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Sample records for molecular orbital energies

  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. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

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

  3. Imaging molecular orbitals using photoionization

    NASA Astrophysics Data System (ADS)

    Santra, Robin

    2006-10-01

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

  4. 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.

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

    SciTech Connect

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

    2015-11-15

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

  6. 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.

  7. 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...

  8. 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)

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

    PubMed

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

    2016-07-12

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

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

    PubMed

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

    2015-03-21

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

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

    PubMed

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

    2013-11-01

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

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

    SciTech Connect

    Thirman, Jonathan Head-Gordon, Martin

    2015-08-28

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

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

    PubMed

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

    2016-08-17

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

  15. 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

  16. 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

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

    PubMed

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

    2015-03-28

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

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

  1. Quantitative molecular orbital energies within a G0W0 approximation

    NASA Astrophysics Data System (ADS)

    Sharifzadeh, S.; Tamblyn, I.; Doak, P.; Darancet, P. T.; Neaton, J. B.

    2012-09-01

    Using many-body perturbation theory within a G 0 W 0 approximation, with a plane wave basis set and using a starting point based on density functional theory within the generalized gradient approximation, we explore routes for computing the ionization potential (IP), electron affinity (EA), and fundamental gap of three gas-phase molecules — benzene, thiophene, and (1,4) diamino-benzene — and compare with experiments. We examine the dependence of the IP and fundamental gap on the number of unoccupied states used to represent the dielectric function and the self energy, as well as the dielectric function plane-wave cutoff. We find that with an effective completion strategy for approximating the unoccupied subspace, and a well converged dielectric function kinetic energy cutoff, the computed IPs and EAs are in excellent quantitative agreement with available experiment (within 0.2 eV), indicating that a one-shot G 0 W 0 approach can be very accurate for calculating addition/removal energies of small organic molecules.

  2. 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.)

  3. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    NASA Astrophysics Data System (ADS)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

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

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  6. Simple orbital theory for the molecular electrician.

    PubMed

    Ernzerhof, Matthias

    2011-07-01

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

  7. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

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

    2014-05-14

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

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

    PubMed

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

    2011-10-01

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

  9. 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.

  10. Molecular orbitals for properties and spectroscopies

    SciTech Connect

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

    2015-12-31

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

  11. Coulomb-corrected molecular orbital tomography of nitrogen

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  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. Optimization of selected molecular orbitals in group basis sets.

    PubMed

    Ferenczy, György G; Adams, William H

    2009-04-01

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

  15. Energy and the Elliptical Orbit

    NASA Astrophysics Data System (ADS)

    Nettles, Bill

    2009-03-01

    In the January 2007 issue of The Physics Teacher, Prentis, Fulton, Hesse, and Mazzino describe a laboratory exercise in which students use a geometrical analysis inspired by Newton to show that an elliptical orbit and an inverse-square law force go hand in hand. The historical, geometrical, and teamwork aspects of the exercise are useful and important. This paper presents an exercise which uses an energy/angular momentum conservation model for elliptical orbits. This exercise can be done easily by an individual student and on regular notebook-sized paper.

  16. 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.

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

    ERIC Educational Resources Information Center

    Keeports, David

    1986-01-01

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

  18. Conformation effects on the molecular orbitals of serine

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    SciTech Connect

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

    2012-12-28

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

  20. Vanishing rainbows near orbiting and the energy dependence of rainbow scattering - Relation to properties of the potential. [molecular beam scattering cross sections

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

    The energy threshold behavior of elastic rainbow scattering near the transition to orbiting is derived. Analysis of the energy dependence of the rainbow angle shows that the full range from high energies down to orbiting can be fitted with two parameters. Thus, measurements of the rainbow angle can give essentially only two pieces of information about the potential. For potentials of common shapes, such measurements are sensitive to regions of the potential just beyond the minimum and give information about the shape of the potential in this range. However, neither a minimum nor a point of inflection in the potential is necessary for rainbow scattering.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Sung; Kim, Taekyeong

    2016-01-01

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

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

    SciTech Connect

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

    1990-11-21

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

  4. 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

  5. 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.

  6. 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

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

    PubMed

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

    2006-01-26

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

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  9. 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.

  10. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

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

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  11. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

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

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  12. 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.

  13. 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

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

    PubMed

    Heßelmann, Andreas

    2016-06-14

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

  15. 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

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

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

    SciTech Connect

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

    1988-01-01

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

  18. Energy and the Elliptical Orbit

    ERIC Educational Resources Information Center

    Nettles, Bill

    2009-01-01

    In the January 2007 issue of "The Physics Teacher," Prentis, Fulton, Hesse, and Mazzino describe a laboratory exercise in which students use a geometrical analysis inspired by Newton to show that an elliptical orbit and an inverse-square law force go hand in hand. The historical, geometrical, and teamwork aspects of the exercise are useful and…

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

    SciTech Connect

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

    2013-08-01

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

  20. The Energy of Substituted Ethanes. Asymmetry Orbitals

    PubMed Central

    Salem, Lionel; Hoffmann, Roald; Otto, Peter

    1973-01-01

    The leading terms in the energy of a general substituted ethane are derived in explicit form as a function of the torsional angle θ, the substituent electronegativities, and their mutual overlaps. The energy is found to be the sum of all four overlaps between pairs of asymmetry orbitals, and satisfies the requisite symmetry properties. PMID:16592060

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

    NASA Astrophysics Data System (ADS)

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

    2002-02-01

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

  2. Exploring chemistry with the fragment molecular orbital method.

    PubMed

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

    2012-06-01

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

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

    PubMed

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

    2004-11-01

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

  4. Towards simple orbital-dependent density functionals for molecular dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Igor Ying; Richter, Patrick; Scheffler, Matthias

    2015-03-01

    Density functional theory (DFT) is one of the leading first-principles electronic-structure theories. However, molecular dissociation remains a challenge, because it requires a well-balanced description of the drastically different electronic structure at different bond lengths. One typical and well-documented case is the dissociation of both H2+ and H2, for which all popular DFT functionals fail. We start from the Bethe-Goldstone equation to propose a simple orbital-dependent correlation functional which generalizes the linear adiabatic connection approach. The resulting scheme is based on second-order perturbation theory (PT2), but includes the self-consistent coupling of electron-hole pairs, which ensures the correct H2 dissociation limit and gives a finite correlation energy for systems with a (near)-degenerate energy gap. This coupling PT2-like (CPT2) approximation delivers a significant improvement over all existing functionals for both H2 and H2+ dissociation. We will demonstrate the reason for this improvement analytically for H2 in a minimal basis.

  5. [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

  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 π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure. PMID:25756689

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Bâldea, Ioan

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

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

  11. 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)

  12. 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…

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

    PubMed

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

    2016-09-13

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

  14. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Autschbach, Jochen; King, Harry F.

    2010-07-01

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

  16. 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.

  17. 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.

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

    SciTech Connect

    Zwan, Elmar V. van der; Lein, Manfred

    2007-11-29

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

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

    SciTech Connect

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

    1992-01-01

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

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

    SciTech Connect

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

    1992-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  2. 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

  3. Atomic-orbital expansion model for describing ion-atom collisions at intermediate and low energies

    SciTech Connect

    Lin, C.D.; Fritsch, W.

    1983-01-01

    In the description of inelastic processes in ion-atom collisions at moderate energies, the semiclassical close-coupling method is well established as the standard method. Ever since the pioneering work on H/sup +/ + H in the early 60's, the standard procedure is to expand the electronic wavefunction in terms of molecular orbitals (MO) or atomic orbitals (AO) for describing collisions at, respectively, low or intermediate velocities. It has been recognized since early days that traveling orbitals are needed in the expansions in order to represent the asymptotic states in the collisions correctly. While the adoption of such traveling orbitals presents no conceptual difficulties for expansions using atomic orbitals, the situation for molecular orbitals is less clear. In recent years, various forms of traveling MO's have been proposed, but conflicting results for several well-studied systems have been reported.

  4. 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

  5. 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.

  6. 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.

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

    SciTech Connect

    Feng, Min; Zhao, Jin; Petek, Hrvoje

    2008-04-17

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

  8. Band effects on inelastic scattering of low-energy ions from metallic and ionic surfaces: A formalism beyond the adiabatic molecular-orbitals calculation

    NASA Astrophysics Data System (ADS)

    García, Evelina A.; Goldberg, E. C.

    1998-03-01

    Charge exchange and inelastic excitation processes have been analyzed in the scattering of low-energy He+ from metallic and ionic surfaces. An Anderson-like Hamiltonian is proposed, where the parameters are defined taking into account the electronic band structure of the surface as well as the atomic nature of the interaction between the projectile and the target atoms. The time-dependent collisional process is solved by using a Green-function formalism, which allows us to calculate not only the charge-state probabilities but also the one-electron interband excitations in the solid. Competitive effects of the hybridizations among the localized state at the projectile site and the localized and extended surface states are contemplated. In this way we can explain the observed energy dependences of the neutralization probability, as well as the occurrence of energy-loss processes due to the excitation of valence and core surface electrons induced by the collision.

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

    PubMed

    Proppe, Jonny; Herrmann, Carmen

    2015-02-01

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

  10. 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.

  11. A concept of the energy storable orbital power station (ESOPS)

    NASA Astrophysics Data System (ADS)

    Akiba, Ryojiro; Takano, Tadashi; Yokota, Hiroki

    To save foreseeable difficulties and risks associated with large scale development of the Space Power Station on GEO at a remote distance, the Energy Storable Orbital Power Station (ESOPS) placed in a near earth orbit is proposed. Most promising orbit for ESOPS is a fixed periapsis pseudo sun synchronous orbit. A thermodynamical power generation is preferable owing to its inherent insensitive nature against radiation suffered on the medium altitude orbit. Thermal energy storage using latent heat of fusion seems the best choice for this system. The power transmission from ESOPS to ground station presents most critical problems due to non-stationary characteristics.

  12. Orbital relaxation effects on Kohn–Sham frontier orbital energies in density functional theory

    SciTech Connect

    Zhang, DaDi; Zheng, Xiao; Li, Chen; Yang, Weitao

    2015-04-21

    We explore effects of orbital relaxation on Kohn–Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn–Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn–Sham frontier orbital energies by Hartree–Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scaling correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems.

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

    PubMed

    Mitxelena, Ion; Piris, Mario

    2016-05-28

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

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    Mitxelena, Ion; Piris, Mario

    2016-05-01

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

  17. P and N compensation in diamond molecular orbital theory

    NASA Astrophysics Data System (ADS)

    Anderson, Alfred B.; Kostadinov, Lubomir N.

    1997-01-01

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

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

    SciTech Connect

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

    1986-09-01

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

  19. 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.

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

    SciTech Connect

    Chen, N.; Yang, R.T.

    1996-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Fukushima, Kimichika

    1993-07-01

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

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

    PubMed

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

    2011-03-01

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

  4. 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.

  5. Targeting Low-Energy Transfers to Low Lunar Orbit

    NASA Technical Reports Server (NTRS)

    Parker, Jeffrey S.; Anderson, Rodney L.

    2011-01-01

    A targeting scheme is presented to build trajectories from a specified Earth parking orbit to a specified low lunar orbit via a low-energy transfer and up to two maneuvers. The total transfer delta V (velocity) is characterized as a function of the Earth parking orbit inclination and the departure date for transfers to each given low lunar orbit. The transfer delta V (velocity) cost is characterized for transfers constructed to low lunar polar orbits with any longitude of ascending node and for transfers that arrive at the Moon at any given time during a month.

  6. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2010-06-11

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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Chakraborty, Debajit; Karasiev, Valentin; Trickey, Samuel

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

  11. 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.

  12. 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…

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

    PubMed

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

    2016-07-28

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

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

    PubMed

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

    2009-01-29

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

  15. Energy offsets within a molecular monolayer: the influence of the molecular environment

    NASA Astrophysics Data System (ADS)

    Willenbockel, M.; Stadtmüller, B.; Schönauer, K.; Bocquet, F. C.; Lüftner, D.; Reinisch, E. M.; Ules, T.; Koller, G.; Kumpf, C.; Soubatch, S.; Puschnig, P.; Ramsey, M. G.; Tautz, F. S.

    2013-03-01

    The compressed 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) herringbone monolayer structure on Ag(110) is used as a model system to investigate the role of molecule-molecule interactions at metal-organic interfaces. By means of the orbital tomography technique, we can not only distinguish the two inequivalent molecules in the unit cell but also resolve their different energy positions for the highest occupied and the lowest unoccupied molecular orbitals. Density functional theory calculations of a freestanding PTCDA layer identify the electrostatic interaction between neighboring molecules, rather than the adsorption site, as the main reason for the molecular level splitting observed experimentally.

  16. Exploring three-dimensional orbital imaging with energy-dependent photoemission tomography

    PubMed Central

    Weiß, S.; Lüftner, D.; Ules, T.; Reinisch, E. M.; Kaser, H.; Gottwald, A.; Richter, M.; Soubatch, S.; Koller, G.; Ramsey, M. G.; Tautz, F. S.; Puschnig, P.

    2015-01-01

    Recently, it has been shown that experimental data from angle-resolved photoemission spectroscopy on oriented molecular films can be utilized to retrieve real-space images of molecular orbitals in two dimensions. Here, we extend this orbital tomography technique by performing photoemission initial state scans as a function of photon energy on the example of the brickwall monolayer of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on Ag(110). The overall dependence of the photocurrent on the photon energy can be well accounted for by assuming a plane wave for the final state. However, the experimental data, both for the highest occupied and the lowest unoccupied molecular orbital of PTCDA, exhibits an additional modulation attributed to final state scattering effects. Nevertheless, as these effects beyond a plane wave final state are comparably small, we are able, with extrapolations beyond the attainable photon energy range, to reconstruct three-dimensional images for both orbitals in agreement with calculations for the adsorbed molecule. PMID:26437297

  17. Exploring three-dimensional orbital imaging with energy-dependent photoemission tomography.

    PubMed

    Weiß, S; Lüftner, D; Ules, T; Reinisch, E M; Kaser, H; Gottwald, A; Richter, M; Soubatch, S; Koller, G; Ramsey, M G; Tautz, F S; Puschnig, P

    2015-01-01

    Recently, it has been shown that experimental data from angle-resolved photoemission spectroscopy on oriented molecular films can be utilized to retrieve real-space images of molecular orbitals in two dimensions. Here, we extend this orbital tomography technique by performing photoemission initial state scans as a function of photon energy on the example of the brickwall monolayer of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on Ag(110). The overall dependence of the photocurrent on the photon energy can be well accounted for by assuming a plane wave for the final state. However, the experimental data, both for the highest occupied and the lowest unoccupied molecular orbital of PTCDA, exhibits an additional modulation attributed to final state scattering effects. Nevertheless, as these effects beyond a plane wave final state are comparably small, we are able, with extrapolations beyond the attainable photon energy range, to reconstruct three-dimensional images for both orbitals in agreement with calculations for the adsorbed molecule. PMID:26437297

  18. Exploring three-dimensional orbital imaging with energy-dependent photoemission tomography

    NASA Astrophysics Data System (ADS)

    Weiß, S.; Lüftner, D.; Ules, T.; Reinisch, E. M.; Kaser, H.; Gottwald, A.; Richter, M.; Soubatch, S.; Koller, G.; Ramsey, M. G.; Tautz, F. S.; Puschnig, P.

    2015-10-01

    Recently, it has been shown that experimental data from angle-resolved photoemission spectroscopy on oriented molecular films can be utilized to retrieve real-space images of molecular orbitals in two dimensions. Here, we extend this orbital tomography technique by performing photoemission initial state scans as a function of photon energy on the example of the brickwall monolayer of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on Ag(110). The overall dependence of the photocurrent on the photon energy can be well accounted for by assuming a plane wave for the final state. However, the experimental data, both for the highest occupied and the lowest unoccupied molecular orbital of PTCDA, exhibits an additional modulation attributed to final state scattering effects. Nevertheless, as these effects beyond a plane wave final state are comparably small, we are able, with extrapolations beyond the attainable photon energy range, to reconstruct three-dimensional images for both orbitals in agreement with calculations for the adsorbed molecule.

  19. 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.

  20. Characterizing metastable states beyond energies and lifetimes: Dyson orbitals and transition dipole moments

    NASA Astrophysics Data System (ADS)

    Jagau, Thomas-C.; Krylov, Anna I.

    2016-02-01

    The theoretical description of electronic resonances is extended beyond calculations of energies and lifetimes. We present the formalism for calculating Dyson orbitals and transition dipole moments within the equation-of-motion coupled-cluster singles and doubles method for electron-attached states augmented by a complex absorbing potential (CAP-EOM-EA-CCSD). The capabilities of the new methodology are illustrated by calculations of Dyson orbitals of various transient anions. We also present calculations of transition dipole moments between transient and stable anionic states as well as between different transient states. Dyson orbitals characterize the differences between the initial neutral and final electron-attached states without invoking the mean-field approximation. By extending the molecular-orbital description to correlated many-electron wave functions, they deliver qualitative insights into the character of resonance states. Dyson orbitals and transition moments are also needed for calculating experimental observables such as spectra and cross sections. Physically meaningful results for those quantities are obtained only in the framework of non-Hermitian quantum mechanics, e.g., in the presence of a complex absorbing potential (CAP), when studying resonances. We investigate the dependence of Dyson orbitals and transition moments on the CAP strength and illustrate how Dyson orbitals help understand the properties of metastable species and how they are affected by replacing the usual scalar product by the so-called c-product.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

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

    2014-01-24

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

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Lai, Wei; Guo, Chunlei

    2016-04-01

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

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

    PubMed

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

    2015-04-16

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

  8. 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

  9. 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.

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

    PubMed

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

    2009-05-15

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

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

    SciTech Connect

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

    2009-10-15

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

  12. 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.

  13. 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.

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

    SciTech Connect

    Roemelt, Michael

    2015-07-28

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

  15. 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.

  16. 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

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

    PubMed

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

    2015-11-01

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

  18. 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.

  19. Fragmented Molecular Orbital with Diffusion Monte Carlo for large molecular systems

    NASA Astrophysics Data System (ADS)

    Benali, Anouar; Pruitt, Spencer R.; Fedorov, Dmitri G.

    Performing accurate quantum mechanics (QM) calculations on larger and larger systems, while maintaining a high level of accuracy is an ongoing effort in many ab initio fields. Many different attempts have been made to develop highly scalable and accurate methods. The fragment molecular orbital (FMO) method is an ab initio method capable of taking advantage of modern supercomputers, such as the Blue Gene Q system Mira at the Argonne National Laboratory Leadership Computing Facility (ALCF). FMO is based on dividing molecules into fragments and performing ab initio calculations on fragments, their dimers and, optionally, trimers. This decomposition makes it possible to perform QM calculations of real size biological molecules. In contrast to many other fragment-based methods, the effect of the environment is rigorously accounted for by computing the electrostatic potential (ESP) due to remaining fragments that are not explicitly included in a given monomer, dimer, or trimer calculation. The use of highly accurate levels of theory, such as Diffusion Monte Carlo (DMC-QMC), in conjunction with FMO allows for the goal of highly scalable and accurate all electron calculations demonstrated in this study, on a variety of relevant systems (H2O)[3-6] and protein using GAMESS and QMCPACK.

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

    PubMed

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

    2016-09-01

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

  1. 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.

  2. Low-Energy Ballistic Transfers to Lunar Halo Orbits

    NASA Technical Reports Server (NTRS)

    Parker, Jeffrey S.

    2009-01-01

    Recent lunar missions have begun to take advantage of the benefits of low-energy ballistic transfers between the Earth and the Moon rather than implementing conventional Hohmann-like lunar transfers. Both Artemis and GRAIL plan to implement low-energy lunar transfers in the next few years. This paper explores the characteristics and potential applications of many different families of low-energy ballistic lunar transfers. The transfers presented here begin from a wide variety of different orbits at the Earth and follow several different distinct pathways to the Moon. This paper characterizes these pathways to identify desirable low-energy lunar transfers for future lunar missions.

  3. An efficient algorithm for energy gradients and orbital optimization in valence bond theory.

    PubMed

    Song, Lingchun; Song, Jinshuai; Mo, Yirong; Wu, Wei

    2009-02-01

    An efficient algorithm for energy gradients in valence bond theory with nonorthogonal orbitals is presented. A general Hartree-Fock-like expression for the Hamiltonian matrix element between valence bond (VB) determinants is derived by introducing a transition density matrix. Analytical expressions for the energy gradients with respect to the orbital coefficients are obtained explicitly, whose scaling for computational cost is m(4), where m is the number of basis functions, and is thus approximately the same as in HF method. Compared with other existing approaches, the present algorithm has lower scaling, and thus is much more efficient. Furthermore, the expression for the energy gradient with respect to the nuclear coordinates is also presented, and it provides an effective algorithm for the geometry optimization and the evaluation of various molecular properties in VB theory. Test applications show that our new algorithm runs faster than other methods. PMID:18629879

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  5. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.

    PubMed

    Pruitt, Spencer R; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, Mark S

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Møller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed. PMID:26913837

  6. K/S Lambert problem. [energy requirements for transfer orbits

    NASA Technical Reports Server (NTRS)

    Jezewski, D. J.

    1975-01-01

    The Lambert problem in orbital mechanics is formulated in Kustaanheimo/Stiefel variables. The problem is to determine the required energy and the value of the generalized eccentric anomaly such that a particle at the initial position vector will transfer to the final position vector in a physical time interval. The fictitious time solution results in two nonlinear equations in the two unknowns, energy and fictitious time. The generalized eccentric anomaly solution, however, results in only one nonlinear equation in the one unknown, the eccentric anomaly. This simplification is possible because the energy equation is separable in the eccentric anomaly formulation.

  7. 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.

  8. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Fedorov, Dmitri G.; Kitaura, Kazuo

    2004-08-01

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

  11. 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…

  12. 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.

  13. Separated-orbit bisected energy-recovered linear accelerator

    DOEpatents

    Douglas, David R.

    2015-09-01

    A separated-orbit bisected energy-recovered linear accelerator apparatus and method. The accelerator includes a first linac, a second linac, and a plurality of arcs of differing path lengths, including a plurality of up arcs, a plurality of downgoing arcs, and a full energy arc providing a path independent of the up arcs and downgoing arcs. The up arcs have a path length that is substantially a multiple of the RF wavelength and the full energy arc includes a path length that is substantially an odd half-integer multiple of the RF wavelength. Operation of the accelerator includes accelerating the beam utilizing the linacs and up arcs until the beam is at full energy, at full energy executing a full recirculation to the second linac using a path length that is substantially an odd half-integer of the RF wavelength, and then decelerating the beam using the linacs and downgoing arcs.

  14. Energy storage for low earth orbit operations at high power

    NASA Technical Reports Server (NTRS)

    Trout, J. B.

    1979-01-01

    Results are presented of an in-house study of relative sizes and technology needs of three energy storage systems for high power, low earth orbit power systems. The systems compared are nickel-cadmium batteries, nickel-hydrogen batteries, and regenerative fuel cell systems (RFCS). RFCS based on hydrogen-oxygen and hydrogen-chlorine reactants are examined. Those components of the total power system which are significantly impacted by energy storage system selection; e.g., solar array, reactant storage tanks and radiator sizes, are included incrementally in the weights of the systems compared.

  15. A Frontier orbital energy approach to redox potentials

    NASA Astrophysics Data System (ADS)

    Conradie, Jeanet

    2015-09-01

    The prediction of the oxidation and reduction potentials of molecules is important in many research areas. A review of relationships obtained between frontier orbital energies (eV), the calculated ionization potentials (IP in eV), or adiabatic electron affinities (EA in eV) with the experimental oxidation and reduction potentials is presented, for selected series of β- diketones, rhodium-β-diketonato complexes, as well as metal-tris-β-diketonato complexes, with the metal Fe or Mn. The good linear relationships obtained for related series of complexes show that the oxidation and reduction potentials of these complexes can be predicted by their DFT-calculated energies.

  16. Rotational Doppler Effect: A Probe for Molecular Orbitals Anisotropy.

    PubMed

    Miao, Quan; Travnikova, Oksana; Gel'mukhanov, Faris; Kimberg, Victor; Sun, Yu-Ping; Thomas, T Darrah; Nicolas, Christophe; Patanen, Minna; Miron, Catalin

    2015-05-01

    The vibrationally resolved X-ray photoelectron spectra of X2Σg+(3σg−1) and B2Σu+(2σu−1) states of N2+ were recorded for different photon energies and orientations of the polarization vector. Clear dependencies of the spectral line widths on the X-ray polarization as well as on the symmetry of the final electronic states are observed. Contrary to the translational Doppler, the rotational Doppler broadening is sensitive to the photoelectron emission anisotropy. On the basis of theoretical modeling, we suggest that the different rotational Doppler broadenings observed for gerade and ungerade final states result from a Young's double-slit interference phenomenon. PMID:26263315

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  18. 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

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

    PubMed

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

    2016-04-28

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

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

    PubMed

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

    2007-11-01

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

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Romere, P. O.

    1982-03-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1996-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-10-01

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

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

    PubMed

    Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi

    2016-01-01

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

  11. 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.

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

    PubMed

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

    2013-06-01

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

  13. Optimal aeroassisted coplanar orbital transfer using an energy model

    NASA Technical Reports Server (NTRS)

    Halyo, Nesim; Taylor, Deborah B.

