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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. Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations.

    PubMed

    van Meer, R; Gritsenko, O V; Baerends, E J

    2014-10-14

    In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent density functional theory (TDDFT) calculations of excitation energies have been performed. The tested functionals do not approximate exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of molecular excitations. Benchmark calculations are performed for the statistical average of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential does not only perform satisfactorily for calculated vertical excitation energies of both valence and Rydberg transitions but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calculated with local density, generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in molecules: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).

  3. Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.

    PubMed

    Simoncini, David; Nakata, Hiroya; Ogata, Koji; Nakamura, Shinichiro; Zhang, Kam Yj

    2015-02-01

    Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

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

    PubMed

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

    2013-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  6. 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.

  7. 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.

  8. Basis set effects on frontier molecular orbital energies and energy gaps: a comparative study between plane waves and localized basis functions in molecular systems.

    PubMed

    Matus, Myrna H; Garza, Jorge; Galván, Marcelo

    2004-06-01

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

  9. 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.

  10. Fake molecular-orbital calculations

    NASA Astrophysics Data System (ADS)

    Harris, Frank E.; Trautwein, Alfred; Delhalle, Joseph

    1980-06-01

    The FAKE method of approximate molecular-orbital calculations is presented and illustrated by application to a number of molecules. The method is of the extended Huckel type but uses accurately computed kinetic-energy matrix elements and avoids scale factors of the Wolfsberg—Helmholtz type. It also includes neighbor-atom charge effects and single-center off-diagonal matrix elements. These features permit FAKE occupied-orbital energies and charge distributions to come into close agreement with corresponding ab initio quantities.

  11. Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method.

    PubMed

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

    2016-07-28

    The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well. PMID:27475354

  12. Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nakata, Hiroya; Nishimoto, Yoshio; Fedorov, Dmitri G.

    2016-07-01

    The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well.

  13. 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.

  14. 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.

  15. Orbiting molecular-beam laboratory

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.; Brock, F. J.

    1977-01-01

    The composition of the atmosphere within the planned orbital envelope of the Space Shuttle and the velocity necessary to maintain a stable orbit within that envelope provide unique conditions for forming a high-purity, moderate energy beam (about 5 eV) of atomic oxygen. At 500 km, for example, atomic oxygen comprises approximately 90% of the atmosphere. Since the mean thermal speed of the ambient atomic oxygen is substantially less than the orbital speed, a high-purity beam can be generated by sweeping through the gas with a series of beam-forming truncated conical shells. Characteristics of the beam, including energy distribution, flux, and purity variation with orbital altitude and methods for lowering the mean energy, are presented. Gas-surface interaction experiments that have been proposed for this laboratory are also discussed.

  16. 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

  17. 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.

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

    PubMed

    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. PMID:26328835

  19. 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

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

    PubMed

    Otsuka, Takao; Okimoto, Noriaki; Taiji, Makoto

    2015-11-15

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-15

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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.)

  8. Tuning molecular orbitals in molecular electronics and spintronics.

    PubMed

    Kim, Woo Youn; Kim, Kwang S

    2010-01-19

    With the advance of nanotechnology, a variety of molecules, from single atoms to large-scale structures such as graphene or carbon nanotubes, have been investigated for possible use as molecular devices. Molecular orbitals (MOs) are a key ingredient in determining the transport properties of molecules, because they contain all the quantum mechanical information of molecular electronic structures and offer spatial conduction channels for electron transport. Therefore, the delicate modulation of the MOs enables us to tune the performance of electron transport through the molecule. Electric and magnetic fields are powerful and readily accessible means for that purpose. In this Account, we describe the effects of external fields on molecular electronic and spintronic devices. Quantum transport through a molecule that connects source and drain electrodes depends strongly on the alignment of molecular energy levels with respect to the chemical potentials at both electrodes. This dependence results from the energy levels being exploited in resonant tunneling processes when the molecule is weakly coupled to the electrodes in the molecular junction. Molecular energy levels can be shifted by the Stark effect of an external electric field. For a molecule with no permanent dipole moment, the polarizability is the primary factor determining the energy shift of each MO, according to the second-order Stark effect; more polarizable MOs undergo a larger energy shift. Interestingly, even a small shift may lead to a completely nontrivial result. For example, we show a magnetic on-off switching phenomenon of a molecule controlled by an electric field. If a molecule has a nonmagnetic ground state but a highly polarizable magnetic excited state with an energy slightly above the ground state, the magnetic excited state can have lower energy than the ground state under a sufficiently strong electric field. A magnetic field is normally used to control spin orientation in a ferromagnetic

  9. Examination of the hydrogen-bonding networks in small water clusters (n = 2-5, 13, 17) using absolutely localized molecular orbital energy decomposition analysis.

    PubMed

    Cobar, Erika A; Horn, Paul R; Bergman, Robert G; Head-Gordon, Martin

    2012-11-28

    Using the ωB97X-D and B3LYP density functionals, the absolutely localized molecular orbital energy decomposition method (ALMO-EDA) is applied to the water dimer through pentamer, 13-mer and 17-mer clusters. Two-body, three-body, and total interaction energies are decomposed into their component energy terms: frozen density interaction energy, polarization energy, and charge transfer energy. Charge transfer, polarization, and frozen orbital interaction energies are all found to be significant contributors to the two-body and total interaction energies; the three-body interaction energies are dominated by polarization. Each component energy term for the two-body interactions is highly dependent on the associated hydrogen bond distance. The favorability of the three-body terms associated with the 13- and 17-mer structures depends on the hydrogen-donor or hydrogen-acceptor roles played by each of the three component waters. Only small errors arise from neglect of three-body interactions without two adjacent water molecules, or beyond three-body interactions. Interesting linear correlations are identified between the contributions of charge-transfer and polarization terms to the two and three-body interactions, which permits elimination of explicit calculation of charge transfer to a good approximation.

  10. Molecular Electronic Terms and Molecular Orbital Configurations.

    ERIC Educational Resources Information Center

    Mazo, R. M.

    1990-01-01

    Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)

  11. 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.

