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1

Visualization of Molecular Orbitals: Formaldehyde  

ERIC Educational Resources Information Center

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

Olcott, Richard J.

1972-01-01

2

Energy level diagrams for black hole orbits  

NASA Astrophysics Data System (ADS)

A spinning black hole with a much smaller black hole companion forms a fundamental gravitational system, like a colossal classical analog to an atom. In an appealing if imperfect analogy with atomic physics, this gravitational atom can be understood through a discrete spectrum of periodic orbits. Exploiting a correspondence between the set of periodic orbits and the set of rational numbers, we are able to construct periodic tables of orbits and energy level diagrams of the accessible states around black holes. We also present a closed-form expression for the rational q, thereby quantifying zoom-whirl behavior in terms of spin, energy and angular momentum. The black hole atom is not just a theoretical construct, but corresponds to extant astrophysical systems detectable by future gravitational wave observatories.

Levin, Janna

2009-12-01

3

Molecular orbitals of solids  

SciTech Connect

The molecular orbital contains, in general, a linear combination of orbitals of all equivalent atoms in the molecule, and for its construction one can use the method projection operators or induced representation. In this paper, for the expansion of space group representations obtained on induction of representation of local symmetry groups into a space group, the authors use the Mackey linkage theory and the generalized Frobenius reciprocity theorem. On the basis of the Mackey theory a classification of the chemical interactions in crystals composed of one orbital was obtained. Molecular orbitals for the O/sub h//sup 7/ groups of diamond were obtained, and a symmetric analysis of the zone structure of diamond, silicon, and germanium was performed.

Yarzhemskii, V.G.; Murav'ev, E.N.

1987-11-01

4

Energy level diagrams for black hole orbits  

Microsoft Academic Search

A spinning black hole with a much smaller black hole companion forms a fundamental gravitational system, like a colossal classical analog to an atom. In an appealing if imperfect analogy with atomic physics, this gravitational atom can be understood through a discrete spectrum of periodic orbits. Exploiting a correspondence between the set of periodic orbits and the set of rational

Janna Levin

2009-01-01

5

Pseudosymmetry analysis of molecular orbitals.  

PubMed

We introduce a pseudosymmetry analysis of molecular orbitals by means of the newly proposed irreducible representation measures. To do that we define first what we consider as molecular pseudosymmetry and the relationships of this concept with those of approximate symmetry and quasisymmetry. We develop a general algorithm to quantify the pseudosymmetry content of a given object within the framework of the finite group algebra. The obtained mathematical expressions are able to decompose molecular orbitals by means of the irreducible representations of any reference symmetry point group. The implementation and usefulness of the pseudosymmetry analysis of molecular orbitals is demonstrated in the study of ? and ? orbitals in planar and nonplanar polycyclic aromatic hydrocarbons and the t2 g and eg character of the d-orbitals in the [FeH6](3-) anion in its high spin state along the Bailar twist pathway. PMID:23436743

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

2013-02-22

6

Observation of molecular orbital gating.  

PubMed

The control of charge transport in an active electronic device depends intimately on the modulation of the internal charge density by an external node. For example, a field-effect transistor relies on the gated electrostatic modulation of the channel charge produced by changing the relative position of the conduction and valence bands with respect to the electrodes. In molecular-scale devices, a longstanding challenge has been to create a true three-terminal device that operates in this manner (that is, by modifying orbital energy). Here we report the observation of such a solid-state molecular device, in which transport current is directly modulated by an external gate voltage. Resonance-enhanced coupling to the nearest molecular orbital is revealed by electron tunnelling spectroscopy, demonstrating direct molecular orbital gating in an electronic device. Our findings demonstrate that true molecular transistors can be created, and so enhance the prospects for molecularly engineered electronic devices. PMID:20033044

Song, Hyunwook; Kim, Youngsang; Jang, Yun Hee; Jeong, Heejun; Reed, Mark A; Lee, Takhee

2009-12-24

7

Atomic Electron Populations by Molecular Orbital Theory.  

National Technical Information Service (NTIS)

The detailed distribution of electrons in molecules can be broken down into atomic orbital populations if an atomic orbital basis is used for a molecular orbital wave function (LCAO). A total assignment of all electrons in a molecule to atomic orbitals (a...

W. J. Hehre R. F. Stewart J. A. Pople

1968-01-01

8

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

9

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

ERIC Educational Resources Information Center

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

Lee, Victor R.

2010-01-01

10

Phase Diagram of Spin and Orbital Ordering in Perovskite-type Vanadates  

Microsoft Academic Search

Perovskite-type RVO3 undergoes not only an antiferromagnetic transition but also a structural phase transition coupled with orbital ordering of the t_2g orbital in V^3+ ions with the decrease of temperature. We have investigated specific heat and Raman spectra in these vanadates to clarify the phase diagram of RVO3 and the relationship between the spin and orbital ordering. The specific heat

Shigeki Miyasaka; Masayuki Iwama; Yoichi Okimoto; Hiroshi Okamoto; Yoshinori Tokura

2003-01-01

11

Nucleon Molecular Orbitals and the Transition Mechanism Between Molecular Orbitals in Nucleus-Nucleus Collisions.  

National Technical Information Service (NTIS)

The molecular orbitals of the nucleon(s) in nucleus-nucleus collisions are dynamically defined as a linear combination of nucleon single-particle orbits (LCNO) in a rotating frame by using the coupled-reaction-channel (CRC) theory. Nucleon molecular orbit...

B. Imanishi S. Misono W. von Oertzen H. Voit

1988-01-01

12

MOPAC Manual: A General Molecular Orbital Package.  

National Technical Information Service (NTIS)

MOPAC is a general purpose, semi empirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semi-empirical Hamiltonians MNDO, AMI, PM3, and MINDO/3 and combines the calculation...

J. M. Stewart

1988-01-01

13

Molecular orbital model of atomic collisions  

Microsoft Academic Search

Molecular orbitals and their behavior under promotion are important concepts introduced by Robert Mulliken. A molecular analysis of atomic collisions uses these concepts in a modified form. Such an analysis works well within the limits of its validity, namely, in slow atomic collisions involving excitaton of inner-shell electrons by MO promotion, with subsequent coupling between a few states. To succeed

William Lichten

1980-01-01

14

MOPAC: A semiempirical molecular orbital program  

Microsoft Academic Search

Before we start, we need a working definition for MOPAC. The following description has been used many times to describe MOPAC: MOPAC is a general-purpose, semiempirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semiempirical Hamiltonians MNDO, AM 1, MINDO\\/3, and MNDOPM3, and combir_es the calculations of vibrational spectra, thermodynamic

James J. P. Stewart

1990-01-01

15

Molecular degrees of freedom: resonances and orbiting  

SciTech Connect

Studies of orbiting and other gross features of heavy ion induced reactions show that molecular degrees of freedom play a significant role. The formation of a rotating dinuclear molecule appears as a general feature, and the radii derived for these dinuclear systems are larger than the radii of the conventional nucleus-nucleus potential. These large radii for the molecular bonding potential are similar to those derived from systematic studies performed recently on resonances in the /sup 12/C + /sup 12/C + /sup 16/O systems.

Shapira, D.; Erb, K.A.

1983-01-01

16

Imaging a Molecular Orbital Wave Function Using High Harmonic Emission  

Microsoft Academic Search

Single-electron molecular orbital wave functions are mathematical constructs that are used to describe the multi-electron wave function of molecules. The highest lying orbitals are of particular interest since they are responsible for the chemical properties of molecules. To observe them change as molecular bonds are formed and broken is to observe the essence of chemistry. Yet single orbitals are difficult

David Villeneuve

2005-01-01

17

Molecular orbital model for Be isotopes  

NASA Astrophysics Data System (ADS)

The chain of Be isotopes is an interesting object because of the unique combination of shell, cluster, pairing, deformation and halo effects. Nuclear structure of Be isotopes is studied in the framework of the fully microscopic model where the trial wave function of the ^8Be skeleton has a two-center spatial configuration with the parameters determined by variation of energy (an expectation value of the total hamiltonian of interacting nucleons) after projecting out a proper value of angular momentum. Additional neutrons in heavier Be isotopes are placed on the molecular orbitals with energy minimization for different geometrical configurations. The energy spectra, quadrupole moments and mean square radii are calculated. The extension of the approach for the case of hole configurations in ^7Li is suggested.

Sakharuk, Alexander; Zelevinsky, Vladimir

2000-04-01

18

Molecular Orbital Theoretical Studies of Some Organic Corrosion Inhibitors  

Microsoft Academic Search

Molecular orbital theoretical calculations based on the modified neglect of differential overlap (MNDO) method were performed on some substituted methyl pyridines and substituted ethane derivatives in common use as corrosion inhibitors for iron in acid media. New correlations of corrosion rates with the energy of the highest occupied molecular orbital (E{sub HOMO}), the energy gap or difference between the lowest

V. S. Sastri; J. R. Perumareddi

1997-01-01

19

Phase diagram of kaolinite from Molecular Dynamics calculations  

NASA Astrophysics Data System (ADS)

Structural and thermal behaviors of uncharged 1:1 phyllosilicates kaolinite were investigated from molecular dynamics simulations based on the CLAYFF force field. The focus is on the variation of structural properties including bulk modulus with pressure from 0 to 20 GPa under various range of temperature. The largest bulk modulus between the pressures of 200 and 800 MPa varies from 80 GPa at 298 K to 50 GPa at 1473 K. The obtained value of Cp varies between 7.8 and 13.6 Kcal mol-1 K-1 in the pressure range of 0.1 MPa-20 GPa. Besides, a huge difference was noticed regarding the computed properties at the superheating point. Finally, we show the relationship between superheating point temperature and pressure leading to a phase diagram of kaolinite.

Benazzouz, B. K.; Zaoui, A.

2012-07-01

20

Tuning molecular orbitals in molecular electronics and spintronics.  

PubMed

With the advance of nanotechnology, a variety of molecules, from single atoms to large-scale structures such as graphene or carbon nanotubes, have been investigated for possible use as molecular devices. Molecular orbitals (MOs) are a key ingredient in determining the transport properties of molecules, because they contain all the quantum mechanical information of molecular electronic structures and offer spatial conduction channels for electron transport. Therefore, the delicate modulation of the MOs enables us to tune the performance of electron transport through the molecule. Electric and magnetic fields are powerful and readily accessible means for that purpose. In this Account, we describe the effects of external fields on molecular electronic and spintronic devices. Quantum transport through a molecule that connects source and drain electrodes depends strongly on the alignment of molecular energy levels with respect to the chemical potentials at both electrodes. This dependence results from the energy levels being exploited in resonant tunneling processes when the molecule is weakly coupled to the electrodes in the molecular junction. Molecular energy levels can be shifted by the Stark effect of an external electric field. For a molecule with no permanent dipole moment, the polarizability is the primary factor determining the energy shift of each MO, according to the second-order Stark effect; more polarizable MOs undergo a larger energy shift. Interestingly, even a small shift may lead to a completely nontrivial result. For example, we show a magnetic on-off switching phenomenon of a molecule controlled by an electric field. If a molecule has a nonmagnetic ground state but a highly polarizable magnetic excited state with an energy slightly above the ground state, the magnetic excited state can have lower energy than the ground state under a sufficiently strong electric field. A magnetic field is normally used to control spin orientation in a ferromagnetic system. Here we show that the magnetic field can also be used to control MOs. A graphene nanoribbon with zig-zag-shaped edges (ZGNR) has a ferromagnetic spin ordering along the edges, and the spin states have unique orbital symmetries. Both spin polarizations and orbital symmetries can simultaneously be controlled by means of an external magnetic field. The ZGNR spin-valve devices incorporating this effect are predicted to show an extreme enhancement (compared with conventional devices) of magnetoresistance due to the double spin-filtering process. In such a system, spins are filtered not only by spin matching-mismatching between both electrodes as in normal spin-valve devices, but also by the orbital symmetry matching-mismatching. Thus, a new type of magnetoresistance, and with extremely large values, so-called super-magnetoresistance (distinct from the conventional tunneling or giant magnetoresistance), is available with this method. MOs are at the heart of understanding and tuning transport properties in molecular systems. Therefore, investigating the effects of external fields on MOs is important not only for understanding fundamental quantum phenomena in molecular devices but also for practical applications in the development of interactive devices. PMID:19769353

Kim, Woo Youn; Kim, Kwang S

2010-01-19

21

Orbiting resonances and bound states in molecular scattering  

NASA Astrophysics Data System (ADS)

A family of orbiting resonances in molecular scattering is globally described by using a single pole moving in the complex angular momentum plane. The extrapolation of this pole at negative energies gives the location of the bound states. Then a single pole trajectory, which connects a rotational band of bound states and orbiting resonances, is obtained. These complex angular momentum singularities are derived through a geometrical theory of the orbiting. The downward crossing of the phase shifts through ?/2, due to the repulsive region of the molecular potential, is estimated by using a simple hard-core model. Some remarks about the difference between diffracted rays and orbiting are also given.

de Micheli, Enrico; Viano, Giovanni Alberto

2002-03-01

22

Empirical LCAO parameters for ? molecular orbitals in planar organic molecules  

Microsoft Academic Search

A novel parametrization within a simplified LCAO model (a type of Hückel model) is presented for the description of ? molecular orbitals in organic molecules containing ?-bonds between carbon, nitrogen, or oxygen atoms with sp hybridization. It is shown that the model is quite accurate in predicting the energy of the highest occupied ? orbital and the first ?–?* transition

L. G. D. Hawke; G. Kalosakas; C. Simserides

2009-01-01

23

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

24

MOPAC Manual. A General Molecular Orbital Package. Fourth Edition.  

National Technical Information Service (NTIS)

MOPAC is a general purpose, semi empirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semi-empirical Hamiltonians MNDO, AM1, and MINDO/3 and combines the calculations of ...

J. J. Stewart

1987-01-01

25

Ab initio molecular orbital calculations for magnesium-containing systems  

Microsoft Academic Search

Ab initio molecular orbital calculations for selected magnesium-containing systems have been performed with extended basis sets to examine the convergence of the electrical dipole moment and the total electronic energy.

P. J. Gardner; D. Steele

1992-01-01

26

Phase diagrams and Thomas-Fermi estimates for spin-orbit-coupled Bose-Einstein condensates under rotation  

NASA Astrophysics Data System (ADS)

We provide complete phase diagrams describing the ground state of a trapped spinor Bose-Einstein condensate under the combined effects of rotation and a Rashba spin-orbit coupling. The interplay between the different parameters (magnitude of rotation, strength of the spin-orbit coupling, and interaction) leads to a rich ground-state physics that we classify. We explain some features analytically in the Thomas-Fermi approximation, writing the problem in terms of the total density, total phase, and spin. In particular, we analyze the giant skyrmion and find that it is of degree 1 in the strong-segregation case. In some regions of the phase diagrams, we relate the patterns to a ferromagnetic energy.

Aftalion, Amandine; Mason, Peter

2013-08-01

27

Metastability of Molecular Phases of Nitrogen: Implications to the Phase Diagram  

SciTech Connect

Despite their simplicity, diatomic molecules of first row elements can exhibit very complex phase diagrams. Determination of the phase diagrams can be further complicated by the existence of hysteretic molecular phases that can be observed over large regions of coexistence. Here we present evidence for a previously unreported molecular phase of nitrogen existing at room temperature at least over the range of 33-74 GPa. Our measurements show that sample history may have a significant impact on the thermodynamic states accessed by the molecular nitrogen solid and, by extension, also on the established phase diagram.

Lorenzana, H E; Evans, W J; Lipp, M J

2001-09-12

28

Ab initio molecular simulations with numeric atom-centered orbitals  

Microsoft Academic Search

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 \\

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

2009-01-01

29

Ground-state phase diagram and critical temperature of two-component Bose gases with Rashba spin-orbit coupling  

NASA Astrophysics Data System (ADS)

Ground-state phase diagram of two-component Bose gases with Rashba spin-orbit coupling is determined via a variational approach. A phase in which the fully polarized condensate occupies zero momentum is identified. This zero-momentum phase competes with the spin density wave phase when interspecies interaction is stronger than intraspecies interaction, and the former one is always the ground state for weak spin-orbit coupling. When the energies of these two phases are close, there is a phase separation between them. At finite temperature, such a zero-momentum condensation can be induced by a ferromagnetic phase transition in normal state. The spontaneous spin polarization removes the degeneracy of quasiparticles’ energy minima, and consequently the modified density of state accommodates a Bose condensation to appear below a critical temperature.

Yu, Zeng-Qiang

2013-05-01

30

Molecular orbital study of acyclical nitramine compounds  

NASA Astrophysics Data System (ADS)

The results of MNDO and MINDO/3 semiempirical self-consistent field calculations for the ground state structures, hears of formation, and dipole moments of several acyclical nitramine compounds are compared with each other and experiment. Because the reactions of such molecules are complicated, it may happen that the first steps of their decompositions are not amenable to experimental study, and, in order to attempt to obtain an understanding of the complete dynamics, it is necessary to perform theoretical calculations. The small value of the ratio of electron to proton masses, 1/1823, leads to a decoupling of the electronic motion from that of the heavy particles, the Born-Oppenheimer approximation. The quantum mechanical treatment of the electronic motion for fixed positions of the nuclei forms the basis of quantum chemistry which generates a potential energy surface that determines the heavy particle motion classically, semiclassically, or quantum mechanically. In Sec 2, the Hartree-Fock (HF) self-consistent field (SCF) method is briefly described. The reduction of the HF equations by means of atomic orbitals (AO's) is described as is the problem of multifold proliferation of matrix elements. In Sec 3, the reduction of the full SCF Hamiltonian to the MINDO/3 and MNDO forms is discussed, and the empirical parameterization of matrix elements is described. In Sec. 4, the results obtained for the ground state properties of several acyclical nitramine compounds using MINDO/3 and MNDO Hamiltonians are compared with each other and with experiment.

Herling, G. H.

1985-09-01

31

Binding Energy Calculations Using the Molecular Orbital Wave Function.  

National Technical Information Service (NTIS)

The molecular orbital wave function is used in describing the 4 N-nuclei internal wave function. Using the variational technique the binding energies of the nuclei exp 12 C, exp 16 O, exp 20 Ne and exp 24 Mg are calculated using different Skyrm interactio...

M. Y. M. Hassan A. Rabie E. H. Ismail

1982-01-01

32

Atomlike, Hollow-Core–Bound Molecular Orbitals of C??  

SciTech Connect

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

Feng, Min; Zhao, Jin; Petek, Hrvoje

2008-04-17

33

Chemical bond descriptors from molecular information channels in orbital resolution  

NASA Astrophysics Data System (ADS)

The inter and intraorbital flows of the Fisher and Shannon informations in the molecular communication networks defined in the condensed atomic orbital (AO) resolution are investigated, and the effect of the basis set overlap is examined. The Schrödinger equation is interpreted as solution of the variation principle for the extreme Fisher information, subject to the wave-function-normalization (geometric) and potential-energy (physical) constraints. Its orbital contributions determine the information scattering of the underlying Fisher channel in the adopted AO basis set. This communication network is compared with the associated information system of the Shannon theory of communication. The new set of conditional probabilities between orbitals is compared to that used in the previous, sequential-cascade approach to the effective information promotion of AO in the molecular environment. Both geometrical and physical probabilities are reexamined using the quantum-mechanical superposition principle. The former characterizes the whole orbital space, whereas the latter describes only its occupied part, which determines the system chemical bonds. It is argued that the squares of corresponding elements of the charge and bond-order (CBO) matrix of the LCAO MO theory replace in the physical set of conditional probabilities the corresponding squares of the overlap integrals, which determine the geometrical set. The chain-rule interpretation of conditional probabilities is given. The modified 2-AO channel reproduces fully the earlier predictions from the molecular information channel in atomic resolution. The familiar bond criteria for an effective mixing of AO into molecular orbitals (MO) are shown to remain valid in the communication theory of the chemical bond (CTCB).

Nalewajski, Roman F.

34

Recovering molecular orientation from convoluted orbitals  

NASA Astrophysics Data System (ADS)

Scanning probe microscopy lets us “see” atoms and molecules with unprecedented detail, particularly when the resolution is enhanced by functionalizing the tip of the microscope through deliberate adsorption of atomic or molecular species. However, interpreting the resultant images is often far from trivial as they contain features of both the tip and the sample. Here, a computationally simple theoretical approach is presented that allows the orientations of the tip and sample molecules to be determined from a single scanning tunneling microscopy (STM) image, which in turn reveals information on the bonding interaction between the molecules and the tip and surface. We use the approach to deconvolve the experimental STM images arising from the interaction between a C60-functionalized tip and a C60 molecule adsorbed on a Si(111)-(7×7) surface. The results provide experimental verification of the surface orientations postulated theoretically by Rurali . [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.81.075419 81, 075419 (2010)].

Lakin, Andrew J.; Chiutu, Cristina; Sweetman, Adam M.; Moriarty, Philip; Dunn, Janette L.

2013-07-01

35

Three-Center Bonds in Electron-Deficient Compounds. The Localized Molecular Orbital Approach.  

National Technical Information Service (NTIS)

The authors derive localized molecular orbitals (LMO's) objectively from accurate self-consistent field (SCF) molecular orbital (MO) theory, and explore the limits of transferability of these LMO's in the boranes, carboranes, and their related ionic speci...

W. N. Lipscomb

1972-01-01

36

Influence of large permanent dipoles on molecular orbital tomography.  

PubMed

The influence of large permanent dipoles on molecular orbital tomography via high-order harmonic generation (HHG) is investigated in this work. It is found that, owing to the modification of the angle-dependent ionization rate resulting from the Stark shift, the one-side-recollision condition for the tomographic imaging can not be satisfied even with the few-cycle driving pulses. To overcome this problem, we employ a tailored driving pulse by adding a weak low-frequency pulse to the few-cycle laser pulse to control the HHG process and the recollision of the continuum electrons are effectively restricted to only one side of the core. Then we carried out the orbital reconstruction in both the length and velocity forms. The results show that, the orbital structure can only be successfully reproduced by using the dipole matrix elements projected perpendicular to the permanent dipole in both forms. PMID:23482097

Zhu, Xiaosong; Qin, Meiyan; Zhang, Qingbin; Li, Yang; Xu, Zhizhan; Lu, Peixiang

2013-03-11

37

Mechanically controlled molecular orbital alignment in single molecule junctions.  

PubMed

Research in molecular electronics often involves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4'-Benzenedithiol is the most widely studied molecule in molecular electronics, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4'-benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4'-benzenedithiol, which often differ by orders of magnitude. PMID:22138861

Bruot, Christopher; Hihath, Joshua; Tao, Nongjian

2011-12-04

38

Application of explicitly localized molecular orbitals to electronic structure calculations.  

PubMed

We have recently generalized the method for localizing orbitals on a set of predefined molecular fragments [Phys. Chem. Chem. Phys. 2012, 14, 546]. The regional localized molecular orbitals (RLMO) are well suited for exploiting the locality of electronic correlation at post-Hartree-Fock level of theory. In this paper, the adequacy of RLMO representation is tested in the second-order local Møller-Plesset (LMP2) perturbation theory. Two model systems, namely, n-pentadecane and trans-retinal, are considered. Adequacy of RLMO/LMP2 method is discussed in conjunction with 'exact' MP2 and Pipek-Mezey LMP2 calculations. It is demonstrated that RLMO/MP2 method reduces correlation space and reproduces more than 99% of the correlation energy. PMID:22613144

de Silva, Piotr; Makowski, Marcin; Korchowiec, Jacek

2012-01-01

39

Analyzing molecular static linear response properties with perturbed localized orbitals  

NASA Astrophysics Data System (ADS)

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

Autschbach, Jochen; King, Harry F.

2010-07-01

40

Analyzing molecular static linear response properties with perturbed localized orbitals.  

PubMed

Perturbed localized molecular orbitals (LMOs), correct to first order in an applied static perturbation and consistent with a chosen localization functional, are calculated using analytic derivative techniques. The formalism is outlined for a general static perturbation and variational localization functionals. Iterative and (formally) single-step approaches are compared. The implementation employs an iterative sequence of 2x2 orbital rotations. The procedure is verified by calculations of molecular electric-field perturbations. Boys LMO contributions to the electronic static polarizability and the electric-field perturbation of the r(2) expectation value are calculated and analyzed for ethene, ethyne, and fluoroethene (H(2)C=CHF). For ethene, a comparison is made with results from a Pipek-Mezey localization. The calculations show that a chemically intuitive decomposition of the calculated properties is possible with the help of the LMO contributions and that the polarizability contributions in similar molecules are approximately transferable. PMID:20687635

Autschbach, Jochen; King, Harry F

2010-07-28

41

Electronic and magnetic structure of vivianite: cluster molecular orbital calculations  

Microsoft Academic Search

The electronic and magnetic structure of the octahydrophosphate vivianite, Fe3(PO4)2·8H2O, has been investigated by cluster molecular orbital calculations in local spin density approximation. Optical and Mössbauer\\u000a spectra are well reproduced by the calculations, and the differences between the two iron sites can be correlated with differences\\u000a in the geometrical structure of the first coordination sphere. The spin structure within the

M. Grodzicki; G. Amthauer

2000-01-01

42

Bonding in Transition Metal Silyl Dimers. Molecular Orbital Theory.  

National Technical Information Service (NTIS)

Molecular orbital studies of Mn2(CO)8 (Si(C6H5)2)2 and Pt2(H3P)4(SiC6H5C1)2 have been made by interacting disilene fragments with transition metal dimers. In the former complex, it is found that the Mn-Mn distance is close to the sum of the atomic radii b...

A. B. Anderson C. A. Tessier-Youngs E. A. Zarate P. Shiller W. J. Youngs

1989-01-01

43

Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations  

Microsoft Academic Search

Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was

S. Ono; M. Kuroda; J. Higo; N. Kamiya; N. Nakajima; H. Nakamura

2002-01-01

44

Manipulating Localized Molecular Orbitals by Single-Atom Contacts  

Microsoft Academic Search

We have fabricated atom-molecule contacts by attachment of single Cu atoms to terpyridine side groups of bis-terpyridine tetra-phenyl ethylene molecules on a Cu(111) surface. By means of scanning tunneling microscopy, spectroscopy, and density functional calculations, we have found that, due to the localization characteristics of molecular orbitals, the Cu-atom contact modifies the state localized at the terpyridine side group which

Weihua Wang; Xingqiang Shi; Chensheng Lin; Rui Qin Zhang; Christian Minot; Michel A. van Hove; Yuning Hong; Ben Zhong Tang; Nian Lin

2010-01-01

45

Molecular orbital theory of ballistic electron transport through molecules  

NASA Astrophysics Data System (ADS)

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

Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

2009-03-01

46

Communication: Highest occupied molecular orbital-lowest unoccupied molecular orbital gaps of doped silicon clusters from core level spectroscopy.  

PubMed

A method to determine band gaps of size-selected and isolated nanoparticles by combination of valence band and core-level photoionization spectroscopy is presented. This approach is widely applicable and provides a convenient alternative to current standard techniques for the determination of band gaps by optical or photoelectron spectroscopy. A first application to vanadium doped silicon clusters confirms a striking size-dependence of their highest occupied-lowest unoccupied molecular orbital gaps. PMID:21280677

Lau, J T; Vogel, M; Langenberg, A; Hirsch, K; Rittmann, J; Zamudio-Bayer, V; Möller, T; von Issendorff, B

2011-01-28

47

Polarized Molecular Orbital Model Chemistry. II. The PMO Method  

PubMed Central

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

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

2012-01-01

48

Active Transport Orbitals in Electron Propagator Calculations on Molecular Wires.  

NASA Astrophysics Data System (ADS)

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

Dahnovsky, Yuri; Zakrzewski, V. G.; Kletsov, Alexey; Ortiz, J. V.

2006-03-01

49

On the diabatic separate-atom limit of molecular orbitals in atomic collisions  

Microsoft Academic Search

The authors examine the possibility of establishing a one to one correlation between molecular orbitals and the separate-atom orbitals corresponding to substates with a given principal quantum number. They consider the specific case of the 3 sigma and 4 sigma molecular orbitals for various asymmetric diatomic systems. They discuss the influence of the ionisation state of the system on this

C. Falcon; A. Macias; A. Riera; A. Salin

1981-01-01

50

alpha-clustering and molecular-orbital states in sd-shell nuclei  

SciTech Connect

The alpha-clustering and molecular-orbitals of {sup 22}Ne and F isotopes are investigated based on antisymmetrized molecular dynamics (AMD). The observed candidates for the alpha cluster state of {sup 22}Ne are understood as the molecular-orbital states and alpha+{sup 18}O di-nuclei states. The presence of the molecular-orbital states in the O and F isotopes and the drastic reduction of their excitation energy near the neutron-drip line are predicted.

Kimura, M. [Creative Research Institution Sousei Research Department, Hokkaido University, Sapporo 011-0021 (Japan); Furutachi, N. [Meme Media Laboratory, Hokkaido University, Sapporo 060-8628 (Japan)

2010-05-12

51

Electronic and magnetic structure of vivianite: cluster molecular orbital calculations  

NASA Astrophysics Data System (ADS)

The electronic and magnetic structure of the octahydrophosphate vivianite, Fe3(PO4)2.8H2O, has been investigated by cluster molecular orbital calculations in local spin density approximation. Optical and Mössbauer spectra are well reproduced by the calculations, and the differences between the two iron sites can be correlated with differences in the geometrical structure of the first coordination sphere. The spin structure within the crystallographic ac plane is derived and explained on the basis of different superexchange pathways via edges of the phosphate tetrahedra. The calculations demonstrate that quite large clusters (up to 118 atoms) are necessary to arrive at reliable results.

Grodzicki, M.; Amthauer, G.

52

Revealing molecular orbital gating by transition voltage spectroscopy  

NASA Astrophysics Data System (ADS)

Recently, Song et al. [Nature 462, 1039 (2009)] employed transition voltage spectroscopy to demonstrate that the energy ?H of the highest occupied molecular orbital (HOMO) of single-molecule transistors can be controlled by a gate potential VG. To demonstrate the linear dependence ?H - VG, the experimental data have been interpreted by modeling the molecule as an energy barrier spanning the spatial source-drain region of molecular junctions. Since, as shown in this work, that crude model cannot quantitatively describe the measured I- V-characteristics, it is important to get further support for the linear dependence of ?H on VG. The results presented here, which have been obtained within a model of a point-like molecule, confirm this linear dependence. Because the two models rely upon complementary descriptions, the present results indicate that the interpretation of the experimental results as evidence for a gate controlled HOMO is sufficiently general.

Bâldea, Ioan

2010-11-01

53

Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient  

NASA Astrophysics Data System (ADS)

The energy gradient of the second-order Møller-Plesset perturbation theory (MP2) has been implemented in conjunction with the fragment molecular orbital-based molecular dynamics (FMO-MD) method including up to three-body correction (FMO3). A hybrid integral-direct approach of both atomic and molecular orbital indices was utilized with parallelism for the gradient calculations. A droplet model consisting of 64 water molecules was then simulated with the 6-31G ? basis set. The first peak position of O-O radial distribution function was evaluated to be 2.75 Å at the FMO3-MP2 level, whereas the corresponding Hartree-Fock (FMO3-HF) value was 2.89 Å. Comparison with an X-ray value of 2.73 Å indicated better reliability of the MP2 gradient for FMO-MD.

Mochizuki, Yuji; Nakano, Tatsuya; Komeiji, Yuto; Yamashita, Katsumi; Okiyama, Yoshio; Yoshikawa, Hikaru; Yamataka, Hiroshi

2011-03-01

54

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

SciTech Connect

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

Kafafi, S.A. (Johns Hopkins Univ., Baltimore, MD (USA)); LaFemina, J.P. (Battelle Pacific Northwest Lab., Richland, WA (USA)); Nauss, J.L. (Walter Reed Army Inst. of Research, Washington, DC (USA))

1990-11-21

55

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

SciTech Connect

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

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

2012-12-28

56

Metastable region of phase diagram: optimum parameter range for processing ultrahigh molecular weight polyethylene blends.  