    1989-01-01

    The atmospheric portion of the trajectories for the aeroassisted coplanar orbit transfer was investigated. The equations of motion for the problem are expressed using reduced order model and total vehicle energy, kinetic plus potential, as the independent variable rather than time. The order reduction is achieved analytically without an approximation of the vehicle dynamics. In this model, the problem of coplanar orbit transfer is seen as one in which a given amount of energy must be transferred from the vehicle to the atmosphere during the trajectory without overheating the vehicle. An optimal control problem is posed where a linear combination of the integrated square of the heating rate and the vehicle drag is the cost function to be minimized. The necessary conditions for optimality are obtained. These result in a 4th order two-point-boundary-value problem. A parametric study of the optimal guidance trajectory in which the proportion of the heating rate term versus the drag varies is made. Simulations of the guidance trajectories are presented.

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

    PubMed

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

    2015-08-18

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

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

    PubMed

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

    2016-03-01

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

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Tada, Tomofumi; Aoki, Yuriko; Imamura, Akira

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

  20. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

  2. 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.

  3. Molecular quantum magnetism with strong spin-orbit coupling in inorganic solid Ba3Yb2Zn5O11

    NASA Astrophysics Data System (ADS)

    Park, Sang-Youn; Ji, Sungdae; Park, Jae-Hoon; Do, Seunghwan; Choi, Kwang-Yong; Jang, Dongjin; Schmidt, Burkhard; Brando, Manuel; Butch, Nicholas

    The molecular magnet, assembly of finite number of spins which are isolated from environment, is a model system to study the quantum information process such as the qubit or spintronic devices. In past decades, the molecular magnet has been mostly realized in organic material, however, it has difficulty synthesizing materials or controlling their properties, meanwhile tremendous endeavors to search inorganic molecular magnet are continuing. Here, we propose Ba3Yb2Zn5O11 as a candidate of inorganic molecular magnet. This material consists of an alternating 3D-array of small and large tetrahedron containing antiferromagnetically coupled four pseudospin-1/2 Yb ions, and magnetic properties are described by an isolated tetrahedron without long-range magnetic ordering. Inelastic neutron scattering measurement with external magnetic field reveals that extraordinarily huge Dzyaloshinsky-Moriya (DM) interaction originating from strong spin-orbit coupling in Yb isospin is the key to explain energy level of tetrahedron in addition to Heisenberg exchange interaction and Zeeman effect. Magnetization measurement shows the Landau-Zener transition between avoided crossing levels caused by DM interaction.

  4. Differential neutron energy spectra measured on spacecraft low Earth orbit

    NASA Technical Reports Server (NTRS)

    Benton, E. V.; Frank, A. L.; Dudkin, E. V.; Potapov, Yu. V.; Akopova, A. B.; Melkumyan, L. V.

    1995-01-01

    Two methods for measuring neutrons in the range from thermal energies to dozens of MeV were used. In the first method, alpha-particles emitted from the (sup 6) Li(n.x)T reaction are detected with the help of plastic nuclear track detectors, yielding results on thermal and resonance neutrons. Also, fission foils are used to detect fast neutrons. In the second method, fast neutrons are recorded by nuclear photographic emulsions (NPE). The results of measurements on board various satellites are presented. The neutron flux density does not appear to correlate clearly with orbital parameters. Up to 50% of neutrons are due to albedo neutrons from the atmosphere while the fluxes inside the satellites are 15-20% higher than those on the outside. Estimates show that the neutron contribution to the total equivalent radiation dose reaches 20-30%.

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  6. 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.

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

    NASA Technical Reports Server (NTRS)

    Tai, H.

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  9. 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

  10. 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

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

    PubMed

    Nishimoto, Yoshio; Fedorov, Dmitri G

    2016-08-10

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

  12. 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.

  13. 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.

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

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

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

  15. 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…

  16. Curvature and Frontier Orbital Energies in Density Functional Theory

    SciTech Connect

    Stein, Tamar; Autschbach, Jochen; Govind, Niranjan; Kronik, Leeor; Baer, Roi

    2012-12-20

    Perdew et al. [Phys. Rev. Lett 49, 1691 (1982)] discovered and proved two different properties that exact Kohn-Sham density functional theory (DFT) must obey: (i) The exact total energy versus particle number must be a series of linear segments between integer electron points; (ii) Across an integer number of electrons, the exchange-correlation potential may ``jump’’ by a constant, known as the derivative discontinuity (DD). Here, we show analytically that in both the original and the generalized Kohn-Sham formulation of DFT, the two are in fact two sides of the same coin. Absence of a derivative discontinuity necessitates deviation from piecewise linearity, and the latter can be used to correct for the former, thereby restoring the physical meaning of the orbital energies. Using selected small molecules, we show that this results in a simple correction scheme for any underlying functional, including semi-local and hybrid functionals as well as Hartree-Fock theory, suggesting a practical correction for the infamous gap problem of density functional theory. Moreover, we show that optimally-tuned range-separated hybrid functionals can inherently minimize both DD and curvature, thus requiring no correction, and show that this can be used as a sound theoretical basis for novel tuning strategies.

  17. Effects of Exchange Energy and Spin-Orbit Coupling on Bond Energies

    ERIC Educational Resources Information Center

    Smith, Derek W.

    2004-01-01

    Since chemical reactions involve the breaking and making of bonds, understanding the relative strengths of bonds is of paramount importance in the study, teaching, and practice of chemistry. Further, it is showed that free atoms having p(super n) configuration with n = 2,3, or 4 are stabilized by exchange energy, and by spin-orbit coupling for n =…

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

    PubMed

    Shinagawa, Y

    1992-02-01

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

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

    PubMed

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

    2015-05-01

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

  20. Potential energy hypersurface and molecular flexibility

    NASA Astrophysics Data System (ADS)

    Koča, Jaroslav

    1993-02-01

    The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.

  1. 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.

  2. Quasi-relativistic modeltotential approach. Spin-orbit effects on energies and geometries of several di- and tri-atomic molecules

    NASA Astrophysics Data System (ADS)

    Hafner, P.; Habitz, P.; Ishikawa, Y.; Wechsel-Trakowski, E.; Schwarz, W. H. E.

    1981-06-01

    Calculations on ground and valence-excited states of Au +2, Tl 2 and Pb 2, and on the ground states of HgCl 2, PbCl 2 and PbH 2 have teen performed within the Kramers-restricteu self-consistent-field approach using a quasi-relativitistic model-potential hamiltonian. The influence of spin—orbit coupling on molecular orbitals, bond energies and geometries is discussed.

  3. Orbit-orbit relativistic corrections to the pure vibrational non-Born-Oppenheimer energies of H(2).

    PubMed

    Stanke, Monika; Kedziera, Dariusz; Bubin, Sergiy; Molski, Marcin; Adamowicz, Ludwik

    2008-03-21

    We report the derivation of the orbit-orbit relativistic correction for calculating pure vibrational states of diatomic molecular systems with sigma electrons within the framework that does not assume the Born-Oppenheimer (BO) approximation. The correction is calculated as the expectation value of the orbit-orbit interaction operator with the non-BO wave function expressed in terms of explicitly correlated Gaussian functions multiplied by even powers of the internuclear distance. With that we can now calculate the complete relativistic correction of the order of alpha(2) (where alpha=1/c). The new algorithm is applied to determine the full set of the rotationless vibrational levels and the corresponding transition frequencies of the H(2) molecule. The results are compared with the previous calculations, as well as with the frequencies obtained from the experimental spectra. The comparison shows the need to include corrections higher than second order in alpha to further improve the agreement between the theory and the experiment. PMID:18361577

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  6. 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.

  7. 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.

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

    SciTech Connect

    Ipatov, A. N.

    2010-02-15

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

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

    PubMed Central

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

    2013-01-01

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

  10. 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

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Gee, Myrlene; Wasylishen, Roderick E.

    2001-06-01

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

  15. 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

  16. Design of Acceptors with Suitable Frontier Molecular Orbitals to Match Donors via Substitutions on Perylene Diimide for Organic Solar Cells

    PubMed Central

    Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa

    2016-01-01

    A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The –CN substituent can improve the electron transport properties of PDI-BI. The –CH3 group in different positions slightly affects the electron transport properties of PDI-BI. PMID:27187370

  17. Molecular energies from an incremental fragmentation method

    NASA Astrophysics Data System (ADS)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  18. Ionisation potential theorem in the presence of the electric field: Assessment of range-separated functional in the reproduction of orbital and excitation energies

    NASA Astrophysics Data System (ADS)

    Borpuzari, Manash Protim; Boruah, Abhijit; Kar, Rahul

    2016-04-01

    Recently, the range-separated density functionals have been reported to reproduce gas phase orbital and excitation energies with good accuracy. In this article, we have revisited the ionisation potential theorem in the presence of external electric field. Numerical results on six linear molecules are presented and the performance of the range-separated density functionals in reproducing highest occupied molecular orbital (HOMO) energies, LUMO energies, HOMO-LUMO gaps in the presence of the external electric field is assessed. In addition, valence and Rydberg excitation energies in the presence of the external electric field are presented. It is found that the range-separated density functionals reproduce orbital and excitation energies accurately in the presence of the electric field. Moreover, we have performed fractional occupation calculation using cubic spline equation and tried to explain the performance of the functional.

  19. Relationship between orbital energy gaps and excitation energies for long-chain systems.

    PubMed

    Tsuneda, Takao; Singh, Raman K; Nakata, Ayako

    2016-06-15

    The difference between the excitation energies and corresponding orbital energy gaps, the exciton binding energy, is investigated based on time-dependent (TD) density functional theory (DFT) for long-chain systems: all-trans polyacetylenes and linear oligoacenes. The optimized geometries of these systems indicate that bond length alternations significantly depend on long-range exchange interactions. In TDDFT formalism, the exciton binding energy comes from the two-electron interactions between occupied and unoccupied orbitals through the Coulomb-exchange-correlation integral kernels. TDDFT calculations show that the exciton binding energy is significant when long-range exchange interactions are involved. Spin-flip (SF) TDDFT calculations are then carried out to clarify double-excitation effects in these excitation energies. The calculated SF-TDDFT results indicate that double-excitation effects significantly contribute to the excitations of long-chain systems. The discrepancies between the vertical ionization potential minus electron affinity (IP-EA) values and the HOMO-LUMO excitation energies are also evaluated for the infinitely long polyacetylene and oligoacene using the least-square fits to estimate the exciton binding energy of infinitely long systems. It is found that long-range exchange interactions are required to give the exciton binding energy of the infinitely long systems. Consequently, it is concluded that long-range exchange interactions neglected in many DFT calculations play a crucial role in the exciton binding energies of long-chain systems, while double-excitation correlation effects are also significant to hold the energy balance of the excitations. © 2016 Wiley Periodicals, Inc. PMID:27010365

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

    PubMed

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

    2004-11-01

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

  1. 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

  2. Solar Energy Economics Revisited: The Promise and Challenge of Orbiting Reflectors for World Energy Supply

    NASA Technical Reports Server (NTRS)

    Billman, Kenneth W.; Gilbreath, William P.; Bowen, Stuart W.

    1978-01-01

    A system of orbiting, large-area, low mass density reflector satellites which provide nearly continuous solar energy to a world-distributed set of conversion sites is examined under the criteria for any potential new energy system: technical feasibility, significant and renewable energy impact, economic feasibility and social/political acceptability. Although many technical issues need further study, reasonable advances in space technology appear sufficient to implement the system. The enhanced insolation is shown to greatly improve the economic competitiveness of solar-electric generation to circa 1995 fossil/nuclear alternatives. The system is shown to have the potential for supplying a significant fraction of future domestic and world energy needs. Finally, the environmental and social issues, including a means for financing such a large shift to a world solar energy dependence, is addressed.

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

    PubMed

    Balachandran, V; Karunakaran, V

    2014-06-01

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

  4. 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.

  5. 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.

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

    PubMed

    Saito, N; Fuwa, A

    2000-01-01

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

  7. 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…

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

    NASA Astrophysics Data System (ADS)

    Mahalakshmi, G.; Balachandran, V.

    2014-10-01

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

  9. Investigation of the energy dependence of the orbital light curve in LS 5039

    NASA Astrophysics Data System (ADS)

    Chang, Z.; Zhang, S.; Ji, L.; Chen, Y. P.; Kretschmar, P.; Kuulkers, E.; Collmar, W.; Liu, C. Z.

    2016-08-01

    LS 5039 is so far the best studied γ-ray binary system at multi-wavelength energies. A time resolved study of its spectral energy distribution (SED) shows that above 1 keV its power output is changing along its binary orbit as well as being a function of energy. To disentangle the energy dependence of the power output as a function of orbital phase, we investigated in detail the orbital light curves as derived with different telescopes at different energy bands. We analysed the data from all existing INTEGRAL/IBIS/ISGRI observations of the source and generated the most up-to-date orbital light curves at hard X-ray energies. In the γ-ray band, we carried out orbital phase-resolved analysis of Fermi-LAT data between 30 MeV and 10 GeV in 5 different energy bands. We found that, at ≲100 MeV and ≳1 TeV the peak of the γ-ray emission is near orbital phase 0.7, while between ˜100 MeV and ˜1 GeV it moves close to orbital phase 1.0 in an orbital anti-clockwise manner. This result suggests that the transition region in the SED at soft γ-rays (below a hundred MeV) is related to the orbital phase interval of 0.5-1.0 but not to the one of 0.0-0.5, when the compact object is "behind" its companion. Another interesting result is that between 3 and 20 GeV no orbital modulation is found, although Fermi-LAT significantly (˜18σ) detects LS 5039. This is consistent with the fact that at these energies, the contributions to the overall emission from the inferior conjunction phase region (INFC, orbital phase 0.45 to 0.9) and from the superior conjunction phase region (SUPC, orbital phase 0.9 to 0.45) are equal in strength. At TeV energies the power output is again dominant in the INFC region and the flux peak occurs at phase ˜0.7.

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

    NASA Astrophysics Data System (ADS)

    Itoh, H.; Ertl, G.

    1982-04-01

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

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

    PubMed

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

    2011-08-01

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

  12. Development of Molecular Electrocatalysts for Energy Storage

    SciTech Connect

    DuBois, Daniel L.

    2014-02-20

    Molecular electrocatalysts can play an important role in energy storage and utilization reactions needed for intermittent renewable energy sources. This manuscript describes three general themes that our laboratories have found useful in the development of molecular electrocatalysts for reduction of CO2 to CO and for H2 oxidation and production. The first theme involves a conceptual partitioning of catalysts into first, second, and outer coordination spheres. This is illustrated with the design of electrocatalysts for CO2 reduction to CO using first and second coordination spheres and for H2 production catalysts using all three coordination spheres. The second theme focuses on the development of thermodynamic models that can be used to design catalysts to avoid high energy and low energy intermediates. In this research, new approaches to the measurement of thermodynamic hydride donor and acceptor abilities of transition metal complexes were developed. Combining this information with other thermodynamic information such as pKa values and redox potentials led to more complete thermodynamic descriptions of transition metal hydride, dihydride, and related species. Relationships extracted from this information were then used to develop models that are powerful tools for predicting and understanding the relative free energies of intermediates in catalytic reactions. The third theme is the control of proton movement during electrochemical fuel generation and utilization reactions. This research involves the incorporation of pendant amines in the second coordination sphere that can facilitate H-H bond heterolysis and heteroformation, intramolecular and intermolecular proton transfer steps, and the coupling of proton and electron transfer steps. Studies also indicate an important role for outer coordination sphere in the delivery of protons to the second coordination sphere. Understanding these proton transfer reactions and their

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  14. 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.

  15. 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.

  16. 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.

  17. Energy spectrum and Landau levels in bilayer graphene with spin-orbit interaction

    NASA Astrophysics Data System (ADS)

    Mireles, Francisco; Schliemann, John

    2012-09-01

    We present a theoretical study of the band structure and Landau levels in bilayer graphene at low energies in the presence of a transverse magnetic field and Rashba spin-orbit interaction in the regime of negligible trigonal distortion. Within an effective low-energy approach the (Löwdin partitioning theory), we derive an effective Hamiltonian for bilayer graphene that incorporates the influence of the Zeeman effect, the Rashba spin-orbit interaction and, inclusively, the role of the intrinsic spin-orbit interaction on the same footing. Particular attention is paid to the energy spectrum and Landau levels. Our modeling unveils the strong influence of the Rashba coupling λR in the spin splitting of the electron and hole bands. Graphene bilayers with weak Rashba spin-orbit interaction show a spin splitting linear in momentum and proportional to λR, but scaling inversely proportional to the interlayer hopping energy γ1. However, at robust spin-orbit coupling λR, the energy spectrum shows a strong warping behavior near the Dirac points. We find that the bias-induced gap in bilayer graphene decreases with increasing Rashba coupling, a behavior resembling a topological insulator transition. We further predict an unexpected asymmetric spin splitting and crossings of the Landau levels due to the interplay between the Rashba interaction and the external bias voltage. Our results are of relevance for interpreting magnetotransport and infrared cyclotron resonance measurements, including situations of comparatively weak spin-orbit coupling.

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

    PubMed

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

  1. Energy pooling upconversion in organic molecular systems.

    PubMed

    LaCount, Michael D; Weingarten, Daniel; Hu, Nan; Shaheen, Sean E; van de Lagemaat, Jao; Rumbles, Garry; Walba, David M; Lusk, Mark T

    2015-04-30

    A combination of molecular quantum electrodynamics, perturbation theory, and ab initio calculations was used to create a computational methodology capable of estimating the rate of three-body singlet upconversion in organic molecular assemblies. The approach was applied to quantify the conditions under which such relaxation rates, known as energy pooling, become meaningful for two test systems, stilbene-fluorescein and hexabenzocoronene-oligothiophene. Both exhibit low intramolecular conversion, but intermolecular configurations exist in which pooling efficiency is at least 90% when placed in competition with more conventional relaxation pathways. For stilbene-fluorescein, the results are consistent with data generated in an earlier experimental investigation. Exercising these model systems facilitated the development of a set of design rules for the optimization of energy pooling. PMID:25793313

  2. Classifying orbits of low and high energy stars in axisymmetric disk galaxies

    NASA Astrophysics Data System (ADS)

    Zotos, Euaggelos E.

    The ordered or chaotic character of orbits of stars moving in the meridional (R,z) plane of an analytic axisymmetric time-independent disk galaxy model with an additional spherically symmetric central nucleus is investigated. Our aim is to determine how the total energy influences the orbital structure of the galaxy. For this purpose we monitor how the percentage of chaotic orbits as well as the rates of orbits composing the main regular families evolve as a function of the value of the energy. In order to distinguish with certainty between chaotic and ordered motion we use the SALI method in extensive sets of initial conditions of orbits. Moreover, a spectral method is applied for identifying the various regular families and also for recognizing the secondary resonances that bifurcate from them. Our numerical computations suggest that for low energy levels the observed amount of chaos is high and the orbital content is rather poor, while for high energy levels, corresponding to global motion, regular motion dominates and many secondary higher resonances emerge. We also compared our results with previous related work.

  3. High-order moments of spin-orbit energy in a multielectron configuration.

    PubMed

    Na, Xieyu; Poirier, M

    2016-07-01

    In order to analyze the energy-level distribution in complex ions such as those found in warm dense plasmas, this paper provides values for high-order moments of the spin-orbit energy in a multielectron configuration. Using second-quantization results and standard angular algebra or fully analytical expressions, explicit values are given for moments up to 10th order for the spin-orbit energy. Two analytical methods are proposed, using the uncoupled or coupled orbital and spin angular momenta. The case of multiple open subshells is considered with the help of cumulants. The proposed expressions for spin-orbit energy moments are compared to numerical computations from Cowan's code and agree with them. The convergence of the Gram-Charlier expansion involving these spin-orbit moments is analyzed. While a spectrum with infinitely thin components cannot be adequately represented by such an expansion, a suitable convolution procedure ensures the convergence of the Gram-Charlier series provided high-order terms are accounted for. A corrected analytical formula for the third-order moment involving both spin-orbit and electron-electron interactions turns out to be in fair agreement with Cowan's numerical computations. PMID:27575229

  4. High-order moments of spin-orbit energy in a multielectron configuration

    NASA Astrophysics Data System (ADS)

    Na, Xieyu; Poirier, M.

    2016-07-01

    In order to analyze the energy-level distribution in complex ions such as those found in warm dense plasmas, this paper provides values for high-order moments of the spin-orbit energy in a multielectron configuration. Using second-quantization results and standard angular algebra or fully analytical expressions, explicit values are given for moments up to 10th order for the spin-orbit energy. Two analytical methods are proposed, using the uncoupled or coupled orbital and spin angular momenta. The case of multiple open subshells is considered with the help of cumulants. The proposed expressions for spin-orbit energy moments are compared to numerical computations from Cowan's code and agree with them. The convergence of the Gram-Charlier expansion involving these spin-orbit moments is analyzed. While a spectrum with infinitely thin components cannot be adequately represented by such an expansion, a suitable convolution procedure ensures the convergence of the Gram-Charlier series provided high-order terms are accounted for. A corrected analytical formula for the third-order moment involving both spin-orbit and electron-electron interactions turns out to be in fair agreement with Cowan's numerical computations.

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

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaolei; Zeng, X. C.

    2003-02-01

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

  6. Angular-overlap calculation of the Jahn-Teller stabilization energie for f-orbital degeneracies

    SciTech Connect

    Warren, K.D.

    1980-03-01

    The angular-overlap model is applied to the calculation of the linear Jahn-Teller coupling constants for f-orbital degeneracies. The MX/sub 6/, O/sub h/, chromophore is treated as representative of the highest symmetry commonly occurring in the lanthanide and actinide series, and it is shown that, even when spin-orbit effects are taken into account, 5f orbital degeneracies may lead to significant Jahn-Teller stabilization energies. The operation of this effect for F/sup 1/ GAMMA/sub 8/ states is considered. 2 tables.

  7. Thermodynamic energy balance equations for Space Shuttle Orbiter gas compartment during ascent and re-entry

    NASA Technical Reports Server (NTRS)

    Ting, P. C.

    1982-01-01

    Thermodynamic energy balance equations are derived and applied to midsection Orbiter-payload atmospheric thermal math models (TMMs) to predict Orbiter component, element, compartment, internal insolation and structure temperatures in support of NASA/JSC mission planning, postflight thermal analysis and payload thermal integration planning. The equations are extended and applied to the forward section, midsection, and aft section of the TMMs for five Orbiter mission phases: prelaunch on pad with purge, lift-off to ascent, re-entry to touchdown, post landing without purge, and post-landing with purge. Predicted results from the 390 node/DFI atmospheric TMM are in good agreement with STS-1 flight measurement data.

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

    NASA Technical Reports Server (NTRS)

    Ehlers, H. K. F.

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Humbel, Stéphane; Sieber, Stefan; Morokuma, Keiji

    1996-08-01

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

  10. Anomalous Orbital-Energy Changes Observed during Spacecraft Flybys of Earth

    NASA Astrophysics Data System (ADS)

    Anderson, John D.; Campbell, James K.; Ekelund, John E.; Ellis, Jordan; Jordan, James F.

    2008-03-01

    We report and characterize anomalous orbital-energy changes observed during six Earth flybys by the Galileo, NEAR, Cassini, Rosetta, and MESSENGER spacecraft. These anomalous energy changes are consistent with an empirical prediction formula which is proportional to the total orbital energy per unit mass and which involves the incoming and outgoing geocentric latitudes of the asymptotic spacecraft velocity vectors. We use this formula to predict a potentially detectable flyby velocity increase of less than 1mm/s for a second Rosetta flyby on November 13, 2007.

  11. Anomalous orbital-energy changes observed during spacecraft flybys of earth.

    PubMed

    Anderson, John D; Campbell, James K; Ekelund, John E; Ellis, Jordan; Jordan, James F

    2008-03-01

    We report and characterize anomalous orbital-energy changes observed during six Earth flybys by the Galileo, NEAR, Cassini, Rosetta, and MESSENGER spacecraft. These anomalous energy changes are consistent with an empirical prediction formula which is proportional to the total orbital energy per unit mass and which involves the incoming and outgoing geocentric latitudes of the asymptotic spacecraft velocity vectors. We use this formula to predict a potentially detectable flyby velocity increase of less than 1 mm/s for a second Rosetta flyby on November 13, 2007. PMID:18352689

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

    PubMed

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

    2016-04-15

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

  13. 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…

  14. Aplication of Kohn-Sham Theory for Orbital Dependent (Self-Interaction-Corrected) Exchange-Correlation Energy Functionals to First Row Homonuclear Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Chen, Jiqiang; Krieger, J. B.; Iafrate, G. J.

    1996-03-01

    We have attempted to employ the LSD approximation with orbital self-interaction-correction (LSDSIC) for the exchange-correlation energy functional in the calculation of the ground state properties of first row homonuclear diatomic molecules. As a higher symmetry is involved in these systems, a different LSDSIC approach has to be taken in order to obtain an appropriate self-interaction correction.( M. R. Pederson, R. A. Heaton, and C. C. Lin, J. Chem. Phys. \\underline82), 2688 (1985) Two methods of employing LSDSIC are considered: Localizing all the "paired" orbitals from an LSD calculation at the experimental bond length, and then calculating LSDSIC total energy and dissociation energy; (2)Employing SIC only to electrons in the outer-shell with the inner-shell electrons treated in the LSD, and then obtaining the Kohn-Sham molecular orbitals by fully numerical solution in the KLI approximation. We find that the total energies are much improved with method (1), but this does not always lead to improved dissociation energies; Method (2) results in better highest occupied orbital energies, and better dissociation energies for most molecules, but the bond length is less accurately given and the vibration frequency is significantly in error.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  16. Molecular Multipole Potential Energy Functions for Water.

