to the molecular bond.

Gaj, A; Ilzhöfer, P; Löw, R; Hofferberth, S; Pfau, T

2015-01-01

393

Lunar Reconnaissance Orbiter Orbit Determination Accuracy Analysis  

NASA Technical Reports Server (NTRS)

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

Slojkowski, Steven E.

2014-01-01

394

Labeled floor diagrams for plane curves  

Microsoft Academic Search

Floor diagrams are a class of weighted oriented graphs introduced by E. Brugalle and the second author. Tropical geometry arguments lead to combinatorial descriptions of (ordinary and relative) Gromov-Witten invariants of projective spaces in terms of floor diagrams and their generalizations. In a number of cases, these descriptions can be used to obtain explicit (direct or recursive) formulas for the

Sergey Fomin; Grigory Mikhalkin

2009-01-01

395

Empirical Validation of Class Diagram Metrics  

Microsoft Academic Search

As a key early artefact in the development of OO software, the quality of class diagrams is crucial for all later design work and could be a major determinant for the quality of the software product that is finally delivered. Quantitative measurement instruments are useful to assess class diagram quality in an objective way, thus avoiding bias in the quality

Marcela Genero; Mario Piattini; Coral Calero

2002-01-01

396

Activity Diagrams Patterns for Modeling Business Processes  

E-print Network

on Software Engineering Research, Management and Applications (SERA 2013). The final publication is available consider in this paper the UML since it offers also many other diagrams (classes, state ma- chine, etc so as to build complex activity diagrams. Our ap- proach also takes classes into account. We have

André, Étienne

397

Timing Diagrams: Formalization and Algorithmic Verification  

E-print Network

generated by B¨uchi automata in timing diagram languages is decidable. The result relies on a correlation foundation for both reasoning and theoretical analyses. This paper presents a timing dia­ gram logicTiming Diagrams: Formalization and Algorithmic Verification Kathi Fisler \\Lambda Department

Fisler, Kathryn

398

DECISION DIAGRAMS AND PASS TRANSISTOR LOGIC SYNTHESIS  

E-print Network

DECISION DIAGRAMS AND PASS TRANSISTOR LOGIC SYNTHESIS V. Bertacco S. Minato P. Verplaetse L. Benini by ARPA, under grant No. DABT63-95-C-0049. #12;Decision Diagrams and Pass Transistor Logic Synthesis V transistors and domino logic. The synthesis of these cells is based on BDD and ZBDD representations

De Micheli, Giovanni

399

Resummation of Cactus Diagrams in Lattice QCD  

E-print Network

We show how to perform a resummation, to all orders in perturbation theory, of a certain class of gauge invariant diagrams in Lattice QCD. These diagrams are often largely responsible for lattice artifacts. Our resummation leads to an improved perturbative expansion. Applied to a number of cases of interest, this expansion yields results remarkably close to corresponding nonperturbative estimates.

H. Panagopoulos; E. Vicari

1998-06-08

400

THE QCD PHASE DIAGRAM AT FINITE DENSITY.  

SciTech Connect

We study the density of states method to explore the phase diagram of the chiral transition on the temperature and quark chemical potential plane. Four quark flavours are used in the analysis. Though the method is quite expensive small lattices show an indication for a triple-point connecting three different phases on the phase diagram.

SCHMIDT, C.; FODOR, Z.; KATZ, S.

2005-07-25

401

Penrose diagram for a transient black hole  

Microsoft Academic Search

A Penrose diagram is constructed for a spatially coherent black hole that smoothly begins an accretion, and then excretes symmetrically as measured by a distant observer, with the initial and final states described by a metric of the Minkowski form. Coordinate curves on the diagram are computationally derived. Causal relationships between spacetime regions are briefly discussed. The life cycle of

James Lindesayand; Paul Sheldon

2010-01-01

402

Building Path Diagrams for Multilevel Models  

ERIC Educational Resources Information Center

Multilevel models have come to play an increasingly important role in many areas of social science research. However, in contrast to other modeling strategies, there is currently no widely used approach for graphically diagramming multilevel models. Ideally, such diagrams would serve two functions: to provide a formal structure for deriving the…

Curran, Patrick J.; Bauer, Daniel J.

2007-01-01

403

Formalizing Spider Diagrams Joseph (Yossi) Gil  

E-print Network

]. The Swiss mathemati- cian Leonhard Euler (1707-1783) introduced the notation we now call Euler circles (or- lar and intuitive Venn diagrams and Euler circles. The language design emphasized scalability Euler diagrams) [1] to illus- trate relations between sets. This notation uses the topo- logical

Kent, University of

404

Simplifying computation of dynamic influence diagrams  

Microsoft Academic Search

Influence diagrams (EDs) are based on Bayesian networks (BNs) and decision theory, and they are powerful tools for representing and processing problems of agents. An approach of decomposition and incorporation is developed to solve problems of multi-agent system based on influence diagrams and dynamic Bayesian networks (DBNs) that is intractable for exact calculation. In additional, we discuss realizing decision of

Hong-Liang Yao; Hao Wang; You-Sheng Zhang; Xue-Gang Hu; Bao-Fu Fang

2004-01-01

405

Abstract Voronoi Diagrams Revisited Elmar Langetepe  

E-print Network

bisectors have infinitely many intersections, so that it was not covered by the existing AVD theory Voronoi Diagrams (AVDs) were introduced by the first author in [20], as a unifying concept for both, structure theory and algorithmic computation. The basic observation behind AVDs was that Voronoi diagrams

Klein, Rolf

406

A Formal Semantics of Data Flow Diagrams  

Microsoft Academic Search

semantics Abstract. This paper presents a formal semantics of data flow diagrams as used in Structured Analysis, based on an abstract model for data flow transformations. The semantics consists of a collection of VDM functions, transforming an abstract syntax representation of a data flow diagram into an abstract syntax representation of a VDM specification. Since this transformation is executable, it

407

Local helioseismology using ring diagram analysis  

Microsoft Academic Search

Ring diagram analysis is an extension of global helioseismology that is applied to small areas on the Sun. It can be used to infer the horizontal components of large scale flows as well as the structure, and variations thereof, in the outer convection zone. We describe below the ring-diagram analysis technique, and some results obtained using this technique.