  12. Orbitals and orbital energies in DFT and TDDFT

    NASA Astrophysics Data System (ADS)

    Baerends, Evert Jan

    The status and meaning of orbitals and orbital energies in the Kohn-Sham one-electron model of DFT has been controversial, in contrast to Hartree-Fock orbitals and orbital energies. We will argue the opposite: the exact Kohn-Sham orbitals of DFT are ''better'' than HF orbitals and their orbital energies are much closer to ionization energies than HF orbital energies are. This follows from the relation between the KS potential and the wavefunction, which can be cast in the form vs =vc , kin +vH +vxchole +vresp, where each term depends on the KS orbitals and the wavefunction (the one- or two-particle density matrices). The response potential vresp (r) = ∑ j ∞|/dj(r) | 2 ρ (r) Ij - ∑ i H|/ψs , i(r) | 2 ρ (r) (-ɛi) (dj is the Dyson orbital corresponding to ion state ΨjN - 1 , ψs , i is a Kohn-Sham orbital) enables the connection between ionization energies Ii and orbital energies ɛi to be made. For virtual orbitals and orbital energies similar statements can be made: the shapes and energies of the (exact) KS orbitals are much more realistic than those of the Hartree-Fock model or hybrid functionals. The HOMO-LUMO gap in molecules is very close to the optical gap, and very different from the fundamental gap. In solids the situation is very different, which is the well-known ''KS gap problem''. Again the response potential vresp (a good approximation to it) helps to solve this problem, affording a straigtforward correction method of the KS gap to the fundamental gap.

  13. Density functional theory for comprehensive orbital energy calculations.

    PubMed

    Nakata, Ayako; Tsuneda, Takao

    2013-08-14

    This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.

  14. 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.

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

    PubMed

    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(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.

  16. 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.

  17. 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.

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

    PubMed

    Liu, Shubin; Schauer, Cynthia K

    2015-02-01

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

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

    SciTech Connect

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

    2015-02-07

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

  20. 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.

  1. Molecular diagnosis of orbital inflammatory disease.

    PubMed

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

    2015-04-01

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

  2. 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

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

    PubMed

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

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

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

    PubMed

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

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

  5. 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.

  6. Angle resolved photoemission from organic semiconductors: orbital imaging beyond the molecular orbital interpretation

    NASA Astrophysics Data System (ADS)

    Dauth, M.; Wiessner, M.; Feyer, V.; Schöll, A.; Puschnig, P.; Reinert, F.; Kümmel, S.

    2014-10-01

    Fascinating pictures that can be interpreted as showing molecular orbitals have been obtained with various imaging techniques. Among these, angle resolved photoemission spectroscopy (ARPES) has emerged as a particularly powerful method. Orbital images have been used to underline the physical credibility of the molecular orbital concept. However, from the theory of the photoemission process it is evident that imaging experiments do not show molecular orbitals, but Dyson orbitals. The latter are not eigenstates of a single-particle Hamiltonian and thus do not fit into the usual simple interpretation of electronic structure in terms of molecular orbitals. In a combined theoretical and experimental study we thus check whether a Dyson-orbital and a molecular-orbital based interpretation of ARPES lead to differences that are relevant on the experimentally observable scale. We discuss a scheme that allows for approximately calculating Dyson orbitals with moderate computational effort. Electronic relaxation is taken into account explicitly. The comparison reveals that while molecular orbitals are frequently good approximations to Dyson orbitals, a detailed understanding of photoemission intensities may require one to go beyond the molecular orbital picture. In particular we clearly observe signatures of the Dyson-orbital character for an adsorbed semiconductor molecule in ARPES spectra when these are recorded over a larger momentum range than in earlier experiments.

  7. 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)

  8. Frontier orbital control of molecular conductance and its switching.

    PubMed

    Tsuji, Yuta; Hoffmann, Roald

    2014-04-14

    For transmission of electrons through a π system, when the Landauer theory of molecular conductance is viewed from a molecular orbital (MO) perspective, there obtains a simple perturbation theoretic dependence, due to Yoshizawa and Tada, on a) the product of the orbital coefficients at the sites of electrode attachment, and b) the MO energies. The frontier orbitals consistently and simply indicate high or low transmission, even if other orbitals may contribute. This formalism, with its consequent reinforcement and/or interference of conductance, accounts for the (previously explained) difference in direct vs. cross conjugated transmission across an ethylene, as well as the comparative ON/OFF ratios in the experimentally investigated dimethyldihydropyrene and dithienylethene-type single-molecule switches. A strong dependence of the conductance on the site of attachment of the electrodes in a π system is an immediate extrapolation; the theory then predicts that for some specified sites the switching behavior will be inverted; i.e. the "open" molecular form of the switch will be more conductive.

  9. 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

  10. 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.

  11. Interpretation of intermolecular geometric isotope effect in hydrogen bonds: nuclear orbital plus molecular orbital study.

    PubMed

    Ikabata, Yasuhiro; Imamura, Yutaka; Nakai, Hiromi

    2011-03-01

    The intermolecular geometric isotope effect (GIE) in hydrogen bond A-X···B (X = H and D) is investigated theoretically using the nuclear orbital plus molecular orbital (NOMO) theory. To interpret the GIE in terms of physically meaningful energy components such as electrostatic and exchange-repulsion interactions, the reduced variational space self-consistent-field method is extended to the NOMO scheme. The intermolecular GIE is analyzed as a two-stage process: the intramolecular bond shrinkage and the intermolecular bond elongation. According to the isotopic shifts of energy components described by the NOMO/MP2 method, the intermolecular GIE is approximately interpreted as a process reducing the exchange-repulsion interaction after the decrease of electrostatic interaction. PMID:21306139

  12. 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

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

    PubMed Central

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

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    1997-01-01

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

  15. Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

    NASA Astrophysics Data System (ADS)

    Datta, Dipayan; Kossmann, Simone; Neese, Frank

    2016-09-01

    The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the

  16. Molecular orbital analysis of the hydrogen bonded water dimer.

    PubMed

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

    2016-02-24

    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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method.

    PubMed

    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.

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

    SciTech Connect

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

    1995-11-01

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

  4. 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.

  5. 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…

  6. 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

  7. 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

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

    PubMed

    Bâldea, Ioan

    2014-11-14

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  10. Molecular design of electron transport with orbital rule: toward conductance-decay free molecular junctions.