PubMed

Numerous studies suggest that two-phase morphology and thick interface are separately beneficial to the viscosity reduction and mechanical property maintainence of the matrix when normal molecular weight polymer (NMWP) is used for modification of ultrahigh molecular weight polyethylene (UHMWPE). Nevertheless, it is very difficult to obtain a UHMWPE/NMWP blend which may demonstrate both two-phase morphology and thick interface. In this work, dissipative particle dynamics simulations and Flory-Huggins theory are applied in predicting the optimum NMWP and the corresponding conditions, wherein the melt flowability of UHMWPE can be improved while its mechanical properties can also be retained. As is indicated by dissipative particle dynamics simulations and phase diagram calculated from Flory-Huggins theory, too small Flory-Huggins interaction parameter (?) and molecular chain length of NMWP (N(NMWP)) may lead to the formation of a homogeneous phase, whereas very large interfacial tension and thin interfaces might also appear when parameters N(NMWP) and ? are too large. When these parameters are located in the metastable region of the phase diagram, however, two-phase morphology occurs and interfaces of the blends are extremely thick. Therefore, metastable state is found to be advisable for both the viscosity reduction and mechanical property improvement of the UHMWPE/NMWP blends. PMID:22038460

Gai, Jing-Gang; Zuo, Yuan

2011-10-27

57

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

58

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

PubMed

The efficiency at maximum power (EMP) for tight-coupling molecular motors is investigated within the framework of irreversible thermodynamics. It is found that the EMP depends merely on the constitutive relation between the thermodynamic current and force. The motors are classified into four generic types (linear, superlinear, sublinear, and mixed types) according to the characteristics of the constitutive relation, and then the corresponding ranges of the EMP for these four types of molecular motors are obtained. The exact bounds of the EMP are derived and expressed as the explicit functions of the free energy released by the fuel in each motor step. A phase diagram is constructed which clearly shows how the region where the parameters (the load distribution factor and the free energy released by the fuel in each motor step) are located can determine whether the value of the EMP is larger or smaller than 1/2. This phase diagram reveals that motors using ATP as fuel under physiological conditions can work at maximum power with higher efficiency (> 1/2) for a small load distribution factor (< 0.1). PMID:23404567

Tu, Z C

2013-02-12

59

The Fueling Diagram: Linking Galaxy Molecular-to-atomic Gas Ratios to Interactions and Accretion  

NASA Astrophysics Data System (ADS)

To assess how external factors such as local interactions and fresh gas accretion influence the global interstellar medium of galaxies, we analyze the relationship between recent enhancements of central star formation and total molecular-to-atomic (H2/H I) gas ratios, using a broad sample of field galaxies spanning early-to-late type morphologies, stellar masses of 107.2-1011.2 M ?, and diverse stages of evolution. We find that galaxies occupy several loci in a "fueling diagram" that plots H2/H I ratio versus mass-corrected blue-centeredness, a metric tracing the degree to which galaxies have bluer centers than the average galaxy at their stellar mass. Spiral galaxies of all stellar masses show a positive correlation between H2/H I ratio and mass-corrected blue-centeredness. When combined with previous results linking mass-corrected blue-centeredness to external perturbations, this correlation suggests a systematic link between local galaxy interactions and molecular gas inflow/replenishment. Intriguingly, E/S0 galaxies show a more complex picture: some follow the same correlation, some are quenched, and a distinct population of blue-sequence E/S0 galaxies (with masses below key scales associated with transitions in gas richness) defines a separate loop in the fueling diagram. This population appears to be composed of low-mass merger remnants currently in late- or post-starburst states, in which the burst first consumes the H2 while the galaxy center keeps getting bluer, then exhausts the H2, at which point the burst population reddens as it ages. Multiple lines of evidence suggest connected evolutionary sequences in the fueling diagram. In particular, tracking total gas-to-stellar mass ratios within the fueling diagram provides evidence of fresh gas accretion onto low-mass E/S0s emerging from their central starburst episodes. Drawing on a comprehensive literature search, we suggest that virtually all galaxies follow the same evolutionary patterns found in our broad sample.

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

2013-05-01

60

Visualization of Molecular Orbitals and the Related Electron Densities  

SciTech Connect

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

Haranczyk, Maciej; Gutowski, Maciej S.

2008-02-10

61

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

PubMed

The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries. PMID:23704835

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

2013-01-01

62

Development of the explicitly correlated Gaussian-nuclear orbital plus molecular orbital theory: Incorporation of electron-electron correlation  

NASA Astrophysics Data System (ADS)

This Letter proposes a scheme to incorporate electron-electron (e-e) correlation for the explicitly correlated Gaussian-nuclear orbital plus molecular orbital (ECG-NOMO) theory, which offers accurate descriptions for electronic and nuclear states. The second order Møller-Plesset perturbation theory and coupled-cluster theory with singles and doubles in the ECG-NOMO framework are adopted for evaluating the e-e correlation. Illustrative applications for dihydrogen, trihydrogen cation molecules, and their isotopomers confirm significant improvement for the total energies and zero-point energies.

Nishizawa, Hiroaki; Imamura, Yutaka; Ikabata, Yasuhiro; Nakai, Hiromi

2012-04-01

63

Evaluation of electron repulsion integral of the explicitly correlated Gaussian-nuclear orbital plus molecular orbital theory  

NASA Astrophysics Data System (ADS)

This Letter proposes two schemes for the efficient evaluation of electron repulsion integrals required for the explicitly correlated Gaussian-nuclear orbital plus molecular orbital (ECG-NOMO) theory, which offers accurate descriptions for electrons and nuclei. Two schemes, i.e., fully analytical and hybrid schemes for analytical and numerical integrations, for the ECG-NOMO/Hartree-Fock theory are assessed. Illustrative applications of these schemes to two-electron diatomic molecules demonstrate that the ECG-NOMO/HF theory provides significantly accurate zero-point energies within 123.5 cm?1 deviation when compared with the experimental data.

Nishizawa, Hiroaki; Hoshino, Minoru; Imamura, Yutaka; Nakai, Hiromi

2012-01-01

64

Basis Set Orbital Relaxation in Atomic and Molecular Hydrogen Systems  

Microsoft Academic Search

Orbital relaxation (OR) amounts to variation of the orbital exponents in hydrogen molecules and ions relative to the exponents of the isolated atom; it is represented as the sum of the one- and two-center contributions depending on the effective atomic charge and on the presence of other atoms in the molecule. The procedure for isolating the contributions of the exponent

A. I. Ermakov; A. E. Merkulov; A. A. Svechnikova; V. V. Belousov

2004-01-01

65

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

66

Molecular Orbital Approach to Interpret High Pressure Phenomena – Case of Elusive Gold Monofluoride  

Microsoft Academic Search

\\u000a Usefulness of Molecular Orbital analysis for prediction and interpretation of a variety of high-pressure phenomena will be\\u000a illustrated for the case of elusive gold monofluoride, Au(I)F.

Wojciech Grochala; Dominik Kurzydlowski

2010-01-01

67

Alternant molecular-orbital excitations by the generator-coordinate method in the electron gas  

NASA Astrophysics Data System (ADS)

A combination of the generator-coordinate method and the alternant molecular-orbital method is applied to the electron-gas problem. The resulting ground and collective excited states are analyzed and discussed with reference to their density and spin density. The restricted Hartree-Fock alternant molecular-orbital instability found earlier now shows up as a vanishing excitation frequency. Supported in part by Aerospace Research Laboratories (AFSC), United States Air Force under Grant AFOSR 73-2546.

Laskowski, B.; van Leuven, P.; Calais, J.-L.

68

Alternant molecular-orbital excitations by the generator-coordinate method in the electron gas  

Microsoft Academic Search

A combination of the generator-coordinate method and the alternant molecular-orbital method is applied to the electron-gas problem. The resulting ground and collective excited states are analyzed and discussed with reference to their density and spin density. The restricted Hartree-Fock alternant molecular-orbital instability found earlier now shows up as a vanishing excitation frequency. Supported in part by Aerospace Research Laboratories (AFSC),

B. Laskowski; P. van Leuven; J.-L. Calais

1975-01-01

69

Orbital  

NASA Astrophysics Data System (ADS)

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

Hanson, Robert M.

2003-06-01

70

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

PubMed

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

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

2009-05-15

71

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

SciTech Connect

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

Lagmago Kamta, G. [Department of Medical Physics, Ottawa Hospital Cancer Centre, Ottawa, Ontario, K1H 8L6 (Canada); Bandrauk, A. D. [Departement de Chimie, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada)

2009-10-15

72

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

Microsoft Academic Search

The integral bottleneck in evaluating molecular energies arises from the two-electron contributions. These are difficult and time-consuming to evaluate, especially over exponential type orbitals, used here to ensure the correct behavior of atomic orbitals. The two-center two-electron integrals are essential to describe atom pairs in molecules and distinguish those that are bound. In this work on analytical integration, it is

Noureddine Absi; Philip Hoggan

2006-01-01

73

Atomic Orbitals  

NSDL National Science Digital Library

The Atomic Orbitals website is a distribution point for the orbital image generating program "Orbital Viewer" as well as the home of a collection of images generated with the program. Atomic and molecular orbitals are constructed. For atoms, the hydrogenic solution, up to n=30, is generated and for molecules the linear combination of atomic orbitals method is used.

Manthey, David

2009-03-24

74

Correlation of the molecular orbitals of organic sulfides (selenides) and five-membered heterocyclic compounds by photoelectron spectroscopy  

Microsoft Academic Search

The structure and the correlation of the molecular orbitals were studied for divinyl chalcogenides and the isoelectronic five-membered heterocyclic compounds by photoelectron spectroscopy (PES). It was shown that the two frontier p orbitals are inverted in the transition from divinyl sulfide to thiophene, while the heterocyclization of divinyl selenide is accompanied by quasidegeneration. According to PES, the orbital structure of

V. K. Turchaninov; L. M. Sinegovskaya; S. V. Eroshchenko; A. F. Ermikov; B. A. Trofimov

1991-01-01

75

A Direct Molecular Orbital–Molecular Dynamics (MO–MD) Study on the Diffusion of Alkaline Ions on Amorphous Carbon  

Microsoft Academic Search

Hybrid density functional theory (DFT) calculations have been carried out for the lithium ion-carbon cluster model systems to elucidate the nature of lithium-carbon surface interaction. Also, direct molecular orbital-molecular dynamics (MO–MD) calculation [Tachikawa and Shimizu, J. Phys. Chem. B, 109 (2005) 13255] was applied to diffusion processes of the Li ion on the model surfaces of amorphous carbon. Seven cluster

Tetsuji Iyama; Hiroshi Kawabata; Hiroto Tachikawa

2007-01-01

76

Molecular contamination of an EUV instrument in geosynchronous orbit  

NASA Astrophysics Data System (ADS)

Molecular contamination of ultraviolet (UV) optics has been well characterized at wavelengths longer than 120 nm, and some tests have been done at very short wavelengths (10 nm). Characterization of molecular contamination effects at intermediate wavelengths is scarce. This paper draws a parallel between organic light filters and molecular contaminants, considering the contaminant as an extra organic film on an existing filter. This allows the analyst to use Henke light absorptance analysis to characterize extreme ultraviolet (EUV) light attenuation. This technique shows that peak light attenuation occurs near 73 nm (17 eV), rather than the previously assumed 121.6 nm, due to the preferential ejection of 2s electrons in carbon near 17 eV.

Sanders, Jack T., Jr.

2004-10-01

77

Phosphate bonding configuration on ferrihydrite based on molecular orbital calculations and XANES fingerprinting  

NASA Astrophysics Data System (ADS)

Sorption of phosphate by Fe(III)- and Al(III)-(hydr)oxide minerals regulates the mobility of this potential water pollutant in the environment. The objective of this research was to determine the molecular configuration of phosphate bound on ferrihydrite at pH 6 by interpreting P K-edge XANES spectra in terms of bonding mode. XANES and UV-visible absorption spectra for aqueous Fe(III)-PO 4 solutions (Fe/P molar ratio = 0-2.0) provided experimental trends for energies of P(3p)-O(2p) and Fe(3d)-O(2p) antibonding molecular orbitals. Molecular orbitals for Fe(III)-PO 4 or Al(III)-PO 4 complexes in idealized monodentate or bidentate bonding mode were generated by conceptual bonding arguments, and Extended-Hückel molecular orbital computations were used to understand and assign XANES spectral features to bound electronic states. The strong white line at the absorption edge in P K-edge XANES spectra for Fe-PO 4 or Al-PO 4 systems is attributable to an electronic transition from a P 1s atomic orbital into P(3p)-O(2p) or P(3p)-O(2p)-Al(3p) antibonding molecular orbitals, respectively. For Fe-PO 4 systems, a XANES peak at 2-5 eV below the edge was assigned to a P 1s electron transition into Fe(4p)-O(2p) antibonding molecular orbitals. Similarly, a shoulder on the low-energy side of the white line for variscite corresponds to a transition into Al(3p)-O(2p) orbitals. In monodentate-bonded phosphate, Fe-O bonding is optimized and P-O bonding is weakened, and the converse is true of bidentate-bonded phosphate. These differences explained an inverse correlation between energies of P(3p)-O(2p) and Fe(3d)-O(2p) antibonding molecular orbitals consistent with a monodentate-to-bidentate transition in aqueous Fe(III)-PO 4 solutions. The intensity of the XANES pre-edge feature in Fe(III)-bonded systems increased with increasing number of Fe(III)-O-P bonds. Based on the similarity of intensity and splitting of the pre-edge feature for phosphate sorbed on ferrihydrite at 750 mmol/kg at pH 6 and aqueous Fe-PO 4 solutions containing predominantly bidentate complexes, XANES results indicated that phosphate adsorbed on ferrihydrite was predominantly a bidentate-binuclear surface complex.

Khare, Nidhi; Martin, James D.; Hesterberg, Dean

2007-09-01

78

Phosphate Bonding Configuration on Ferrihydrite Based on Molecular Orbital Calculations and XANES Fingerprinting  

SciTech Connect

Sorption of phosphate by Fe(III)- and Al(III)-(hydr)oxide minerals regulates the mobility of this potential water pollutant in the environment. The objective of this research was to determine the molecular configuration of phosphate bound on ferrihydrite at pH 6 by interpreting P K-edge XANES spectra in terms of bonding mode. XANES and UV-visible absorption spectra for aqueous Fe(III)-PO4 solutions (Fe/P molar ratio = 0-2.0) provided experimental trends for energies of P(3p)-O(2p) and Fe(3d)-O(2p) antibonding molecular orbitals. Molecular orbitals for Fe(III)-PO4 or Al(III)-PO4 complexes in idealized monodentate or bidentate bonding mode were generated by conceptual bonding arguments, and Extended-Hueckel molecular orbital computations were used to understand and assign XANES spectral features to bound electronic states. The strong white line at the absorption edge in P K-edge XANES spectra for Fe-PO4 or Al-PO4 systems is attributable to an electronic transition from a P 1s atomic orbital into P(3p)-O(2p) or P(3p)-O(2p)-Al(3p) antibonding molecular orbitals, respectively. For Fe-PO4 systems, a XANES peak at 2-5 eV below the edge was assigned to a P 1s electron transition into Fe(4p)-O(2p) antibonding molecular orbitals. Similarly, a shoulder on the low-energy side of the white line for variscite corresponds to a transition into Al(3p)-O(2p) orbitals. In monodentate-bonded phosphate, Fe-O bonding is optimized and P-O bonding is weakened, and the converse is true of bidentate-bonded phosphate. These differences explained an inverse correlation between energies of P(3p)-O(2p) and Fe(3d)-O(2p) antibonding molecular orbitals consistent with a monodentate-to-bidentate transition in aqueous Fe(III)-PO4 solutions. The intensity of the XANES pre-edge feature in Fe(III)-bonded systems increased with increasing number of Fe(III)-O-P bonds. Based on the similarity of intensity and splitting of the pre-edge feature for phosphate sorbed on ferrihydrite at 750 mmol/kg at pH 6 and aqueous Fe-PO4 solutions containing predominantly bidentate complexes, XANES results indicated that phosphate adsorbed on ferrihydrite was predominantly a bidentate-binuclear surface complex.

Khare,N.; Martin, J.; Hesterberg, D.

2007-01-01

79

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

PubMed

In our quest to explore molecules with chemically significant regions where the Fukui function is negative, we explored reactions where the frontier orbital that indicates the sites for electrophilic attack is not the highest occupied molecular orbital. The highest occupied molecular orbital (HOMO) controls the location of the regions where the Fukui function is negative, supporting the postulate that negative values of the Fukui function are associated with orbital relaxation effects and nodal surfaces of the frontier orbitals. Significant negative values for the condensed Fukui function, however, were not observed. PMID:23090502

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

2012-10-23

80

Optimum atomic orbitals for molecular calculations A review  

Microsoft Academic Search

This review is intended to give a broad outline of the many techniques used in the calculation of atomic structure and the methods of using the information gained from this work in molecular calculations. Consequently, no topic is considered in full depth and only selected examples from the literature are used to illustrate the main points. Extensive tabulatios of atomic

F. R. Burden; R. M. Wilson

1972-01-01

81

Ab initio molecular orbital calculations on the pyrazine-lithium ion pair  

Microsoft Academic Search

The results of ab initio molecular orbital calculations are presented for the pyrazine-\\/Li+ ion pair. It is shown that the lowest energy conformation is where the lithium occupies a position in the plane of the pyrazine ring, along the C2 axis passing through the nitrogen atoms.

A. Hinchliffe; J. C. Cobb; A. J. Duke

1974-01-01

82

Assessment of lithium ion doping into low crystallized carbonaceous materials using molecular orbital calculations  

Microsoft Academic Search

Using molecular orbital calculation, the Li doping reaction in low crystallized carbonaceous material was investigated. As the Li doping reaction occurs on the surface of the graphite layer, the influence on the electric charge of the graphite layer was examined with graphitic models attached with functional groups (-OH, -CHO). As a result, it is suggested that Li was doped at

Satoru Komoda; Mikio Watanabe; Shinichi Komaba; Tetsuya Osaka; Susumu Kikuyama; Kohji Yuasa

1998-01-01

83

An extension of ab initio molecular orbital theory to nuclear motion  

Microsoft Academic Search

We propose an extension of the quantum chemical molecular orbital (MO) method to describe the nuclear motion. Both electronic and nuclear wavefunctions are simultaneously solved with the full variational MO method, by which exponents and centers of gaussian-type function (GTF) basis sets are optimized as well as the linear combination of GTF coefficients. Applications of the method to [F?;e+], FH

Masanori Tachikawa; Kazuhide Mori; Hiromi Nakai; Kaoru Iguchi

1998-01-01

84

The Nonlocalized Molecular Orbital Model to Analyze Infrared and Vibrational Circular Dichroism Spectra: a Database Approach  

Microsoft Academic Search

The nonlocalized molecular orbital model (NMO) of Nafie and Freedman is implemented at the ab initio level to calculate IR and VCD intensities based on contributions of fixed partial charges (FPC), charge flow along bonds (CF) and atomic polarizations (PP). It is theoretically demonstrated that NMO is equivalent to the ab initio RHF formalism for IR intensities. Using local symmetry

Felix Maurer

1993-01-01

85

Study of the electronic structure and reactivity of 4-hydroxyisoquinoline by the molecular orbital method  

Microsoft Academic Search

The reactivity indexes of the neutral, cationic, anionic, and dipolar forms of 4-hydroxyisoquinoline, calculated by the molecular orbital method using dynamic and static approximations, were compared with the experimental data on electrophilic substitution reactions in various media. Good agreement between the experimentally found orientations (3> 1>8, 7, 6, 5) and the localization energies and boundary densities was obtained. The reactivity

B. E. Zaitsev; N. A. Andronova; V. T. Grachev; V. P. Lezina; K. M. Dyumaev; L. D. Smirnov

1972-01-01

86

A molecular orbital study of bond length and angle variations in framework structures  

Microsoft Academic Search

Molecular orbital calculations on a variety of silicate and aluminosilicate molecules have been used to explore the bonding forces that govern tetrahedral bond length variations, r(TO), in framework silicates and aluminosilicates. Not only do the calculations provide insight into the variety of structural types and the substitution limits of one tetrahedral atom for another, but they also provide an understanding

K. L. Geisinger; G. V. Gibbs; A. Navrotsky

1985-01-01

87

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

88

Molecular-orbital model of heat-induced effective exchange coupling in magnetic multilayers  

PubMed

Heat-induced effective exchange coupling between two ferromagnets across a semiconductor spacer layer is described by the interaction of localized, weakly bound electron states which are situated at the two interfaces. These states overlap across the spacer layer and form large molecular orbitals. The energies of these orbitals depend on the spin configuration of the electrons and therefore determine the exchange coupling. Thermal repopulation of the levels yields a positive temperature coefficient of the coupling. The results are found to well reproduce the experimental observations. PMID:10990778

Hunziker; Landolt

2000-05-15

89

Spin-orbit-induced bound state and molecular signature of the degenerate Fermi gas in a narrow Feshbach resonance  

NASA Astrophysics Data System (ADS)

In this paper we explore the spin-orbit-induced bound state and molecular signature of the degenerate Fermi gas in a narrow Feshbach resonance based on a generalized two-channel model. Without the atom-atom interactions, only one bound state can be found even if spin-orbit coupling exists. Moreover, the corresponding bound-state energy depends strongly on the strength of spin-orbit coupling, but is influenced slightly by its type. In addition, we find that when increasing the strength of spin-orbit coupling, the critical point at which the molecular fraction vanishes shifts from zero to the negative detuning. In the weak spin-orbit coupling, this shifting is proportional to the square of its strength. Finally, we also show that the molecular fraction can be well controlled by spin-orbit coupling.

Zhang, Kuang; Chen, Gang; Jia, Suotang

2013-07-01

90

Interaction of HIV-1 aspartic protease with its inhibitor, by molecular dynamics and ab initio fragment molecular orbital method  

PubMed Central

For the three complex crystal structures of HIV-1 aspartic protease (an enzyme of AIDS) with its inhibitor in the Protein Data Bank, molecular dynamics of the generalized Born surface area and the ab initio fragment molecular orbital of an ABINIT-MP calculation was performed to obtain the binding free energy, the molecular orbital energy, the interaction energy of residues with an inhibitor and the charge transfer at the active site. The inhibitors are five symmetric cyclic ureas, of which three were modelled, and an asymmetric dipeptide. The interaction energy of the inhibitor at the active sites of aspartic acid is as great as 50?kcal?mol?1, coinciding with a tetrahedral transition state. For the inhibitor with a higher affinity, charge was transferred to the inhibitor from the active site. The difference in symmetry of the inhibitor was not evident. Binding free energy corresponds to the experimental value of the binding constant, while molecular orbital energy does not always, which is considered to be an entropy effect.

Koyano, Kazuo; Nakano, Tatsuya

2008-01-01

91

Toward internal cooling of trapped molecular ions using a spin-orbit split ground state  

NASA Astrophysics Data System (ADS)

Preparation of state-selected trapped molecular ensembles is a promising starting point for precision measurements on trapped molecular samples. Translational cooling of trapped molecular ions can be accomplished sympathetically by laser cooling a co-trapped atomic species. To date, in situ cooling of rotational degrees of freedom has been demonstrated only for polar hydrides, by optical pumping into an excited vibrational level. However, with increasing reduced mass, the time for vibrational relaxation within the ground state increases, making this scheme problematic for heavy species. We introduce a new cooling scheme, exploiting the diagonal Franck-Condon factors present for molecular ions with spin-orbit split ground states, applicable to certain heavy as well as non-polar species. Progress towards the experimental realization of this scheme for cooling IF?+, including the molecular ion production technique, details of the state-preparation, and the proposed state-resolved detection scheme will be discussed.

Rajagopal, V.; Marler, J. P.; Ruth, L. C.; Seck, C. M.; Odom, B. C.

2011-06-01

92

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

93

Molecular orbital calculation on the chemical bonding character of phosphate glasses  

Microsoft Academic Search

Chemical bonding character of various bonds in phosphate glasses was investigated on the basis of bond overlap population which was evaluated from molecular orbital calculations. Cluster models were constructed from various phosphate crystals. There are two terminal PO bonds in phosphates, that is, P=O double bonds and PNBO (non-bridging oxygen) bonds. In bond overlap population, P=O bonds were much larger

Y. Asano; S. Sakida; T. Nanba; Y. Miura

94

Molecular orbital study on antiferromagnetic coupling mechanism in a silver (I) complex  

Microsoft Academic Search

The mechanism of antiferromagnetic coupling in an Ag (I) complex of nitronyl nitroxide is investigated by means of the broken-symmetry approach within the density functional method (DFT-BS). The magneto-structural corre- lation and the single-occupied molecular orbital (SOMO) analysis reveal the existence of the antiferromagnetic cou- pling pathway along nitronyl nitroxide units via Ag (I) ion, and that the Ag (I)

Guiqin ZHANG; HUANG Jiangen; HUANG Yuanhe; FANG Decai; ZHANG Deqing

2005-01-01

95

Nuclear quantum effects on the He2H+ complex with the nuclear molecular orbital approach  

Microsoft Academic Search

The nuclear quantum effects (NQE) on the geometries and energies of the HeH+ and He2H+ complexes and their hydrogen isotopologues are investigated with the recently developed APMO\\/MP2 code. This code implements the Nuclear Molecular Orbital Approach (NMO) at a MP2 level of theory for electrons and quantum nuclei. In a first investigation of NQE on HeH+, we have observed a

Sergio A. González; Andrés Reyes

2010-01-01

96

Molecular orbital view of the electronic coupling between two metal nanoparticles  

SciTech Connect

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

Troparevsky, Claudia [University of Tennessee, Knoxville (UTK); Zhao, Ke [University of Tennessee, Knoxville (UTK); Xiao, Di [ORNL; Eguiluz, Adolfo G [ORNL; Zhang, Zhenyu [ORNL

2010-01-01

97

Ab initio molecular orbital cluster studies of the zeolite ZSM-5. 1. Proton affinites  

Microsoft Academic Search

In this study we carried out ab initio molecular orbital calculations using the STO-3G, 3-21G, and 6-31G basis sets on aluminosilicate clusters representing ZSM-5 containing up to 46 tetrahedrally coordinated tetravalent atoms and including (SiO)[sub n] rings. The proton affinity and OH stretching frequency of the central bridging oxygen site (O(24)site) are examined as a function of cluster size and

H. V. Brand; L. A. Curtiss; L. E. Iton

1993-01-01

98

Infrared spectra and molecular orbital studies of hydrogen bonded complexes of 2-chloro-4-nitrobenzoic acid  

Microsoft Academic Search

Infrared spectra from complexes of 2-chloro-4-nitrobenzoic acid and some amines with proton affinities (PA) ranging from 205.9 to 229.4 kcal mol?1 are studied. A characteristic relationship between the center of gravity of the infrared protonic vibrational band and proton affinity is obtained. A theoretical study using the atom superposition and electron delocalization molecular orbital method (ASED-MO) is performed. A good

Mohamed K. Awad; Moustafa M. Habeeb

1996-01-01

99

Calculations of molecular-orbital — separated-atom x-ray coincidences  

Microsoft Academic Search

The calculated cross section for the production of 1ss molecular orbital (MO) x-rays in coincidence with projectile and targetK x-rays is a factor of 0.2 to 0.3 smaller than the non-coincident cross section. TheK-coincident MO x-rays are emitted with a much larger anisotropy than the non-coincident MO x-rays.

R. Anholt

1983-01-01

100

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

PubMed

From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I(3) and the single-component molecular conductor [Au(tmdt)(2)]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy. PMID:22299903

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

2012-01-28

101

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

2013-02-13

102

The effect of molecular distortions on spin-orbit coupling in simple hydrocarbons  

NASA Astrophysics Data System (ADS)

Recent work [D.N.S. Parker et al., Chem. Phys. Lett. 469 (2009) 43-49] has found intersystem crossing (ISC) on an ultrafast timescale in electronically excited benzene, a surprise as hydrocarbons generally have small spin-orbit coupling. In this paper, the effect of molecular distortions on spin-orbit coupling (SOC) is calculated for cyclobutadiene and benzene. At equilibrium the SOC in both molecules is negligible, and therefore terms arising from molecular distortions must play a significant role in any fast ISC. We show that out-of-plane C-H bends, which leads to the hybridisation of ? and ? orbitals, are responsible for the most significant effect. The S 1/S 0 conical intersection is an important feature for understanding the photochemistry of these molecules. We examine the SOC along the vector from the Franck-Condon point to the lowest energy point on the crossing seam and discuss the potential importance of the SOC to the ultrafast dynamics.

Penfold, T. J.; Worth, G. A.

2010-09-01

103

Phase diagram of the one-dimensional molecular-crystal model with Coulomb interactions: Half-filled-band sector  

NASA Astrophysics Data System (ADS)

We discuss the ground-state phase diagram of the molecular-crystal model for electron-phonon interactions in the presence of on-site (U) and nearest-neighbor (V) electron-electron interactions in the half-filled-band sector. The system is analyzed as a function of the phonon frequency (?), electron-phonon coupling constant (?), and U and V in the physically relevant case (U,V>0). We discuss various limiting cases with perturbation theory, as well as intermediate-coupling cases using a numerical simulation technique. In particular, we study in detail the limit ?-->?, which corresponds to the extended Hubbard model. The phase diagram is divided into regions of long-range charge-density-wave (CDW) order, algebraic spin-density-wave (SDW) order, and coexisting algebraic singlet superconducting and CDW order. The transition between CDW and SDW phases is continuous for small U and first order for large U. For the physical parameter range (U,V>0), there is no regime where superconductivity dominates. Modification of this picture for the non-half-filled-band sector is indicated.

Hirsch, J. E.

1985-05-01

104

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

105

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

NASA Astrophysics Data System (ADS)

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

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

1997-07-01

106

Comment on ``Phase diagram of MgO from density-functional theory and molecular-dynamics simulations''  

NASA Astrophysics Data System (ADS)

The paper by Strachan et al. [Phys. Rev. B 60, 15 084 (1999)] presents a theoretical phase diagram for MgO. I argue that the B1-liquid phase boundary and the triple point B1-B2-liquid, if calculated correctly using the same model for MgO, might be significantly different from the presented ones. I argue further that the chosen method for calculating the B1-liquid boundary does not provide melting temperatures with a reasonable accuracy, is more time consuming than the two-phase simulation method, and less precise. The only molecular-dynamics simulation in which the MgO melting curve was determined is that by Belonoshko and Dubrovinsky.

Belonoshko, Anatoly B.

2001-03-01

107

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

108

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

NASA Astrophysics Data System (ADS)

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

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

2010-11-01

109

Eutectics and Phase Diagrams of Molten Salts from Molecular Dynamics simulations  

NASA Astrophysics Data System (ADS)

The use of alkali nitrate salt mixtures as heat transfer fluids in solar thermal power plants is limited by their relatively high melting point. Certain compositions of quaternary and higher dimensional mixtures of alkali and alkaline earth nitrates and nitrites have low melting points. However, the high dimensionality of the search space makes it difficult to find lowest melting compositions. Molecular simulations offer an efficient way to screen for promising mixtures. A molecular dynamics scheme general enough to identify eutectics of any HTF candidate mixture will be presented. The eutectic mixture and temperature are located as the tangent point between free energies of mixing for the liquid and a linear plane connecting the pure solid-liquid free energy differences. The free energy of mixing of the liquid phase is obtained using thermodynamic integration over "alchemical" transmutations sampled with molecular dynamics, in which particle identities are swapped gradually. Numerical results for binary and ternary mixtures of alkali nitrates agree well with experimental measurements.

Jayaraman, Saivenkataraman; von Lilienfeld, Anatole; Thompson, Aidan

2011-03-01

110

Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital method  

NASA Astrophysics Data System (ADS)

The fragment molecular orbital method (FMO) was applied to the geometry optimization of several heparin oligosaccharides at the RHF/6-31(+)G(d) level combined with the polarizable continuum model (PCM). For comparison, GLYCAM force field optimization in explicit solvent was also conducted. Good accuracy of FMO was demonstrated in comparison to ab initio at the MP2/PCM level. The interaction analysis was conducted using the pair interaction energy decomposition analysis (PIEDA), and the role of hydrogen bonding and solvent was elucidated in the helix formation of heparin in solution. Content:text/plain; charset="UTF-8"

Sawada, Toshihiko; Fedorov, Dmitri G.; Kitaura, Kazuo

111

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

NASA Astrophysics Data System (ADS)

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.