    PubMed

    Tan, Ming-Liang; Tran, Kelly N; Pickard, Frank C; Simmonett, Andrew C; Brooks, Bernard R; Ichiye, Toshiko

    2016-03-01

    Water is the most common liquid on this planet, with many unique properties that make it essential for life as we know it. These properties must arise from features in the charge distribution of a water molecule, so it is essential to capture these features in potential energy functions for water to reproduce its liquid state properties in computer simulations. Recently, models that utilize a multipole expansion located on a single site in the water molecule, or "molecular multipole models", have been shown to rival and even surpass site models with up to five sites in reproducing both the electrostatic potential around a molecule and a variety of liquid state properties in simulations. However, despite decades of work using multipoles, confusion still remains about how to truncate the multipole expansions efficiently and accurately. This is particularly important when using molecular multipole expansions to describe water molecules in the liquid state, where the short-range interactions must be accurate, because the higher order multipoles of a water molecule are large. Here, truncation schemes designed for a recent efficient algorithm for multipoles in molecular dynamics simulations are assessed for how well they reproduce results for a simple three-site model of water when the multipole moments and Lennard-Jones parameters of that model are used. In addition, the multipole analysis indicates that site models that do not account for out-of-plane electron density overestimate the stability of a non-hydrogen-bonded conformation, leading to serious consequences for the simulated liquid. PMID:26562223

  17. Scalable Quantum Simulation of Molecular Energies

    NASA Astrophysics Data System (ADS)

    O'Malley, P. J. J.; Babbush, R.; Kivlichan, I. D.; Romero, J.; McClean, J. R.; Barends, R.; Kelly, J.; Roushan, P.; Tranter, A.; Ding, N.; Campbell, B.; Chen, Y.; Chen, Z.; Chiaro, B.; Dunsworth, A.; Fowler, A. G.; Jeffrey, E.; Lucero, E.; Megrant, A.; Mutus, J. Y.; Neeley, M.; Neill, C.; Quintana, C.; Sank, D.; Vainsencher, A.; Wenner, J.; White, T. C.; Coveney, P. V.; Love, P. J.; Neven, H.; Aspuru-Guzik, A.; Martinis, J. M.

    2016-07-01

    We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Second, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors. This error tolerance inspires hope that variational quantum simulations of classically intractable molecules may be viable in the near future.

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

    SciTech Connect

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

    1999-04-15

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

  19. Monthly Variations of Low-Energy Ballistic Transfers to Lunar Halo Orbits

    NASA Technical Reports Server (NTRS)

    Parker, Jeffrey S.

    2010-01-01

    The characteristics of low-energy transfers between the Earth and Moon vary from one month to the next largely due to the Earth's and Moon's non-circular, non-coplanar orbits in the solar system. This paper characterizes those monthly variations as it explores the trade space of low-energy lunar transfers across many months. Mission designers may use knowledge of these variations to swiftly design desirable low-energy lunar transfers in any given month.

  20. Methods of performing downhole operations using orbital vibrator energy sources

    DOEpatents

    Cole, Jack H.; Weinberg, David M.; Wilson, Dennis R.

    2004-02-17

    Methods of performing down hole operations in a wellbore. A vibrational source is positioned within a tubular member such that an annulus is formed between the vibrational source and an interior surface of the tubular member. A fluid medium, such as high bulk modulus drilling mud, is disposed within the annulus. The vibrational source forms a fluid coupling with the tubular member through the fluid medium to transfer vibrational energy to the tubular member. The vibrational energy may be used, for example, to free a stuck tubular, consolidate a cement slurry and/or detect voids within a cement slurry prior to the curing thereof.

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

    PubMed

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

    2013-11-01

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

  2. Scattering framework for two particles with isotropic spin-orbit coupling applicable to all energies

    NASA Astrophysics Data System (ADS)

    Guan, Q.; Blume, D.

    2016-08-01

    Previous work developed a K -matrix formalism applicable to positive energies for the scattering between two s -wave interacting particles with two internal states, isotropic spin-orbit coupling and vanishing center-of-mass momentum [H. Duan, L. You, and B. Gao, Phys. Rev. A 87, 052708 (2013)., 10.1103/PhysRevA.87.052708]. This work extends the formalism to the entire energy regime. Explicit solutions are obtained for the total angular momentum J =0 and 1 channels. The behavior of the partial cross sections in the negative energy regime is analyzed in detail. We find that the leading contributions to the partial cross sections at the negative energy thresholds are governed by the spin-orbit coupling strength kso and the mass ratio. The fact that these contributions are independent of the two-body scattering length as is a direct consequence of the effective reduction of the dimensionality, and hence of the density of states, near the scattering thresholds due to the single-particle spin-orbit coupling terms. The results are analytically continued to the energy regime where bound states exist. It is shown that our results are consistent with results obtained by alternative approaches. Our formulation, which can be regarded as an extension of the standard textbook partial wave decomposition, can be generalized to two-body systems with other types of spin-orbit coupling, including cases where the center-of-mass momentum does not vanish.

  3. 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.

  4. CSR Interaction for a 2D Energy-Chirped Bunch on a General Orbit

    SciTech Connect

    Rui Li

    2009-05-01

    When an electron bunch with initial linear energy chirp traverses a bunch compression chicane, the bunch interacts with itself via coherent synchrotron radiation (CSR) and space charge force. The effective longitudinal CSR force for such kind of 2D bunch on a circular orbit has been analyzed earlier [1]. In this paper, we present the analytical results of the effective longitudinal CSR force for a 2D energy-chirped bunch going through a general orbit, which includes the entrance and exit of a circular orbit. In particular, we will show the behavior of the force in the last bend of a chicane when the bunch is under extreme compression. This is the condition when bifurcation of bunch phase space occurs in many CSR measurements. [1] R. Li, Phys. Rev. ST Accel. Beams 11, 024401 (2008)

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

    SciTech Connect

    Kimura, M.; Lane, N.F.

    1987-01-01

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

  6. Energy Balance and Power Performance Analysis for Satellite in Low Earth Orbit

    NASA Astrophysics Data System (ADS)

    Jang, Sung-Soo; Kim, Sung-Hoon; Lee, Sang-Ryool; Choi, Jaeho

    2010-09-01

    The electrical power system (EPS) of Korean satellites in low-earth-orbit is designed to achieve energy balance based on a one-orbit mission scenario. This means that the battery has to be fully charged at the end of a one-orbit mission. To provide the maximum solar array (SA) power generation, the peak power tracking (PPT) method has been developed for a spacecraft power system. The PPT is operated by a software algorithm, which tracks the peak power of the SA and ensures the battery is fully charged in one orbit. The EPS should be designed to avoid the stress of electronics in order to handle the main bus power from the SA power. This paper summarizes the results of energy balance to achieve optimal power sizing and the actual trend analysis of EPS performance in orbit. It describes the results of required power for the satellite operation in the worst power conditions at the end-of-life, the methods and input data used in the energy balance, and the case study of energy balance analyses for the normal operation in orbit. Both 10:35 AM and 10:50 AM crossing times are considered, so the power performance in each case is analyzed with the satellite roll maneuver according to the payload operation concept. In addition, the data transmission to the Korea Ground Station during eclipse is investigated at the local-time-ascending-node of 11:00 AM to assess the greatest battery depth-of-discharge in normal operation.

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

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-01

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

  8. 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.

  9. Regenerative fuel cell energy storage system for a low Earth orbit space station

    SciTech Connect

    Martin, R.E.; Garow, J.; Michaels, K.B.

    1984-08-01

    Results of a study to define the characteristics of a regenerative fuel cell energy storage system for a large space station operating in low earth orbit (LEO) are presented. The regenerative fuel cell system employs an alkaline electrolyte fuel cell with the option of employing either an alkaline or a solid polymer electrolyte electrolyzer.

  10. Metabolic energy requirements during manned orbital Skylab missions.

    PubMed

    Rambaut, P C; Leach, C S; Whedon, G D

    1977-01-01

    An investigation was undertaken to determine the metabolic cost of life in space. Energy intake was determined throughout the 28-, 59- and 84-day flights for each of the nine Skylab astronauts. Metabolic excretions were quantitatively collected and analyzed for a variety of biochemical constituents. Body mass was determined each day and body volume was ascertained by stereophotogrammetric means immediately pre- and post-flight. A ground-based control period of at least 3 weeks preceded each flight, and one of at least 18 days followed each flight. Examination of the data reveals that all crew members lost mass in flight, and that this loss did not result in a net increase in density. Elevated urinary and blood nitrogen, a net negative calcium and nitrogen balance and a decrease in the radiographic density of certain bones support the conclusion that lean body mass decreased. That the loss was primarily proteinaceous in nature is evidenced by the comparatively small net change in total body water and by a decrease in total body potassium each measured by isotopic dilution techniques. These changes in body composition, despite a constant caloric intake in flight and on the ground, suggest that the body's demand for exogenous nutrient energy is not measurably changed by exposure to null gravity flight up to 84 days in duration. PMID:11958214

  11. An ab initio molecular orbital study of the argon hydride molecule-ions, ArH + and ArD +, at the MP4(SDQ)/6-311++G(3df,3dp) level. II. The changes in bonding MOs during the Born-Oppenheimer stepwise scan of the internuclear potential energy of the X 1Σ+ ground state of the 40Ar1H+ molecule-ion

    NASA Astrophysics Data System (ADS)

    Schutte, C. J. H.

    2001-12-01

    An analysis of the shapes of the MOs obtained during a Born-Oppenheimer scan of the PE of ArH + by MP4/6-311++G(3df,3dp) MO calculations, allows the successive disengagement of bonding orbitals to be determined. This clearly shows how the different MOs influence the vibrational-rotational properties of ArH + and underlines the importance of the concept of orbital following for molecular spectroscopy and the understanding of chemical bonds in molecules. From this follows an explanation why the first excited state of ArH + and the ground state of ArH are unstable.

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

    NASA Astrophysics Data System (ADS)

    Kalfaoǧlu, Emel; Karabulut, Bünyamin

    2016-03-01

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

  13. 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.

  14. 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.

  15. 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…

  16. Energy preserving low-thrust guidance for orbit transfers in KS variables

    NASA Astrophysics Data System (ADS)

    Hernandez, Sonia; Akella, Maruthi R.

    2016-05-01

    A Lyapunov-based approach is presented to design finite-thrust closed-loop guidance schemes in a two-body model, to perform any general orbit transfer. The design is performed in the Kustaanheimo-Stiefel (KS) model, a regularized two-body framework. The KS model aids in the design of the guidance schemes, but the new guidance solutions can be explicitly characterized in the regular two-body model. The control scheme covers two main phases: first, a matching of the semi-major axis of the target orbit; and second, a matching of the remaining desired orbital elements by holding energy constant. No constraint is imposed on the magnitude of the thrust; however, an emphasis is placed on low-thrust examples.

  17. Super-orbital variability of LS I +61°303 at TeV energies

    NASA Astrophysics Data System (ADS)

    Ahnen, M. L.; Ansoldi, S.; Antonelli, L. A.; Antoranz, P.; Babic, A.; Banerjee, B.; Bangale, P.; Barres de Almeida, U.; Barrio, J. A.; Becerra González, J.; Bednarek, W.; Bernardini, E.; Biasuzzi, B.; Biland, A.; Blanch, O.; Bonnefoy, S.; Bonnoli, G.; Borracci, F.; Bretz, T.; Buson, S.; Carosi, A.; Chatterjee, A.; Clavero, R.; Colin, P.; Colombo, E.; Contreras, J. L.; Cortina, J.; Covino, S.; Da Vela, P.; Dazzi, F.; De Angelis, A.; De Lotto, B.; de Oña Wilhelmi, E.; Delgado Mendez, C.; Di Pierro, F.; Domínguez, A.; Dominis Prester, D.; Dorner, D.; Doro, M.; Einecke, S.; Eisenacher Glawion, D.; Elsaesser, D.; Fernández-Barral, A.; Fidalgo, D.; Fonseca, M. V.; Font, L.; Frantzen, K.; Fruck, C.; Galindo, D.; García López, R. J.; Garczarczyk, M.; Garrido Terrats, D.; Gaug, M.; Giammaria, P.; Godinović, N.; González Muñoz, A.; Gora, D.; Guberman, D.; Hadasch, D.; Hahn, A.; Hanabata, Y.; Hayashida, M.; Herrera, J.; Hose, J.; Hrupec, D.; Hughes, G.; Idec, W.; Kodani, K.; Konno, Y.; Kubo, H.; Kushida, J.; La Barbera, A.; Lelas, D.; Lindfors, E.; Lombardi, S.; Longo, F.; López, M.; López-Coto, R.; López-Oramas, A.; Majumdar, P.; Makariev, M.; Mallot, K.; Maneva, G.; Manganaro, M.; Mannheim, K.; Maraschi, L.; Marcote, B.; Mariotti, M.; Martínez, M.; Mazin, D.; Menzel, U.; Miranda, J. M.; Mirzoyan, R.; Moralejo, A.; Moretti, E.; Nakajima, D.; Neustroev, V.; Niedzwiecki, A.; Nievas Rosillo, M.; Nilsson, K.; Nishijima, K.; Noda, K.; Orito, R.; Overkemping, A.; Paiano, S.; Palacio, J.; Palatiello, M.; Paneque, D.; Paoletti, R.; Paredes, J. M.; Paredes-Fortuny, X.; Pedaletti, G.; Persic, M.; Poutanen, J.; Prada Moroni, P. G.; Prandini, E.; Puljak, I.; Rhode, W.; Ribó, M.; Rico, J.; Rodriguez Garcia, J.; Saito, T.; Satalecka, K.; Schultz, C.; Schweizer, T.; Shore, S. N.; Sillanpää, A.; Sitarek, J.; Snidaric, I.; Sobczynska, D.; Stamerra, A.; Steinbring, T.; Strzys, M.; Takalo, L.; Takami, H.; Tavecchio, F.; Temnikov, P.; Terzić, T.; Tescaro, D.; Teshima, M.; Thaele, J.; Torres, D. F.; Toyama, T.; Treves, A.; Verguilov, V.; Vovk, I.; Ward, J. E.; Will, M.; Wu, M. H.; Zanin, R.; MAGIC Collaboration; Casares, J.; Herrero, A.

    2016-06-01

    Context. The gamma-ray binary LS I +61°303 is a well-established source from centimeter radio up to very high energy (VHE; E> 100 GeV). The broadband emission shows a periodicity of ~26.5 days, coincident with the orbital period. A longer (super-orbital) period of 1667 ± 8 days was proposed from radio variability and confirmed using optical and high-energy (HE; E> 100 MeV) gamma-ray observations. In this paper, we report on a four-year campaign performed by MAGIC together with archival data concentrating on a search for a long-timescale signature in the VHE emission from LS I +61°303. Aims: We focus on the search for super-orbital modulation of the VHE emission, similar to that observed at other energies, and on the search for correlations between TeV emission and an optical determination of the extension of the circumstellar disk. Methods: A four-year campaign has been carried out using the MAGIC telescopes. The source was observed during the orbital phases when the periodic VHE outbursts have occurred (φ = 0.55-0.75, one orbit = 26.496 days). Additionally, we included archival MAGIC observations and data published by the VERITAS collaboration in these studies. For the correlation studies, LS I +61°303 has also been observed during the orbital phases where sporadic VHE emission had been detected in the past (φ = 0.75-1.0). These MAGIC observations were simultaneous with optical spectroscopy from the LIVERPOOL telescope. Results: The TeV flux of the periodical outburst in orbital phases φ = 0.5-0.75 was found to show yearly variability consistent with the long-term modulation of ~4.5 years found in the radio band. This modulation of the TeV flux can be well described by a sine function with a best-fit period of 1610 ± 58 days. The complete data, including archival observations, span two super-orbital periods. There is no evidence for a correlation between the TeV emission and the mass-loss rate of the Be star, but this may be affected by the strong, short

  18. Inspiralling compact binaries in quasi-elliptical orbits: The complete third post-Newtonian energy flux

    SciTech Connect

    Arun, K. G.; Iyer, Bala R.; Qusailah, Moh'd S. S.

    2008-03-15

    The instantaneous contributions to the third post-Newtonian (3PN) gravitational wave luminosity from the inspiral phase of a binary system of compact objects moving in a quasi-elliptical orbit is computed using the multipolar post-Minkowskian wave generation formalism. The necessary inputs for this calculation include the 3PN accurate mass quadrupole moment for general orbits and the mass octupole and current quadrupole moments at 2PN. Using the recently obtained 3PN quasi-Keplerian representation of elliptical orbits, the flux is averaged over the binary's orbit. Supplementing this by the important hereditary contributions arising from tails, tails of tails, and tails-squared terms calculated in a previous paper, the complete 3PN energy flux is obtained. The final result presented in this paper would be needed for the construction of ready-to-use templates for binaries moving on noncircular orbits, a plausible class of sources not only for the space-based detectors like LISA but also for the ground-based ones.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

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

    PubMed

    Prabavathi, N; Nilufer, A; Krishnakumar, V

    2013-10-01

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

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

    SciTech Connect

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

    2009-06-15

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

  2. 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

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2010-11-01

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

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

    PubMed Central

    Sure, Rebecca; Brandenburg, Jan Gerit

    2015-01-01

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

  6. Density functional theory studies of structural properties, energies and natural band orbital for two new aluminate compounds

    NASA Astrophysics Data System (ADS)

    Sahebalzamani, Hajar; Ghammamy, Shahriare; Mehrani, Kheyrollah; Jahandide, Shahram; Salimi, Farshid

    2012-05-01

    Two new aluminate compounds was prepared by the reaction of AlCl3 with KX (X = SCN-, CN-) in a 1:1 mole ratio. In these salts the aluminum atom is surrounded by three chlorine atoms and a ligand (X = SCN-, CN-). In AlCl3SCN anion, the SCN coordinates to the Al through sulfur and AlCl3CN anion the CN- coordinates to the Al center through carbon. The molecular geometry, vibrational frequencies, energies and natural bond orbital (NBO) in the ground state are calculated by using the DFT (B3LYP) methods with 6-311G* basis sets. The geometries and normal modes of vibrations obtained from B3LYP calculations are in good agreement with the experimentally observed data.

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

    PubMed

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

    2016-03-24

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

  8. Engineering Molecular Transformations for Sustainable Energy Conversion

    SciTech Connect

    Neurock, Matthew

    2010-12-03

    Future strategies for sustainable energy production will undoubtedly require processes and materials that can efficiently convert renewable resources into fuels. Nature’s enzymes can exquisitely integrate highly active catalytic centers within flexible environments that can adaptively guide reactants to products with very high activities and selectivities. They are limited, however, by their stability and ability to integrate into large scale production processes. The design of more robust heterogeneous catalytic materials that mimic the performance of enzymes, however, has been hindered by our limited understanding of how such transformations proceed. The tremendous advances in ab initio quantum mechanical methods, atomistic simulations, and high performance computing that have occurred over the past two decades, however, provide unprecedented ability to track molecular transformations and how they proceed at specific sites and within particular environments. This information together with the advances in in situ spectroscopic methods that follow such transformations can begin to enable the design of atomic surface ensembles and nanoscale reaction environments. This paper provides the author’s perspective on how theory and simulation can be used to move from current onedimensional design efforts based on catalytic descriptors to the design of two-dimensional surfaces, threedimensional reaction environments, and proton-coupled electron transfer systems that mimic enzymes in the transformation of molecules.

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

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Porchelvi, E Elamurugu; Muthu, S

    2015-01-01

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

  12. Accurate Energies and Orbital Description in Semi-Local Kohn-Sham DFT

    NASA Astrophysics Data System (ADS)

    Lindmaa, Alexander; Kuemmel, Stephan; Armiento, Rickard

    2015-03-01

    We present our progress on a scheme in semi-local Kohn-Sham density-functional theory (KS-DFT) for improving the orbital description while still retaining the level of accuracy of the usual semi-local exchange-correlation (xc) functionals. DFT is a widely used tool for first-principles calculations of properties of materials. A given task normally requires a balance of accuracy and computational cost, which is well achieved with semi-local DFT. However, commonly used semi-local xc functionals have important shortcomings which often can be attributed to features of the corresponding xc potential. One shortcoming is an overly delocalized representation of localized orbitals. Recently a semi-local GGA-type xc functional was constructed to address these issues, however, it has the trade-off of lower accuracy of the total energy. We discuss the source of this error in terms of a surplus energy contribution in the functional that needs to be accounted for, and offer a remedy for this issue which formally stays within KS-DFT, and, which does not harshly increase the computational effort. The end result is a scheme that combines accurate total energies (e.g., relaxed geometries) with an improved orbital description (e.g., improved band structure).

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

    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.

  14. Prospects for ultrahigh-energy particle observation based on the lunar orbital LORD space experiment

    NASA Astrophysics Data System (ADS)

    Ryabov, V. A.; Chechin, V. A.; Gusev, G. A.; Maung, K. T.

    2016-08-01

    The problem of searching for highest-energy cosmic rays and neutrinos in the Universe is reviewed. Possibilities for using the radio method for detecting particles of energies above the GZK cut-off are analyzed. The method is based on the registration of coherent radio emission produced by cascades of most energetic particles in radio-transparent lunar regolith. The Luna-Resurs Orbiter space mission to be launched in the near future (2020) involves the Lunar Orbital Radio Detector (LORD). The design of the LORD space instrument and its scientific potentialities for registration of low-intense cosmic ray particle fluxes of energies above the GZK cut-off up to 1024eV are discussed. The designed LORD module (including the antenna, amplification, and data-acquisition systems) now is under construction. Exposure and capabilities of the LORD space experiment for detection of ultrahigh-energy cosmic rays and neutrinos have been compared with those for well-known current and proposed experiments. The LORD space experiment will make it possible to obtain important information on the highest-energy particles in the Universe, to verify modern models for the origin and the propagation of ultrahigh-energy cosmic rays and neutrinos.

  15. The Bond Order of C2 from a Strictly N-Representable Natural Orbital Energy Functional Perspective.

    PubMed

    Piris, Mario; Lopez, Xabier; Ugalde, Jesus M

    2016-03-14

    The bond order of the ground electronic state of the carbon dimer has been analyzed in the light of natural orbital functional theory calculations carried out with an approximate, albeit strictly N-representable, energy functional. Three distinct solutions have been found from the Euler equations of the minimization of the energy functional with respect to the natural orbitals and their occupation numbers, which expand upon increasing values of the internuclear coordinate. In the close vicinity of the minimum energy region, two of the solutions compete around a discontinuity point. The former, corresponding to the absolute minimum energy, features two valence natural orbitals of each of the following symmetries, σ, σ*, π and π*, and has three bonding interactions and one antibonding interaction, which is very suggestive of a bond order large than two but smaller than three. The latter, features one σ-σ* linked pair of natural orbitals and three degenerate pseudo-bonding like orbitals, paired each with one triply degenerate pseudo-antibonding orbital, which points to a bond order larger than three. When correlation effects, other than Hartree-Fock for example, between the paired natural orbitals are accounted for, this second solution vanishes yielding a smooth continuous dissociation curve. Comparison of the vibrational energies and electron ionization energies, calculated on this curve, with their corresponding experimental marks, lend further support to a bond order for C2 intermediate between acetylene and ethylene. PMID:26822104

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    SciTech Connect

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

    2008-05-20

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

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

    PubMed

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

    2011-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Karna, Shashi P.

    2002-01-01

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

  20. 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.

  1. Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors.

    PubMed

    Oliveira, Fernanda G; Sant'Anna, Carlos M R; Caffarena, Ernesto R; Dardenne, Laurent E; Barreiro, Eliezer J

    2006-09-01

    In the present work, several computational methodologies were combined to develop a model for the prediction of PDE4B inhibitors' activity. The adequacy of applying the ligand docking approach, keeping the enzyme rigid, to the study of a series of PDE4 inhibitors was confirmed by a previous molecular dynamics analysis of the complete enzyme. An exhaustive docking procedure was performed to identify the most probable binding modes of the ligands to the enzyme, including the active site metal ions and the surrounding structural water molecules. The enzyme-inhibitor interaction enthalpies, refined by using the semiempirical molecular orbital approach, were combined with calculated solvation free energies and entropy considerations in an empirical free energy model that enabled the calculation of binding free energies that correlated very well with experimentally derived binding free energies. Our results indicate that both the inclusion of the structural water molecules close to the ions in the binding site and the use of a free energy model with a quadratic dependency on the ligand free energy of solvation are important aspects to be considered for molecular docking investigations involving the PDE4 enzyme family. PMID:16843671

  2. 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.

  3. Linear energy transfer (LET) spectra of cosmic radiation in low Earth orbit

    NASA Technical Reports Server (NTRS)

    Akopova, A. B.; Magradze, N. V.; Dudkin, V. E.; Kovalev, E. E.; Benton, E. V.; Frank, A. L.; Benton, E. R.; Parnell, T. A.; Watts, J. W. Jr

    1990-01-01

    Integral linear energy transfer (LET) spectra of cosmic radiation (CR) particles were measured on five Cosmos series spacecraft in low Earth orbit (LEO). Particular emphasis is placed on results of the Cosmos 1887 biosatellite which carried a set of joint U.S.S.R.-U.S.A. radiation experiments involving passive detectors that included thermoluminescent detectors (TLDs), plastic nuclear track detectors (PNTDs), fission foils, nuclear photo-emulsions, etc. which were located both inside and outside the spacecraft. Measured LET spectra are compared with those theoretically calculated. Results show that there is some dependence of LET spectra on orbital parameters. The results are used to estimate the CR quality factor (QF) for the Cosmos 1887 mission.