    PubMed

    Tada, Tomofumi; Yoshizawa, Kazunari

    2015-12-28

    In this study, we report our viewpoint of single molecular conductance in terms of frontier orbitals. The orbital rule derived from orbital phase and amplitude is a powerful guideline for the qualitative understanding of molecular conductance in both theoretical and experimental studies. The essence of the orbital rule is the phase-related quantum interference, and on the basis of this rule a constructive or destructive pathway for electron transport is easily predicted. We have worked on the construction of the orbital rule for more than ten years and recently found from its application that π-stacked molecular junctions fabricated experimentally are in line with the concept for conductance-decay free junctions. We explain the orbital rule using benzene molecular junctions with the para-, meta- and ortho-connections and discuss linear π-conjugated chains and π-stacked molecular junctions with respect to their small decay factors in this manuscript.

  11. 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.

  12. Computation of orbits using total energy

    NASA Technical Reports Server (NTRS)

    Bond, Victor R.; Mulcihy, David D.

    1988-01-01

    The computation of orbits can be done more efficiently by the use of any of several new formulations of the perturbed two body problem which consider the total energy of the orbital system as one of the dependent variables. The total energy is the osculating two body energy plus the potential energy due to perturbing masses. The use of the total energy as the dependent variable instead of the two body energy is a relatively new idea. The advantage of using total energy arises from the fact that the more perturbing potential energy that is accounted for in the total energy variable, the more nearly constant is the total energy. In fact, except for dissipative forces such as drag, the only reason for the total energy not being constant is the rotation or revolution of the perturbing mass. This near constancy of the total energy has the effect of inhibiting error growth during numerical solution. This paper will present the results of an application of total energy formulation to the problem of the precise computation of orbits.

  13. 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

  14. Spin-orbit coupled molecular quantum magnetism realized in inorganic solid.

    PubMed

    Park, Sang-Youn; Do, S-H; Choi, K-Y; Kang, J-H; Jang, Dongjin; Schmidt, B; Brando, Manuel; Kim, B-H; Kim, D-H; Butch, N P; Lee, Seongsu; Park, J-H; Ji, Sungdae

    2016-01-01

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-½ Yb(3+) ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets. PMID:27650796

  15. Spin–orbit coupled molecular quantum magnetism realized in inorganic solid

    PubMed Central

    Park, Sang-Youn; Do, S.-H.; Choi, K.-Y.; Kang, J.-H.; Jang, Dongjin; Schmidt, B.; Brando, Manuel; Kim, B.-H.; Kim, D.-H.; Butch, N. P.; Lee, Seongsu; Park, J.-H.; Ji, Sungdae

    2016-01-01

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal–organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin–orbit coupled pseudospin-½ Yb3+ ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky–Moriya interaction originating from strong spin–orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky–Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets. PMID:27650796

  16. Spin-orbit coupled molecular quantum magnetism realized in inorganic solid.

    PubMed

    Park, Sang-Youn; Do, S-H; Choi, K-Y; Kang, J-H; Jang, Dongjin; Schmidt, B; Brando, Manuel; Kim, B-H; Kim, D-H; Butch, N P; Lee, Seongsu; Park, J-H; Ji, Sungdae

    2016-09-21

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-½ Yb(3+) ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets.

  17. Spin-orbit coupled molecular quantum magnetism realized in inorganic solid

    NASA Astrophysics Data System (ADS)

    Park, Sang-Youn; Do, S.-H.; Choi, K.-Y.; Kang, J.-H.; Jang, Dongjin; Schmidt, B.; Brando, Manuel; Kim, B.-H.; Kim, D.-H.; Butch, N. P.; Lee, Seongsu; Park, J.-H.; Ji, Sungdae

    2016-09-01

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-1/2 Yb3+ ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets.

  18. Crystal field and molecular orbital theory of MBm centres in glasses

    NASA Astrophysics Data System (ADS)

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

    2010-01-01

    The spectral phenomena in optical fibres with bismuth-doped aluminosilicate glass core are explicated on the basis of a molecular orbital theory and of a Schrödinger equation solution, taking into account the exchange, spin-orbit and crystal field interactions of s, p and d electrons of M atoms (M signifies Bi, Sb, Pb, Sn, In, Te, etc) with ligand orbits of environmental B atoms (B signifies O, S, Se, etc). Energy level diagrams and selection rules of transitions between molecular orbital states of s and p electrons of MBm molecule permit us to determine the energies of the main spectral transitions of absorption and luminescent spectra and their correspondence with experimental spectra of different types of optical fibres is obtained.

  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. 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'.

  1. Nonorthogonal molecular orbital method: single-determinant theory.

    PubMed

    Watanabe, Yoshihiro; Matsuoka, Osamu

    2014-05-28

    Using the variational principle, we have derived a variant of the Adams-Gilbert equation for nonorthogonal orbitals of a single-determinant wave function, which we name the modified Adams-Gilbert equation. If we divide the molecular system into several subsystems, such as bonds, lone pairs, and residues, we can solve the equations for the subsystems one by one. Thus, this procedure has linear scaling. We have presented a practical procedure for solving the equations that is also applicable to macromolecular calculations. The numerical examples show that the procedure yields, with reasonable effort, results comparable with those of the Hartree-Fock-Roothaan method for orthogonal orbitals. To resolve the convergence difficulty in the self-consistent-field iterations, we have found that virtual molecular-orbital shifts are very effective.

  2. [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

  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. Molecular orbital calculations on tumour-inhibitory aniline mustards: QSARs.

    PubMed

    Lewis, D F

    1989-02-01

    1. Molecular orbital calculations by the MINDO/3 method are reported for a series of 23 para-substituted aniline mustards. 2. Quantitative structure-activity relationships are presented which show that electronic structural parameters can be related to a number of features of aniline mustard reactivity.

  5. 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)

  6. Local reactivity descriptors from degenerate frontier molecular orbitals

    NASA Astrophysics Data System (ADS)

    Martínez, Jorge

    2009-08-01

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

  7. 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…

  8. MOPAC manual. Sixth edition. A general molecular orbital package

    NASA Astrophysics Data System (ADS)

    Stewart, James J.

    1990-11-01

    MOPAC is a general-purpose, semi-empirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semi-empirical Hamiltonians MNDO, AM1, PM3, and MINDO/3 and combines the calculations of vibrational spectra, thermodynamic quantities, isotopic substitution effects, time-dependent effects, and force constants in a fully integrated program. Elements parameterized at the PM3 level are H, Be, C, N, O, F, Mg, Al, Si, P, S, Cl, Zn, lja, lje, As, Br, Cd, In, Sn, Sb, Te, I, Hg, Tl, Pb, and Bi. Within the electronic part of the calculation, molecular and localized orbitals excited states up to sextets, chemical bond indices, charges, etc. are computed. Both intrinsic and dynamic reaction coordinates can be calculated. A transition-state location routine and two transition-state optimizing routines are available for studying chemical reactions.