Fedorov, Dmitri G.; Kitaura, Kazuo

2009-11-01

112

Effect of the highest occupied molecular orbital energy level offset on organic heterojunction photovoltaic cells  

Microsoft Academic Search

The effect of the highest occupied molecular orbital energy level offset, DeltaEHOMO, on organic photovoltaic cells has been investigated using a set of donor\\/C60 heterojunction structures with DeltaEHOMO up to 1.1 eV provided by various donors. The open-circuit voltage decreases with DeltaEHOMO whereas the short-circuit current and fill factor increase with DeltaEHOMO but roll off with DeltaEHOMO>0.7 eV. These characteristics

Minlu Zhang; Hui Wang; C. W. Tang

2010-01-01

113

Fragment molecular orbital calculation using the RI-MP2 method  

NASA Astrophysics Data System (ADS)

The resolution of the identity second-order Møller-Plesset perturbation theory (RI-MP2) was introduced into the fragment molecular orbital (FMO) method, where the program of the RI-MP2 method was newly developed. After some test calculations with a small peptide, the performance of the RI-MP2 method with the FMO scheme was demonstrated for two biomolecular systems: the human immunodeficiency virus type 1 protease with the lopinavir molecule, and the prion protein with the GN8 molecule. These calculations showed the great advantage of FMO calculations using the RI-MP2 method over ordinary FMO calculations.

Ishikawa, Takeshi; Kuwata, Kazuo

2009-05-01

114

Density functional theory (DFT) investigation of molecular structure and frontier molecular orbitals (FMOs) of P-N,N-dimethylaminobenzylidenemalononitrile (DBM).  

PubMed

P-N,N-dimethylaminobenzylidenemalononitrile (DBM) dye belongs to a class of organic compounds known as molecular rotors. Its optimized geometry and frontier molecular orbitals (FMOs), before and after ultraviolet (UV) irradiation, were obtained by DFT/B3LYP level with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. It is found that the length of C-C bonds of the DBM molecule increases after the UV irradiation, which leads to an increase in its dipole moment making it as a promising material for solar cell applications. Also, its HOMO-LUMO gap decreased from 3.46 to 3.34 eV. From the cyclic voltammetry measurements the value of HOMO-LUMO gap is equal to 3.21 eV. This means that B3LYP/6-311++G(d,p) level of theory is the best one for calculations. PMID:21640638

El-Nahass, M M; Kamel, M A; El-Deeb, A F; Atta, A A; Huthaily, S Y

2011-05-12

115

Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)  

NASA Astrophysics Data System (ADS)

The fragment molecular orbital-based molecular dynamics (FMO-MD) was improved by the introduction of the three-body extension (FMO3) and the generalized dynamic fragmentation. An analytical energy gradient was derived for FMO3 to realize FMO3-MD. An algorithm of generalized dynamic fragmentation was devised to treat each covalent-bonded and, optionally, hydrogen-bonded atom cluster as a fragment in the course of FMO-MD. The new algorithms were tested by performing conventional MO-MD, FMO2-MD, based on two-body extension, and FMO3-MD simulations of (H 2O) 32 and H +(H 2O) 32. FMO2-MD resulted in lower precision, especially in H +(H 2O) 32, while FMO3-MD gave a precision comparable to that of MO-MD.

Komeiji, Yuto; Mochizuki, Yuji; Nakano, Tatsuya

2010-01-01

116

Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion  

NASA Astrophysics Data System (ADS)

Recently, the method of fragment molecular orbital-based molecular dynamics (FMO-MD) was enhanced by including the three-body corrections (FMO3) [Y. Komeiji, Y. Mochizuki, T. Nakano, Chem. Phys. Lett. 484 (2010) 380]. This simulation protocol was applied to a droplet model consisting of a divalent zinc ion and 64 water molecules, in order to investigate the hydration structure in ab initio fashion. The first peak position of the Zn-O radial distribution function (RDF) was evaluated to be 2.05 Å at the FMO3-HF/6-31G level of theory, which was in agreement with an X-ray value of 2.06 ± 0.02 Å. The coordination number was evaluated to be 6, corresponding to an octahedral coordination.

Fujiwara, Takayuki; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Mori, Hirotoshi; Nakano, Tatsuya; Miyoshi, Eisaku

2010-04-01

117

a Time-Dependent Molecular Orbital Approach to Ion-Solid Surface Collisions  

NASA Astrophysics Data System (ADS)

A time-dependent molecular orbital method has been developed to study charge transfer in collisions of ions with metal surfaces at energies between 1 au and 170 au. A set of localized basis functions, consisting of generalized Wannier functions for the surface and s- and p-atomic functions for the ion, is used to separate the system into primary and secondary regions. An effective Hamiltonian and time-dependent equations for the electron density matrix are obtained in the primary region, where most charge transfer occurs. The equations for the electron density matrix are solved with a linearization scheme. The method is suitable to study atomic orbital polarization for collisions of ions and surfaces. A model calculation for Na^+ + W(110) collisions with a prescribed trajectory is presented. The interaction potentials between the W(110) surface and Na 3s and 3p orbitals are calculated from a Na pseudopotential and a step potential for W(110). Results show that the yield of neutralized atoms oscillates with the collision energy as the result of the near-resonance charge transfer mechanism. The time-dependence of the density matrix provides insight on the dynamics of electron transfer along the atomic trajectory.

Feng, Eric Quinn

1991-02-01

118

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

119

Theoretical studies on tunneling ionizations from the doubly degenerate highest occupied molecular orbitals of benzene in intense laser fields.  

PubMed

Combining our generalized Keldysh theory [Sov. Phys. JETP 20, 1307 (1965)] with the molecular orbital theory, the authors theoretically study tunneling ionizations of neutral benzene in intense linearly polarized Ti:sapphire laser fields (800 nm). They consider the ionizations from the highest occupied molecular orbitals (HOMOs) of the ground electronic state. The double degeneracy of the HOMOs is properly taken into account. In the theory, molecular ionizations consist of the individual ionizations from each atom and the quantum interferences between them. The theory reproduces the experimental data well. The authors also show that the polarization dependence of the ionization rates is strongly influenced by the quantum interferences. PMID:17228951

Nagaya, K; Lu, H-F; Mineo, H; Mishima, K; Hayashi, M; Lin, S H

2007-01-14

120

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

121

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

122

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

NASA Astrophysics Data System (ADS)

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.

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

2012-07-01

123

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); Blake, G.A. [California Institute of Technology, Pasadena, CA (United States)

1997-03-01

124

Molecular quantum defect orbital study of the Stark effect in the H{sub 3} molecule  

SciTech Connect

Stark maps and the distribution of oscillator strengths within a Stark manifold in the H{sub 3} molecule have been calculated by diagonalization of the Hamiltonian matrix using a molecular quantum defect orbital (MQDO) basis set. Our perturbative treatment, in which only experimental quantum defects have been used and no fitting parameters are required, explicitly accounts for the coupling between the rotation of the molecular core and the Rydberg-electron motion. A pure Hund's case (d) has been adopted for all the Rydberg states except for the np series, for which Hund's case (b) is considered to be more realistic. A mixing of some of the np Stark states with those belonging to other Rydberg series appears to occur. The presently achieved results conform very well with other reliable theoretical values, in the absence of experimental data. The adequacy of the MQDO procedure for accurately dealing with properties related to the Stark effect in molecules is suggested.

Menendez, J. M.; Martin, I.; Velasco, A. M. [Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid (Spain)

2006-10-15

125

Methane activation by metals and semiconductors. Molecular orbital theory. Annual report, September 1987-August 1988  

SciTech Connect

An atom-superposition and electron delocalization molecular orbital study was made of CHn and CO reactions over coordinatively unsaturated Mo(IV) edge cations in MoS2. Coupling to C2H6 and C2H5(a) proceed with high barriers. CH2(a) coupling to strongly adsorbed ethylene proceeds with a lower barrier, and hydrogenation to ethane is possible. CO binds relatively weakly to 5-fold coordinated Mo and strongly to 4-fold coordinated sites. Over two such sites, CO easily tilts to a di-Sigma bridging orientation and dissociates with a low barrier. In the Fischer-Tropsch process hydrogenation to CH3(ads) and H2O(g) is expected. CO inserts into the Mo-CH3 bond with a low barrier, and subsequent hydrogenations to form C2H6+H2O or CH3CH2OH are favorable. It is proposed that the selectivity toward alcohol formation over alkali-doped MoS2 (the DOW process) may stem from the ability of the alkali cations to stabilize alkoxy intermediates. A second molecular orbital study shows AlN behaves similarly to MgO toward CH4. Stoichiometric AlN is inactive. CH4 is activated by surface N(2-) hole sites, forming surface HN(2-) and methyl radicals.

Anderson, A.B.

1988-09-01

126

Image-charge-induced localization of molecular orbitals at metal-molecule interfaces: Self-consistent GW calculations  

NASA Astrophysics Data System (ADS)

Quasiparticle (QP) wave functions, also known as Dyson orbitals, extend the concept of single-particle states to interacting electron systems. Here we employ many-body perturbation theory in the GW approximation to calculate the QP wave functions for a semiempirical model describing a ?-conjugated molecular wire in contact with a metal surface. We find that image charge effects pull the frontier molecular orbitals toward the metal surface, while orbitals with higher or lower energy are pushed away. This affects both the size of the energetic image charge shifts and the coupling of the individual orbitals to the metal substrate. Full diagonalization of the QP equation and, to some extent, self-consistency in the GW self-energy, is important to describe the effect, which is not captured by standard density functional theory or Hartree-Fock. These results should be important for the understanding and theoretical modeling of electron transport across metal-molecule interfaces.

Strange, M.; Thygesen, K. S.

2012-11-01

127

Spectra of porphyrins Part III. Self-consistent molecular orbital calculations of porphyrin and related ring systems  

Microsoft Academic Search

Self-consistent molecular orbital calculations on the porphin ring by the method of Pariser, Parr, and Pople (SCMO-PPP) confirm earlier conclusions of Gouterman and Platt that the visible and Soret bands of the porphin absorption spectrum can be explained by a four-orbital model. According to this model, the lowest two pairs of excited configurations are accidentally degenerate, and the extensive interaction

Charles Weiss; Hiroshi Kobayashi; Martin Gouterman

1965-01-01

128

Radio Emission Line Surveys of the Molecular Disks Orbiting TW Hya and V4046 Sgr  

NASA Astrophysics Data System (ADS)

We have conducted the first comprehensive mm-wave molecular emission line surveys of the evolved circumstellar disks orbiting the nearby pre-main sequence stars TW Hya (D = 54 pc) and V4046 Sgr AB (D = 73 pc). Both systems have relatively advanced ages of roughly 10 Myr; nevertheless, these disks are known to retain significant residual gaseous components, as evidenced by previous radio and infrared detections of molecular and atomic emission lines and optical/X-ray spectral signatures of ongoing stellar accretion. Our unbiased broad-band radio spectral surveys were performed with the Atacama Pathfinder Experiment (APEX) 12 meter telescope and are intended to yield a complete census of bright molecular emission lines in the 0.85-1.0 mm wavelength range. Here, we present initial results, with particular emphasis on newly detected molecular species and emission lines that are potential diagnostics of the effects of high-energy radiation from pre-main sequence stars on disk gas chemistry and physical conditions. This research is supported by National Science Foundation grant AST-1108950 to RIT.

Kastner, Joel H.; Hily-Blant, P.; Rodriguez, D.; Punzi, K.; Forveille, T.

2013-01-01

129

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

Microsoft Academic Search

Full geometry optimizations using molecular mechanics and the quantum chemical AM1 method have been carried out to determine the minimum energy conformation of pyromellitic dianhydride-oxydianiline polyimide (PMDA-ODA PI). The phenyl-imide twist angle for this compound was determined to be â¼30. These computations also provided a quantitative determination of the energy gap (7 eV), electron affinity (-2 eV), and ionization potential

Sherif A. Kafafi; John P. LaFemina; Jeffrey L. Nauss

1990-01-01

130

Study of the high-pressure helium phase diagram using molecular dynamics  

NASA Astrophysics Data System (ADS)

The rich occurrence of helium and hydrogen in space makes their properties highly interesting. By means of molecular dynamics (MD), we have examined two interatomic potentials for 4He. Both potentials are demonstrated to reproduce high-pressure solid and liquid equation of state (EOS) data. The EOS, solid-solid transitions and melting at high pressures (P) were studied using a two-phase method. The Buckingham potential shows a good agreement with theoretical and experimental EOS, but does not reproduce experimental melting data. The Aziz potential shows a perfect match with theoretical melting data. We conclude that there is a stable body-centred-cubic (bcc) phase for 4He at temperatures (T) above 340 K and pressures above 22 GPa for the Buckingham potential, whereas no bcc phase is found for the Aziz potential in the applied PT range.

Koci, L.; Ahuja, R.; Belonoshko, A. B.; Johansson, B.

2007-01-01

131

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

PubMed

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

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

2011-01-01

132

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

133

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

PubMed Central

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

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

2010-01-01

134

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

PubMed Central

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

Scheiner, S; Lipscomb, W N

1976-01-01

135

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

136

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

NASA Astrophysics Data System (ADS)

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

2011-09-01

137

Anomalous molecular orbital variation upon adsorption on a wide band gap insulator  

NASA Astrophysics Data System (ADS)

It is commonly believed that organic molecules are physisorbed on the ideal nonpolar surfaces of wide band gap insulators with limited variation in the electronic properties of the adsorbate molecule. On the basis of first principles calculations within density functional theory (DFT) and GW approximation, we show that this is not generally true. We find that the molecular frontier orbitals undergo significant changes when a hydroxy acid (here we chose gluconic acid) is adsorbed on MgSO4.H2O(100) surface due to the complex interaction between the molecule and the insulating surface. The predicted trend of the adsorption effect on the energy gap obtained by DFT is reversed when the surface polarization effect is taken into account via the many-body corrections.

Chen, Wei; Tegenkamp, Christoph; Pfnür, Herbert; Bredow, Thomas

2010-06-01

138

Effective preconditioning for ab initio ground state energy minimization with non-orthogonal localized molecular orbitals.  

PubMed

The non-orthogonal localized molecular orbital (NOLMO) is the most localized representation of electronic degrees of freedom. As such, NOLMOs are thus potentially the most efficient for linear-scaling calculations of electronic structures for large systems. However, direct ab initio calculations with NOLMO have not been fully implemented and widely used, partly because of the slow convergence issue in the optimization of NOLMO. Towards realizing the potential of NOLMO for large systems, we applied an energy minimum variational principle for carrying out ab initio self-consistent-field (SCF) calculations with NOLMOs. We developed an effective preconditioning approach using the diagonal part of the second order derivatives and show that the convergence of the energy optimization is significantly improved. The speed of convergence of the energy and density are comparable with that of the conventional SCF approach, thus paving the way for the optimization of NOLMO in linear scaling calculations for large systems. PMID:23943010

Peng, Liang; Gu, Feng Long; Yang, Weitao

2013-08-28

139

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

140

Crystallographic and molecular-orbital studies on the geometry of antifolate drugs.  

PubMed Central

In the common dihydrofolate reductase inhibitors an amino substituent replaces the pteridine carbonyl oxygen atom of folates, with altered hydrogen-bonding properties and size. Flexibility in the amino groups could facilitate enzyme binding. Studies of cycloguanil hydrochloride by neutron diffraction show both in-plane and out-of-plane deformation of amino groups. Molecular-orbital calculations ab initio on 2,4-diamino-5-methylpyrimidinium cation confirm that the 4-amino group is readily deformable. The 2,4-diaminoquinazoline structure is reported. Atomic co-ordinates, thermal parameters, bond distances and bond angles for cycloguanil and 2,4-diaminoquinazoline have been deposited as Supplementary Publication SUP 50108 (13 pages) at the British Library Lending Division, Boston Spa. Wetherby, West Yorkshire LS23, 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1978) 169, 5.

Hunt, W E; Schwalbe, C H; Bird, K; Mallinson, P D

1980-01-01

141

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

PubMed

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

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

2011-03-01

142

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

PubMed

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

Saito, N; Fuwa, A

2000-01-01

143

Physical chemistry of nanostructured molecular sieves by the study of phase diagrams: the case of the cetyltrimethylammonium bromide–tetramethylammonium silicate–water system  

Microsoft Academic Search

A phase diagram for the system cetyltrimethylammonium bromide (CTAB)\\/tetramethylammonium silicate (TMASi)\\/water has been constructed in order to better understand the interactions between these precursors of the MCM-41 mesoporous molecular sieves. Three different CTAB concentration regions were analyzed: the dilute and semidilute regions, where simple surfactant species, such as monomers and spherical and nonspherical CTAB micelles, are found, and the concentrated

A. Albuquerque; C. Vautier-Giongo; H. O. Pastore

2005-01-01

144

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

145

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

PubMed Central

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

Liu, Shubin; Pedersen, Lee G.

2009-01-01

146

?????????????????????????????????????????????????????????????? ????? ????????????????????? ????????? 3 ???? ILLUSTRATING THE DIMENSIONS OF THE BONDING MOLECULAR ORBITALS OF ETHANE, ETHENE, AND ETHYNE BY USING THE 3D ANIMATION MOVIES  

Microsoft Academic Search

In teaching Organic chemistry 1, the instructor developed the three 3D animation movies to illustrate the virtual models of the bonding molecular orbitals of the carbon-carbon bonds in the molecules of ethane, ethene, and ethyne. The created movies illustrated the dimensions around the bonding molecular orbitals. These computer assisted instruction (CAI) media could excite the students in class well. Introduction:

Itsara Khantikaew

147

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

148

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.

2007-09-01

149

Duality Diagrams  

Microsoft Academic Search

The duality between the s- and t-channel descriptions of strong-interaction scattering amplitudes and the assumption that in every channel the scattering proceeds via nonexotic resonances are exhibited by simple diagrams. The diagrams lead to simple derivations of some known consequences of these assumptions as well as to many new predictions which can be tested experimentally.

Haim Harari

1969-01-01

150

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

2007-07-16

151

Calculated Spectroscopic Parameters and the Intermediate Spin-Orbit Coupling Diagram in the Interpretation of 5f4 AmO2+ Spectra  

Microsoft Academic Search

Ab initio relativistic SCF Dirac-Fock and Dirac-Slater calculations of the free-ion Coulomb interaction parameter, F2, and the spin-orbit coupling parameter, &zgr;, have been made for all known oxidation states of actinides, thorium through nobelium. These calculated parameters, when normalized to the experimental spectroscopic parameters, were used to initiate least-squares fits to nine experimental electronic energy levels of anhydrous KAmO2CO3, and

L. P. Varga; J. B. Mann; L. B. Asprey; M. J. Reisfeld

1971-01-01

152

Lattice relaxation, electronic screening, and spin and orbital phase diagram of LaTiO3/SrTiO3 superlattices  

NASA Astrophysics Data System (ADS)

The effect of lattice relaxation on the electronic charge density, band structure, and phase diagram in oxide heterostructure, LaTiO3/SrTiO3 superlattices, the structure grown and measured by Ohtomo et al.[1], is investigated using density functional theory LDA and LDA+U (VASP implementation). We observe substantial ferroelectric-like distortion of TiO6 octahedra at the nearest-to-La region which screens the electrostatic force originating from La^3+ ion reducing the charge density in the La-rich region. We determine the changes in the low energy electronic Hamiltonian caused by the lattice relaxation and investigate the consequences for the ground state phase diagram using the Hartree-Fock approximation. Finally, we present a detailed comparison with previous calculations which neglected the lattice effect. [2] Support from DOE ER 46169. [1]Ohtomo et al., Nature 419, 378 (2002). [2]Okamoto and Millis, Nature (London) 428, 630 (2004), and Phys. Rev. B 70, 195120 (2004).

Okamoto, Satoshi; Millis, Andrew; Spaldin, Nicola

2006-03-01

153

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method  

PubMed Central

Background The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. Results We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. Conclusions Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone.

2011-01-01

154

The extension of the fragment molecular orbital method with the many-particle Green's function.  

PubMed

By using the many-particle Green's function (GF) the extension of the fragment molecular orbital (FMO) method by Kitaura et al. [Chem. Phys. Lett. 313, 701 (1999)] is proposed. It is shown that the partial summation of the cluster expansion of GF reproduces the same extrapolation formula as that of FMO. Therefore we can determine the excitation energy, the transition moment, and the linear response of a molecule from GF approximated with the FMO procedure. It is also shown that no wave function exists which is consistent to the FMO results. The perturbation expansion in which the self-consistent charge approximation defines the unperturbed state is reported. By using it the three-body effects missing in the pair approximation of FMO are analyzed and the corrections to the energy and the reduced density matrices are proposed. In contrast to the previous works these new corrections are not expressed as the addition or the subtraction of the energies of fragments. They are size extensive and require only the quantities available by the FMO calculation. The accuracy of these corrections is validated with the extended Hubbard model and the several test molecules. PMID:17059233

Yasuda, Koji; Yamaki, Daisuke

2006-10-21

155

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

NASA Astrophysics Data System (ADS)

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

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

2002-12-01

156

Spectral-luminescent properties and molecular orbital treatment of some mono- and difluoroquinolones.  

PubMed

Electronic absorption and luminescent spectra of nonfluorinated nalidixic (nlqH) and pipemidic acid (pifqH), monofluoroquinolones - norfloxacin (nfqH) and pefloxacin (pfqH) as well as of their difluorinated analogs 1-ethyl-6,8-difluoro-1,4-dihydro-7-(1-(4-methylpiperazinyl) - 4-oxo-3-quinolinecarboxylic (mdfqH) acid and 1-ethyl-6,8-difluoro-1,4-dihydro-7-(1-piperazinyl) - 4-oxo-3-quinolinecarboxylic acid (dfqH) - were investigated. Quantum yields, lifetimes of excited states and rate constants of radiative and nonradiative transitions of the compounds were measured. The Mulliken charges of atoms from these compounds were calculated by quantum-chemical complex GAMESS. Differences in the electronic structures of these compounds and their spectral-luminescent characteristics were compared with the data of the phototoxicity degree of fluoroquinolones. Analysis of the Mulliken charges of the difluoroquinolones points to the changes of the redistribution of the electron density along ?-conjugated system, and on the oxygen atoms of the carbonyl and carboxyl groups. The analysis of the molecular orbitals involved in the electronic transitions of the compounds revealed that both defluorination and piperazine photolysis are photodecomposition mechanisms which may take place in the excited states of these compounds. The relationship between the location order of the ?-?* excited levels of the FQs and the degree of their phototoxicity has been determined. PMID:21229296

Polishchuk, Anna V; Karaseva, Emilya T; Emelina, Tatyna B; Cramariuc, Oanna; Karasev, Vladimir E

2011-01-13

157

Ab initio molecular orbital study of the GaAs hydrides  

SciTech Connect

The interaction of GaH{sub x} (x = 0{minus}3), electron deficient in the valence shell, and of AsH{sub x} (x = 0{minus}3), electron rich in the valence shell, has been studied by using ab initio molecular orbital methods, which include Moller-Plesset correlation corrections to the fourth order, MP4SDTQ. In most instances, Hartree-Fock (HF) optimizations were used to determine local minima, and in a few cases, MP2 = Full optimizations or MCSCF optimizations were also employed. This research corroborates the work reported by others for the electronic states of GaH, GaH{sub 2}, GaH, AsH, AsH{sub 2}, AsH{sub 3}, and GaAs. The authors report two structures for (GaAs){sub 2}(dimer); the lowest energy conformer appears to be a special case of {mu}-bridged Ga-As{sub 2}-Ga. Monovalent Ga is proposed to explain the lowest energy structure of GaAsH{sub 2}. The lowest energy tetrahydride, H{sub 2}Ga-AsH{sub 2}, is a classical Lewis structure. A double Lewis acid/base adduct, (H{sub 2}Ga-AsH{sub 2}){sub 2}, which can be interpreted in terms of {mu}-bridging, is the dimer structure. This research supports the formations of Lewis acid/base adducts in the thin-film deposition of GaAs by chemical vapor deposition.

Bock, C.W.; Trachtman, M. (Philadelphia Coll. of Textiles and Sciences, PA (United States)); Dobbs, K.D. (Univ. of Delaware, Newark (United States)); Mains, G.J. (Oklahoma State Univ., Stillwater (United States))

1991-10-03

158

Spin-orbit interactionsand magnetic field in antiferromagnetic triangular molecular magnets  

NASA Astrophysics Data System (ADS)

Frustrated triangular molecular magnets such as Cu3 are characterized by a doubly generate S=1/2 ground-state (GS) with opposite chirality. Recently it has been proposed theoretically [1] and verified by ab-initio calculations [2] that an external electric field can efficiently couple these two chiral spin states, even in the absence of spin-orbit interaction (SOI). SOIs are nevertheless important, since they introduce a splitting in the GS manifold. In this talk we will discuss different schemes on how to evaluate within spin density functional theory the effect of the SOIs on the chiral states. The connection between SOI and the Dzyalozhinsky-Moriya interaction will be discussed. We will also present calculations of the energy dependence on an external magnetic field, whose presence is important to achieve full control of the spin-electric coupling within the manifold of the GS chiral doublets. [4pt] [1] M. Trif et. al. Phys. Rev. B 82, 045429 (2010) and M. Trif et. al. Phys. Rev. Lett. 101, 217201 (2008) [0pt] [2] F. Islam et. al. Phys. Rev. B 82, 155446 (2010)

Nossa, J. F.; Islam, M. F.; Canali, C. M.; Pederson, M. R.

2011-03-01

159

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

160

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

161

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

Microsoft Academic Search

Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12–20). Selected geometric isomers include those predicted by Ho &etal; [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding\\/genetic algorithm, as well as those found by Rata &etal; [Phys. Rev. Lett. 85, 546 (2000)] based on density-functional tight-binding\\/single-parent

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

2004-01-01

162

Structures and stability of medium silicon clusters. II. Ab initio molecular orbital calculations of Si12Si20  

Microsoft Academic Search

Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12-20). Selected geometric isomers include those predicted by Ho et al. [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding\\/genetic algorithm, as well as those found by Rata et al. [Phys. Rev. Lett. 85, 546 (2000)] based on

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

2004-01-01

163

Conformational analysis of cis-? 1, -? 2, -? 3 and -? 4-tetrahydrophthalic anhydrides by semiempirical and ab initio molecular orbital calculations  

Microsoft Academic Search

Semiempirical and ab initio molecular orbital calculations have been used to study the conformational geometries and the relative stability of the conformers of cis-?1, -?2, -?3 and -?4-tetrahydrophthalic anhydrides (THPA). The total energy and the structure of the transition states for the interconversion of conformers were calculated with PM3 semiempirical method. It is found that PM3, AM1 and MNDO semiempirical

A. Ben Fredj; S. Ben Rejeb; Z. Ben Lakhdar

2000-01-01

164

Investigations in Semi-Empirical Molecular Orbital Methods. IV. A Modified Wolfsberg-Helmholz Method for Inorganic Systems.  

National Technical Information Service (NTIS)

Semi-empirical molecular orbital calculations were performed for MF6(3-) where M=Ti(3+), V(3+), Cr(3+). Fe(3+) and Co(3+), MnF6(4-), MnF6(2-), MnCl6(4-), MnCl4(2-), MnCl2, VCl6(2-), and VCl4, using a modified semi-empirical MWH method. The method of calcu...

L. E. Harris E. A. Boudreaux

1973-01-01

165

Molecular orbital calculations on electronic and Li-adsorption properties of sulfur-, phosphorus- and silicon-substituted disordered carbons  

Microsoft Academic Search

To clarify the effect of atom substitution on electronic and lithium (Li) adsorption properties of disordered carbons, we employed circum-coronene (C54H18) as a model cluster for disordered carbons and investigated the stable structures, electronic and Li-adsorption properties of its sulfur-, phosphorus- and silicon-substituted sheets, by using a semiempirical molecular orbital method. Among the three substituted sheets, the silicon-substituted Si2C52H18 sheet

Noriyuki Kurita; Morinobu Endo

2002-01-01

166

Calculation of hopping-conduction energy of holes in SiO 2 based on molecular orbital theory  

Microsoft Academic Search

We have developed a new molecular-orbital (MO)-theory-based procedure for calculating activation energies for hole-hopping in dielectrics. The hole-hopping is assumed to consist of two steps. First, the hole hops directly from one trap site to another by electronic excitation without changing atomic structure. Then, the atomic structure gradually relaxes as the hole remains at the newly trapped site. We calculated

Yoshiaki Takemura; Jiro Ushio; Takuya Maruizumi; Katsuhiko Kubota; Masanobu Miyao

1999-01-01

167

Magnetic properties of binuclear complexes with an oxygen bridge in the light of methods of valence schemes and molecular orbits  

Microsoft Academic Search

Using the results of investigations and x ray diffraction data given in the literature for the metal-oxygen bond, we assume that there is a double bond in the nucleus Me=O=Me. A nucleus of this kind shouldbe considered as one whole in which the properties of the bond belong to the oxygen. A scheme of molecular orbits is pr op0sed which

B. Jezowska-Trzebiatowska; W. Wojciechowski

1963-01-01

168

The generalized hybrid orbital method for combined quantum mechanical\\/molecular mechanical calculations: formulation and tests of the analytical derivatives  

Microsoft Academic Search

.  ?Hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials are becoming increasingly important for studying\\u000a condensed-phase systems but one of the outstanding problems in the field has been how to treat covalent bonds between atoms\\u000a of the QM and MM regions. Recently, we presented a generalized hybrid orbital (GHO) method that was designed to tackle this\\u000a problem for hybrid potentials

Patricia Amara; Martin J. Field; Cristobal Alhambra; Jiali Gao

2000-01-01

169

Direct observation of molecular orbitals in an individual single-molecule magnet Mn12 on Bi(111).  

PubMed

Single-molecule nanomagnets have unique quantum properties, and their potential applications require characterization and accessibility of individual single-molecule magnets on various substrates. We develop a gentle tip-deposition method to bring individual prototype single-molecule magnets, manganese-12-acetate (Mn12) molecules, onto the semimetallic Bi(111) surface without linker molecules, using low-temperature scanning tunneling microscopy. We are able to identify both the almost flat-lying and side-lying orientations of Mn12 molecules at 4.5 K. Energy-resolved spectroscopic mapping enables the first observation of several molecular orbitals of individual Mn12 molecules in real space, which is consistent with density functional theory calculations. Both experimental and theoretical results suggest that an energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the almost flat-lying Mn12 is only 40% of such a gap for an isolated (free) Mn12 molecule, which is caused by charge transfer from the metallic surface states of Bi to the Mn12. Despite the reduction of this gap, STM images show that the local lattices of Bi(111) covered with Mn12 remain essentially intact, indicating that Mn12-Bi interactions are not strong. Our findings open an avenue to address directly the local structural and electronic properties of individual single-molecule magnets on solid substrates. PMID:23829481

Sun, Kai; Park, Kyungwha; Xie, Jiale; Luo, Jiyong; Yuan, Hongkuan; Xiong, Zuhong; Wang, Junzhong; Xue, Qikun

2013-07-11

170

The performance of KSC Fixation Tubes with RNALater for orbital experiments: A case study in ISS operations for molecular biology  

NASA Astrophysics Data System (ADS)

Molecular biology experiments on the International Space Station (ISS) continue to face challenges of sample harvesting and sample return to earth for post flight analysis; however, the use of Kennedy Space Center Fixation Tubes filled with RNALater has proven to be a robust solution to many of these challenges. While it is clear that one direction of future spaceflight experimentation may be towards enhanced on-orbit analytical capabilities, the rapid progress of earth-bound analytical capacity dictates that facile return of molecular biology samples from the ISS will continue to be a mainstay of space life sciences research and flight operations. In this paper we present a case study of the successful performance of KFTs and RNALater over a broad set of operational conditions of ascent configuration, on-orbit experiment use, on-orbit storage and sample return configurations that are unique to ISS current operations and constraints. We also provide observations on performance limits and discuss deployment opportunities and scenarios that are consistent with continued successful ISS molecular biology experimentation.

