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Sample records for molecular orbital diagrams

  1. Visualization of Molecular Orbitals: Formaldehyde

    ERIC Educational Resources Information Center

    Olcott, Richard J.

    1972-01-01

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

  2. ISS EPS Orbital Replacement Unit Block Diagrams

    NASA Technical Reports Server (NTRS)

    Schmitz, Gregory V.

    2001-01-01

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

  3. Magnetically dressed one-electron molecular orbitals

    SciTech Connect

    Wille, U.

    1988-10-01

    A general method for solving the stationary one-electron, two-center Coulomb problem with a superimposed (uniform) strong magnetic field is described and applied. For arbitrary orientation of the field with respect to the line connecting the centers, the pertinent Schroedinger equation is solved by evaluating analytically the Hamiltonian matrix in a basis of (nonorthogonal) Hylleraas functions and solving numerically the generalized eigenvalue problem for this matrix. A detailed study of the properties of ''magnetically dressed'' (diatomic) one-electron molecular orbitals is performed by calculating energies and wave functions for the H/sub 2//sup +/ and (H-He)/sup 2+/ systems for field strengths up to about 10/sup 8/ T. Molecular-orbital correlation diagrams are presented and discussed, in which dressed-orbital energies are displayed as a function of internuclear distance R at fixed angle theta between field direction and internuclear axis, and as a function of theta at fixed R. Equilibrium internuclear distances and total binding energies are calculated as functions of field strength for the magnetically dressed H/sub 2//sup +/ system in its lowest gerade and ungerade states at theta = 0 and theta = 90/sup 0/. The influence of the magnetic field on molecular binding properties as well as on the separation behavior of molecular orbitals at large internuclear distances is illustrated by means of wave-function plots. Whenever possible, our results are compared to those of previous investigations. The convergence properties of our method are discussed.

  4. Basic primitives for molecular diagram sketching

    PubMed Central

    2010-01-01

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

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

    PubMed

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

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Mller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Mller-Plesset perturbation theory or higher. PMID:24754304

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

    ERIC Educational Resources Information Center

    Lee, Victor R.

    2010-01-01

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

  7. Some Observations on Molecular Orbital Theory

    ERIC Educational Resources Information Center

    Journal of Chemical Education, 2005

    2005-01-01

    A few flawed predictions in the context of homonuclear diatomic molecules are presented in order to introduce students to molecular orbital (MO) theory. A common misrepresentation of the relationship between the energy of an atomic orbital and the energy of the MO associated with the atomic orbital is illustrated.

  8. A Simple Huckel Molecular Orbital Plotter

    ERIC Educational Resources Information Center

    Ramakrishnan, Raghunathan

    2013-01-01

    A program is described and presented to readily plot the molecular orbitals from a Huckel calculation. The main features of the program and the scope of its applicability are discussed through some example organic molecules. (Contains 2 figures.)

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

    NASA Astrophysics Data System (ADS)

    Fu, Guoepeng; Kyu, Thein

    2014-03-01

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

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

    Orenha, Renato P.; Galembeck, Srgio E.

    2014-01-01

    This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations

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

    ERIC Educational Resources Information Center

    Orenha, Renato P.; Galembeck, Sérgio E.

    2014-01-01

    This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

  14. Spinorbit interaction mediated molecular dissociation

    SciTech Connect

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

    2014-05-14

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

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

    NASA Astrophysics Data System (ADS)

    De Silva, Theja N.

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    PubMed

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

    2016-03-01

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

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

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    1997-01-01

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

  19. Molecular orbitals for properties and spectroscopies

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    The description and clarification of spectroscopies and properties goes through ab initio calculations. Wave function based calculations (CASSCF/CASPT2) are particularly appealing since they offer spectroscopic accuracy and means of interpretation. we performed such calculations to elucidate the origin of unusual structural changes and intramolecular electron transfer phenomenon. Based on optimized molecular orbitals and a reading of the multireference wave function, it is suggested that intimate interactions are likely to considerably modify the standard pictures. A so-called PIMA (polarization-induced metal?arene) interaction similar to the more familiar anion-? interaction is responsible for a significant deviation from sp3 geometry and an energetic stabilization of 50 kJ/mol in Cr(II) benzyl organometallic complexes. In a similar fashion, it is proposed that the energetic profile of the IVCT (inter valence charge transfer) exhibits strong similarities to the Marcus' theory, suggesting a response behaviour of the ensemble of electrons as electron transfer occurs in Fe2+/Fe3+ bimetallic compound. The electronic reorganization induced by the IVCT process accounts for 11.8 eV, a very large effect that reduces the transfer energy down to 0.89 eV, in very good agreement with experiments.

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

    PubMed

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

    2015-04-20

    We present ab initio numerical study of ultrafast ionization dynamics of H(2)(+) as well as CO(2) and N(2) exposed to linearly polarized attosecond extreme ultraviolet pulses. When the molecules are aligned perpendicular to laser polarization direction, photonionization of these molecules show clear and distinguishing diffraction patterns in molecular attosecond photoelectron momentum distributions. The internuclear distances of the molecules are related to the position of the associated diffraction patterns, which can be determined with high accuracy. Moreover, the relative heights of the diffraction fringes contain fruitful information of the molecular orbital structures. We show that the diffraction spectra can be well produced using the two-center interference model. By adopting a simple inversion algorithm which takes into account the symmetry of the initial molecular orbital, we can retrieve the molecular orbital from which the electron is ionized. Our results offer possibility for imaging of molecular structure and orbitals by performing molecular attosecond photoelectron diffraction. PMID:25969107

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

    ERIC Educational Resources Information Center

    Willis, Christopher J.

    1988-01-01

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

  2. Superatomic Molecular Orbitals of C60: First-Principles calculation

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  3. Periodic orbits of the hydrogen molecular ion and their quantization

    SciTech Connect

    Duan, Y.; Yuan, J.; Bao, C.

    1995-11-01

    In a classical study of the hydrogen molecular ion beyond the Born-Oppenheimer approximation (BOA), we have found that segments of trajectories resemble that of the Born-Oppenheimer approximation periodic orbits. The importance of this fact to the classical understanding of chemical bonding leads us to a systematic study of the periodic orbits of the planar hydrogen molecular ion within the BOA. Besides introducing a classification scheme for periodic orbits, we discuss the convergence properties of families of periodic orbits and their bifurcation patterns according to their types. Semiclassical calculations of the density of states based on these periodic orbits yield results in agreement with the exact quantum eigenvalues of the hydrogen molecular ion system.

  4. Molecular orbital theoretical studies of some organic corrosion inhibitors

    SciTech Connect

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

    1997-08-01

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

  5. Open-Shell Formulation of the Fragment Molecular Orbital Method.

    PubMed

    Pruitt, Spencer R; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, Mark S

    2010-01-12

    Performing accurate calculations on large molecular systems is desirable for closed- and open-shell systems. In this work, the fragment molecular orbital method is extended to open-shell systems and implemented in the GAMESS (General Atomic and Molecular Electronic Structure System) program package. The accuracy of the method is tested, and the ability to reproduce reaction enthalpies is demonstrated. These tests also demonstrate its utility in providing an efficient means to model large open-shell systems. PMID:26614313

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed

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

    2014-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  9. Imaging a Molecular Orbital Wave Function Using High Harmonic Emission

    NASA Astrophysics Data System (ADS)

    Villeneuve, David

    2005-05-01

    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 to observe experimentally --- until now impossible on the time scale of chemical reactions. We show that the full 3-dimensional structure of a single orbital can be imaged using a seemingly unlikely technique --- high harmonic generation from aligned molecules using intense femtosecond laser pulses. We show how the broadband harmonic spectra, measured for a series of molecular alignments, lead to a tomographic reconstruction of the single electron orbital wave function of dinitrogen. This leads to ontological discussions about the meaning of a wave function, particularly in a multielectron system. A non-ionizing femtosecond laser pulse creates a rotational wavepacket that causes periodic molecular alignment. A more intense pulse induces high harmonic emission from the aligned molecules. The recollision electron current pulse is characterized as it returns to a reference argon atom. Assuming that we know the shape of the 3p orbital of argon, we can determine the spectral phase and amplitude of the recollision current. The phase of the harmonic emission from nitrogen is referenced to the phase of argon by measuring the interference in a mixed target gas. The polarization of the emission is also recorded by polarimetry. All of these measurements lead to the reconstruction of the nitrogen sigma-g orbital shape. We also show that attosecond dynamics of an electron wave packet can be measured in the high harmonic spectrum.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    SciTech Connect

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

    2000-01-01

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

  12. Coulomb-corrected molecular orbital tomography of nitrogen.

    PubMed

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

    2016-01-01

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

  13. Coulomb-corrected molecular orbital tomography of nitrogen

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Chen, Zhu; Liang, Zhaoxin

    2016-01-01

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

  15. Dissociative electron attachment in nonplanar chlorocarbons with ??/??-coupled molecular orbitals

    NASA Astrophysics Data System (ADS)

    Aflatooni, K.; Gallup, G. A.; Burrow, P. D.

    2010-03-01

    Total absolute cross sections for the dissociative electron attachment (DEA) process are reported for a series of nonplanar ethylenic and phenylic compounds monosubstituted with (CH2)nCl groups, where n=1-4. Coupling between the local ?? molecular orbitals provided by the unsaturated moieties and the ?? (C-Cl) orbital is thus examined as a function of the separation of these groups. In particular, the coupling is viewed from the perspective of the interacting temporary negative ions formed by short lived occupation of these orbitals and their decay into the DEA channel. A theoretical treatment of "remote" bond breaking, presented elsewhere, satisfactorily accounts for DEA in the chloroethylenic compounds presented here and emphasizes not only the delocalization of the coupled anionic wave functions but the importance of their relative phases. The dependence of the cross sections on the vertical attachment energies, measured by electron transmission spectroscopy, is also explored and compared to that found previously in chlorinated alkanes.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed

    Liu, Shubin; Schauer, Cynthia K

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Liu, Shubin; Schauer, Cynthia K.

    2015-02-01

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

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

    SciTech Connect

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

    2015-02-07

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  2. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  3. A low Earth orbit molecular beam space simulation facility

    NASA Technical Reports Server (NTRS)

    Cross, J. B.

    1984-01-01

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

  4. Fragment molecular orbital calculations under periodic boundary condition

    NASA Astrophysics Data System (ADS)

    Fujita, Takatoshi; Nakano, Tatsuya; Tanaka, Shigenori

    2011-04-01

    The periodic boundary condition (PBC) is incorporated in the fragment molecular orbital (FMO) method to appropriately describe systems with aqueous solutions. We present benchmark calculations for (H2O)64 and show that this PBC-FMO method can eliminate artificial surface effects. An application to molecular dynamics simulation for liquid water is also shown, and calculated radial distribution functions are in reasonable agreement with those obtained from experiments. It is thus confirmed that the present PBC-FMO method is useful for ab initio simulations in aqueous solution.

  5. Hydrogen outgassing considerations for an orbiting aluminum molecular shield

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.

    1982-01-01

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

  6. Benzobisoxazole cruciforms: heterocyclic fluorophores with spatially separated frontier molecular orbitals.

    PubMed

    Lim, Jaebum; Albright, Thomas A; Martin, Benjamin R; Miljani?, Ognjen

    2011-12-16

    We report the synthesis of nine conjugated cruciform-shaped molecules based on the central benzo[1,2-d:4,5-d']bisoxazole nucleus, at which two conjugated currents intersect at a ~90 angle. Cruciforms' substituents were varied pairwise among the electron-neutral phenyl groups, electron-rich 4-(N,N-dimethylamino)phenyl substituents, and electron-poor pyridines. Hybrid density functional theory calculations revealed that the highest occupied molecular orbitals (HOMOs) are localized (24-99%) in all cruciforms, in contrast to the lowest unoccupied molecular orbitals (LUMOs) which are strongly dependent on the substitution and less localized (6-64%). Localization of frontier molecular orbitals (FMOs) along different axes of these cruciforms makes them promising as sensing platforms, since analyte binding to the cruciform should mandate a change in the HOMO-LUMO gap and the resultant optical properties. This prediction was verified using UV/vis absorption and emission spectroscopy: cruciforms' protonation results in hypsochromic and bathochromic shifts consistent with the preferential stabilization of HOMO and LUMO, respectively. In donor-acceptor-substituted systems, a two-step optical response to protonation was observed, wherein an initial bathochromic shift is followed by a hypsochromic one with continued acidification. X-ray diffraction studies of three selected cruciforms revealed the expected ~90 angle between the cruciform's substituents, and crystal packing patterns dominated by [??] stacking and edge-to-face [C-H?] contacts. PMID:22077919

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

    SciTech Connect

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

    2013-05-20

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

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

    PubMed

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

    2014-09-16

    Conspectus Localized molecular orbitals (LMO) not only serve as an important bridge between chemical intuition and molecular wave functions but also can be employed to reduce the computational cost of many-body methods for electron correlation and excitation. Therefore, how to localize the usually completely delocalized canonical molecular orbitals (CMO) into confined physical spaces has long been an important topic: It has a long history but still remains active to date. While the known LMOs can be classified into (exact) orthonormal and nonorthogonal, as well as (approximate) absolutely localized MOs, the ways for achieving these can be classified into two categories, a posteriori top-down and a priori bottom-up, depending on whether they invoke the global CMOs (or equivalently the molecular density matrix). While the top-down approaches have to face heavy tasks of minimizing or maximizing a given localization functional typically of many adjacent local extrema, the bottom-up ones have to invoke some tedious procedures for first generating a local basis composed of well-defined occupied and unoccupied subsets and then maintaining or resuming the locality when solving the Hartree-Fock/Kohn-Sham (HF/KS) optimization condition. It is shown here that the good of these kinds of approaches can be combined together to form a very efficient hybrid approach that can generate the desired LMOs for any kind of gapped molecules. Specifically, a top-down localization functional, applied to individual small subsystems only, is minimized to generate an orthonormal local basis composed of functions centered on the preset chemical fragments. The familiar notion for atomic cores, lone pairs, and chemical bonds emerges here automatically. Such a local basis is then employed in the global HF/KS calculation, after which a least action is taken toward the final orthonormal localized molecular orbitals (LMO), both occupied and virtual. This last step is very cheap, implying that, after the CMOs, the LMOs can be obtained essentially for free. Because molecular fragments are taken as the basic elements, the approach is in the spirit of "from fragments to molecule". Two representatives of highly conjugated molecules, that is, C12H2 and C60, are taken as showcases for demonstrating the success of the proposed approach. The use of the so-obtained LMOs will lead naturally to low-order scaling post-HF/KS methods for electron correlation or excitation. In addition, the underlying fragment picture allows for easy and pictorial interpretations of the correlation/excitation dynamics. PMID:25019464

  9. Molecular orbital analysis of the hydrogen bonded water dimer

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-01-01

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

  11. Ab Initio NMR Chemical Shift Calculations Using Fragment Molecular Orbitals

    NASA Astrophysics Data System (ADS)

    Yokojima, Satoshi; Gao, Qi; Nakamura, Shinichiro

    2009-03-01

    The recently proposed method to calculate NMR chemical shift of large biomolecular systems using fragment molecular orbitals (FMO) is evaluated in comparison with the conventional ab initio results using a ?-sheet (32 residues). The errors in isotropic shielding constants are slightly larger than the previous errors. [Q. Gao, S. Yokojima, T. Kohno, T. Ishida, D. G. Fedorov, K. Kitaura, M. Fujihira, and S. Nakamura, Chem. Phys. Lett. 445, 331-339 (2007).] The increase of the errors in anisotropic shielding constants of 15N is attributed to the neglect of the shielding of the neighboring hydrogen bonded residue, which suggests the crucial importance of hydrogen bonds in biomolecular systems.

  12. Molecular orbital analysis of the hydrogen bonded water dimer

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  13. Molecular integrals over the gauge-including atomic orbitals

    NASA Astrophysics Data System (ADS)

    Ishida, Kazuhiro

    2003-03-01

    Each general formula can be derived by the use of the solid harmonic gradient operator [K. Ishida, Recent Res. Dev. Quantum Chem. 2, 147 (2001)] for each of the ten kinds of molecular integral over the gauge-including atomic orbitals (GIAOs). Each is obtained with the accompanying coordinate expansion (ACE) formula. These ten kinds are the overlap, the kinetic energy, the nuclear attraction, the electron repulsion, the angular momentum, the quadrupole moment, the field, the first kind field gradient, the second kind field gradient, and the "dipole-field" integrals. Except for the overlap and angular momentum integrals, we derive the general formula of these eight molecular integrals at the first level. These ACE formulas will be useful, for example, for a calculation of a molecule in a uniform magnetic field, for a relativistic calculation, and so on, using GIAO as a basis function.

  14. Effective fragment molecular orbital method: a merger of the effective fragment potential and fragment molecular orbital methods.

    PubMed

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

    2010-08-26

    We present a new method called the effective fragment molecular orbital (EFMO) method. The EFMO method is a hybrid between the fragment molecular orbital (FMO) electronic structure method ( Kitaura , K. ; Ikeo , E. ; Asada , T. ; Nakano , T. ; Uebayasi , M. Chem. Phys. Lett. 1999 , 313 , 701 - 706 ) and the effective fragment potential multipole-based polarizable force field ( Day , P. N. ; Jensen , J. H. ; Gordon , M. S. ; Webb , S. P. ; Stevens , W. J. ; Krauss , M. ; Garmer , D. ; Basch , H. ; Cohen , D. J. Chem. Phys. 1996 , 105 , 1968 - 1986 ). The EFMO method is based on the FMO molecular fragmentation scheme and the many-body energy expression but uses the EFP multipole-based energy expressions for long-range interactions and for evaluating the many-body polarization. The accuracy and performance of the EFMO method is compared to FMO and conventional electronic structure theory for water clusters. The difference in the EFMO energy compared to that of conventional Hartree-Fock theory is roughly 0.5 kcal/mol per hydrogen using the 6-31G(d) basis set but less than 0.1 kcal/mol using the 6-31+G(d) basis set. The EFMO method is roughly two times faster than the FMO2 method using Hartree-Fock and five times when computing Hartree-Fock energy and gradients; preliminary density functional theory results are also presented. PMID:20446697

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

    SciTech Connect

    Kimura, M.; Furutachi, N.

    2010-05-12

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C36. We first show that free energies obtained via thermodynamic integrations along isotherms displaying "van der Waals loops," are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C36, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400-1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C36 fullerite and of its liquid state, at variance with what previously experienced for C60.