  9. 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.

  10. 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.

  11. Inversion of strong-field photoelectron spectra for molecular orbital imaging

    NASA Astrophysics Data System (ADS)

    Puthumpally-Joseph, R.; Viau-Trudel, J.; Peters, M.; Nguyen-Dang, T. T.; Atabek, O.; Charron, E.

    2016-08-01

    Imaging structures at the molecular level is a developing interdisciplinary research field that spans the boundaries of physics and chemistry. High-spatial-resolution images of molecules can be obtained with photons or ultrafast electrons. In addition, images of valence molecular orbitals can be extracted via tomographic techniques based on the coherent extreme UV radiation emitted by a molecular gas exposed to an intense ultrashort infrared laser pulse. In this paper, we demonstrate that similar information can be obtained by inverting energy-resolved photoelectron spectra using a simplified analytical model.

  12. 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.

  13. 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.

  14. Elimination of translational and rotational motions in nuclear orbital plus molecular orbital theory.

    PubMed

    Nakai, Hiromi; Hoshino, Minoru; Miyamoto, Kaito; Hyodo, Shiaki

    2005-04-22

    The nuclear orbital plus molecular orbital (NOMO) theory was developed in order to determine the nonadiabatic nuclear and electronic wave functions. This study presents a formulation to remove the contamination of rotational motion as well as translational motion in the NOMO theory. We have formulated the translation- and rotation-free (TRF)-NOMO theory by introducing the TRF Hamiltonian. The principal moment of inertia, which is the denominator in the rotational Hamiltonian, is expanded in a Taylor series. The zeroth-order of the Taylor expansion corresponds to a rigid-body rotator. The first-order terms contribute the coupling between the vibration and the rotation. Hartree-Fock equations have been derived in the framework of the TRF-NOMO theory. Numerical assessments, which were preformed for H2, D2, T2, mu2 (muon dimmer), and H2O, confirmed the importance of the TRF treatment. PMID:15945666

  15. Molecular vibrational energy flow

    NASA Astrophysics Data System (ADS)

    Gruebele, M.; Bigwood, R.

    This article reviews some recent work in molecular vibrational energy flow (IVR), with emphasis on our own computational and experimental studies. We consider the problem in various representations, and use these to develop a family of simple models which combine specific molecular properties (e.g. size, vibrational frequencies) with statistical properties of the potential energy surface and wavefunctions. This marriage of molecular detail and statistical simplification captures trends of IVR mechanisms and survival probabilities beyond the abilities of purely statistical models or the computational limitations of full ab initio approaches. Of particular interest is IVR in the intermediate time regime, where heavy-atom skeletal modes take over the IVR process from hydrogenic motions even upon X H bond excitation. Experiments and calculations on prototype heavy-atom systems show that intermediate time IVR differs in many aspects from the early stages of hydrogenic mode IVR. As a result, IVR can be coherently frozen, with potential applications to selective chemistry.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  3. Intra- versus Inter-dimer Charge Inhomogeneity in the Triangular Lattice Compounds of β'-Cs[Pd(dmit)2]2: A Degree of Freedom Characteristic of an Interchange of Energy Levels in the Molecular Orbitals

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takashi; Tamura, Masafumi; Yakushi, Kyuya; Kato, Reizo

    2016-10-01

    We have carried out the complete analyses of the C=C stretching modes in the vibrational spectra in the triangular lattice of β'-Cs[Pd(dmit)2]2 in order to solve the puzzling phenomenon that the ground state is neither spin frustration nor anti-ferromagnetic state but octamerization. We found that both charge-rich and charge-poor dimers are non-centrosymmetric dimers with the inhomogeneous charges. Because the energy levels of HOMO and LUMO are interchanged due to the tight dimerization, the cooperative interaction between the inter-site Coulomb repulsions and the valence-bond formation operates within and between dimers, those which contribute to the inter-dimer and intra-dimer charge separations, respectively. Octamer is the minimal unit under both cooperative interactions. In the high-temperature phase of β'-Cs[Pd(dmit)2]2, the competition between octamerization and tetramerization is observed because of the suppression of the intra-dimer cooperative interaction. The competition between two different states indicates the degree of freedom characteristic of the molecular orbital due to the tight dimerization. The cooperative interactions of the various X[Pd(dmit)2]2 salts are quantitatively evaluated from the C=C stretching modes.

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

    SciTech Connect

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

    2007-03-15

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

  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. Computing Ligand Field Potentials and Relative Energies of d Orbitals

    ERIC Educational Resources Information Center

    Krishnamurthy, R.; Schaap, Ward B.

    1969-01-01

    Presents a method for calculating the relative energies of d orbitals in various geometric configurations having coordination numbers 1 to 12. Discusses the changes in orbital degeneracies and energies due to symmetry differences. Shows that the addivity principle of Dq values gives results identical to the complete perturbation treatment. Also…

  7. 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.

  8. 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.

  9. 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.

  10. Elimination of Translational and Rotational Motions in Nuclear Orbital Plus Molecular Orbital Theory:  Contribution of the First-Order Rovibration Coupling.

    PubMed

    Miyamoto, Kaito; Hoshino, Minoru; Nakai, Hiromi

    2006-11-01

    The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed to determine nonadiabatic nuclear and electronic wave functions. This study implemented a computational program for the TRF-NOMO method including first-order rotational terms, which corresponds to rovibronic coupling. Numerical assessments of first-order TRF-NOMO Hartree-Fock as well as second-order Møller-Plesset perturbation methods were carried out for several small molecules. The first-order contributions give small corrections in energy. Thus, we confirm that the approximate zeroth-order treatment is sufficient for eliminating the rotational contamination. PMID:26627025

  11. Testing time-dependent density functional theory with depopulated molecular orbitals for predicting electronic excitation energies of valence, Rydberg, and charge-transfer states and potential energies near a conical intersection

    SciTech Connect

    Li, Shaohong L.; Truhlar, Donald G.