Ferl, Robert J.; Zupanska, Agata; Spinale, April; Reed, David; Manning-Roach, Susan; Guerra, George; Cox, David R.; Paul, Anna-Lisa

2011-07-01

171

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

SciTech Connect

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

Figueira de Morisson Faria, C.; Augstein, B. B. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom)

2010-04-15

172

Molecular orbital modeling of aqueous organosilicon complexes: implications for silica biomineralization  

NASA Astrophysics Data System (ADS)

Researchers recently have proposed that hypercoordinate Si-organic complexes can form in biologically relevant fluids, and they have reported the first evidence for a transient organosilicon complex generated within the life cycle of an organism (Kinrade et al., 2001b, 2002). These interpretations are based upon peak assignments of 29Si NMR spectra that invoke Si-polyol (e.g., Si-sorbitol) complexes with Si in five- and six-fold coordination states. However, ab initio analyses of the proposed organosilicon structures do not reproduce the experimentally observed 29Si NMR chemical shifts (Sahai and Tossell 2001, 2002 and this work). In place of the originally proposed structures, we have modeled one of the observed ? 29Si values with a 5-fold Si-disorbitol complex involving 5-membered ring configurations (i.e., Si-O-C-C-O). The calculated ? 29Si value of this new structure closely matches the observed ? 29Si peaks in the -100 to -102 ppm range. Likewise, 29Si NMR peaks near -144 ppm were well fit by a model complex in which a 6-fold Si was complexed to three sorbitol molecules in 5-membered ring configurations. The ability to reproduce the observed NMR peaks using molecular orbital calculations provides support for the controversial role of hypercoordinate organosilicon species in the uptake and transport of silica by biological systems. The existence of such complexes in turn may explain other puzzles in Si biogeochemistry, such as the persistence of dissolved silica in concentrated biological fluids, the biofractionation of Si isotopes, and fractionation of Ge from Si.

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

2003-11-01

173

The Nonlocalized Molecular Orbital Model to Analyze Infrared and Vibrational Circular Dichroism Spectra: a Database Approach.  

NASA Astrophysics Data System (ADS)

The nonlocalized molecular orbital model (NMO) of Nafie and Freedman is implemented at the ab initio level to calculate IR and VCD intensities based on contributions of fixed partial charges (FPC), charge flow along bonds (CF) and atomic polarizations (PP). It is theoretically demonstrated that NMO is equivalent to the ab initio RHF formalism for IR intensities. Using local symmetry coordinates suitable for creating intensity parameters that are transferable among structurally related molecular fragments, NMO is applied to various molecules to test its validity, and its utility for a database approach for predicting IR and VCD intensities of larger systems. The IR intensities of propane are investigated in terms of FPC, CF and PP, which provides new conceptual insight into electronic effects of vibrations. The VCD spectra of (S)-1,1,1,2-tetradeuteropropane, (S)-1-deuteroethanol and (R)-2-methyloxetane are calculated with NMO, reproducing high level ab initio vibronic coupling and experimental intensities. Procedures are developed to create and retrieve transferable parameters for IR and VCD intensity databases. The concept is examined by compiling an intensity database from parameters of 10 small organic molecules and subsequently predicting the IR and VCD spectra of (R)-1-deutero-ethyl methyl ether and (R)-3-deutero-1-butene. The resulting absorption intensities correspond to those determined directly with NMO. The VCD spectrum of only the former is reproduced well. Discrepancies in the spectrum of the latter are mainly due to CF but also PP terms neglected in the database approach. The NMO-VCD model is tested on a series of terpenes. The measured IR and Raman spectra of alpha -pinene, beta-pinene, nopinone and verbenone are assigned based on non-uniformly scaled ab initio 6-31G^{*0.3} force fields in the range 0-1500 cm^{-1} . A total of 210 observed transitions are reproduced with an average error of 3.7 cm^{-1 }. The NMO-VCD intensities are shown to compare well to experimental features for well determined normal modes. Discrepancies observed in the range 1100-1350 cm ^{-1} are attributed to inaccuracies in the normal mode descriptions rather than shortcomings of the model. In general, the NMO model was shown to be a valid and useful method for predicting VCD intensities and expedient for database applications.

Maurer, Felix

174

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

175

Na2IrO3 as a Molecular Orbital Crystal  

NASA Astrophysics Data System (ADS)

Contrary to previous studies that classify Na2IrO3 as a realization of the Heisenberg-Kitaev model with a dominant spin-orbit coupling, we show that this system represents a highly unusual case in which the electronic structure is dominated by the formation of quasimolecular orbitals (QMOs), with substantial quenching of the orbital moments. The QMOs consist of six atomic orbitals on an Ir hexagon, but each Ir atom belongs to three different QMOs. The concept of such QMOs in solids invokes very different physics compared to the models considered previously. Employing density functional theory calculations and model considerations we find that both the insulating behavior and the experimentally observed zigzag antiferromagnetism in Na2IrO3 naturally follow from the QMO model.

Mazin, I. I.; Jeschke, Harald O.; Foyevtsova, Kateryna; Valentí, Roser; Khomskii, D. I.

2012-11-01

176

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

SciTech Connect

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

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

1985-01-01

177

Chemical bonds from through- bridge orbital communications in prototype molecular systems  

Microsoft Academic Search

The indirect components of chemical interactions between atomic orbitals are explored within the Orbital Communication Theory\\u000a of the chemical bond. The conditional probabilities for such through-bridge probability propagation and the associated entropy\\/information measures of the bond covalency are examined. The illustrative\\u000a example of the bridge components of the chemical bonds between bridgehead carbons in small propellanes is discussed using\\u000a the

Roman F. Nalewajski

2011-01-01

178

Effects of nucleobase metalation on frontier molecular orbitals: potential implications for pi-stacking interactions with tryptophan.  

PubMed

Biochemical recognition processes mediated through pi-stacking interactions are a potential target for rational drug synthesis. A combination of electrostatic, hydrophobic, solvation, charge-transfer, induction, and dispersion interactions has been used to account for the three-dimensional arrangements observed in such motifs. A principal example involves the interaction of purine and pyrimidine rings of nucleic acids with aromatic amino-acid residues such as tryptophan, phenylalanine, and tyrosine. Protonation, alkylation, or coordination of a metal ion such as Pd(II) or Pt(II) to a nucleobase strengthens this interaction by lowering the energy of the lowest unoccupied molecular orbital (LUMO) of the modified nucleobase and improving overlap with the highest occupied molecular orbital (HOMO) in N-acetyl tryptophan. The relative energy difference between the frontier orbitals of isolated molecules, obtained using Density Functional Theory (DFT), is explored as a predictive tool for the strength of the pi-stacking interaction of the nucleobase/tryptophan pair. From the optimized structures of these species, evaluation of the donor-acceptor HOMO-LUMO gap (Deltaepsilon d-->a) suggests that this parameter is a promising predictor of pi-stacking strength for the donor-acceptor pairs presented in this study. The analysis correlates well with experimental association constants, measured by fluorescence spectroscopy, of metallated and alkylated nucleobases with tryptophan in comparison to free nucleobases. PMID:18939818

Anzellotti, Atilio I; Bayse, Craig A; Farrell, Nicholas P

2008-10-22

179

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.

Perkins, Dexter

180

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

181

Thermodynamic Diagrams  

NASA Astrophysics Data System (ADS)

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

Chaston, Scot

1999-02-01

182

Correlation between Molecular Orbitals and Doping Dependence of the Electrical Conductivity in Electron-Doped Metal?Phthalocyanine Compounds  

Microsoft Academic Search

We have performed a comparative study of the electronic properties of six\\u000adifferent electron-doped metal phthalocyanine (MPc) compounds (ZnPc, CuPc,\\u000aNiPc, CoPc, FePc, and MnPc), in which the electron density is controlled by\\u000ameans of potassium intercalation. In spite of the complexity of these systems,\\u000awe find that the nature of the underlying molecular orbitals produce observable\\u000aeffects in the

Monica F. Craciun; Sven Rogge; Alberto F. Morpurgo

2005-01-01

183

BetaMol: Molecular Modeling, Analysis, and Visualization Software Based on the Beta-Complex Derived from the Voronoi Diagram  

Microsoft Academic Search

Molecular shape is one of the most critical factors that determine molecular function. To properly understand the function of a molecule, it is necessary to explore its geometric properties more effectively and efficiently in addition to its physicochemical properties. Due to the complexity of the problems in biomolecular structure, in-silico approach is inevitable for many cases and is becoming more

Youngsong Cho; Jae-Kwan Kim; Chung-In Won; Joonghyun Ryu; Chong-Min Kim; Deok-Soo Kim

2011-01-01

184

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

National Technical Information Service (NTIS)

An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of ...

R. L. Augustine K. M. Lahanas

1992-01-01

185

The bonding of ferrous iron to sulfur and oxygen in tetrahedral coordination: A comparative study using SCF X scattered wave molecular orbital calculations  

Microsoft Academic Search

Molecular quantum mechanical calculations have been performed on high-spin ferrous iron tetrahedrally coordinated to sulfur and oxygen, respectively. The molecular orbital energies obtained from the calculations are compared with experimental optical and X-ray emission spectra. Good agreement was found between calculated and experimental spectral transition energies for the optical absorption spectra of Fe 2+ in sphalerite, of Fe 2+ in

D. J. Vaughan; K. H. Johnson; J. A. Tossell

1974-01-01

186

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

SciTech Connect

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.

Danel, J-F.; Kazandjian, L.; Zerah, G. [Centre DAM Ile-de-France, CEA, Bruyeres-le-Chatel, 91297 Arpajon Cedex (France)

2009-06-15

187

Length-dependence of electron transfer coupling matrix in polyene wires: Ab initio molecular orbital theory study  

NASA Astrophysics Data System (ADS)

The electron transfer (ET) properties of ?-electron conjugated quasi-one-dimensional molecular wires, consisting of polyene, [>C=C<]n (n = 1-11), including ?-carotene, is investigated using ab initio molecular orbital theory within Koopmans theorem (KT) approach. The ET coupling matrix element, VDA, for 1,3-trans-butadiene molecule calculated with the KT approach shows excellent agreement with the corresponding results obtained with two-state model. The calculated values of VDA for the polyene oligomers exhibit exponential decrease in magnitude with increasing length of the wire. However, the decay curve exhibits three different regimes. The magnitude of the decay constant, ?, decreases with the increase in length of the wire. A highly delocalized ?-electron cloud in the polyene chain appears to facilitate retention of the electronic coupling at large separations between the donor and acceptor centers. Publishe

Mallick, Govind; Karna, Shashi P.; He, Haiying; Pandey, Ravindra

188

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

PubMed

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

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

2011-07-28

189

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

190

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

PubMed

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 (BH(4)) in water and the change in the interaction energy of solvated BH(4) (described by MM) with the P(450) heme described by QM. The model can be employed for the development of an extensive classical polarizable force-field. PMID:19045177

Biswas, P K; Gogonea, Valentin

2008-10-21

191

Venn Diagrams  

NSDL National Science Digital Library

Unions, intersections, and differences: This can all be quite confusing to students trying to enter the potentially tricky world of Venn Diagrams. Fortunately, Alfredo Jiminez of Pennsylvania State University, Hazleton has created this handy Flash-enabled teaching application designed to provide students with an engaging way to learn about this subject. The project is party of the Digital Classroom Resources at the MAA Mathematical Sciences Digital Library, and visitors will find this particular learning activity quite easy to use. The interactive tool contains seven sections, including those dealing with the principles of union and intersection, distributive properties, and De Morgan's laws. Within each section, visitors can try their hand with a series of short questions and then take advantage of some review materials and, of course, a few basic tests.

Jiminez, Alfredo

192

Galactic-Center Molecular Arms, Ring, and Expanding Shell. I. Kinematical Structures in Longitude--Velocity Diagrams  

Microsoft Academic Search

Analyzing the (l, b, V_LSR) data cube of (13) CO(J=1--0)-line emission from the Bell-Telephone-Laboratory survey, we have investigated the molecular gas distribution and kinematics in the central +\\/- 1(deg) (+\\/- 150 pc) region of the Galaxy. We have applied the pressing method to remove the local- and foreground-gas components at low velocities in order to estimate the intensity more quantitatively.

Yoshiaki Sofue

1995-01-01

193

Phase Diagram of Tetragonal Manganites  

Microsoft Academic Search

The phase diagram of La1-xSrxMnO3, as a function of hole doping x and tetragonal distortion c\\/a, which consists of ferromagnetic (FM), A-, C-, and G-type antiferromagnetic (AF) states, is obtained by the first-principles band structure calculations. Effects of tetragonal distortion on the magnetic ordering are discussed in terms of orbital ordering and anisotropy in the hopping integrals. The general sequence

Z. Fang; I. V. Solovyev; K. Terakura

2000-01-01

194

Efficient and accurate approximations to the molecular spin-orbit coupling operator and their use in molecular g-tensor calculations  

NASA Astrophysics Data System (ADS)

Approximations to the Breit-Pauli form of the spin-orbit coupling (SOC) operator are examined. The focus is on approximations that lead to an effective quasi-one-electron operator which leads to efficient property evaluations. In particular, the accurate spin-orbit mean-field (SOMF) method developed by Hess, Marian, Wahlgren, and Gropen is examined in detail. It is compared in detail with the ``effective potential'' spin-orbit operator commonly used in density functional theory (DFT) and which has been criticized for not including the spin-other orbit (SOO) contribution. Both operators contain identical one-electron and Coulomb terms since the SOO contribution to the Coulomb term vanishes exactly in the SOMF treatment. Since the DFT correlation functional only contributes negligibly to the SOC the only difference between the two operators is in the exchange part. In the SOMF approximation, the SOO part is equal to two times the spin-same orbit contribution. The DFT exchange contribution is of the wrong sign and numerically shown to be in error by a factor of 2-2.5 in magnitude. The simplest possible improvement in the DFT-SOC treatment [Veff(-2X)-SOC] is to multiply the exchange contribution to the Veff operator by -2. This is verified numerically in calculations of molecular g-tensors and one-electron SOC constants of atoms and ions. Four different ways of handling the computationally critical Coulomb part of the SOMF and Veff operators are discussed and implemented. The resolution of the identity approximation is virtually exact for the SOC with standard auxiliary basis sets which need to be slightly augmented by steep s functions for heavier elements. An almost as efficient seminumerical approximation is equally accurate. The effective nuclear charge model gives results within ~10% (on average) of the SOMF treatment. The one-center approximation to the Coulomb and one-electron SOC terms leads to errors on the order of ~5%. Small absolute errors are obtained for the one-center approximation to the exchange term which is consequently the method of choice [SOMF(1X)] for large molecules.

Neese, Frank

2005-01-01

195

Ion solvation and association in LiClO4/sulfolane solution: a vibrational spectroscopic and molecular orbital study.  

PubMed

Solvation interaction and ion association in solutions of lithium perchlorate/sulfolane have been studied by using infrared and Raman spectra as a function of concentration of lithium perchlorate. The band changes of antisymmetric OSO stretch, antisymmetric CSC stretch, -SO2 wag and twist suggest that there is an interaction between Li+ and sulfolane molecules, and the site of solvation is the oxygen atom of -SO2 group. The molecular orbital calculation supports this suggestion. On the other hand, the apparent solvation number was calculated, and the band fitting for the ClO4- band reveals the presence of contact ion pair, solvent separated ion pair and free ClO4- anion in the concentrated solutions. PMID:11471707

Xuan, X; Wang, J; Lu, J; Pei, N; Mo, Y

2001-07-01

196

Modeling of peptide-silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations  

NASA Astrophysics Data System (ADS)

We have applied the four-body corrected fragment molecular orbital (FMO4) method to the investigation of the interaction between an artificially designed peptide, with sequence of Arg1-Lys2-Leu3-Pro4-Asp5-Ala6 [Sano et al., Langmuir, 21 (2005) 3090], and the silica surface modeled by a large cluster model including 257 silicon atoms. The second-order Møller-Plesset perturbation calculation was accelerated by the Cholesky decomposition with adaptive metric technique (CDAM-MP2). Systematic analyses were made for inter-fragment interaction energies (IFIEs) with and without a statistical correction for screening. As the result, the importance of three charged residues (Arg1, Lys2 and Asp5) in the peptide-silica interaction was illuminated.

Okiyama, Yoshio; Tsukamoto, Takayuki; Watanabe, Chiduru; Fukuzawa, Kaori; Tanaka, Shigenori; Mochizuki, Yuji

2013-04-01

197

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

PubMed

Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator strengths in the molecular-adapted quantum defect orbital formalism from a distorted Cs geometry selected on the basis of outer valence green function calculations. The present work provides a wide range of data of excitation energies and absolute oscillator strengths which correspond to the Rydberg series converging to the three lower ionization potential values of the distorted methane molecule, in energy regions for which experimentally measured data appear to be unavailable. PMID:16599680

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

2006-03-28

198

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

NASA Astrophysics Data System (ADS)

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

Toroz, Dimitrios; Rontani, Massimo; Corni, Stefano

2013-01-01

199

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

SciTech Connect

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

Woerner, H. J.; Bertrand, J. B.; Hockett, P.; Corkum, P. B.; Villeneuve, D. M. [Joint Laboratory for Attosecond Science, National Research Council of Canada and University of Ottawa, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6 (Canada)

2010-06-11

200

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

PubMed

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

Taha, Mohamed; Lee, Ming-Jer

2013-06-28

201

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

NASA Astrophysics Data System (ADS)

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

Taha, Mohamed; Lee, Ming-Jer

2013-06-01

202

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

PubMed

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

Moncho, Salvador; Autschbach, Jochen

2010-12-01

203

Unconventional magnetism as a consequence of the charge disproportionation and the molecular orbital formation in Ba4Ru3O10  

NASA Astrophysics Data System (ADS)

The magnetic and electronic properties of Ba4Ru3O10 were investigated by the ab initio and model calculations. It is shown that nonmagnetic ground state of the one-third Ru4+ ions is not due to the correlation effects. It is rather caused by the charge disproportionation between crystallographically different Ru and the molecular orbital formation in the Ru's trimer.

Streltsov, S. V.; Khomskii, D. I.

2012-08-01

204

Localized Molecular Orbitals for 1,2- and 1,6-Dicarbahexaborane(6). The Open Three-Center Bond and Implications for Carborane Topology.  

National Technical Information Service (NTIS)

Localized molecular orbitals (LMO's) have been calculated for the 1,2 and 1,6 isomers of C2B4H6 by the Edmiston-Ruedenberg procedure. The 1,2 isomer is the first example found in LMO calculations of the existence of the open three-center bond, and it occu...

I. R. Epstein D. S. Marynick W. N. Lipscomb

1972-01-01

205

Physical Methods in Studying Polyoxometalates: Extended HÜCkel Molecular Orbital Calculations and Spectroscopic Properties  

Microsoft Academic Search

\\u000a Polyoxometalates (POMs) of vanadium, molybdenum and tungsten and to some extent, niobium and tantalum are very important and\\u000a interesting classes of complexes with great potential in many applications [1–4]. Since in many cases their structures prove to be unchanged in solution, many methods are applicable for studying their\\u000a molecular and electronic structures. These studies are expected to be useful for

L. P. KAZANSKY

206

Comparison of the local structural stabilities of mammalian prion protein (PrP) by fragment molecular orbital calculations  

PubMed Central

Bovine spongiform encephalopathy (BSE), a member of the prion diseases, is a fatal neurodegenerative disorder suspected to be caused by a malfunction of prion protein (PrP). Although BSE prions have been reported to be transmitted to a wide range of animal species, dogs and hamsters are known to be BSE-resistant animals. Analysis of canine and hamster PrP could elucidate the molecular mechanisms supporting the species barriers to BSE prion transmission. The structural stability of 6 mammalian PrPs, including human, cattle, mouse, hamster, dog and cat, was analyzed. We then evaluated intramolecular interactions in PrP by fragment molecular orbital (FMO) calculations. Despite similar backbone structures, the PrP side-chain orientations differed among the animal species examined. The pair interaction energies between secondary structural elements in the PrPs varied considerably, indicating that the local structural stabilities of PrP varied among the different animal species. Principal component analysis (PCA) demonstrated that different local structural stability exists in bovine PrP compared with the PrP of other animal species examined. The results of the present study suggest that differences in local structural stabilities between canine and bovine PrP link diversity in susceptibility to BSE prion infection.

Hasegawa, Koji; Mohri, Shirou; Yokoyama, Takashi

2013-01-01

207

Phase diagram of Ag-Pd bimetallic nanoclusters by molecular dynamics simulations: solid-to-liquid transition and size-dependent behavior.  

PubMed

This report on the solid-to-liquid transition region of an Ag-Pd bimetallic nanocluster is based on a constant energy microcanonical ensemble molecular dynamics simulation combined with a collision method. By varying the size and composition of an Ag-Pd bimetallic cluster, we obtained a complete solid-solution type of binary phase diagram of the Ag-Pd system. Irrespective of the size and composition of the cluster, the melting temperature of Ag-Pd bimetallic clusters is lower than that of the bulk state and rises as the cluster size and the Pd composition increase. Additionally, the slope of the phase boundaries (even though not exactly linear) is lowered when the cluster size is reduced on account of the complex relations of the surface tension, the bulk melting temperature, and the heat of fusion. The melting of the cluster initially starts at the surface layer. The initiation and propagation of a five-fold icosahedron symmetry is related to the sequential melting of the cluster. PMID:19562138

Kim, Da Hye; Kim, Hyun You; Ryu, Ji Hoon; Lee, Hyuck Mo

2009-04-03

208

Vibrational investigation, molecular orbital studies and molecular electrostatic potential map analysis on 3-chlorobenzoic acid using hybrid computational calculations.  

PubMed

The FT-IR and FT-Raman spectra of 3-chlorobenzoic acid (3CBA) are recorded in the liquid state. The fundamental vibrational frequencies, intensity of vibrational bands and the optimized geometrical parameters of the compound are evaluated using HF and DFT (LSDA/B3LYP/B3PW91/MPW1PW91) methods with 6-311+G(d,p) basis set. The theoretical wave numbers are scaled down and compared with the experimental values which showed very good agreement. Comparison of stimulated spectra with the experimental spectra provides important information about the ability of the hybrid computational method to describe the vibrational modes. The HOMO, LUMO, chemical hardness (?), chemical potential (?), electrophilicity values (?) and maximum amount of electronic charge transfer (?N(max)) are calculated. The molecular electrostatic potential (MESP) is calculated and the corresponding graphs are drawn. Some thermodynamic parameters and physico-chemical properties are calculated and discussed. PMID:21993254

Ramalingam, S; Babu, P David Suresh; Periandy, S; Fereyduni, E

2011-09-20

209

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

PubMed

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

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

2007-11-01

210

Prediction of cytochrome P450 xenobiotic metabolism: tethered docking and reactivity derived from ligand molecular orbital analysis.  

PubMed

Metabolism of xenobiotic and endogenous compounds is frequently complex, not completely elucidated, and therefore often ambiguous. The prediction of sites of metabolism (SoM) can be particularly helpful as a first step toward the identification of metabolites, a process especially relevant to drug discovery. This paper describes a reactivity approach for predicting SoM whereby reactivity is derived directly from the ground state ligand molecular orbital analysis, calculated using Density Functional Theory, using a novel implementation of the average local ionization energy. Thus each potential SoM is sampled in the context of the whole ligand, in contrast to other popular approaches where activation energies are calculated for a predefined database of molecular fragments and assigned to matching moieties in a query ligand. In addition, one of the first descriptions of molecular dynamics of cytochrome P450 (CYP) isoforms 3A4, 2D6, and 2C9 in their Compound I state is reported, and, from the representative protein structures obtained, an analysis and evaluation of various docking approaches using GOLD is performed. In particular, a covalent docking approach is described coupled with the modeling of important electrostatic interactions between CYP and ligand using spherical constraints. Combining the docking and reactivity results, obtained using standard functionality from common docking and quantum chemical applications, enables a SoM to be identified in the top 2 predictions for 75%, 80%, and 78% of the data sets for 3A4, 2D6, and 2C9, respectively, results that are accessible and competitive with other recently published prediction tools. PMID:23701380

Tyzack, Jonathan D; Williamson, Mark J; Torella, Rubben; Glen, Robert C

2013-05-24

211

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

NASA Astrophysics Data System (ADS)

A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption ?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.

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

2013-11-01

212

Molecular orbital calculations of /sup 13/C-/sup 13/C and /sup 1/H-/sup 1/H nuclear spin-spin coupling constants  

SciTech Connect

Theoretical studies are presented for the conformational dependencies of vicinal /sup 13/C-/sup 13/C coupling constants within a variety of saturated and unsaturated molecular frameworks. Using the molecular orbital approach of Blizzard and Santry, it is shown that three distinct patterns of dihedral angle versus /sup 3/H/sub CC/sup contract/ coupling are produced, depending upon the degree of double bonding present within the direct coupling path. By means of calculations that involve modifying the various exchange integrals, two of these coupling patterns are found to depend on sigma-..pi.. exchange. A rationalization of the origin of these coupling patterns is presented. In all systems studied, the orbital and dipolar contributions to the vicinal coupling constant are calculated to be negligible compared to the Fermi contact mechanism except in conjugated systems. The FP/INDO molecular orbital method is employed in the investigation of substitutent effects on /sup 1/H-/sup 1/H coupling constants in substituted ethanes, ethylenes, and benzenes. Substituent effects are simulated by varying the (1/2)(I + A) INDO parameters on two different types of pseudoatoms, one essentially a pseudo-hydrogen and the other involving 2s and 2p orbitals on two centers. A review of the theory of nuclear spin-spin coupling is presented.

Severson, M.L.

1984-01-01

213

Surface behavior and imaging of the lowest unoccupied molecular orbital of indolo[2,1-b]quinazoline-6,12-dione (tryptanthrin) via scanning tunneling microscopy  

NASA Astrophysics Data System (ADS)

Indolo[2,1-b]quinazoline-6,12-dione (tryptanthrin) was imaged at the solution-graphite interface using scanning tunneling microscopy. STM images of the molecular monolayers show clear lobe-to-lobe resolution of the lowest unoccupied molecular orbitals of the molecules, as well as a somewhat unusual parallel arrangement of the molecular dipoles. Evaluation of the dipole-dipole interactions reveals that the interactions of the closest molecule pairs are reduced due to a magic angle-like effect. These results represent an important step toward a more in-depth understanding of the behavior of tryptanthrins, which are of interest due to their potential as pharmaceutical compounds.

Sriraman, Krishnan; Novak, Mark J.; Baum, J. Clayton; Herron, Andrew; Olson, Joel A.

2013-10-01

214

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

215

An ab initio molecular orbital study on effect of electric field strength on ionic selectivity of the sodium channel.  

PubMed

The effect of electric field strength of the selectivity filter on ionic selectivity of the sodium channel has been studied by ab initio molecular orbital calculations. On the basis of the previous method, two kinds of model systems, the FCO2M system and the FCO2M-H2O system, were studied. In this study, a FCO2- molecule, which is substituted for a HCO2- molecule, was used as a model for the selectivity filter. This substitution corresponds to weakening the electric field strength of the selectivity filter. For this system, geometries of ground and transition states were optimized with MINI-3 basis sets. The FCO2-H2O system, for which we evaluated thermochemical parameters and cross-sections, is a good model for ionic permeation of the sodium channel. When the results of the FCO2M-H2O system were compared with those of the HCO2M-H2O system, we concluded that permeabilities of Li+ and Na+ are smaller and that of K+ is larger as the field strength of the selectivity filter is weakened. Namely, the permeation of K+ is relatively favorable when the field strength of the selectivity filter is weakened. This conclusion is in accordance with the prediction of Eisenman's theory. PMID:8392652

Suenobu, K; Tani, S; Imamura, A

1993-04-01

216

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

PubMed Central

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

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

1975-01-01

217

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

SciTech Connect

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

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

1986-08-01

218

Phase diagram of tetragonal manganites  

PubMed

The phase diagram of La1-xSrxMnO3, as a function of hole doping x and tetragonal distortion c/a, which consists of ferromagnetic (FM), A-, C-, and G-type antiferromagnetic (AF) states, is obtained by the first-principles band structure calculations. Effects of tetragonal distortion on the magnetic ordering are discussed in terms of orbital ordering and anisotropy in the hopping integrals. The general sequence of the magnetic ground states, FM --> A-AF --> C-AF --> G-AF with increasing of x, is also explained based on the instability of FM states with respect to the spin-wave excitations. PMID:11019039

Fang; Solovyev; Terakura

2000-04-01

219

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

220

Comparative molecular-orbital and atomic-orbital study of electron transfer and excitation in He sup + +Na(3 s ) collisions at energies of 0. 05 to 20 keV/amu  

SciTech Connect

Electron transfer and excitation in 0.05- to 20-keV/amu He{sup +}+Na(3{ital s}) collisions is studied theoretically within the close-coupling method with two-electron molecular- and atomic-orbital expansion basis sets. Results agree with the trend of other information on this system. Remaining discrepancies that are larger than those in similar contemporary studies of one-electron systems are discussed with reference to the convergence of this two-electron study. Results for the integral alignment parameter {ital A}{sub 20} are also presented as a guideline for future experimental study.

Fritsch, W. (Bereich Kern- und Strahlenphysik, Hahn-Meitner-Institut Berlin, D-1000 Berlin 39, West Germany (DE) Department of Physics, Rice University, Houston, Texas 77251 (USA)); Kimura, M. (Argonne National Laboratory, Argonne, Illinois 60439 Department of Physics, Rice University, Houston, Texas 77251 (USA)); Lane, N.F. (Department of Physics and Rice Quantum Institute, Rice University, Houston, Texas 77251 (USA))

1990-01-01

221

Solvation of Lithium Ion in Organic Electrolyte Solutions and Its Isotopic Reduced Partition Function Ratios Studied by ab initio Molecular Orbital Method  

Microsoft Academic Search

To explore local structures around lithium ions and to estimate lithium isotopic reduced partition function ratios (RPFRs) of solvated lithium ions in ethylene carbonate (EC), methylethyl carbonate (MEC) and EC\\/MEC mixed solvent systems, ab initio molecular orbital calculations at the HF\\/6-31G(d) level of theory were carried out. Both EC and MEC were coordinated to lithium ions using their carboxyl oxygens

Satoshi YANASE; Takao OI

2002-01-01

222

Solvation of Lithium Ion in Organic Electrolyte Solutions and Its Isotopie Reduced Partition Function Ratios Studied by ab initio Molecular Orbital Method  

Microsoft Academic Search

To explore local structures around lithium ions and to estimate lithium isotopic reduced partition function ratios (RPFRs) ofsolvated lithium ions in ethylene carbonate (EC), methylethyl carbonate (MEC) and EC\\/MEC mixed solvent systems, ab initio molecular orbital calculations at the HF\\/6-31G(d) level of theory were carried out. Both EC and MEC were coordinated to lithium ions using their carboxyl oxygens and

Satoshi YANASE; Takao OI

2002-01-01

223

Calculations of Reduced Partition Function Ratios of Monomeric and Dimeric Boric Acids and Borates by the ab initio Molecular Orbital Theory  

Microsoft Academic Search

With the final goal to elucidate boron isotope fractionation observed experimentally, molecular orbital calculations were performed on boric acid and borate monomers and dimers. The geometries of B(OH)3 and B(OH)4 were first optimized and their vibrational frequencies were calculated at their optimized structures. The estimated B-to-B isotopic reduced partition function ratios (RPFRs) of B(OH)3 and B(OH) and the calculated equilibrium

Takao OI

2000-01-01

224

Ab initio molecular orbital calculations of DNA bases and their racdical ions in various protonation states: Evidence for proton transfer in GC base pair radical anions  

Microsoft Academic Search

Ab initio molecular orbital calculations of various protonation states of DNA base and DNA base radical ions were performed to aid our understanding of primary radiation processes in DNA. Each of the structures was optimized at the STO-3G and 3-21 levels of theory, and single point calculations were performed at the 6-31G*\\/\\/3-21G and 6-31+G(d)\\/\\/3-21G levels. Each of the protonation states

Anny Odile Colson; M. D. Sevilla; B. Besler; D. M. Close

1992-01-01

225

Molecular-orbital studies of transition and noble-metal clusters by the SCF-X alpha scattered-wave method  

Microsoft Academic Search

The electronic structures of small copper, nickel, palladium, and platinum clusters having simple-cubic and cubo-octahedral geometries have been calculated, using the self-consistent-field X-alpha scattered-wave approach to molecular-orbital (MO) theory. As the cluster size and coordination number are increased, the MO results show increasing similarity to the electronic structures of the corresponding crystalline metals. The calculated ionization potentials decrease gradually with

K. H. Johnson; J. B. Diamond; C. Y. Yang; R. P. Messmer; S. K. Knudson

1975-01-01

226

Observation of anisotropic interactions and molecular orbitals of CO upon collision with He*(23S) atoms by two-dimensional Penning ionization electron spectroscopy  

Microsoft Academic Search

By collision-energy\\/electron-energy-resolved 2D Penning ionization electron spectroscopy as well as by theoretical calculations of the collisional ionization dynamics, the outer shape of molecular orbitals for ionization to X(2?+) and A(2?) states of CO+ was sensitively probed, and the anisotropy of the interaction between He*(23S) and CO was determined. Ionization to the B(2?+) state of CO+ was assigned to autoionization from

N Kishimoto; M Yamazaki; Y Hanzawa; T Horio; K Ohno

2007-01-01

227

Diagrams about Thoughts about Thoughts about Diagrams  

Microsoft Academic Search

The study of diagrammatic reasoning often focuses on computational models of diagram use rather than on studies of human performance. This paper considers diagrams as a notational system that can be used and studied in an experimental context. It presents a review of the experimental psychology literature rather than a complete theoretical framework, and is intended as an introduction to

Alan F. Blackwell

1997-01-01

228

Neutral-fragmentation paths of methane induced by intense ultrashort IR laser pulses: ab initio molecular orbital approach.  