H. M. Antia; S. Basu

2007-01-01

408

Architecture flow diagrams under teamwork reg sign  

Microsoft Academic Search

The Teamwork CASE tool allows Data Flow Diagrams (DFDs) to be maintained for structured analysis. Fermilab has extended teamwork under UNIX{trademark} to permit Hatley and Pirbhai Architecture Flow Diagrams (AFDs) to be associated with DFDs and subsequently maintained. This extension, called TWKAFD, allows a user to open an AFD, graphically edit it, and replace it into a TWKAFD maintained library.

Nicinski

1992-01-01

409

HMI ring diagram analysis II. Data products  

Microsoft Academic Search

The combination of high resolution, spatial coverage, and continuity of photospheric Doppler and other data from HMI has allowed us to embark on a program of systematic exploration of solar subsurface flows and thermal structure variations using the technique of ring-diagram analysis on an unprecedented scale. There are two ring-diagrams pipelines, as described in [1]. In this paper we discuss

R. S. Bogart; C. Baldner; S. Basu; D. A. Haber; M. C. Rabello-Soares

2011-01-01

410

Chord Diagrams and Coxeter Links Eriko Hironaka  

E-print Network

Chord Diagrams and Coxeter Links Eriko Hironaka April 23, 2003 Abstract This paper presents a construction of #12;bered links (K; #6;) out of chord diagrams L. Let be the incidence graph of L. Under; S). Lehmer's problem is solved for the monodromy of these Coxeter links. 1 1 Introduction A chord

Hironaka, Eriko

411

Chord Diagrams and Coxeter Links Eriko Hironaka  

E-print Network

Chord Diagrams and Coxeter Links Eriko Hironaka February 28, 2003 Abstract This paper presents a construction of #12;bered links (K; #6;) out of chord diagrams L. Let be the incidence graph of L. Under; S). Lehmer's problem is solved for the monodromy of these Coxeter links. 1 1 Introduction A chord

Aluffi, Paolo

412

Aerothermal analysis for the Mars Reconnaissance Orbiter  

Microsoft Academic Search

The force on and the heat flux to the NASA Mars Reconnaissance Orbiter (MRO) during drag passes are analyzed. Aerobraking takes place in the higher\\/rarefied levels of the Martian atmosphere, where traditional continuum flui d dynamics methods cannot be applied. Therefore, molecular gas dynamics simulations such as the Direct Simulation Monte Carlo Method are used to calculate these flow fields

Michail A. Gallis; Wahid L. Hermina; James D. Chapel; Mark A. Johnson

2004-01-01

413

Painless orbital myositis.  

PubMed

Idiopathic orbital inflammation is the third most common orbital disease, following Graves orbitopathy and lymphoproliferative diseases. We present a 11 year old girl with 15 days history of painless diplopia. There was no history of fluctuation of symptoms, drooping of eye lids or diminished vision. She had near total restricted extra-ocular movements and mild proptosis of the right eye. There was no conjunctival injection, chemosis, or bulb pain. There was no eyelid retraction or lid lag. Rest of the neurological examination was unremarkable.Erythrocyte sedimentation rate was raised with eosinophilia. Antinuclear antibodies were positive. Liver, renal and thyroid functions were normal. Antithyroid, double stranded deoxyribonucleic acid and acetylcholine receptor antibodies were negative. Repetitive nerve stimulation was negative. Magnetic resonance imaging (MRI) of the orbit was typical of orbital myositis. The patient responded to oral steroids. Orbital myositis can present as painless diplopia. MRI of orbit is diagnostic in orbital myositis. PMID:22919201

Chakor, Rahul T; Santhosh, N S

2012-07-01

414

Controlling the NGST Orbit  

NASA Astrophysics Data System (ADS)

NGST will likely be placed in an elliptical orbit around the external collinear Lagrange point L2. However, the orbit is dynamically unstable and on-board thrusters must be used to make corrections to the orbit over time. The limited fuel available for such corrections may well limit the mission lifetime. Due to its large (200 m2) heat shield, NGST will be subject to significant perturbations by solar radiation pressure. We present an analysis for controlling the orbit against various perturbations, including solar radiation pressure. Ignoring effects of nonlinearity, we obtain an analytic description of the orbital evolution subject to arbitrary time-dependent perturbations. Orbital instability can be controlled by minimizing the effects of secular growing terms. Several control strategies are described. These strategies include the optimal use of thrusters and the selection of an appropriate orbit which compensates for perturbations.

Lubow, S. H.

2001-11-01

415

Efficient orbit integration by orbital longitude methods  

NASA Astrophysics Data System (ADS)

Triggered by the desire to investigate numerically the planetary precession through a long-term numerical integration of the solar system, we developed a new formulation of numerical integration of orbital motion named manifold correction methods. The main trick is to keep rigorously the consistency of some physical relations such as that of the orbital energy, of the orbital angular momentum, or of the Laplace integral of a binary subsystem. This maintenance is done by applying a sort of correction to the integrated variables at every integration step. Typical methods of correction are certain geometric transformation such as the spatial scaling and the spatial rotation, which are commonly used in the comparison of reference frames, or mathematically-reasonable operations such as the modularization of angle variables into the standard domain [-?,?). The finally-evolved form of the manifold correction methods is the orbital longitude methods, which enable us to conduct an extremely precise integration of orbital motions. In the unperturbed orbits, the integration errors are suppressed at the machine epsilon level for an infinitely long period. In the perturbed cases, on the other hand, the errors initially grow in proportion to the square root of time and then increase more rapidly, the onset time of which depends on the type and the magnitude of perturbations. This feature is also realized for highly eccentric orbits by applying the same idea to the KS-regularization. Especially the introduction of time element greatly enhances the performance of numerical integration of KS-regularized orbits whether the scaling is applied or not.

Fukushima, T.

2005-09-01

416

Mining and integration of pathway diagrams from imaging data  

PubMed Central

Motivation: Pathway diagrams from PubMed and World Wide Web (WWW) contain valuable highly curated information difficult to reach without tools specifically designed and customized for the biological semantics and high-content density of the images. There is currently no search engine or tool that can analyze pathway images, extract their pathway components (molecules, genes, proteins, organelles, cells, organs, etc.) and indicate their relationships. Results: Here, we describe a resource of pathway diagrams retrieved from article and web-page images through optical character recognition, in conjunction with data mining and data integration methods. The recognized pathways are integrated into the BiologicalNetworks research environment linking them to a wealth of data available in the BiologicalNetworks' knowledgebase, which integrates data from >100 public data sources and the biomedical literature. Multiple search and analytical tools are available that allow the recognized cellular pathways, molecular networks and cell/tissue/organ diagrams to be studied in the context of integrated knowledge, experimental data and the literature. Availability: BiologicalNetworks software and the pathway repository are freely available at www.biologicalnetworks.org. Contact: baitaluk@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22267504

Kozhenkov, Sergey; Baitaluk, Michael

2012-01-01

417

Phase diagram of a reentrant gel of patchy particles  

SciTech Connect

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.