    2014-09-14

    Kohn-Sham (KS) time-dependent density functional theory (TDDFT) with most exchange-correlation functionals is well known to systematically underestimate the excitation energies of Rydberg and charge-transfer excited states of atomic and molecular systems. To improve the description of Rydberg states within the KS TDDFT framework, Gaiduk et al. [Phys. Rev. Lett. 108, 253005 (2012)] proposed a scheme that may be called HOMO depopulation. In this study, we tested this scheme on an extensive dataset of valence and Rydberg excitation energies of various atoms, ions, and molecules. It is also tested on a charge-transfer excitation of NH{sub 3}-F{sub 2} and on the potential energy curves of NH{sub 3} near a conical intersection. We found that the method can indeed significantly improve the accuracy of predicted Rydberg excitation energies while preserving reasonable accuracy for valence excitation energies. However, it does not appear to improve the description of charge-transfer excitations that are severely underestimated by standard KS TDDFT with conventional exchange-correlation functionals, nor does it perform appreciably better than standard TDDFT for the calculation of potential energy surfaces.

  12. Modeling Photodetachment from HO2- Using the pd Case of the Generalized Mixed Character Molecular Orbital Model

    NASA Astrophysics Data System (ADS)

    Blackstone, Christopher C.; Sanov, Andrei

    2016-06-01

    Using the generalized model for photodetachment of electrons from mixed-character molecular orbitals, we gain insight into the nature of the HOMO of HO2- by treating it as a coherent superpostion of one p- and one d-type atomic orbital. Fitting the pd model function to the ab initio calculated HOMO of HO2- yields a fractional d-character, γp, of 0.979. The modeled curve of the anisotropy parameter, β, as a function of electron kinetic energy for a pd-type mixed character orbital is matched to the experimental data.

  13. 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.

  14. Extended Lagrangian free energy molecular dynamics.

    PubMed

    Niklasson, Anders M N; Steneteg, Peter; Bock, Nicolas

    2011-10-28

    Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated.

  15. Construction of the Fock Matrix on a Grid-Based Molecular Orbital Basis Using GPGPUs.

    PubMed

    Losilla, Sergio A; Watson, Mark A; Aspuru-Guzik, Alán; Sundholm, Dage

    2015-05-12

    We present a GPGPU implementation of the construction of the Fock matrix in the molecular orbital basis using the fully numerical, grid-based bubbles representation. For a test set of molecules containing up to 90 electrons, the total Hartree-Fock energies obtained from reference GTO-based calculations are reproduced within 10(-4) Eh to 10(-8) Eh for most of the molecules studied. Despite the very large number of arithmetic operations involved, the high performance obtained made the calculations possible on a single Nvidia Tesla K40 GPGPU card.

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

    NASA Astrophysics Data System (ADS)

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

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

  17. Molecular-orbital-free algorithm for excited states in time-dependent perturbation theory.

    PubMed

    Lucero, Melissa J; Niklasson, Anders M N; Tretiak, Sergei; Challacombe, Matt

    2008-08-14

    A nonlinear conjugate gradient optimization scheme is used to obtain excitation energies within the random phase approximation (RPA). The solutions to the RPA eigenvalue equation are located through a variational characterization using a modified Thouless functional, which is based upon an asymmetric Rayleigh quotient, in an orthogonalized atomic orbital representation. In this way, the computational bottleneck of calculating molecular orbitals is avoided. The variational space is reduced to the physically-relevant transitions by projections. The feasibility of an RPA implementation scaling linearly with system size N is investigated by monitoring convergence behavior with respect to the quality of initial guess and sensitivity to noise under thresholding, both for well- and ill-conditioned problems. The molecular-orbital-free algorithm is found to be robust and computationally efficient, providing a first step toward large-scale, reduced complexity calculations of time-dependent optical properties and linear response. The algorithm is extensible to other forms of time-dependent perturbation theory including, but not limited to, time-dependent density functional theory. PMID:18715058

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

    PubMed

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

    2015-07-14

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

  19. 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.

  20. 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.

  1. Quantum Monte Carlo Method for Heavy Atomic and Molecular Systems with Spin-Orbit Interactions

    NASA Astrophysics Data System (ADS)

    Melton, Cody; Mitas, Lubos

    We present a new quantum Monte Carlo (QMC) method that can treat spin-orbit and other types of spin-depentent interactions explicitly. It is based on generalization of the fixed-phase and projection of the nonlocal operators with spinor trial wave functions. For testing the method we calculate several atomic and molecular systems such as Bi, W, Pb, PbH and PbO, some of them with both large- and small-core pseudopotentials. We validate the quality of the results against other correlated methods such as configuration interaction in two-component formalism. We find excellent agreement with extrapolated values for the total energies and we are able to reliably reproduce experimental values of excitation energies, electron affinity and molecular binding. We show that in order to obtain the agreement with experimental values the explicit inclusion of the spin-orbit interactions is crucial. U.S. D.O.E. grant de-sc0012314 and NERSC Contract No. DE-AC02-05CH11231.

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

    PubMed

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

    2014-12-01

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

  3. 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…

  4. Elimination of translational and rotational motions in nuclear orbital plus molecular orbital theory: application of Moller-Plesset perturbation theory.

    PubMed

    Hoshino, Minoru; Nakai, Hiromi

    2006-05-21

    The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed to determine the nonadiabatic nuclear and electronic wave functions. This study presents a formulation of TRF-NOMO second-order Moller-Plesset (MP2) perturbation and Epstein-Nesbet (EN) theory with the use of the TRF Hamiltonian. Numerical assessment of the TRF-NOMO/MP2 and EN is performed for several molecules. We confirm the importance of the elimination of translational and rotational motions in the many-body calculations. PMID:16729806

  5. 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

  6. A Simple Molecular Orbital Treatment of the Barrier to Internal Rotation in the Ethane Molecule

    NASA Astrophysics Data System (ADS)

    Smith, Derek W.

    1998-07-01

    The origin of the barrier to internal rotation in the ethane molecule is explored in terms of elementary molecular orbital (MO) considerations. Emphasis is placed on the antibonding effect, i.e. the result that an antibonding MO is more destabilized than its bonding counterpart is stabilized, relative to the parent atomic orbitals (AOs). It is shown that, in the case of two equivalent AOs, this effect is approximately proportional to the square of the overlap integral. By constructing the ethane Mos from those of two methyl fragments, it is shown that the most important orbital energy changes consequent upon rotation about the C-C bond can be expressed in terms of the antibonding effect arising from the filled twofold-degenerate p-bonding and -antibonding MOs. This can be reduced to the dependence on the rotation angle of the vicinal H-H overlap integrals, which are calculated explicitly, showing that the antibonding effect is minimised in the staggered conformation. A letter from Lawrence J. Sacks in our April 2000 issue addresses the above.