PubMed

Instantaneous (laser-field-dependent) potential energy curves leading to neutral fragmentations of methane were calculated at several laser intensities from 1.4 × 10(13) to 1.2 × 10(14) W/cm(2) (from 1.0 × 10(10) to 3.0 × 10(10) V/m) using ab initio molecular orbital (MO) methods to validate the observation of neutral fragmentations induced by intense femtosecond IR pulses (Kong et al. J. Chem. Phys. 2006, 125, 133320). Two fragmentation paths, CH(2) + 2H and CH(2) + H(2), in (1)T(2) superexcited states that are located in the energy range of 12-16 eV were considered as the reaction paths because these states are responsible for Jahn-Teller distortion opening up reaction paths during ultrashort pulses. As field intensity increased, the low-lying excited (1)A(1) states originated from the Jahn-Teller (1)T(2) states were substantially stabilized along the neutral-fragment path CH(4) ? CH(2) + 2H and were located below the ionization threshold. On the other hand, the low-lying excited (1)B(1) states, which also originate from the Jahn-Teller (1)T(2) states, were embedded on the ionized state along the dissociation path to CH(2) + H(2). This indicates that ionic fragments, rather than neutral ones, are produced along the CH(2) + H(2) path. The computational results support neutral fragmentations through superexcited states proposed by Kong et al. PMID:23231683

Koseki, Shiro; Shimakura, Noriyuki; Teranishi, Yoshiaki; Lin, Sheng Hsien; Fujimura, Yuichi

2013-01-03

229

Structures, molecular orbitals and UV-vis spectra investigations on Br2C6H4: A computational study  

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

230

H/D isotope effect in methyl torsional interaction of acetone as calculated by a multicomponent molecular orbital method.  

PubMed

We analyzed the H/D isotope effect in the methyl torsional interactions accompanying two methyl internal rotations for acetone (CH(3)COCH(3)) and deuterated acetone (CD(3)COCD(3) and CH(3)COCD(3)) in the ground state by means of the multicomponent molecular orbital (MC_MO) method, which directly accounts for the quantum effects of protons and deuterons. Our estimated rotational constants and moments of inertia for CH(3)COCH(3) and CD(3)COCD(3) agreed well with the experimental results because of the adequate treatment of protonic and deuteronic quantum effects afforded by the MC_MO method. Because the C-D bond distance in the CD(3) group was shorter than the C-H distance in CH(3) owing to the anharmonicity of the potential, the difference in potential energy surfaces of CH(3)COCH(3), CD(3)COCD(3), and CH(3)COCD(3) was strongly related to the differences induced in geometrical parameters by the H/D isotope effect. The potential energy obtained by the MC_MO method was estimated as 290.88 cm(-1) for CH(3)COCH(3), which is in excellent agreement with the experimental results. For CH(3)COCD(3), two potential energies were obtained for CH(3) and CD(3) internal rotations. The MC_MO method successfully elucidated the H/D isotope effect for methyl-methyl repulsive interactions by allowing the adequate treatment of protonic and deuteronic wave functions. The potential energies and bond distances associated with methyl internal rotation induced by the H/D isotope effect were also controlled by the distribution of wave functions of protons and deuterons. PMID:19063553

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

2008-12-01

231

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

232

Nesting in Euler Diagrams  

Microsoft Academic Search

This paper outlines the notion of nesting in Euler diagrams, and how nesting aects the interpretation and construction of such diagrams. After setting up the necessary definitions for Euler diagrams at concrete syntax and abstract levels, the notion of nestedness is introduced at the concrete level, then an equivalent notion is given at the abstract level. The natural progression to

Jean Flower; John Howse; John Taylor

2003-01-01

233

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

SciTech Connect

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

Sadrai, M.; Hadel, L.; Sauers, R.R. [State Univ. of New Jersey, New Brunswick, NJ (United States)] [and others

1992-10-01

234

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

SciTech Connect

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

Alcami, M.; Mo, O.; Yanez, M. [Univ. Autonoma de Madrid (Spain). Dept. de Quimica; Cooper, I.L. [Univ. of Newcastle upon Tyne (United Kingdom). Dept. of Chemistry

1999-04-15

235

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

PubMed

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

Ferenczy, György G

2012-12-28

236

Probing the shape and stereochemistry of molecular orbitals in locally flexible aromatic chains: a penning ionization electron spectroscopy and Green's function study of the electronic structure of biphenyl.  

PubMed

We report on the results of an exhaustive study of the interplay between the valence electronic structure, the topology and reactivity of orbitals, and the molecular structure of biphenyl by means of Penning ionization electron spectroscopy in the gas phase upon collision with metastable He*(2(3)S) atoms. The measurements are compared with one-particle Green's function calculations of one-electron and shake-up valence ionization spectra employing the third-order algebraic diagrammatic construction scheme [ADC(3)]. Penning ionization intensities are also analyzed by means of the exterior electron-density model and comparison with photoelectron spectra: in contrast with the lines originating from sigma orbitals, ionization lines belonging to the pi-band system have large Penning ionization cross sections due to their greater extent outside the molecular van der Waals surface. The involved chemi-ionization processes are further experimentally investigated using collision-energy-resolved Penning ionization electron spectroscopy. The cross sections of pi-ionization bands exhibit a markedly negative collision-energy dependence and indicate that the interaction potential that prevails between the molecule and the He*(2(3)S) atom is strongly attractive in the pi-orbital region. On the other hand, the partial ionization cross sections pertaining to sigma-ionization channels are characterized by more limited collision-energy dependencies, as a consequence of rather repulsive interactions within the sigma-orbital region. A comparison of ADC(3) simulations with the Penning ionization electron spectra and UV photoelectron spectra measured by Kubota et al. [Chem. Phys. Lett. 1980, 74, 409] on thin films of biphenyl deposited at 170 and 109 K on copper demonstrates that biphenyl molecules lying at the surface of polycrystalline layers adopt predominantly a planar configuration, whereas within an amorphous sample most molecules have twisted structures similar to those prevailing in the gas phase. PMID:16834309

Kishimoto, Naoki; Hagihara, Yusuke; Ohno, Koichi; Knippenberg, Stefan; François, Jean-Pierre; Deleuze, Michael S

2005-11-24

237

Symmetry and broken-symmetry in molecular orbital descriptions of unstable molecules. 3. The nature of chemical bonds of spin frustrated systems.  

PubMed

Symmetry and broken symmetry in the molecular orbital description of spin frustration systems have been investigated in relation to the resonating valence bond (RVB) theory of the spin liquid state and non-BCS superconductivity. Broken symmetry (BS) and resonating BS (RBS) molecular orbital (MO) methods have been employed to obtain resonating valence bond (RVB)-type explanations of spin frustrated systems. RBS MO solutions are expanded using the localized molecular orbitals (LMO) to elucidate a universal MO-VB description. The BS and RBS MO descriptions of triangular spin frustrated systems corresponding to transition structures for exchange-forbidden radical insertions were investigated in comparison with the RVB-type explanations of such systems. The BS and RBS calculations by the use of three different axial (SDW) solutions or three noncollinear GSO (helical SDW) solutions of a triangular hydrogen cluster were performed to obtain potential curves with and without resonance (quantum) effects. The resonating GSO (noncollinear) state responsible for short-range correlation was found to be the most stable for the system. The reliability of the approximate spin projection (AP) procedure to eliminate the high-spin component was also elucidated, comparing with the AP BS and RBS potential curves. The BS GSO (GHF) computations of several triangular systems, N(CH(2))(3), (CH(2))(3), and Mn(II)(3)O(4), were performed to obtain total energies and total spin angular momentums and effective exchange integrals (J) between local spins, which are crucial for construction of effective spin Hamiltonian models. The exact diagonalization of the Heisenberg models was also performed to depict the energy levels and magnetic susceptibility curves for triangular and kagome lattices to elucidate spin frustration effects and related quantum spin behaviors. Implications of the computational results have been discussed in relation to magnetic properties of several triangular and kagome systems synthesized recently and the superconductivity of triangular systems discovered recently. PMID:19908878

Kawakami, T; Takeda, R; Nishihara, S; Saito, T; Shoji, M; Yamada, S; Yamanaka, S; Kitagawa, Y; Okumura, M; Yamaguchi, K

2009-12-31

238

Local orbitals by minimizing powers of the orbital variance.  

PubMed

It is demonstrated that a set of local orthonormal Hartree-Fock (HF) molecular orbitals can be obtained for both the occupied and virtual orbital spaces by minimizing powers of the orbital variance using the trust-region algorithm. For a power exponent equal to one, the Boys localization function is obtained. For increasing power exponents, the penalty for delocalized orbitals is increased and smaller maximum orbital spreads are encountered. Calculations on superbenzene, C(60), and a fragment of the titin protein show that for a power exponent equal to one, delocalized outlier orbitals may be encountered. These disappear when the exponent is larger than one. For a small penalty, the occupied orbitals are more local than the virtual ones. When the penalty is increased, the locality of the occupied and virtual orbitals becomes similar. In fact, when increasing the cardinal number for Dunning's correlation consistent basis sets, it is seen that for larger penalties, the virtual orbitals become more local than the occupied ones. We also show that the local virtual HF orbitals are significantly more local than the redundant projected atomic orbitals, which often have been used to span the virtual orbital space in local correlated wave function calculations. Our local molecular orbitals thus appear to be a good candidate for local correlation methods. PMID:21599041

Jansík, Branislav; Høst, Stinne; Kristensen, Kasper; Jørgensen, Poul

2011-05-21

239

Local orbitals by minimizing powers of the orbital variance  

NASA Astrophysics Data System (ADS)

It is demonstrated that a set of local orthonormal Hartree-Fock (HF) molecular orbitals can be obtained for both the occupied and virtual orbital spaces by minimizing powers of the orbital variance using the trust-region algorithm. For a power exponent equal to one, the Boys localization function is obtained. For increasing power exponents, the penalty for delocalized orbitals is increased and smaller maximum orbital spreads are encountered. Calculations on superbenzene, C60, and a fragment of the titin protein show that for a power exponent equal to one, delocalized outlier orbitals may be encountered. These disappear when the exponent is larger than one. For a small penalty, the occupied orbitals are more local than the virtual ones. When the penalty is increased, the locality of the occupied and virtual orbitals becomes similar. In fact, when increasing the cardinal number for Dunning's correlation consistent basis sets, it is seen that for larger penalties, the virtual orbitals become more localthan the occupied ones. We also show that the local virtual HF orbitals are significantly more local than the redundant projected atomic orbitals, which often have been used to span the virtual orbital space in local correlated wave function calculations. Our local molecular orbitals thus appear to be a good candidate for local correlation methods.

Jansík, Branislav; Høst, Stinne; Kristensen, Kasper; Jørgensen, Poul

2011-05-01

240

Energetic Studies and Phase Diagram of Thioxanthene  

NASA Astrophysics Data System (ADS)

The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p° = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 ± 4.1 kJ·mol-1) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p° = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 ± 0.8 kJ·mol-1), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p° = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 ± 4.2 kJ·mol-1. Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data.

Freitas, Vera L. S.; Monte, Manuel J. S.; Santos, Luís M. N. B. F.; Gomes, José R. B.; Ribeiro da Silva, Maria D. M. C.

2009-10-01

241

Energetic studies and phase diagram of thioxanthene.  

PubMed

The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p degrees = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 +/- 4.1 kJ x mol(-1)) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p degrees = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 +/- 0.8 kJ x mol(-1)), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p degrees = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 +/- 4.2 kJ x mol(-1). Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data. PMID:19821598

Freitas, Vera L S; Monte, Manuel J S; Santos, Luís M N B F; Gomes, José R B; Ribeiro da Silva, Maria D M C

2009-11-19

242

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

PubMed

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. PMID:24070283

Gersten, Joel; Kaasbjerg, Kristen; Nitzan, Abraham

2013-09-21

243

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

244

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

NASA Astrophysics Data System (ADS)

The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (?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.

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

2013-10-01

245

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

246

Structure Flow Diagram Generator.  

National Technical Information Service (NTIS)

The Structure Flow Diagram Generator provides the user with a convenient, easy-to-use, and less time-consuming way of diagramming the overall structure of a program. It allows for several options including segment and overlay numbers, and the inclusion of...

S. M. Adams

1989-01-01

247

Formalizing Spider Diagrams  

Microsoft Academic Search

Geared to complement UML and to the specification of large software systems by non-mathematicians,spider di- agrams are a visual language that generalizes the popu- lar and intuitive Venn diagrams and Euler circles. The language design emphasized scalability and expressiveness while retaining intuitiveness. In this extended abstract we describe spider diagrams from a mathematical standpoint and show how their formal semantics

Joseph Gil; John Howse; Stuart Kent

1999-01-01

248

Sequence Diagrams for Mobility  

Microsoft Academic Search

There are several kinds of UML diagrams for convenient modelling of behaviour, but these diagrams can be hardly used for modelling mobility. The situa- tion is not very different in the case of agent languages. There exist already some pro- posals for modelling mobility of interacting agents by graphical notations, but these notations are rather not very intuitive and hard

Piotr Kosiuczenko

2002-01-01

249

Lenses and Ray Diagrams  

NSDL National Science Digital Library

This is the first time that students will draw technical ray diagrams (in previous experiments, they simply sketched the rays). They need a little instruction in drawing ray diagrams before they can do it, so the activity is not purely inquiry. But it is

Horton, Michael

2009-05-30

250

Failure diagrams for unidirectional  

Microsoft Academic Search

Pertinent failure processes in unidirectional fiber metal-matrix composites (MMCs) have been identified and analyzed. The critical conditions for interface delamination in several composites are compared with the theoretical delamination diagram proposed by He and Hutchinson, in which interface delamination and fiber fracture are delineated on the basis of their relative tough-ness values. It is shown that the delamination diagram does

K. S. Chan

1993-01-01

251

Hertzsprung-Russell Diagram  

NASA Astrophysics Data System (ADS)

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

Chiosi, C.; Murdin, P.

2000-11-01

252

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

PubMed

The O-N-N-O-type tetradentate ligands H2S,S-eddp (H2S,S-eddp stands for S,S-ethylenediamine-N,N'-di-2-propionic acid) and H2edap (H2edap stands for ethylenediamine-N-acetic-N'-3-propionic acid) and the corresponding novel octahedral nickel(ii) complexes have been prepared and characterized. N2O2 ligands coordinate to the nickel(ii) ion via four donor atoms (two deprotonated carboxylate atoms and two amine nitrogens) affording octahedral geometry in the case of all investigated Ni(ii) complexes. A six coordinate, octahedral geometry has been verified crystallographically for the s-cis-[Ni(S,S-eddp)(H2O)2] complex. Structural data correlating similarly chelated Ni(ii) complexes have been used to carry out an extensive configuration analysis. Molecular mechanics and Density Functional Theory (DFT) have been used to model the most stable geometric isomer, yielding, at the same time, significant structural and spectroscopic (TDDFT) data. The results from density functional studies have been compared to X-ray data. Natural Bond Orbital (NBO) and Natural Energetic Decomposition Analysis (NEDA) have been done for the [Ni(edda-type)(H2O)2-n] and nH2O fragments. Molecular orbital analysis (MPA) is given as well. The infra-red and electronic absorption spectra of the complexes are discussed in comparison to the related complexes of known geometries. PMID:23884426

Trifunovi?, Sre?ko R; Mileti?, Vesna D; Jevti?, Verica V; Meetsma, Auke; Matovi?, Zoran D

2013-07-25

253

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

PubMed

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

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

2011-09-12

254

Lymphoid tumor in the orbit: malignant or benign? MRI, histomorphological and molecular genetic analysis of eight cases  

Microsoft Academic Search

Differentiation between benign and malignant lymphoid infiltrates of the conjunctiva and the orbit is difficult even on the basis of histopathological appearance. We describe eight cases with low-grade malignant lymphoma, mucosa-associated lesion tissue (MALT) lymphoma. Laboratory analysis was done using microscopy, immunophenotyping and gene rearrangement using the Southern blot technique. DNA-rearrangement analysis allows a very precise determination of the benign

Seishu Abe; Mitsuharu Tamakawa; Masakatu Andoh; Kyuhei Kohda; Chihiro Teranishi; Isao Ohta

2005-01-01

255

How to Interpret Circuit Diagrams  

NSDL National Science Digital Library

This site presents an explanation of how to interpret circuit diagrams. Two diagrams show the difference between a "short hand" circuit diagram and a more detailed one. The detailed circuit diagram is useful for those first learning circuits in an effort to eventually understand the "short hand" diagram without difficulty.

Lesurf, Jim

2013-06-07

256

Molecular spin-orbit excitations in the Jeff=(1)/(2) frustrated spinel GeCo2O4  

NASA Astrophysics Data System (ADS)

We describe powder and single-crystal inelastic neutron scattering experiments on a spinel-type antiferromagnet GeCo2O4, represented by an effective total angular momentum Jeff=1/2. Several types of nondispersive short-range magnetic excitations were discovered. The scattering intensity maps in Q space are well reproduced by dynamical structure factor analyses using molecular model Hamiltonians. The results of analyses suggest that the molecular excitations below TN arise from molecular ground states, one of which consists of antiferromagnetically coupled ferromagnetic subunits. The quasielastic excitations above TN are interpreted as its precursor. A combination of frustration and Jeff=1/2 might induce these quantum phenomena.

Tomiyasu, K.; Crawford, M. K.; Adroja, D. T.; Manuel, P.; Tominaga, A.; Hara, S.; Sato, H.; Watanabe, T.; Ikeda, S. I.; Lynn, J. W.; Iwasa, K.; Yamada, K.

2011-08-01

257

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)

1994-02-01

258

Plutonium Predominance Region Diagrams.  

National Technical Information Service (NTIS)

Four plutonium predominance region diagrams, a technique for estimating the solubility of hydrous plutonium(IV) oxide, and a method for comparing valence state distributions of uranium, neptunium and plutonium are described.

G. L. Silver

1975-01-01

259

Venn Diagram Shape Sorter  

NSDL National Science Digital Library

This interactive Java applet helps students explore attributes of objects by sorting different sized, colored, shapes into Venn Diagrams. The user chooses the type of Venn Diagram including 2 intersecting circles, 2 non-intersecting circles, or a single circle. Two modes include "make the rule," where users create the rules of the circles and then sort, or "guess the rule," where users attempt to sort the shapes into the circles in order to guess the rule the computer has chosen.

2005-01-01

260

Failure diagrams for unidirectional  

Microsoft Academic Search

Pertinent failure processes in unidirectional fiber metal-matrix composites (MMCs) have been identified and analyzed. The\\u000a critical conditions for interface delamination in several composites are compared with the theoretical delamination diagram\\u000a proposed by He and Hutchinson, in which interface delamination and fiber fracture are delineated on the basis of their relative\\u000a tough-ness values. It is shown that the delamination diagram does

K. S. Chan

1993-01-01

261

On the lack of activity of substitutional Sn atoms toward the electro-oxidation of CO on Pt anodes: Molecular orbital theory  

SciTech Connect

An atom superposition and electron delocalization molecular orbital (ASED-MO) study shows that tin atoms alloyed substitutionally into platinum electrode surfaces are inactive in generating OH(ads) for the electro-oxidation of the CO(ads) poison generated during the operation of methanol fuel cells. Such tin atoms, though they donate to Pt, are not good acceptors for H{sub 2}O lone-pair donation bond formation because of the way in which their 5p orbitals mix with the Pt valence band. Thus substitutional Sn atoms in the Pt surface do not attract or activate H{sub 2}O. OH is also found to adsorb weakly to substitutional Sn atoms compared to surface Pt atoms, the opposite of the diatomic SnO and PtO bond strengths. This is because the OH is essentially reduced by neighboring Pt atoms and not the Sn atom to which it is bound. When bound to substitutional Sn atoms, OH is calculated to be relatively active in oxidizing CO(ads) on adjacent Pt atoms, but the inability of the surface to generate such OH implies a different mechanism must be responsible for-the electrocatalysis, perhaps involving adsorbed Sn atoms or Sn complexes.

Anderson, A.B.; Grantscharova, E. [Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Chemistry; Shiller, P. [Packard Electric DELPHI Systems, Warren, OH (United States)

1995-06-01

262

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

263

Molecular Spin-Orbit Interaction for d5 Ions in Crystals. Spin-Lattice Coupling Coefficients and First-Order Spin-Orbit Interaction for the Fluorescent Levels of d5 Ions  

NASA Astrophysics Data System (ADS)

The first-order spin-orbit (SO) interaction for the fluorescent 4T1-levels of Mn2+ in the common cation series ZnX (X: S, Se, Te) has been calculated by using the molecular SO interaction HSO mol and a very elaborated ligand-field (LF) model. With respect to the splittings predicted by the crystal-field (CF) model, the first-order SO splittings are very strongly reduced for Mn in ZnS, while for Mn in ZnSe and ZnTe, the splittings are inversed and strongly enhanced. A theoretical check of the validity of the LF model is performed by relating the matrix elements of the total angular momentum for the monoelectronic wave functions 2e and 2t2 which intervene in the calculation of the matrix elements of the first-order SO interaction to those which intervene in the calculation of the spin-lattice coupling coefficients (SLCC). Another check of the validity of the LF model from a previous analysis of the four vibronic lines of the fluorescent level of Mn2+ in ZnS is briefly recalled.

Parrot, R.; Boulanger, D.

1997-06-01

264

UV-diagram: A Voronoi diagram for uncertain data  

Microsoft Academic Search

The Voronoi diagram is an important technique for answering nearest-neighbor queries for spatial databases. In this paper, we study how the Voronoi diagram can be used on uncertain data, which are inherent in scientific and busines s applications. In particular, we propose the Uncertain-Voronoi Diagram (or UV-diagram in short). Conceptually, the data space is divided into distinct \\

Reynold Cheng; Xike Xie; Man Lung Yiu; Jinchuan Chen; Liwen Sun

2010-01-01

265

Ion-molecule interactions in solutions of lithium perchlorate in propylene carbonate + diethyl carbonate mixtures: an IR and molecular orbital study.  

PubMed

FTIR spectra have been recorded and analyzed for solutions of lithium perchlorate in propylene carbonate (PC), diethyl carbonate (DEC), and PC + DEC mixtures. It has been shown that the carbonyl stretch bands for PC and DEC are very sensitive to the interaction between Li+ and the solvent molecules. They split with addition of LiClO4, indicating a strong interaction of Li+ with PC and DEC through the oxygen group of PC and both oxygen and ether oxygen atoms of DEC. In conjunction with molecular orbital calculation, the optimized geometries of solvation are given. In addition, solvent separated ion pairs and contact ion pairs were observed in LiClO4/DEC solutions, and no preferential solvation of Li+ in LiClO4/PC + DEC solutions were detected. PMID:12212734

Wang, Jianji; Wu, Yanping; Xuan, Xiaopeng; Wang, Hanqing

2002-08-01

266

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

267

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

268

Hydrogen transfer in photoexcited phenol/ammonia clusters by UV-IR-UV ion dip spectroscopy and ab initio molecular orbital calculations. I. Electronic transitions  

NASA Astrophysics Data System (ADS)

The electronic spectra of reaction products via photoexcited phenol/ammonia clusters (1:2-5) have been measured by UV-near-IR-UV ion dip spectroscopy. Compared with the electronic spectra of hydrogenated ammonia cluster radicals the reaction products have been proven to be (NH3)n-1NH4 (n=2-5), which are generated by excited-state hydrogen transfer in PhOH-(NH3)n. By comparing the experimental results with ab initio molecular orbital calculations at multireference single and double excitation configuration interaction level, it has been found that the reaction products (NH3)n-1NH4 (for n=3 and 4), contain some isomers.

Ishiuchi, Shun-Ichi; Daigoku, Kota; Saeki, Morihisa; Sakai, Makoto; Hashimoto, Kenro; Fujii, Masaaki

2002-10-01

269

Hydrogen transfer in photo-excited phenol/ammonia clusters by UV-IR-UV ion dip spectroscopy and ab initio molecular orbital calculations. II. Vibrational transitions  

NASA Astrophysics Data System (ADS)

The vibrational spectra of phenol/ammonia clusters (1:2-5) in S0 and those of their photochemical reaction products, (NH3)n-1NH4 (n=2-5), which are generated by excited-state hydrogen transfer, have been measured by UV-IR-UV ion dip spectroscopy. The geometries, IR spectra and normal modes of phenol-(NH3)n (n=1-5) have been examined by ab initio molecular orbital calculations, at the second-order Møller-Plesset perturbation theory level with large basis sets. For the n=2 and 3 reaction products, similar vibrational analyses have been carried out. From the geometrical information of reactants and products, it has been suggested that the reaction products have memories of the reactant's structure, which we call ``memory effect.''

Ishiuchi, Shun-Ichi; Daigoku, Kota; Saeki, Morihisa; Sakai, Makoto; Hashimoto, Kenro; Fujii, Masaaki

2002-10-01

270

Ab initio molecular orbital study of the reactivity of active alkyl groups. V. Nitrosation mechanism of acetone with syn-form of methyl nitrite.  

PubMed

The mechanisms of nitrosation of acetone through sodium enolate [CH3CO1CH2]-Na+ (1) or naked enolate [CH3CO1CH2]- (2) with methyl nitrite CH3O3NO2 (3), and the reactivity of the syn-form of 3 (syn-3) during the C-N bond formation process were investigated using ab initio molecular orbital (MO) methods. Our results have demonstrated the predominant formation of E-1-hydroxyimino-2-oxo-propane CH3COCH=NOH (4E) when the complex [CH3CO1CH2NO2(O3CH3)]-Na+ was produced kinetically via a metal-chelated pericyclic transition state (TS(CHELATED)), in which the O3 atom of syn-3 was coordinated to the Na+ atom of 1. PMID:12419919

Niiya, Tokihiro; Ikeda, Hirohito; Yukawa, Miho; Goto, Yoshinobu

2002-11-01

271

Molecular orbital study of polarity and hydrogen bonding effects on the g and hyperfine tensors of site directed NO spin labelled bacteriorhodopsin  

NASA Astrophysics Data System (ADS)

Semiempirical molecular orbital methods (PM3, INDO, ZINDO/S) have been used to calculate the effects of local electric fields and of hydrogen bonding on the g and hyperfine tensors of a nitroxide spin label model system. The results yield a linear correlation between the two principal tensor components gxx and A Nzz at label sites of varying polarity. Hydrogen bonding with a single water molecule produces a constant shift of ? gxx ? -4 x 10-4. These theoretical results are used to interpret recent high field (3.4T, 95GHz) electron paramagnetic resonance investigations on site-directed spin labelled bacteriorhodopsin. This protein reveals a close correlation between proticity and polarity at the various label sites. The slope of the gxx versus ANzz dependence is affected strongly by polarity induced structural strains of the spin label.

Plato, Martin; Steinhoff, Heinz-Jürgen; Wegener, Christoph; Törring, Jens T.; Savitsky, Anton; Möbius, Klaus

272

Atomic Orbitals  

NSDL National Science Digital Library

The Atomic Orbitals Web site "was established as part of an (ongoing) project at Purdue University to develop 'visualization modules' for general chemistry students." Using the Chime plug-in, which allows unique and stunning visualizations, visitors can learn what an atomic orbital is; what the 1s, 2s, 3s, 2p, 3p, and 3d orbitals are; what hybrid orbitals are; and more. The combination of easy-to-read descriptions and educational graphics make the site a great learning resource for high school and even college level chemistry students.

2007-06-05

273

Risk Mitigation for Managing On-Orbit Anomalies.  

National Technical Information Service (NTIS)

This slide presentation reviews strategies for managing risk mitigation that occur with anomalies in on-orbit spacecraft. It reviews the risks associated with mission operations, a diagram of the method used to manage undesirable events that occur which i...

J. La

2010-01-01

274

Ionic Radical Theory of Crystalline Electro-Optical and Nonlinear Optical Effects. II. Calculation of Second Harmonic Generation Coefficient of alpha -LiIO sub 3 Crystal Using (IO Sub 3 ) exp -1 Radical Molecular Orbitals.  

National Technical Information Service (NTIS)

An (IO sub 3 ) exp -1 ionic radical model is proposed for the SHG effect of iodate crystals. The SHG coefficient for alpha LiIO sub 3 is calculated using (IO sub 3 ) exp -1 radical molecular orbitals and the calculated value agrees well with experimental ...

C. Chen

1977-01-01

275

Intramolecular Nonbonded Interactions Between Oxygen and Group VIA Elements: An Ab Initio Molecular Orbital and Density Functional Theory Investigation of the Structures of HX—CH 2 —COOH (X=S, Se, and Te)  

Microsoft Academic Search

Ab initio molecular orbital and density functional methods have been used to study the potential energy surfaces of the substituted acetic acids HX—CH2—COOH, where X is one of the Group VIA Chalcophiles S, Se, or Te. The various conformers adopted by these compounds provide information regarding the energetic importance of nonbonded \\u000a

George D. Markham; Cindy L. Bock; Mendel Trachtman; Charles W. Bock

1999-01-01

276

Strong Rotational Coupling Effects on the Transition /sup 17/O(/sup 16/O, /sup 16/O)/sup 17/O*(0.87 MeV, 1/2/sup +/) Between Nucleon Molecular Orbitals.  

National Technical Information Service (NTIS)

It is pointed out that the rotational coupling interactions play essential role in the transition between nucleon molecular orbitals leading to the excitation of /sup 17/O*(0.87 MeV;1/2/sup +/) in the scattering of /sup 16/O on /sup 17/O. (ERA citation 13...

B. Imanishi S. Misono W. Oertzen

1987-01-01

277

Minkowski Diagram Model  

NSDL National Science Digital Library

The Minkowski Diagram model displays the spacetime diagrams for two inertial observers. One or two events may be displayed and moved with the mouse. Optionally, the corresponding light cones may be shown, as well as the simultaneity lines in both reference frames. The spacetime interval is automatically computed. The simulation may be used to discuss simultaneity and causality in special relativity. You can modify this simulation if you have Ejs installed by right-clicking within the plot and selecting "Open Ejs Model" from the pop-up menu item. The Minkowski Diagram model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_ehu_special_relativity_minkowski.jar file will run the program if Java is installed. Please note that this resource requires at least version 1.5 of Java (JRE).