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

    NASA Astrophysics Data System (ADS)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

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

  18. The activation strain model and molecular orbital theory

    PubMed Central

    Wolters, Lando P; Bickelhaupt, F Matthias

    2015-01-01

    The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324–343. doi: 10.1002/wcms.1221 PMID:26753009

  19. Assessing the Bonding Properties of Individual Molecular Orbitals.

    PubMed

    Robinson, Paul J; Alexandrova, Anastassia N

    2015-12-24

    Molecular orbitals (MOs), while one of the most widely used representations of the electronic structure of a system, are often too complex to intuit properties. Aside from the simplest of cases, it is not necessarily possible to visually tell which orbitals are bonding or antibonding along particular directions, especially in cases of highly delocalized and nontrivial bonding like metal clusters or solids. We propose a method for easily assessing and comparing the relative bonding contributions of MOs, by calculating their response to stress (e.g., compression). We find that this approach accurately describes relative bonding or antibonding character in both the simplest cases and provides new insight in more complex cases. We test the approach on four systems: H2, Am2, benzene, and the Pt4 cluster. In exploring this methodology, a scheme became elucidated, for predicting changes in the ground electronic configuration upon compression, including changes in bonding order, angular momenta of occupied MOs, and trends in MO ordering. We note that the applications of this work go beyond simple molecules and could be straightforwardly extended to, for example, solids and their response to stress along the specific crystallographic plane. Additionally, predictions of structures and properties of chemical systems under stress could result from the emerging intuition about changes in the electronic structure. PMID:26616443

  20. Molecular orbital dependence of high-order harmonic generation

    NASA Astrophysics Data System (ADS)

    Marangos, J. P.; Altucci, C.; Velotta, R.; Heesel, E.; Springate, E.; Pascolini, M.; Poletto, L.; Villoresi, P.; Vozzi, C.; Sansone, G.; Anscombe, M.; Caumes, J.-P.; Stagira, S.; Nisoli, M.

    2006-01-01

    We examine the role of the electronic orbital of a molecule in the process of high-order harmonic generation. To do this, measurements of high-order harmonic generation in molecules (O2, N2, H2, CO2 and small alkanes) and atoms (Xe, Ar and Kr) have been carried out with intense few-optical-cycle pulses. Comparison between molecules and their companion' atoms (i.e. those with nearly equal ionization potential) was made. The molecule response in the high-field regime is treated by adopting an atom-like' model for the forms of the molecular orbitals employing the Lewenstein et al. model, properly modified in order to account for the nonlinear dipole moment of a randomly oriented molecule ensemble. The calculation procedure is described here in detail. There is good agreement between the spectra calculated using this model and the harmonic cut-off position and the shape of the measured spectra. The cut-offs of O2 and CO2 extend far beyond the cut-offs of Xe and Kr respectively, in contrast with N2 and H2 which exhibit cutoffs very close to that of Ar. This behaviour is well explained by adopting the atom-like approximation. A series of alkanes has also been investigated and again the spectra are well matched by this simple model.

  1. Sulfur at nickel-alumina interfaces - Molecular orbital theory

    NASA Technical Reports Server (NTRS)

    Hong, S. Y.; Anderson, Alfred B.; Smialek, James L.

    1990-01-01

    Previous studies on Al-Ni alloys containing sulfur as an impurity suggest that, when S is in the interface between a metal and an oxide scale, it weakens the chemical bonding between them. This paper investigates factors responsible for this effect, using a molecular orbital theory to predict sulfur structures and electronic properties on the Ni-Al2O3 interface. It is shown that, in absence of S, the basal plane of Al2O3 will bind strongly through the Al(3+) cation surface to Ni (111). When segregated S impurity is present on the Ni surface, there are too few interfacial AlS bonds to effect good adhesion, leading to an inhibition of the oxide scale adhesion in NiCrAl alloys.

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

    PubMed

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

    2014-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

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

    SciTech Connect

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

    2012-12-28

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

  5. Growth diagram and morphologies of AlN thin films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Koblmueller, G.; Averbeck, R.; Geelhaar, L.; Riechert, H.; Hsler, W.; Pongratz, P.

    2003-06-01

    A growth diagram for molecular beam epitaxy of AlN on sapphire and 6H-SiC was established using reflection high energy electron diffraction, atomic force microscopy, and Rutherford backscattering spectrometry. In varying the Al/N ratio and growth temperature, distinctive surface morphologies emerge, which are assigned to three regimes of growth, one N-rich (Al/N<1) and two Al-rich (Al/N>1) regimes. Under N-rich conditions, AlN films exhibit rough surface morphologies. In contrast, Al-rich conditions produce excellent smooth surface morphologies, but with the constraint of Al droplet formation at very high Al/N ratios and low temperatures. The differentiation between N-rich and Al-rich regimes is given only by the Al/N ratio, while the two Al-rich regimes (intermediate self-regulated and droplet regime) are separated by the boundary line of Al droplet formation. For this boundary an Arrhenius dependence of growth temperature was found, yielding an activation energy of 3.40.1 eV. The observed morphology transitions are attributed to varying surface adatom mobilities present under the different Al/N ratios.

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

    PubMed Central

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

    2015-01-01

    The frontier orbitals of molecules are the prime determinants of their chemical, optical and electronic properties. Arguably, the most direct method of addressing the (filled) frontier orbitals is ultra-violet photoemission spectroscopy (UPS). Although UPS is a mature technique from the early 1970s on, the angular distribution of the photoemitted electrons was thought to be too complex to be analysed quantitatively. Recently angle resolved UPS (ARUPS) work on conjugated molecules both, in ordered thick films and chemisorbed monolayers, has shown that the angular (momentum) distribution of the photocurrent from orbital emissions can be simply understood. The approach, based on the assumption of a plane wave final state is becoming known as orbital tomography. Here we will demonstrate, with selected examples of pentacene (5A) and sexiphenyl (6P), the potential of orbital tomography. First it will be shown how the full angular distribution of the photocurrent (momentum map) from a specific orbital is related to the real space orbital by a Fourier transform. Examples of the reconstruction of 5A orbitals will be given and the procedure for recovering the lost phase information will be outlined. We then move to examples of sexiphenyl where we interrogate the original band maps of thick sexiphenyl in the light of our understanding of orbital tomography that has developed since then. With comparison to theoretical simulations of the molecular band maps, the molecular conformation and orientation will be concluded. New results for the sexiphenyl monolayer on Al(110) will then be presented. From the band maps it will be concluded that the molecule is planarised and adopts a tilted geometry. Finally the momentum maps down to HOMO-11 will be analysed and real space orbitals reconstructed. PMID:26752804

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

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

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

    SciTech Connect

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

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  9. Applications of the Fragment Molecular Orbital Method in Drug Discovery.

    PubMed

    Ishikawa, Takeshi

    2016-01-01

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

  10. Orbital-Free Molecular Dynamics Simulations at Extreme Conditions

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  11. Fuzzy symmetries of molecule and molecular orbital: characterization and simple application

    NASA Astrophysics Data System (ADS)

    Zhao, Xuezhuang; Xu, Xiufang; Wang, Guichang; Pan, Yinming; Cai, Zunsheng

    A fuzzy point group has been constructed to describe imperfect molecular symmetry by using fuzzy set theory. Then the fuzzy symmetry of the molecular orbital has also been analyzed, and several concepts, such as fuzzy irreducible representation and fuzzy characters (fuzzy generalized parity) for molecular orbitals have been advanced. The results show that sometimes the symmetry of the molecule as a whole is not obvious, however, that of some molecular orbital may be obvious. Although oscillator strength in the electronic spectrum is not determined solely by fuzzy symmetry, it is obviously related to the fuzzy symmetry, which seems to be a fuzzy rule for the electronic spectrum.

  12. Visualization of Molecular Orbitals and the Related Electron Densities

    SciTech Connect

    Haranczyk, Maciej; Gutowski, Maciej S.

    2008-02-10

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    ERIC Educational Resources Information Center

    Johnson, Adam R.

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Johnson, Adam R.

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Cass, Marion E.; Hollingsworth, William E.

    2004-01-01

    It is suggested that molecular theory should be taught earlier in the inorganic chemistry curriculum even in the introductory chemistry course in order to integrate molecular orbital arguments more effectively throughout the curriculum. The method of teaching relies on having access to molecular modeling software as having access to such software

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. d3z2-r2 orbital in high-Tc cuprates: Excitonic spectrum, metal-insulator phase diagram, optical conductivity, and orbital character of doped holes

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Dang, Hung The; Millis, Andrew J.

    2011-07-01

    The single-site dynamical mean-field approximation is used to solve a model of high-Tc cuprate superconductors, which includes both dx2-y2 and d3z2-r2 orbitals on the Cu as well as the relevant oxygen states. Both T (with apical oxygen) and T' (without apical oxygen) crystal structures are considered. In both phases, inclusion of the d3z2-r2 orbital is found to broaden the range of stability of the charge-transfer insulating phase. For equal charge-transfer energies and interaction strengths, the T' phase is found to be less strongly correlated than the T phase. For both structures, d-d excitons are found within the charge-transfer gap. However, for all physically relevant dopings, the Fermi surface is found to have only one sheet and the admixture of d3z2-r2 into the ground-state wave function remains negligible (<5%). Inclusion of the extra orbitals is found not to resolve the discrepancy between computed and observed conductivity in the insulating state.

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

    SciTech Connect

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

    2009-12-15

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

  1. Phase diagram of n-heneicosane and n-tricosane molecular alloys

    NASA Astrophysics Data System (ADS)

    Jouti, B.; Provost, E.; Petitjean, D.; Bouroukba, M.; Dirand, M.

    1996-08-01

    The phase diagram of the mixtures n-C 21H 44:n-C 23H 48 has been established by joint calorimetric and structural analyses. This study indicates the existence of nine solid single-phase domains of equilibrium: four terminal solid solutions, denoted ?o( C21), ?' o( C21), ?' o( C23) and ?' o( C23) with the n-heneicosane and n-tricosane structures, three orthorhombic intermediate solid phases, called ?? 1, ?' 1 and ?? 2 ( ?? 1 and ?? 2 on both sides of ?? 1 are isostructural), with increasing temperature, a total miscibility field: ?, with the orthorhombic structure Fmmm, above the intermediate solid solution regions (a second order transition which is characterized by the Rotator RI state is observed in this phase) and below the solidus line ?-RII with the rhombohedral structure R3m. These results complete the literature diagrams which only presented two solid single-phase domains.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  4. Homolytic molecular dissociation in natural orbital functional theory.

    PubMed

    Matxain, J M; Piris, M; Ruiprez, F; Lopez, X; Ugalde, J M

    2011-12-01

    The dissociation of diatomic molecules of the 14-electron isoelectronic series N(2), O(2)(2+), CO, CN(-) and NO(+) is examined using the Piris natural orbital functional. It is found that the method describes correctly the dissociation limit yielding an integer number of electrons on the dissociated atoms, in contrast to the fractional charges obtained when using the variational two-particle reduced density matrix method under the D, Q and G positivity necessary N-representability conditions. The chemistry of the considered systems is discussed in terms of their dipole moments, natural orbital occupations and bond orders as well as atomic Mulliken populations at the dissociation limit. The values obtained agree well with accurate multiconfigurational wave function based CASSCF results and the available experimental data. PMID:21904734

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

    NASA Astrophysics Data System (ADS)

    Habasaki, J.; Ngai, K. L.

    2013-08-01

    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.

  6. Solution of multi-center molecular integrals of Slater-type orbitals

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1989-01-01

    The troublesome multi-center molecular integrals of Slater-type orbitals (STO) in molecular physics calculations can be evaluated by using the Fourier transform and proper coupling of the two center exchange integrals. A numerical integration procedure is then readily rendered to the final expression in which the integrand consists of well known special functions of arguments containing the geometrical arrangement of the nuclear centers and the exponents of the atomic orbitals. A practical procedure was devised for the calculation of a general multi-center molecular integrals coupling arbitrary Slater-type orbitals. Symmetry relations and asymptotic conditions are discussed. Explicit expressions of three-center one-electron nuclear-attraction integrals and four-center two-electron repulsion integrals for STO of principal quantum number n=2 are listed. A few numerical results are given for the purpose of comparison.

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

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

    SciTech Connect

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

    2011-10-03

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

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

    SciTech Connect

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

    2014-09-07

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C{sub 36}. We first show that free energies obtained via thermodynamic integrations along isotherms displaying van der Waals loops, are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C{sub 36}, with resulting triple point and critical temperatures about 1770K and 2370K, respectively. We thus predict a 600K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 14001300K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C{sub 36} fullerite and of its liquid state, at variance with what previously experienced for C{sub 60}.

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

    SciTech Connect

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

    2008-11-10

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

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

    PubMed

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

    2007-11-01

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

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

    SciTech Connect

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

    2007-01-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Dias, Jerry Ray

    2016-03-01

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

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

    PubMed

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

    2014-07-28

    We made use of synchrotron radiation to perform near edge X-ray absorption fine structure spectroscopy, NEXAFS, at the carbon K-edge of perylene and perylene-tetracarboxylic-diimide, PTCDI. Reference spectra measured for isolated molecules in the gas phase are compared with polarization dependent NEXAFS spectra measured on highly oriented thin films in order to study the symmetry of the molecular orbitals. The molecular overlayers are grown onto the rutile TiO2(110) surface for which the large anisotropic corrugation effectively drives the molecular orientation, while its dielectric nature prevents the rehybridization of the molecular orbitals. We employed density functional theory, DFT, calculations to disentangle the contribution of specific carbon atoms to the molecular density of states. Numerical simulations correctly predict the observed NEXAFS azimuthal dichroism of the ?* resonances above the ionization threshold, from which we determine the full geometric orientation of the overlayer molecules. A discrepancy observed for the spectral contribution of the imide carbon atom to the calculated unoccupied molecular orbitals has been explained in terms of initial state effects, as determined by Hartree-Fock corrections and in full agreement with the corresponding shift of the C 1s core level measured by X-ray photoelectron spectroscopy, XPS. PMID:24924641

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

    NASA Technical Reports Server (NTRS)

    Luther, George W., III

    1987-01-01

    In this paper, molecular orbital theory is used to explain a heterogeneous reaction mechanism for both pyrite oxidation and reduction. The mechanism demonstrates that the oxidation of FeS2 by Fe(3+) may occur as a result of three important criteria: (1) the presence of a suitable oxidant having a vacant orbital (in case of liquid phase) or site (solid phase) to bind to the FeS2 via sulfur; (2) the initial formation of a persulfido (disulfide) bridge between FeS2 and the oxidant, and (3) an electron transfer from a pi(asterisk) orbital in S2(2-) to a pi or pi(asterisk) orbital of the oxidant.

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

    NASA Astrophysics Data System (ADS)

    Gutman, Ivan

    2016-02-01

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

  18. Extending electron orbital precession to the molecular case: Use of orbital alignment for observation of wavepacket dynamics

    SciTech Connect

    Martay, Hugo E. L.; England, Duncan G.; McCabe, David J.; Walmsley, Ian A.

    2011-04-15

    The complexity of ultrafast molecular photoionization presents an obstacle to the modeling of pump-probe experiments. Here, a simple optimized model of atomic rubidium is combined with a molecular dynamics model to predict quantitatively the results of a pump-probe experiment in which long-range rubidium dimers are first excited, then ionized after a variable delay. The method is illustrated by the outline of two proposed feasible experiments and the calculation of their outcomes. Both of these proposals use Feshbach {sup 87}Rb{sub 2} molecules. We show that long-range molecular pump-probe experiments should observe spin-orbit precession given a suitable pump pulse, and that the associated high-frequency beat signal in the ionization probability decays after a few tens of picoseconds. If the molecule was to be excited to only a single fine-structure state, then a low-frequency oscillation in the internuclear separation would be detectable through the time-dependent ionization cross section, giving a mechanism that would enable observation of coherent vibrational motion in this molecule.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    PubMed

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

    2011-01-01

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

  1. New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Choi, Cheol Ho; Sugita, Yuji; Ten-no, Seiichiro

    2007-11-01

    Two new techniques are introduced in the generalized hybrid orbital (GHO) method [Pu et al., J. Phys. Chem. A 108, 632 (2004)] and tested on small molecules. The first is a way to determine occupation numbers dependent on the molecular mechanical (MM) atoms linked to the boundary. The method takes account of the inhomogeneity in the occupation numbers of the auxiliary orbitals from different types of MM atoms in such a way that the formal charge condition is fulfilled. The second technique is a rigorous orthogonalization procedure of auxiliary orbitals for more than two boundary atoms. It is shown that the new implementation widens the realm of the GHO method with flexible quantum mechanical/MM partitionings.

  2. Molecular contamination of spacecraft surfaces in thermostatic control and orbital injection of launch vehicle nose cone

    NASA Astrophysics Data System (ADS)

    Shuvalov, V. A.; Tykhyy, V. G.; Potapovych, L. P.; Priymak, A. I.; Pismenniy, N. I.; Kochubey, G. S.

    The authors developed calculation and experimental procedures for engineering evaluation of surface roughness levels and mass of spacecraft molecular contamination level in thermostatic control of the Dnepr LV's nose cone by high-pressure air and in orbital injection of the space head module. It is shown that spacecraft surface molecular contamination corresponds to A/65 ? &xi ? A/25 levels in thermostatic control of the space head module by air of a purity class of 5000, and the particle mass of condensed phase of volatile compounds deposited on spacecraft surfaces during 930 seconds of flight is within 0.333 ? M? ? 2.690 mg/m2 in orbital injection, which is not worse than a purity level of ? ? A/3.6 according to the MILSTD 1246C standard.

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

    NASA Technical Reports Server (NTRS)

    Romere, P. O.

    1982-01-01

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

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

    SciTech Connect

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

    1985-05-01

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

  5. Semiempirical molecular orbital estimation of the relative stability of bianthryls produced by anthracene pyrolysis

    SciTech Connect

    Mulholland, J.A.; Mukherjee, J.; Wornat, M.J.; Sarofim, A.F.; Rutledge, G.C. . Dept. of Chemical Engineering)

    1993-08-01

    The pyrolysis of pure anthracene at temperatures between 1,200 and 1,500 K produced all six bianthryl isomers whose relative yields appear to be related to steric factors. To evaluate the hypothesis that thermodynamic factors govern the product distribution of bianthryls in this system, the relative enthalpies and entropies of biaryl isomers were estimated by molecular orbital modeling, using the semiempirical AM1 (Austin Model 1). Computational analysis of several isomer sets demonstrates that the relative stabilities of a large number of biaryl isomers are determined largely by steric interactions caused by structural features defined as bays, coves, and fjords. These steric factors affect both the degree of biaryl twist in the preferred conformation and the freedom of internal rotation. Molecular orbital modeling supports the hypothesis that a thermodynamic distribution of bianthryl isomers is produced by anthracene pyrolysis.

  6. Effect of vacuum processing on outgassing within an orbiting molecular shield

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.

    1982-01-01

    The limiting hydrogen number density in an orbiting molecular shield is highly dependent on the outgassing rates from the materials of construction for the shield, experimental apparatus, and other hardware contained within the shield. Ordinary degassing temperatures used for ultrahigh vacuum studies (less than 450 C) are not sufficient to process metals so that the contribution to the number density within the shield due to outgassing is less than the theoretically attainable level (approximately 200 per cu. cm). Pure aluminum and type 347 stainless steel were studied as candidate shield materials. Measurements of their hydrogen concentration and diffusion coefficients were made, and the effects of high temperature vacuum processing (greater than 600 C) on their resulting outgassing rates was determined. The densities in a molecular shield due to the outgassing from either metal were substantially less ( 0.003) than the density due to the ambient atomic hydrogen flux at an orbital altitude of 500 km.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  9. Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

    SciTech Connect

    Kress, Joel David; Ticknor, Christopher; Collins, Lee A.