  4. Linear Energy Transfer (LET) spectra of cosmic radiation in low Earth orbit

    NASA Technical Reports Server (NTRS)

    Parnell, T. A.; Watts, J. W., Jr.; Akopova, A. B.; Magradze, N. V.; Dudkin, V. E.; Kovalev, E. E.; Potapov, Yu. V.; Benton, E. V.; Frank, A. L.; Benton, E. R.

    1995-01-01

    Integral linear energy transfer (LET) spectra of cosmic radiation (CR) particles were measured on five Cosmos series spacecraft in low Earth orbit (LEO). Particular emphasis is placed on results of the Cosmos 1887 biosatellite which carried a set of joint U.S.S.R.-U.S.A. radiation experiments involving passive detectors that included thermoluminescent detectors (TLD's), plastic nuclear track detectors (PNTD's), fission foils, nuclear photo-emulsions, etc. which were located both inside and outside the spacecraft. Measured LET spectra are compared with those theoretically calculated. Results show that there is some dependence of LET spectra on orbital parameters. The results are used to estimate the CR quality factor (QF) for the COSMOS 1887 mission.

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

    PubMed

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

    2016-07-18

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

  6. 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.

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

    PubMed

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

    2012-05-28

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

  8. 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.

  9. Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

    NASA Astrophysics Data System (ADS)

    Blum, Volker

    This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

  10. Molecular structure, vibrational spectra and DFT molecular orbital calculations (TD-DFT and NMR) of the antiproliferative drug Methotrexate

    NASA Astrophysics Data System (ADS)

    Ayyappan, S.; Sundaraganesan, N.; Aroulmoji, V.; Murano, E.; Sebastian, S.

    2010-09-01

    The FT-IR and FT-Raman spectral studies of the Methotrexate (MTX) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of MTX have been investigated with the help of B3LYP density functional theory (DFT) using 6-31G(d) as basis set. Detailed analysis of the vibrational spectra has been made with the aid of theoretically predicted vibrational frequencies. The vibrational analysis confirms the differently acting ring modes, steric repulsion, conjugation and back-donation. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complement with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Good correlations between the experimental 1H and 13C NMR chemical shifts in DMSO solution and calculated GIAO shielding tensors were found.

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

    PubMed

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

    2015-05-01

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

  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)

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

    2015-05-01

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

  13. 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.

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

    PubMed Central

    Song, Lingchun; Mo, Yirong; Gao, Jiali

    2009-01-01

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

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

    PubMed

    Song, Lingchun; Mo, Yirong; Gao, Jiali

    2009-01-01

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

  16. Observation of ultrahigh-energy cosmic rays and neutrinos from lunar orbit: LORD space experiment

    NASA Astrophysics Data System (ADS)

    Ryabov, Vladimir; Chechin, Valery; Gusev, German

    The problem of detecting highest-energy cosmic rays and neutrinos in the Universe is reviewed. Nowadays, there becomes clear that observation of these particles requires approaches based on novel principles. Projects based on orbital radio detectors for particles of energies above the CZK cut-off are discussed. We imply the registration of coherent Cherenkov radio emission produced by cascades of most energetic particles in radio-transparent lunar regolith. The Luna-Glob space mission proposed for launching in the near future involves the Lunar Orbital Radio Detector (LORD). The feasibility of LORD space instrument to detect radio signals from cascades initiated by ultrahigh-energy particles interacting with lunar regolith is examined. The comprehensive Monte Carlo calculations were carried out within the energy range of 10 (20) -10 (25) eV with the account for physical properties of the Moon such as its density, the lunar-regolith radiation length, the radio-wave absorption length, the refraction index, and the orbital altitude of a lunar satellite. We may expect that the LORD space experiment will surpass in its apertures and capabilities the majority of well-known current and proposed experiments dealing with the detection of both ultrahigh-energy cosmic rays and neutrinos. The design of the LORD space instrument and its scientific potentialities in registration of low-intense cosmic-ray particle fluxes above the GZK cut-off up to 10 (25) eV is discussed as well. The designed LORD module (including an antenna system, amplifiers, and a data acquisition system) now is under construction. The LORD space experiment will make it possible to obtain important information on the highest-energy particles in the Universe, to verify modern models for the origin and the propagation of ultrahigh-energy cosmic rays and neutrinos. Successful completion of the LORD experiment will permit to consider the next step of the program, namely, a multi-satellite lunar systems to

  17. Molecular geometry, vibrational spectra, atomic charges, frontier molecular orbital and Fukui function analysis of antiviral drug zidovudine

    NASA Astrophysics Data System (ADS)

    Ramkumaar, G. R.; Srinivasan, S.; Bhoopathy, T. J.; Gunasekaran, S.

    2012-12-01

    The solid phase FT-IR and FT-Raman spectra of zidovudine (AZT) were recorded in the regions 4000-400 and 3500-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of zidovudine were obtained by the Restricted Hartree-Fock (RHF) density functional theory (DFT) with complete relaxation in the potential energy surface using 6-31G(d,p) basis set. The harmonic vibrational frequencies for zidovudine were calculated and the scaled values have been compared with experimental values of FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The harmonic vibrational wave numbers and intensities of vibrational bands of zidovudine with its cation and anion were calculated and compared with the neutral AZT. The DFT calculated HOMO and LUMO energies 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 AZT.

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

    PubMed

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

    Conradie, Jeanet; Ghosh, Abhik

    2014-05-19

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

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

    PubMed

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

    2011-11-15

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

  2. Aplication of Kohn-Sham Theory for Orbital Dependent (Self-Interaction-Corrected) Exchange-Correlation Energy Functionals to First Row Heteropolar Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Krieger, J. B.; Chen, Jiqiang; Iafrate, G. J.

    1996-03-01

    We have employed the local-spin-density approximation with orbital self-interaction-correction (LSDSIC) for the exchange-correlation energy functional in the calculation of the ground state properties of first row heteropolar diatomic molecules. The Kohn-Sham molecular orbitals are obtained by fully numerical solution of a Schrodinger equation including the Optimized Effective Potential in the KLIfootnote J. B. Krieger, Y. Li and G. J Iafrate in "Density Functional Theory" eds. E. K. U. Gross and R. M. Dreizler, NATO ASI SERIES, Plenum, New York (1995) approximation. We find that in the exchange-only case, our results closely approximate those of non-local Hartree-Fock calculations. Results for the bond length, total energy, dissociation energy, single particle energy eigenvalue, ɛ _m, for the highest lying occupied state, and vibration frequency obtained by employing the LSDSIC for exchange and correlation will be presented. These results will be compared to experimental values as well as to the results obtained by employing the LSD exchange-correlation energy functional. We find that the total energy, dissociation energy and ɛ m are given with greater accuracy than the corresponding LSD results. However, the bond length is less accurately given and the vibration frequency is significantly in error.

  3. Global calculations of microscopic energies and nuclear deformations: Isospin dependence of the spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Wu, Zhe-Ying; Qi, Chong; Wyss, Ramon; Liu, Hong-Liang

    2015-08-01

    Background: The deviation between different model calculations that may occur when one goes toward regions where the masses are unknown is getting increased attention. This is related to the uncertainties of the different models which may have not been fully understood. Purpose: To explore in detail the effect of the isospin dependence of the spin-orbital force in the Woods-Saxon potential on global binding energy and deformation calculations. Method: The microscopic energies and nuclear deformations of about 1850 even-even nuclei are calculated systematically within the macroscopic-microscopic framework using three Woods-Saxon parametrizations, with different isospin dependencies, which were constructed mainly for nuclear spectroscopy calculations. Calculations are performed in the deformation space (β2,γ ,β4) . Both the monopole and doubly stretched quadrupole interactions are considered for the pairing channel. Results: The ground-state deformations obtained by the three calculations are quite similar to each other. Large differences are seen mainly in neutron-rich nuclei and in superheavy nuclei. Systematic calculations on the shape-coexisting second minima are also presented. As for the microscopic energies of the ground states, the results are also very close to each other. Only in a few cases the difference is larger than 2 MeV. The total binding energy is estimated by adding the macroscopic energy provided by the usual liquid drop model with its parameters fitted through the least square root and minimax criteria. Calculations are also compared with the results of other macroscopic-microscopic mass models. Conclusions: All the three calculations give similar values for the deformations, microscopic energies, and binding energies of most nuclei. One may expect to have a better understanding of the isospin dependence of the spin-orbital force with more data on proton- and neutron-rich nuclei.

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

    PubMed

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

    2016-04-26

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

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

    PubMed

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

    2013-05-30

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

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

    PubMed

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

    2016-05-12

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

  7. Minimum energy-loss guidance for aero-assisted orbital plane change

    NASA Technical Reports Server (NTRS)

    Hull, D. G.; Giltner, J. M.; Speyer, J. L.; Mapar, J.

    1984-01-01

    Minimum energy-loss guidance for the aero-assisted plane change of an orbiting vehicle is developed and applied to the plane change of a circular orbit. First, trajectories which minimize the fuel required to change the orbital plane are computed for a realistic vehicle. From these trajectories, it is observed that the fuel weight is minimized if the velocity at exit from the atmosphere is maximized. Next, for the atmospheric turn, approximate optimal controls (angle of attack and bank angle) which maximize the exit velocity are derived. Finally, the minimum-fuel problem is resolved using optimal guidance for the atmospheric part of the trajectory, and the optimization problem reduces to a one-dimensional parameter minimization. Successful plane changes up to 40 deg are demonstrated. Optimal guidance requires up to 14 percent more fuel than the 'true' optimum but only 50 percent of the fuel required by the single-impulse maneuver. Finally, the guidance law developed here is implementable because only algebraic manipulations are required.

  8. 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.

  9. 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.

  10. Laser orbital energy moduleâ'the first step to space power station

    NASA Astrophysics Data System (ADS)

    Babaev, Igor K.; Leontiev, Alexandr I.; Samsonov, Vladimir L.; Schmidt, Konstantin L.; Katorgin, Boris I.; Ponomarov-Stepney, Niokolay N.

    1995-01-01

    The possibility of power module development as the first step for the development of an orbital power state (OPS) is reviewed in this report. The most probable OPS scheme is a laser system with direct nuclear pumping. Since this task is not yet been defined well enough in its technical form, a better developed prototype has been selected in the form of a free electron laser with the power system on the basis of a gas core nuclear reactor (MGD)—generator and multi-modular closed gas turbine system. Taking into consideration that many of the elements of this orbital complex are in the stage of advanced development within current programs in different countries, we propose to continue the research and development of the remainder of the key elements. This work was carried out earlier for military purposes but was halted after the end of the cold war. It is proposed to perform this work within the framework of international cooperation, and a lot of the achievements of the Russian nuclear and aerospace technology will be utilized in the project. It will be a worthwhile task to achieve within 6-8 years the development of an orbital power module with a shortwave laser having the power of NL=100 kW for short-time periodical energy transmision from the 500 km orbital to a stationary site in Eastern Siberia. The power supply for this laser is based upon a closed high temperature gas turbine system with a graphite heat accumulator, which is charged with electricity generated by the ``Topaz''-type nuclear power system.

  11. Ab Initio determination of Cu 3d orbital energies in layered copper oxides

    PubMed Central

    Hozoi, Liviu; Siurakshina, Liudmila; Fulde, Peter; van den Brink, Jeroen

    2011-01-01

    It has long been argued that the minimal model to describe the low-energy physics of the high Tc superconducting cuprates must include copper states of other symmetries besides the canonical one, in particular the orbital. Experimental and theoretical estimates of the energy splitting of these states vary widely. With a novel ab initio quantum chemical computational scheme we determine these energies for a range of copper-oxides and -oxychlorides, determine trends with the apical Cu–ligand distances and find excellent agreement with recent Resonant Inelastic X-ray Scattering measurements, available for La2CuO4, Sr2CuO2Cl2, and CaCuO2. PMID:22355584

  12. Low-Energy Structures in Strong Field Ionization Revealed by Quantum Orbits

    SciTech Connect

    Yan, Tian-Min; Popruzhenko, S. V.; Vrakking, M. J. J.; Bauer, D.

    2010-12-17

    Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schroedinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the 'strong field approximation' (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered 'low-energy structure' [C. I. Blaga et al., Nature Phys. 5, 335 (2009) and W. Quan et al., Phys. Rev. Lett. 103, 093001 (2009)].

  13. Low-energy structures in strong field ionization revealed by quantum orbits.

    PubMed

    Yan, Tian-Min; Popruzhenko, S V; Vrakking, M J J; Bauer, D

    2010-12-17

    Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schrödinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the "strong field approximation" (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered "low-energy structure" [C. I. Blaga, Nature Phys. 5, 335 (2009) and W. Quan, Phys. Rev. Lett. 103, 093001 (2009). PMID:21231586

  14. Russian measurements of neutron energy spectra on the Mir orbital station.

    PubMed

    Lyagushin, V I; Dudkin, V E; Potapov, Y V; Sevastianov, V D

    2001-06-01

    Results of the experiments on neutron energy spectra measurements within broad energy range from 5 x 10(-7) to 2 x 10(2) MeV aboard the Mir orbital station and equivalent neutron dose estimation are presented. Four measurement techniques were used during the experiments. The shape of spectra and their absolute values are in good agreement. According to those experiments, an equivalent neutron dose depends upon effective shielding thickness and spacecraft mass. The neutron dose mentioned is comparable with that of ionizing radiation. Neutron flux levels measured aboard the Mir station have shown that a neutron spectrometer involving broad energy range will be used within the radiation monitoring systems in manned space flights. PMID:11855413

  15. Regenerative Hydrogen-oxygen Fuel Cell-electrolyzer Systems for Orbital Energy Storage

    NASA Technical Reports Server (NTRS)

    Sheibley, D. W.

    1984-01-01

    Fuel cells have found application in space since Gemini. Over the years technology advances have been factored into the mainstream hardware programs. Performance levels and service lives have been gradually improving. More recently, the storage application for fuel cell-electrolyzer combinations are receiving considerable emphasis. The regenerative system application described here is part of a NASA Fuel Cell Program which was developed to advance the fuel cell and electrolyzer technology required to satisfy the identified power generation and energy storage need of the Agency for space transportation and orbital applications to the year 2000.

  16. Improvements on the minimax algorithm for the Laplace transformation of orbital energy denominators

    NASA Astrophysics Data System (ADS)

    Helmich-Paris, Benjamin; Visscher, Lucas

    2016-09-01

    We present a robust and non-heuristic algorithm that finds all extremum points of the error distribution function of numerically Laplace-transformed orbital energy denominators. The extremum point search is one of the two key steps for finding the minimax approximation. If pre-tabulation of initial guesses is supposed to be avoided, strategies for a sufficiently robust algorithm have not been discussed so far. We compare our non-heuristic approach with a bracketing and bisection algorithm and demonstrate that 3 times less function evaluations are required altogether when applying it to typical non-relativistic and relativistic quantum chemical systems.

  17. Low Molecular Weight Norbornadiene Derivatives for Molecular Solar-Thermal Energy Storage.

    PubMed

    Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl; Moth-Poulsen, Kasper

    2016-09-01

    Molecular solar-thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193-260 g mol(-1) ) norbornadiene-quadricyclane systems. The molecules feature cyano acceptor and ethynyl-substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo-thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396-629 kJ kg(-1) ). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. PMID:27492997

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

    PubMed

    Moncho, Salvador; Autschbach, Jochen

    2010-12-01

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

  19. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods.

    PubMed

    Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua

    2015-01-13

    We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207

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

    PubMed

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

    1995-01-01

    stoichiometry was in fact prepared. (13)C spin-lattice relaxation rates of neutral, zwitterionic and anionic piroxicam, in DMSO solution are explained by the thermal equilibrium between the three most stable structures of the three forms, thus confirming the high quality of the force field. The EPR spectrum of [Cu(II)(Pir)(2)(DMF)(2)] (DMSO/GLY, 2:1, v/v, 298 and 110 K) agrees with a N2O2+O2 pseudo-octahedral coordination geometry. The EPR spectrum of [Cu(II)(Pir)(2).0.5DMF agrees with a pseudo-tetrahedral coordination geometry. The parameters extracted from the room temperature spectra of the solution phases are in agreement with the data reported for powder and frozen solutions. The extended-Hückel calculations on minimum energy structures of [Cu(II)(Pir)(2)(DMF)(2)] and [Cu(II)(Pir)(2)] (square planar) revealed that the HOMOs have a relevant character of d(x) (2)-y(2). On the other hand the HOMO of a computer generated structure for [Cu(II)(Pir)(2)] (pseudo-tetrahedral) has a relevant character of d(xy) atomic orbital. A d(xy) orbital is better suited to allow a dpi-ppi interaction to the O(2) (-) anion. Therefore this work shows that the anti-inflammatory activity of piroxicam could be due in part to the formation of [Cu(II)(Pir)(2)] chelates, which can exert a SOD-like activity. PMID:18472745

  1. 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

  2. Confinement effects on excitation energies and regioselectivity as probed by the Fukui function and the molecular electrostatic potential

    NASA Astrophysics Data System (ADS)

    Borgoo, Alex; Tozer, David; Geerlings, Paul; de Proft, Frank

    2009-03-01

    When a molecule is placed as a guest inside a zeolite pore, its electronic structure will be altered, among others by the effect of the so-called ``confinement". It has been established that the compression of the molecular orbitals influences a system's reactivity. In this work we use a simple potential barrier method to quantify the importance of confinement effects on chemical reactivity. In the first part, excitation energies and molecular orbital energy gaps are evaluated for molecules placed in cavities of different sizes. Our results for ethylene and formaldehyde reveal an increase in excitation energy and the gap between the occupied and the unoccupied levels. In the case of the larger molecules naphthalene and anthracene, the HOMO-LUMO gap shows very little sensitivity to the confinement. To investigate the role of confinement effects on local aspects of chemical reactivity and on regioselectivity, we evaluated its effect on the Fukui function and the molecular electrostatic potential, reactivity indices that are central in the description of orbital and charge controlled reactions. The results indicate that confinement can influence the regioselectivity and that the reactivity of anions is expected to change, due to the artificial binding of the exess electron.

  3. A Molecular orbital study of the rotation about the CC bond in styrene

    NASA Astrophysics Data System (ADS)

    Bock, Charles W.; Trachtman, Mendel; George, Philip

    1985-03-01

    The geometry and energy of styrene have been calculated using the 6-31G basis set as a function of the C βC 2C 1C 2 dihedral angle-Φ = 0°(cis), 15°, 30°, 60° and 90° — assuming that the vinyl and phenyl groups remain planar, but otherwise with full geometry optimization. Similar calculations have been carried out for 1,3-butadiene and 3-methylene-1,4-pentadiene (MPD) where rotation about 180° generates a different and not the same conformer. The torsional potential energy curve for styrene has a very flat minimum Φ = 0, i.e. the cis structure is the most stable, whereas butadiene and MPD have minima in the region Φ = 37° to 40°, indicative of more stable gauche structures. For styrene the barrier height Φ = 90° is 131.1 KJ mol -1. These results provide strong support for the potential function obtained by Hollas and Ridley from single level vibronic fluorescence and other spectroscopic data. The distortion of the benzene ring brought about the vinyl group substitution is discussed, also the variation of the C/C and H/C bond lenghts with Φ and the change in charge on the vinyl group and the polarity of the various bonds in the conversion of the cis into the 90° gauche conformer. The stabilization energy for styrene relative to that for benzene has been evaluated according to various criteria, and, in addition, the energy associated with the distortion of the ring.

  4. Two-center interference in molecular photoelectron energy spectra with intense attosecond circularly polarized XUV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bian, Xue-Bin; Bandrauk, André D.

    2014-08-01

    We study two-center electron interference in molecular photoionization processes by intense attosecond circularly polarized extreme ultraviolet (XUV) laser pulses in both symmetric H2+ and nonsymmetric HHe2+ one-electron diatomic systems. Simulations from numerical solutions of time-dependent Schrödinger equations for the oriented symmetric molecular ion H2+ exhibit a signature of interference with double peaks (minima) in molecular attosecond photoelectron energy spectra (MAPES) at critical angles ϑc between the continuum electron momentum pe and the molecular internuclear R axis. The interference patterns are shown to be influenced by the molecular Coulomb potential, leading to a shift of the critical angle ϑc. Dependence of the two-center interference on the pulse ellipticity is also investigated. Furthermore, it is found that the interference phenomena are critically sensitive to the molecular orbital symmetry. For the nonsymmetric molecular ion HHe2+, such double peaks in MAPES also occur, thus suggesting a method for imaging orbitals in molecules by intense ultrashort circularly polarized XUV pulses on the attosecond time scale.

  5. Localization of energy on the molecular scale

    SciTech Connect

    Lindenberg, K.; Brown, D.W.

    1997-12-31

    We discuss the spontaneous localization of vibrational energy in translationally invariant anharmonic chains at finite temperatures. In addition to the familiar energy-driven coherent mechanisms, which are rapidly degraded by thermal fluctuations, we identify the entropy-driven phenomenon we call {open_quotes}stochastic localization{close_quotes}, within which we include a number of characteristics of soft anharmonic oscillators in thermal equilibrium. Principal among these are a tendency for soft oscillators to spend more time at higher energies than comparable harmonic oscillators, and for high-energy fluctuations in soft oscillators to persist for longer times than lower-energy fluctuations, leading to a tendency for energy fluctuations to be organized into {open_quotes}bursts{close_quotes} separated by intervals of relative quiet. We illustrate the effects of stochastic localization on a bistable impurity embedded in a chain of soft oscillators by comparing it to an impurity embedded in a harmonic chain. Effects on transition rates at a given system energy can be quite dramatic.

  6. A proposal for the proper use of pseudopotentials in molecular orbital cluster model studies of chemisorption

    NASA Technical Reports Server (NTRS)

    Bagus, P. S.; Bauschlicher, C. W., Jr.; Nelin, C. J.; Laskowski, B. C.; Seel, M.

    1984-01-01

    The interaction of CO with Cu5, Ni5, and Al4 are treated as model systems for molecular adsorption on metal surfaces. The effect of the use of pseudopotentials for the metal atoms is studied by considering three types of clusters. In the first case, all of the metal electrons are explicitly included in the wave function; an all electron (AE) treatment. In the second case, the metal atom which directly interacts with the CO is described by AE but the remaining metal atoms include a pseudopotential for their core electrons. Finally, in the third case, all of the metal atoms in the cluster have a pseudopotential treatment for the core electrons. The AE cluster results are taken as reference values for the two pseudopotential treatments. The mixed cluster results are in excellent agreement with those of the all AE clusters; however, the results for the all pseudopotential cluster of Ni5CO or of Cu5CO are qualitatively different. The pseudopotential treatment for all of the metal atoms often leads to results that contain serious errors and it is not a reliable approach.

  7. Influence of radiant energy exchange on the determination of convective heat transfer rates to Orbiter leeside surfaces during entry

    NASA Technical Reports Server (NTRS)

    Throckmorton, D. A.

    1982-01-01

    Temperatures measured at the aerodynamic surface of the Orbiter's thermal protection system (TPS), and calorimeter measurements, are used to determine heating rates to the TPS surface during atmospheric entry. On the Orbiter leeside, where convective heating rates are low, it is possible that a significant portion of the total energy input may result from solar radiation, and for the wing, cross radiation from the hot (relatively) Orbiter fuselage. In order to account for the potential impact of these sources, values of solar- and cross-radiation heat transfer are computed, based upon vehicle trajectory and attitude information and measured surface temperatures. Leeside heat-transfer data from the STS-2 mission are presented, and the significance of solar radiation and fuselage-to-wing cross-radiation contributions to total energy input to Orbiter leeside surfaces is assessed.

  8. Potential energy surface for C2H4I2+ dissociation including spin-orbit effects

    SciTech Connect

    Siebert, Matthew R.; Aquino, Adelia J.; De Jong, Wibe A.; Granucci, Giovanni; Hase, William L.

    2012-10-24

    Previous experiments [Baer, et al. J. Phys. Chem. A 116, 2833 (2012)] have studied the dissociation of 1,2-diiodoethane radical cation (C2H4I2+•) and found a one-dimensional distribution of translational energy; an odd finding considering most product relative translational energy distributions are two-dimensional. The goal of this study is to obtain an accurate understanding of the potential energy surface (PES) topology for the unimolecular decomposition reaction C2H4I2+• - C2H4I+ + I•. This is done through comparison of many single-reference electronic structure methods, coupled-cluster single point (energy) calculations, and multi-reference calculations used to quantify spin-orbit (SO) coupling effects. We find that the structure of the C2H4I2+• reactant has a substantial effect on the role of SO coupling on the reaction energy. Both the BHandH and MP2 theories with an ECP/6-31++G** basis set, and without SO coupling corrections, provide accurate models for the reaction energetics. MP2 theory gives an unsymmetric structure with different C-I bond lengths, resulting in a SO energy for C2H4I2+• similar to that for the product I-atom and a negligible SO correction to the reaction energy. In contrast, DFT gives a symmetric structure for C2H4I2+•, similar to that of the neutral C2H4I2 parent, resulting in a substantial SO correction and increasing the reaction energy by 6.0-6.5 kcal/mol. Also, we find that for this system single point energy calculations are inaccurate, since a small change in geometry can lead to a large change in energy.

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

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

  10. Free energy calculations for molecular solids using GROMACS

    NASA Astrophysics Data System (ADS)

    Aragones, J. L.; Noya, E. G.; Valeriani, C.; Vega, C.