Aguirregabiria, Juan

2011-09-09

278

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

2012-03-01

279

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

280

Bifurcation diagrams and fractal brain boundaries of phase-locked loop circuits  

Microsoft Academic Search

Several 2-parameter bifurcation diagrams and the boundaries of the basin attraction of various periodic orbits associated with a typical phase-locked loop circuit widely used in modern communication systems are presented. Using these diagrams, the authors have identified and confirmed various routes to chaos reported previously for this circuit. Moreover, they have discovered that over certain regions in the parameter space,

T. Endo; L. O. Chua

1990-01-01

281

Activating multistep charge-transfer processes in fullerene-subphthalocyanine-ferrocene molecular hybrids as a function of ?-? orbital overlap.  

PubMed

We have synthesized two different fullerene-subphthalocyanine-ferrocene conjugates. The molecules were designed so that the ferrocene unit is linked at the subphthalocyanine axial position through a phenoxy spacer while the C(60) is rigidly held close to the concave face of the macrocycle via a 3-fold C(3)-symmetrical anchoring. The Bingel trisaddition reaction leading to the final products proceeded with very high regioselectivities and full diastereoselectivity. The only difference between both systems is the length of the triple tether employed, which finely regulates the regioselectivity of the trisaddition reaction and the distance between the subphthalocyanine and the C(60) complementary ?-? surfaces. Thus, when the tether is connected to the subphthalocyanine through a direct C-C bond, a short ?-? distance of 3.25-3.30 Å was calculated. In contrast, when it is connected through a slightly longer C-O-C bond, the distance increases to 3.5-3.6 Å. This ?-? distance has a strong influence on the ground-state electronic interactions between the subphthalocyanine and the C(60), as determined from electronic absorption and cyclic voltammetry measurements. In addition, fluorescence and time-resolved transient absorption experiments demonstrated that different mechanisms operate in the two systems after photoexcitation. Despite the similar HOMO-LUMO gaps, only when the two complementary ?-? surfaces of the subphthalocyanine and the C(60) are held at a close distance, therefore showing a high degree of orbital overlap, is a multistep electron transfer process triggered, ultimately leading to the long-lived, spatially separated C(60) radical anion and ferrocenium radical cation pair. A full account of the synthesis, characterization, and studies of the ground- and excited-state electronic interactions occurring in these conjugates, as well as in their reference C(60)-subphthalocyanine and subphthalocyanine-ferrocene dyads, is presented in this article. PMID:21033683

González-Rodríguez, David; Carbonell, Esther; Rojas, Gustavo de Miguel; Castellanos, Carmen Atienza; Guldi, Dirk M; Torres, Tomás

2010-10-29

282

Functional schematic diagrams  

Microsoft Academic Search

A carefully planned schematic diagram will simplify the study and servicing of electronic equipment. Whereas a conventional schematic merely shows the electrical components and how they are connected, a functional schematic will place these parts on the drawing in such a way as to delineate the circuits they build. This circuit concept versus component concept is the main thesis of

S. H. Larick

1946-01-01

283

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

284

Hierarchical Hybrid Block Diagrams  

Microsoft Academic Search

Block diagram languages are now commonly used to design and even implement embedded systems. In the design phase, they are used to model both plant and controller, typically with continuous and discrete modeling respectively. The semantics of these lan- guages are often vague and\\/or complex, which is fine for some users but leaves others puzzled by the behav- iors they

Ben Denckla; Pieter J. Mosterman

285

Knots and Feynman Diagrams  

NASA Astrophysics Data System (ADS)

1. Introduction; 2. Perturbative quantum field theory; 3. The Hopf algebra structure of renormalization; 4. Rationality: no knots, no transcendentals; 5. The simplest link diagrams; 6. Necessary topics from knot theory; 7. Knots to numbers; 8. One-loop words; 9. Euler-Zagier sums; 10. Knots and transcendentals; 11. The 4-term relation; 12. Hopf algebras, non-commutative geometry, and what else?

Kreimer, Dirk

2000-07-01

286

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

287

Acyclic Jacobi Diagrams  

Microsoft Academic Search

We propose a simple new combinatorial model to study spaces of acyclic Jacobi diagrams, in which they are identified with algebras of words modulo operations. This provides a starting point for a word-problem type combinatorial investigation of such spaces, and provides fresh insights on known results.

Daniel Moskovich

2005-01-01

288

Chromatic Number of Diagrams.  

National Technical Information Service (NTIS)

Conditions concerning a partially ordered set (poset (P)) and an orientation for an undirected graph diagram are given. An explicit construction of an order P with given chi(D(P)) is given. This order is the interval order, as N free. This leads to specia...

J. Gustedt S. Felsner M. Morvan J. Rampon

1991-01-01

289

Simultaneity Spacetime Diagram Model  

NSDL National Science Digital Library

The Simultaneity Spacetime Diagram model uses light-trajectories to show the effect of relative motion when observing (recording) events in special relativity. In the default scenario, an explosion (an event) at the center of a right-moving stick occurs at t=0 and the arrival of the explosion light signal at each end is recorded. The arrival event at the left end occurs before the arrival event at the right end because the stick is moving. How do the location and time of these events change if they are observed in a reference frame (the Other Frame) in which the stick is stationary?   The Simultaneity Spacetime Diagram model was written for the study of special relativity the Lorentz transformation using spacetime diagrams and is a supplemental simulation for an article by Sebastien Cromier and Richard Steinberg "The Twin Twin Paradox: Exploring Student Approaches to Understanding Relativistic Concepts" in the The Physics Teacher 48 (9), 598-601 (2010). Initial conditions, such as the locations of the explosion and the detectors, can be adjusted by dragging before the simulation is run. The slider can be used to change the speed of the stick. A third view shows the stick and the wavefront in space. More importantly, a checkbox allows users to compare the predictions of Galilean and special relativity in order to observe how the assumption of a constant speed of light leads to the relativity of simultaneity.   The Simultaneity Spacetime Diagram model was created using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_sr_SimultaneitySpacetimeDiagram.jar file will run the program if Java is installed.

Christian, Wolfgang

2010-10-07

290

Orbital Dzyaloshinskii-Moriya exchange interaction  

NASA Astrophysics Data System (ADS)

A superexchange calculation is performed for multiorbital band models with broken inversion symmetry. Orbital-changing hopping terms allowed by the symmetry-breaking electric field lead to a new kind of orbital exchange interaction closely resembling the Dzyaloshinskii-Moriya spin exchange. Inversion symmetry breaking as present in surfaces and interfaces and a strong on-site repulsion, but not the spin-orbit interaction, are the requirements to observe the proposed effect. The mean-field phase diagram exhibits a rich structure including anti-ferro-orbital, ferro-orbital, and both single and multiple spiral-orbital phases, in close analogy with the Skyrmion spin crystal phase recently discovered in thin-film chiral magnets.

Kim, Panjin; Han, Jung Hoon

2013-05-01

291

The Workup of Penetrometer Diagrams (Snyatie i Obrabotka Plotnomernykh Diagram).  

National Technical Information Service (NTIS)

During studies of operation and testing of agricultural machines and tools, penetrometers are used to plot diagrams for determining the density of the soil. The recorded registrations of the penetrometer diagrams as a function of the depth of cone submerg...

V. I. Buromski

1972-01-01

292

Elements of a Chemical Orbital Theory  

NASA Astrophysics Data System (ADS)

Interaction is important in chemistry. Interactions of atoms form chemical bonds. Bonds interact with each other in molecules to determine the molecular properties. Interactions of molecules give rise to chemical reactions. Electrons control atoms, bonds, and molecules. The behavior of electrons is simply and effectively represented by orbitals, which contain wave properties, i.e., phase and amplitude. In our chemical orbital theory we consider the interactions of the orbitals of atoms, bonds and molecules. The elements of the chemical orbital theory are separated into three groups: (1) interactions of two orbitals, (2) interactions of three orbitals, and (3) cyclic interactions of more than two orbitals. Here, general aspects of the interactions of two orbitals are summarized to show the background of this volume and assist nonspecialists to read the following chapters. Among the keywords are: phase and amplitude of orbitals, strength of orbital interactions, electron delocalization, electron localization, exchange repulsion, ionization energy, electronic spectrum, frontier orbitals, reactivity, selectivity, orbital symmetry, and so on. The remaining elements of the chemical orbital theory, i.e., an orbital mixing rule for the three-orbital interactions and an orbital phase theory for the cyclic interactions, are introduced briefly.

Inagaki, Satoshi

293

Orbital Dynamics  

NSDL National Science Digital Library

This video from SpaceTEC National Aerospace Technical Education Center explains the mechanics of orbital dynamics and Newton's first law of motion. This three minute video is one of the aerospace certification readiness courses.

2011-07-27

294

Automatic construction of intelligent diagram editors  

Microsoft Academic Search

The intelligent diagram is a recent metaphor for diagramming in which the underlying graphic editor parses the diagram as it is being constructed, performing error correction and collecting geometric constraints which capture the relationships between diagram components. During diagram manipulation a constraint solver uses these geometric constraints to maintain the diagram’s semantics. We describe the Penguins system. This automates the

Sitt Chen Chok; Kim Marriott

1998-01-01

295

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

SciTech Connect

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

Iskin, M. [Department of Physics, Koc University, Rumelifeneri Yolu, 34450 Saryer, Istanbul (Turkey); Subasi, A. L. [Department of Physics, Faculty of Science and Letters, Istanbul Technical University, 34469 Maslak, Istanbul (Turkey)

2011-10-15

296

Quaternary ammonium room-temperature ionic liquid including an oxygen atom in side chain/lithium salt binary electrolytes: ab initio molecular orbital calculations of interactions between ions.  

PubMed

Interactions of the lithium bis(trifluoromethylsulfonyl)amide (LiTFSA) complex with N, N-diethyl-N-methyl-N-(2-methoxyethyl) ammonium (DEME), 1-ethyl-3-methylimidazolium (EMIM) cations, neutral diethylether (DEE), and the DEMETFSA complex were studied by ab initio molecular orbital calculations. An interaction energy potential calculated for the DEME cation with the LiTFSA complex has a minimum when the Li atom has contact with the oxygen atom of DEME cation, while potentials for the EMIM cation with the LiTFSA complex are always repulsive. The MP2/6-311G**//HF/6-311G** level interaction energy calculated for the DEME cation with the LiTFSA complex was -18.4 kcal/mol. The interaction energy for the neutral DEE with the LiTFSA complex was larger (-21.1 kcal/mol). The interaction energy for the DEMETFSA complex with LiTFSA complex is greater (-23.2 kcal/mol). The electrostatic and induction interactions are the major source of the attraction in the two systems. The substantial attraction between the DEME cation and the LiTFSA complex suggests that the interaction between the Li cation and the oxygen atom of DEME cation plays important roles in determining the mobility of the Li cation in DEME-based room temperature ionic liquids. PMID:18636771

Tsuzuki, Seiji; Hayamizu, Kikuko; Seki, Shiro; Ohno, Yasutaka; Kobayashi, Yo; Miyashiro, Hajime

2008-07-18

297

A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin  

NASA Astrophysics Data System (ADS)

The gradient for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO/EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic tetraglycine immersed in water layers of 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 A? are investigated by performing FMO/EFP geometry optimizations at the RHF/cc-pVDZ level of theory for the solutes. The geometries optimized with FMO-RHF/EFP are compared to those from the conventional RHF/EFP and are found to be in very close agreement. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order Møller-Plesset theory (MP2)/cc-pVDZ level. To demonstrate the potential of the method for proteins, the geometry of hydrated chignolin (protein data bank ID: 1UAO) was optimized, and the importance of the inclusion of water was examined by comparing the solvated and gas phase structures of chignolin with the experimental NMR structure.

Nagata, Takeshi; Fedorov, Dmitri G.; Sawada, Toshihiko; Kitaura, Kazuo; Gordon, Mark S.

2011-01-01

298

Interpretation of excited state Hartree-Fock analytic derivative anomalies for NO2 and HCO2 using the molecular orbital Hessian  

NASA Astrophysics Data System (ADS)

A simple procedure utilizing the molecular orbital (MO) Hessian, the second derivative of the Hartree-Fock (HF) energy with respect to MO coefficient perturbations, has been proposed in the interpretation of anomalous analytic HF energy derivatives. The nature of the anomalous analytic self-consistent field (SCF) harmonic vibrational frequencies and infrared (IR) intensities of the 2B2 and 2A2 excited states of NO2 and HCO2 have been studied in detail. By suitable partitioning of the HF second energy derivative expression, an association between the abnormal force constants, the dipole moment derivatives, and specific solutions to the SCF coupled perturbed HF equations is established. This connection to unstable wave functions can now be used with the MO Hessian to predict these anomalies at the HF level. In addition, appropriate small complete active space SCF methods have been utilized to overcome the inherent shortcomings of the HF wave functions, and determine more realistic values for the force constants and IR intensities.

Burton, Neil A.; Yamaguchi, Yukio; Alberts, Ian L.; Schaefer, Henry F., III

1991-11-01

299

Schematic transformation diagrams for steel  

Microsoft Academic Search

This paper examines the diffusional transformations of austenite and concludes that separate C-curves are required for pearlite, upper bainite, lower bainite and isothermal martensite. A schematic isothermal transformation diagram incorporating the four curves is presented for a plain carbon eutectoid steel and used to develop a schematic continuous cooling transformation diagram. These diagrams are shown to be more compatible with

Noel F. Kennon

1978-01-01

300

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

301

Sorting Helps for Voronoi Diagrams  

Microsoft Academic Search

It is well known that, using standard models of computation, ?(n logn) time is required to build a Voronoi diagram forn point sites. This follows from the fact that a Voronoi diagram algorithm can be used to sort. However, if the sites are sorted\\u000a before we start, can the Voronoi diagram be built any faster? We show that for certain

L. Paul Chew; Steven Fortune

1997-01-01

302

Diagram Techniques for Confluence  

Microsoft Academic Search

We,develop,diagram,techniques,for proving,confluence,in abstract reductions,systems. The underlying,theory,gives a systematic,and,uniform framework in which a number of known results, widely scattered throughout the literature, can be understood. These results include Newman’s lemma, Lemma 3.1 of Winkler and Buchberger, the HindleyRosen lemma, the Request lemmas of Staples, the Strong Confluence lemma of Huet, the lemma,of De Bruijn.,, 1998 Academic,Press

Marc Bezem; Jan Willem Klop; Vincent Van Oostrom

1998-01-01

303

Diagram Techniques for Confluence  

Microsoft Academic Search

We develop diagram techniques for proving confluence in abstract reductions systems. The underlying theory gives a systematic and uniform framework in which a number of known results, widely scattered throughout the literature, can be understood. These results include Newman's\\u000aLemma (1942), Lemma 3.1 of Winkler and Buchberger (1985), the\\u000aHindley-Rosen Lemma (1964), the Request Lemmas of Staples (1975),\\u000athe Strong

M. A. Bezem; J. W. Klop; V. van Oostrom

1996-01-01

304

TEP process flow diagram  

SciTech Connect

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

Wilms, R Scott [Los Alamos National Laboratory; Carlson, Bryan [Los Alamos National Laboratory; Coons, James [Los Alamos National Laboratory; Kubic, William [Los Alamos National Laboratory

2008-01-01

305

Phosphatidylcholine: cholesterol phase diagrams.  

PubMed

Two mono-cis-unsaturated phosphatidylcholine (PC) lipid molecules, having very different gel-liquid crystalline phase transition temperatures as a consequence of the relative positions of the double bond, exhibit PC:cholesterol phase diagrams that are very similar to each other and to that obtained previously for a fully saturated PC:cholesterol mixture (Vist, M. R., and J. H. Davis. 1990. Biochemistry 29:451-464). This leads to the conjecture that PC:cholesterol membrane phase diagrams have a universal form which is relatively independent of the precise chemical structure of the PC molecule. One feature of this phase diagram is the observation over a wide temperature range of a fluid but highly conformationally ordered phase at bilayer concentrations of more than approximately 25 mol% cholesterol. This ;liquid ordered' phase is postulated to be the relevant physical state for many biological membranes, such as the plasma membrane of eukaryotic cells, that contain substantial amounts of cholesterol or equivalent sterols. PMID:19431848

Thewalt, J L; Bloom, M

1992-10-01

306

Intramolecular non-bonded interactions between oxygen and group VIA elements. An ab initio molecular orbital and density functional theory investigation of the structures of HX–CH 2–CHO (X=S, Se and Te)  

Microsoft Academic Search

Non-bonded interactions between the group VIA elements and oxygen atoms play roles in numerous chemical processes, however, the geometries and energetics of these interactions are not yet well defined. Ab initio molecular orbital and density functional methods have been used to study the potential energy surfaces of the substituted acetaldehydes, HX–CH2–CH?O, where X is one of the Group VIA chalcophiles

George D. Markham; Cindy L. Bock; Mendel Trachtman; Charles W. Bock

1999-01-01

307

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!"

308

Orbital pseudotumor.  

PubMed

Orbital pseudotumor is a benign condition that accounts for approximately 10% of all orbital mass lesions. Any part of the orbit may be involved. The etiology is unknown. The presentation may be either acute or subacute. Patients may present with a palpable mass, a swollen eyelid, congestion, pain, diminished ocular motility, and/or decreased visual acuity. Approximately, 25% of patients present with bilateral disease. A modest proportion of patients experience resolution of their symptoms without treatment. Biopsy is indicated for those who do not respond to, or relapse after, first-line therapy. Oral corticosteroids are the initial treatment and approximately 80% of patients respond. Roughly half of those who respond to corticosteroids relapse. Second-line therapy consists of either low-dose radiotherapy (20-30 Gy at 2 Gy per fraction), cytotoxic chemotherapy, or immunosuppressive agents. Radiotherapy results in long-term local control rates of 50% or higher. Limited lesions may be successfully resected. A small subset of patients may experience inexorable progression to a fixed, painful, sightless eye and require orbital exenteration. PMID:19738455

Mendenhall, William M; Lessner, Alan M

2010-06-01

309

Nuclear orbiting  

SciTech Connect

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

Shapira, D.

1988-01-01

310

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

Horton, Michael

2009-05-30

311

Unusual regioselective electrophilic substitutions in quinoline foldamers: conceptual DFT and frontier molecular orbital analysis reveal the crucial role of folding and substituents.  

PubMed

We carried out a detailed computational investigation of an earlier experimentally observed, unusual, regioselective, electrophilic halogenation in helically folded quinoline oligoamides. In the experimental studies, halogenation occurred selectively at a given monomer of a foldamer substituted with electron-withdrawing groups at the N terminus, although apparently identical reactive sites were available to react with the incoming electrophile. On the other hand, the selectivity was lost with weakly electron-donating groups. To gain an insight into the regioselective preference of bromination in quinoline foldamers, conceptual DFT was used to calculate the local nucleophilicity index of various foldamers of different sizes and with different substituents, and it was found that the predicted reaction centers were in line with the experimental results. Frontier molecular orbital analysis was used to understand this behavior. A detailed study of the hypothetical linear conformation of the tetramer for comparison with the folded conformation was carried out. In the case of a linear conformer, the HOMO is localized on specific monomers irrespective of substitution, but upon folding delocalization is observed, which is larger for the weakly electron-donating groups when compared with the electron-withdrawing groups. In the case of strongly donating groups there is no delocalization, even upon folding. The behavior remains the same when the size of the helix is increased (octamer). Thus, it is clearly seen in this work that the combined effects of conformations and substituents dictate the regioselectivity in the folded oligoamides; this knowledge will have a profound effect on the field of foldamer chemistry. PMID:22887893

Shravani, Madishetti; Balaiah, Shanigaram; Srinivas, Kolupula; Bhanuprakash, K; Huc, Ivan

2012-08-07

312

Interpretation of indirect nuclear spin-spin couplings in isomers of adenine: novel approach to analyze coupling electron deformation density using localized molecular orbitals.  

PubMed

Adenine, an essential building block of nucleic acids present in all living systems, can occur in several tautomeric forms. The phenomenon of tautomerism can be investigated by several experimental methods, including nuclear magnetic resonance. In this study, long-range (1)H-(13)C and (1)H-(15)N coupling constants for N-alkyl derivatives related to four tautomers of adenine are investigated in DMSO and DMF solutions. To investigate the structural dependence of the coupling constants and to understand how polarization propagates in the system, Fermi contact (FC) terms were calculated for the individual isomers and analyzed by using density functional theory (DFT), and the coupling pathways were visualized using real-space functions. The coupling electron deformation densities (CDD) of several (1)H-X (X = (13)C, (15)N) pairs are evaluated and compared. In order to analyze the CDD in more detail, a new approach to break down the CDD into contributions from Boys or Pipek-Mezey localized molecular orbitals (LMOs) has been developed. A similar approach has been applied to split the value of the FC contribution to the J coupling into the LMO contributions. On the basis of chemical concepts, the contributions of sigma-bonds, pi-electrons, and lone pairs of electrons are discussed. The lone pair of electrons at the nitrogen atom contributes significantly to the (1)H-C horizontal line(15)N coupling, whereas the (1)H-C=N-(13)C coupling is affected in a somewhat different way. Surprisingly, the contribution of the intervening C horizontal lineN bond to the FC term for (1)H-C=(15)N coupling originates exclusively in sigma-electrons, with a vanishingly small contribution calculated for the pi-electrons of this fragment. This behavior is rationalized by introducing the concept of "hard and soft J elements" derived from the polarizability of the individual components. PMID:20518482

Marek, Radek; Krístková, Anezka; Malináková, Katerina; Tousek, Jaromír; Marek, Jaromír; Hocek, Michal; Malkina, Olga L; Malkin, Vladimir G

2010-06-24

313

Covalently bound molecular structures in the ? + 16O system  

NASA Astrophysics Data System (ADS)

Using the concept of covalent molecular orbitals for neutrons and the known properties of the local ? + 16O potential the formation of asymmetric molecular structures in neon isotopes is discussed. Experimental evidence for parity doublets in 21Ne is reviewed and a corresponding band structure for the states in 21Ne at moderate excitation energy of Ex = 0-8 MeV is proposed. The structure of some bands can be interpreted as consisting of an instrinsic asymmetric ( 4He + 16O) structure bound by a covalent neutron in ? and ? orbitals. An extension of the observed structures to symmetric molecular structures in isotopes of Mg and heavier nuclei is suggested. In particular shape isomers in isotopes of magnesium, namely (He)2O molecules, can be predicted and an extended Ikeda diagram is proposed.

von Oertzen, W.

314

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

315

Schematic transformation diagrams for steel  

Microsoft Academic Search

This paper examines the diffusional transformations of austenite and concludes that separateC-curves are required for pearlite, upper bainite, lower bainite and isothermal martensite. A schematic isothermal transformation\\u000a diagram incorporating the four curves is presented for a plain carbon eutectoid steel and used to develop a schematic continuous\\u000a cooling transformation diagram. These diagrams are shown to be more compatible with the

Noel F. Kennon

1978-01-01

316

Graphical process diagrams ion—views and diagrams  

Microsoft Academic Search

Process design (and description) is largely an ad hoc discipline composed of several diagramming techniques with no clear definition of the process characteristics described by any one, usually with no definition of the relationship between the diagrams, and in most cases with no definition of the process design stages. This is in sharp contrast with product description and design, where

KOSTIA MANDEL

1990-01-01

317

Molecular orbital cluster calculation study of electron correlation and local lattice instability in La{sub 2-2x}Sr{sub 1+2x}Mn{sub 2}O{sub 7}  

SciTech Connect

In order to examine covalence and polaron effects in the bilayer manganite La{sub 2-2x}Sr{sub 1+2x}Mn{sub 2}O{sub 7}, we have performed molecular orbital cluster calculations. Two types of (Mn{sub 2}O{sub 11}){sup 15-} clusters, one with the manganese aligned in the a direction and the other in the c direction, were embedded in a point charge environment that mimicked the crystal environment of the bilayer manganite at x=0.40, and their electronic states were calculated by the unrestricted Hartree-Fock (UHF) and the complete active-space self-consistent field (CASSCF) methods. The CASSCF result for the cluster along the a direction exhibits double-well potential energy surfaces for symmetry-breaking deformations. This indicates small polaron formation in this system. On the other hand, the UHF calculation did not give double-well potential surfaces, showing the importance of the electron correlation for the polaron formation. Significantly large wells are obtained for the in-plane antiphase breathing and in-plane antiphase O-Mn-O stretching deformations. The double-well barrier for the former is 68 meV and that for the latter is 92 meV, where the former is close to the experimentally obtained polaron hopping activation energy above T{sub c}. A similar calculation for the cluster along the c direction exhibits a negligibly small double well, indicating that the polaron effect is very small in the carrier hopping in the c direction within a bilayer. Electronic structures have been investigated using natural orbitals. At a double-well minimum, a localized polaron orbital is seen. In the ground state, a small but significant hole population is found in p orbitals of the bridging oxygen, and a slight electron population is found in the e{sub g} orbital above the localized polaron orbital. For the cluster along the a direction and without deformation, the first excited state is an electron-transfer state where an electron is moved from the bridging oxygen p{sub z} to a manganese e{sub g} orbital. This excited state couples with the ground state by the pseudo-Jahn-Teller effect, thus, the polaron is the 'pseudo-Jahn-Teller polaron'. Using the natural orbitals, we have calculated magnetic Compton profiles and compared with experiment. Comparison between the experimental and theoretical results suggests the presence of polarons below T{sub c}. We briefly discuss the implication of this result in relation to the colossal magnetoresistance effect.

Miyaki, Satoru; Uzuhara, Shinji; Terada, Kazuto; Makoshi, Kenji; Koizumi, Hiroyasu [Graduate School of Material Science, University of Hyogo, Kamigori, Ako-gun, Hyogo 678-1297 (Japan); Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573 (Japan)

2005-02-15

318

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

NASA Astrophysics Data System (ADS)

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

Lee, Sung Keun; Stebbins, Jonathan F.

2006-08-01

319

Phase diagram of half-doped manganites  

SciTech Connect

The phase diagram of half-doped manganites which may consist of experimentally observed ferromagnetic (FM), A-,C-, and charge-exchange (CE)-type antiferromagnetic (AF) states is obtained in terms of a model which is based on double exchange via degenerate e{sub g} orbitals, the on-site Coulomb interaction (U), and the nearest-neighbor Coulomb interaction (V). We find that, because of the strong spatial anisotropy of the electron hoppings, the on-site Coulomb interaction has different effects on these magnetic order states. As a result, large values of U suppress the FM state and favor the A- and C-type AF states. Moreover, we show that it is the interplay between the on-site and nearest-neighbor Coulomb repulsions that stabilizes the CE phase and results in the charge ordering in the state.

Shu, Zhenghuang; Dong, Jinming; Xing, D. Y.

2001-06-01

320

Schematic Diagrams, XML and Accessibility  

Microsoft Academic Search

This paper describes work in progress at Oxford Brookes University. The aim of the project is to define a higher-level diagram description language for the World Wide Web, which captures the structure and the semantics of a diagram and enables the generation of accessible presentations in different modalities such as speech, text, graphic, etc. This project, called Graphical Structure Semantic

Zaineb Ben Fredj; David A. Duce

2003-01-01

321

Potential-pH Diagrams.  

ERIC Educational Resources Information Center

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

Barnum, Dennis W.

1982-01-01

322

Constructing Precise Object Relation Diagrams  

Microsoft Academic Search

The Object Relation Diagram (ORD) of a program is a class interdependence diagram which has applications in a wide variety of software engineering problems (e.g., in- tegration testing, integration coverage analysis, regression testing, impact analysis, program understanding, and re- verse engineering). Because the imprecision of the ORD directly affects the practicality of its usage, it is important to investigate techniques

Ana Milanova; Atanas Rountev; Barbara G. Ryder

2002-01-01

323

CLIMATE DIAGRAM - MILES CITY, MT  

Technology Transfer Automated Retrieval System (TEKTRAN)

Research conducted across the Great Plains has shown precipitation and temperature are the main factors affecting plant growth and development. A climate diagram was constructed with long-term (96-year) climate records from Miles City, Montana. The diagram describes the climate of the area. Maximum ...

324

VORONOI DIAGRAMS AND ORNAMENTAL DESIGN  

Microsoft Academic Search

A set of points in the plane induces a Voronoi diagram, a division of the plane based on proximity to points in the set. Voronoi diagrams have been used extensively in engineering and scientific disciplines, but the possibility of using them for creating abstract ornamental designs is largely unexplored. I present some techniques for creating attractive ornamental designs using Voronoi

Craig S. Kaplan

1999-01-01

325

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

326

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

327

Theoretical phase diagrams for solid H{sub 2}  

SciTech Connect

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

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

1993-07-01

328

Spider Diagrams: A Diagrammatic Reasoning System  

Microsoft Academic Search

Spider diagrams combine and extend Venn diagrams and Euler circles to express constraints on sets and their relationships with other sets. These diagrams can be used in conjunction with object-oriented modelling notations such as the Unified Modelling Language. This paper summarises the main syntax and semantics of spider diagrams. It also introduces inference rules for reasoning with spider diagrams and

John Howse; Fernando Molina; John Taylor; Stuart Kent; JOSEPH YOSSI GIL

2001-01-01

329

Integrating UML diagrams for production control systems  

Microsoft Academic Search

This paper proposes to use SDL block diagrams, UML class diagrams, and UML behavior diagrams like collaboration diagrams, activity diagrams, and statecharts as a visual programming language. We describe a modeling approach for flexible, autonomous production agents, which are used for the decentralization of production control systems. In order to generate a (Java) implementation of a production control system from

Hans J. Köhler; Ulrich Nickel; Jörg Niere; Albert Zündorf

2000-01-01

330

Particles, Feynman Diagrams and All That  

ERIC Educational Resources Information Center

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

Daniel, Michael

2006-01-01

331

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 C2v 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

332

Quantum theory of the charge-stability diagram of semiconductor double-quantum-dot systems  

NASA Astrophysics Data System (ADS)

We complete our recently introduced theoretical framework treating the double-quantum-dot system with a generalized form of Hubbard model. The effects of all quantum parameters involved in our model on the charge-stability diagram are discussed in detail. A general formulation of the microscopic theory is presented and, truncating at one orbital per site, we study the implication of different choices of the model confinement potential on the Hubbard parameters as well as the charge-stability diagram. We calculate the charge-stability diagram keeping three orbitals per site and find that the effect of additional higher-lying orbitals on the subspace with lowest-energy orbitals only can be regarded as a small renormalization of Hubbard parameters, thereby justifying our practice of keeping only the lowest orbital in all other calculations. The role of the harmonic-oscillator frequency in the implementation of the Gaussian model potential is discussed, and the effect of an external magnetic field is identified to be similar to choosing a more localized electron wave function in microscopic calculations. The full matrix form of the Hamiltonian, including all possible exchange terms and several peculiar charge-stability diagrams due to unphysical parameters, is presented in the Appendices, thus emphasizing the critical importance of a reliable microscopic model in obtaining the system parameters defining the Hamiltonian.

Wang, Xin; Yang, Shuo; Das Sarma, S.

2011-09-01

333

Mass-imbalanced Fermi gases with spin-orbit coupling  

SciTech Connect

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

Iskin, M. [Department of Physics, Koc University, Rumelifeneri Yolu, TR-34450 Sariyer, Istanbul (Turkey); Subasi, A. L. [Department of Physics, Faculty of Science and Letters, Istanbul Technical University, TR-34469 Maslak, Istanbul (Turkey)

2011-10-15

334

Atemporal diagrams for quantum circuits  

SciTech Connect

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

Griffiths, Robert B.; Wu Shengjun; Yu Li; Cohen, Scott M. [Physics Department, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Physics Department, Duquesne University, Pittsburgh, Pennsylvania 15282 (United States)

2006-05-15

335

Phase diagrams of magnetic nanotubes  

NASA Astrophysics Data System (ADS)

Analytical expressions for the total magnetic energy of two characteristic internal configurations of nanometric tubes are calculated. A magnetic phase diagram with respect to the aspect ratio of the tubes is obtained which allows a discussion about the possibility of getting ensembles of nanotubes with low coercive fields. A comparison with recently reported coercive fields of three different cobalt nanotube arrays agrees well with the phase diagram derived here.