Roldán-Vargas, Sándalo; Smallenburg, Frank; Sciortino, Francesco [Department of Physics, Sapienza, Università di Roma, Piazzale Aldo Moro 2, I-00185 Roma (Italy)] [Department of Physics, Sapienza, Università di Roma, Piazzale Aldo Moro 2, I-00185 Roma (Italy); Kob, Walter [Laboratoire Charles Coulomb, UMR 5221, CNRS and Université Montpellier 2, 34095 Montpellier (France)] [Laboratoire Charles Coulomb, UMR 5221, CNRS and Université Montpellier 2, 34095 Montpellier (France)

2013-12-28

418

Phase diagram of a reentrant gel of patchy particles.  

PubMed

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. PMID:24387399

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

2013-12-28

419

Reading fitness landscape diagrams through HSAB concepts  

NASA Astrophysics Data System (ADS)

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.

Vigneresse, Jean-Louis

2014-10-01

420

Reactivity index based on orbital energies.  

PubMed

This study shows that the chemical reactivities depend on the orbital energy gaps contributing to the reactions. In the process where a reaction only makes progress through charge transfer with the minimal structural transformation of the reactant, the orbital energy gap gradient (OEGG) between the electron-donating and electron-accepting orbitals is proven to be very low. Using this relation, a normalized reaction diagram is constructed by plotting the normalized orbital energy gap with respect to the normalized intrinsic reaction coordinate. Application of this reaction diagram to 43 fundamental reactions showed that the majority of the forward reactions provide small OEGGs in the initial stages, and therefore, the initial processes of the forward reactions are supposed to proceed only through charge transfer. Conversely, more than 60% of the backward reactions are found to give large OEGGs implying very slow reactions associated with considerable structural transformations. Focusing on the anti-activation-energy reactions, in which the forward reactions have higher barriers than those of the backward ones, most of these reactions are shown to give large OEGGs for the backward reactions. It is also found that the reactions providing large OEGGs in the forward directions inconsistent with the reaction rate constants are classified into SN 2, symmetric, and methyl radical reactions. Interestingly, several large-OEGG reactions are experimentally established to get around the optimum pathways. This indicates that the reactions can take significantly different pathways from the optimum ones provided no charge transfer proceeds spontaneously without the structural transformations of the reactants. PMID:24740548

Tsuneda, Takao; Singh, Raman K

2014-05-30

421

Phase diagram of ammonium nitrate  

SciTech Connect

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.

Dunuwille, Mihindra; Yoo, Choong-Shik, E-mail: csyoo@wsu.edu [Department of Chemistry and Institute for Shock Physics, Washington State University, Pullman, Washington 99164 (United States)] [Department of Chemistry and Institute for Shock Physics, Washington State University, Pullman, Washington 99164 (United States)

2013-12-07

422

The morphological diagram of spinels  

SciTech Connect

Catalytic anisotropy in mild oxidation reactions results from the varying activity of different crystal faces. Here, spinels exposing (100), (110), and (111) faces have been considered and their Curie-Wulff plots have been drawn, admitting that the relative G(hkl) surface free energies may change in a wide range as a function of composition, inversion, and segregation degree. The normalized free surface energies are defined as A = G(100)/G(111), B = G(110)/G(111), and C = G(111)/G(111) = 1 = const. This made it possible to construct bidimensional morphological diagrams (morphology = f(A,B) at C = const) in the exposed-face-type, solid-type, and exposure-percentage versions. Eleven morphological habits of grains have been identified, including (100)-cube, (110)-dodecahedron, (111)-hexagons, 18-hedron, 20-hedron, and up to 26-hedra bordered with (i) 6 (100)-octagons, 12 (110)-rectangles, and 8 (111)-hexagons, (ii) 6 (100)-squares, 12 (110)-rectangles, and 8 (111)-triangles, or (iii) 6 (100)-squares, 12 (110)-octagons, and 8 (100)-triangles. The analysis is valid for all compounds crystallizing in the cubic system and preferentially exposing the three enumerated faces.

Ziolkowski, J. [Institute of Catalysis and Surface Chemistry, Krakow (Poland)] [Institute of Catalysis and Surface Chemistry, Krakow (Poland)

1996-02-01

423

Towards the QCD phase diagram  

E-print Network

We summarize our recent results on the phase diagram of QCD with N_f=2+1 quark flavors, as a function of temperature T and quark chemical potential \\mu. Using staggered fermions, lattices with temporal extent N_t=4, and the exact RHMC algorithm, we first determine the critical line in the quark mass plane (m_{u,d},m_s) where the finite temperature transition at \\mu=0 is second order. We confirm that the physical point lies on the crossover side of this line. Our data are consistent with a tricritical point at (m_{u,d},m_s) = (0,\\sim 500) MeV. Then, using an imaginary chemical potential, we determine in which direction this second-order line moves as the chemical potential is turned on. Contrary to standard expectations, we find that the region of first-order transitions shrinks in the presence of a chemical potential, which is inconsistent with the presence of a QCD critical point at small chemical potential. The emphasis is put on clarifying the translation of our results from lattice to physical units, and on discussing the apparent contradiction of our findings with earlier lattice studies.