    2013-07-01

    In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

  11. Generation of Equal-Energy Orbital Angular Momentum Beams via Photopatterned Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Chen, Peng; Ge, Shi-Jun; Ma, Ling-Ling; Hu, Wei; Chigrinov, Vladimir; Lu, Yan-Qing

    2016-04-01

    Orbital angular momentum (OAM) has been extensively studied to date and has become topical in the last few years due to its potential for increasing bandwidth in optical communications. The so-called Dammann vortex grating (DVG) can generate a series of equal-energy OAM beams and satisfactorily realize OAM parallel detection, an important challenge in this field. However, previously reported DVGs suffer from polarization sensitivity, low efficiency, or the lack of tunability and mode variety. Here, a design of liquid-crystal DVGs is proposed and demonstrated for the generation of various equal-energy OAM beams. The DVGs, featured by alternative orthogonally planar-aligned regions, are carried out via photopatterning technology. Beam arrays composed of arbitrary OAM modes, as well as two-dimensional ones, are generated in good quality and high efficiency. The liquid-crystal DVGs exhibit merits of excellent polarization independency, electrical switchability, and tunability. This supplies a promising approach towards OAM generation, manipulation, and detection.

  12. Alkaline regenerative fuel cell energy storage system for manned orbital satellites

    NASA Technical Reports Server (NTRS)

    Martin, R. E.; Gitlow, B.; Sheibley, D. W.

    1982-01-01

    It is pointed out that the alkaline regenerative fuel cell system represents a highly efficient, lightweight, reliable approach for providing energy storage in an orbiting satellite. In addition to its energy storage function, the system can supply hydrogen and oxygen for attitude control of the satellite and for life support. A summary is presented of the results to date obtained in connection with the NASA-sponsored fuel cell technology advancement program, giving particular attention to the requirements of the alkaline regenerative fuel cell and the low-earth mission. Attention is given to system design guidelines, weight considerations, gold-platinum cathode cell performance, matrix development, the electrolyte reservoir plate, and the cyclical load profile tests.

  13. A comparative study of isoelectronic and isogyric reactions: Molecular orbital calculations of diatomic hydrides and halides

    SciTech Connect

    Deakyne, C.A. ); Liebman, J.F. ); Frenking, G. ); Koch, W. )

    1990-03-22

    MP4/6-311G(2df,2pd)//MP2/6-31G{sup **} and MPn/6-31G{sup **}//ClD/6-31G{sup **} (n = 2-4) calculations have been carried out for HeF{sup +}, NeF{sup +}, ArF{sup +}, ArH{sup +}, HCl, HCl{sup +}, ClF, Cl{sub 2}, HF, HF{sup +}, F{sub 2}, H{sub 2}, and H{sub 2}{sup +}. Structures, vibrational frequencies, ionization potentials, reaction enthalpies, and triplet vs singlet energies (for HeF{sup +}, NeF{sup +}, and ArF{sup +}) have been examined. The reactions considered include hydrogenolysis and bond dissociation reactions.

  14. Relative Photoionization Cross Sections of Super-Atom Molecular Orbitals (SAMOs) in C60.

    PubMed

    Bohl, Elvira; Sokół, Katarzyna P; Mignolet, Benoit; Thompson, James O F; Johansson, J Olof; Remacle, Francoise; Campbell, Eleanor E B

    2015-11-25

    The electronic structure and photoinduced dynamics of fullerenes, especially C60, is of great interest because these molecules are model systems for more complex molecules and nanomaterials. In this work we have used Rydberg Fingerprint Spectroscopy to determine the relative ionization intensities from excited SAMO (Rydberg-like) states in C60 as a function of laser wavelength. The relative ionization intensities are then compared to the ratio of the photoionization widths of the Rydberg-like states, computed in time-dependent density functional theory (TD-DFT). The agreement is remarkably good when the same photon order is required to energetically access the excited states. This illustrates the predictive potential of quantum chemistry for studying photoionization of large, complex molecules as well as confirming the assumption that is often made concerning the multiphoton excitation and rapid energy redistribution in the fullerenes. PMID:26551039

  15. Nondynamical correlation energy in model molecular systems

    NASA Astrophysics Data System (ADS)

    Chojnacki, Henryk

    The hypersurfaces for the deprotonation processes have been studied at the nonempirical level for H3O+, NH+4, PH+4, and H3S+ cations within their correlation consistent basis set. The potential energy curves were calculated and nondynamical correlation energies analyzed. We have found that the restricted Hartree-Fock wavefunction leads to the improper dissociation limit and, in the three latest cases requires multireference description. We conclude that these systems may be treated as a good models for interpretation of the proton transfer mechanism as well as for testing one-determinantal or multireference cases.

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

    SciTech Connect

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

    2015-07-07

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

  17. 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.

  18. 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

  19. Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

    SciTech Connect

    Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F. Ingrosso, Francesca

    2014-07-21

    In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the

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

    NASA Astrophysics Data System (ADS)

    Li, Yanli; Dabo, Ismaila

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-01-01

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

  2. A perovskite oxide optimized for oxygen evolution catalysis from molecular orbital principles.

    PubMed

    Suntivich, Jin; May, Kevin J; Gasteiger, Hubert A; Goodenough, John B; Shao-Horn, Yang

    2011-12-01

    The efficiency of many energy storage technologies, such as rechargeable metal-air batteries and hydrogen production from water splitting, is limited by the slow kinetics of the oxygen evolution reaction (OER). We found that Ba(0.5)Sr(0.5)Co(0.8)Fe(0.2)O(3-δ) (BSCF) catalyzes the OER with intrinsic activity that is at least an order of magnitude higher than that of the state-of-the-art iridium oxide catalyst in alkaline media. The high activity of BSCF was predicted from a design principle established by systematic examination of more than 10 transition metal oxides, which showed that the intrinsic OER activity exhibits a volcano-shaped dependence on the occupancy of the 3d electron with an e(g) symmetry of surface transition metal cations in an oxide. The peak OER activity was predicted to be at an e(g) occupancy close to unity, with high covalency of transition metal-oxygen bonds. PMID:22033519

  3. Energy Transformation in Molecular Electronic Systems

    SciTech Connect

    Kasha, Michael

    1999-05-17

    This laboratory has developed many new ideas and methods in the electronic spectroscopy of molecules. This report covers the contract period 1993-1995. A number of the projects were completed in 1996, and those papers are included in the report. The DOE contract was terminated at the end of 1995 owing to a reorganizational change eliminating nationally the projects under the Office of Health and Environmental Research, U. S. Department of Energy.

  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. Modulation of Energy Conversion Processes in Carbonaceous Molecular Bearings.

    PubMed

    Hitosugi, Shunpei; Ohkubo, Kei; Kawashima, Yuki; Matsuno, Taisuke; Kamata, Sho; Nakamura, Kosuke; Kono, Hirohiko; Sato, Sota; Fukuzumi, Shunichi; Isobe, Hiroyuki

    2015-11-01

    The energetics and photodynamics of carbonaceous molecular bearings with discrete molecular structures were investigated. A series of supramolecular bearings comprising belt-persistent tubular cycloarylene and fullerene molecules accepted photonic stimuli to afford charge-separated species via a photoinduced electron transfer process. The energy conversion processes associated with the photoexcitation, however, differed depending on the molecular structure. A π-lengthened tubular molecule allowed for the emergence of an intermediary triplet excited state at the bearing, which should lead to an energy conversion to thermal energy. On the other hand, low-lying charge-separated species induced by an endohedral lithium ion in fullerene enabled back electron transfer processes to occur without involving triplet excited species. The structure-photodynamics relationship was analyzed in terms of the Marcus theory to reveal a large electronic coupling in this dynamic supramolecular system. PMID:26195132

  6. ARPES Studies of Low-energy electronic structure of the strong spin-orbit semimetal SrIrO3

    NASA Astrophysics Data System (ADS)

    Nie, Yuefeng; King, Philip D. C.; Wei, Haofei; Uchida, Masaki; Harter, John; Monkman, Eric; Shai, Daniel; Schlom, Darrell; Shen, Kyle

    2013-03-01

    The similar energy scales of spin-orbit coupling and electron-electron correlation strength lead to exotic Jeff = 1/2 Mott insulating ground states for layered Ruddlesden-Popper 5d iridates, Srn+1IrnO3n+1. A metal-insulator transition occurs upon increasing dimensionality from the two-dimensional layered Sr2IrO4 to the three-dimensional perovskite SrIrO3. However, little is known about the electronic structure and nature of the metallic states in SrIrO3. We synthesized epitaxial SrIrO3 films on (001) LSAT substrates by molecular beam epitaxy and investigated their electronic structure using angle-resolved photoemission spectroscopy. We find an exotic semi-metallic state comprised of massive hole-like bands, whose extrema are pinned very close to the chemical potential, and rapidly dispersive electron bands which dominate the transport. Intriguingly, the bandwidths of SrIrO3 are smaller than in its Mott insulating counterpart Sr2IrO4, indicating that metal-insulator transitions in Ruddlesden-Popper iridates are not simply driven by band narrowing resulting from reduced dimensionality.

  7. State-to-state dynamics of molecular energy transfer

    SciTech Connect

    Gentry, W.R.; Giese, C.F.

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

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

    NASA Astrophysics Data System (ADS)

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

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

  9. Potential seal candidates for high-energy propellants. [for Space Shuttle orbital maneuvering system

    NASA Technical Reports Server (NTRS)

    Merz, P. L.

    1975-01-01

    Five potential seal candidates (linear Tefzel, linear Halar, crosslinked Halar, Viton ECD-006, and phosphazine fluoroelastomer) were evaluated for the orbital maneuvering system of the space shuttle. Since this system employs nitrogen tetroxide (N2O4) and monomethyl hydrazine (MMH) as hypergolic propellants, the seal candidates were selected on the basis of projected chemical resistance as well as rheological behavior. Chemical resistance to these high-energy fuels was determined via conventional isothermal and thermal cycling immersion tests. Rheological measurements, however, were performed on O-rings molded from the subject seal candidates. Properties determined, such as cyclic work and hysteresis, stress relaxation, and indicated modulus, therefore, relate to the O-ring seals themselves.

  10. Differential neutron energy spectra measured on spacecraft in low Earth orbit

    NASA Technical Reports Server (NTRS)

    Dudkin, V. E.; Akopova, A. B.; Melkumyan, L. V.; Benton, E. V.; Frank, A. L.

    1990-01-01

    Two methods for measuring neutrons in the range from thermal energies to dozens of MeV were used. In the first method, alpha-particles emitted from the 6Li(n,alpha)T reaction are detected with the help of plastic nuclear track detectors, yielding results on thermal and resonance neutrons. Also, fission foils are used to detect fast neutrons. In the second method, fast neutrons are recorded by nuclear photographic emulsions (NPE). The results of measurements on board various satellites are presented. The neutron flux density does not appear to correlate clearly with orbital parameters. Up to 50% of neutrons are due to albedo neutrons from the atmosphere while the fluxes inside the satellites are 15-20% higher than those on the outside. Estimates show that the neutron contribution to the total equivalent radiation dose reaches 20-30%.

  11. Study on Properties of Energy Spectra of the Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-Feng; Chen, Xiang-Rong

    The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

  12. Molecular dynamics simulation of threshold displacement energies in zircon

    SciTech Connect

    Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.

    2009-10-15

    Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.

  13. Electron energy-loss spectra in molecular fluorine

    NASA Technical Reports Server (NTRS)

    Nishimura, H.; Cartwright, D. C.; Trajmar, S.

    1979-01-01

    Electron energy-loss spectra in molecular fluorine, for energy losses from 0 to 17.0 eV, have been taken at incident electron energies of 30, 50, and 90 eV and scattering angles from 5 to 140 deg. Features in the spectra above 11.5 eV energy loss agree well with the assignments recently made from optical spectroscopy. Excitations of many of the eleven repulsive valence excited electronic states are observed and their location correlates reasonably well with recent theoretical results. Several of these excitations have been observed for the first time and four features, for which there are no identifications, appear in the spectra.

  14. Energy-loss rate of a fast particle in two-dimensional semiconductors with Rashba spin-orbit coupling

    SciTech Connect

    Feng, W.; Tawfiq, Asya; Cao, J. C.; Zhang, C.

    2013-02-04

    The energy-loss rate (ELR) of a charged particle in a two-dimensional semiconductor with Rashba spin-orbit coupling is studied. Our model takes into account of the temperature and density dependence of the electronic properties of the Rashba system. The energy and temperature dependence of the ELR are presented. It is found that a finite Rashba spin-orbit coupling offers a mechanism of tuning the mean scattering time in narrow-gap semiconductors. With a change of Rashba parameter of around 3 times, the mean scattering time can change by one to two orders of magnitude.

  15. Beyond the Lorentzian Model in Quantum Transport: Energy-Dependent Resonance Broadening in Molecular Junctions

    NASA Astrophysics Data System (ADS)

    Liu, Zhenfei; Neaton, Jeffrey B.

    In quantum transport calculations, transmission functions of molecular junctions, as well as spectral functions of metal-organic interfaces, often feature peaks originating from molecular resonances. These resonance peaks are often assumed to be Lorentzian, with an energy-independent broadening function Γ. However, in the general case, the wide-band-limit breaks down, and the Lorentzian approximation is no longer valid. Here, we develop a new energy-dependent broadening function Γ (E) , based on diagonalization of non-Hermitian matrices within a non-equilbrium Green's function (NEGF) formalism. As defined, Γ (E) can describe resonances of non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively; and it is particularly useful in understanding transport properties in terms of molecular orbitals in asymmetric junctions. We compute this quantity via an ab initio NEGF approach based on density functional theory and illustrate its utility with several junctions of experimental relevance, including recent work on rectification in Au-graphite junctions. This work is supported by the DOE, and computational resources are provided by NERSC.

  16. Molecular ion sources for low energy semiconductor ion implantation (invited).

    PubMed

    Hershcovitch, A; Gushenets, V I; Seleznev, D N; Bugaev, A S; Dugin, S; Oks, E M; Kulevoy, T V; Alexeyenko, O; Kozlov, A; Kropachev, G N; Kuibeda, R P; Minaev, S; Vizir, A; Yushkov, G Yu

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4(+) ion beams were extracted. Results from devices and some additional concepts are described. PMID:26932065

  17. Molecular ion sources for low energy semiconductor ion implantation (invited)

    NASA Astrophysics Data System (ADS)

    Hershcovitch, A.; Gushenets, V. I.; Seleznev, D. N.; Bugaev, A. S.; Dugin, S.; Oks, E. M.; Kulevoy, T. V.; Alexeyenko, O.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S.; Vizir, A.; Yushkov, G. Yu.

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4+ ion beams were extracted. Results from devices and some additional concepts are described.

  18. Energy dissipation in an adaptive molecular circuit

    NASA Astrophysics Data System (ADS)

    Wang, Shou-Wen; Lan, Yueheng; Tang, Lei-Han

    2015-07-01

    The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth and survival. Sensory adaptation allows a cell to recover its sensitivity after a transient response to a shift in the strength of extracellular stimulus. The working principles of adaptation have been established previously based on rate equations which do not consider fluctuations in a thermal environment. Recently, Lan et al (2012 Nat. Phys. 8 422-8) performed a detailed analysis of a stochastic model for the Escherichia coli sensory network. They showed that accurate adaptation is possible only when the system operates in a nonequilibrium steady-state (NESS). They further proposed an energy-speed-accuracy (ESA) trade-off relation. We present here analytic results on the NESS of the model through a mapping to a one-dimensional birth-death process. An exact expression for the entropy production rate is also derived. Based on these results, we are able to discuss the ESA relation in a more general setting. Our study suggests that the adaptation error can be reduced exponentially as the methylation range increases. Finally, we show that a nonequilibrium phase transition exists in the infinite methylation range limit, despite the fact that the model contains only two discrete variables.

  19. The contribution of low-energy protons to the total on-orbit SEU rate

    DOE PAGESBeta

    Dodds, Nathaniel Anson; Martinez, Marino J.; Dodd, Paul E.; Shaneyfelt, Marty R.; Sexton, Frederick W.; Black, Jeffrey D.; Lee, David S.; Swanson, Scot E.; Bhuva, B. L.; Warren, K. M.; et al

    2015-11-10

    Low- and high-energy proton experimental data and error rate predictions are presented for many bulk Si and SOI circuits from the 20-90 nm technology nodes to quantify how much low-energy protons (LEPs) can contribute to the total on-orbit single-event upset (SEU) rate. Every effort was made to predict LEP error rates that are conservatively high; even secondary protons generated in the spacecraft shielding have been included in the analysis. Across all the environments and circuits investigated, and when operating within 10% of the nominal operating voltage, LEPs were found to increase the total SEU rate to up to 4.3 timesmore » as high as it would have been in the absence of LEPs. Therefore, the best approach to account for LEP effects may be to calculate the total error rate from high-energy protons and heavy ions, and then multiply it by a safety margin of 5. If that error rate can be tolerated then our findings suggest that it is justified to waive LEP tests in certain situations. Trends were observed in the LEP angular responses of the circuits tested. As a result, grazing angles were the worst case for the SOI circuits, whereas the worst-case angle was at or near normal incidence for the bulk circuits.« less

  20. The contribution of low-energy protons to the total on-orbit SEU rate

    SciTech Connect

    Dodds, Nathaniel Anson; Martinez, Marino J.; Dodd, Paul E.; Shaneyfelt, Marty R.; Sexton, Frederick W.; Black, Jeffrey D.; Lee, David S.; Swanson, Scot E.; Bhuva, B. L.; Warren, K. M.; Reed, R. A.; Trippe, J.; Sierawski, B. D.; Weller, R. A.; Mahatme, N.; Gaspard, N.; Assis, T.; Austin, R.; Massengill, L. M.; Swift, G.; Wirthlin, M.; Cannon, M.; Liu, R.; Chen, L.; Kelly, A. T.; Marshall, P.; Trinczek, M.; Blackmore, E. W.; Wen, S. -J.; Wong, R.; Narasimham, B.; Pellish, J. A.; Puchner, H.; Weeden-Wright, S. L.

    2015-11-10

    Low- and high-energy proton experimental data and error rate predictions are presented for many bulk Si and SOI circuits from the 20-90 nm technology nodes to quantify how much low-energy protons (LEPs) can contribute to the total on-orbit single-event upset (SEU) rate. Every effort was made to predict LEP error rates that are conservatively high; even secondary protons generated in the spacecraft shielding have been included in the analysis. Across all the environments and circuits investigated, and when operating within 10% of the nominal operating voltage, LEPs were found to increase the total SEU rate to up to 4.3 times as high as it would have been in the absence of LEPs. Therefore, the best approach to account for LEP effects may be to calculate the total error rate from high-energy protons and heavy ions, and then multiply it by a safety margin of 5. If that error rate can be tolerated then our findings suggest that it is justified to waive LEP tests in certain situations. Trends were observed in the LEP angular responses of the circuits tested. As a result, grazing angles were the worst case for the SOI circuits, whereas the worst-case angle was at or near normal incidence for the bulk circuits.

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

    PubMed

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

    2016-01-01

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

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

    SciTech Connect

    Tachikawa, Masanori

    2015-12-31

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

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  4. Photoinduced charge and energy transfer in molecular wires.

    PubMed

    Gilbert, Mélina; Albinsson, Bo

    2015-02-21

    Exploring charge and energy transport in donor-bridge-acceptor systems is an important research field which is essential for the fundamental knowledge necessary to develop future applications. These studies help creating valuable knowledge to respond to today's challenges to develop functionalized molecular systems for artificial photosynthesis, photovoltaics or molecular scale electronics. This tutorial review focuses on photo-induced charge/energy transfer in covalently linked donor-bridge-acceptor (D-B-A) systems. Of utmost importance in such systems is to understand how to control signal transmission, i.e. how fast electrons or excitation energy could be transferred between the donor and acceptor and the role played by the bridge (the "molecular wire"). After a brief description of the electron and energy transfer theory, we aim to give a simple yet accurate picture of the complex role played by the bridge to sustain donor-acceptor electronic communication. Special emphasis is put on understanding bridge energetics and conformational dynamics effects on the distance dependence of the donor-acceptor electronic coupling and transfer rates. Several examples of donor-bridge-acceptor systems from the literature are described as a support to the discussion. Finally, porphyrin-based molecular wires are introduced, and the relationship between their electronic structure and photophysical properties is outlined. In strongly conjugated porphyrin systems, limitations of the existing electron transfer theory to interpret the distance dependence of the transfer rates are also discussed. PMID:25212903

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

    PubMed

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

    2014-01-01

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

  6. Potential energy surfaces for the HBr+ + CO2 → Br + HOCO+ reaction in the HBr+ 2Π3/2 and 2Π1/2 spin-orbit states

    NASA Astrophysics Data System (ADS)

    Sun, Rui; Granucci, Giovanni; Paul, Amit K.; Siebert, Matthew; Liang, Hongliang J.; Cheong, Grace; Hase, William L.; Persico, Maurizio

    2015-03-01

    Quantum mechanical (QM) + molecular mechanics (MM) models are developed to represent potential energy surfaces (PESs) for the HBr+ + CO2 → Br + HOCO+ reaction with HBr+ in the 2Π3/2 and 2Π1/2 spin-orbit states. The QM component is the spin-free PES and spin-orbit coupling for each state is represented by a MM-like analytic potential fit to spin-orbit electronic structure calculations. Coupled-cluster single double and perturbative triple excitation (CCSD(T)) calculations are performed to obtain "benchmark" reaction energies without spin-orbit coupling. With zero-point energies removed, the "experimental" reaction energy is 44 ± 5 meV for HBr+(2Π3/2) + CO2 → Br(2P3/2) + HOCO+, while the CCSD(T) value with spin-orbit effects included is 87 meV. Electronic structure calculations were performed to determine properties of the BrHOCO+ reaction intermediate and [HBr⋯OCO]+ van der Waals intermediate. The results of different electronic structure methods were compared with those obtained with CCSD(T), and UMP2/cc-pVTZ/PP was found to be a practical and accurate QM method to use in QM/MM direct dynamics simulations. The spin-orbit coupling calculations show that the spin-free QM PES gives a quite good representation of the shape of the PES originated by 2Π3/2HBr+. This is also the case for the reactant region of the PES for 2Π1/2 HBr+, but spin-orbit coupling effects are important for the exit-channel region of this PES. A MM model was developed to represent these effects, which were combined with the spin-free QM PES.

  7. Potential energy surfaces for the HBr(+) + CO2 → Br + HOCO(+) reaction in the HBr(+)  (2)Π3/2 and (2)Π1/2 spin-orbit states.

    PubMed

    Sun, Rui; Granucci, Giovanni; Paul, Amit K; Siebert, Matthew; Liang, Hongliang J; Cheong, Grace; Hase, William L; Persico, Maurizio

    2015-03-14

    Quantum mechanical (QM) + molecular mechanics (MM) models are developed to represent potential energy surfaces (PESs) for the HBr(+) + CO2 → Br + HOCO(+) reaction with HBr(+) in the (2)Π3/2 and (2)Π1/2 spin-orbit states. The QM component is the spin-free PES and spin-orbit coupling for each state is represented by a MM-like analytic potential fit to spin-orbit electronic structure calculations. Coupled-cluster single double and perturbative triple excitation (CCSD(T)) calculations are performed to obtain "benchmark" reaction energies without spin-orbit coupling. With zero-point energies removed, the "experimental" reaction energy is 44 ± 5 meV for HBr(+)((2)Π3/2) + CO2 → Br((2)P3/2) + HOCO(+), while the CCSD(T) value with spin-orbit effects included is 87 meV. Electronic structure calculations were performed to determine properties of the BrHOCO(+) reaction intermediate and [HBr⋯OCO](+) van der Waals intermediate. The results of different electronic structure methods were compared with those obtained with CCSD(T), and UMP2/cc-pVTZ/PP was found to be a practical and accurate QM method to use in QM/MM direct dynamics simulations. The spin-orbit coupling calculations show that the spin-free QM PES gives a quite good representation of the shape of the PES originated by (2)Π3/2HBr(+). This is also the case for the reactant region of the PES for (2)Π1/2 HBr(+), but spin-orbit coupling effects are important for the exit-channel region of this PES. A MM model was developed to represent these effects, which were combined with the spin-free QM PES. PMID:25770535

  8. Calculation of molecular free energies in classical potentials

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2016-02-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.

  9. A molecularly based theory for electron transfer reorganization energy

    NASA Astrophysics Data System (ADS)

    Zhuang, Bilin; Wang, Zhen-Gang

    2015-12-01

    Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule's permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.

  10. A molecularly based theory for electron transfer reorganization energy

    SciTech Connect

    Zhuang, Bilin; Wang, Zhen-Gang

    2015-12-14

    Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule’s permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.

  11. Photoswitchable Molecular Rings for Solar-Thermal Energy Storage

    SciTech Connect

    Durgun, E; Grossman, JC

    2013-03-21

    Solar-thermal fuels reversibly store solar energy in the chemical bonds of molecules by photoconversion, and can release this stored energy in the form of heat upon activation. Many conventional photoswichable molecules could be considered as solar thermal fuels, although they suffer from low energy density or short lifetime in the photoinduced high-energy metastable state, rendering their practical use unfeasible. We present a new approach to the design of chemistries for solar thermal fuel applications, wherein well-known photoswitchable molecules are connected by different linker agents to form molecular rings. This approach allows for a significant increase in both the amount of stored energy per molecule and the stability of the fuels. Our results suggest a range of possibilities for tuning the energy density and thermal stability as a function of the type of the photoswitchable molecule, the ring size, or the type of linkers.