    2015-09-16

    Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

  10. Molecular orbital calculations of octahedral molybdenum cluster complexes with the DV-X{alpha} method

    SciTech Connect

    Imoto, Hideo; Saito, Taro; Adachi, Hirohiko

    1995-04-26

    Discrete variational-{Chi}{alpha} molecular orbital methods were applied to octahedral cluster complexes, [Mo{sub 6}X{sub 8}-(PH{sub 3}){sub 6}](X = S and Se). This structure is of interest due to its role in superconductivity of Chevrel plates. Level energies are discussed and factors contributing to their separations are categorized. Agreement with empirical XPS data is excellent.

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

    USGS Publications Warehouse

    Sherman, David M.

    1986-01-01

    A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

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

    NASA Astrophysics Data System (ADS)

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

    1994-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    ERIC Educational Resources Information Center

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

    1984-01-01

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

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

    SciTech Connect

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

    1983-03-30

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

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

    PubMed

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

    2016-02-23

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

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

    NASA Astrophysics Data System (ADS)

    Absi, Noureddine; Hoggan, Philip

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

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

    PubMed

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

    2013-02-01

    We have performed a systematic study of lithium hydride (LiH), using orbital-free molecular dynamics, with a focus on mass transport properties such as diffusion and viscosity by extending our previous studies at the lower end of the warm, dense matter regime to cover a span of densities from ambient to 10-fold compressed and temperatures from 10 eV to 10 keV. We determine analytic formulas for self- and mutual-diffusion coefficients, and viscosity, which are in excellent agreement with our molecular dynamics results, and interpolate smoothly between liquid and dense plasma regimes. In addition, we find the orbital-free calculations begin to agree with the Brinzinskii-Landau formula above about 250 eV at which point the medium becomes fully ionized. A binary-ion model based on a bare Coulomb interaction within a neutralizing background with the effective charges determined from a regularization prescription shows good agreement above about 100 eV with the orbital-free results. Finally, we demonstrate the validity of a pressure-based mixing rule in determining the transport properties from the pure-species quantities. PMID:23496628

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  20. Fluorination-dependent molecular orbital occupancy in ring-shaped perfluorocarbons.

    PubMed

    Brandenburg, Tim; Petit, Tristan; Neubauer, Antje; Atak, Kaan; Nagasaka, Masanari; Golnak, Ronny; Kosugi, Nobuhiro; Aziz, Emad F

    2015-07-28

    Perfluorocarbons are a family of molecules consisting mainly of carbon and fluorine atoms. They have interesting chemical properties and have diverse applications in biomedicine, physical chemistry and polymer science. In this work, carbon K-edge absorption and emission spectra of liquid decalin are presented and compared to perfluorodecalin. A comprehensive picture of the electronic structure of decalin is provided based on soft X-ray absorption and emission spectroscopies. Experimental data are compared to theoretical time-dependent density functional theory for the hydrocarbon, the perfluorocarbon and the stepwise fluorinated derivatives. We observed a molecular orbital change from unoccupied to occupied orbitals for perfluorodecalin, which was induced through the fluorination process. PMID:26105104

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

    PubMed

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

    2015-01-01

    The aim of this study is to compare magnetic resonance imaging (MRI) with computed tomography (CT) for visualization of an orbital alloplastic prosthesis made of ultra-high-molecular-weight polyethylene (UHMW-PE) both in vitro and in vivo. A study of 15 test implants from UHMW-PE visualized in vitro in CT and MRI and an in vivo visualization in a patient who suffered from orbital injury and underwent reconstructive surgery is presented. The postsurgery MRI showed the UHMW-PE material clearly, with no significant artifacts. The surrounding tissues could be satisfactorily evaluated. The CT scans did not present the graft material. Both techniques were sufficient tools for in vitro evaluation of the shape and measurement of the prosthesis. PMID:25830408

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

    SciTech Connect

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

    2007-03-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

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

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

    SciTech Connect

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

    2010-11-10

    We have used the Atacama Pathfinder Experiment 12 m telescope to detect circumstellar CO emission from MP Muscae (MP Mus; K1 IVe), a nearby (D {approx} 100 pc), actively accreting, {approx}7 Myr old pre-main-sequence (pre-MS) star. The CO emission line profile measured for MP Mus is indicative of an orbiting disk with radius {approx}120 AU, assuming that the central star mass is 1.2 M {sub sun} and the disk inclination is i {approx} 30{sup 0}. The inferred disk molecular gas mass is {approx}3 M {sub +}. MP Mus thereby joins TW Hya and V4046 Sgr as the only late-type (low-mass), pre-MS star systems within {approx}100 pc of Earth that are known to retain orbiting, molecular disks. We also report the nondetection (with the Institut de Radio Astronomie Millimetrique 30 m telescope) of CO emission from another 10 nearby (D {approx_lt} 100 pc), dusty, young (age {approx}10-100 Myr) field stars of spectral type A-G. We discuss the implications of these results for the timescales for stellar and Jovian planet accretion from, and dissipation of, molecular disks around young stars.

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

    PubMed

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

    2015-05-22

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

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

    PubMed

    Zhu, Xun; Aoki, Yuriko

    2015-06-15

    Predicting the high spin stability of organic radicals correctly for designing organic ferromagnets remains a significant challenge. We have developed a method with an index (L(min)) for predicting the high spin stability of conjugated organic radicals at the restricted open-shell Hartree-Fock level. Unitary transformations were performed for localizing the coefficients of nonbonding molecular orbitals, and subsequently the localized coefficients were used to calculate L(min) that indicates the high spin stability of conjugated organic radicals. This method can be combined with the elongation method to treat huge high spin open-shell systems. Thus, this method is useful for designing organic ferromagnets. PMID:25903426

  7. Parallel Fock matrix construction program for molecular orbital calculation--specific computer with a hierarchical network.

    PubMed

    Umeda, Hiroaki; Inadomi, Yuichi; Honda, Hiroaki; Nagashima, Umpei

    2009-04-15

    A parallel Fock matrix construction program for a hierarchical network has been developed on the molecular orbital calculation-specific EHPC system. To obtain high parallelization efficiency on the hierarchical network system, a multilevel dynamic load-balancing scheme was adopted, which provides equal load balance and localization of communications on a tree-structured hierarchical network. The parallelized Fock matrix construction routine was implemented into a GAMESS program on the EHPC system, which has a tree-structured hierarchical network. Benchmark results on a 63-processor system showed high parallelization efficiency even on the tree-structured hierarchical network. PMID:18727159

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

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1989-01-01

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

  9. An ab initio molecular orbital study of ion-solid interaction in carbon deposition processes

    NASA Astrophysics Data System (ADS)

    Kiuchi, Masato; Takeuchi, Takae; Yamamoto, Masao

    1997-04-01

    The charge effects of incident carbon ions on the chemical bond formation are discussed by using ab initio molecular orbital calculations. There are two kinds of bonds which are formed in the incident carbon and graphite surface; one is a covalent bond of a carbon cation with the surface, and the other is a van der Waals bond of a carbon nonion and the surface. A carbon anion can not have a stable bond to the graphite surface. The calculated results at the MP2 level are qualitatively consistent with the results at the UHF level.

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

    NASA Astrophysics Data System (ADS)

    Runge, Keith; Karasiev, Valentin; Deymier, Pierre

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  12. Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Watanabe, Hirofumi; Okiyama, Yoshio; Nakano, Tatsuya; Tanaka, Shigenori

    2010-11-01

    We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17 β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation.

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

    SciTech Connect

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

    1992-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  15. Ab initio molecular orbital study on the reaction of TMA with H 2

    NASA Astrophysics Data System (ADS)

    Hiraoka, Yishiko Someya; Mashita, Masao; Tada, Tsukasa; Yoshimura, Reiko

    1993-03-01

    The reaction of trimethylaluminium (Al(CH 3) 3, TMA) with H 2 has been investigated using ab initio molecular orbital calculations. It has been shown that the activation energy of the reaction, TMA + H 2 ? AlH(CH 3) 2 + CH 4, is about 1/2 of the dissociation energy of radical decomposition, TMA ? Al(CH 3) 2 + CH 3. This means that TMA decomposition under conditions where collisions between TMA and H 2 are sufficiently frequent is dominated by hydrogenolysis. This explains the experimental result that the decomposition temperature of TMA becomes lower with increasing H 2 pressure.

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

    PubMed

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

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

  17. Ab initio molecular orbital theory: a tool for THz spectroscopic investigation

    NASA Astrophysics Data System (ADS)

    Jones, Inke; Rainsford, Tamath J.; Mickan, Samuel P.; Abbott, Derek

    2006-01-01

    Terahertz spectroscopy, which investigates the electromagnetic spectrum of samples between 0.1 and 10 THz, allows not only for exploration of molecular structures but also of molecular dynamics. One difficulty in performing THz spectroscopy is that the data can be noisy and difficult to interpret. Ab initio molecular modelling has recently become more and more useful in the prediction of, for example, molecular structures, dynamic states and isomeric forms. Since the structure of biomolecules is closely related to their functionality there are broad ranging applications in biomedicine, for example in DNA sensing. An a priori knowledge of the expected THz spectra allows for improved experimentation. There is a growing and recognised need for THz spectroscopic databases to be created and made available along with classifiers that are able to effectively detect a specific substance. We show, for a specific example, the 9-cis and all-trans retinal isomers, how ab initio molecular orbital calculations and quantum chemical modelling programs, such as Gamess, can aid in this endeavour.

  18. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    del Rio, B. G.; Gonzlez, L. E.

    2015-08-01

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

    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.

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

    PubMed

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

    2012-07-28

    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

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

    NASA Astrophysics Data System (ADS)

    Kato, Koichiro; Fukuzawa, Kaori; Mochizuki, Yuji

    2015-06-01

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

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

    ERIC Educational Resources Information Center

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

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

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

    ERIC Educational Resources Information Center

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

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel

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

    NASA Astrophysics Data System (ADS)

    Dogaru, Daniela; Motiu, Stefan; Gogonea, Valentin

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

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

    SciTech Connect

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

    2015-04-21

    Organic-inorganic nanoparticle molecular hybrid materials are interesting candidates for improving exciton separation in organic solar cells. The orbital alignment at the internal interface of cadmium selenide (ArS-CdSe) hybrid materials functionalized with covalently attached arylthiolate moieties was investigated through X-ray photoemission spectroscopy (XPS) and ultraviolet photoemission spectroscopy (UPS). A physisorbed interface between arylthiol (ArSH) ligands and CdSe nanoparticles was also investigated for comparison. This interface was created via a multi-step thin film deposition procedure in-vacuo, where the surface was characterized after each experimental step. This enabled the direct comparison of ArSH/CdSe interfaces produced via physisorption and ArS-CdSe covalently attached hybrid materials, which rely on a chemical reaction for their synthesis. All material depositions were performed using an electrospray deposition, which enabled the direct injection of solution-originating molecular species into the vacuum system. This method allows XPS and UPS measurements to be performed immediately after deposition without exposure to the atmosphere. Transmission electron microscopy was used to determine the morphology and particle size of the deposited materials. Ultraviolet-visible spectroscopy was used to estimate the optical band gap of the CdSe nanoparticles and the HOMO-LUMO gap of the ArSH ligands. These experiments showed that hybridization via covalent bonds results in an orbital realignment at the ArSH/CdSe interface in comparison to the physisorbed interface. The orbital alignment within the hybrid caused a favorable electron injection barrier, which likely facilitates exciton-dissociation while preventing charge-recombination.

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

    PubMed

    Govindasamy, P; Gunasekaran, S; Srinivasan, S

    2014-09-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    EPA Science Inventory

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

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

    NASA Astrophysics Data System (ADS)

    Strange, M.; Thygesen, K. S.

    2012-11-01

    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.

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

    SciTech Connect

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

    1986-01-01

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

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

    SciTech Connect

    Luo, Qinlong; Dagotto, Elbio R

    2014-01-01

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

  12. Orbit Functions

    NASA Astrophysics Data System (ADS)

    Klimyk, Anatoliy; Patera, Jiri

    2006-01-01

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

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

    SciTech Connect

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M.

    2014-10-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

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

    PubMed

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

    2015-01-01

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

  15. Equation of state of dense plasmas by ab initio simulations: Bridging the gap between quantum molecular dynamics and orbital-free molecular dynamics at high temperature

    SciTech Connect

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

    2012-12-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on the Thomas-Fermi semiclassical approximation and possibly on a gradient correction, is the only simulation method currently available at high temperature. We show in the case of a dense boron plasma that the two approaches give pressures differing by a few percent even at temperatures as high as a few tens of electron-volts. We indicate how the pressures obtained by orbital-free molecular dynamics can be corrected in order to appear as a limit of the quantum molecular dynamics results as temperature increases. We thus obtain a method to calculate the equation of state of a dense plasma up to high temperatures where quantum molecular dynamics cannot be directly implemented.

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

    SciTech Connect

    Zhou, Xin

    1998-11-30

    Photoemission intensities from the molecular orbitals of c(2x2)CO/Pt(111) over a wide photon energy range were measured and analyzed by the same methods developed for structural studies using core levels. The 4{sigma} orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5{sigma} orbital lies between the C atom and the Pt surface. The C 1s photoelectron diffraction was used to determine the adsorption geometry. The earlier ambiguity that multiple scattering is needed to correctly model a {chi} curve while single scattering is sufficient for understanding major peaks in the ARPEFS-FTS is clarified by studying the clean Ni(111) surface. In the normal emission case, several different combinations of scattering events have similar path length differences (PLDs), and can either cancel each other or enhance the corresponding FT peak. In the off-normal case the degeneracy is greatly reduced due to the lower degree of symmetry. In normal emission AR PEFS, up to third order multiple scattering is needed to describe fully both the {chi} curve and its FT spectrum. To improve the spectral resolution in the ARPEFS-FT analysis, several new spectral analysis methods are introduced. With both autocorrelation autoregression (ACAR) and autocorrelation eigenvector (ACE), we can produce a reliable power spectrum by following the order-closing procedure. The best spectra are usually obtained when the autocorrelation sequence is computed with lags up to half the data range. A simple way of determining surface adsorption sites is proposed as follows: First use a single scattering cluster for possible adsorption sites to construct the geometrical PLDs from the strong backscattering events; then compare these PLDs with those obtained from the ARPEFS-FT analysis of the experimental data. After the preferred adsorption site is determined, fine tune the interlayer distances according to the positional R-factor.

  17. Predicting the solid solubility limit in high-entropy alloys using the molecular orbital approach

    NASA Astrophysics Data System (ADS)

    Sheikh, Saad; Klement, Uta; Guo, Sheng

    2015-11-01

    High-entropy alloys (HEAs) are currently at the research frontier of metallic materials. Understanding the solid solubility limit in HEAs, such a highly concentrated multicomponent alloy system, is scientifically intriguing. It is also technically important to achieve desirable mechanical properties by controlling the formation of topologically or geometrically closed packed phases. Previous approaches to describe the solid solubilities in HEAs could not accurately locate the solubility limit and have to utilize at least two parameters. Here, we propose to use a single parameter, the average energy of d-orbital levels, Md, to predict the solid solubility limit in HEAs. It is found that Md can satisfactorily describe the solid solubilities in fcc structured HEAs containing 3 d transition metals, and also in bcc structured HEAs. This finding will greatly simplify the alloys design and lends more flexibility to control the mechanical properties of HEAs. When 4 d transition metals are alloyed, Md alone cannot describe the solid solubility limit in fcc structured HEAs, due to the large increase of the bond strength that can be gauged by the bond order, Bo. The potential opportunities and challenges with applying the molecular orbital approach to HEAs are discussed.

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

    SciTech Connect

    Varsano, Daniele; Barborini, Matteo; Dipartimento di Scienze Fisiche e Chimiche, Universit degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila ; Guidoni, Leonardo

    2014-02-07

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

  19. Imaging superatomic molecular orbitals in a C60 molecule through four 800-nm photons

    NASA Astrophysics Data System (ADS)

    Zhang, G. P.; Zhu, H. P.; Bai, Y. H.; Bonacum, J.; Wu, X. S.; George, Thomas F.

    2015-05-01

    Superatomic molecular orbitals (SAMOs) in C60 are ideal building blocks for functional nanostructures. However, imaging them spatially in the gas phase has been unsuccessful. It is found experimentally that if C60 is excited by an 800-nm laser, the photoelectron casts an anisotropic velocity image, but the image becomes isotropic if excited at a 400-nm wavelength. This diffuse image difference has been attributed to electron thermal ionization, but more recent experiments (800 nm) reveal a clear nondiffuse image superimposed on the diffuse image, whose origin remains a mystery. Here we show that the nondiffuse anisotropic image is the precursor of the f SAMOs. We predict that four 800-nm photons can directly access the 1f SAMO, and with one more photon, can image the orbital, with the photoelectron angular distribution having two maxima at 0 and 180 and two humps separated by 56.5. Since two 400-nm photons only resonantly excite the spherical 1s SAMO and four 800-nm photons excite the anisotropic 1f SAMO, our finding gives a natural explanation of the nondiffuse image difference, complementing the thermal scenario.

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-04-28

    We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm(-1) in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed. PMID:23635107

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

    NASA Astrophysics Data System (ADS)

    Yuan, Wenjuan; Yang, Hongping; Luo, Jun; Zhu, Jing

    2015-11-01

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

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

    PubMed

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

    2015-07-14

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

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

    NASA Technical Reports Server (NTRS)

    Anderson, A. B.

    1985-01-01

    The chemical mechanisms for sulfate formation from sodium chloride and sulfur trioxide, which is a product of jet fuel combustion was determined. Molten sodium sulfate leads to hot corrosion of the protective oxide layers on turbine blades. How yttrium dopants in nidkel-aluminum alloys used in turbine blades reduce the spalling rate of protective alumina films and enhance their adhesion was also determined. Two other fulfate mechanisms were deduced and structure of carbon monoxide on a clean chronium and clean platinum-titanium alloys surfaces was determined. All studies were by use of the atom superposition and electron delocalization molecular orbital (ASED-MO) theory. Seven studies were completed. Their titles and abstracts are given.

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Safouhi, Hassan; Hoggan, Philip

    2003-01-01

    This review on molecular integrals for large electronic systems (MILES) places the problem of analytical integration over exponential-type orbitals (ETOs) in a historical context. After reference to the pioneering work, particularly by Barnett, Shavitt and Yoshimine, it focuses on recent progress towards rapid and accurate analytic solutions of MILES over ETOs. Software such as the hydrogenlike wavefunction package Alchemy by Yoshimine and collaborators is described. The review focuses on convergence acceleration of these highly oscillatory integrals and in particular it highlights suitable nonlinear transformations. Work by Levin and Sidi is described and applied to MILES. A step by step description of progress in the use of nonlinear transformation methods to obtain efficient codes is provided. The recent approach developed by Safouhi is also presented. The current state of the art in this field is summarized to show that ab initio analytical work over ETOs is now a viable option.

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

    PubMed Central

    Scheiner, S; Lipscomb, W N

    1976-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  13. AM1 and ab initio molecular orbital study of water dimer

    SciTech Connect

    Dannenberg, J.J.

    1988-12-01

    Several structures for the water dimer, including trifurcated structures similar to the optimized AM1 geometry, have been calculated by using the MP4/6-311G** level of ab initio molecular orbital theory. The relative energies of the structures become quite close at the higher levels of calculation. The best trifurcated is only 0.2 kcal/mol higher than the optimized HF/6-31G* structure and only 0.4 kcal/mol higher than the lowest energy structure found (optimized by using AM1 with the H bond constrained to be linear). It appears likely that the potential surface of the water dimer is extremely flat. The experimental geometry, which corresponds to the minimum on the free energy surface, is likely to be dominated by entropy contributions.