Philippe de Forcrand; Owe Philipsen

2006-11-22

424

Hooke, orbital motion, and Newton's Principia  

NASA Astrophysics Data System (ADS)

A detailed analysis is given of a 1685 graphical construction by Robert Hooke for the polygonal path of a body moving in a periodically pulsed radial field of force. In this example the force varies linearly with the distance from the center. Hooke's method is based directly on his original idea from the mid-1660s that the orbital motion of a planet is determined by compounding its tangential velocity with a radial velocity impressed by the gravitational attraction of the sun at the center. This hypothesis corresponds to the second law of motion, as formulated two decades later by Newton, and its geometrical implementation constitutes the cornerstone of Newton's Principia. Hooke's diagram represents the first known accurate graphical evaluation of an orbit in a central field of force, and it gives evidence that he demonstrated that his resulting discrete orbit is an approximate ellipse centered at the origin of the field of force. A comparable calculation to obtain orbits for an inverse square force, which Hooke had conjectured to be the gravitational force, has not been found among his unpublished papers. Such a calculation is carried out here numerically with the Newton-Hooke geometrical construction. It is shown that for orbits of comparable or larger eccentricity than Hooke's example, a graphical approach runs into convergence difficulties due to the singularity of the gravitational force at the origin. This may help resolve the long-standing mystery why Hooke never published his controversial claim that he had demonstrated that an attractive force, which is ``...in a duplicate proportion to the Distance from the Center Reciprocall...'' implies elliptic orbits.

Nauenberg, Michael

1994-04-01

425

Orbital Debris Engineering Model (ORDEM) v.3  

NASA Technical Reports Server (NTRS)

A model of the manmade orbital debris environment is required by spacecraft designers, mission planners, and others in order to understand and mitigate the effects of the environment on their spacecraft or systems. A manmade environment is dynamic, and can be altered significantly by intent (e.g., the Chinese anti-satellite weapon test of January 2007) or accident (e.g., the collision of Iridium 33 and Cosmos 2251 spacecraft in February 2009). Engineering models are used to portray the manmade debris environment in Earth orbit. The availability of new sensor and in situ data, the re-analysis of older data, and the development of new analytical and statistical techniques has enabled the construction of this more comprehensive and sophisticated model. The primary output of this model is the flux [#debris/area/time] as a function of debris size and year. ORDEM may be operated in spacecraft mode or telescope mode. In the former case, an analyst defines an orbit for a spacecraft and "flies" the spacecraft through the orbital debris environment. In the latter case, an analyst defines a ground-based sensor (telescope or radar) in terms of latitude, azimuth, and elevation, and the model provides the number of orbital debris traversing the sensor's field of view. An upgraded graphical user interface (GUI) is integrated with the software. This upgraded GUI uses project-oriented organization and provides the user with graphical representations of numerous output data products. These range from the conventional flux as a function of debris size for chosen analysis orbits (or views), for example, to the more complex color-contoured two-dimensional (2D) directional flux diagrams in local spacecraft elevation and azimuth.

Matney, Mark; Krisko, Paula; Xu, Yu-Lin; Horstman, Matthew

2013-01-01

426

The amplituhedron from momentum twistor diagrams  

NASA Astrophysics Data System (ADS)

We propose a new diagrammatic formulation of the all-loop scattering amplitudes/Wilson loops in planar = 4 SYM, dubbed the "momentum-twistor diagrams". These are on-shell-diagrams obtained by gluing trivalent black and white vertices in momentum twistor space, which, in the reduced diagram case, are known to be related to diagrams in the original twistor space. The new diagrams are manifestly Yangian invariant, and they naturally represent factorization and forward-limit contributions in the all-loop BCFW recursion relations in momentum twistor space, in a fashion that is completely different from those in momentum space. We show how to construct and evaluate momentum-twistor diagrams, and how to use them to obtain tree-level amplitudes and loop-level integrands; in particular the latter involve isolated bubble-structures for loop variables arising from forward limits, or the entangled removal of particles. From each diagram, the generalized "boundary measurement" directly gives the C, D matrices, thus a cell in the amplituhedron associated with the amplitude, and we expect that our diagrammatic representations of the amplitude provide triangulations of the amplituhedron. To demonstrate the computational power of the formalism, we give explicit results for general two-loop integrands, and the cells of the amplituhedron for two-loop MHV amplitudes.

Bai, Yuntao; He, Song

2015-02-01

427

Frustration and Entanglement in Compass and Spin-Orbital Models  

E-print Network

We review the consequences of intrinsic frustration of the orbital superexchange and of spin-orbital entanglement. While Heisenberg perturbing interactions remove frustration in the compass model, the lowest columnar excitations are robust in the nanoscopic compass clusters and might be used for quantum computations. Entangled spin-orbital states determine the ground states in some cases, while in others concern excited states and lead to measurable consequences, as in the $R$VO$_3$ perovskites. On-site entanglement for strong spin-orbit coupling generates the frustrated Kitaev-Heisenberg model with a rich magnetic phase diagram on the honeycomb lattice. Frustration is here reflected in hole propagation which changes from coherent in an antiferromagnet via hidden quasiparticles in zigzag and stripe phases to entirely incoherent one in the Kitaev spin liquid.

Andrzej M. Ole?

2014-10-24

428

Orbit Determination of the Lunar Reconnaissance Orbiter  

NASA Technical Reports Server (NTRS)

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

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

2011-01-01

429

Breviz: Visualizing Spreadsheets using Dataflow Diagrams  

E-print Network

Spreadsheets are used extensively in industry, often for business critical purposes. In previous work we have analyzed the information needs of spreadsheet professionals and addressed their need for support with the transition of a spreadsheet to a colleague with the generation of data flow diagrams. In this paper we describe the application of these data flow diagrams for the purpose of understanding a spreadsheet with three example cases. We furthermore suggest an additional application of the data flow diagrams: the assessment of the quality of the spreadsheet's design.

Hermans, Felienne; van Deursen, Arie

2011-01-01

430

Determination of the g-tensors and their orientations for cis,trans-(L-N2S2)Mo(V)OX (X = Cl, SCH2Ph) by single-crystal EPR spectroscopy and molecular orbital calculations.  