  12. Energy transfer in a molecular motor in the Kramers regime.

    PubMed

    Challis, K J; Jack, Michael W

    2013-10-01

    We present a theoretical treatment of energy transfer in a molecular motor described in terms of overdamped Brownian motion on a multidimensional tilted periodic potential. The tilt represents a thermodynamic force driving the system out of equilibrium and, for nonseparable potentials, energy transfer occurs between degrees of freedom. For deep potential wells, the continuous theory transforms to a discrete master equation that is tractable analytically. We use this master equation to derive formal expressions for the hopping rates, drift and diffusion, and the efficiency and rate of energy transfer in terms of the thermodynamic force. These results span both strong and weak coupling between degrees of freedom, describe the near and far from equilibrium regimes, and are consistent with generalized detailed balance and the Onsager relations. We thereby derive a number of diverse results for molecular motors within a single theoretical framework. PMID:24229123

  13. 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.

  14. Low Energy Interplanetary Transfers Using the Invariant Manifolds of L(sub 1), L(sub 2) and Halo Orbits

    NASA Technical Reports Server (NTRS)

    Lo, M.

    1998-01-01

    The invariant manifolds associated with the outer planets are extremely large objects in phase space. They are trajectories in the ecliptic which intersect one another. This enables a low energy single impulse transfer between the planets which requries several orbital periods.

  15. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    PubMed

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-01

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces. PMID:23039583

  16. Molecular partitioning based on the kinetic energy density

    NASA Astrophysics Data System (ADS)

    Noorizadeh, Siamak

    2016-05-01

    Molecular partitioning based on the kinetic energy density is performed to a number of chemical species, which show non-nuclear attractors (NNA) in their gradient maps of the electron density. It is found that NNAs are removed using this molecular partitioning and although the virial theorem is not valid for all of the basins obtained in the being used AIM, all of the atoms obtained using the new approach obey this theorem. A comparison is also made between some atomic topological parameters which are obtained from the new partitioning approach and those calculated based on the electron density partitioning.

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

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Taha, Ali

    2003-04-01

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

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

    SciTech Connect

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

    1989-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Qi, Jianbing

    2016-05-01

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

  1. Trajectory Planning for Pushing Motion Based on Extended Orbital Energy of Humanoid Robot

    NASA Astrophysics Data System (ADS)

    Motoi, Naoki; Ohnishi, Kouhei

    This paper describes the trajectory planning for the pushing motion of a humanoid robot. In the design of a humanoid robot for pushing an object, it is necessary to take into account many parameters such as stride length, pushing force, and walking velocity. However, there are no standard methods for evaluating these parameters. Additionally, the robot may fall down if these parameters are not chosen correctly. In this paper, a method for determining these parameters for pushing motion is proposed. The extended orbital energy (EOE) is considered as the design index. Here, the EOE describes the relation between walking motion and pushing motion. By using the proposed method, the COG trajectory, pushing force and stride length can be modified on the basis of the EOE. In other words, the suitable values of theses parameters can be obtained by determining only the desired EOE. As a result, the humanoid robot walks stably during pushing motion. The effectiveness of the proposed method was confirmed by experimental results.

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

    PubMed Central

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

    2009-01-01

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

  3. Accurate calculations on the 22 electronic states and 54 spin-orbit states of the O2 molecule: potential energy curves, spectroscopic parameters and spin-orbit coupling.

    PubMed

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue; Shulin, Zhang

    2014-04-24

    The potential energy curves (PECs) of 54 spin-orbit states generated from the 22 electronic states of O2 molecule are investigated for the first time for internuclear separations from about 0.1 to 1.0nm. Of the 22 electronic states, the X(3)Σg(-), A(')(3)Δu, A(3)Σu(+), B(3)Σu(-), C(3)Πg, a(1)Δg, b(1)Σg(+), c(1)Σu(-), d(1)Πg, f(1)Σu(+), 1(5)Πg, 1(3)Πu, 2(3)Σg(-), 1(5)Σu(-), 2(1)Σu(-) and 2(1)Δg are found to be bound, whereas the 1(5)Σg(+), 2(5)Σg(+), 1(1)Πu, 1(5)Δg, 1(5)Πu and 2(1)Πu are found to be repulsive ones. The B(3)Σu(-) and d(1)Πg states possess the double well. And the 1(3)Πu, C(3)Πg, A'(3)Δu, 1(5)Δg and 2(5)Σg(+) states are the inverted ones when the spin-orbit coupling is included. The PEC calculations are done by the complete active space self-consistent field (CASSCF) method, which is followed by the internally contracted multireference configuration interaction (icMRCI) approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections are taken into account. The convergence of present calculations is evaluated with respect to the basis set and level of theory. The vibrational properties are discussed for the 1(5)Πg, 1(3)Πu, d(1)Πg and 1(5)Σu(-) states and for the second well of the B(3)Σu(-) state. The spin-orbit coupling effect is accounted for by the state interaction method with the Breit-Pauli Hamiltonian. The PECs of all the electronic states and spin-orbit states are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and compared with available experimental and other theoretical results. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is obtained that the effect of spin-orbit coupling on the spectroscopic parameters are small almost for all the electronic states involved in this paper except for the 1(5)Σu(-), 1(5)Πg and 1(3)Πu. PMID:24486866

  4. Ionization Energies, Electron Affinities, and Polarization Energies of Organic Molecular Crystals: Quantitative Estimations from a Polarizable Continuum Model (PCM)-Tuned Range-Separated Density Functional Approach.

    PubMed

    Sun, Haitao; Ryno, Sean; Zhong, Cheng; Ravva, Mahesh Kumar; Sun, Zhenrong; Körzdörfer, Thomas; Brédas, Jean-Luc

    2016-06-14

    We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a nonempirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values, as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials. PMID:27183355

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

    PubMed

    Ferenczy, György G

    2013-04-01

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

  6. Low energy stage study. Volume 4: Cost benefits analysis and recommendations. [orbital launching of space shuttle payloads

    NASA Technical Reports Server (NTRS)

    1978-01-01

    The costs and benefits of existing/planned systems, new propulsion concepts, and adaptations of existing/planned systems (as supported by Orbiter interface requirements and operations requirements) were quantified. Scenarios of these propulsion approaches were established which accommodate the low energy regime as defined by the new low energy payload mission model. These scenarios were screened on a cost and then a benefits basis. A propulsion approach comprising existing/planned systems and a new propulsion concept were selected as the most cost effective approach to accommodate the model payloads and the low energy regime they represent. Key cost drivers and sensitivity trends were identified. All costs were derived in 1977 dollars.

  7. Efficient quantum mechanical calculation of solvation free energies based on density functional theory, numerical atomic orbitals and Poisson Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Wang, Mingliang; Wong, Chung F.; Liu, Jianhong; Zhang, Peixin

    2007-07-01

    We have successfully coupled the Kohn-Sham with Poisson-Boltzmann equations to predict the solvation free energy, where the Kohn-Sham equations were solved by implementing the flexible pseudo atomic orbitals as in S IESTA package. It was found that the calculated solvation free energy is in good agreement with experimental results for small neutral molecules, and its standard error is 1.33 kcal/mol, the correlation coefficient is 0.97. Due to its high efficiency and accuracy, the proposed model can be a promising tool for computing solvation free energies in computer aided drug design in future.

  8. Theoretical study of valence orbital response to guanine tautomerization in coordinate and momentum spaces

    NASA Astrophysics Data System (ADS)

    Yang, Zejin; Duffy, Patrick; Zhu, Quan; Takahashi, Masahiko; Wang, Feng

    2015-10-01

    The binding energy spectra and electron momentum spectra of eight stable guanine tautomers are calculated in the complete valence space. The present results show that the canonical keto (C=O) guanine N(9)H tautomer (GU1) possesses the largest dipole moment, molecular electronic spatial extent, molecular hardness value, and the minimum first vertical ionization potential (VIP). Valence orbital profile investigations find that several orbitals remain almost unchanged during tautomerization, such as frontier highest occupied molecular orbital 39a and 18a. Several orbitals with interchanged order and inverse direction in charge spatial orientations are also detected. Outer valence orbitals (with smaller VIPs) show more complex orbital shapes in the momentum space than those of inner ones (larger VIPs) due mainly to the relatively strong inter-orbital interaction and delocalized electronic distributions. Proton rotation along C-O(H) and C-N(H) axes within hexagonal ring causes smaller influence to orbital profiles than those of proton migration within pentagonal and/or hexagonal rings. Orbital variation trends between enol (GU3-GU5) and keto (GU1, GU2, GU6-GU8) tautomers are observed, including the signature orbitals of enol form, the variation tendency of total orbital intensity, and the variation order of the maximum orbital intensity. In the outer valence momentum space (outside 26a), orbital composed by pz electrons show single peak with a gradual increasing peak site from 0.5 a.u. of inner valence orbital to 1.0 a.u. of outer valence orbital, whereas orbitals composed by px,y electrons form double peaks with respective sites at about 0.5 and 1.5 a.u., only three px,y-orbitals present single peaks (33a,34a,36a). The general variation trends in the complete valence space for all the valence orbitals on their intensities, peak sites, and orbital components are concluded.

  9. Selective excitation, relaxation, and energy channeling in molecular systems

    SciTech Connect

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems.

  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. Use of excess solar array power by regenerative fuel cell energy storage systems in low earth orbit

    SciTech Connect

    Hoberecht, M.A.; Green, R.D.

    1997-12-31

    Regenerative Fuel Cells (RFC`s) are a competing energy storage system technology for a number of low-earth-orbit applications. The system is comprised of an electrolyzer which utilizes solar array power to convert water into hydrogen and oxygen reactants, a fuel cell that recombines the reactants back into water and produces power during eclipse, and associated controls and reactant storage. Round-trip electrical efficiencies of RFC systems are typically lower than competing battery energy storage systems. This results in larger solar arrays for the same application, with inherent drag, mass, and cost penalties. However, the increase in solar array size can be limited, if not totally eliminated, because of the ability of RFC systems to use excess solar array power. For this paper, the International Space Station (ISS) application was chosen for evaluation and comparison of battery and RFC energy storage systems. This selection was based on the authors` familiarity with the ISS design and the availability of a detailed in-house computer model specific to the ISS electrical power system (SPACE). Combined altitude and orientation effects, seasonal variations, and beginning-of-life solar array performance were examined for individual orbits at and above specified reference points. Charging characteristics of the battery system were also investigated. The evaluation allowed a comparison of the solar array size required with the existing battery energy storage system to the projected solar array size required with a possible RFC system. The results of the examination indicated that no increase in solar array size would be necessary for the ISS if outfitted with a RFC energy storage system, in spite of the lower round-trip electrical efficiency. For orbits with a minimum of excess power, the battery energy storage system used only 73% of the available solar array power as compared to 100% usage for a RFC system. The usage by the battery system was far less for the orbits

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

    NASA Astrophysics Data System (ADS)

    Mazin, Igor; Streltsov, Sergey; Foyevtseva, Kateryna

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

  13. Zero-Magnetic-Field Spin Splitting of Polaron's Ground State Energy Induced by Rashba Spin-Orbit Interaction

    NASA Astrophysics Data System (ADS)

    Liu, Jia; Xiao, Jing-Ling

    2006-10-01

    We study theoretically the ground state energy of a polaron near the interface of a polar-polar semiconductor by considering the Rashba spin-orbit (SO) coupling with the Lee-Low-Pines intermediate coupling method. Our numerical results show that the Rashba SO interaction originating from the inversion asymmetry in the heterostructure splits the ground state energy of the polaron. The electron areal density and vector dependence of the ratio of the SO interaction to the total ground state energy or other energy composition are obvious. One can see that even without any external magnetic field, the ground state energy can be split by the Rashba SO interaction, and this split is not a single but a complex one. Since the presents of the phonons, whose energy gives negative contribution to the polaron's, the spin-splitting states of the polaron are more stable than electron's.

  14. An improved model electronic Hamiltonian for potential energy surfaces and spin−orbit couplings of low-lying d−d states of [Fe(bpy){sub 3}]{sup 2+}

    SciTech Connect

    Iuchi, Satoru Koga, Nobuaki

    2014-01-14

    With the aim of exploring excited state dynamics, a model electronic Hamiltonian for several low-lying d−d states of [Fe(bpy){sub 3}]{sup 2+} complex [S. Iuchi, J. Chem. Phys. 136, 064519 (2012)] is refined using density-functional theory calculations of singlet, triplet, and quintet states as benchmarks. Spin−orbit coupling elements are also evaluated within the framework of the model Hamiltonian. The accuracy of the developed model Hamiltonian is determined by examining potential energies and spin−orbit couplings at surface crossing regions between different spin states. Insights into the potential energy surfaces around surface crossing regions are also provided through molecular dynamics simulations. The results demonstrate that the constructed model Hamiltonian can be used for studies on the d−d excited state dynamics of [Fe(bpy){sub 3}]{sup 2+}.

  15. Molecular insights into the terminal energy acceptor in cyanobacterial phycobilisome.

    PubMed

    Gao, Xiang; Wei, Tian-Di; Zhang, Nan; Xie, Bin-Bin; Su, Hai-Nan; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Wang, Zhi-Xin; Wu, Jia-Wei; Zhang, Yu-Zhong

    2012-09-01

    The linker protein L(CM) (ApcE) is postulated as the major component of the phycobilisome terminal energy acceptor (TEA) transferring excitation energy from the phycobilisome to photosystem II. L(CM) is the only phycobilin-attached linker protein in the cyanobacterial phycobilisome through auto-chromophorylation. However, the underlying mechanism for the auto-chromophorylation of L(CM) and the detailed molecular architecture of TEA is still unclear. Here, we demonstrate that the N-terminal phycobiliprotein-like domain of L(CM) (Pfam00502, LP502) can specifically recognize phycocyanobilin (PCB) by itself. Biochemical assays indicated that PCB binds into the same pocket in LP502 as that in the allophycocyanin α-subunit and that Ser152 and Asp155 play a vital role in LP502 auto-chromophorylation. By carefully conducting computational simulations, we arrived at a rational model of the PCB-LP502 complex structure that was supported by extensive mutational studies. In the PCB-LP502 complex, PCB binds into a deep pocket of LP502 with a distorted conformation, and Ser152 and Asp155 form several hydrogen bonds to PCB fixing the PCB Ring A and Ring D. Finally, based on our results, the dipoles and dipole-dipole interactions in TEA are analysed and a molecular structure for TEA is proposed, which gives new insights into the energy transformation mechanism of cyanobacterial phycobilisome. PMID:22758351

  16. 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.

  17. Tail effects in the third post-Newtonian gravitational wave energy flux of compact binaries in quasi-elliptical orbits

    SciTech Connect

    Arun, K. G.; Iyer, Bala R.; Qusailah, Moh'd S. S.

    2008-03-15

    The far-zone flux of energy contains hereditary (tail) contributions that depend on the entire past history of the source. Using the multipolar post-Minkowskian wave generation formalism, we propose and implement a semianalytical method in the frequency domain to compute these contributions from the inspiral phase of a binary system of compact objects moving in quasi-elliptical orbits up to third post-Newtonian (3PN) order. The method explicitly uses the quasi-Keplerian representation of elliptical orbits at 1PN order and exploits the doubly periodic nature of the motion to average the 3PN fluxes over the binary's orbit. Together with the instantaneous (nontail) contributions evaluated in a companion paper, it provides crucial inputs for the construction of ready-to-use templates for compact binaries moving on quasi-elliptic orbits, an interesting class of sources for the ground-based gravitational-wave detectors such as LIGO and Virgo, as well as space-based detectors like LISA.

  18. 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.

  19. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    NASA Technical Reports Server (NTRS)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  20. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of 3-hydroxy-6-methyl-2-nitropyridine

    NASA Astrophysics Data System (ADS)

    Karnan, M.; Balachandran, V.; Murugan, M.

    2012-10-01

    The optimized molecular structure and corresponding vibrational assignments of 3-hydroxy-6-methyl-2-nitropyridine have been investigated using density functional theory (DFT) B3LYP method with 6-311++G(d,p), 6-311++G(2d,2p) and 6-311++G(3d,3p) basis sets. Investigation of the relative orientation of the hydroxyl group with respect to the nitro group has shown that two conformers (O-cis) and (O-trans) exist. The vibrational analysis of the stable conformer of the title compound is performed by means of infrared absorption and Raman spectroscopy in combination with theoretical simulations. The molecular stability and bond strength were investigated by applying the natural bond orbital (NBO) analysis. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with electrostatic potential (ESP). The isotropic chemical shift computed by 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the HMNP calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations.

  1. Low energy stage study. Volume 2: Requirements and candidate propulsion modes. [orbital launching of shuttle payloads

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A payload mission model covering 129 launches, was examined and compared against the space transportation system shuttle standard orbit inclinations and a shuttle launch site implementation schedule. Based on this examination and comparison, a set of six reference missions were defined in terms of spacecraft weight and velocity requirements to deliver the payload from a 296 km circular Shuttle standard orbit to the spacecraft's planned orbit. Payload characteristics and requirements representative of the model payloads included in the regime bounded by each of the six reference missions were determined. A set of launch cost envelopes were developed and defined based on the characteristics of existing/planned Shuttle upper stages and expendable launch systems in terms of launch cost and velocity delivered. These six reference missions were used to define the requirements for the candidate propulsion modes which were developed and screened to determine the propulsion approaches for conceptual design.

  2. Molecular understanding of mutagenicity using potential energy methods

    SciTech Connect

    Broyde, S.; Shapiro, R.

    1992-07-01

    Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.

  3. Enhanced spin polarization in graphene with spin energy gap induced by spin-orbit coupling and strain

    SciTech Connect

    Liu, Zheng-Fang; Wu, Qing-Ping E-mail: aixichen@ecjtu.jx.cn; Chen, Ai-Xi E-mail: aixichen@ecjtu.jx.cn; Xiao, Xian-Bo; Liu, Nian-Hua

    2014-05-28

    We investigate the possibility of spin polarization in graphene. The result shows that a spin energy gap can be opened in the presence of both spin-orbit coupling and strain. We find that high spin polarization with large spin-polarized current is achieved in the spin energy gap. However, only one of the two modulations is present, no spin polarization can be generated. So the combination of the two modulations provides a way to design tunable spin polarization without need for a magnetic element or an external magnetic field.

  4. The energy-level crossing behavior and quantum Fisher information in a quantum well with spin-orbit coupling

    PubMed Central

    Wang, Z. H.; Zheng, Q.; Wang, Xiaoguang; Li, Yong

    2016-01-01

    We study the energy-level crossing behavior in a two-dimensional quantum well with the Rashba and Dresselhaus spin-orbit couplings (SOCs). By mapping the SOC Hamiltonian onto an anisotropic Rabi model, we obtain the approximate ground state and its quantum Fisher information (QFI) via performing a unitary transformation. We find that the energy-level crossing can occur in the quantum well system within the available parameters rather than in cavity and circuit quantum eletrodynamics systems. Furthermore, the influence of two kinds of SOCs on the QFI is investigated and an intuitive explanation from the viewpoint of the stationary perturbation theory is given. PMID:26931762

  5. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    NASA Astrophysics Data System (ADS)

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  6. Communication: energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach.

    PubMed

    Liu, Zhen-Fei; Neaton, Jeffrey B

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals. PMID:25296777

  7. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    SciTech Connect

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-07

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  8. Formation of quantum spin Hall state on Si surface and energy gap scaling with strength of spin orbit coupling

    SciTech Connect

    Zhou, Miao; Ming, Wenmei; Liu, Zheng; Wang, Zhengfei; Yao, Yugui; Liu, Feng

    2014-11-19

    For potential applications in spintronics and quantum computing, it is desirable to place a quantum spin Hall insulator [i.e., a 2D topological insulator (TI)] on a substrate while maintaining a large energy gap. Here, we demonstrate a unique approach to create the large-gap 2D TI state on a semiconductor surface, based on first-principles calculations and effective Hamiltonian analysis. We show that when heavy elements with strong spin orbit coupling (SOC) such as Bi and Pb atoms are deposited on a patterned H-Si(111) surface into a hexagonal lattice, they exhibit a 2D TI state with a large energy gap of ≥0.5 eV. The TI state arises from an intriguing substrate orbital filtering effect that selects a suitable orbital composition around the Fermi level, so that the system can be matched onto a four-band effective model Hamiltonian. Furthermore, it is found that within this model, the SOC gap does not increase monotonically with the increasing strength of SOC. These interesting results may shed new light in future design and fabrication of large-gap topological quantum states.

  9. Formation of quantum spin Hall state on Si surface and energy gap scaling with strength of spin orbit coupling

    DOE PAGESBeta

    Zhou, Miao; Ming, Wenmei; Liu, Zheng; Wang, Zhengfei; Yao, Yugui; Liu, Feng

    2014-11-19

    For potential applications in spintronics and quantum computing, it is desirable to place a quantum spin Hall insulator [i.e., a 2D topological insulator (TI)] on a substrate while maintaining a large energy gap. Here, we demonstrate a unique approach to create the large-gap 2D TI state on a semiconductor surface, based on first-principles calculations and effective Hamiltonian analysis. We show that when heavy elements with strong spin orbit coupling (SOC) such as Bi and Pb atoms are deposited on a patterned H-Si(111) surface into a hexagonal lattice, they exhibit a 2D TI state with a large energy gap of ≥0.5more » eV. The TI state arises from an intriguing substrate orbital filtering effect that selects a suitable orbital composition around the Fermi level, so that the system can be matched onto a four-band effective model Hamiltonian. Furthermore, it is found that within this model, the SOC gap does not increase monotonically with the increasing strength of SOC. These interesting results may shed new light in future design and fabrication of large-gap topological quantum states.« less

  10. Formation of quantum spin Hall state on Si surface and energy gap scaling with strength of spin orbit coupling

    PubMed Central

    Zhou, Miao; Ming, Wenmei; Liu, Zheng; Wang, Zhengfei; Yao, Yugui; Liu, Feng

    2014-01-01

    For potential applications in spintronics and quantum computing, it is desirable to place a quantum spin Hall insulator [i.e., a 2D topological insulator (TI)] on a substrate while maintaining a large energy gap. Here, we demonstrate a unique approach to create the large-gap 2D TI state on a semiconductor surface, based on first-principles calculations and effective Hamiltonian analysis. We show that when heavy elements with strong spin orbit coupling (SOC) such as Bi and Pb atoms are deposited on a patterned H-Si(111) surface into a hexagonal lattice, they exhibit a 2D TI state with a large energy gap of ≥0.5 eV. The TI state arises from an intriguing substrate orbital filtering effect that selects a suitable orbital composition around the Fermi level, so that the system can be matched onto a four-band effective model Hamiltonian. Furthermore, it is found that within this model, the SOC gap does not increase monotonically with the increasing strength of SOC. These interesting results may shed new light in future design and fabrication of large-gap topological quantum states. PMID:25407432

  11. G W with linearized augmented plane waves extended by high-energy local orbitals

    NASA Astrophysics Data System (ADS)

    Jiang, Hong; Blaha, Peter

    2016-03-01

    Many-body perturbation theory in the G W approximation is currently the most accurate and robust first-principles approach to determine the electronic band structure of weakly correlated insulating materials without any empirical input. Recent G W results for ZnO with more careful investigation of the convergence with respect to the number of unoccupied states have led to heated debates regarding the numerical accuracy of previously reported G W results using either pseudopotential plane waves or all-electron linearized augmented plane waves (LAPWs). The latter has been arguably regarded as the most accurate scheme for electronic-structure theory for solids. This work aims to solve the ZnO puzzle via a systematic investigation of the effects of including high-energy local orbitals (HLOs) in the LAPW-based G W calculations of semiconductors. Using ZnO as the prototypical example, it is shown that the inclusion of HLOs has two main effects: it improves the description of high-lying unoccupied states by reducing the linearization errors of the standard LAPW basis, and in addition it provides an efficient way to achieve the completeness in the summation of states in G W calculations. By investigating the convergence of G W band gaps with respect to the number of HLOs for several other typical examples, it was found that the effects of HLOs are highly system-dependent, and in most cases the inclusion of HLOs changes the band gap by less than 0.2 eV. Compared to its effects on the band gap, the consideration of HLOs has even stronger effects on the G W correction to the valence-band maximum, which is of great significance for the G W prediction of the ionization potentials of semiconductors. By considering an extended set of semiconductors with relatively well-established experimental band gaps, it was found that in general using a HLO-enhanced LAPW basis significantly improves the agreement with experiment for both the band gap and the ionization potential, and overall

  12. Scaling properties of the kinetic energy density of atoms - towards an orbital-free meta-GGA

    NASA Astrophysics Data System (ADS)

    Cancio, Antonio; Redd, Jeremy

    The scaling properties of atoms, combining periodicity with gradual increase in density, make a fruitful probe of relationships in density functional theory, and have driven advances in understanding the exchange and correlation energy. Although focus is normally upon the properties of integrated energies, insights can be generated from studying energy density functions as well. We visualize the behavior of the positive-definite kinetic energy density (KED) in closed-shell atoms, in comparison to invariant quantities based upon the gradient and Laplacian of the density. The latter are potential variables for constructing orbital-free functionals for the KE and can be used for analyzing the electronic structure of atoms and molecules. We notice a striking fit of the KED within the core of any atom to a gradient expansion model using both the gradient and the Laplacian, but one different from that derived from first principles for a slowly-varying electron gas. Correlated with this feature, we notice unexpected structure to the KED near the nucleus that cannot be explained simply by the von Weizsacker model, as is often presumed. These unexpected features provide potential insights for developing better orbital-free meta-GGA models for the kinetic energy.