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  9. 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.

  10. Theory of Covalent Adsorbate Frontier Orbital Energies on Functionalized Light-Absorbing Semiconductor Surfaces.

    PubMed

    Yu, Min; Doak, Peter; Tamblyn, Isaac; Neaton, Jeffrey B

    2013-05-16

    Functional hybrid interfaces between organic molecules and semiconductors are central to many emerging information and solar energy conversion technologies. Here we demonstrate a general, empirical parameter-free approach for computing and understanding frontier orbital energies - or redox levels - of a broad class of covalently bonded organic-semiconductor surfaces. We develop this framework in the context of specific density functional theory (DFT) and many-body perturbation theory calculations, within the GW approximation, of an exemplar interface, thiophene-functionalized silicon (111). Through detailed calculations taking into account structural and binding energetics of mixed-monolayers consisting of both covalently attached thiophene and hydrogen, chlorine, methyl, and other passivating groups, we quantify the impact of coverage, nonlocal polarization, and interface dipole effects on the alignment of the thiophene frontier orbital energies with the silicon band edges. For thiophene adsorbate frontier orbital energies, we observe significant corrections to standard DFT (∼1 eV), including large nonlocal electrostatic polarization effects (∼1.6 eV). Importantly, both results can be rationalized from knowledge of the electronic structure of the isolated thiophene molecule and silicon substrate systems. Silicon band edge energies are predicted to vary by more than 2.5 eV, while molecular orbital energies stay similar, with the different functional groups studied, suggesting the prospect of tuning energy alignment over a wide range for photoelectrochemistry and other applications.

  11. 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.

  12. 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).

  13. Calculation of the paramagnetism of large carbon nanotubes, using a parameter-independent molecular orbital model

    NASA Astrophysics Data System (ADS)

    Collado, J. R. Alvarez

    A previous self-consistent field molecular orbital method, able to describe systems having a large number of unpaired electrons, n, is reviewed and improved. This method is applied to the study of paramagnetism in large (1,000-16,000 atoms) zigzag carbon nanotubes, represented by their n values. The computational scheme is based on the Hückel neglect differential overlap approach. It is shown that dependence of n on the semiempirical parameters is very small, and so they can be removed from the calculation. Enhancement of the paramagnetism (increase of n), by use of a strong external magnetic field, is also studied. Finally, the dependence of the Fermi one-electron potential energies and the spin atomic densities on both the parameters and the shape of the nanotubes is analyzed.0

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

    PubMed

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

    2015-12-24

    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.

  15. 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.

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

    PubMed

    Hoshino, Minoru; Nishizawa, Hiroaki; Nakai, Hiromi

    2011-07-14

    The present study proposes a rigorous non-Born-Oppenheimer theory combining between the explicitly correlated Gaussian (ECG) method and the nuclear orbital plus molecular orbital (NOMO) method. The new method, called ECG-NOMO, adopts the ECG functions between the electronic and nuclear coordinates and, therefore, is capable of describing the nucleus-electron correlation effect accurately. The basic formalism of the ECG-NOMO method is close to the NOMO method, which starts with the Hartree-Fock type equations for NOs and MOs. The present method requires more computational cost than the original NOMO method. However, its cost is significantly smaller than that of the ECG method. The numerical tests was performed for hydrogen-like atoms (H-Ne(9+)) and dihydrogen cations (H(2)(+), D(2)(+) and T(2)(+)), and clarified that the ECG-NOMO method shows the sufficient accuracy. PMID:21766929

  17. 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.

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

    PubMed

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

    2013-08-27

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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

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

    PubMed

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

    2015-01-01

    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.

  4. Orbital

    NASA Astrophysics Data System (ADS)

    Hanson, Robert M.

    2003-06-01

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

  5. 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

  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. 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.

  8. 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.

  9. Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method.

    PubMed

    Tokuda, Kana; Watanabe, Chiduru; Okiyama, Yoshio; Mochizuki, Yuji; Fukuzawa, Kaori; Komeiji, Yuto

    2016-09-01

    The fragment molecular orbital (FMO) method was applied to quantum chemical calculations of neuramic acid, the natural substrate of the influenza virus neuraminidase, and two of its competitive inhibitors, Oseltamivir (Tamiful(®)) and Zanamivir (Relenza(®)), to investigate their hydrated structures and energetics. Each of the three ligands was immersed in an explicit water solvent, geometry-optimized by classical MM and QM/MM methods, and subjected to FMO calculations with 2-, 3-, and 4-body corrections under several fragmentation options. The important findings were that QM/MM optimization was preferable to obtain reliable hydrated structures of the ligands, that the 3-body correction was important for quantitative evaluation of the solvation energy, and that the dehydration effect was most remarkable near the hydrophobic sections of the ligands. In addition, the hydration energy calculated by the explicit solvent was compared with the hydration free energy calculated by the implicit solvent via the Poisson-Boltzmann equation, and the two showed a fairly good correlation. These findings will serve as useful information for rapid drug design. PMID:27611645

  10. 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.

  11. Orbital order switching in molecular calculations using GGA functionals: Qualitative errors in materials modeling for electrochemical power sources and how to fix them

    NASA Astrophysics Data System (ADS)

    Sk, Mahasin Alam; Chen, Yingqian; Manzhos, Sergei

    2016-08-01

    We report a qualitative difference in molecular band structures and frontier orbital nodal structures in DFT calculations using GGA vs. hybrid functionals and Hartree Fock in molecules used in electrochemical power sources. This can have a significant effect in applications sensitive to redox potentials and to orbital overlaps (excitations, electron transfer rates) but for which the use of hybrid functionals is impractical, such as solids or interfaces used in electrochemical energy conversion and storage technologies. We show that correct band structures and nodal structures (ordering) of frontier orbitals can be obtained by applying a Hubbard correction to selected atomic states.

  12. 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.

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

    PubMed

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

    2016-04-12

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

  14. 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.

  15. 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.

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

    PubMed

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

    2014-07-28

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

  17. 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…

  18. 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…

  19. 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.

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

    PubMed

    Govindasamy, P; Gunasekaran, S; Srinivasan, S

    2014-09-15

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

  1. Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units.