PubMed

A single-crystal study of cis,trans-(L-N2S2)MoVOCl (1) doped into cis,trans-(N2S2)MoVIO2 (3) has enabled the g-tensor of 1 and its orientation with respect to the molecular structure to be determined. The EPR parameters (g1, 2.004; g2, 1.960; g3, 1.946; A1, 71.7 x 10(-4) cm(-1); A2, 11.7 x 10(-4) cm(-1); A3, 32.0 x 10(-4) cm(-1)) of cis,trans-(L-N2S2)MoVOCl [L-N2S2H2 = N,N'-dimethyl-N,N'-bis(mercaptophenyl)ethylenediamine] mimic those of the low-pH form of sulfite oxidase and the "very rapid" species of xanthine oxidase. The principal axis that corresponds to g1 is rotated approximately 10 degrees from the Mo[triple bond]O vector, while the principal axis that corresponds to g3 is located in the equatorial plane and approximately 38 degrees from the Mo-Cl vector. Independent theoretical calculations of the g-tensor of 1 were performed using two types of techniques: (1) the spectroscopically parametrized intermediate neglect of differential overlap technique (INDO/S) combined with single-excitation configuration interaction (CIS); (2) a scalar relativistic DFT (BP86 and B3LYP functionals) treatment using the zeroth order regular approximation to relativistic effects (ZORA) in combination with recently developed accurate multicenter mean field spin-orbit operators (RI-SOMF) and the estimation of solvent effects using dielectric continuum theory at the conductor-like screening model (COSMO) level. The excellent agreement between experiment and theory, as well as the high consistency between the INDO/S and BP86/ZORA results, provides a sound basis for analysis of the calculated orientation of the g-tensor for cis,trans-(L-N2S2)MoVO(SCH2Ph) (2), for which single-crystal EPR data are not available but which contains three equatorial sulfur donor atoms, as occurs in sulfite oxidase and xanthine oxidase. The implications of these results for the EPR spectra of the Mo(V) centers of enzymes are discussed. PMID:15732969

Cosper, Michele Mader; Neese, Frank; Astashkin, Andrei V; Carducci, Michael D; Raitsimring, Arnold M; Enemark, John H

2005-03-01

431

Family of Orbiters  

NASA Technical Reports Server (NTRS)

This image shows the paths of three spacecraft currently in orbit around Mars, as well as the path by which NASA's Phoenix Mars Lander will approach and land on the planet. The t-shaped crosses show where the orbiters will be when Phoenix enters the atmosphere, while the x-shaped crosses show their location at landing time.

All three orbiters, NASA's Mars Reconnaissance Orbiter, NASA's Mars Odyssey and the European Space Agency's Mars Express, will be monitoring Phoenix during the final steps of its journey to the Red Planet.

Phoenix will land just south of Mars's north polar ice cap.

2008-01-01

432

Orbital Debris: A Chronology  

NASA Technical Reports Server (NTRS)

This chronology covers the 37-year history of orbital debris concerns. It tracks orbital debris hazard creation, research, observation, experimentation, management, mitigation, protection, and policy. Included are debris-producing, events; U.N. orbital debris treaties, Space Shuttle and space station orbital debris issues; ASAT tests; milestones in theory and modeling; uncontrolled reentries; detection system development; shielding development; geosynchronous debris issues, including reboost policies: returned surfaces studies, seminar papers reports, conferences, and studies; the increasing effect of space activities on astronomy; and growing international awareness of the near-Earth environment.

Portree, Davis S. F. (Editor); Loftus, Joseph P., Jr. (Editor)

1999-01-01

433

Pseudoatom molecular dynamics.  

PubMed

An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient. PMID:25679720

Starrett, C E; Daligault, J; Saumon, D

2015-01-01

434

Pseudoatom molecular dynamics  

NASA Astrophysics Data System (ADS)

An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient.

Starrett, C. E.; Daligault, J.; Saumon, D.

2015-01-01

435

Anderson localization of cold atomic gases with effective spin-orbit interaction in a quasiperiodic optical lattice  

NASA Astrophysics Data System (ADS)

We theoretically investigate the localization properties of a spin-orbit-coupled spin-1/2 particle moving in a one-dimensional quasiperiodic potential, which can be experimentally implemented using cold atoms trapped in a quasiperiodic optical lattice potential and external laser fields. We present the phase diagram in the parameter space of the disorder strength and those related to the spin-orbit coupling. The phase diagram is verified via multifractal analysis of the atomic wave functions and the numerical simulation of diffusion dynamics. We found that spin-orbit coupling can lead to spectra mixing (coexistence of extended and localized states) and the appearance of mobility edges.

Zhou, Lu; Pu, Han; Zhang, Weiping

2013-02-01

436

PC-402 Pioneer Venus orbiter spacecraft mission operational characteristics document  

NASA Technical Reports Server (NTRS)

The operational characteristics of the Orbiter spacecraft and its subsystems are described. In extensive detail. Description of the nominal phases, system interfaces, and the capabilities and limitations of system level performance are included along with functional and operational descriptions at the subsystem and unit level the subtleties of nominal operation as well as detailed capabilities and limitations beyond nominal performance are discussed. A command and telemetry logic flow diagram for each subsystem is included. Each diagram encountered along each command signal path into, and each telemetry signal path out of the subsystem. Normal operating modes that correspond to the performance of specific functions at the time of specific events in the mission are also discussed. Principal backup means of performing the normal Orbiter operating modes are included.

Barker, F. C.; Butterworth, L. W.; Daniel, R. E.; Drean, R. J.; Filetti, K. A.; Fisher, J. N.; Nowak, L. A.; Porzucki, J.; Salvatore, J. O.; Tadler, G. A.

1978-01-01

437

ConcepTest: Relative Time Diagram #3  

NSDL National Science Digital Library

Match the features in the relative time diagram below with the events described in the short sentence. Assume all rocks are sedimentary unless otherwise indicated. Which unit is composed of granite and older than ...

438

A Phase Diagram for Solar Flares  

NASA Astrophysics Data System (ADS)

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

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

2015-04-01

439

Architecture flow diagrams under teamwork reg sign  

SciTech Connect

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

Nicinski, T.

1992-02-01

440

Sequential Influence Diagrams: A Unified Asymmetry Framework  

E-print Network

We describe a new graphical language for specifying asymmetric decision problems. The language is based on a filtered merge of several existing languages including sequential valuation networks, asymmetric influence diagrams, ...

Jensen, Finn V.; Nielsen, Thomas D.; Shenoy, Prakash P.

2004-10-01

441

An Improved Mnemonic Diagram for Thermodynamic Relationships.  

ERIC Educational Resources Information Center

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)

Rodriguez, Joaquin; Brainard, Alan J.