  13. Molecular Dynamics and Energy Minimization Based on Embedded Atom Method

    Energy Science and Technology Software Center (ESTSC)

    1995-03-01

    This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less

  14. Molecularly Designed, Nitrogen-Functionalized Graphene Quantum Dots for Optoelectronic Devices.

    PubMed

    Tetsuka, Hiroyuki; Nagoya, Akihiro; Fukusumi, Takanori; Matsui, Takayuki

    2016-06-01

    Nitrogen-functionalized graphene quantum dots (NGQDs) with tailorable optical properties are prepared by a versatile technique, which allows the highest occupied molecular orbital/lowest unoccupied molecular orbital energy levels and energy gaps to be continuously varied. The integration of NGQD layers into the structures significantly improves the performance of optoelectronic devices. PMID:27042953

  15. Camera for detection of cosmic rays of energy more than 10 Eev on the ISS orbit

    SciTech Connect

    Garipov, G. K.; Khrenov, B. A.; Panasyuk, M. I.; Nikitsky, V. P.; Saprykin, O. A.; Sholokhov, A. V.; Syromyatnikov, V. S.

    1998-06-15

    Concept of the EHE CR observation from the ISS orbit is discussed. A design of the camera at the Russian segment of the ISS comprising a large area (60 m{sup 2}) parabolic mirror with a photo multiplier pixel retina in its focal plane is described.

  16. Monte Carlo simulation of energy deposition by low-energy electrons in molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Heaps, M. G.; Furman, D. R.; Green, A. E. S.

    1975-01-01

    A set of detailed atomic cross sections has been used to obtain the spatial deposition of energy by 1-20-eV electrons in molecular hydrogen by a Monte Carlo simulation of the actual trajectories. The energy deposition curve (energy per distance traversed) is quite peaked in the forward direction about the entry point for electrons with energies above the threshold of the electronic states, but the peak decreases and broadens noticeably as the electron energy decreases below 10 eV (threshold for the lowest excitable electronic state of H2). The curve also assumes a very symmetrical shape for energies below 10 eV, indicating the increasing importance of elastic collisions in determining the shape of the curve, although not the mode of energy deposition.

  17. Effect of Rashba spin-orbit interaction on the ground state energy of a D0 centre in a GaAs quantum dot with Gaussian confinement

    NASA Astrophysics Data System (ADS)

    Kumar, D. Sanjeev; Boda, Aalu; Mukhopadhyay, Soma; Chatterjee, Ashok

    2015-12-01

    The ground state energy of a neutral hydrogenic donor impurity (D0) trapped in a three-dimensional GaAs quantum dot with Gaussian confinement is calculated in the presence of Rashba spin-orbit interaction. The effect of the spin-orbit interaction is incorporated by performing a unitary transformation and retaining terms up to quadratic in the spin-orbit interaction coefficient. For the resulting Hamiltonian, the Rayleigh-Ritz variational method is employed with a simple wave function within the framework of effective-mass envelope function theory to determine the ground state energy and the binding energy of the donor complex. The results show that the Rashba spin-orbit interaction reduces the total GS energy of the donor impurity.

  18. Orbital simulations on the deflection of Near Earth Objects by directed energy

    NASA Astrophysics Data System (ADS)

    Zhang, Qicheng; Walsh, Kevin J.; Melis, Carl; Hughes, Gary B.; Lubin, Philip M.

    2015-09-01

    Laser ablation of a Near Earth Object (NEO) on a collision course with Earth produces a cloud of ejecta which exerts a thrust on the asteroid, deflecting it from its original trajectory. The DE-STAR system provides such a thrust by illuminating an Earth-targeting asteroid or comet from afar with a stand-off system consisting of a large phased-array laser in Earth orbit. A much smaller version of the same system called DE-STARLITE travels alongside the target, operating in a stand-on mode, slowly deflecting it over a long period. Such a stand-on system would also permit directing the thrust in any desired direction through careful positioning of the laser relative to the asteroid. We present orbital simulations comparing the effectiveness of both systems across a range of laser and asteroid parameters. Simulated parameters include magnitude, duration and, for the stand-on system, direction of the thrust, as well as the size and orbital characteristics of the target asteroid. These simulations indicate that deflection distance is, in general, proportional to the magnitude of thrust, proportional to the square of the laser on time, and inversely proportional to the mass. Furthermore, deflection distance shows strong dependence on thrust direction with optimal direction varying with the asteroid's orbital eccentricity. As one example, we consider a 325 m asteroid in an orbit of eccentricity e=0.2; given 15 years of warning, a force of just 2 N from a stand-on DE-STARLITE system is sufficient to deflect the asteroid by 2 Earth radii. We discuss numerous scenarios and discuss a practical implementation of such a system consistent with current launch vehicle capabilities.

  19. Effect of Rasbha spin-orbit interaction on the ground state energy of a hydrogenic D{sup 0} complex in a Gaussian quantum dot

    SciTech Connect

    Boda, Aalu Kumar, D. Sanjeev; Chatterjee, Ashok; Mukhopadhyay, Soma

    2015-06-24

    The ground state energy of a hydrogenic D{sup 0} complex trapped in a three-dimensional GaAs quantum dot with Gaussian confinement is calculated variationally incorporating the effect of Rashba spin-orbit interaction. The results are obtained as a function of the quantum dot size and the Rashba spin-orbit interaction. The results show that the Rashba interaction reduces the ground state energy of the system.

  20. 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.

  1. An orbital angular momentum spectrometer for electrons

    NASA Astrophysics Data System (ADS)

    Harvey, Tyler; Grillo, Vincenzo; McMorran, Benjamin

    2016-05-01

    With the advent of techniques for preparation of free-electron and neutron orbital angular momentum (OAM) states, a basic follow-up question emerges: how do we measure the orbital angular momentum state distribution in matter waves? Control of both the energy and helicity of light has produced a range of spectroscopic applications, including molecular fingerprinting and magnetization mapping. Realization of an analogous dual energy-OAM spectroscopy with matter waves demands control of both initial and final energy and orbital angular momentum states: unlike for photons, final state post-selection is necessary for particles that cannot be annihilated. We propose a magnetic field-based mechanism for quantum non-demolition measurement of electron OAM. We show that OAM-dependent lensing is produced by an operator of form U =exp iLzρ2/ℏb2 where ρ =√{x2 +y2 } is the radial position operator, Lz is the orbital angular momentum operator along z, and b is the OAM dispersion length. We can physically realize this operator as a term in the time evolution of an electron in magnetic round lens. We discuss prospects and practical challenges for implementation of a lensing orbital angular momentum measurement. This work was supported by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences (BES), under the Early Career Research Program Award # DE-SC0010466.

  2. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  3. Molecular potential energy surfaces for interstellar chemistry and fusion applications

    NASA Astrophysics Data System (ADS)

    Braams, Bastiaan J.; Huang, Xinchuan; Jin, Zhong; Xie, Zhen; Zhang, Xiubin; Bowman, Joel M.; Sharma, Amit Raj; Scheider, Ralf

    2006-04-01

    In the Born-Oppenheimer approximation the electronic Schr"odinger equation is solved given the nuclear positions as parameters, and this defines the potential energy surface. We have used computational invariant theory and the MAGMA computer algebra system as an aid to develop representations for the potential energy and dipole moment surfaces that are fully invariant under permutations of like nuclei, extending an approach that for 3-body and 4-body systems has a long history, e.g. [J. N. Murrell et al. Molecular Potential Energy Functions, Wiley, 1984]. A many-body (cluster) expansion is used to describe reaction complexes. The methods have been applied in an almost routine way for systems of up to 7 nuclei, including several molecules that are of interest for interstellar chemistry and for the issue of hydrocarbon breakdown in fusion edge plasma: H5^+, CH5, CH5^+, C2H3^+, and their fragments, with C2H5^+ on the way. The mathematical and computional methods and the hydrocarbon applications will be presented.

  4. Modification of earth-satellite orbits using medium-energy pulsed lasers

    SciTech Connect

    Phipps, C.R.

    1992-10-01

    Laser Impulse Space Propulsion (LISP) has become an attractive concept, due to recent advances in gas laser technology, high-speed segmented mirrors and improved coeffici-ents for momentum coupling to targets in pulsed laser ablation. There are numerous specialized applications of the basic concept to space science-ranging from far-future and high capital cost to the immediate and inexpensive, such as: LEO-LISP (launch of massive objects into low-Earth-Orbit at dramatically improved cost-per-kg relative to present practice); LEGO-LISP (LEO to geosynchronous transfers); LO-LISP) (periodic re-boost of decaying LEO orbits); and LISK (geosynchronous satellite station-keeping). It is unlikely that one type of laser will be best for all scenarios. In this paper, we will focus on the last two applications.

  5. Modification of earth-satellite orbits using medium-energy pulsed lasers

    SciTech Connect

    Phipps, C.R.

    1992-01-01

    Laser Impulse Space Propulsion (LISP) has become an attractive concept, due to recent advances in gas laser technology, high-speed segmented mirrors and improved coeffici-ents for momentum coupling to targets in pulsed laser ablation. There are numerous specialized applications of the basic concept to space science-ranging from far-future and high capital cost to the immediate and inexpensive, such as: LEO-LISP (launch of massive objects into low-Earth-Orbit at dramatically improved cost-per-kg relative to present practice); LEGO-LISP (LEO to geosynchronous transfers); LO-LISP) (periodic re-boost of decaying LEO orbits); and LISK (geosynchronous satellite station-keeping). It is unlikely that one type of laser will be best for all scenarios. In this paper, we will focus on the last two applications.

  6. On the properties of Se⋯N interaction: the analysis of substituent effects by energy decomposition and orbital interaction.

    PubMed

    Zhou, Fangfang; Liu, Ruirui; Tang, Jia; Li, Ping; Cui, Yahui; Zhang, Houyu

    2016-01-01

    The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive electrostatic potential of Se atoms and the accepting electron ability of X-Se σ(∗) antibonding orbital. Energy decomposition of the Se ⋯N interaction reveals that electrostatic and induction forces are comparable in the weak-bonded complexes and induction becomes more significant in the complexes with strong electron-withdrawing substituents. Natural bond orbital (NBO) analysis indicates that the primary source of the induction is the electron transfer from the N lone pair to the X-Se σ(∗) antibonding orbital. The geometry of the complex and the interaction directionality of NH3 to X-Se bond can be regarded as a consequence of the exchange-repulsion. The topological analysis on the electron density reveals the nature of closed-shell interaction in these X-Se⋯N contacts. The Se⋯N interaction in the complexes with the strong electron-withdrawing substituent has a partly covalent character. PMID:26755190

  7. (Molecular understanding of mutagenicity using potential energy methods)

    SciTech Connect

    Broyde, S.

    1990-01-01

    The objective of our work has been, for many year, to elucidate on a molecular level at atomic resolution the structures of DNAs modified by highly mutagenic polycyclic aromatic amines and hydrocarbons, and their less mutagenic chemically related analogs and unmodified DNAs, as controls. The ultimate purpose of this undertaking is to obtain an understanding of the relationship DNA structures and mutagenicity. Our methods for elucidating structures are computational, but we keep in close contact with experimental developments, and have, very recently, been able to incorporate the first experimental information from NMR studies by other workers in our calculations. The specific computational methods we employ are minimized potential energy calculations using the torsion angle space program DUPLEX, developed and written by Dr. Brain Hingerty to yield static views. Molecular dynamics simulations of the important static structures with full solvation and salt are carried out with the program AMBER; this yields mobile views in a milieu that best mimics the natural environment of the cell. In addition, we have been developing new strategies for searching conformation space and building DNA duplexes from favored subunit structures. 30 refs., 12 figs.

  8. Exploring the free energy surface using ab initio molecular dynamics

    DOE PAGESBeta

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-22

    Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less

  9. Low energy stage study. Volume 1: Executive summary. [propulsion system configurations for orbital launching of space shuttle payloads

    NASA Technical Reports Server (NTRS)

    1978-01-01

    Cost effective approaches for placing automated payloads into circular and elliptical orbits using energy requirements significantly lower than that provided by the smallest, currently planned shuttle upper stage, SSUS-D, were investigated. Launch costs were derived using both NASA existing/planned launch approaches as well as new propulsion concepts meeting low-energy regime requirements. Candidate new propulsion approaches considered were solid (tandem, cluster, and controlled), solid/liquid combinations and all-liquid stages. Results show that the most economical way to deliver the 129 low energy payloads is basically with a new modular, short liquid bipropellant stage system for the large majority of the payloads. For the remainder of the payloads, use the shuttle with integral OMS and the Scout form for a few specialized payloads until the Shuttle becomes operational.

  10. Photoinduced Charge and Energy Transfer Processes in Molecular Aggregates

    SciTech Connect

    John F. Endicott

    2009-10-20

    This project involved the experimental probing of the electronic excited states generated by photoinduced (center-to-center) electron and energy transfer processes in several classes of transition metal donor/acceptor (D/A) complexes. Some of the general properties inferred from these studies should be useful in the design of new systems for energy conversion applications. Pursuit of the project goals has involved the determination of electron transfer efficiencies and the detailed study of variations in the electronic spectra of D/A complexes. This has resulted in the study of some very fundamental issues of photoinduced charge transfer and the identification of some of the constraints on its efficiency. The experimental studies of the competition between the degradative non-radiative unimolecular relaxation of transition metal excited states and their transfer of charge from these excited states to external acceptors have involved a range of techniques such as transient decay kinetics, photoacoustic calorimetry and transient or stationary state spectroscopy. The substrates synthesized for these studies were selected to provide model systems, or series of model systems to probe the validity of models of electronic excited states and their reactivity. The work during the last few years has focused largely, but not exclusively, on the use of emission spectral band shapes to probe the properties of charge transfer (CT) excited states. Bandshape variations are one of the very few approaches for systematically probing electronic excited states and good band shape resolution is necessary in order to gain information about the structural variations that correlate with excited state reactivity. Differences in molecular structure correlate with differences in chemical reactivity, and the variations in emission bandshapes are well known to relate to variations in the molecular structural differences between the excited and ground electronic states. However, it is has been

  11. Preliminary On-Orbit Neutron Dose Equivalent and Energy Spectrum Results from the ISS-RAD Fast Neutron Detector (FND)

    NASA Technical Reports Server (NTRS)

    Semones, Edward; Leitgab, Martin

    2016-01-01

    The ISS-RAD instrument was activated on ISS on February 1st, 2016. Integrated in ISS-RAD, the Fast Neutron Detector (FND) performs, for the first time on ISS, routine and precise direct neutron measurements between 0.5 and 8 MeV. Preliminary results for neutron dose equivalent and neutron flux energy distributions from online/on-board algorithms and offline ground analyses will be shown, along with comparisons to simulated data and previously measured neutron spectral data. On-orbit data quality and pre-launch analysis validation results will be discussed as well.

  12. 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.

  13. 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.

  14. 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. 

  15. 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.

  16. Intramolecular electronic energy transfer in bichromophoric molecular macrocyclic systems

    NASA Astrophysics Data System (ADS)

    Speiser, Shammai

    1993-01-01

    The structures and spectral properties of several bichromophoric molecules, suitable for optical data processing, are presented. The bichromophoric molecules are composed of an aromatic ring connected by two methylene chains to an (alpha) -diketone moiety. Both the absorption and emission spectra of these compounds can be attributed to a superposition of the individual spectra of the separate chromophores. The critical transfer radia for electronic energy transfer from the aromatic (donor) chromophore to the (alpha) -diketone (acceptor) chromophore was calculated from the spectral overlap between the fluorescence spectrum of the aromatic ring with the absorption spectrum of the (alpha) -diketone chromophore. The results show that this series of molecules is well suited for a mechanistic study of short-range intramolecular electronic energy transfer (intra-EET). The temperature and the molecular structure dependence of the intra-EET efficiency in this series was measured and analyzed for both singlet-singlet and triplet-triplet routes. The results show that the transfer efficiency is strongly temperature and structure dependent, indicating that exchange interaction is responsible for intra-EET between close chromophores in a bichromophoric molecule. The relative contributions of interchromophoric distance and that of the relative orientation of the two chromophores to exchange interaction are discussed.

  17. Equiparatition of energy for turbulent astrophysical fluids: Accounting for the unseen energy in molecular clouds

    NASA Technical Reports Server (NTRS)

    Zweibel, Ellen G.; Mckee, Christopher F.

    1995-01-01

    Molecular clouds are observed to be partially supported by turbulent pressure. The kinetic energy of the turbulence is directly measurable, but the potential energy, which consists of magnetic, thermal, and gravitational potential energy, is largly unseen. We have extended previous results on equipartition between kinetic and potential energy to show that it is likely to be a very good approximation in molecular clouds. We have used two separate approaches to demonstrate this result: For small-amplitude perturbations of a static equilibrium, we have used the energy principle analysis of Bernstein et al. (1958); this derivation applies to perturbations of arbitary wavelength. To treat perturbations of a nonstatic equilibrium, we have used the Lagrangian analysis of Dewar (1970); this analysis applies only to short-wavelength perturbations. Both analysis assume conservation of energy. Wave damping has only a small effect on equipartition if the wave frequency is small compared to the neutral-ion collision frequency; for the particular case we considered, radiative losses have no effect on equipartition. These results are then incorporated in a simple way into analyses of cloud equilibrium and global stability. We discuss the effect of Alfvenic turbulence on the Jeans mass and show that it has little effect on the magnetic critical mass.

  18. Orbital Simulations on Deflecting Near-Earth Objects by Directed Energy

    NASA Astrophysics Data System (ADS)

    Zhang, Qicheng; Walsh, Kevin J.; Melis, Carl; Hughes, Gary B.; Lubin, Philip M.

    2016-04-01

    Laser ablation of a near-Earth object (NEO) on a collision course with Earth produces a cloud of ejecta that exerts a thrust on the NEO, deflecting it from its original trajectory. Ablation may be performed from afar by illuminating an Earth-targeting asteroid or comet with a stand-off “DE-STAR” system consisting of a large phased-array laser in Earth orbit. Alternatively, a much smaller stand-on “DE-STARLITE” system may travel alongside the target, slowly deflecting it from nearby over a long period. This paper presents orbital simulations comparing the effectiveness of both systems across a range of laser and NEO parameters. Simulated parameters include magnitude, duration and, for the stand-on system, direction of the thrust, as well as the type, size, and orbital characteristics of the target NEO. These simulations indicate that deflection distance is approximately proportional to the magnitude of thrust and to the square of the duration of ablation, and is inversely proportional to the mass. Furthermore, deflection distance shows strong dependence on thrust direction with the optimal direction of thrust varying with the duration of laser activity. As one example, consider a typical 325 m asteroid: beginning 15 years in advance, just 2 N of thrust from a ∼20 kW stand-on DE-STARLITE system is sufficient to deflect the asteroid by 2 {R}\\oplus . Numerous scenarios are discussed as is a practical implementation of such a system consistent with current launch vehicle capabilities.

  19. The energy spectrometer for particles (ESP): Instrument description and orbital performance

    SciTech Connect

    Meier, M.; Belian, D.; Cayton, T.; Christensen, R.; Garcia, B.; Grace, K.; Ingraham, C.; Laros, J.; Reeves, G.

    1994-12-31

    The ESP detector is functionally described, along with the pertinent orbital and spin properties of the spacecraft that supports it. The phoswiched plastic/BGO scintillators sensor design, electronic implementation, and resulting data types are recounted, and the ground calibration procedures are reported. Several illustrative examples of data are given, including the solar proton event of 29 September 1989, and the nearly periodic episodes of high relativistic electron flux that are associated with solar coronal holes which have been a dominant feature of the space weather over the past few years.

  20. The energy spectrometer for particles (ESP): Instrument description and orbital performance

    SciTech Connect

    Meier, M.M.; Belian, R.D.; Cayton, T.E.; Christensen, R.; Garcia, B.; Grace, K.; Ingraham, J.C.; Laros, J.; Reeves, G.D.

    1994-12-31

    The ESP detector is functionally described, along with the pertinent orbital and spin properties of the spacecraft that supports it. The phoswiched plastic/BGO scintillators sensor design, electronic implementation, and resulting data types are recounted, and the ground calibration procedures are reported. Several illustrative examples of data are given, including the solar proton event of 29 September 1989, and the nearly periodic episodes of high relativistic electron flux that are associated with solar coronal holes which have been a dominant feature of the space weather over the past few years. 2 refs., 10 figs., 1 tab.

  1. The energy spectrometer for particles (ESP): Instrument description and orbital performance

    SciTech Connect

    Meier, M.M.; Belian, R.D.; Cayton, T.E.; Christensen, R.A.; Garcia, B.; Grace, K.M.; Ingraham, J.C.; Laros, J.G.; Reeves, G.D.

    1996-07-01

    The ESP detector is functionally described, along with the pertinent orbital and spin properties of the spacecraft that supports it. The phoswiched plastic/BGO scintillators sensor design, electronic implementation, and resulting data types are recounted, and the ground calibration procedures are reported. Several illustrative examples of data are given, including the solar proton event of 29 September 1989, and the nearly periodic episodes of high relativistic electron flux that are associated with solar coronal holes which have been a dominant feature of the space weather over the past few years. {copyright} {ital 1996 American Institute of Physics.}

  2. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    PubMed

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  3. Quasiparticle band gap of organic-inorganic hybrid perovskites: Crystal structure, spin-orbit coupling, and self-energy effects

    NASA Astrophysics Data System (ADS)

    Gao, Weiwei; Gao, Xiang; Abtew, Tesfaye; Sun, Yiyang; Zhang, Shengbai; Zhang, Peihong

    The quasiparticle band gaps of organic-inorganic hybrid perovskites are often determined (and can be controlled) by various factors, complicating predictive materials optimization. Here we report a comprehensive investigation on the band gap formation mechanism in CH3NH3PbI3 by decoupling various contributing factors which ultimately determine their electronic structure and quasiparticle band gap. Four major factors, namely, quasiparticle self-energy, spin-orbit coupling, volume (lattice constant) effects, and structural distortions due to the presence of organic molecules, and their influences on the quasiparticle band structure of organometal hybrid perovskites are illustrated. We find that although methylammonium cations do not contribute directly to the electronic states near band edges, they play an important role in defining the band gap through a lattice distortion mechanism and by controlling the overall lattice constants (thus the chemical bonding of the optically active PbI3-). The spin-orbit coupling effects drastically reduce the electron and hole effective masses in these systems, which is beneficial for high carrier mobilities and small exciton binding energies. This work is supported by the National Natural Science Foundation of China (Grant No. 11328401), NSF (Grant No. DMR-0946404 and DMR-1506669), and the SUNY Networks of Excellence.

  4. Protons Are Spinning On regular Orbits And Neutrons Have Different Binding Energies Inside Atoms

    NASA Astrophysics Data System (ADS)

    Elfikky, Niazi

    2014-03-01

    Preface. With the centennial of the discovery of the atomic nucleus by the Chemist, Professor Ernest Rutherford (1871-1937), it is worthwhile to memorize such occasion. For the structure of the atom where he had postulated that atoms have their positive charge concentrated in a very small nucleus. It was a great breakthrough when he introduced his imagination for the structure of the atom. Furthermore, he proposed a dynamic planetary model in which the nucleus plays the role of the sun and electrons correspond to the individual planets of the solar system although he fixed the atom's nucleus of the solar system, (He resembled the nucleus of the atom with the sun although he had dropped an essential fact that the sun is also rotating in its specific orbit surrounded by the outer orbit for the rotating planets like the whirling electrons. For studying the stable atom of the steady state elements like hydrogen 1H1, the particles of the 1H1 atoms are simle just one proton 1p1 and one electron 0e1, both the proton and electron have equal electric charge (q = 1.6 × 10-19 Coulomb) but in different sign (positive charge for proton and negative for electron), also they have different masses (mp = 1.67 × 10-27 Kg, me = 9.11 × 10-31 kg), proton is heavier than electron by 1.834 × 103. What does it mean?

  5. Energy-dependent finite-orbit treatment for plasma buildup in mirror fusion devices

    SciTech Connect

    Campbell, M.M.

    1980-01-01

    A computer simulation of hot plasma buildup in mirror fusion devices and results from this model are presented. In a small, hot magnetically confined plasma, the ion orbit radius (rho/sub i/) can be comparable to the plasma radius (R/sub p/). It a mirror-confined plasma were rho/sub i//R/sub p/ > 1/25 (such as 2XII-B), a point kinetic treatment of ion interactions becomes inaccurate and a finite gyro-radius (FGR) treatment must be used to adequately describe plasma buildup processes. This is particularly true for describing losses due to cold-gas charge exchange (c-x) near the plasma surface, since a particle lost near the vacuum interface may have contributed to the density as far as 2 rho/sub i/ radially inward from the c-x point. A similar FGR effect applies to beam-deposited ions whose large orbits influence the density up to 2 rho/sub i/ from the trapping point.

  6. Mechanical Evidence of the Orbital Angular Momentum to Energy Ratio of Vortex Beams

    NASA Astrophysics Data System (ADS)

    Demore, Christine E. M.; Yang, Zhengyi; Volovick, Alexander; Cochran, Sandy; MacDonald, Michael P.; Spalding, Gabriel C.

    2012-05-01

    We measure, in a single experiment, both the radiation pressure and the torque due to a wide variety of propagating acoustic vortex beams. The results validate, for the first time directly, the theoretically predicted ratio of the orbital angular momentum to linear momentum in a propagating beam. We experimentally determine this ratio using simultaneous measurements of both the levitation force and the torque on an acoustic absorber exerted by a broad range of helical ultrasonic beams produced by a 1000-element matrix transducer array. In general, beams with helical phase fronts have been shown to contain orbital angular momentum as the result of the azimuthal component of the Poynting vector around the propagation axis. Theory predicts that for both optical and acoustic helical beams the ratio of the angular momentum current of the beam to the power should be given by the ratio of the beam’s topological charge to its angular frequency. This direct experimental observation that the ratio of the torque to power does convincingly match the expected value (given by the topological charge to angular frequency ratio of the beam) is a fundamental result.