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

    PubMed

    Mohri, Fumihito

    2003-04-01

    The bond-valence sum rule has been examined by molecular-orbital methods related to spin-coupling matrix theory [Okada & Fueno (1976). Bull. Chem. Soc. Jpn, 49, 1524-1530], to give a new formulation of the Lewis-electron pair concept. It is shown that the 'pair-coupling population' between atoms M and X exhibits the same behaviour as the bond valence between them. A quantum chemical definition for bond valence is proposed and successfully applied to Al(2)Cl(6), Te(4)Cl(16) and Al(2)Be(3)(SiO(3))(6) (beryl). Using an alternative bond-valence definition it is shown that for oxides the bond valence can possibly be taken as the double pair-coupling population. PMID:12657813

  15. Oxygen evolution on a SrFeO3 anode - Mechanistic considerations from molecular orbital theory

    NASA Technical Reports Server (NTRS)

    Mehandru, S. P.; Anderson, Alfred B.

    1989-01-01

    Various pathways proposed in the literature for the evolution of O2 in electrochemical oxidations are explored using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory and the cluster models of the SrFeO3 surface as a prototype material. Calculations indicate that oxygen atoms can be easily formed on the (100) surface as well as on the edge cation sites of a SrFeO3 anode by the discharge of OH(-), followed by its deprotonation and electron transfer to the electrode. The O atoms can form O2 on the edge and corner sites, where the Fe(4+) is coordinated to four and three bulk oxygen anions, respectively. The calculations strongly disfavor mechanisms involving coupling of oxygen atoms adsorbed on different cations as well as a mechanism featuring an ozone intermediate.

  16. Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory

    NASA Astrophysics Data System (ADS)

    Yang, Weitao; Cohen, Aron J.; Mori-Snchez, Paula

    2012-05-01

    The conventional analysis of Perdew and Levy, and Sham and Schlter shows that the functional derivative discontinuity of the exchange-correlation density functional plays a critical role in the correct prediction of bandgaps, or the chemical hardness. In a recent work by the present authors, explicit expressions for bandgap prediction with all common types of exchange-correlation functionals have been derived without invoking the concept of exchange-correlation energy functional derivative discontinuity at all. We here analyze the two approaches and establish their connection and difference. The present analysis further leads to several important results: (1) The lowest unoccupied molecular orbital (LUMO) in DFT has as much meaning in describing electron addition as the highest occupied molecular orbital (HOMO) in describing electron removal. (2) Every term in the total energy functional contributes to the energy gap because of the discontinuity of the derivative of the density (or density matrix) with respect to the number of electrons, ((partial ? s({r^' }},{r}))/partial N )_{vs}, at integers. (3) Consistent with the Perdew-Levy-Sham-Schlter conclusion that the exact Kohn-Sham energy gap differs from the fundamental bandgap by a finite correction due to the functional derivative discontinuity of the exchange-correlation energy, we show that the exchange-correlation functional cannot be an explicit and differentiable functional of the electron density, either local or nonlocal. The last result is further strengthened when we consider Mott insulators. There, the exact exchange-correlation functional needs to have an explicitly discontinuous (nondifferentiable) dependence on the density or the density matrix. (4) We obtain exact conditions on the derivatives of total energy with respect to the spin-up and spin-down number of electrons.

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

    SciTech Connect

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

    2014-07-14

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

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

    PubMed

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

    2014-07-14

    The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results. PMID:25028021

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

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

    PubMed Central

    Liu, Shubin; Pedersen, Lee G.

    2009-01-01

    An effective approach of estimating molecular pKa values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pKa values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pKa data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pKa values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules. PMID:19317439

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

    PubMed

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

    2013-06-01

    Charge transfer complex formation between 2-aminopyridine (donor, 2AP) with 2,3-dichloro-5,6-dicyano-p-benzoquinone (acceptor, DDQ) has been studied spectrophotometrically in acetonitrile (CH3CN). The newly formed CT-complex has reddish brown color and is characterized by the appearance of new absorption bands in the 375-650 nm regions where acceptor and donor do not have any absorption. Maximum and constant absorbance of the complex was obtained after 10 min at 20 C with 1 mL 510(-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. PMID:23583852

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    PubMed

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed

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

    2015-05-01

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

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

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Taylor, Peter R.

    1990-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Almloef, Jan; Taylor, Peter R.

    1989-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  9. Introduction to Computational Chemistry: Teaching Huckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    ERIC Educational Resources Information Center

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrdinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hckel molecular orbital theory for p bonding in molecules. We present details and results of

  10. Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    ERIC Educational Resources Information Center

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

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

    SciTech Connect

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

    2015-03-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

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

    PubMed

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

    2015-03-14

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system. PMID:25770496

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  16. Hubble Diagram

    NASA Astrophysics Data System (ADS)

    Djorgovski, S.; Murdin, P.

    2000-11-01

    Initially introduced as a way to demonstrate the expansion of the universe, and subsequently to determine the expansion rate (the HUBBLE CONSTANT H0), the Hubble diagram is one of the classical cosmological tests. It is a plot of apparent fluxes (usually expressed as magnitudes) of some types of objects at cosmological distances, against their REDSHIFTS. It is used as a tool to measure the glob...

  17. Extended analysis of satellite structures in particle induced X-ray emission spectra using molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Uda, U.

    Methods for estimating intensity distributions of X-ray satellite spectra induced by accelerated ions with energies of a few McVlamu are reviewed, where the orbitals responsible for X-ray emission are written in the molecular frame, not in the atomic frame. The ionization cross section is written here in the frame of the direct Coulomb interaction and the shake process. The following two factors are taken into account: (1) changes in the number of orbital electrons due to molecular orbital formation and (2) deviation of the number of electric charges on the projectile ion from the nuclear charge Z. Here the semiclassical approximation (SCA) has been used to calculate the Coulomb interaction between the projectile ion and the orbital electrons. In order to estimate the intensity of X-rays emitted from multiply ionized states changes in the fluorescence yield from the yield of isolated atoms caused by resonant orbital rearrangement (ROR), were also taken into account. Furthermore the energy loss of the projectile ions and absorption of emitted X-rays in the material were taken into account. The agreement between the calculated and the observed X-ray satellite intensities is satisfactory when we use all the correction terms mentioned above.

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

    PubMed

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

    2011-05-01

    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

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

    PubMed

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

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

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

    PubMed

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

    2014-07-01

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

  1. Molecular-orbital description of the states of two-electron systems

    SciTech Connect

    Feagin, J.M.; Briggs, J.S.

    1988-06-15

    The molecular-orbital (MO) method introduced previously by us (Phys. Rev. Lett. 57, 984 (1986)) to treat two-electron atoms is developed further. The states of systems consisting of two electrons and one positively charged particle are analyzed with use of the interelectronic distance as an adiabatic coordinate in analogy to the interprotonic distance in H/sub 2//sup +/. The motion of two electrons then separates into rotational, vibrational, and internal motion, the latter being described by MO, exactly as in molecules. Indeed, adiabatic MO potential curves for atomic systems are obtained by scaling the corresponding curves for H/sub 2//sup +/. Approximate quantum numbers for two-electron states, derived previously by empirical methods or from an ad hoc rovibrational model, arise naturally since the two-center Coulomb problem is exactly separable in MO coordinates and the corresponding nodal surfaces are conserved for all interelectronic separations. In addition, the gerade-ungerade symmetry of MO is exactly preserved and appears as a fundamental symmetry of two-electron states.

  2. Molecular orbital calculations of two-electron states for P-donor solid-state spin qubits

    NASA Astrophysics Data System (ADS)

    Kettle, L. M.; Goan, Hsi-Sheng; Smith, Sean C.

    2006-03-01

    We theoretically study the Hilbert space structure of two neighboring P-donor electrons in silicon-based quantum computer architectures. To use electron spins as qubits, a crucial condition is the isolation of the electron spins from their environment, including the electronic orbital degrees of freedom. We provide detailed electronic structure calculations of both the single donor electron wave function and the two-electron pair wave function. We adopted a molecular orbital method for the two-electron problem, forming a basis with the calculated single donor electron orbitals. Our two-electron basis contains many singlet and triplet orbital excited states, in addition to the two simple ground state singlet and triplet orbitals usually used in the Heitler-London approximation to describe the two-electron donor pair wave function. We determined the excitation spectrum of the two-donor system, and study its dependence on strain, lattice position, and interdonor separation. This allows us to determine how isolated the ground state singlet and triplet orbitals are from the rest of the excited state Hilbert space. In addition to calculating the energy spectrum, we are also able to evaluate the exchange coupling between the two donor electrons, and the double occupancy probability that both electrons will reside on the same P donor. These two quantities are very important for logical operations in solid-state quantum computing devices, as a large exchange coupling achieves faster gating times, while the magnitude of the double occupancy probability can affect the error rate.

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

    ERIC Educational Resources Information Center

    Halkides, Christopher J.

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Halkides, Christopher J.

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  6. Mixed ab initio quantum mechanics/molecular mechanics methods using frozen orbitals with applications to peptides and proteins

    NASA Astrophysics Data System (ADS)

    Philipp, Dean Michael

    Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.

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

    PubMed Central

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

    2015-01-01

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

  8. Reactivity of chromate, molybdate, and tungstate on ferrihydrite by XAFS and molecular orbital calculation

    NASA Astrophysics Data System (ADS)

    Ariga, D.; Tanaka, M.; Kashiwabara, T.; Takahashi, Y.

    2012-12-01

    Chromium(Cr), molybdenum(Mo), and tungsten(W) are congeners which have some stable isotopes. Isotope ratios of Cr and Mo are used as tools to estimate redox state in paleocean. In addition, adsorption on Fe (hydr) oxide surfaces sometimes causes isotope fractionation for the oxyanions in the ocean. For example, the adsorption mechanisms of molybdate and tungstate on ferrihydrite are different although these elements are congeners: molybdate forms outersphere complex, but tungstate forms innersphere complex. This difference of adsorption mechanisms is related to isotope fractionation. However, adsorption mechanism of chromate on ferrihydrite has been unknown. Then, we performed EXAFS analysis to reveal adsorption mechanisms of chromate on Fe (hydr) oxides and molecular orbital (MO) calculation to consider the reactivity of oxyanions (chromate, molybdate, tungstate) on ferrihydrite. From the EXAFS analysis, it is suggested that chromate mainly forms outersphere complex on ferrihydrite. In addition, adsorption amount of chromate decreased as the ionic strength increased, which can be regarded as another evidence of the formation of outersphere complex. The results of MO calculations show that chromate and tungstate also showed that outersphere and innersphere complexes are stable on Fe (hydr) oxide, respectively. This result supports our experimental results using EXAFS. Moreover, the stabilities of hydration complex in water decreased in the order of chromate > molybdate > tungstate. Based on these results, it is suggested that formation of outersphere complex is less stable for tungstate, which allows us to conclude that chromate and molybdate prefer to form outersphere complexes, whereas tungstate to innersphere complex.

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

    PubMed

    Roemelt, Michael

    2015-07-28

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

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

    NASA Astrophysics Data System (ADS)

    Roemelt, Michael

    2015-07-01

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

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

    ERIC Educational Resources Information Center

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

    2013-01-01

    The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

    The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many

  13. Comparative molecular field analysis (CoMFA) of anionic azo dye-fiber affinities I: gas-phase molecular orbital descriptors.

    PubMed

    Funar-Timofei, Simona; Schrmann, Gerrit

    2002-01-01

    This paper presents quantitative structure-activity relationship (QSAR) models for a series of 30 anionic azo dyes applied to cellulose fiber by comparative molecular field analysis. Two forms of the dye molecules (neutral and anionic) are compared. Neutral structures give better statistical results than the anionic species. The electronic and structural properties of these dyes were calculated by the semiempirical AM1 method. The results indicate the predominance of electrostatic interactions in dye-cellulose binding. The dominant contribution of the HOMO orbital molecular energy, used as descriptor, can be explained by the donor ability of the dye molecules in the dye adsorption on cellulose. PMID:12132879

  14. Gradient Architecture as Means of Phase Diagram Manipulation in Copolymers: Accessing Both LCOT and UCOT in High Molecular Weight Styrene/n-Butyl Acrylate Systems

    NASA Astrophysics Data System (ADS)

    Mok, Michelle; Burghardt, Wesley; Ellison, Christopher; Torkelson, John

    2009-03-01

    Traditionally, phase transitions of block copolymers could only be tuned through molecular weight and relative block length. Here, we introduce comonomer sequence design through gradient compositions as a means of further manipulating phase diagram boundaries. In such gradient copolymers, the reduced repulsion between chain segments allows access to phase transitions even at high molecular weights (MW). Rheological and x-ray scattering studies were performed to study the impact of comonomer sequence on phase behavior in styrene/n-butyl acrylate (S/nBA) systems. In S/nBA block copolymers, only upper critical ordering behavior was observed. In contrast, by using a gradient architecture of higher MW we observed both upper and lower ordering transitions similar to those seen in very weakly segregating S/n-butyl methacrylate block copolymers, where such dual ordering transitions were first detected by Russell et al. This is the first study to access a miscibility gap in gradient copolymers. Access to such behavior is very rare in blends and block copolymers, limited to low MW and/or very weakly segregating systems.

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

    SciTech Connect

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

    2010-04-15

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

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

    PubMed

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n=1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts ((1)H and (13)C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results. PMID:25448933

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

    NASA Astrophysics Data System (ADS)

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

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

    NASA Astrophysics Data System (ADS)

    Taha, Mohamed; Lee, Ming-Jer

    2013-06-01

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

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

    PubMed

    Taha, Mohamed; Lee, Ming-Jer

    2013-06-28

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

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

    NASA Technical Reports Server (NTRS)

    Jones, H. W.

    1986-01-01

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

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

    PubMed

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

    1997-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    SciTech Connect

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

    2015-05-07

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    The metal L-edge (2p ? 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d5) model systems with well-known electronic structure, viz., atomic Fe3+, high-spin [FeCl6]3- with ligand donor bonding, and low-spin [Fe(CN)6]3- that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

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

    SciTech Connect

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

    2014-09-28

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

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

    PubMed

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

    2014-09-28

    The metal L-edge (2p → 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe(3+), high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)6](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture. PMID:25273421

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

    PubMed

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

    2008-11-17

    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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  10. Molecular-orbital-free algorithm for the excited-state force in time-dependent density functional theory.

    PubMed

    Liu, Jie; Liang, Wan Zhen

    2011-01-28

    Starting from the equation of motion in the density matrix formulation, we reformulate the analytical gradient of the excited-state energy at the time-dependent density functional theory level in the nonorthogonal Gaussian atom-centered orbital (AO) basis. Analogous to the analytical first derivative in molecular-orbital (MO) basis, a Z-vector equation has been derived with respect to the reduced one-electronic density matrix in AO basis, which provides a potential possibility to exploit quantum locality of the density matrix and avoids the matrix transformation between the AO and the MO basis. Numerical tests are finished for the excited-state geometry optimization and adiabatic excitation energy calculation of a series of small molecules. The results demonstrate the computational efficiency and accuracy of the current AO-based energy gradient expression in comparison with the MO-based scheme. PMID:21280694

  11. Formation of giant molecular clouds in global spiral structures: The role of orbital dynamics and cloud-cloud collisions

    NASA Technical Reports Server (NTRS)

    Roberts, W. W., Jr.; Stewart, G. R.

    1987-01-01

    The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes.

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

    SciTech Connect

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

    2014-01-06

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

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

    NASA Astrophysics Data System (ADS)

    Sand, Andrew M.; Mazziotti, David A.

    2013-06-01

    Different sets of molecular orbitals and the rotations connecting them are of great significance in molecular electronic structure. Most electron correlation methods depend on a reference wave function that separates the orbitals into occupied and unoccupied spaces. Energies and properties from these methods depend upon rotations between the spaces. Some electronic structure methods, such as modified coupled electron pair approximations and the recently developed parametric two-electron reduced density matrix (2-RDM) methods [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], 10.1103/PhysRevLett.101.253002, also depend upon rotations between occupied orbitals and rotations between unoccupied orbitals. In this paper, we explore the sensitivity of the ground-state energies from the parametric 2-RDM method to rotations within the occupied space and within the unoccupied space. We discuss the theoretical origin of the rotational dependence and provide computational examples at both equilibrium and non-equilibrium geometries. We also study the effect of these rotations on the size extensivity of the parametric 2-RDM method. Computations show that the orbital rotations have a small effect upon the parametric 2-RDM energies in comparison to the energy differences observed between methodologies such as coupled cluster and parametric 2-RDM. Furthermore, while the 2-RDM method is rigorously size extensive in a local molecular orbital basis set, calculations reveal negligible deviations in nonlocal molecular orbital basis sets such as those from canonical Hartree-Fock calculations.

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

    PubMed

    Sand, Andrew M; Mazziotti, David A

    2013-06-28

    Different sets of molecular orbitals and the rotations connecting them are of great significance in molecular electronic structure. Most electron correlation methods depend on a reference wave function that separates the orbitals into occupied and unoccupied spaces. Energies and properties from these methods depend upon rotations between the spaces. Some electronic structure methods, such as modified coupled electron pair approximations and the recently developed parametric two-electron reduced density matrix (2-RDM) methods [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], also depend upon rotations between occupied orbitals and rotations between unoccupied orbitals. In this paper, we explore the sensitivity of the ground-state energies from the parametric 2-RDM method to rotations within the occupied space and within the unoccupied space. We discuss the theoretical origin of the rotational dependence and provide computational examples at both equilibrium and non-equilibrium geometries. We also study the effect of these rotations on the size extensivity of the parametric 2-RDM method. Computations show that the orbital rotations have a small effect upon the parametric 2-RDM energies in comparison to the energy differences observed between methodologies such as coupled cluster and parametric 2-RDM. Furthermore, while the 2-RDM method is rigorously size extensive in a local molecular orbital basis set, calculations reveal negligible deviations in nonlocal molecular orbital basis sets such as those from canonical Hartree-Fock calculations. PMID:23822222

  15. Gas-Phase Tautomerism in the Triazoles and Tetrazoles: A Study by Photoelectron Spectroscopy and ab Initio Molecular Orbital Calculations

    NASA Astrophysics Data System (ADS)

    Palmer, Michael H.; Simpson, Isobel; Wheeler, J. Ross

    1981-11-01

    The photoelectron spectra of the tautomeric 1,2,3,- and 1,2,4-triazole and 1,2,3,4-tetrazole systems have been compared with the corresponding N-methyl derivatives. The dominant tautomers in the gas phase have been identified as 2 H-1,2,3-triazole, 1 H-1,2,4-triazole and 2H-tetrazole. Full optimisation of the equilibrium geometry by ab initio molecular orbital methods leads to the same conclusions, for relative stability of the tautomers in each of the triazoles, but the calculations wrongly predict the tetrazole tautomerism.

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

    ERIC Educational Resources Information Center

    Gillespie, Ronald J.; And Others

    1996-01-01

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

  17. Molecular orbital (SCF-Xα-SW) theory of metal-metal charge transfer processes in minerals

    USGS Publications Warehouse

    Sherman, David M.