1989-01-01

442

Voronoi diagram generation on the ellipsoidal earth  

NASA Astrophysics Data System (ADS)

Voronoi diagram on the earth surface is a powerful tool to study spatial proximity at continental or global scale. However, its computation remains challenging because geospatial features have complex shapes. This paper presents a raster-based algorithm to generate Voronoi diagrams on earth's surface. The algorithm approximates the exact point-to-point geographical distances using the cell-to-cell geographical distances calculated by a geographical distance transform. The result is a distance image on which Voronoi diagram is delineated. Compared to existing methods, the proposed algorithm calculates geographical distances based on an earth ellipsoid and allows Voronoi generators to take complex shapes. Most importantly, its approximation error is bounded thus enabling users to control the accuracy of the Voronoi diagram through grid resolution.

Hu, Hai; Liu, XiaoHang; Hu, Peng

2014-12-01

443

Sloan Digital Sky Survey - Hubble Diagram  

NSDL National Science Digital Library

This website, containing information from the Sloan Digital Sky Survey, provides projects and activities for advanced astronomy students. In this particular one, the user retraces Edwin Hubble's steps to discover that the Universe is expanding, by making a Hubble Diagram.

444

Minimum Energy Diagrams for Multieffect Distillation Arrangements  

E-print Network

Minimum Energy Diagrams for Multieffect Distillation Arrangements Hilde K. Engelien and Sigurd distillation arrangements for separating a ternary mixture have been considered. The focus is on a heat-integrated complex distillation configuration, called a multieffect prefractionator arrangement. The comparison

Skogestad, Sigurd

445

Attribute Reduction Based on Property Pictorial Diagram  

PubMed Central

This paper mainly studies attribute reduction which keeps the lattice structure in formal contexts based on the property pictorial diagram. Firstly, the property pictorial diagram of a formal context is defined. Based on such diagram, an attribute reduction approach of concept lattice is achieved. Then, through the relation between an original formal context and its complementary context, an attribute reduct of complementary context concept lattice is obtained, which is also based on the property pictorial diagram of the original formal context. Finally, attribute reducts in property oriented concept lattice and object oriented concept lattice can be acquired by the relations of attribute reduction between these two lattices and concept lattice of complementary context. In addition, a detailed illustrative example is presented. PMID:25247200

Wan, Qing; Wei, Ling

2014-01-01

446

Interfaces for creating quantitative conceptual diagrams  

E-print Network

Modern chart-making, illustration, and mathematical tools poorly support the use of conceptual components in quantitative graphs such as Economics diagrams. The substantial time those tools require to achieve the desired ...

Stewart, Robin S. (Robin Scott)

2008-01-01

447

Fluctuations and the QCD phase diagram  

SciTech Connect

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.

Schaefer, B.-J., E-mail: bernd-jochen.schaefer@uni-graz.at [Karl-Franzens-Universitaet, Institut fuer Physik (Austria)

2012-06-15

448

Steps toward a radio HR diagram  

Microsoft Academic Search

We discuss the possibility of establishing a set of observational parameters for radio galaxies which could be used to study radio source evolution in the same way that the Hertzsprung-Russell diagram is used to understand stellar evolution. As a first step towards a radio H-R diagram, we show that the FRI\\/II break is a function of both radio and optical

Frazer Owen

449

Algebraic decision diagrams and their applications  

Microsoft Academic Search

In this paper we present theory and experiments on the AlgebraicDecision Diagrams (ADD's). These diagrams extend BDD'sby allowing values from an arbitrary finite domain to be associatedwith the terminal nodes. We present a treatment foundedin boolean algebras and discuss algorithms and results in applicationslike matrix multiplication and shortest path algorithms.Furthermore, we outline possible applications of ADD's to logicsynthesis, formal verification,

R. Iris Bahar; Erica A. Frohm; Charles M. Gaona; Gary D. Hachtel; Enrico Macii; Abelardo Pardo; Fabio Somenzi

1993-01-01

450

A universal structured-design diagramer  

NASA Technical Reports Server (NTRS)

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.

1981-01-01

451

Implications of Cladistics: Understanding Branching Diagrams  

NSDL National Science Digital Library

This site explains how a cladogram is formed and its implications. The cladogram is compared to a family tree, however unlike family trees, ancestors in cladistics ideally give rise to only two descendent species. Also unlike family trees, new species form from splitting of old species. Three possible diagrams showing the relationship between humans, gorillas, baboons, and chimpanzees are demonstrated. The author explains why one diagram is favored and also explains the meaning of nodes and clades.

452

Reliability computation from reliability block diagrams  

NASA Technical Reports Server (NTRS)

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.

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

1971-01-01

453

Drawing conformal diagrams for a fractal landscape  

Microsoft Academic Search

Generic models of cosmological inflation and the recently proposed scenarios of a recycling universe and the string theory landscape predict spacetimes whose global geometry is a stochastic, self-similar fractal. To visualize the complicated causal structure of such a universe, one usually draws a conformal (Carter-Penrose) diagram. I develop a new method for drawing conformal diagrams, applicable to arbitrary 1+1-dimensional spacetimes.

Sergei Winitzki; Sergei

2005-01-01

454

Sets and The Venn Diagram (Beginner)  

NSDL National Science Digital Library

This lesson is designed to introduce students to sets, what it means to be part of a set, and how Venn diagrams relate to sets. This lesson provides links to discussions and activities related to sets and Venn diagrams as well as suggested ways to integrate them into the lesson. Finally, the lesson provides links to follow-up lessons designed for use in succession with the current one.

2011-05-23

455

Weyl group orbits on Kac–Moody root systems  

NASA Astrophysics Data System (ADS)

Let D be a Dynkin diagram and let \\Pi =\\{{{? }1},...,{{? }\\ell }\\} be the simple roots of the corresponding Kac–Moody root system. Let h denote the Cartan subalgebra, let W denote the Weyl group and let ? denote the set of all roots. The action of W on h, and hence on ?, is the discretization of the action of the Kac–Moody algebra. Understanding the orbit structure of W on ? is crucial for many physical applications. We show that for i\

Carbone, Lisa; Conway, Alexander; Freyn, Walter; Penta, Diego

2014-11-01

456

Class diagram based evaluation of software performance  

NASA Astrophysics Data System (ADS)

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.

Pham, Huong V.; Nguyen, Binh N.

2013-03-01

457

Congenital orbital encephalocele, orbital dystopia, and exophthalmos.  