  7. Mechanical evidence of the orbital angular momentum to energy ratio of vortex beams.

    PubMed

    Demore, Christine E M; Yang, Zhengyi; Volovick, Alexander; Cochran, Sandy; MacDonald, Michael P; Spalding, Gabriel C

    2012-05-11

    We measure, in a single experiment, both the radiation pressure and the torque due to a wide variety of propagating acoustic vortex beams. The results validate, for the first time directly, the theoretically predicted ratio of the orbital angular momentum to linear momentum in a propagating beam. We experimentally determine this ratio using simultaneous measurements of both the levitation force and the torque on an acoustic absorber exerted by a broad range of helical ultrasonic beams produced by a 1000-element matrix transducer array. In general, beams with helical phase fronts have been shown to contain orbital angular momentum as the result of the azimuthal component of the Poynting vector around the propagation axis. Theory predicts that for both optical and acoustic helical beams the ratio of the angular momentum current of the beam to the power should be given by the ratio of the beam's topological charge to its angular frequency. This direct experimental observation that the ratio of the torque to power does convincingly match the expected value (given by the topological charge to angular frequency ratio of the beam) is a fundamental result. PMID:23003045

  8. On the errors of local density (LDA) and generalized gradient (GGA) approximations to the Kohn-Sham potential and orbital energies.

    PubMed

    Gritsenko, O V; Mentel, Ł M; Baerends, E J

    2016-05-28

    In spite of the high quality of exchange-correlation energies Exc obtained with the generalized gradient approximations (GGAs) of density functional theory, their xc potentials vxc are strongly deficient, yielding upshifts of ca. 5 eV in the orbital energy spectrum (in the order of 50% of high-lying valence orbital energies). The GGAs share this deficiency with the local density approximation (LDA). We argue that this error is not caused by the incorrect long-range asymptotics of vxc or by self-interaction error. It arises from incorrect density dependencies of LDA and GGA exchange functionals leading to incorrect (too repulsive) functional derivatives (i.e., response parts of the potentials). The vxc potential is partitioned into the potential of the xc hole vxchole (twice the xc energy density ϵxc), which determines Exc, and the response potential vresp, which does not contribute to Exc explicitly. The substantial upshift of LDA/GGA orbital energies is due to a too repulsive LDA exchange response potential vxresp (LDA) in the bulk region. Retaining the LDA exchange hole potential plus the B88 gradient correction to it but replacing the response parts of these potentials by the model orbital-dependent response potential vxresp (GLLB) of Gritsenko et al. [Phys. Rev. A 51, 1944 (1995)], which has the proper step-wise form, improves the orbital energies by more than an order of magnitude. Examples are given for the prototype molecules: dihydrogen, dinitrogen, carbon monoxide, ethylene, formaldehyde, and formic acid. PMID:27250286

  9. 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.

  10. Heating rates in a High-Energy Propulsion System (HEPS) Orbital Transfer Vehicle (OTV). Final report, June-August 1989

    SciTech Connect

    Miller, R.L.

    1989-10-01

    Rocket-propulsion systems that use nuclear-energy sources present unique challenges to the design, safety, and reliability of the concept. Since the vehicle and its components must operate in high radiation fields, nuclear heating and radiation effects must be determined and factored into the system design. This report analyzes the nuclear heating in a High-Energy Propulsion System (HEPS) Orbital Transfer Vehicle (OTV) nozzle. Using the FEMP2D (Finite Element, Multigroup, Pn, 2-Dimensional) code for an aluminum and carbon-carbon nozzle, it was determined that the heating contribution was found to be the significant source of heating for both materials. The overall heating rate in the aluminum nozzle (approx. 12 W/cc) was significantly higher than that found in the carbon-carbon nozzle (approx. 8 W/cc).

  11. All-electron formalism for total energy strain derivatives and stress tensor components for numeric atom-centered orbitals

    NASA Astrophysics Data System (ADS)

    Knuth, Franz; Carbogno, Christian; Atalla, Viktor; Blum, Volker; Scheffler, Matthias

    2015-05-01

    We derive and implement the strain derivatives of the total energy of solids, i.e., the analytic stress tensor components, in an all-electron, numeric atom-centered orbital based density-functional formalism. We account for contributions that arise in the semi-local approximation (LDA/GGA) as well as in the generalized Kohn-Sham case, in which a fraction of exact exchange (hybrid functionals) is included. In this work, we discuss the details of the implementation including the numerical corrections for sparse integrations grids which allow to produce accurate results. We validate the implementation for a variety of test cases by comparing to strain derivatives performed via finite differences. Additionally, we include the detailed definition of the overlapping atom-centered integration formalism used in this work to obtain total energies and their derivatives.

  12. Ab initio molecular orbital investigation of the unimolecular decomposition of CH[sub 3]SiH[sub 2][sup +

    SciTech Connect

    Gordon, M.S.; Pederson, L.A. Ames Research Lab., IA ); Bakhtiar, R.; Jacobson, D.B. )

    1995-01-05

    The potential energy surface for the decomposition of CH[sub 3]SiH[sub 2][sup +] was studied by ab initio electronic structure theory. At the MP2/6-31G(d,p) level of theory, CH[sub 3]SiH[sub 2][sup +] is the only minimum energy structure on the SiCH[sub 3][sup +] potential energy surface. Lower levels of theory reported that [sup +]CH[sub 2]SiH[sub 3] was also a local minimum, about 40 kcal/mol higher in energy with only a small (ca. 1-2 kcal/mol) barrier for conversion back to CH[sub 3]SiH[sub 2][sup +]. However, at higher levels of theory, the C[sub s] structure of [sup +]CH[sub 2]SiH[sub 3] has an imaginary frequency, indicating that it is a saddle point rather than a local minimum on the potential energy surface. The 0 K reaction enthalpies for 1,1-dehydrogenation from silicon, 1,2-dehydrogenation, 1,1-dehydrogenation from carbon, and demethanation were calculated to be 30.2, 69.1, 107.3, and 45.3 kcal/mol, respectively. Activation energies (0 K) were calculated at the MP4/6-311++G(2df,2pd) level of theory with the classical barriers subsequently adjusted for zero-point vibrational energies. The 0 K activation energies for 1,1-dehydrogenation from silicon, 1,2-dehydrogenation, and demethanation are predicted to be 66.6, 72.7, and 73.0 kcal/mol, respectively. 52 refs., 5 figs., 2 tabs.

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

    SciTech Connect

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

    2015-01-22

    In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.

  14. Energy landscape of LeuT from molecular simulations

    NASA Astrophysics Data System (ADS)

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-12-01

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ˜40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

  15. Energy landscape of LeuT from molecular simulations.

    PubMed

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-12-28

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates. PMID:26723619

  16. Orbit to orbit transportation

    NASA Technical Reports Server (NTRS)

    Bergeron, R. P.

    1980-01-01

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

  17. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  18. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  19. Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

    ERIC Educational Resources Information Center

    Halpern, Arthur M.; Glendening, Eric D.

    2013-01-01

    A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

  20. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    PubMed

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-01

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197

  1. The Pairwise Correlated Generalized Valence Bond Model of Electronic Structure I; The Estimation of Pair Energies from Orbital Overlaps

    PubMed Central

    Petersson, G. A.

    1974-01-01

    A new method for the accurate a priori calculation of atomic and molecular energies is proposed. The new method agrees with experiment to within less than 1 kcal/mole in all cases examined thus far, and is applicable to excited states and to transition states for chemical reactions. Since the new method corrects the results of generalized valence bond calculations for the effects of electron pair correlations, we call the new method the pairwise correlated generalized valence bond method. PMID:16592172

  2. Construction of the energy matrix for complex atoms. Part V: Electrostatically correlated spin-orbit and electrostatically correlated hyperfine interactions

    NASA Astrophysics Data System (ADS)

    Elantkowska, Magdalena; Ruczkowski, Jarosław; Dembczyński, Jerzy

    2016-02-01

    The continuation of the previous series of papers related to the construction of the energy matrix for complex atoms is presented. The contributions from the second-order perturbation theory concerning electrostatically correlated spin-orbit interactions (CSO), as well as electrostatically correlated hyperfine interactions (CHFS) to the atomic structure of nlN, nlNn1l1^{N_1} and nlNn1l1^{N_1}n2l2^{N_2} configurations, are considered. This theory assumes that the electron excitation n0l0→ nl affects spin-orbit splitting and magnetic dipole and electric quadrupole hyperfine structure in the same way which will be discussed below. Part I of the series presented, in general terms, a method allowing the analysis of complex electronic systems. Parts II, III and IV provided a description of an electrostatic interaction up to second-order perturbation theory; they constitute the basis for the design of an efficient computer program package for large-scale calculations of accurate wave functions. Analyses presented in the entire series of our papers clearly demonstrate that obtaining the precise wave functions is impossible without considering the contribution from the second-order effects into fine and hyperfine atomic structure.

  3. Measurements of the linear energy transfer spectra on the Mir orbital station and comparison with radiation transport models

    NASA Technical Reports Server (NTRS)

    Badhwar, G. D.; Konradi, A.; Atwell, W.; Golightly, M. J.; Cucinotta, F. A.; Wilson, J. W.; Petrov, V. M.; Tchernykh, I. V.; Shurshakov, V. A.; Lobakov, A. P.

    1996-01-01

    A tissue equivalent proportional counter designed to measure the linear energy transfer spectra (LET) in the range 0.2-1250 keV/micrometer was flown in the Kvant module on the Mir orbital station during September 1994. The spacecraft was in a 51.65 degrees inclination, elliptical (390 x 402 km) orbit. This is nearly the lower limit of its flight altitude. The total absorbed dose rate measured was 411.3 +/- 4.41 microGy/day with an average quality factor of 2.44. The galactic cosmic radiation (GCR) dose rate was 133.6 microGy/day with a quality factor of 3.35. The trapped radiation belt dose rate was 277.7 microGy/day with an average quality factor of 1.94. The peak rate through the South Atlantic Anomaly was approximately 12 microGy/min and nearly constant from one pass to another. A detailed comparison of the measured LET spectra has been made with radiation transport models. The GCR results are in good agreement with model calculations; however, this is not the case for radiation belt particles and again points to the need for improving the AP8 omni-directional trapped proton models.

  4. Hydrogen bonded C-H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2016-03-01

    Hydrogen bonded C-H···Y complexes formed by H2O, H2S molecules, hydrogen halides, and halogen-ions with methane, halogen substituted methane as well as with the C2H2 and NCH molecules were studied at the MP2/aug-cc-pVDZ level. The structure of NBOs corresponding to lone pair of acceptor Y, n Y, and vacant anti-σ-bond C-H of proton donor was analyzed and estimates of second order perturbation energy E(2) characterizing donor-acceptor n Y → σ C-H * charge-transfer interaction were obtained. Computational results for complexes of methane and its halogen substituted derivatives show that for each set of analogous structures, the EnY→σ*C-H (2) energy tends to grow with an increase in the s-component percentage in the lone pair NBO of acceptor Y. Calculations for different C···Y distances show that the equilibrium geometries of complexes lie in the region where the E(2) energy is highest and it changes symbatically with the length of the covalent E-H bond when the R(C···Y) distance is varied. The performed analysis allows us to divide the hydrogen bonded complexes into two groups, depending on the pattern of overlapping for NBOs of the hydrogen bridge.

  5. Visualization of atom's orbits.

    PubMed

    Kim, Byungwhan

    2014-02-01

    High-resolution imaging techniques have been used to obtain views of internal shapes of single atoms or columns of atoms. This review article focuses on the visualization of internal atomic structures such as the configurations of electron orbits confined to atoms. This is accomplished by applying visualization techniques to the reported images of atoms or molecules as well as static and dynamic ions in a plasma. It was found that the photon and electron energies provide macroscopic and microscopic views of the orbit structures of atoms, respectively. The laser-imaged atoms showed a rugged orbit structure, containing alternating dark and bright orbits believed to be the pathways for an externally supplied laser energy and internally excited electron energy, respectively. By contrast, the atoms taken by the electron microscopy provided a structure of fine electron orbits, systematically formed in increasing order of grayscale representing the energy state of an orbit. This structure was identical to those of the plasma ions. The visualized electronic structures played a critical role in clarifying vague postulates made in the Bohr model. Main features proposed in the atomic model are the dynamic orbits absorbing an externally supplied electromagnetic energy, electron emission from them while accompanying light radiation, and frequency of electron waves not light. The light-accompanying electrons and ionic speckles induced by laser light signify that light is composed of electrons and ions. PMID:24749452

  6. Orbital pseudotumor

    MedlinePlus

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

  7. Kepler's Orbit

    NASA Video Gallery

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

  8. Orbital cellulitis

    MedlinePlus

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

  9. Energy-dependent Orbital Modulation of X-rays and Constraints on Emission of the Jet in Cyg X-3

    NASA Technical Reports Server (NTRS)

    Zdziarski, Andrzej A.; Maitra, Chandreyee; Frankowski, Adam; Skinner, Gerald K.; Misra, Ranjeev

    2012-01-01

    We study orbital modulation of X-rays from Cyg X-3, using data from Swift, INTEGRAL and RXTE. Using the wealth of the presently available data and an improved averaging method, we obtain energy-dependent folded and averaged light curves with unprecedented accuracy. We find that above 5 keV, the modulation depth decreases with the increasing energy, which is consistent with the modulation being caused by both bound-free absorption and Compton scattering in the stellar wind of the donor, with minima corresponding to the highest optical depth, which occurs around the superior conjunction. We find a decrease of the depth below 3 keV, which appears to be due to re-emission of the absorbed continuum by the wind in soft X-ray lines. Based on the shape of the folded light curves, any X-ray contribution from the jet in Cyg X-3, which emits ?-rays detected at energies > 0.1 GeV in soft spectral states, is found to be minor up to 100 keV. This implies the presence of a rather sharp low-energy break in the jet MeV-range spectrum.We also calculate phase-resolved RXTE X-ray spectra, and show the difference between the spectra corresponding to phases around the superior and inferior conjunctions can indeed be accounted for by a combined effect of bound-free absorption in an ionized medium and Compton scattering.

  10. 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.

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

    PubMed

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

    2015-03-01

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

  12. A molecular orbital study of pyridine and the rotation about the CC bond in 4-vinylpyridine

    NASA Astrophysics Data System (ADS)

    Bock, Charles W.; Trachtman, Mendel; George, Philip

    1986-06-01

    The geometry and energy of pyridine and the planar conformer of 4-vinylpyridine have been calculated using the 6-31G basis set. The distortion of the pyridyl ring brought about by the vinyl substitution is compared to the distortion of the phenyl ring in styrene. Δ ET for the exchange reaction, 4-vinylpyridine + benzene → pyridine + styrene, is very small, 1.73 kJ mol -1, showing that such additional stabilization as there may be in the two vinyl derivatives relative to that in the parent molecules is almost identical. The geometry and energy of 4-vinyl-pyridine have also been calculated as a function of the C βC αC 4C 5 dihedral angle (φ = 0°, 30°, and 90°) assuming that the vinyl group and pyridyl group remain planar but otherwise with full geometry optimization. The torsional potential energy curve is almost identical to that calculated for styrene (Bock, Trachtman and George, 1985), which, in turn, was found to follow closely the experimental curve derived from single vibronic level fluorescence and other spectroscopic data. The curve has a very flat minimum at φ = 0° with a barrier height of 12.7 kJ mol -1. The changes in key geometrical parameters as the planar conformer is converted into the 90°-gauche conformer are likewise very similar to those in styrene, as are the changes in total atomic charge throughout the molecule, despite the profound differences in charge distribution in the two ring systems. Utilizing the increments between the calculated and experimental bond lengths for pyridine and trans-1,3-butadiene an experimental geometry is predicted for 4-vinylpyridine; and the "superimposition hypothesis", proposed by Domenicano and Murray-Rust (1979) for para-disubstituted benzene derivatives, is tested using the 6-31G optimized geometries for pyridine and styrene.

  13. Regenerative fuel cell energy storage system for a low earth orbit space station

    NASA Technical Reports Server (NTRS)

    Martin, R. E.; Garow, J.; Michaels, K. B.

    1988-01-01

    A study was conducted to define characteristics of a Regenerative Fuel Cell System (RFCS) for low earth orbit Space Station missions. The RFCS's were defined and characterized based on both an alkaline electrolyte fuel cell integrated with an alkaline electrolyte water electrolyzer and an alkaline electrolyte fuel cell integrated with an acid solid polymer electrolyte (SPE) water electrolyzer. The study defined the operating characteristics of the systems including system weight, volume, and efficiency. A maintenance philosophy was defined and the implications of system reliability requirements and modularization were determined. Finally, an Engineering Model System was defined and a program to develop and demonstrate the EMS and pacing technology items that should be developed in parallel with the EMS were identified. The specific weight of an optimized RFCS operating at 140 F was defined as a function of system efficiency for a range of module sizes. An EMS operating at a nominal temperature of 180 F and capable of delivery of 10 kW at an overall efficiency of 55.4 percent is described. A program to develop the EMS is described including a technology development effort for pacing technology items.

  14. Regenerative fuel cell energy storage system for a low earth orbit space station

    NASA Astrophysics Data System (ADS)

    Martin, R. E.; Garow, J.; Michaels, K. B.

    1988-04-01

    A study was conducted to define characteristics of a Regenerative Fuel Cell System (RFCS) for low earth orbit Space Station missions. The RFCS's were defined and characterized based on both an alkaline electrolyte fuel cell integrated with an alkaline electrolyte water electrolyzer and an alkaline electrolyte fuel cell integrated with an acid solid polymer electrolyte (SPE) water electrolyzer. The study defined the operating characteristics of the systems including system weight, volume, and efficiency. A maintenance philosophy was defined and the implications of system reliability requirements and modularization were determined. Finally, an Engineering Model System was defined and a program to develop and demonstrate the EMS and pacing technology items that should be developed in parallel with the EMS were identified. The specific weight of an optimized RFCS operating at 140 F was defined as a function of system efficiency for a range of module sizes. An EMS operating at a nominal temperature of 180 F and capable of delivery of 10 kW at an overall efficiency of 55.4 percent is described. A program to develop the EMS is described including a technology development effort for pacing technology items.

  15. Structure of expanded porphyrins: electron-nuclear multiple resonance and molecular orbital studies of texaphyrin anion radicals in solution

    NASA Astrophysics Data System (ADS)

    Endeward, B.; Regev, A.; Plato, M.; Levanon, H.; Sessler, J. L.; Möbius, K.

    1994-08-01

    Liquid solution ENDOR and TRIPLE resonance experiments have been performed on texaphyrin radical anions generated by sodium reduction in tetrahydrofuran. Six proton and two nitrogen hyperfine couplings could be determined, including their signs. The results were compared with theoretical isotropic hyperfine couplings. They were calculated for energy-minimized texaphyrin structures, including the sodium metallo-derivative, by state-of-the-art SCF-MO methods (RHF-INDO/SP). This comparison suggests that in the course of the alkali metal reduction of texaphyrin the acidic hydrogen in the macrocycle is replaced by sodium.

  16. High-energy electrons from the muon decay in orbit: Radiative corrections

    SciTech Connect

    Szafron, Robert; Czarnecki, Andrzej

    2015-12-07

    We determine the Ο(α) correction to the energy spectrum of electrons produced in the decay of muons bound in atoms. We focus on the high-energy end of the spectrum that constitutes a background for the muon-electron conversion and will be precisely measured by the upcoming experiments Mu2e and COMET. As a result, the correction suppresses the background by about 20%.

  17. Accurate potential energy functions, non-adiabatic and spin-orbit couplings in the ZnH+ system

    NASA Astrophysics Data System (ADS)

    Liang, Guiying; Liu, Xiaoting; Zhang, Xiaomei; Xu, Haifeng; Yan, Bing

    2016-03-01

    A high-level ab initio calculation on the ZnH+ cation has been carried out with the multi-reference configuration interaction method plus Davison correction (MRCI + Q). The scalar relativistic effect is included by using the Douglas-Kroll-Hess (DKH) method. The calculated potential energy curves (PECs) of the 7 Λ-S states are associated with the dissociation limits of Zn+(2Sg) + H(2Sg), Zn(1Sg) + H+(1Sg), and Zn+(2Pu) + H(2Sg), respectively (The Λ-S state is labeled as 2S + 1Λ, in which Λ is the quantum number for the projection along the internuclear axis of the total electronic orbital angular momentum and S is the total electron spin). The spectroscopic constants of the bound states are determined and in good agreement with the available theoretical and experimental results. The permanent dipole moments (PDMs) of Λ-S states and the spin-orbit (SO) matrix elements between Λ-S states are also computed. The results show that the abrupt changes of the PDMs and SO matrix elements come into being for the reason of the avoided crossing between the states with the same symmetry. In addition, the non-adiabatic couplings matrix elements between Λ-S states are also evaluated. Finally, the spin-orbit couplings (SOCs) for the low-lying states are considered with Breit-Pauli operator. The SOC effect makes the 7 Λ-S states of the ZnH+ cation split into 12 Ω states (Ω = Λ + Sz, in which Sz is projection of the total electron spin S along the internuclear Z-axis). For the (3)0+ state, the two energy minima exhibit in the potential, which could be attributed to the formation of the new avoided crossing point. The transition dipole moments (TDMs), Franck-Condon factors, and the radiative lifetimes of the selected transitions (2)0+-X0+, (3)0+-X0+, (2)1-X0+ and (3)1-X0+ have been reported.

  18. Accurate potential energy functions, non-adiabatic and spin-orbit couplings in the ZnH(+) system.

    PubMed

    Liang, Guiying; Liu, Xiaoting; Zhang, Xiaomei; Xu, Haifeng; Yan, Bing

    2016-03-01

    A high-level ab initio calculation on the ZnH(+) cation has been carried out with the multi-reference configuration interaction method plus Davison correction (MRCI+Q). The scalar relativistic effect is included by using the Douglas-Kroll-Hess (DKH) method. The calculated potential energy curves (PECs) of the 7 Λ-S states are associated with the dissociation limits of Zn(+)((2)Sg)+H((2)Sg), Zn((1)Sg)+H(+)((1)Sg), and Zn(+)((2)Pu)+H((2)Sg), respectively (The Λ-S state is labeled as (2S+1)Λ, in which Λ is the quantum number for the projection along the internuclear axis of the total electronic orbital angular momentum and S is the total electron spin). The spectroscopic constants of the bound states are determined and in good agreement with the available theoretical and experimental results. The permanent dipole moments (PDMs) of Λ-S states and the spin-orbit (SO) matrix elements between Λ-S states are also computed. The results show that the abrupt changes of the PDMs and SO matrix elements come into being for the reason of the avoided crossing between the states with the same symmetry. In addition, the non-adiabatic couplings matrix elements between Λ-S states are also evaluated. Finally, the spin-orbit couplings (SOCs) for the low-lying states are considered with Breit-Pauli operator. The SOC effect makes the 7 Λ-S states of the ZnH(+) cation split into 12 Ω states (Ω=Λ+Sz, in which Sz is projection of the total electron spin S along the internuclear Z-axis). For the (3)0(+) state, the two energy minima exhibit in the potential, which could be attributed to the formation of the new avoided crossing point. The transition dipole moments (TDMs), Franck-Condon factors, and the radiative lifetimes of the selected transitions (2)0(+)-X0(+), (3)0(+)-X0(+), (2)1-X0(+) and (3)1-X0(+) have been reported. PMID:26637984

  19. Orbit correction in an orbit separated cyclotron

    NASA Astrophysics Data System (ADS)

    Plostinar, C.; Rees, G. H.

    2014-04-01

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

  20. Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Tantakitti, Faifan

    a controlled local release of the soluble growth factor bone morphogenetic protein 4 (BMP-4) was realized from the particle's core composed of cross-linked alginate. The alginate-core and PA-shell microparticles were found to allow independent tuning of the bioactivity of a PA and a release of the growth factor for specific signaling to cells. Using microcarriers which encapsulated BMP-4 and coated with RGDS PA nanofibers, it was shown that a control over spatial distribution, proliferation, and osteogenic differentiation of premyoblastic cells on the surface of microcarriers can be effectively achieved. Finally, in drastic contrast to the traditional approach to material development based on altering molecular structure, chapter 4 presents the energy landscapes in which supramolecular assemblies of unique architecture exist in different thermodynamic wells. Experimental results and calculations revealed that the energy landscapes are rooted in competing interactions between PA monomers, namely beta-sheet hydrogen bonds and repulsion among charged groups. Switching off or on the repulsive electrostatic interactions by changing the ionic strength promoted or suppressed the dominant ?-sheet hydrogen bonding interactions respectively. However, the dominant forces can prevail if the assemblies are above a certain size and thereby can exist in a kinetically trapped state. Preparative pathways involving dilution, annealing, and addition of salt were investigated in which the structures belonging to different energy states could be accessed and demonstrated that these energy landscapes involving competitive interactions was applicable not only to PA systems but also to a non-peptide supramolecular system based on pi-orbital overlaps as the dominant attraction among molecules and electrostatic repulsion. In chapter 5, structure and biological function relationships of long or short PA nanofibers are reported, and such fibers were prepared from identical monomers based on