    1987-01-01

    Electronic transitions between the Fe-Fe bonding and Fe-Fe antibonding orbitals results in the optically-induced intervalence charge transfer bands observed in the electronic spectra of mixed valence minerals. Such transitions are predicted to be polarized along the metal-metal bond direction, in agreement with experimental observations.

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

    PubMed

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

    2011-07-28

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

  19. Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

    PubMed

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

    2015-12-17

    The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well. PMID:26623658

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

    PubMed Central

    Biswas, P. K.; Gogonea, Valentin

    2008-01-01

    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. PMID:19045177

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

    PubMed

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

    2015-12-24

    The precise control of on-off switching is essential to the design of ideal molecular sensors. To understand the switching mechanism theoretically, we selected as representative example a 9-anthryltriphenylstibonium cation, which was reported as a fluoride ion sensor. In this molecule, the first excited singlet state exhibits two minimum geometries, where one of them is emissive and the other one dark. The excited state at the geometry with bright emission is of ?-?* character, whereas it is of ?-?* character at the "dark" geometry. Geometry changes in the excited state were identified by geometry optimization and partial potential energy surface (PES) mapping. We also studied Group V homologues of this molecule. A barrierless relaxation pathway after vertical excitation to the "dark" geometry was found for the Sb-containing compound on the excited-states PES, whereas barriers appear in the case of P and As. Molecular orbital analysis suggests that the ?* orbital of the antimony compound is stabilized along such relaxation and that the excited state changes its nature correspondingly. Our results indicate that the size of the central atom is crucial for the design of fluoride sensors with this ligand framework. PMID:26647787

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

    NASA Astrophysics Data System (ADS)

    Omori, Yukiko; Tsuchiizu, Masahisa; Suzumura, Yoshikazu

    2011-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2015-12-18

    Correlated electron systems can undergo ultrafast photoinduced phase transitions involving concerted transformations of electronic and lattice structure. Understanding these phenomena requires identifying the key structural modes that couple to the electronic states. We report the ultrafast photoresponse of the molecular crystal Me4P[Pt(dmit)2]2, which exhibits a photoinduced charge transfer similar to transitions between thermally accessible states, and demonstrate how femtosecond electron diffraction can be applied to directly observe the associated molecular motions. Even for such a complex system, the key large-amplitude modes can be identified by eye and involve a dimer expansion and a librational mode. The dynamics are consistent with the time-resolved optical study, revealing how the electronic, molecular, and lattice structures together facilitate ultrafast switching of the state. PMID:26680192

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

    PubMed

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

    2016-01-25

    Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design. PMID:26642258

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

    SciTech Connect

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

    2008-05-20

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

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

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Karna, Shashi P.

    2002-01-01

    The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the ?-bonded molecules. The calculated decay constant, ?, shows good agreement with previously reported data. For molecular length?15 , the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    SciTech Connect

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

    2010-06-11

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

  10. Ab initio molecular orbital studies of low-energy, metastable isomers of the ubiquitous cyclopropenylidene. [in interstellar space

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

    The discovery of cyclopropenylidene in space suggests that other C3H2 isomers may be present, and a tentative detection of one such isomer, propargylene (HCCCH), has been reported. Ab initio molecular orbital theory has been used to characterize five low-lying, metastable isomers of cyclopropenylidene. Extended calculations including the electron correlation energy, show that the lowest in energy is singlet propadienylidene, followed by propargylene; the singlet and triplet of the latter are too close in energy to allow an assignment of the ground state; triplet propadienylidene is at a significantly higher energy. Rotational frequencies computed to an expected accuracy of + or - 1 -2 percent do not confirm the tentative detection of propargylene in space, although the discrepancy between theory and the observation is not so great as to unequivocally rule out this possibility.

  11. Electronic structure of the benzene-tetracyanoethylene complex: A synthesis of molecular orbital and density functional descriptions

    SciTech Connect

    Cioslowski, J.

    1994-12-31

    The electronic structure of the benzene-tetracyanoethylene electron donor-acceptor complex is investigated at the HF/6-311G level of theory. The computed electronic wave function is analyzed with rigorous interpretive tools that involve both molecular orbital and density functional approaches. The in situ electronegativity difference is calculated at 3.32 eV, resulting in a charge transfer of 0.016. This extent of charge transfer is found to account for only ca. 17% of the interacting energy of ca. 33% of the dipole moment. The remaining part of the dipole moment originates from buckling of the tetracyanoethylene moiety. The dependence of the electronegativity difference on the magnitude of charge transfer is found to be highly nonlinear. 28 refs., 4 figs., 5 tabs.

  12. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    NASA Astrophysics Data System (ADS)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kalfaoğlu, Emel; Karabulut, Bünyamin

    2011-03-01

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

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

    SciTech Connect

    Yoshida, Norio

    2014-06-07

    The three-dimensional reference interaction site model (3D-RISM) method was efficiently implemented in the fragment molecular orbital (FMO) method. The method is referred to as the FMO/3D-RISM method, and allows us to treat electronic structure of the whole of a macromolecule, such as a protein, as well as the solvent distribution around a solute macromolecule. The formalism of the FMO/3D-RISM method, for the computationally available form and variational expressions, are proposed in detail. A major concern leading to the implementation of the method was decreasing the computational costs involved in calculating the electrostatic potential, because the electrostatic potential is calculated on numerous grid points in three-dimensional real space in the 3D-RISM method. In this article, we propose a procedure for decreasing the computational costs involved in calculating the electrostatic potential in the FMO method framework. The strategy involved in this procedure is to evaluate the electrostatic potential and the solvated Fock matrix in different manners, depending on the distance between the solute and the solvent. The electrostatic potential is evaluated directly in the vicinity of the solute molecule by integrating the molecular orbitals of monomer fragments of the solute molecule, whereas the electrostatic potential is described as the sum of multipole interactions when an analog of the fast multipole method is used. The efficiency of our method was demonstrated by applying it to a water trimer system and three biomolecular systems. The FMO/3D-RISM calculation can be performed within a reasonable computational time, retaining the accuracy of some physical properties.

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

    ERIC Educational Resources Information Center

    Martin, R. Bruce

    1988-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  18. A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO).

    PubMed

    Fedorov, Dmitri G; Olson, Ryan M; Kitaura, Kazuo; Gordon, Mark S; Koseki, Shiro

    2004-04-30

    A two-level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle-point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80-90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks. PMID:15011259

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

    PubMed

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

    2016-03-15

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

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

    PubMed Central

    Hasegawa, Koji; Mohri, Shirou; Yokoyama, Takashi

    2013-01-01

    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. PMID:23232497

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

    PubMed Central

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

    2016-01-01

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

  2. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  3. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane.

    PubMed

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

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes--SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane. PMID:25338873

  4. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    SciTech Connect

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

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

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

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-05-01

    The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. PMID:24556133

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

    NASA Astrophysics Data System (ADS)

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

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

  7. Structural Characterization of MAO and Related Aluminum Complexes. 1. Solid-State 27 Al NMR with Comparison to EFG Tensors from ab Initio Molecular Orbital Calculations

    SciTech Connect

    Bryant, Pamela L.; Harwell, Chris; Mrse, Anthony A.; Emery, Earl F.; Gan, Zhedong; Caldwell, Tod; Reyes, Arneil P.; Kuhns, Philip; Hoyt, David W.; Simeral, Larry S.; Hall, Randall W.; Butler, Leslie G.

    2001-11-07

    Aminato and propanolato aluminum clusters with 3-, 4-, and 6-coordinate aluminum sites are studied with three 27Al NMR techniques optimized for large 27Al Quadrupole coupling constants: field-swept, frequency-stepped, and high-field MAS NMR. The 27Al quadrupole coupling constants and asymmetry parameters of molecular species, both experimental and derived from ab initio molecular orbital calculations, are correlated with structure.

  8. Caution: Venn Diagrams Ahead!

    ERIC Educational Resources Information Center

    Kimmins, Dovie L.; Winters, J. Jeremy

    2015-01-01

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

  9. Caution: Venn Diagrams Ahead!

    ERIC Educational Resources Information Center

    Kimmins, Dovie L.; Winters, J. Jeremy

    2015-01-01

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

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

    PubMed

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

    2015-02-01

    Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (μ) and hyperpolarizability β0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP). PMID:25459510

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  12. Exploring the Nature of the H[subscript 2] Bond. 1. Using Spreadsheet Calculations to Examine the Valence Bond and Molecular Orbital Methods

    ERIC Educational Resources Information Center

    Halpern, Arthur M.; Glendening, Eric D.

    2013-01-01

    A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital-configuration interaction (MO-CI) treatments of H[subscript 2]. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several

  13. Exploring the Nature of the H[subscript 2] Bond. 1. Using Spreadsheet Calculations to Examine the Valence Bond and Molecular Orbital Methods

    ERIC Educational Resources Information Center

    Halpern, Arthur M.; Glendening, Eric D.

    2013-01-01

    A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital-configuration interaction (MO-CI) treatments of H[subscript 2]. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several…

  14. Phase Equilibria Diagrams Database

    National Institute of Standards and Technology Data Gateway

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

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

    PubMed

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

    2012-12-14

    We examine the performance of Density Functional Theory (DFT) approaches based on the Zeroth-Order Regular Approximation (ZORA) Hamiltonian (with and without inclusion of spin-orbit coupling) for predictions of electric field gradients (EFGs) at the heavy atom Hg nucleus. This is achieved by comparing with benchmark DFT and CCSD-T data (Arcisauskaite et al., Phys. Chem. Chem. Phys., 2012, 14, 2651-2657) obtained from 4-component Dirac-Coulomb Hamiltonian calculations. The investigated set of molecules comprises linear HgL(2) (L = Cl, Br, I, CH(3)) and bent HgCl(2) mercury compounds as well as the trigonal planar [HgCl(3)](-) system. In 4-component calculations we used the dyall.cv3z basis set for Hg, Br, I and the cc-pCVTZ basis set for H, C, Cl, whereas in ZORA calculations we used the QZ4P basis set for all the atoms. ZORA-4 reproduces the fully relativistic 4-component DFT reference values within 6% for all studied Hg compounds and employed functionals (BH&H, BP86, PBE0), whereas scalar relativistic (SR)-ZORA-4 results show deviations of up to 15%. Compared to our 4-component CCSD-T benchmark the BH&H functional performs best at both 4-component and ZORA levels. We furthermore observe that changes in the largest component of the diagonalised EFG tensor, V(zz), of linear HgCl(2) show a slightly stronger dependence than the r(-3) scaling upon bond length r(Hg-Cl) alterations. The 4-component/BH&H V(zz) value of -9.26 a.u. for a bent HgCl(2) (?Cl-Hg-Cl = 120) is close to -9.60 a.u. obtained for the linear HgCl(2) structure. Thus a point charge model for EFG calculations completely fails in this case. By means of a projection analysis of molecular orbital (MO) contributions to V(zz) in terms of the atomic constituents, we conclude that this is due to the increased importance of the Hg 5d orbitals upon bending HgCl(2) compared to the linear HgCl(2) structure. Changing ligand leads to only minor changes in V(zz) (from -9.60 a.u. (HgCl(2)) to -8.85 a.u. (HgI(2)) at the 4-component/BH&H level). This appears to be due to cancellation of contributions with opposite signs to V(zz) arising from: (i) increasing electron donation from occupied ligand orbitals to the formally empty Hg 6p orbitals and (ii) an increasing bond length and a decreasing negative charge on the ligand along the series. PMID:23111689

  16. Molecular structures and conformational compositions of 2-chlorobutane and 2-bromobutane; an investigation using gas-phase electron-diffraction data and ab initio molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjrn; Stlevik, Reidar

    2001-06-01

    The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G-). The symbols refer to anti (A) with a torsion angle ?2(X 8-C 2-C 3-C 4) of about 180 and gauche (G+ and G-) with torsion angles ?2(X 8-C 2-C 3-C 4) of about +60 and 300(-60), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G-) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G- 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G- 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G- 17%). The results for the principal distances ( rg) and angles ? ? for the G+ conformer of 2-chlorobutane, with estimated 2 ? uncertainties, obtained from the combined GED/ab initio study are: r( C1- C2)=1.524(3) , r( C2- C3)=1.528(3) , r( C3- C4)=1.539(3) , r( C- Cl)=1.812(3) , r( C- H) ave=1.098(4) , ?C 1C 2C 3=111.5(16), ?C 2C 3C 4=113.3(5), ?C 1C 2C1=110.4(9). The results for the G+ conformer of 2-bromobutane are: r( C1- C2)=1.526(4) , r( C2- C3)=1.530(4) , r( C3- C4)=1.540(4) , r( C- Br)=1.982(5) , r( C- H) ave=1.111(8) , ?C 1C 2C 3=112.5(16), ?C 2C 3C 4=114.6(15), ?C 1C 2Br=110.1(16). Only average values for r(C-C), r(C-H), ?CCC, and ?CCH could be determined in the least-squares refinements, the differences between these parameters in the same conformer, and between the different conformers, were kept constant at the values obtained in the ab initio molecular orbital calculations.

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

    PubMed

    Otsuka, Takao; Okimoto, Noriaki; Taiji, Makoto

    2015-11-15

    In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics-based force fields, although they cannot fully describe protein-ligand interactions. A noteworthy computational method in development involves large-scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large-scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange-correlation functionals, and solvation effects) on the binding energies of the FK506-binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2-MP2/6-31G(d), is suitable for evaluating the protein-ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R?=?0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure-activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R?=?0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein-ligand interaction distance. Our acceleration scheme, which uses FMO2-HF/STO-3G:MP2/6-31G(d) at R(int)?=?7.0 , reduces computational costs, while maintaining accuracy in the evaluation of binding energy. PMID:26400829

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

    SciTech Connect

    Severson, M.L.

    1984-01-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed

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

    2015-07-01

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

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

    SciTech Connect

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

    1986-08-01

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

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

    SciTech Connect

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

    2015-03-28

    Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed

    Mahalakshmi, G; Balachandran, V

    2014-10-15

    The FT-IR and FT-Raman spectra of 4-Aminomethylpiperidine have been recorded using Perkin Elmer Spectrophotometer and Nexus 670 spectrophotometer. The equilibrium geometrical parameters, various bonding features, the vibrational wavenumbers, the infrared intensities and the Raman scattering activities were calculated using Hartree-Fock and density functional method (B3LYP) with 6-311+G(d,p) basis set. Detailed interpretations of the vibrational spectra have been carried out with the aid of the normal coordinate analysis. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of intra molecular hydrogen bonds, electron delocalization and steric effects. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of 4-Aminomethylpiperidine (4AMP) were calculated. The theoretical UV-Visible spectrum of the compound was computed in the region 200-400nm by time-dependent TD-DFT approach. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. The dipole moment (?) and polarizability (?), anisotropy polarizability (??) and hyperpolarizability (?) of the molecule have been reported. PMID:24853994

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

    PubMed Central

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

    1975-01-01

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

  7. Curvature in orbital dynamics

    NASA Astrophysics Data System (ADS)

    Nauenberg, Michael

    2005-04-01

    The physical basis and the geometrical significance of the equation for the orbit of a particle moving under the action of external forces is exhibited by deriving this equation in a coordinate-independent representation in terms of the radius of curvature of the orbit. Although this formulation appeared in Newton's Principia, it has been ignored in contemporary classical mechanics textbooks. For small eccentricities, the orbit equation is used to obtain approximate solutions that illustrate the role of curvature. It is shown that this approach leads to a simple graphical method for determining the orbits for central forces. This method is similar to one attributed to Newton, who applied it to a constant central force, and sent a diagram of the orbit to Hooke in 1679. The result is compared to the corresponding orbit of a ball revolving inside an inverted cone which Hooke described in his response to Newton.

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

    PubMed

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

    2015-02-25

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Kim, Heung-Sik; Kee, Hae-Young

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  12. Hertzsprung-Russell Diagram

    NASA Astrophysics Data System (ADS)

    Chiosi, C.; Murdin, P.

    2000-11-01

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

  13. Integrating Diagrams and Text.

    ERIC Educational Resources Information Center

    Wright, Patricia; And Others

    1990-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  15. Energetic studies and phase diagram of thioxanthene.

    PubMed

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

    2009-11-19

    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

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

    SciTech Connect

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  17. E-Orbit Functions

    NASA Astrophysics Data System (ADS)

    Klimyk, Anatoliy U.; Patera, Jiri

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

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

  19. Square Source Type Diagram

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  1. Upgrading Diagnostic Diagrams

    NASA Astrophysics Data System (ADS)

    Proxauf, B.; Kimeswenger, S.; ttl, S.

    2014-04-01

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

  2. Trace element indiscrimination diagrams

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

    Danel, J-F; Kazandjian, L

    2015-01-01

    We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C(2)H(3) and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm(3) for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm(3) for orbital-free molecular dynamics. Simulations for the full C(2)H(3) mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot. PMID:25679719

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    SciTech Connect

    Nakata, Hiroya; RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 ; Fedorov, Dmitri G.; Yokojima, Satoshi; Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachioji-shi, Tokyo 192-0392 ; Kitaura, Kazuo; Sakurai, Minoru; Nakamura, Shinichiro

    2014-04-14

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

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

    SciTech Connect

    Curtiss, L.A.

    1993-01-01

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

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

    SciTech Connect

    Curtiss, L.A.

    1993-04-01

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

  8. Analysis of Bonding Patterns in the Valence Isoelectronic series O-3, S-3, SO2 and OS2 in Terms of Oriented Quasi-Atomic Molecular Orbitals

    SciTech Connect

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

    2010-08-26

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

  9. Orbital Exponent Optimization in Elementary VB Calculations of the Chemical Bond in the Ground State of Simple Molecular Systems

    ERIC Educational Resources Information Center

    Magnasco, Valerio

    2008-01-01

    Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and…

  10. Orbital Exponent Optimization in Elementary VB Calculations of the Chemical Bond in the Ground State of Simple Molecular Systems

    ERIC Educational Resources Information Center

    Magnasco, Valerio

    2008-01-01

    Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and

  11. Gravity wave transmission diagram

    NASA Astrophysics Data System (ADS)

    Tomikawa, Y.

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

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

    SciTech Connect

    Burakovsky, Leonid; Kress, Joel D.; Collins, Lee A.

    2012-05-31

    Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD){sub x}U{sub (1-x)} compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, {rho}, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk{sub B}T/V + P{sub e}, is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species {alpha}, D{sub {alpha}}, the mutual diffusion coefficient for species {alpha} and {beta}, D{alpha}{beta}, and the shear viscosity, {eta}, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.

  14. Impulse-Momentum Diagrams

    ERIC Educational Resources Information Center

    Rosengrant, David

    2011-01-01

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

  15. Understanding Network Diagrams.

    ERIC Educational Resources Information Center

    Waller, Robert

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

  16. Impulse-Momentum Diagrams

    ERIC Educational Resources Information Center

    Rosengrant, David

    2011-01-01

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

  17. Reading Diagrams. Pipefitter.

    ERIC Educational Resources Information Center

    Greater Baton Rouge Chamber of Commerce, LA.

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

  18. Reading Diagrams. E & I.

    ERIC Educational Resources Information Center

    Greater Baton Rouge Chamber of Commerce, LA.

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

  19. Reading Diagrams. Millwright.

    ERIC Educational Resources Information Center

    Greater Baton Rouge Chamber of Commerce, LA.