    PubMed

    Hohenstein, Edward G; Bouduban, Marine E F; Song, Chenchen; Luehr, Nathan; Ufimtsev, Ivan S; Martínez, Todd J

    2015-07-01

    The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate. PMID:26156469

  2. Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units.

    PubMed

    Hohenstein, Edward G; Bouduban, Marine E F; Song, Chenchen; Luehr, Nathan; Ufimtsev, Ivan S; Martínez, Todd J

    2015-07-01

    The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.

  3. Measurement of Thermopower and Current-Voltage Characteristics of Molecular Junctions to Identify Orbital Alignment

    SciTech Connect

    Tan, Aaron; Sadat, Seid; Reddy, Pramod

    2010-01-08

    We report an experimental technique that concurrently measures the Seebeck coefficient and the current-voltage (I-V) characteristics of a molecular junction to determine the identity and the effective energetic separation of the molecular orbital closest to the electrodes’ Fermi level. Junctions created by contacting a gold-coated atomic force microscope tip with a monolayer of molecules assembled on a gold substrate were found to have a Seebeck coefficient of (+16.9±1.4) μV/K. This positive value unambiguously shows that the highest occupied molecular orbital (HOMO) dominates charge transport. Further, by analyzing the (I-V) characteristics, the HOMO level is estimated to be ~ 0.69 eV with respect to the Fermi level.

  4. Energy transformation in molecular electronic systems

    SciTech Connect

    Kasha, M.

    1985-07-25

    Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species /sup 1/..delta../sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on ..pi..-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs.

  5. Energy transformation in molecular electronic systems

    NASA Astrophysics Data System (ADS)

    Kasha, M.

    1985-07-01

    Our new optical pumping spectroscopy allows the production and study of the unstable rate tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole 3-hydroxyflavone, lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worthy of industrial development. The excited and highly reactive singlet molecular oxygen species (1) DELTA sub g has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of trisdibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on (PI)--electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved.

  6. 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.

  7. 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

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

    PubMed

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

    2014-10-28

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

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

    PubMed

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

    2015-07-28

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

  10. Orbital Analysis of Molecular Optical Activity Based on Configuration Rotatory Strength.

    PubMed

    Caricato, Marco

    2015-04-14

    We present a method to analyze the origin of molecular optical activity in terms of orbital contributions and rotatory strength in configuration space. The method uses quantities already available at completion of standard linear-response calculations of specific rotation and requires minimal manipulation. Preliminary application to (1S,4S)-norborne-none and (P)-2,3-pentadiene shows that only a few orbitals (6 and 4, respectively) contribute significantly to the specific rotation and can be used directly for a qualitative interpretation of this fundamental property.

  11. 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

  12. 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.

  13. 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.

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

    PubMed

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

    2007-11-01

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

  15. Optimal aeroassisted coplanar orbital transfer using an energy model

    NASA Astrophysics Data System (ADS)

    Halyo, Nesim; Taylor, Deborah B.

    1989-05-01

    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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    PubMed

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

    2015-02-01

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

  1. 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.

  2. 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.

  3. 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.

  4. Control of Electronic Symmetry and Rectification through Energy Level Variations in Bilayer Molecular Junctions.

    PubMed

    Bayat, Akhtar; Lacroix, Jean-Christophe; McCreery, Richard L

    2016-09-21

    Two layers of molecular oligomers were deposited on flat carbon electrode surfaces by electrochemical reduction of diazonium reagents, then a top contact applied to complete a solid-state molecular junction containing a molecular bilayer. The structures and energy levels of the molecular layers included donor molecules with relatively high energy occupied orbitals and acceptors with low energy unoccupied orbitals. When the energy levels of the two molecular layers were similar, the device had electronic characteristics similar to a thick layer of a single molecule, but if the energy levels differed, the current voltage behavior exhibited pronounced rectification. Higher current was observed when the acceptor molecule was biased negatively in eight different bilayer combinations, and the direction of rectification was reversed if the molecular layers were also reversed. Rectification persisted at very low temperature (7 K), and was activationless between 7 and 100 K. The results are a clear example of a "molecular signature" in which electronic behavior is directly affected by molecular structure and orbital energies. The rectification mechanism is discussed, and may provide a basis for rational design of electronic properties by variation of molecular structure.

  5. Control of Electronic Symmetry and Rectification through Energy Level Variations in Bilayer Molecular Junctions.

    PubMed

    Bayat, Akhtar; Lacroix, Jean-Christophe; McCreery, Richard L

    2016-09-21

    Two layers of molecular oligomers were deposited on flat carbon electrode surfaces by electrochemical reduction of diazonium reagents, then a top contact applied to complete a solid-state molecular junction containing a molecular bilayer. The structures and energy levels of the molecular layers included donor molecules with relatively high energy occupied orbitals and acceptors with low energy unoccupied orbitals. When the energy levels of the two molecular layers were similar, the device had electronic characteristics similar to a thick layer of a single molecule, but if the energy levels differed, the current voltage behavior exhibited pronounced rectification. Higher current was observed when the acceptor molecule was biased negatively in eight different bilayer combinations, and the direction of rectification was reversed if the molecular layers were also reversed. Rectification persisted at very low temperature (7 K), and was activationless between 7 and 100 K. The results are a clear example of a "molecular signature" in which electronic behavior is directly affected by molecular structure and orbital energies. The rectification mechanism is discussed, and may provide a basis for rational design of electronic properties by variation of molecular structure. PMID:27563739

  6. Time-dependent multiconfiguration theory for ultrafast electronic dynamics of molecules in an intense laser field: Electron correlation and energy redistribution among natural orbitals

    NASA Astrophysics Data System (ADS)

    Kato, Tsuyoshi; Kono, Hirohiko

    2009-12-01

    We propose a new definition of molecular orbital energy in order to investigate the energetics of constituent molecular orbitals in the many-electron wave function calculated based on time-dependent multiconfiguration theory. It is shown that when energies are assigned to natural orbitals by a similar manner to that used in the Hartree-Fock theory, we can quantify a correction energy to the total electronic energy that represents electron correlation, and thus we can evaluate the time-dependence of the correlation energy. Our attempt is illustrated by numerical results on the time-dependence of the spatial density of the correlation energy and the orbital energies for a H 2 molecule interacting with an intense, near-infrared laser field. We compared the energy ζj( t) supplied by the applied field with the net energy gain Δɛ(t) for respective natural orbitals ϕj( t). ϕj and found that the natural orbitals with Δɛ(t)>ζj(t) play a key role in the ionization process.