Escrig, J.; Landeros, P.; Altbir, D.; Vogel, E. E.; Vargas, P.

2007-01-01

336

Introduction to Ternary Phase Diagrams  

NSDL National Science Digital Library

This exercise is intended as a group exercise to help students learn the fundamentals of using ternary phase diagrams. It is a much better way for students to learn about the diagrams than to lecture to them. Good students will be able to walk through this with little assistance from the instructor.Weaker students will struggle and need help from peers or instructors. The entire exercise takes 1-2 hours for most.

Perkins, Dexter

337

Diagram Designer 1.23  

NSDL National Science Digital Library

Turning out flowcharts and diagrams for presentations can be quite a hassle, so it's nice to lean about the Diagram Designer application. With the program's interface, visitors can take advantage of the customizable object palette, slide show viewer, and the ability to plot mathematical expressions. This version also allows users to import various image file formats, such as jpeg and gif files. This version is compatible with computers running Windows 98 and newer.

Vinther, Michael

338

Drawing Euler Diagrams with Circles  

Microsoft Academic Search

\\u000a Euler diagrams are a popular and intuitive visualization tool which are used in a wide variety of application areas, including\\u000a biological and medical data analysis. As with other data visualization methods, such as graphs, bar charts, or pie charts,\\u000a the automated generation of an Euler diagram from a suitable data set would be advantageous, removing the burden of manual\\u000a data

Gem Stapleton; Leishi Zhang; John Howse; Peter Rodgers

2010-01-01

339

Electronic eigenvalue (EEVA): a new QSAR/QSPR descriptor for electronic substituent effects based on molecular orbital energies. A QSAR approach to the Ah receptor binding affinity of polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs).  

PubMed

A new descriptor of molecular structure for use in the derivation of predictive QSAR and QSPR models, electronic eigenvalue (EEVA), is described. This is a modification of the recently proposed EVA approach, but is based on computationally-derived molecular orbital energies instead of vibrational frequencies. Like EVA, it is also invariant as to the alignment of the structures concerned. Its performance has been tested with respect to the Ah receptor binding of PCBs, PCDDs and PCDFs, and its predictive ability has been clearly demonstrated. In particular, it seems to be suitable for 'pure' electronic substituent effects. i.e., for cases in which both hydrophobic and steric factors are of minor importance. PMID:10864156

Tuppurainen, K; Ruuskanen, J

2000-09-01

340

Molecular orbitals of the oxocarbons (CO)n, n = 2-6. Why does (CO)4 have a triplet ground state?  

PubMed

Cyclobutane-1,2,3,4-tetrone has been both predicted and found to have a triplet ground state, in which a b(2g) ? MO and an a(2u) ? MO are each singly occupied. The nearly identical energies of these two orbitals of (CO)(4) can be attributed to the fact that both of these MOs are formed from a bonding combination of C-O ?* orbitals in four CO molecules. The intrinsically stronger bonding between neighboring carbons in the b(2g) ? MO compared to the a(2u) ? MO is balanced by the fact that the non-nearest-neighbor, C-C interactions in (CO)(4) are antibonding in b(2g), but bonding in a(2u). Crossing between an antibonding, b(1g) combination of carbon lone-pair orbitals in four CO molecules and the b(2g) and a(2u) bonding combinations of ?* MOs is responsible for the occupation of the b(2g) and a(2u) MOs in (CO)(4). A similar orbital crossing occurs on going from two CO molecules to (CO)(2), and this crossing is responsible for the triplet ground state that is predicted for (CO)(2). However, such an orbital crossing does not occur on formation of (CO)(2n+1) from 2n + 1 CO molecules, which is why (CO)(3) and (CO)(5) are both calculated to have singlet ground states. Orbital crossings, involving an antibonding, b(1), combination of lone-pair MOs, occur in forming all (CO)(2n) molecules from 2n CO molecules. Nevertheless, (CO)(6) is predicted to have a singlet ground state, in which the b(2u) ? MO is doubly occupied and the a(2u) ? MO is left empty. The main reason for the difference between the ground states of (CO)(4) and (CO)(6) is that interactions between 2p AOs on non-nearest-neighbor carbons, which stabilize the a(2u) ? MO in (CO)(4), are much weaker in (CO)(6), due to the much larger distances between non-nearest-neighbor carbons in (CO)(6) than in (CO)(4). PMID:22687146

Bao, Xiaoguang; Zhou, Xin; Flener Lovitt, Charity; Venkatraman, Amruth; Hrovat, David A; Gleiter, Rolf; Hoffmann, Roald; Borden, Weston Thatcher

2012-06-11

341

ERS Orbit Control.  

National Technical Information Service (NTIS)

The European remote sensing mission orbit control is addressed. For the commissioning phase, the orbit is defined by the following requirements: Sun synchronous, local time of descending node 10:30; three days repeat cycle with 43 orbital revolutions; ove...

M. Rosengren

1991-01-01

342

Vibrational (FT-IR and FT-Raman) spectra and quantum chemical studies on the molecular orbital calculations, chemical reactivity and thermodynamic parameters of 2-chloro-5-(trifluoromethyl) aniline.  

PubMed

In this work, the vibrational characteristics of 2-chloro-5-(trifluoromethyl) aniline have been investigated and both the experimental and theoretical vibrational data indicate the presence of various functional groups within the title molecule. The influence of chlorine substituent on the vibrational wavenumbers of a molecule in comparison with aniline and trifluoromethyl aniline has been discussed in detail. The density functional theoretical (DFT) computations were performed at the B3LYP/6-31++G(3df,3pd)/6-31G(3df,3pd) levels to derive the optimized geometry, vibrational wavenumbers with IR and Raman intensities. Furthermore, the molecular orbital calculations such as; natural bond orbitals (NBOs) and HOMO-LUMO energy gap and mapped molecular electrostatic potential (MEP) surfaces were also performed with the same level of DFT. The temperature dependence thermodynamic parameters of a molecule were illustrated on the basis of their correlation graphs. The detailed interpretation of the vibrational spectra has been carried out with the aid of potential energy distribution (PED) results obtained from MOLVIB program. The delocalization of electron density in various constituents of the molecule has been discussed with the aid of NBO and HOMO-LUMO energy gap analysis. PMID:23416911

Karthick, T; Balachandran, V; Perumal, S; Nataraj, A

2013-01-24

343

Vibrational (FT-IR and FT-Raman) spectra and quantum chemical studies on the molecular orbital calculations, chemical reactivity and thermodynamic parameters of 2-chloro-5-(trifluoromethyl) aniline  

NASA Astrophysics Data System (ADS)

In this work, the vibrational characteristics of 2-chloro-5-(trifluoromethyl) aniline have been investigated and both the experimental and theoretical vibrational data indicate the presence of various functional groups within the title molecule. The influence of chlorine substituent on the vibrational wavenumbers of a molecule in comparison with aniline and trifluoromethyl aniline has been discussed in detail. The density functional theoretical (DFT) computations were performed at the B3LYP/6-31++G(3df,3pd)/6-31G(3df,3pd) levels to derive the optimized geometry, vibrational wavenumbers with IR and Raman intensities. Furthermore, the molecular orbital calculations such as; natural bond orbitals (NBOs) and HOMO-LUMO energy gap and mapped molecular electrostatic potential (MEP) surfaces were also performed with the same level of DFT. The temperature dependence thermodynamic parameters of a molecule were illustrated on the basis of their correlation graphs. The detailed interpretation of the vibrational spectra has been carried out with the aid of potential energy distribution (PED) results obtained from MOLVIB program. The delocalization of electron density in various constituents of the molecule has been discussed with the aid of NBO and HOMO-LUMO energy gap analysis.

Karthick, T.; Balachandran, V.; Perumal, S.; Nataraj, A.

2013-04-01

344

Analytic calculation of phase diagrams for solutions containingcolloids or globular proteins  

Microsoft Academic Search

Molecular thermodynamics is used to calculate phase diagrams for aqueous charged dipolar colloids or globular proteins. Because normal pressures are not important for condensed systems, here a phase diagram is a plot of temperature versus colloid concentration. Properties of the fluid phase are obtained from the random-phase approximation, whereas those for the solid phase correspond to a perfect crystal. Crystal

Frederico W. Tavares; John M. Prausnitz

2003-01-01

345

ATOMIC AND MOLECULAR PHYSICS: Spin---orbit ab initio curves of 80 Se2+ ion and the assignment of photoelectron spectra of 80 Se2 molecule  

Microsoft Academic Search

This paper carries out ab initio calculations to study the 80 Se2(X3Sigmag-) state and 80 Se2+(X2 IIg), 80 Se2+(a4 IIg) states by using completed active space self-consistent field and multi-reference second order perturbation theory. The electronic curves of these states including spin---orbit coupling are calculated, and then the spectroscopic parameters are obtained. The photoelectron spectra of 80 Se2 molecule in

Bing Yan; Shou-Fu Pan; Qing-Qun Guo

2008-01-01

346

Ab initio molecular orbital study of the first two bands in the photoelectron spectrum of hydroxylamine (NH/sub 2/OH)  

SciTech Connect

The geometries and energies of the cationic states of NH/sub 2/OH corresponding to electron loss from the nitrogen lone pair and from the oxygen lone pair have been investigated with an extended basis set. The results confirm previously assigned orbital characters for the first two bands in the photoelectron spectrum of NH/sub 2/OH, help to explain the width and vibrational structure of the bands, and provide information on the symmetries of the ionic states.

Curtiss, L.A.

1982-10-01

347

Problems in causal loop diagrams revisited  

Microsoft Academic Search

A reemerging problem Word-and-arrow diagrams (causal-loop diagrams, influence diagrams, cognitive maps, and the like) are enjoying widespread use in the system dynamics and systems thinking communities. It is increasingly common to see these diagrams with links labeled \\

George P. Richardson

1997-01-01

348

Characteristics of Group Development of Diagrams  

Microsoft Academic Search

One contributing factor to the lack of widespread usage of software for collaborative development of diagrams is the high degree of variability in the requirements for such software. The requirements are categorized in terms of diagram characteristics and diagram creation strategies. Various measures are proposed to characterize a potential collaborative diagramming need and to compare it to potential software systems.

Jeffrey D. Campbell

2002-01-01

349

Orbital Gating of Single Molecule Transistors  

NASA Astrophysics Data System (ADS)

Electron devices containing molecules as the active region have been an active area of research over the last few years. In molecular-scale devices, a longstanding challenge has been to create a true three-terminal device; e.g., one that operates by modifying the internal energy structure of the molecule, analogous to conventional FETs. Here we report the observation of such a solid-state molecular device, in which transport current is directly modulated by an external gate voltage. We have realized a molecular transistor made from the prototype molecular junction, benzene dithiol, and have used a combination of spectroscopies to determine the internal energetic structure of the molecular junction. Resonance-enhanced coupling to the nearest molecular orbital is revealed by electron tunneling spectroscopy, demonstrating for the first time direct molecular orbital gating in a molecular electronic device.

Reed, Mark

2011-03-01

350

Surface Reconstruction Phase Diagrams for InAs, AlSb, and GaSb.  

National Technical Information Service (NTIS)

We present experimental flux-temperature phase diagrams for surface reconstruction transitions on the 6.1As compound semiconductors. The phase transitions occur within or near typical substrate temperature ranges for growth of these materials by molecular...

A. S. Bracker B. R. Bnnett J. C. Culbertson M. J. Yang W. J. Moore

2000-01-01

351

Diagrams for laser materials processing  

NASA Astrophysics Data System (ADS)

An analytical heat flow model is used to identify dimensionless parameter groups which determine the temperature field produced in a material by a scanning laser beam. The groups are used to plot experimental data for metallic alloys on a processing diagram for a range of continuous CO2 laser treatments. Practical operating regions for each type of treatment are thus identified, which coincide with those predicted using the heat flow model. The model is extended in order to construct more detailed diagrams for transformation hardening, surface melting and keyhole welding, which quantify the depth of treatment. By using realistic estimates of certain poorly-known process variables, good agreement is observed between measured and predicted data. Methods for optimizing processing parameters with respect to various criteria are presented for transformation hardening. The diagrams, which are constructed on a personal computer, are a useful tool for summarizing current data, optimizing practical processing parameters, and assessing the potential of novel laser treatments on new materials.

Ion, J. C.; Shercliff, H. R.; Ashby, M. F.

1992-07-01

352

Matched designs and causal diagrams.  

PubMed

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

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

2013-06-01

353

ATOMIC AND MOLECULAR PHYSICS: Spin—orbit ab initio curves of 80 Se2+ ion and the assignment of photoelectron spectra of 80 Se2 molecule  

NASA Astrophysics Data System (ADS)

This paper carries out ab initio calculations to study the 80 Se2(X3?g-) state and 80 Se2+(X2 IIg), 80 Se2+(a4 IIg) states by using completed active space self-consistent field and multi-reference second order perturbation theory. The electronic curves of these states including spin—orbit coupling are calculated, and then the spectroscopic parameters are obtained. The photoelectron spectra of 80 Se2 molecule in gas phase are assigned according to Franck-Condon analysis based on calculated potential energy curves. The ionization energies of 80 Se2 molecule are determined by the present calculation.

Yan, Bing; Pan, Shou-Fu; Guo, Qing-Qun

2008-09-01

354

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

355

Pseudohaptic interaction with knot diagrams  

NASA Astrophysics Data System (ADS)

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

Weng, Jianguang; Zhang, Hui

2012-07-01

356

Viking satellite orbit determination  

Microsoft Academic Search

During the summer of 1976, the two Viking spacecraft, each consisting of an orbiter-lander combination, were inserted into orbit about Mars. The paper describes the experiences of the Viking Satellite Orbit Determination Team in determining Mars centered ephemerides of the orbiters and positions of the landers from the two-way Doppler and range data, and synthesizes the different phases of the

C. E. Hildebrand; E. J. Christensen; D. H. Boggs; G. H. Born; H. Hokikian; J. F. Jordan; W. B. Howard

1977-01-01

357

Concepts of orbital mechanics  

Microsoft Academic Search

Parameters determining an orbit, perturbations acting on a satellite and orbital deviations resulting from them, and a study of the particular types of orbits relevant to the use of artificial earth satellites for finding and developing natural resources are presented. The discussion shows the constraints imposed on teledetective search by certain characteristics of the orbits.

A. Alouges

1974-01-01

358

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.

Hamilton, Douglas

359

Vibrational spectra, molecular structure, natural bond orbital, first order hyperpolarizability, TD-DFT and thermodynamic analysis of 4-amino-3-hydroxy-1-naphthalenesulfonic acid by DFT approach  

NASA Astrophysics Data System (ADS)

Vibrational spectral analysis of 4-amino-3-hydroxy-1-naphthalenesulfonicacid (4A3HNSA) molecule were carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, harmonic vibrational wavenumbers, various bonding features have been computed using density functional B3LYP method with 6-31G(d,p) as basis set. The Non-Linear Optical (NLO) behavior of 4A3HNSA has been studied by determination of the electric dipole moment (?) and hyperpolarizability ? using HF/6-31G(d,p) method. 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 ?* and ?* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of Intramolecular Charge Transfer (ICT) within the molecule. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental spectra.

Sebastian, S.; Sylvestre, S.; Sundaraganesan, N.; Amalanathan, M.; Ayyapan, S.; Oudayakumar, K.; Karthikeyan, B.

2013-04-01

360

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

ERIC Educational Resources Information Center

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

Shubbar, Khalil E.

2003-01-01

361

Finite-perturbation intermediate neglect of differential overlap molecular orbital calculations of nuclear magnetic resonance spin-spin coupling constants for polycyclic aromatic hydrocarbons and aromatic nitrogen heterocyclics  

NASA Astrophysics Data System (ADS)

The H-H, C-H, and C-C spin-spin coupling constants were calculated by the finite-perturbation, intermediate neglect of differential overlap method using the Fermi contat interaction for benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations were made using both the actual and the average molecular geometries. For all six of these molecules, the agreements between the calculated and the experimental coupling constants were comparable to those previously reported for other, predominantly smaller, molecules. The actual molecular geometries always gave the correct relative order of values for the H-H coupling constants, whereas the average molecular geometries did not always do so. The magnitudes, but not the signs, of the calculated coupling constants were sensitive to small changes in molecular geometry. The results were the best (next best) for the H-H (C-H) coupling constants.

Long, S. A. T.

362

Spontaneous subperiosteal orbital hemorrhage.  

PubMed

Abstract Subperiosteal orbital hemorrhage typically results from trauma. Spontaneous subperiosteal orbital hemorrhage (SSOH) is rare and has been reported with sudden elevation of cranial venous pressure, bleeding diathesis, and sinusitis. This article presents a series of 9 patients (11 orbits) with SSOH and review the associated systemic conditions. 10 out of 11 orbits (91%) underwent surgical intervention due to advanced orbital signs or poor vision. PMID:23895577

Elia, Maxwell D; Shield, David; Kazim, Michael; Shinder, Roman; Yoon, Michael; McCulley, Timothy J; Shore, John W; Greene, Daniel; Servat, Juan J; Levin, Flora

2013-07-29

363

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.

Joseph, Jeffrey M; Glavas, Ioannis P

2011-01-01

364

ERS orbit control  

Microsoft Academic Search

The European remote sensing mission orbit control is addressed. For the commissioning phase, the orbit is defined by the following requirements: Sun synchronous, local time of descending node 10:30; three days repeat cycle with 43 orbital revolutions; overhead Venice tower (12.508206 deg east, 45.314222 deg north). The launch, maneuvers for the initial acquisition of the operational orbit, orbit maintenance maneuvers,

Mats Rosengren

1991-01-01

365

The Butterfly Diagram internal structure .  

NASA Astrophysics Data System (ADS)

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

Ternullo, M.

366

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

367

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

368

Animated Diagram: Sedimentary Rock Identification  

NSDL National Science Digital Library

This Flash-enabled diagram provides a scheme for sedimentary rock identification accompanied by pop-up images of the rocks. Rolling the mouse over highlighted boxes links texture, grain size, composition, and map symbols to images of a variety of sedimentary rocks. The animation is downloadable.

369

Validation of Causal Loop Diagrams  

Microsoft Academic Search

In this paper, we present techniques for manually assessing the structural validity of each link in a causal loop diagram (CLD). A link is defined as consisting of an origination quantity, a destination quantity and a connection edge between them. Each link is considered as a separate and distinct causal hypothesis whose validity should stand on its own merits. Following

James R. Burns

370

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

371

QCD phase diagram: an overview  

NASA Astrophysics Data System (ADS)

The aim of this review is to summarize the contemporary understanding of the QCD phase di- agram as a function of temperature T and baryo-chemical potential µB . The focus is on recent theoretical developments due to lattice simulations of the phase diagram.

Stephanov, Misha

2006-12-01

372

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.

Nielsen-Gammon, John

1996-01-01

373

Stability diagrams for Landau damping  

Microsoft Academic Search

Coherent modes which are present when there is no incoherent tune spread may be absent when such a spread exists. Such modes are “Landau damped”. There is instead an incoherent spectrum, a continuum of an infinite number of frequencies, which will decohere (filament), thus not leading to collective instabilities. A stability diagram indicates when Landau damping will be effective. It

J. Scott Berg; Francesco Ruggiero

1997-01-01

374

Voronoi Diagrams on Periodic Graphs  

Microsoft Academic Search

A periodic graph models various natural and artificial periodic patterns with repetitions of a given static graph, and have vast applications in crystallography, scheduling, VLSI circuits and systems of uniform recurrence equations. This paper considers a graph Voronoi diagram for a given subset of vertices on a periodic graph. The simplest two-dimensional periodic graph is a square lattice, and the

Norie Fu; Hiroshi Imai; Sonoko Moriyama

2010-01-01

375

Orbit-Orbit Interactions in Atomic Spectra  

Microsoft Academic Search

Empirical spectroscopic evidence suggests the existence of an orbit-orbit interaction between electrons, of the form alphal1.l2, and of a magnitude comparable to the spin-orbit interaction. The direct magnetic interaction is of this form, but previous calculations have yielded too small a magnitude. We suggest that the magnetic interaction is uniquely sensitive to the correlation of the interacting electrons, and that

C. W. Ufford; H. B. Callen

1958-01-01

376

Ionospheric Imaging from Geostationary Orbit  

Microsoft Academic Search

An ultraviolet imager is under development to image the ionosphere and thermosphere from geostationary orbit. The instrument will consist of two telescopes, one with a filter wheel to measure the atomic oxygen airglow emission at 130.4 nm and 135.6 nm and molecular nitrogen Lyman-Birge-Hopfield bands near 142.5 nm. The second telescope will image the atomic oxygen ion resonance multiplet at

R. P. McCoy; K. S. Wood; K. F. Dymond; S. E. Thonnard

2001-01-01

377

Rhenium oxide as an efficient p-dopant to overcome S-shaped current density-voltage curves in organic photovoltaics with a deep highest occupied molecular orbital level donor layer  

NASA Astrophysics Data System (ADS)

Effect of p-dopants in a p-doped hole transport layer inserted between indium tin oxide and a donor layer of ?,?'-bis(2,2-dicyanovinyl)-quinquethiophene with a deep highest occupied molecular orbital level is reported to remove the S-shape in the organic photovoltaics (OPV) cell. Among the p-dopants of ReO3, MoO3, WO3, and CuI, ReO3 possesses the largest work function and turns out to be the most efficient p-dopant to remove the S-shape of the current density-voltage curve in the OPV cells. The rest of the dopants could not get rid of the S-shape, even with a doping concentration of 25 mol. %. The difference among the dopants can be understood by the different charge generation efficiency of the dopants.

Kim, Dae-Ho; Kim, Tae-Min; Jeong, Won-Ik; Kim, Jang-Joo

2012-10-01

378

Characterisation of Maillard reaction products derived from LEKFD - A pentapeptide found in ?-lactoglobulin sequence, glycated with glucose - By tandem mass spectrometry, molecular orbital calculations and gel filtration chromatography coupled with continuous photodiode array.  

PubMed

Maillard reaction peptides (MRPs) contribute to taste, aroma, colour, texture and biological activity. However, peptide degradation or the cross-linking of MRPs in the Maillard reaction has not been investigated clearly. A peptide of LEKFD, a part of ?-lactoglobulin, was heated at 110°C for 24h with glucose and the reaction products were analysed by HPLC with ODS, ESI-MS, ESI-MS/MS and HPLC with gel-filtration column and DAD detector. In the HPLC fractions, an imminium ion of LEK*FD, a pyrylium ion or a hydroxymethyl furylium ion of LEK*FD, and KFD and EK were detected by ESI-MS. Therefore, those products may be produced by the Maillard reaction. The molecular orbital of glycated LEKFD at the lysine epsilon-amino residue with Schiff base form was calculated by MOPAC. HPLC with gel-filtration column showed cross-linking and degradation of peptides. PMID:24128561

Yamaguchi, Keiko; Homma, Takeshi; Nomi, Yuri; Otsuka, Yuzuru

2013-09-07

379

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

SciTech Connect

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

Ito, K.; Lee, G. H.; Harada, K.; Suzuno, M.; Suemasu, T. [Institute of Applied Physics, University of Tsukuba, Ibaraki 305-8573 (Japan); Takeda, Y.; Saitoh, Y. [Japan Atomic Energy Agency, SPring-8, Hyogo 679-5198 (Japan); Ye, M.; Kimura, A. [Graduate School of Science, Hiroshima University, Hiroshima 739-8526 (Japan); Akinaga, H. [National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8568 (Japan)

2011-03-07

380

Transfer orbit determination accuracy for orbit maneuvers  

NASA Astrophysics Data System (ADS)

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

Pinheiro, Mery Passos

381

Phase diagram of water between hydrophobic surfaces.  

PubMed

Molecular dynamics simulations demonstrate that there are at least two classes of quasi-two-dimensional solid water into which liquid water confined between hydrophobic surfaces freezes spontaneously and whose hydrogen-bond networks are as fully connected as those of bulk ice. One of them is the monolayer ice and the other is the bilayer solid which takes either a crystalline or an amorphous form. Here we present the phase transformations among liquid, bilayer amorphous (or crystalline) ice, and monolayer ice phases at various thermodynamic conditions, then determine curves of melting, freezing, and solid-solid structural change on the isostress planes where temperature and intersurface distance are variable, and finally we propose a phase diagram of the confined water in the temperature-pressure-distance space. PMID:15836349

Koga, Kenichiro; Tanaka, Hideki

2005-03-01

382

Phase diagram of water in carbon nanotubes.  

PubMed

A phase diagram of water in single-walled carbon nanotubes at atmospheric pressure is proposed, which summarizes ice structures and their melting points as a function of the tube diameter up to 1.7 nm. The investigation is based on extensive molecular dynamics simulations over numerous thermodynamic states on the temperature-diameter plane. Spontaneous freezing of water in the simulations and the analysis of ice structures at 0 K suggest that there exist at least nine ice phases in the cylindrical space, including those reported by x-ray diffraction studies and those unreported by simulation or experiment. Each ice has a structure that maximizes the number of hydrogen bonds under the cylindrical confinement. The results show that the melting curve has many local maxima, each corresponding to the highest melting point for each ice form. The global maximum in the melting curve is located at approximately 11 A, where water freezes in a square ice nanotube. PMID:18162549

Takaiwa, Daisuke; Hatano, Itaru; Koga, Kenichiro; Tanaka, Hideki

2007-12-27

383

Orbital mission profile of geostationary satellites for HI launch vehicle payload  

Microsoft Academic Search

The planned orbital mission profile of the ETS-V satellite to be launched by the H-I launch vehicle is described. The ETS-V is a 550-kg class, three-axis stabilized geostationary satellite. A diagram of the typical ground trace and the transfer orbit and stations for the satellite is presented. The optimization of the injection orbit parameters, and the launch window of the

M. Horii; M. Kusanagi; K. Ueno; K. Izumida; M. Miyashita

1986-01-01

384

Prediction of orbital ordering in single-layered ruthenates.  

PubMed

The key role of the orbital degree of freedom to understanding the magnetic properties of layered ruthenates is discussed based on the 3-orbital Hubbard model coupled to lattice distortions, using numerical and mean-field techniques. In the G-type antiferromagnetic phase of Ca(2)RuO(4), recent x-ray experiments reported 0.5 holes/site in the d(xy) orbital, while d(yz) and d(zx) orbitals contain 1.5 holes. This unexpected t(2g) hole distribution is explained by a novel orbital ordered (OO) state, stabilized by a combination of Coulombic and lattice effects. The phase diagram suggests the possibility of large magnetoresistance effects and a new ferromagnetic OO phase in ruthenates. PMID:11800983

Hotta, Takashi; Dagotto, Elbio

2001-12-17

385

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

NASA Astrophysics Data System (ADS)

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

Long, Sheila Ann Thibeault

386

Rapidly fluctuating orbital occupancy above the orbital ordering transition in spin-gap compounds  

NASA Astrophysics Data System (ADS)

Low-dimensionality spin systems develop a spin-dimer phase within a molecular orbital that competes with long-range antiferromagnetism below TS. Very often, preferential orbital occupancy and ordering are the actual driving force for dimerization, as in the orbitally-driven spin-Peierls (MgTi2O4, CuIr2S4, La4Ru2O10, NaTiSi2O6, etc.). Through a microscopic analysis of the thermal conductivity in La4Ru2O10, we show that the orbital occupancy fluctuates rapidly above TS, resulting in an orbital-liquid state. Strong orbital-lattice coupling introduces dynamic bond-length fluctuations that scatter the phonons to produce a glass-like thermal conductivity above TS. This phonon-glass to phonon-crystal transition occurs in other spin-dimer systems, like NaTiSi2O6, pointing to a general phenomenon.

Rivadulla, Francisco; Rivas-Murias, Beatriz; Zhou, Haidong; Rivas, Jose

2011-03-01

387

Causal Construction of the Massless Vertex Diagram  

NASA Astrophysics Data System (ADS)

The massless one-loop vertex diagram is constructed by exploiting the causal structure of the diagram in configuration space, which can be translated directly into dispersive relations in momentum space.

Aste, Andreas

2006-11-01

388

Nonorthogonal localized orbitals and orthogonal atomic hybrids derived from Mulliken's population analysis  

Microsoft Academic Search

The construction of non-orthogonal localized molecular orbitals (Wannier functions of extended systems) with maximal degree of localization according to the Magnasco-Perico localization criterion derived from Mulliken's population analysis is discussed and several forms of the equations giving these orbitals are presented. A partial orthogonality property of these orbitals permits an easy determination of the effective orthogonal atomic orbitals characterizing the

I. Mayer

1995-01-01

389

Graphene as a reversible spin manipulator of molecular magnets.  

PubMed

One of the primary objectives in molecular nanospintronics is to manipulate the spin states of organic molecules with a d-electron center, by suitable external means. In this Letter, we demonstrate by first principles density functional calculations, as well as second order perturbation theory, that a strain induced change of the spin state, from S=1?S=2, takes place for an iron porphyrin (FeP) molecule deposited at a divacancy site in a graphene lattice. The process is reversible in the sense that the application of tensile or compressive strains in the graphene lattice can stabilize FeP in different spin states, each with a unique saturation moment and easy axis orientation. The effect is brought about by a change in Fe-N bond length in FeP, which influences the molecular level diagram as well as the interaction between the C atoms of the graphene layer and the molecular orbitals of FeP. PMID:22243106

Bhandary, Sumanta; Ghosh, Saurabh; Herper, Heike; Wende, Heiko; Eriksson, Olle; Sanyal, Biplab

2011-12-15

390

The atomic orbitals of the topological atom.  

PubMed

The effective atomic orbitals have been realized in the framework of Bader's atoms in molecules theory for a general wavefunction. This formalism can be used to retrieve from any type of calculation a proper set of orthonormalized numerical atomic orbitals, with occupation numbers that sum up to the respective Quantum Theory of Atoms in Molecules (QTAIM) atomic populations. Experience shows that only a limited number of effective atomic orbitals exhibit significant occupation numbers. These correspond to atomic hybrids that closely resemble the core and valence shells of the atom. The occupation numbers of the remaining effective orbitals are almost negligible, except for atoms with hypervalent character. In addition, the molecular orbitals of a calculation can be exactly expressed as a linear combination of this orthonormalized set of numerical atomic orbitals, and the Mulliken population analysis carried out on this basis set exactly reproduces the original QTAIM atomic populations of the atoms. Approximate expansion of the molecular orbitals over a much reduced set of orthogonal atomic basis functions can also be accomplished to a very good accuracy with a singular value decomposition procedure. PMID:23758358

Ramos-Cordoba, Eloy; Salvador, Pedro; Mayer, István

2013-06-01

391

The atomic orbitals of the topological atom  

NASA Astrophysics Data System (ADS)

The effective atomic orbitals have been realized in the framework of Bader's atoms in molecules theory for a general wavefunction. This formalism can be used to retrieve from any type of calculation a proper set of orthonormalized numerical atomic orbitals, with occupation numbers that sum up to the respective Quantum Theory of Atoms in Molecules (QTAIM) atomic populations. Experience shows that only a limited number of effective atomic orbitals exhibit significant occupation numbers. These correspond to atomic hybrids that closely resemble the core and valence shells of the atom. The occupation numbers of the remaining effective orbitals are almost negligible, except for atoms with hypervalent character. In addition, the molecular orbitals of a calculation can be exactly expressed as a linear combination of this orthonormalized set of numerical atomic orbitals, and the Mulliken population analysis carried out on this basis set exactly reproduces the original QTAIM atomic populations of the atoms. Approximate expansion of the molecular orbitals over a much reduced set of orthogonal atomic basis functions can also be accomplished to a very good accuracy with a singular value decomposition procedure.

Ramos-Cordoba, Eloy; Salvador, Pedro; Mayer, István

2013-06-01

392

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.

Institute, Howard H.