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

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

    NASA Astrophysics Data System (ADS)

    Chu, Xi; Groenenboom, Gerrit C.

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Johansen, Tore H.; Hagen, Kolbjrn; Stlevik, Reidar

    1999-08-01

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

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

    PubMed

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

    2007-07-01

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

  3. Impulse-Momentum Diagrams

    NASA Astrophysics Data System (ADS)

    Rosengrant, David

    2011-01-01

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

  4. TEP process flow diagram

    SciTech Connect

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

    2008-01-01

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

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

    SciTech Connect

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

    1994-02-01

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

  6. Pioneer Venus orbiter

    NASA Technical Reports Server (NTRS)

    1974-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  8. Orbital transfer vehicle studies overview

    NASA Technical Reports Server (NTRS)

    Perkinson, Don

    1987-01-01

    An overview is given in viewgraph form of orbital transfer vehicle concept definition and systems analysis studies. Project development flow charts are shown for key milestones from 1985 until 1997. Diagrams of vehicles are given. Information is presented in outline form on technology requirements, cooling of propellant tanks, cryogenic fluid management, quick connect/disconnect fluid interfaces and propellant mass transfer.

  9. Antisymmetric Orbit Functions

    NASA Astrophysics Data System (ADS)

    Klimyk, Anatoliy; Patera, Jiri

    2007-02-01

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

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

    PubMed

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

    2013-01-15

    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. PMID:23123244

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

    Porchelvi, E Elamurugu; Muthu, S

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-09-01

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

  15. The tetrazole-azide tautomerism of some nitrotetrazolo [1,5- a]pyridines studied by NMR, IR spectroscopy and molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Cmoch, P.; Wiench, J. W.; Stefaniak, L.; Webb, G. A.

    1999-11-01

    The 6-nitro- and 8-nitro- groups in the tetrazolo[1,5- a]pyridine molecule exhibit completely different influences on the tetrazole-azide equilibrium. Introduction of the methyl-, nitro-, azido groups or a bromine atom in positions 5, 6, 7 or 8 of the nitrotetrazolopyridine produce changes in the equilibrium constants. Based on the IR spectra taken in the solid state, the tetrazole structure was assigned for almost all the compounds studied. Only one of them, 2,6-diazido-3-nitropyridine, exists in the diazido-form in the solid. The 1H, 13C, 15N, and 17O NMR spectral parameters (coupling constants, chemical shifts) as well as ab initio molecular orbital calculations were used to describe the tetrazole-azide tautomerism in solutions. The differences in the NMR parameters between the neutral compound (6,8-dinitrotetrazolo[1,5- a]pyridine) and its ?-adducts are also included as data for distinguishing between both molecules.

  16. Energy Stabilization of the S-Symmetry Superatom Molecular Orbital by Endohedral Doping of C82 Fullerene with a Lanthanum Atom

    SciTech Connect

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

    2013-08-14

    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.

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

    PubMed

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

    2000-01-01

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

  18. 4d-polytopes described by Coxeter diagrams and quaternions

    NASA Astrophysics Data System (ADS)

    Koca, Mehmet

    2011-03-01

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

  19. [Columbia Sensor Diagrams]. Revised

    NASA Technical Reports Server (NTRS)

    2003-01-01

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

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

    USGS Publications Warehouse

    Sherman, David M.

    1990-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

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

  2. Quantum Mhv Diagrams

    NASA Astrophysics Data System (ADS)

    Brandhuber, A.; Travaglini, G.

    2007-03-01

    Over the past two years, the use of on-shell techniques has deepened our understanding of the S-matrix of gauge theories and led to the calculation of many new scattering amplitudes. In these notes we review a particular on-shell technique developed recently, the quantum MHV diagrams, and discuss applications to one-loop amplitudes. Furthermore, we briefly discuss the application of D-dimensional generalised unitarity to the calculation of scattering amplitudes in non-supersymmetric Yang-Mills.

  3. Diagrams of airplane stability

    NASA Technical Reports Server (NTRS)

    Batemen, H

    1921-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  5. Impact decision support diagrams

    NASA Astrophysics Data System (ADS)

    Boslough, Mark

    2014-10-01

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

  6. Warped penguin diagrams

    SciTech Connect

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

    2011-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    SciTech Connect

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

    1994-10-26

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

  9. Space Shuttle Orbiter auxiliary power unit status

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  10. On-orbit flight control algorithm description

    NASA Technical Reports Server (NTRS)

    1975-01-01

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

  11. Space Shuttle Orbiter auxiliary power unit status

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

    Zoba?, Vladimr; Lewis, James P.; Abad, Enrique; Mendieta-Moreno, Jess I.; Hapala, Prokop; Jelnek, Pavel; Ortega, Jos

    2015-05-01

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

  13. Molecular orbital studies (hardness, chemical potential, electrophilicity, and first electron excitation), vibrational investigation and theoretical NBO analysis of 2-hydroxy-5-bromobenzaldehyde by density functional method

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    In this work, the vibrational spectral analysis was carried out using Raman and infrared spectroscopy in the range 4000-400 cm-1 and 3500-100 cm-1, respectively, for the 2-hydroxy-5-bromobenzaldehyde (HBB). The experimental spectra were recorded in the solid phase. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-311G++(d,p) method and basis set. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of related compound. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (?), electrophilicity index (?), hardness (?), chemical potential (?), and first electron excitation (?) are all correlated with the HOMO and LUMO energies with their molecular properties. These show that charge transfer occurs within the molecule. Furthermore, molecular electrostatic potential maps (MESP) of the molecule have been calculated.

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

    SciTech Connect

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

    2015-01-22

    In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (?) of asymmetric ?-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ?(t) and system polarization p(t) are calculated by the QME approach. Dynamic ? in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(?). Spatial contributions of electrons to ? are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2?. We apply the present method to the calculation of the dynamic ? of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.

  15. Polysaccharide-polynucleotide complexes. Part 32. Structural analysis of the curdlan/poly(cytidylic acid) complex with semiempirical molecular orbital calculations.

    PubMed

    Miyoshi, Kentaro; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji

    2005-01-01

    Natural Curdlan adopts a right-handed 6(1) triple helix, in which the constituting glucan chains are underpinned with each other by the intermolecular hydrogen bonds. Curdlan can form a stoichiometric complex with polynucleotides [e.g., poly(cytidylic acid), poly(C)]. In this paper, we carried out the MOPAC (semiempirical molecular-orbital package) calculation to examine the molecular structure of the Curdlan/poly(C) complex. The calculation exhibited that two types of hydrogen bonds are formed between the Curdlan and the poly(C); the third nitrogen (N3) in cytosine forms a hydrogen bond with the second OH of one Curdlan chain, and the proton of N4 is interacting with the O2 of another Curdlan chain. In our model, the helix diameter of poly(C) is expanded from 11.0 to 15.3 A upon complexation. Despite such large conformational changes, the 6(1) helix structure of poly(C) was maintained even after the complexation. This fact is complementary to the experimental fact that the complexation does not change the band shape of the circular dichroism of poly(C). The chain length dependence of the reaction enthalpy indicated that the complexation becomes thermodynamically more favorable with the chain length increasing. This feature is also consistent with the experimental data. PMID:15877376

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

    PubMed

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

    2010-11-15

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

  17. Argument Diagramming: The Araucaria Project

    NASA Astrophysics Data System (ADS)

    Rowe, Glenn; Reed, Chris

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

  18. Faceting diagram for sticky steps

    NASA Astrophysics Data System (ADS)

    Akutsu, Noriko

    2016-03-01

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

  19. Box diagram in Yukawa theory

    SciTech Connect

    Bakker, Bernard L. G.; Boomsma, Jorn K.; Ji, Chueng-Ryong

    2007-03-15

    We present a light-front calculation of the box diagram in Yukawa theory. The covariant box diagram is finite for the case of spin-1/2 constituents exchanging spin-0 particles. In light-front dynamics, however, individual time-ordered diagrams are divergent. We analyze the corresponding light-front singularities and show the equivalence between the light-front and covariant results by taming the singularities.

  20. Program Synthesizes UML Sequence Diagrams

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

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

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

    PubMed

    Sutter, Kiplangat; Autschbach, Jochen

    2012-08-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  3. Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. III. Comparison with Born-Oppenheimer dynamics

    NASA Astrophysics Data System (ADS)

    Schlegel, H. Bernhard; Iyengar, Srinivasan S.; Li, Xiaosong; Millam, John M.; Voth, Gregory A.; Scuseria, Gustavo E.; Frisch, Michael J.

    2002-11-01

    In a recently developed approach to ab initio molecular dynamics (ADMP), we used an extended Lagrangian to propagate the density matrix in a basis of atom centered Gaussian functions. Results of trajectory calculations obtained by this method are compared with the Born-Oppenheimer approach (BO), in which the density is converged at each step rather than propagated. For NaCl, the vibrational frequency with ADMP is found to be independent of the fictitious electronic mass and to be equal to the BO trajectory result. For the photodissociation of formaldehyde, H2CO[right arrow]H2+CO, and the three body dissociation of glyoxal, C2H2O2[right arrow]H2+2CO, very good agreement is found between the Born-Oppenheimer trajectories and the extended Lagrangian approach in terms of the rotational and vibrational energy distributions of the products. A 1.2 ps simulation of the dynamics of chloride ion in a cluster of 25 water molecules was used as a third test case. The Fourier transform of the velocity-velocity autocorrelation function showed the expected features in the vibrational spectrum corresponding to strong hydrogen bonding in the cluster. A redshift of approximately 200 cm-1 was observed in the hydroxyl stretch due to the presence of the chloride ion. Energy conservation and adiabaticity were maintained very well in all of the test cases.

  4. Preparation and Characterization of [pi]-Stacking Quinodimethane Oligothiophenes. Predicting Semiconductor Behavior and Bandwidths from Crystal Structures and Molecular Orbital Calculations

    SciTech Connect

    Janzen, Daron E.; Burand, Michael W.; Ewbank, Paul C.; Pappenfus, Ted M.; Higuchi, Hiroyuki; da Silva, Demetrio A.; Young, Victor G.; Bredas, Jean-Luc; Mann, Kent R.

    2010-11-16

    A series of new quinodimethane-substituted terthiophene and quaterthiophene oligomers has been investigated for comparison with a previously studied quinoid oligothiophene that has demonstrated high mobilities and ambipolar transport behavior in thin-film transistor devices. Each new quinoidal thiophene derivative shows a reversible one-electron oxidation between 0.85 and 1.32 V, a quasi-reversible one-electron second oxidation between 1.37 and 1.96 V, and a reversible two-electron reduction between -0.05 and -0.23 V. The solution UV-vis-NIR spectrum of each compound is dominated by an intense epsilon congruent with 100,000 M{sup -1} cm{sup -1} low energy pi-pi transition that has a lambda(max) ranging between 648 and 790 nm. All X-ray crystal structures exhibit very planar quinoidal backbones and short intermolecular pi-stacking distances (3.335-3.492 A). Structures exhibit a single pi-stacking distance with parallel cofacial stacking (sulfur atoms of equivalent rings pointed in the same direction) or with alternating distances and antiparallel cofacial stacking (sulfur atoms of equivalent rings pointed in the opposite direction). Examples of the layered and herringbone-packing motifs are observed for both the parallel and the antiparallel cofacial stacking. Analysis of the X-ray structures and molecular orbital calculations indicates that all of these compounds have one-dimensional electronic band structures as a result of the pi-stacking. For structures with a unique pi-stacking distance, a simple geometric overlap parameter calculated from the shape of the molecule and the slip from perfect registry in the pi-stack correlates well with the transfer integrals (t) calculated using molecular orbital theory. The calculated valence (633 meV) and conduction (834 meV) bandwidths for a quinoid quaterthiophene structure are similar to those calculated for the benchmark pentacene and indicate that both hole and electron mobilities could be significant.

  5. The Orbital Acceleration Research Experiment

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  7. Potential-pH Diagrams.

    ERIC Educational Resources Information Center

    Barnum, Dennis W.

    1982-01-01

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

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

    PubMed

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

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-11-11

    The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. PMID:24858354

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  13. 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

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

    2008-08-14

    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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

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

    PubMed

    Tang, Shanshan; Zhang, Jingping

    2012-06-01

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

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

    PubMed

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

    2014-10-15

    The methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate (C11H11N3O2) has been studied by theoretically methods. The structure of this compound is optimized by density functional theory (DFT), the second-order Mller-Plesset perturbation theory (MP2) and G3 theory (G3(MP2)) levels. Our calculation results are in very good agreement with experimental values. Compared to a perfect pentagonal structure, the geometrical structures of C11H11N3O2 show a little distortion of 1,2,3-triazole ring due to the highly electronegativity of substitution groups. In addition, dipole moment and frontier molecular orbitals (FMOs) of the C11H11N3O2 are calculated as well. Because of solvent effect, the HOMO-LUMO energy gap in methanol is predicted to be smaller than in gas phase by 0.367eV. The simulated UV-vis spectra are investigated by time-dependent density functional theory (TD-DFT), and two obviously absorption features have been predicted. These two absorption features are located between 170nm and 210nm, which is in ultraviolet C range. Moreover, the UV absorption features in methanol are predicted to be more intense than in gas phase; besides, the red shift is predicted in methanol as well. PMID:24835928

  17. Ab initio molecular orbital study of the molecular and electronic structure of FeCH + 2 and of the reaction mechanism of FeCH + 2+H2

    NASA Astrophysics Data System (ADS)

    Musaev, Djamaladdin G.; Morokuma, Keiji

    1994-12-01

    Both complete active space self-consistent field (CASSCF) and internally contracted single and double configuration interaction from the CASSCF reference functions (MR-SDCI-CASSCF) methods have been used to study the molecular and electronic structures of FeCH+2, as well as the mechanism for the reaction FeCH+2+H2. Three quartet electronic states of FeCH+2 are very low-lying; the ground state is a nearly degenerate pair (4B2 and 4B1), with the 4A2 state only 1-2 kcal/mol higher in energy. The lowest doublet states are about 25-35 kcal/mol higher. The binding energy of FeCH+2(4B2), relative to the dissociation limit Fe+(6D,s1d6)+CH2(3B1), is estimated to be 68 kcal/mol. In the first step of reaction FeCH+2+H2, the reactants yield an ion-molecule complex, (H2)FeCH+2, stabilized by about 6 kcal/mol. Subsequently, the H-H bond is activated, leading to a four-center transition state with an energy barrier of about 24 and 14 kcal/mol for the ground 4A` and excited 2A' states of the reactants. This step is calculated to be the rate-determining for the entire reaction, and therefore the doublet excited state of FeCH+2 is expected to be more reactive than the ground state because of the lower barrier. The resultant HFeCH+3 complex is predicted to be a minimum at the CASSCF level, but at the highest MR-SDCI-CASSCF level this minimum disappears. Thus, following the H-H bond cleavage, an FeCH+4 ion-molecule complex is directly formed. The ground state of the FeCH+4 complex is the sextet 6A2 state, which is stable relative to the ground state dissociation Fe+(6D,s1d6)+CH4 by 16 kcal/mol. The entire FeCH+2 hydrogenolysis reaction FeCH+2(4B2)+H2?Fe+(6D,s1d6)+CH4 (1) is estimated to be exothermic by 29 kcal/mol. The channels leading to formation of FeH++CH3 (2) and FeCH+3+H (3) are thermodynamically almost neutral. The reverse reaction Fe++CH4 for 6D, 4F or 2G states of Fe+ gives only one product, the ion-molecule complex FeCH+4 at moderate temperatures. An increase in the available kinetic energy for 6D and 4F states would make it possible to form dissociation products, FeH++CH3 and FeCH+3+H. Though the channel leading to FeCH+2+H2 is thermodynamically as easy as (2) and (3), a large barrier prevents it from taking place.

  18. Frontier orbital engineering of photo-hydrogen-evolving molecular devices: a clear relationship between the H2-evolving activity and the energy level of the LUMO.

    PubMed

    Masaoka, Shigeyuki; Mukawa, Yuichiro; Sakai, Ken

    2010-07-01

    Two new Ru(II)Pt(II) dimers, [Ru(bpy)(2)(mu-L2)PtCl(2)](2+) (5) and [Ru(bpy)(2)(mu-L3)PtCl(2)](2+) (6), were synthesized and characterized, and their electrochemical and spectroscopic properties together with their photo-hydrogen-evolving activities were evaluated (bpy = 2,2'-bypridine; L2 = 4'-[1,10]phenanthrolin-5-ylcarbamoyl)-[2,2']bipyridinyl-4-carboxylic acid ethyl ester; L3 = 4'-methyl-[2,2']bipyridinyl-4-carboxylic acid [1,10]phenanthrolin-5-ylamide). The structures of 5 and 6 are basically identical with that of the first active model of a photo-hydrogen-evolving molecular device developed in our group, [Ru(bpy)(2)(mu-L1)PtCl(2)](2+) (4) (L1 = 4'-([1,10]phenanthrolin-5-ylcarbamoyl)-[2,2']bipyridinyl-4-carboxylic acid), except for the difference in the substituent group at the 4-position of the bpy moiety bound to Pt(II) (-COOH for 4; -COOEt for 5; -CH(3) for 6). Electrochemical studies revealed that the first reduction potential of 5 (E(1/2) = -1.23 V) is nearly consistent with that of 4 (E(1/2) = -1.20 V) but is more positive than that of 6 (E(1/2) = -1.39 V), where the first reduction is associated with the reduction of the bpy moiety bound to Pt(II), consistent with a general tendency that the first reduction of bpy shows an anodic shift upon introduction of electron-withdrawing group. Density functional theory (DFT) calculations for 5 and 6 also show that the lowest unoccupied molecular orbital (LUMO) corresponds to the pi* orbital of the bpy moiety bound to Pt(II) for all the Ru(II)Pt(II) dimers, and the energy level of the LUMO of 6 is destabilized compared with those of 4 and 5, consistent with the results of the electrochemical studies. The photochemical hydrogen evolution from water driven by 4-6 in the presence a sacrificial electron donor (EDTA) was investigated. 5 was found to be active as an H(2)-evolving catalyst, while 6 shows no activity at all. However, 6 was found to drive photochemical H(2) evolution in the presence of both EDTA and methyl viologen (N,N'-dimethyl-4,4'-bipyridinium, MV(2+)), indicating that the (3)MLCT excited state of the Ru(bpy)(2)(phen)(2+) moiety is once oxidatively quenched by MV(2+) to give MV(+) and then hydrogen evolution from water by MV(+*) proceeds as a dark reaction. Emission decays and transient absorption spectra also show that the intramolecular electron transfer (IET) is accelerated in the active Ru(II)Pt(II) dimers 4 and 5, while such acceleration is not realized for the inactive Ru(II)Pt(II) dimer 6. The driving forces (DeltaG degrees(ET)) for the IET processes are estimated to be -0.16 eV for 4, -0.09 eV for 5 and 0.03 eV for 6, indicating that the IET process in 6 is uphill. It is concluded that efficient IET is required to drive the photochemical H(2) evolution from water with these Ru(II)Pt(II)-based molecular devices. PMID:20502844

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

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.

    2015-02-01

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

  20. Scattering equations and Feynman diagrams

    NASA Astrophysics Data System (ADS)

    Baadsgaard, Christian; Bjerrum-Bohr, N. E. J.; Bourjaily, Jacob L.; Damgaard, Poul H.