PubMed

We present here an exceedingly rare variant of a nonmidline basal encephalocele of the spheno-orbital type, and this was accompanied with orbital dystopia in a 56-year-old man. On examination, his left eye was located more inferolaterally than his right eye, and the patient said this had been this way since his birth. The protrusion of his left eye was aggravated when he is tired. His naked visual acuity was 0.7/0.3, and the ocular pressure was 14/12 mm Hg. The exophthalmometry was 10/14 to 16 mm. His eyeball motion was not restricted, yet diplopia was present in all directions. The distance from the midline to the medial canthus was 20/15 mm. The distance from the midline to the midpupillary line was 35/22 mm. The vertical dimension of the palpebral fissure was 12/9 mm. The height difference of the upper eyelid margin was 11 mm, and the height difference of the lower eyelid margin was 8 mm. Facial computed tomography and magnetic resonance imaging showed left sphenoid wing hypoplasia and herniation of the left anterior temporal pole and dura mater into the orbit, and this resulted into left exophthalmos and encephalomalacia in the left anterior temporal pole. To the best of our knowledge, our case is the second case of basal encephalocele and orbital dystopia. PMID:22801176

Hwang, Kun; Kim, Han Joon

2012-07-01

458

Planetary Orbit Simulator  

NSDL National Science Digital Library

This web page from the University of Nebraska contains a simulation of a planetary orbit. The visitor can control the size of the orbit and the eccentricity. The simulation shows velocity and acceleration factors continually. Each of Kepler's three laws has a separate section, with different display options to illustrate each law.

459

Titan Orbiter Aerorover Mission  

NASA Technical Reports Server (NTRS)

We propose a combined Titan orbiter and Titan Aerorover mission with an emphasis on both in situ and remote sensing measurements of Titan's surface, atmosphere, ionosphere, and magnetospheric interaction. The biological aspect of the Titan environment will be emphasized by the mission (i.e., search for organic materials which may include simple organics to 'amono' analogues of amino acids and possibly more complex, lightening detection and infrared, ultraviolet, and charged particle interactions with Titan's surface and atmosphere). An international mission is assumed to control costs. NASA will provide the orbiter, launch vehicle, DSN coverage and operations, while international partners will provide the Aerorover and up to 30% of the cost for the scientific instruments through collaborative efforts. To further reduce costs we propose a single PI for orbiter science instruments and a single PI for Aerorover science instruments. This approach will provide single command/data and power interface between spacecraft and orbiter instruments that will have redundant central DPU and power converter for their instruments. A similar approach could be used for the Aerorover. The mission profile will be constructed to minimize conflicts between Aerorover science, orbiter radar science, orbiter radio science, orbiter imaging science, and orbiter fields and particles (FP) science. Additional information is contained in the original extended abstract.

Sittler Jr., E. C.; Acuna, M.; Burchell, M. J.; Coates, A.; Farrell, W.; Flasar, M.; Goldstein, B. E.; Gorevan, S.; Hartle, R. E.; Johnson, W. T. K.

2001-01-01

460

Orbital trapdoor fractures  

PubMed Central

Orbital trapdoor fractures are commonly encountered in children. Awareness of trapdoor fractures is of particular importance. This is because early recognition and treatment are necessary to prevent permanent motility abnormities. In this article, we will provide a brief overview of orbital fractures. The clinical and radiographic features of trapdoor fractures will then be reviewed, followed by a discussion on their proper management. PMID:23961006

Phan, Laura T.; Jordan Piluek, W.; McCulley, Timothy J.

2012-01-01

461

Focus on Orbital Physics  

Microsoft Academic Search

The quest for a microscopic understanding of the physical properties of transition metal oxides with orbital degeneracy (`orbital physics') is currently at the forefront of solid-state physics. The field was kicked off nearly 50 years ago by a remarkable pair of papers. In the first, Wollan and Koehler reported using the newly developed technique of neutron scattering to elucidate the

Bernhard Keimer; Andrzej M Oles

2004-01-01

462

Mars Climate Orbiter  

NASA Technical Reports Server (NTRS)

The purpose of this mission is to study the climate history and the water distribution of Mars. Beautiful panoramic views of the shuttle on the launch pad, engine ignition, Rocket launch, and the separation and burnout of the Solid Rocket Boosters are shown. The footage also includes an animation of the mission. Detailed views of the path that the Orbiter traversed were shown. Once the Orbiter lands on the surface of Mars, it will dig a six to eight inch hole and collect samples from the planets' surface. The animation also included the prospective return of the Orbiter to Earth over the desert of Utah. The remote sensor on the Orbiter helps in finding the exact location of the Orbiter so that scientists may collect the sample and analyze it.

1998-01-01

463

Orbital Debris Mitigation  

NASA Technical Reports Server (NTRS)

Policies on limiting orbital debris are found throughout the US Government, many foreign space agencies, and as adopted guidelines in the United Nations. The underlying purpose of these policies is to ensure the environment remains safe for the operation of robotic and human spacecraft in near- Earth orbit. For this reason, it is important to consider orbital debris mitigation during the design of all space vehicles. Documenting compliance with the debris mitigation guidelines occurs after the vehicle has already been designed and fabricated for many CubeSats, whereas larger satellites are evaluated throughout the design process. This paper will provide a brief explanation of the US Government Orbital Debris Mitigation Standard Practices, a discussion of international guidelines, as well as NASA's process for compliance evaluation. In addition, it will discuss the educational value of considering orbital debris mitigation requirements as a part of student built satellite design.

Kelley, R. L.; Jarkey, D. R.; Stansbery, G.

2014-01-01

464

Fingerprints of spin-orbital entanglement in transition metal oxides  

E-print Network

The concept of spin-orbital entanglement on superexchange bonds in transition metal oxides is introduced and explained on several examples. It is shown that spin-orbital entanglement in superexchange models destabilizes the long-range (spin and orbital) order and may lead either to a disordered spin-liquid state or to novel phases at low temperature which arise from strongly frustrated interactions. Such novel ground states cannot be described within the conventionally used mean field theory which separates spin and orbital degrees of freedom. Even in cases where the ground states are disentangled, spin-orbital entanglement occurs in excited states and may become crucial for a correct description of physical properties at finite temperature. As an important example of this behaviour we present spin-orbital entanglement in the $R$VO$_3$ perovskites, with $R$=La,Pr,...,Yb,Lu, where such finite temperature properties of these compounds can be understood only using entangled states: ($i$) thermal evolution of the optical spectral weights, ($ii$) the dependence of transition temperatures for the onset of orbital and magnetic order on the ionic radius in the phase diagram of the $R$VO$_3$ perovskites, and ($iii$) dimerization observed in the magnon spectra for the $C$-type antiferromagnetic phase of YVO$_3$. Finally, it is shown that joint spin-orbital excitations in an ordered phase with coexisting antiferromagnetic and alternating orbital order introduces topological constraints for the hole propagation and will thus radically modify transport properties in doped Mott insulators where hole motion implies simultaneous spin and orbital excitations.