2002-01-01

393

Hero's journey in bifurcation diagram  

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

394

Automatic Generation of Digital System Schematic Diagrams  

Microsoft Academic Search

A systematic approach to the automatic generation of schematic diagrams for digital systems¿diagrams described as networks of modules¿provides useful CAD applications. This approach transforms guidelines. traditionally followed in manual drawings of schematic diagrams, into quantitative objectives. In view of the complex relationship between these objectives, the schematic design process is broken into a lengthy sequence of steps. We will attempt

Anshul Kumar; Anjali Arya; V. V. Swaminathan; Amit Misra

1986-01-01

395

White is green: new schematic diagrams  

Microsoft Academic Search

Two new schematic diagrams are presented here that derive from the study of the value relationships of the primary colors of RGB computer and video color. The first diagram is a 'Truth Table' that presents true-false, on-off states of the three colors of RGB so that the colors are presented in the order of their brightness values. The second diagram

Hal Glicksman

2002-01-01

396

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

397

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

398

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

399

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

400

Arrows in Comprehending and Producing Mechanical Diagrams  

ERIC Educational Resources Information Center

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

Heiser, Julie; Tversky, Barbara

2006-01-01

401

Molecular Crystals  

NSDL National Science Digital Library

In this activity, by the Concord Consortium's Molecular Literacy project, students will learn about molecular crystals. The presentation defines a molecular crystal, and presents its different forms during certain phases, for example polymorphic and amorphic construction. Use of moving diagrams, along with strong textual description, makes this page a useful resource for the classroom. The activity itself is a java-based interactive resource built upon the free, open source Molecular Workbench software. In addition, visitors will find an overview of the activity, assessments, and concepts and their correlation to AAAS and NSES standards.

2008-12-08

402

Calculations of forming limit diagrams  

Microsoft Academic Search

The right-hand side of the forming limit diagram (FLD) was calculated using a Marciniak-Kuczynski analysis with a nonquadratic\\u000a anisotropic yield criterion. Effects of changing the strain-hardening exponent, n, strain-rate exponent, m, strain ratio,\\u000a R, stress exponent in the anisotropic yield criterion, a, and the inhomogeneity factor, f, were explored. For a ? 6, the effect\\u000a of R is negligible. The

Alejandro Graf; William F. Hosford

1990-01-01

403

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.

Perkins, Dexter

404

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.

Perkins, Dexter

405

INCONEL 718: A solidification diagram  

Microsoft Academic Search

As part of a program studying weldability of Ni-base superalloys, results of an integrated analytical approach are used to\\u000a generate a constitution diagram for INCONEL 718* in the temperature range associated with solidification. Differential thermal analysis of wrought material and optical and\\u000a scanning electron microscopy, electron probe microanalysis, and analytical electron microscopy of gas tungsten arc welds are\\u000a used in

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

1989-01-01

406

In Orbit Infrastructure.  

National Technical Information Service (NTIS)

A systematic approach to space activity by using a standardized automated multipurpose system of transportation and accomodation to, in, and from orbit, called In-Orbit Infrastructure (IOI) is discussed. The IOI needs of commercial space platforms for Ear...

J. Lacaze

1983-01-01

407

Causal diagrams in systems epidemiology  

PubMed Central

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

2012-01-01

408

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

409

Photodissociation of the ?(0,0) and ?(1,0) bands of nitric oxide in the stratosphere and the mesosphere: A molecular-adapted quantum defect orbital calculation of photolysis rate constants  

NASA Astrophysics Data System (ADS)

The availability of data concerning the upper atmosphere is essential for an understanding of both the change in solar activity on the Earth and of the different processes that have direct effects on the biosphere, in particular those with harmful environmental consequences. The main goal of the present work is the theoretical analysis of the photodissociation of nitric oxide (NO), which plays an important role in the chemical and energetic balance of the upper atmosphere. Given that the molecular absorption cross section is directly linked to the photodissociation rate of the molecule, we have first determined photoabsorption cross sections and then used the calculated values to obtain the rate constants for the photodissociation processes. The photodissociation of NO at a given wavelength range is triggered by the predissociation of the ?(0,0) and ?(1,0) bands. Through the analysis of the predissociation rate constants, a study of the dissociative behavior of NO by absorption of light within the VUV spectral region has been performed. The dependence on the altitude arises from the temperature changes to the doppler-broaded halfwidth, in addition to the state population, and the solar zenith angle of the atmospheric photodissociation rate constants of this molecule have been calculated with the molecular-adapted quantum defect orbital (MQDO) approach. Altitudes ranging from 20 to 90 km, which comprise the stratosphere and mesosphere, have been considered.

Mayor, E.; Velasco, A. M.; MartíN, I.

2007-07-01

410

Thermodynamic phase diagram of the quantum hall skyrmion system  

PubMed

We numerically study the interacting quantum Hall Skyrmion system based on the Chern-Simons action. By noticing that the action is invariant under global spin rotations in the spin space with respect to the magnetic field direction, we obtain the low-energy effective action for a many-Skyrmion system. Performing extensive molecular dynamics simulations, we establish the thermodynamic phase diagram for a many-Skyrmion system. PMID:11017419

Moon; Mullen

2000-01-31

411

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.

Laboratory, Jet P.; Administration, National A.

412

Ab initio molecular orbital study of the interaction of Li+, Na+ and K+ with the pore components of ion channels: consideration of the size, structure and selectivity of the pore of the channels.  

PubMed

Ab initio molecular orbital calculations were made for the various types of structures of the pore of the ion channel and the results were applied to the permeability model by Hille, an extension of the Eyring rate theory. In Hille's model, ion passage through the channel is regarded as a kinetic process. Accordingly, it is thought that the interaction energy between cation and ligand, the easier the passage is, due to the lower activation energy. The calculated interaction energy was in the order Li+ greater than Na+ greater than K+ for all models. The optimum size of the pore determined from the interaction energy depends on the structure of the filter. The size for the pentagon was largest, followed by the hexagon and tetragon. On the other hand, the size depends hardly at all on the kind of ligand molecules. In the case of the tetragon, the sizes for the Na and K channels were nearly the same as those estimated from the model building and inhibitor-blocking experiment. The interaction energy between the ionized carboxyl group and the cation was extremely large, clearly reflecting the experimental fact that the carboxyl group in the pore has an important role in making the passage of the cation through the channel easier by dehydrating the water molecules. By analysis of the interaction energy, it was revealed that the contribution of the electrostatic energy was predominant, although the contributions of the other effects might not be negligible. Among these effects, the value of the charge transfer energy is largest, and this is noteworthy in connection with the selective transmission of cations through the overlap of orbitals. It is concluded that the quantum-chemical indices such as interaction energy and the electronic charge calculated by the sophisticated ab initio method help to shed light on the nature of the pore of the ion channel. PMID:6097772

Nagata, C; Aida, M

1984-10-21

413

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

Microsoft Academic Search

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

D. J. Stevenson; E. E. Salpeter

1977-01-01

414

Painless orbital myositis  

PubMed Central

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.

Chakor, Rahul T.; Santhosh, N. S.

2012-01-01

415

Chemguide: Atomic Orbitals  

NSDL National Science Digital Library

This web page explains what atomic orbitals are in a way that makes it appropriate for pre-college introductory chemistry or physics courses. It goes into detail on s and p orbitals, including their shapes and energies, while devoting less discussion to d and f orbitals. The author uses an analogy comparing an atom to a multi-story house -- with the nucleus on the ground floor and then various rooms (orbitals) on the higher floors occupied by the electrons. A full page debunks the misconception that "orbitals" are like "orbits" (common among beginning students). Beyond this foundation, the tutorial explores how electrons fill orbitals (from low-to-high energy). It concludes with a set of questions, with answers provided, for self-gauging understanding. This page is part of Chemguide, an informational website developed by a veteran high school teacher to promote deeper understanding of concepts in introductory and intermediate-level chemistry.

Clark, Jim

2013-02-20

416

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

417

Phase diagram of nuclear ``pasta'' and its uncertainties in supernova cores  

Microsoft Academic Search

We examine the model dependence of the phase diagram of inhomogeneous nulcear matter in supernova cores using the quantum molecular dynamics (QMD). Inhomogeneous matter includes crystallized matter with nonspherical nuclei---``pasta'' phases---and the liquid-gas phase-separating nuclear matter. Major differences between the phase diagrams of the QMD models can be explained by the energy of pure neutron matter at low densities and

Hidetaka Sonoda; Gentaro Watanabe; Katsuhiko Sato; Kenji Yasuoka; Toshikazu Ebisuzaki

2008-01-01

418

Phase diagram of nuclear 'pasta' and its uncertainties in supernova cores  

Microsoft Academic Search

We examine the model dependence of the phase diagram of inhomogeneous nulcear matter in supernova cores using the quantum molecular dynamics (QMD). Inhomogeneous matter includes crystallized matter with nonspherical nuclei--''pasta'' phases--and the liquid-gas phase-separating nuclear matter. Major differences between the phase diagrams of the QMD models can be explained by the energy of pure neutron matter at low densities and

Hidetaka Sonoda; Gentaro Watanabe; Katsuhiko Sato; Kenji Yasuoka; Toshikazu Ebisuzaki

2008-01-01

419

Structural Phase Diagram of Ca  

SciTech Connect

To help the understanding of the physical behavior of Ca{sub 1-x}Y{sub x}MnO{sub 3}, its phase diagram in the whole x concentration range was investigated taking into account the stability of phases and the possible coexistence of different structural phases. By careful analysis of powder X-ray diffraction (XRD) patterns, we were able to observe the following phase diagram: (i) Orthorhombic phases were detected both in the region of 0 {le} x {le} 0.25 (O type phase with Ca site twelve fold coordinated) and in the region of 0.5 {le} x {le} 0.75 (O' type phase with Ca site ninefold coordinated). (ii) Phase segregation for 0.25 {le} x {le} 0.5 and for x > 0.75 that have not been reported previously, hexagonal YMnO{sub 3} segregates as a separate phase for x > 0.75, and for 0.25 {le} x {le} 0.5 the coexistence of Ca{sub 0.75}Y{sub 0.25}MnO{sub 3} (O) and Ca{sub 0.5}Y{sub 0.5}MnO{sub 3} (O') have to be included in the refinement for it to converge.

Vega, D.; Polla, G.; Leyva, A. G.; Konig, P.; Lanza, H.; Esteban, A.; Aliaga, H.; Causa, M. T.; Tovar, M.; Alascio, B.

2001-02-01

420

Are there atomic orbitals in a molecule?  

PubMed

Effective atomic orbitals (AOs) have been calculated by the method of the "fuzzy atoms" analysis by using the numerical molecular orbitals (MOs) obtained from plane-wave DFT calculation, i.e., without introducing any atom-centered functions. The results show that in the case of nonhypervalent atoms there are as many effective AOs with non-negligible occupation numbers, as many orbitals are in the classical minimal basis set of the given atom. This means that, for nonhypervalent systems, it is possible to present the MOs as sums of effective atomic orbitals that resemble very much the atomic minimal basis orbitals of the individual atoms (or their hybrids). For hypervalent atoms some additional orbitals basically of d-type are also of some importance; they are necessary to describe the back-donation to these positive atoms. It appears that the d-type orbitals play a similar role also for strongly positive carbon atoms. The method employed here is also useful to decide whether the use of polarization functions of a given type is a matter of conceptual importance or has only a numerical effect. PMID:21699211

Mayer, I; Bakó, I; Stirling, A

2011-06-23

421

Optical activity and electronic absorption spectra of some simple nucleosides related to cytidine and uridine: all-valence-shell molecular orbital calculations.  

PubMed Central

The circular dichroism and electronic absorption of three simple model systems for cytidine and uridine have been measured to 190 nm. The molecular spectral properties (excitation wavelengths, oscillator strengths, rotational strengths, and polarization directions) and electronic transitional patterns were investigated by using wave functions of the entire nucleoside with the goal of establishing the reliability of the theoretical method. The computed electronic absorption quantities were shown to be in satisfactory agreement with experimental data. It was found that the computed optical rotatory strengths of the B2u and E1u electronic transitions and lowest observed n-pi transition are in good agreement with experimental values. Electronic transitions were characterized by their electronic transitional patterns derived from population analysis of the transition density matrix. The theoretical rotational strengths associated with the B2u and E1u transitions stabilize after the use of just a few singly excited configurations in the configuration interaction basis and, hypothetically, are more reliable as indicators of conformation in pyrimidine nucleosides related to cytidine.

Miles, D W; Redington, P K; Miles, D L; Eyring, H

1981-01-01

422

Lorenz Attractor Periodic Orbits  

NSDL National Science Digital Library

The butterfly-like Lorenz attractor is a simplified model of two-dimensional convective fluid flow and is one of the best known images of chaos. Embedded in this attractor are unstable periodic orbits described by Viswanath and this model computes a number of these orbits. Each periodic orbit is classified by the number of times the trajectory orbits the A and B fixed points before it repeats. Note that because the attractor is chaotic and because of numerical errors and the finite precision of the initial conditions, errors accumulate and the trajectory leaves the vicinity of a periodic orbit after a half dozen cycles. The Lorenz Attractor Periodic Orbits Model was created using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_chaos_LorenzAttractor.jar file will run the program if Java is installed.

Christian, Wolfgang

2009-05-20

423

Earth orbiting stations  

Microsoft Academic Search

The earth-orbiting station has evolved through Salyut, Skylab, and the Apollo-Soyuz project. The Shuttle combined with Spacelab will permit low-earth-orbit flights of up to 30 days. Later manned and automated free-flying Spacelabs will extend stay-times to 60 days. Bigger space stations housing 6-12 crewmen for up to six months could be built up from modules carried into orbit. Future space

D. W. Patterson; J. W. Gurr; G. V. Butler

1975-01-01

424

Functional sites of cytochrome c and other electron carrier proteins: semi-empirical molecular orbital program PM3 applied to the conformational analysis of Cys-X1-X2-Cys peptides.  

PubMed

The semi-empirical molecular orbital program, MOPAC version 6.0, PM3 was applied to estimate the distance between two sulfur atoms of two Cys side chains in optimized conformers of Cys-X1-X2-Cys sequences, as well as the total energy of that conformer relative to the most stable one. Some Cys-X1-X2-Cys tetrapeptides found in cytochrome c were optimized to conformers whose sulfur-sulfur distances were just suitable for binding to heme, whereas some tetrapeptides not found in cytochrome c were unable to be optimized to heme-binding conformers. Similarly, Cys-X1-X2-Cys tetrapeptides found in [4Fe-4S]ferredoxin were optimized to [4Fe-4S]-binding conformers, etc. The tetrapeptides found in the redox site of thioredoxin were optimized to conformers in which the two sulfur atoms were in van der Waals contact, so that a disulfide bond may be formed during the function. The conclusion has been drawn that the combination of X1 and X2 in a Cys-X1-X2-Cys sequence may be determining for that sequence to be a functional redox site in an electron carrier protein. PMID:7893813

Shimura, M; Hirota, F; Yagi, T

1994-01-01

425

Spectroscopic (FT-IR, FT-Raman and UV-vis) investigation and frontier molecular orbitals analysis on 3-methyl-2-nitrophenol using hybrid computational calculations.  

PubMed

In the present study, the FT-IR and FT-Raman spectra of 3-methyl-2-nitrophenol (C(7)H(7)O(3)N) (3M2NP) have been recorded in the range of 4000-100 cm(-1). The fundamental modes of vibrational frequencies of 3M2NP are assigned. All the geometrical parameters have been calculated by HF and DFT (LSDA and B3LYP) methods with 6-31G(d,p) and 6-311G(d,p) basis sets. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for phenol and some substituted phenol. The harmonic and anharmonic vibrational wave numbers, IR intensities and Raman activities are calculated at the same theory levels used in geometry optimization. The calculated frequencies are scaled and compared with experimental values. The scaled vibrational frequencies at LSDA/B3LYP/6-311G(d,p) seem to coincide with the experimentally observed values with acceptable deviations. The impact of substitutions on the benzene structure is investigated. The molecular interactions between the substitutions (OH, CH(3) and NO(2)) are also analyzed. A detailed interpretation of the infrared spectra of was also reported more precisely. Charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap are calculated and presented. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H) and temperatures. PMID:22074882

Mahadevan, D; Periandy, S; Karabacak, M; Ramalingam, S; Puviarasan, N

2011-10-19

426

Some interesting color-magnitude diagrams  

NASA Astrophysics Data System (ADS)

Some CCD color-magnitude diagrams for a few open clusters, global clusters, and dwarf spheroidal galaxies in the Local Group are presented. Consideration is given to the open clusters NGC 7789, NGC 2818, NGC 6205, and NGC 6341, the spheroidal galaxy in Draco, the B, R color-magnitude diagram of Carina, and the B, R color-magnitude diagram for the dwarf spheroidal galaxy in Fornax.

Stetson, Peter B.

1997-07-01

427

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

428

Linking the Macroscopic and Submicroscopic Levels: Diagrams  

Microsoft Academic Search

Explanations of chemical phenomena are nearly always focused at the sub-micro level, a level that cannot be observed, yet\\u000a are normally provided with diagrams at the symbolic level. These diagrams represent the macro and sub-micro levels of matter.\\u000a The connections between the macro level and the diagrams of the sub-micro level are not always apparent to students, indicating\\u000a a need

Bette Davidowitz; Gail Chittleborough

429

Multiresolution Approximations of Generalized Voronoi Diagrams  

Microsoft Academic Search

\\u000a A framework to support multiresolution approximations of planar generalized Voronoi diagrams is presented. Our proposal is:\\u000a (1) A multiresolution model based on a quadtree data structure which encodes approximations of a generalized Voronoi diagram\\u000a at different levels of detail. (2) A user driven refinement strategy which generates from the quadtree a continuous polygonal\\u000a approximation of the Voronoi diagram.

Imma Boada; Narcís Coll; Joan Antoni Sellarès

2004-01-01

430

Idiopathic orbital pseudotumour.  

PubMed

Idiopathic orbital pseudotumour (IOP) is a benign inflammatory condition usually confined to the orbit. This may involve single or multiple intraorbital structures. Extraorbital extension can also occur. The imaging appearances often mimic other orbital diseases. Both computed tomography (CT) and magnetic resonance imaging (MRI) are frequently used to investigate orbital diseases, and it is important for radiologists to be aware of the variety of imaging appearances that occur in IOP. We present the imaging appearances in histopathologically confirmed cases of IOP and discuss the clinical features, natural history, and differential diagnosis of this condition. PMID:21546008

Ding, Z X; Lip, G; Chong, V

2011-05-04

431

Updated ephemeris, (O-C) diagrams and light fluctuations of the supersoft X-ray source QR And  

NASA Astrophysics Data System (ADS)

CCD photometry of QR And obtained in 2004 is reported. The lightcurves show changes in overall brightness on timescale of a week in range of ~0.30 mag, contrary to recently published results ~0.15 mag. With our data set we improved the orbital period and construct the first (O-C) diagrams.

Chrastina, M.; Szasz, G.; Petrik, K.; Hric, L.

2006-02-01

432

A Regime Diagram for Subduction  

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

433

Hubble's diagram and cosmic expansion.  

PubMed

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

Kirshner, Robert P

2003-12-26

434

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

435

The new concept of the orbital theory of paleoclimate  

NASA Astrophysics Data System (ADS)

The comparison of the Phanerosoic climatic changes, characterized by the orbital periodicities, with the theories of Croll (1875) and Milankovitch (1930) lead me to the formulation of the new cocept of the orbital theory of paleoclimate (Bol’shakov, 2001). It consists of two main principles: 1)The extent and type of the climatic effect of variations in orbital elements depend on the global paleoclimatic state of the Earth (ranging from glacial to thermal epochs); this state is most probably determined by both terrestrial and extraterrestrial factors; 2)The determination of the climatic significance of variations in individual orbital elements should take into account the following aspects: (a) specific character of the continuous in time (annual) and space (for the whole Earth) insolation variations, related to the variations in all three orbital elements, and (b) terrestrial climatic feedback mechanisms transforming the orbital signals into the global climatic changes. It is obvious from the new concept formulation, that the paleoclimatic simulation (and the plotting of the paleoclimatic curve) is the extremely difficult task. Because I supposed the simplified method for the plotting of the Pleistocene paleoclimatic curve, which was called orbital-climatic diagram (OCD; Bol’shakov, 2000). This method is based on a simple, general and commonly adopted mechanisms of the global climatic influences of the variations in all orbital elements. Generally good similarity between the orbital-climatic diagram and oxygen isotope curves for the fist time directly confirms the determining influence of the orbital insolation variations on the rhythm and tendency of the global climatic changes over the last million years. It should be noted, that the new concept of the orbital theory of paleoclimate allows to solve on the basis of a unified system of notions the majority of problems, such as the problem of the 100-kyr climatic cyclicity, the absence of the eccentricity’s 400 kyr climatic periodicity in the Pleistocene, the transition, about 1 million years ago, the main climatic periodicity from 41 thousand years to about 100 thousand years and so on. Contrary to the widespread opinion, the seasonal precession insolation variations have had the least effect on the global climatic changes in the Quaternary. The new concept leads to new ideas about the main factors, driving the Phanerosoic climatic changes, characterized by the orbital periodicities.

Bolshakov, V. A.

2003-04-01

436

Saturn Orbiter Mission Study.  

National Technical Information Service (NTIS)

A preliminary analysis of the important aspects of missions orbiting the planet Saturn is provided. Orbital missions to Saturn is given serious consideration for the 1980's, or after flybys by Pioneer 10/G and Mariner Jupiter-Saturn 1977. An attempt is ma...

W. C. Wells R. J. Sullivan

1973-01-01

437

Devising geodetic satellite orbits  

Microsoft Academic Search

In the present paper, an intermediate theory of satellite motion, developed within the framework of the problem of six fixed centers with allowance for the influence of eight zonal harmonics of the geopotential, is applied to the analysis of quasi-geosynchronous and heliosynchronous orbits of geodetic satellites. Expressions for selecting nominal parameters for such orbits are proposed.

E. L. Lukashevich

1979-01-01

438

Tethered Orbital Refueling Study.  

National Technical Information Service (NTIS)

One of the major applications of the space station will be to act as a refueling depot for cryogenic-fueled space-based orbital transfer vehicles (OTV), Earth-storable fueled orbit maneuvering vehicles, and refurbishable satellite spacecraft using hydrazi...

D. A. Fester L. K. Rudolph E. R. Kiefel P. W. Abbott P. Grossrode

1986-01-01

439

Stability of halo orbits.  

PubMed

We predict new populations of trapped nonequatorial ("halo") orbits of charged dust grains about an arbitrary axisymmetric planet. Simple equilibrium and stability conditions are derived, revealing dramatic differences between positively and negatively charged grains in prograde or retrograde orbits. Implications for the Cassini mission to Saturn are discussed. PMID:11019061

Howard, J E; Dullin, H R; Horányi, M

2000-04-10

440

From surface to orbit  

Microsoft Academic Search

Space travel is highly expensive and has significant limitations. Among all space activities the process of travelling from the surface to orbit requires the greatest amount of energy, materials and cost. Basically even today, more than 61 years after the first artificial satellite was set to orbit, these difficulties have been the greatest barriers of the dawn of the real

Andras Bela Olah

2011-01-01

441

Spontaneous orbital haemorrhage.  

PubMed Central

A 57-year-old housewife, with controlled hypertension, presented with acute right proptosis and visual loss with external ophthalmoplegia due to spontaneous orbital haemorrhage. Vision and ocular motility were returned to normal by the rapid surgical evacuation of the blood. Acute orbital haemorrhage is an ocular emergency requiring urgent treatment to prevent the usual previously reported outcome of permanent visual loss. Images

Brooks, A. M.; Finkelstein, E.

1984-01-01

442

Space Shuttle orbiter avionics  

Microsoft Academic Search

The paper concerns the Orbiter's integrated avionic system, which consists of multiple computers with attendant software, multifunction man-machine interfaces, digital communications, and multipurpose instrumentation and data handling capability. The design and verification tasks discussed include hardware and software simulation leading to the flight test phases. Some of the major attributes of the orbiter avionic system include redundancy to support time-critical

L. M. Carrier; R. G. Minor

1977-01-01

443

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.

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

2012-01-01

444

Lunar orbiting and landing missions  

Microsoft Academic Search

Orbits for a lunar orbiting spacecraft and unmanned lunar surface rovers are identified. The orbit to the moon is divided into two phases: one is the lunar transfer phase and the other is the landing phase. For each phase standard orbits are designed, and mission profiles are presented. The minimum weight of the lunar orbiting spacecraft is estimated to be

Tsutomu Iwata; Kazumi Okuda; Yutaka Kaneko

1989-01-01

445

Massive congenital orbital teratoma.  

PubMed

Orbital teratomas are rare embryonic tumors composed of a wide diversity of tissues derived from the three germinal layers. The presenting features include, a healthy newborn with extreme unilateral proptosis; marked stretching of the eyelids over a tense, fluctuating mass, with elongation of the palpebral fissure; enlargement of the bony orbit (two to three times normal size) with subsequent nasal and malar deformities; and transillumination of all or part of the orbital mass. Commonly the eye is normally developed but often vision is not preserved either due to exposure or secondary optic atrophy. The objective in the management of orbital teratoma is to save the eye to encourage orbitofacial development, maintain cosmesis and retain some vision. We report a case of massive congenital orbital teratoma successfully removed by an eyelid-sparing exenteration technique. PMID:16304523

Gnanaraj, Lawrence; Skibell, Bentley C; Coret-Simon, Judith; Halliday, William; Forrest, Christopher; DeAngelis, Dan D

2005-11-01

446

Orbital endoscopic surgery  

PubMed Central

Minimally invasive ?keyhole? surgery performed using endoscopic visualization is increasing in popularity and is being used by almost all surgical subspecialties. Within ophthalmology, however, endoscopic surgery is not commonly performed and there is little literature on the use of the endoscope in orbital surgery. Transorbital use of the endoscope can greatly aid in visualizing orbital roof lesions and minimizing the need for bone removal. The endoscope is also useful during decompression procedures and as a teaching aid to train orbital surgeons. In this article, we review the history of endoscopic orbital surgery and provide an overview of the technique and describe situations where the endoscope can act as a useful adjunct to orbital surgery.

Selva, Dinesh

2008-01-01

447

Handling the Handbag Diagram in Compton Scattering on the Proton  

SciTech Connect

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

Miller, Gerald A.

2004-02-25

448

Automatic Generation of Digital System Schematic Diagrams  

Microsoft Academic Search

This paper presents a rigorours approach to automatic generation of schematic diagrams for digital systems described as networks of modules. This is very useful in comprehensive CAD environment. The approach is based on identification of some guidelines which are traditionally followed in mannual drawing of schematic diagrams. Theses guidelines are transformed into quantitative objectives. In view of the complex interrelationship

A. Arya; V. V. Swaminathan; A. Misra; A. Kumar

1985-01-01

449

Automatic generation of digital system schematic diagrams  

Microsoft Academic Search

This paper presents a rigorous approach to automatic generation of schematic diagrams for digital systems described as networks of modules. This is very useful in comprehensive CAD environment. The approach is based on identification of some guidelines which are traditionally followed in manual drawing of schematic diagrams. Theses guidelines are transformed into quantitative objectives. In view of the complex interrelationship

Anjali Arya; Anshul Kumar; V. V. Swaminathan; Amit Misra

1985-01-01

450

Calculation of Binary Eutectic Phase Diagrams.  

National Technical Information Service (NTIS)

The phase diagrams of 65 simple binary eutectic phase diagrams are calculated from the properties of the elemental constituents. The liquid phase is assumed to behave as an ideal solution and the terminal solid solution regions were assumed to be ideal an...

J. E. Davison

1969-01-01

451

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

452

Generic Phase Diagram of Active Polar Films  

Microsoft Academic Search

We study theoretically the phase diagram of compressible active polar gels such as the actin network of eukaryotic cells. Using generalized hydrodynamics equations, we perform a linear stability analysis of the uniform states in the case of an infinite bidimensional active gel to obtain the dynamic phase diagram of active polar films. We predict, in particular, modulated flowing phases and

R. Voituriez; J. F. Joanny; J. Prost

2006-01-01

453

EXTENDING FEATURE DIAGRAMS WITH UML MULTIPLICITIES  

Microsoft Academic Search

Feature diagrams are an important product of domain analysis for product lines or system families, respectively. They describe relations between requirements and distin- guish between common and variable characteristics. Fea- ture diagrams, as part of the feature model, form the basis for configuring the system. Current principles do not sup- ply a complete description of the semantics of relation- ships

Matthias Riebisch; Kai Böllert; Detlef Streitferdt; Ilka Philippow

454

Dynamic Causality Diagram in Fault Diagnosis  

Microsoft Academic Search

In order to overcomes some shortages of Belief Network dynamic causality diagram is put forward. Its knowledge expression, reasoning, probability computing and also the model of causality diagram used for system fault diagnosis, the model constructing method and reasoning algorithm are proposed. At last, an application example in the fault diagnosis of the nuclear power plant is given which shows

Qingsi Shi; Xinyuan Liang

2009-01-01

455

Influence diagram based on rough set theory  

Microsoft Academic Search

In conventional influence diagrams, the numerical models of uncertainty and imprecise knowledge from large-scaled data set is involved in the systems, the suitability of probability distributions is questioned. The influence diagrams model based on rough sets are proposed in this paper. In the framework, the causal relationships among the nodes and the decision rules are expressed with rough set theory.

Yueling Zhao; Hui Jin; Lihong Wang; Shuang Wang

2010-01-01

456

Diagrams based on structural object perception  

Microsoft Academic Search

Most diagrams, particularly those used in software engineering, are line drawings consisting of nodes drawn as rectangles or circles, and edges drawn as lines linking them. In the present paper we review some of the literature on human perception to develop guidelines for effective diagram drawing. Particular attention is paid to structural object recognition theory. According to this theory as

Pourang Irani; Colin Ware

2000-01-01

457

Hasse Diagram Generators and Petri Nets  

Microsoft Academic Search

In (LJ06) Lorenz and Juhas raised the question of whether there exists a suitable formalism for the representation of infinite families of partial orders generated by Petri nets. Restricting ourselves to bounded p\\/t-nets, we propose Hasse diagram generators as an answer. We show that Hasse diagram generators are expressive enough to represent the partial order lan- guage of any bounded

Mateus De Oliveira Oliveira

2009-01-01

458

Fibonacci numbers when counting chord diagrams  

Microsoft Academic Search

1. Introduction. The combinatorics of drawing some chords in some circles arises in a section of knot theory called invariants of finite-type. We will see that the Fibonacci numbers are useful for counting certain forms of these chord diagrams. We also prove that most of the chord diagrams are null. 2. Definitions We begin with a vector space of chord

Jane Kraemer

459

Voronoi diagrams based on convex distance functions  

Microsoft Academic Search

We present an “expanding waves” view of Voronoi diagrams that allows such diagrams to be defined for very general metrics and for distance measures that do not qualify as metrics. If a pebble is dropped into a still pond, circular waves move out from the point of impact. If n pebbles are dropped simultaneously, the places where wave fronts meet

L. Paul Chew

1985-01-01

460

Vesicle deformation by microtubules: A phase diagram  

NASA Astrophysics Data System (ADS)

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

Emsellem, Virginie; Cardoso, Olivier; Tabeling, Patrick

1998-10-01

461

Diagrams and Descriptions in Acquiring Complex Systems  

Microsoft Academic Search

Complex systems such as a car brake, circulatory system, or legislative system can be c onveyed by language or diagrams. Such systems can be presented from structural or functional perspectives. In three e xperiments, we examine c ommunicating structure a nd function of mechanical systems (bike pump, car brake, pulley system) by text and diagrams in relation to mechanical ability.

Julie Heiser; Barbara Tversky

462

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

463

Topology of ternary VLE diagrams: Elementary cells  

Microsoft Academic Search

The classification of ternary vapor-liquid equilibrium (VLE) diagrams is a key to simple azeotropic dis- tillation analysis. We find that all ternary mixtures so far reported occurring in nature can be qualitatively represented by a combination of only four elementary cells. This greatly reduces the number of VLE diagram structures that need to be analyzed in order to reveal the

E. K. Hilmen; V. N. Kiva; S. Skogestad

2002-01-01

464

Semantic and Visual Encoding of Diagrams  

Microsoft Academic Search

Constructed geometric diagrams capture a dynamic relationship between text and image that played a central role in ancient science and math- ematics. Euclid, Theodosius, Ptolemy, Archimedes and others constructed diagra