    2015-09-01

    We show a direct matching between individual Feynman diagrams and integration measures in the scattering equation formalism of Cachazo, He and Yuan. The connection is most easily explained in terms of triangular graphs associated with planar Feynman diagrams in ? 3-theory. We also discuss the generalization to general scalar field theories with ? p interactions, corresponding to polygonal graphs involving vertices of order p. Finally, we describe how the same graph-theoretic language can be used to provide the precise link between individual Feynman diagrams and string theory integrands.

  1. Particles, Feynman Diagrams and All That

    ERIC Educational Resources Information Center

    Daniel, Michael

    2006-01-01

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

  2. Atemporal diagrams for quantum circuits

    SciTech Connect

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

    2006-05-15

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

  3. Phase diagrams of decomposing nanoalloys

    NASA Astrophysics Data System (ADS)

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

    2004-02-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

    Zhang, Huaiyu; Danovich, David; Wu, Wei; Brada, Benot; Hiberty, Philippe C; Shaik, Sason

    2014-06-10

    The charge-shift bonding (CSB) concept was originally discovered through valence bond (VB) calculations. Later, CSB was found to have signatures in atoms-in-molecules and electron-localization-function and in experimental electron density measurements. However, the CSB concept has never been derived from a molecular orbital (MO)-based theory. We now provide a proof of principle that an MO-based approach enables one to derive the CSB family alongside the distinctly different classical family of covalent bonds. In this bridging energy decomposition analysis, the covalent-ionic resonance energy, RECS, of a bond is extracted by cloning an MO-based purely covalent reference state, which is a constrained two-configuration wave function. The energy gap between this reference state and the variational TCSCF ground state yields numerical values for RECS, which correlate with the values obtained at the VBSCF level. This simple MO-based method, which only takes care of static electron correlation, is already sufficient for distinguishing the classical covalent or polar-covalent bonds from charge-shift bonds. The equivalence of the VB and MO-based methods is further demonstrated when both methods are augmented by dynamic correlation. Thus, it is shown from both MO and VB perspectives that the bonding in the CSB family does not arise from electron correlation. Considering that the existence of the CSB family is associated also with quite a few experimental observations that we already reviewed ( Shaik , S. , Danovich , D. , Wu , W. , and Hiberty , P. C. Nat. Chem. , 2009 , 1 , 443 - 449 ), the new bonding concept has passed by now two stringent tests. This derivation, on the one hand, supports the new concept and on the other, it creates bridges between the two main theories of electronic structure. PMID:26580761

  6. Chapter 4 Novel Theoretical Prediction Method of the Haldane Gap among the Azido-Bridged Compounds by DV-X[alpha] Molecular Orbital Calculation

    NASA Astrophysics Data System (ADS)

    Ishii, Tomohiko; Fuke, Yukikazu; Aizawa, Naoko; Yamashita, Masahiro

    The electronic structures of the Haldane gap compounds that include NiII ions having s=1 spin are reported. The azido-bridged Haldane gap compounds, such as NINAZ ([Ni(NH2(CH2)3NH2)2N3]ClO4), NDMAZ ([Ni(NH2CH2C(CH3)2CH2NH2)2N3]ClO4), and NDMAP ([Ni(NH2CH2C(CH3)2 CH2NH2)2N3]PF6) have been synthesized by substituting different in-plane ligands and counteranions. The most powerful advantage of the metal complex based Haldane gap compounds is to control the antiferromagnetic interaction by changing the combination of the counteranions and the in-plane and the bridging ligands. After carrying out a high-precision X-ray structural analysis of NINAZ, the differences of the molecular structures and the electronic structures among these three azido-bridged Haldane gap compounds can be compared in order to clarify the mechanism of the energy difference between the singlet ground state and the triplet excited state. From the result of the energy difference between the singlet and the triplet states using the DV-X[alpha] calculation method, we have observed a trend that the compound having a large Haldane gap energy, such a NINAZ, has a large energy difference between two spin states, implying the larger energy difference should be the harder spin inversion from anti-parallel singlet to the parallel triplet state. Our previous manifestation of the way to predict the value of the Haldane gap by using the analysis of the bond overlap population by means of a DV-X[alpha] molecular orbital calculation was not so suitable for general Haldane gap compounds including the NO2-bridged one-dimensional (1D) chain structure compounds. Therefore in this study the novel way using the analysis of the energy level structures should be reported.

  7. Orbiter Autoland reliability analysis

    NASA Technical Reports Server (NTRS)

    Welch, D. Phillip

    1993-01-01

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

  8. The Hot Orbit: Orbital Cellulitis

    PubMed Central

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

    2012-01-01

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

  9. Energy Tracking Diagrams

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  10. Orbital cellulitis

    MedlinePLUS

    ... be needed to drain the abscess , or relieve pressure in the space around the eye. An orbital cellulitis infection can get worse very quickly. A person with this condition must be checked every few hours.

  11. Orbiter's Skeleton

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The structure of NASA's Mars Reconnaissance Orbiter spacecraft is constructed from composite panels of carbon layers over aluminum honeycomb, lightweight yet strong. This forms a basic structure or skeleton on which the instruments, electronics, propulsion and power systems can be mounted. The propellant tank is contained in the center of the orbiter's structure. This photo was taken at Lockheed Martin Space Systems, Denver, during construction of the spacecraft.

  12. Automatically Assessing Graph-Based Diagrams

    ERIC Educational Resources Information Center

    Thomas, Pete; Smith, Neil; Waugh, Kevin

    2008-01-01

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

  13. Automatically Assessing Graph-Based Diagrams

    ERIC Educational Resources Information Center

    Thomas, Pete; Smith, Neil; Waugh, Kevin

    2008-01-01

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

  14. Matched designs and causal diagrams

    PubMed Central

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

    2013-01-01

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

  15. The Lenz Vector and Orbital Analog Computers

    ERIC Educational Resources Information Center

    Harter, W. G.

    1976-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1985-01-01

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

  17. The Quasar SED Mixing Diagram

    NASA Astrophysics Data System (ADS)

    Hao, Heng; Elvis, M.; Civano, F.

    2011-05-01

    We present a useful new diagram for characterizing the quasar-host-reddening mixture for AGN SEDs. This "mixing diagram" is based on a detailed study of 413 X-ray selected Type 1 AGN SEDs from the XMM-COSMOS Survey (Elvis, Hao, et al., 2011). The mixing diagram plots the near-IR (1-3micron) spectral slope against the optical (0.3-1micron) slope to form a generalized 'color-color' diagram. A pure AGN continuum (Elvis et al., 1994, E94) and pure host galaxies are located at clear and distinct positions on the mixing diagram. The lines joining them indicate the fraction of host contribution to each AGN. The reddening vector is almost perpendicular to these mixing lines, and so is easily measured independently. The mixing diagram shows that 90% of the AGNs lie on mixing curves between the mean E94 AGN SED and a host galaxy, with only modest reddening [E(B-V)=0.1-0.2] (Hao et al., 2011a). Lower luminosity and lower Eddington ratio AGNs have a larger host galaxy fraction, as expected. Optically selected samples (SDSS) have smaller host galaxy fractions. There is some intrinsic scatter around the E94 mean SED. A substantial minority, 10%, of the XMM-COSMOS AGNs are inconsistent with any AGN+host+reddening mix. These AGNs have weak or non-existent near-IR bumps, suggesting a lack of the hot dust characteristic of AGNs (Hao et al., 2010). A similar fraction of these "hot dust poor" (HDP) quasars are found in the Elvis et al. 1994 (BQS) and Richards et al. 2006 (SDSS) samples (Hao et al., 2011b). The fraction of "hot dust poor" AGNs grows to 20% at z>2 (Hao et al. 2010). The proposed 'cosmic cycle' of SMBH and galaxy co-evolution (e.g. Hopkins et al., 2006) can be shown as tracks on the mixing diagram. The mixing diagram definition could also be expanded to other wavelengths.

  18. Voronoi Diagrams and Spring Rain

    ERIC Educational Resources Information Center

    Perham, Arnold E.; Perham, Faustine L.

    2011-01-01

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

  19. Voronoi Diagrams and Spring Rain

    ERIC Educational Resources Information Center

    Perham, Arnold E.; Perham, Faustine L.

    2011-01-01

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

  20. [Orbital exenteration].

    PubMed

    Mouriaux, F; Barraco, P; Patentre, P; Pellerin, P

    2001-10-01

    Exenteration of the orbit is a disfiguring and destructive procedure that is usually reserved for treatment of life-threatening orbital malignancy when a less radical operation such as local surgery, chemotherapy, or irradiation are deemed inadequate or have failed. Many methods have been published for managing the socket, but of primary importance is the need to remove all diseased tissue prior to considering any reconstructive efforts. Options include spontaneous granulation, skin grafting, or muscle flaps. This article will describe the development and the indications for this procedure and will outline the surgical techniques and its complications, the various reconstructive efforts, and survival. The success of orbital exenteration depends on recurrence, histological type, tumor size, and tumor-free margins. PMID:11894540

  1. A frontier orbital study with ab initio molecular dynamics of the effects of solvation on chemical reactivity: solvent-induced orbital control in FeO-activated hydroxylation reactions.

    PubMed

    Bernasconi, Leonardo; Baerends, Evert Jan

    2013-06-19

    Solvation effects on chemical reactivity are often rationalized using electrostatic considerations: the reduced stabilization of the transition state results in higher reaction barriers and lower reactivity in solution. We demonstrate that the effect of solvation on the relative energies of the frontier orbitals is equally important and may even reverse the trend expected from purely electrostatic arguments. We consider the H abstraction reaction from methane by quintet [EDTAH(n)FeO]((n-2)+), (n = 0-4) complexes in the gas phase and in aqueous solution, which we examine using ab initio thermodynamic integration. The variation of the charge of the complex with the protonation of the EDTA ligand reveals that the free energy barrier in gas phase increases with the negative charge, varying from 16 kJ mol(-1) for [EDTAH4FeO](2+) to 57 kJ mol(-1) for [EDTAHnFeO](2-). In aqueous solution, the barrier for the +2 complex (38 kJ mol(-1)) is higher than in gas phase, as predicted by purely electrostatic arguments. For the negative complexes, however, the barrier is lower than in gas phase (e.g., 45 kJ mol(-1) for the -2 complex). We explain this increase in reactivity in terms of a stabilization of the virtual 3?* orbital of FeO(2+), which acts as the dominant electron acceptor in the H-atom transfer from CH4. This stabilization originates from the dielectric screening caused by the reorientation of the water dipoles in the first solvation shell of the charged solute, which stabilizes the acceptor orbital energy for the -2 complex sufficiently to outweigh the unfavorable electrostatic destabilization of the transition-state relative to the reactants in solution. PMID:23634772

  2. Molecular orbital (SCF-Xα-SW) theory of metal-metal charge transfer processes in minerals - II. Application to Fe2+ --> Ti4+ charge transfer transitions in oxides and silicates

    USGS Publications Warehouse

    Sherman, David M.

    1987-01-01

    A molecular orbital description, based on Xα-Scattered wave calculations on a (FeTiO10)14− cluster, is given for Fe2+ → Ti4+ charge transfer transitions in minerals. The calculated energy for the lowest Fe2+ → Ti4+ metal-metal charge transfer transition is 18040 cm−1 in reasonable agreement with energies observed in the optical spectra of Fe-Ti oxides and silicates. As in the case of Fe2+ → Fe3+ charge transfer in mixed-valence iron oxides and silicates, Fe2+ → Ti4+ charge transfer is associated with Fe-Ti bonding across shared polyhedral edges. Such bonding results from the overlap of the Fe(t 2g ) and Ti(t 2g ) 3d orbitals.

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

    PubMed

    Zarycz, M Natalia C; Provasi, Patricio F

    2015-02-01

    The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons. PMID:25266873

  4. Orbital Debris

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    Earth orbital debris issues and recommended future activities are discussed. The workshop addressed the areas of environment definition, hazards to spacecraft, and space object management. It concluded that orbital debris is a potential problem for future space operations. However, before recommending any major efforts to control the environment, more data are required. The most significant required data are on the population of debris smaller than 4 cm in diameter. New damage criteria are also required. When these data are obtained, they can be combined with hypervelocity data to evaluate the hazards to future spacecraft. After these hazards are understood, then techniques to control the environment can be evaluated.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed

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

    2015-06-01

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

  7. The Phase Diagram of Superionic Ice

    NASA Astrophysics Data System (ADS)

    Sun, Jiming; Clark, Bryan; Car, Roberto

    2014-03-01

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

  8. Nuclear orbiting

    SciTech Connect

    Shapira, D.

    1988-01-01

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

  9. Orbital Mechanics.

    ERIC Educational Resources Information Center

    Dalton, Joel B.

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

  10. The role of orbital dynamics and cloud-cloud collisions in the formation of giant molecular clouds in global spiral structures

    NASA Technical Reports Server (NTRS)

    Roberts, William W., Jr.; Stewart, Glen R.

    1987-01-01

    The role of orbit crowding and cloud-cloud collisions in the formation of GMCs and their organization in global spiral structure is investigated. Both N-body simulations of the cloud system and a detailed analysis of individual particle orbits are used to develop a conceptual understanding of how individual clouds participate in the collective density response. Detailed comparisons are made between a representative cloud-particle simulation in which the cloud particles collide inelastically with one another and give birth to and subsequently interact with young star associations and stripped down simulations in which the cloud particles are allowed to follow ballistic orbits in the absence of cloud-cloud collisions or any star formation processes. Orbit crowding is then related to the behavior of individual particle trajectories in the galactic potential field. The conceptual picture of how GMCs are formed in the clumpy ISMs of spiral galaxies is formulated, and the results are compared in detail with those published by other authors.

  11. Spectral Determinants on Mandelstam Diagrams

    NASA Astrophysics Data System (ADS)

    Hillairet, Luc; Kalvin, Victor; Kokotov, Alexey

    2015-11-01

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

  12. Reliability computation from reliability block diagrams

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

    Computer program computes system reliability for very general class of reliability block diagrams. Four factors are considered in calculating probability of system success: active block redundancy, standby block redundancy, partial redundancy, and presence of equivalent blocks in the diagram.

  13. Causal diagrams in systems epidemiology

    PubMed Central

    2012-01-01

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

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

    PubMed

    Muthu, S; Renuga, S

    2014-01-24

    FT-IR and FT-Raman spectra of 5-{1-hydroxy-2-[(propan-2-yl) amino] ethyl} benzene-1,3-diol (abbrevi- 54 ated as HPAEBD) were recorded in the region 4000-450 cm(-1) and 4000-100 cm(-1) respectively. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (B3LYP) and HF method with 6-31 G(d,p) as basis set. The theoretical wave numbers were scaled and compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated Potential energy distribution (PED). Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the ? antibonding orbitals and E (2) energies confirm the occurrence of intra molecular charge transfer (ICT) within the molecule. The molecule orbital contributions were studied by using the total (TDOS), sum of ? and ? electron (??DOS) density of States. Mulliken population analysis of atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in this compound. On the basis of vibrational analyses, the thermodynamic properties of title compound at different temperatures have been calculated. PMID:24096064

  15. Arrows in Comprehending and Producing Mechanical Diagrams

    ERIC Educational Resources Information Center

    Heiser, Julie; Tversky, Barbara

    2006-01-01

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

  16. Arrows in Comprehending and Producing Mechanical Diagrams

    ERIC Educational Resources Information Center

    Heiser, Julie; Tversky, Barbara

    2006-01-01

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

  17. Eye and orbit ultrasound

    MedlinePLUS

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

  18. Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

    PubMed

    Szostak, Roman; Aub, Jeffrey; Szostak, Michal

    2015-08-21

    Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C?O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides. PMID:26154179

  19. Understanding machines from text and diagrams

    NASA Astrophysics Data System (ADS)

    Hegarty, Mary; Just, Marcel A.

    1987-12-01

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

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

    ERIC Educational Resources Information Center

    Py, Dominique; Auxepaules, Ludovic; Alonso, Mathilde

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Py, Dominique; Auxepaules, Ludovic; Alonso, Mathilde

    2013-01-01

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

  2. Payload/orbiter contamination control requirement study

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  3. Thermodynamic phase diagram of the quantum hall skyrmion system

    PubMed

    Moon; Mullen

    2000-01-31

    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

  4. Origin and use of crystallization phase diagrams.

    PubMed

    Rupp, Bernhard

    2015-03-01

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

  5. Orbit analysis

    SciTech Connect

    Michelotti, L.

    1995-01-01

    The past fifteen years have witnessed a remarkable development of methods for analyzing single particle orbit dynamics in accelerators. Unlike their more classic counterparts, which act upon differential equations, these methods proceed by manipulating Poincare maps directly. This attribute makes them well matched for studying accelerators whose physics is most naturally modelled in terms of maps, an observation that has been championed most vigorously by Forest. In the following sections the author sketchs a little background, explains some of the physics underlying these techniques, and discusses the best computing strategy for implementing them in conjunction with modeling accelerators.

  6. Voronoi Diagrams Without Bounding Boxes

    NASA Astrophysics Data System (ADS)

    Sang, E. T. K.

    2015-10-01

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

  7. A Hubble Diagram for Quasars

    NASA Astrophysics Data System (ADS)

    Risaliti, Guido; Lusso, Elisabeta

    2015-09-01

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

  8. Risk Mitigation for Managing On-Orbit Anomalies

    NASA Technical Reports Server (NTRS)

    La, Jim

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

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

    SciTech Connect

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

    2008-10-31

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

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

    NASA Astrophysics Data System (ADS)

    Işık, N.; Doğan, M.; Bahçeli, S.

    2016-03-01

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

  12. Magnetized effective QCD phase diagram

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    PubMed

    Gaudin, Karen; Chaminade, Pierre; Baillet, Arlette

    2002-10-11

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

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

    SciTech Connect

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

    2011-11-15

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

  15. Orbital Winch

    NASA Technical Reports Server (NTRS)

    Hoyt, Robert (Inventor); Slostad, Jeffrey T. (Inventor); Frank, Scott (Inventor); Barnes, Ian M. (Inventor)

    2016-01-01

    Orbital winch having: lower and upper frames; spool having upper and lower flanges with lower flange attached to lower frame; axial tether guide mounted to upper frame; secondary slewing ring coaxial with spool and rotatably mounted to upper frame, wherein secondary slewing ring's outer surface has gearing; upper tether guide mounted to inner surface of secondary slewing ring; linear translation means having upper end mounted to upper frame and lower end mounted on lower frame; primary slewing ring rotatably mounted within linear translation means allowing translation axially between flanges, wherein primary slewing ring's outer surface has gearing; lower tether guide mounted on primary slewing ring's inner surface; pinion rod having upper end mounted to upper frame and lower end mounted to lower frame, wherein pinion rod's teeth engage primary and secondary slewing rings' outer surface teeth; and tether passing through axial, upper, and lower tether guides and winding around spool.

  16. Small orbits

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    NASA Technical Reports Server (NTRS)

    1975-01-01

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

  18. Magnetic and orbital order in overdoped bilayer manganites

    NASA Astrophysics Data System (ADS)

    Maitra, Tulika; Taraphder, A.