Andrzej M. Ole?

2012-07-12

465

Orbital metastatic osteosarcoma.  

PubMed

At an estimated incidence of 2 cases per million persons per year, osteosarcoma is the most common primary malignant bone tumor in children and adults, excluding hematopoietic intraosseous tumors. Orbital metastases of osteosarcoma are very rare. Only 5 cases of orbital metastasis of osteosarcoma previously reported in the literature. We report the case of a 19-year-old man with known history of osteosarcoma of right distal femur who presented with acute visual loss and progressive protrusion of his left eye. Orbital CT scan and MRI revealed orbital mass eroding orbital walls and intracranial invasion. He underwent superotemporal orbitotomy for debulking of orbital mass. Histopathological examination (HPE) of the specimen was reported as metastatic osteosarcoma with extensive tumor necrosis. Then he underwent adjuvant chemotherapy and palliative radiotherapy. Although orbital metastasis of osteosarcoma is a rare event, it seems it has had an increasing trend recently. so, making efforts to palliate the patient's symptoms by multidisciplinary teamwork and proper interaction among ophthalmologist, orthopedic surgeons and oncologists is necessary. PMID:25644802

Rajabi, Mohammad Taher; Saeedi-Anari, Ghasem; Ramezani, Farshid; Tabatabaie, Seyed-Ziaeddin; Rajabi, Mohammad Bagher; Asadi Amoli, Fahimeh

2015-02-01

466

Harmonically excited orbital variations  

SciTech Connect

Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs.

Morgan, T.

1985-08-06

467

Orbit Stabilization of Nanosat  

SciTech Connect

An algorithm is developed to control a pulsed {Delta}V thruster on a small satellite to allow it to fly in formation with a host satellite undergoing time dependent atmospheric drag deceleration. The algorithm uses four short thrusts per orbit to correct for differences in the average radii of the satellites due to differences in drag and one thrust to symmetrize the orbits. The radial difference between the orbits is the only input to the algorithm. The algorithm automatically stabilizes the orbits after ejection and includes provisions to allow azimuthal positional changes by modifying the drag compensation pulses. The algorithm gives radial and azimuthal deadbands of 50 cm and 3 m for a radial measurement accuracy of {+-} 5 cm and {+-} 60% period variation in the drag coefficient of the host. Approaches to further reduce the deadbands are described. The methodology of establishing a stable orbit after ejection is illustrated in an appendix. The results show the optimum ejection angle to minimize stabilization thrust is upward at 86{sup o} from the orbital velocity. At this angle the stabilization velocity that must be supplied by the thruster is half the ejection velocity. An ejection velocity of 0.02 m/sat 86{sup o} gives an azimuthal separation after ejection and orbit stabilization of 187 m. A description of liquid based gas thrusters suitable for the satellite control is included in an appendix.

JOHNSON,DAVID J.

1999-12-01

468

OL- ORBITAL LIFETIME PROGRAM  

NASA Technical Reports Server (NTRS)

The Orbital Lifetime (OL) program analyzes the long-term motion of Earth-orbiting spacecraft at altitudes of up to 2500 kilometers. It models perturbations to the orbit caused by solar radiation pressure, atmospheric drag, and gravitational effects due to the sun, the moon, and Earth oblateness. OL can be used to predict the orbital lifetime and decay rate of a satellite. The atmospheric density models used in OL are the U.S. Standard Atmosphere for altitudes below 90 km and the Jacchia model for altitudes above 90 km. The Jacchia model requires solar flux and geomagnetic index for the date of orbit. An input file containing these values for 1984 to 1998 is supplied with the OL package. The solar radiation pressure calculations in OL will predict the amount of time a spacecraft is subjected to the Earth's shadow. Input to OL includes spacecraft physical characteristics, initial orbit parameters, and launch date/time. OL calculates time histories of the orbital elements, total lifetime, and decay rates. A spacecraft is considered 'down' at an altitude of 64 km. OL also generates a file of plot data which can be input to a user-supplied graphics program for lifetime plots of altitude against time. OL is written in FORTRAN 77 for interactive or batch execution and has been implemented on a DEC VAX series computer operating under VMS. This program was developed in 1985.

Orr, L. H.

1994-01-01

469

External Resource: What is orbit?  

NSDL National Science Digital Library

A 5-8 NASA Education reference answering the question, " What is orbit?" Topics include: satellite, ecliptic plane, perigee, apogee, escape velocity, geosynchronous, polar orbits, and low Earth orbit.

1900-01-01

470

Orbital Debris Environment Monitor (ODEM)  

NASA Technical Reports Server (NTRS)

Viewgraphs on orbital debris environmental monitor (ODEM) are presented. Topics covered include: Long Duration Exposure Facility (LDEF); interplanetary dust experiment; orbital debris clouds; mapping and modeling of orbital debris clouds; and solar maximum mission spacecraft.

Oliver, John P.

1992-01-01

471

Working in orbit and beyond  

SciTech Connect

This book contains papers presented at a conference on the challenges for space medicine. Topics covered include radiation hazards in low earth orbit, polar orbit, geosynchronous orbit, and deep space.

Lorr, D.B. (Space Medicine Systems, Inc. (US)); Garshnek, V. (George Washington Univ., Washington, DC (US)); Cadoux, C. (Union Memorial Hospital, Baltimore, MD (US))

1989-01-01

472

Titan's internal structure inferred from a coupled thermal-orbital model  

Microsoft Academic Search

Through coupled thermal and orbital calculations including a full description of tidal dissipation, heat transfer and the H2ONH3 phase diagram, we propose a model for the internal structure and composition of Titan testable with Cassini–Huygens measurements. The high value of Titan's orbital eccentricity provides a strong constraint on the amount of the tidal energy dissipation on its surface and within

Gabriel Tobie; Olivier Grasset; Jonathan I. Lunine; Antoine Mocquet; Christophe Sotin