    2004-01-01

    The magnetic and orbital orders for the bilayer manganites in the doping region 0.5 < x < 1.0 have been investigated from a model that incorporates the two eg orbitals at each Mn site, the inter-orbital Coulomb interaction and lattice distortions. The usual double exchange operates via the eg orbitals. It is shown that such a model reproduces much of the phase diagram recently obtained for the bilayer systems in this range of doping. The C-type phase with (?,0,?) spin order seen by Ling et al. appears as a natural consequence of the layered geometry and is stabilised by the static distortions of the system. The orbital order is shown to drive the magnetic order while the anisotropic hopping across the eg orbitals, the layered nature of the underlying structure and the associated static distortions largely determine the orbital arrangements.

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

    SciTech Connect

    Iskin, M.; Subasi, A. L.

    2011-10-15

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

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

    SciTech Connect

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

    2015-04-14

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

  1. Phase diagram of ammonium nitrate

    NASA Astrophysics Data System (ADS)

    Dunuwille, M.; Yoo, C. S.

    2014-05-01

    Ammonium Nitrate (AN) has often subjected to uses in improvised explosive devices, due to its wide availability as a fertilizer and its capability of becoming explosive with slight additions of organic and inorganic compounds. Yet, the origin of enhanced energetic properties of impure AN (or AN mixtures) is neither chemically unique nor well understood -resulting in rather catastrophic disasters in the past1 and thereby a significant burden on safety in using ammonium nitrates even today. To remedy this situation, we have carried out an extensive study to investigate the phase stability of AN at high pressure and temperature, using diamond anvil cells and micro-Raman spectroscopy. The present results confirm the recently proposed phase IV-to-IV' transition above 17 GPa2 and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400 C.

  2. A Regime Diagram for Subduction

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  3. Hubble's diagram and cosmic expansion

    PubMed Central

    Kirshner, Robert P.

    2004-01-01

    Edwin Hubble's classic article on the expanding universe appeared in PNAS in 1929 [Hubble, E. P. (1929) Proc. Natl. Acad. Sci. USA 15, 168173]. 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

  4. 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)

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

    2012-10-01

    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.

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

    SciTech Connect

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

    2011-03-07

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

  6. 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

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

    2014-02-15

    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

  7. Satake diagrams of affine Kac Moody algebras

    NASA Astrophysics Data System (ADS)

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

    2006-02-01

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

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

    NASA Technical Reports Server (NTRS)

    Davis, Philip A.; Spudis, Paul D.

    1987-01-01

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

  9. Pressure-temperature phase diagrams of biomolecules.

    PubMed

    Smeller, Lszl

    2002-03-25

    The pressure-temperature phase diagram of various biomolecules is reviewed. Special attention is focused on the elliptic phase diagram of proteins. The phenomenological thermodynamic theory describing this diagram explains the heat, cold and pressure denaturations in a unified picture. The limitations and possible developments of this theory are discussed as well. It is pointed out that a more complex diagram can be obtained when the intermolecular interactions are also taken into account. In this case metastable states appear on the pressure-temperature (p-T) diagram due to intermolecular interactions. Pressure-temperature phase diagrams of other biopolymers are also discussed. While the p-T diagrams of helix-coil transition of nucleic acids and of gel-liquid crystal transition of lipid bilayers are non-elliptical, those of gelatinization of starch and of phase separation of some synthetic polymers show an elliptic profile, similar to that of proteins. Finally, the p-T diagram of bacterial inactivation is shown to be elliptic. From the point of view of basic science, this fact shows that the key factor of inactivation should be the protein type, and from the viewpoint of practical applications, it serves as the theoretical basis of pressure treatment of biosystems. PMID:11983384

  10. Vesicle deformation by microtubules: A phase diagram

    NASA Astrophysics Data System (ADS)

    Emsellem, Virginie; Cardoso, Olivier; Tabeling, Patrick

    1998-10-01

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

  11. Learning from Diagrams: Theoretical and Instructional Considerations.

    ERIC Educational Resources Information Center

    Winn, William D.; Holliday, William G.

    The purpose of the eight studies reported in this paper was two-fold: to identify some of the relationships that exist between the unique properties of diagrams and various aspects of cognitive processes and learning, and, subsequently, to derive principles from these relationships that would direct the design and use of diagrams in the classroom.

  12. THE QCD PHASE DIAGRAM AT FINITE DENSITY.

    SciTech Connect

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

    2005-07-25

    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.

  13. Phase diagrams for surface alloys

    NASA Astrophysics Data System (ADS)

    Christensen, A.; Ruban, A. V.; Stoltze, P.; Jacobsen, K. W.; Skriver, H. L.; Nrskov, J. K.; Besenbacher, F.

    1997-09-01

    We discuss surface alloy phases and their stability based on surface phase diagrams constructed from the surface energy as a function of the surface composition. We show that in the simplest cases of pseudomorphic overlayers there are four generic classes of systems, characterized by the sign of the heat of segregation from the bulk and the sign of the excess interactions between the atoms in the surface (the surface mixing energy). We also consider the more complicated cases with ordered surface phases, nonpseudomorphic overlayers, second layer segregation, and multilayers. The discussion is based on density-functional calculations using the coherent-potential approximation and on effective-medium theory. We give self-consistent density-functional results for the segregation energy and surface mixing energy for all combinations of the transition and noble metals. Finally we discuss in detail the cases Ag/Cu(100), Pt/Cu(111), Ag/Pt(111), Co/Cu(111), Fe/Cu(111), and Pd/Cu(110) in connection with available experimental results.

  14. Phase Diagram of Ammonium Nitrate

    NASA Astrophysics Data System (ADS)

    Dunuwille, Mihindra; Yoo, Choong-Shik

    2013-06-01

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

  15. Phase diagram of ammonium nitrate

    SciTech Connect

    Dunuwille, Mihindra; Yoo, Choong-Shik

    2013-12-07

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

  16. Lattice QCD study of four-quark components of the isosinglet scalar mesons: Significance of disconnected diagrams

    NASA Astrophysics Data System (ADS)

    Wakayama, Masayuki; Kunihiro, Teiji; Muroya, Shin; Nakamura, Atsushi; Nonaka, Chiho; Sekiguchi, Motoo; Wada, Hiroaki; Scalar Collaboration

    2015-05-01

    We study the possible significance of four-quark states in the isosinglet scalar mesons (JP C=0++ , I =0 ) by performing two-flavor full lattice QCD simulations on an 8316 lattice using the improved gauge action and the clover-improved Wilson quark action. In particular, we evaluate the propagators of molecular and tetraquark operators together with singly disconnected diagrams. In the computation of the singly disconnected diagrams we employ the Z2-noise method with the truncated eigenmode approach. We show that the quark loops given by the disconnected diagrams play an essential role in propagators of tetraquark and molecular operators.

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

    PubMed

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

    2015-08-10

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

  18. Mission orbit design

    NASA Astrophysics Data System (ADS)

    Wu, An-Ming

    In this paper we first describe the relations between space mission and orbit design, and then introduce the basic properties of the orbit. Geopotential representation is used to illustrate the common used Earth orbits, including Sun-synchronous orbits and Molniya orbits. Perturbation concept is used to demonstrate the mission orbits of LISA, ASTROD, and SOHO. Finally, for the interplanetary orbit design, the numerical methods of two-point boundary-value problems, the applications of fly-past, and the considerations of optimization are discussed, and are utilized to preliminary design the mission orbit of ASTROD spacecraft to be launched in 2015.

  19. Theoretical analysis (NBO, NPA, Mulliken Population Method) and molecular orbital studies (hardness, chemical potential, electrophilicity and Fukui function analysis) of (E)-2-((4-hydroxy-2-methylphenylimino)methyl)-3-methoxyphenol

    NASA Astrophysics Data System (ADS)

    Demircioğlu, Zeynep; Kaştaş, Çiğdem Albayrak; Büyükgüngör, Orhan

    2015-07-01

    The molecular structure and spectroscopic properties of (E)-2-((4-hydroxy-2-methylphenylimino)methyl)-3-methoxyphenol, were characterized by X-ray diffraction, FT-IR and UV-Vis spectroscopy. All of theoretical calculations and optimized geometric parameters have been calculated by using density functional theory (DFT) with hybrid method B3LYP by 6-31G(d,p) basis set. The title compound of C15H15N1O3 have been analyzed according to electronic and energetics behaviors for enol-imine and keto-amine tautomers. Both these tautomers engender six-membered ring due to intramolecular hydrogen bonded interactions. Two types of intramolecular hydrogen bonds (a) strong O-H⋯N interactions in enol-imine form and (b) N-H⋯O interactions in keto-amine form are compared particularly. The theoretical vibrational frequencies have been found in good agreement with the corresponding experimental data. A study on the electronic and optical properties, absorption wavelengths, excitation energy, dipole moment, molecular electrostatic potential (MEP) and frontier molecular orbital energies are performed using DFT method. Additionally, geometry optimizations in solvent media were performed with the same level of theory by the polarizable continuum model (PCM). The effect of solvents on the tautomeric stability has been investigated. Mulliken Population Method and natural population analysis (NPA) have been studied. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. The local reactivity of the molecule has been studied using the Fukui function. NLO properties related to polarizability and hyperpolarizability are also discussed.

  20. Shuttle Orbiter Uplink Text and Graphics System

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  1. The amplituhedron from momentum twistor diagrams

    NASA Astrophysics Data System (ADS)

    Bai, Yuntao; He, Song

    2015-02-01

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

  2. Equations of state and phase diagrams of hydrogen isotopes

    NASA Astrophysics Data System (ADS)

    Urlin, V. D.

    2013-11-01

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

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

    PubMed

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

    2014-06-01

    We present a new, non-variational orbital-optimization scheme for the antisymmetric product of one-reference orbital geminal wave function. Our approach is motivated by the observation that an orbital-optimized seniority-zero configuration interaction (CI) expansion yields similar results to an orbital-optimized seniority-zero-plus-two CI expansion [L. Bytautas, T. M. Henderson, C. A. Jimenez-Hoyos, J. K. Ellis, and G. E. Scuseria, J. Chem. Phys. 135, 044119 (2011)]. A numerical analysis is performed for the C2 and LiF molecules, for the CH2 singlet diradical as well as for the symmetric stretching of hypothetical (linear) hydrogen chains. For these test cases, the proposed orbital-optimization protocol yields similar results to its variational orbital optimization counterpart, but prevents symmetry-breaking of molecular orbitals in most cases. PMID:24907997

  4. High pressure phase diagram of MgO

    NASA Astrophysics Data System (ADS)

    French, Martin; Cebulla, Daniel; Redmer, Ronald

    2015-06-01

    In order to improve the understanding of the interior of super-Earths (planets in the range of 1-10 Earth masses) and other exoplanets, ab inito calculations for the planetary materials and the equation of state (EOS) and phase diagram of planetary materials are needed. A typical representative is MgO, which is an abundant material in the Earth's mantle and is also expected to be important for the mantle of exoplanets as well as for the rocky cores of gas giants such as Jupiter. Using ab initio molecular dynamic simulations, we have determined the phase diagram for MgO up to 20000 K and 1.5 TPa. In particular, the transition from the solid to the molten salt has been studied using diffusion analyses and pair distribution functions. The transition from the B1 to the B2 structure in solid MgO is determined by calculating the respective free enthalpies. The phase diagram of MgO is constructed based on accurate EOS data. We compare with results from (decaying) shock and ramp compression experiments and theoretical calculations for the B1-B2 and the liquid-solid transition line.

  5. Phase diagram of a reentrant gel of patchy particles

    SciTech Connect

    Roldn-Vargas, Sndalo; Smallenburg, Frank; Sciortino, Francesco; Kob, Walter

    2013-12-28

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

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

    PubMed

    Zhu, X-Y

    2014-07-01

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

  7. Mining and integration of pathway diagrams from imaging data

    PubMed Central

    Kozhenkov, Sergey; Baitaluk, Michael

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2001-01-01

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

  9. Algorithmic Identification for Wings in Butterfly Diagrams.

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    ERIC Educational Resources Information Center

    Shubbar, Khalil E.

    2003-01-01

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

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

    ERIC Educational Resources Information Center

    Shubbar, Khalil E.

    2003-01-01

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

  12. Josephson current in carbon nanotubes with spin-orbit interaction.

    PubMed

    Lim, Jong Soo; Lpez, Rosa; Aguado, Ramn

    2011-11-01

    We demonstrate that curvature-induced spin-orbit coupling induces a 0-? transition in the Josephson current through a carbon nanotube quantum dot coupled to superconducting leads. In the noninteracting regime, the transition can be tuned by applying a parallel magnetic field near the critical field where orbital states become degenerate. Moreover, the interplay between charging and spin-orbit effects in the Coulomb blockade and cotunneling regimes leads to a rich phase diagram with well-defined (analytical) boundaries in parameter space. Finally, the 0 phase always prevails in the Kondo regime. Our calculations are relevant in view of recent experimental advances in transport through ultraclean carbon nanotubes. PMID:22181630

  13. A Hubble Diagram for Quasars

    NASA Astrophysics Data System (ADS)

    Risaliti, G.; Lusso, E.

    2015-12-01

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

  14. 75 FR 61512 - Outer Continental Shelf Official Protraction Diagrams

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-05

    ... Protraction Diagrams AGENCY: Bureau of Ocean Energy Management, Regulation and Enforcement, Interior. ACTION... Outer Continental Shelf Official Protraction Diagrams (OPDs) located within Atlantic Ocean areas, with... informational purposes only. Outer Continental Shelf Official Protraction Diagrams in the North Atlantic,...

  15. Veitch diagram plotter simplifies Boolean functions

    NASA Technical Reports Server (NTRS)

    Rubin, D. K.

    1964-01-01

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

  16. Some Geometric Aspects of the Ternary Diagram.

    ERIC Educational Resources Information Center

    Philip, G. M.; Watson, D. F.

    1989-01-01

    Uses the process of normalization in the Cartesian coordinate system which entails radial projection onto a transect to compare different compositions of minerals. Warns that the ternary diagram should not be used as a framework for calculations. (MVL)

  17. A Smart Thermal Block Diagram Tool

    NASA Technical Reports Server (NTRS)

    Tsuyuki, Glenn; Miyake, Robert; Dodge, Kyle

    2008-01-01

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

  18. A Phase Diagram for Solar Flares

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  19. An Improved Mnemonic Diagram for Thermodynamic Relationships.

    ERIC Educational Resources Information Center

    Rodriguez, Joaquin; Brainard, Alan J.

    1989-01-01

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

  20. Quantum quasicrystals and other exotic states of spin-orbit coupled dipolar bosons

    NASA Astrophysics Data System (ADS)

    Gopalakrishnan, Sarang; Wilson, Ryan; Anderson, Brandon; Lev, Benjamin; Clark, Charles; Martin, Ivar; Demler, Eugene

    2014-03-01

    We study dipolar Bose gases in which the bosons experience a Rashba spin-orbit coupling. We show that the degenerate dispersion minimum due to the spin-orbit coupling, combined with the long-range dipolar interaction, can stabilize a rich phase diagram including a number of exotic phases, such as a quantum quasicrystal (in the quasi-2D limit) and a meron state (in the 3D limit), as one tunes the strength of the dipolar interaction and the spin-orbit coupling. We discuss specific level schemes for exploring this phase diagram using ultracold dysprosium.

  1. Reliability computation from reliability block diagrams

    NASA Technical Reports Server (NTRS)

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

    1971-01-01

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

  2. A universal structured-design diagramer

    NASA Technical Reports Server (NTRS)

    1981-01-01

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

  3. An analysis of Newton's projectile diagram

    NASA Astrophysics Data System (ADS)

    Topper, D.; Vincent, D. E.

    1999-01-01

    Newton's famous mountain projectile diagram, reproduced in countless science books, is analysed in detail - mathematically, graphically, and historically - perhaps for the first time. A study of the relationship between this diagram from Newton's On the System of the World and the written texts on projectile motion in this book and in the Principia reveals an ambiguity in Newton's presentation. We propose an explanation of the ambiguity based on an exploration of its roots in Newton's thought.

  4. Lattice and Phase Diagram in QCD

    SciTech Connect

    Lombardo, Maria Paola

    2008-10-13

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

  5. Preliminary Study of Impulse-Momentum Diagrams

    NASA Astrophysics Data System (ADS)

    Rosengrant, David; Mzoughi, Taha

    2008-10-01

    In this paper we present a new representation to help students learn about momentum, impulse and conservation of momentum which we call an Impulse-Momentum Diagram. We include a description of this diagram as well as examples of how instructors can use them in the classroom. Next we present preliminary quantitative and qualitative data of a study we conducted where students used these representations. Our final analysis shows how students benefited from these representations.

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

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.

    2015-02-01

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

  7. Class diagram based evaluation of software performance

    NASA Astrophysics Data System (ADS)

    Pham, Huong V.; Nguyen, Binh N.

    2013-03-01

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

  8. Pressure-enthalpy diagrams for alternative refrigerants

    SciTech Connect

    Chen, J.; Kruse, H.

    1996-10-01

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

  9. Lunar Reconnaissance Orbiter Orbit Determination Accuracy Analysis

    NASA Technical Reports Server (NTRS)

    Slojkowski, Steven E.

    2014-01-01

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

  10. Transfer orbit determination accuracy for orbit maneuvers

    NASA Astrophysics Data System (ADS)

    Pinheiro, Mery Passos

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    SciTech Connect

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

    2014-08-15

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

  13. Orbital Models Made of Plastic Soda Bottles

    NASA Astrophysics Data System (ADS)

    Samoshin, Vyacheslav V.

    1998-08-01

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

  14. Non-planar on-shell diagrams

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Azadi, Sam; Foulkes, Matthew

    2015-03-01

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

  16. Superfluid helium on-orbit resupply

    NASA Technical Reports Server (NTRS)

    Eberhardt, Ralph N.; Gille, John P.

    1990-01-01

    The requirements for superfluid helium (SFHe) resupply were investigated, and the results were used to develop a conceptual design for a superfluid helium tanker (SFHT) which is designed to meet a 50-mission requirement. The SFHT design uses a conventional dewar approach with multiple vapor cooled shields, and a porous-plug phase separator for on-orbit temperature control. An open loop refrigeration approach is used for ground conversion of normal He to SFHe, allowing near-total fill of the supply tank. Design diagrams of the SFHT concept and of various SFHT subsystems are presented.

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

    ERIC Educational Resources Information Center

    Dimmel, Justin K.; Herbst, Patricio G.

    2015-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Dimmel, Justin K.; Herbst, Patricio G.

    2015-01-01

    Geometry diagrams use the visual features of specific drawn objects to convey meaning about generic mathematical entities. We examine the semiotic structure of these visual features in two parts. One, we conduct a semiotic inquiry to conceptualize geometry diagrams as mathematical texts that comprise choices from different semiotic systems. Two,…

  20. Students' Understanding of Diagrams for Solving Word Problems: A Framework for Assessing Diagram Proficiency

    ERIC Educational Resources Information Center

    Poch, Apryl L.; van Garderen, Delinda; Scheuermann, Amy M.

    2015-01-01

    A visual representation, such as a diagram, can be a powerful strategy for solving mathematical word problems. However, using a representation to solve mathematical word problems is not as simple as it seems! Many students with learning disabilities struggle to use a diagram effectively and efficiently. This article provides a framework for