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

    SciTech Connect

    Curtiss, L.A.

    1993-04-01

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

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

    SciTech Connect

    Curtiss, L.A.

    1993-01-01

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

  9. Generalized average local ionization energy and its representations in terms of Dyson and energy orbitals

    NASA Astrophysics Data System (ADS)

    Kohut, Sviataslau V.; Cuevas-Saavedra, Rogelio; Staroverov, Viktor N.

    2016-08-01

    Ryabinkin and Staroverov [J. Chem. Phys. 141, 084107 (2014)] extended the concept of average local ionization energy (ALIE) to correlated wavefunctions by defining the generalized ALIE as I ¯ ( r ) = - ∑ j λ j | f j ( r ) | 2 / ρ ( r ) , where λj are the eigenvalues of the generalized Fock operator and fj(r) are the corresponding eigenfunctions (energy orbitals). Here we show that one can equivalently express the generalized ALIE as I ¯ ( r ) = ∑ k I k | d k ( r ) | 2 / ρ ( r ) , where Ik are single-electron removal energies and dk(r) are the corresponding Dyson orbitals. The two expressions for I ¯ ( r ) emphasize different physical interpretations of this quantity; their equivalence enables one to calculate the ALIE at any level of ab initio theory without generating the computationally expensive Dyson orbitals.

  10. Generalized average local ionization energy and its representations in terms of Dyson and energy orbitals.

    PubMed

    Kohut, Sviataslau V; Cuevas-Saavedra, Rogelio; Staroverov, Viktor N

    2016-08-21

    Ryabinkin and Staroverov [J. Chem. Phys. 141, 084107 (2014)] extended the concept of average local ionization energy (ALIE) to correlated wavefunctions by defining the generalized ALIE as Ī(r)=-∑jλj|fj(r)|(2)/ρ(r), where λj are the eigenvalues of the generalized Fock operator and fj(r) are the corresponding eigenfunctions (energy orbitals). Here we show that one can equivalently express the generalized ALIE as Ī(r)=∑kIk|dk(r)|(2)/ρ(r), where Ik are single-electron removal energies and dk(r) are the corresponding Dyson orbitals. The two expressions for Ī(r) emphasize different physical interpretations of this quantity; their equivalence enables one to calculate the ALIE at any level of ab initio theory without generating the computationally expensive Dyson orbitals. PMID:27544093

  11. 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

  12. 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

  13. 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%.

  14. Multicomponent Molecular Orbital-Climbing Image-Nudged Elastic Band Method to Analyze Chemical Reactions Including Nuclear Quantum Effect.

    PubMed

    Udagawa, Taro; Suzuki, Kimichi; Tachikawa, Masanori

    2015-10-26

    To analyze the H/D isotope effects on hydrogen transfer reactions in XHCHCHCHY↔XCHCHCHYH (X, Y=O, NH, or CH2 ) including the nuclear quantum effect of proton and deuteron, we propose a multicomponent molecular orbital-climbing image-nudged elastic band (MC_MO-CI-NEB) method. We obtain not only transition state structures but also minimum-energy paths (MEPs) on the MC_MO effective potential energy surface by using MC_MO-CI-NEB method. We find that nuclear quantum effect affects not only stationary-point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate the importance of including nuclear quantum effects for H/D isotope effect on rate constants (kH /kD ).

  15. 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.

  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. Orbit crowding of molecular gas at a bar-spiral arm transition zone in M83

    NASA Technical Reports Server (NTRS)

    Kenney, Jeffrey D. P.; Lord, Steven D.

    1991-01-01

    The southwestern bar-spiral arm transition zone in M83 is been studied in CO, H-alpha, H I, red light, and the radio continuum. A massive molecular gas complex in the heart of the transition zone is composed or two principal components which have the morphology and kinematics expected from orbit crowding, where gas on highly elliptical orbits form the bar region converges with gas on more circular orbits from the spiral arm region. Three mechanisms for the origin of the orbit crowding are investigated, and it is proposed that the crowding is due primarily to density wave streaming motions caused by the bar and spiral arms. The inner CO component is partially coincident with a region of highly polarized radio continuum emission which precedes the H-alpha spiral arm by 15-25 arcsec, indicating that it lies on or just downstream from a shock front. This suggests that the bar gas approaching the transition zone is shocked and explains the ridge of dense gas seen upstream from the spiral arm.

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

    PubMed

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

    2015-02-25

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

  19. 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.

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

    PubMed

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

    2015-12-24

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

  1. 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.

  2. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  5. 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.

  6. Multireference Møller Plesset perturbation theory using spin-dependent orbital energies

    NASA Astrophysics Data System (ADS)

    Kobayashi, Yuka; Nakano, Haruyuki; Hirao, Kimihiko

    2001-03-01

    The use of spin-dependent orbital energies is proposed in the multireference Møller-Plesset perturbation theory. In this method a single canonical Fock orbital set is used for both alpha and beta electrons, while the orbital energies depend on the spin of the electron that occupies the orbital. The method is tested on the energy splitting between states of different spins in the CH 2, CF 2, CO, O 2, N 2+, and o-benzyne molecules. The results agree well with available experimental data; the deviations are within 4 kcal/mol in all cases considered.

  7. 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 =…

  8. 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.

  9. 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.

  10. 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

  11. Sulphur hexaflouride: low energy (e,2e) experiments and molecular three-body distorted wave theory

    NASA Astrophysics Data System (ADS)

    Nixon, Kate L.; Murray, Andrew J.; Chaluvadi, H.; Ning, C. G.; Colgan, James; Madison, Don H.

    2016-10-01

    Experimental and theoretical triple differential ionisation cross-sections (TDCSs) are presented for the highest occupied molecular orbital of sulphur hexafluoride. These measurements were performed in the low energy regime, with outgoing electron energies ranging from 5 to 40 eV in a coplanar geometry, and with energies of 10 and 20 eV in a perpendicular geometry. Complementary theoretical predictions of the TDCS were calculated using the molecular three-body distorted wave formalism. Calculations were performed using a proper average over molecular orientations as well as the orientation-averaged molecular orbital approximation. This more sophisticated model was found to be in closer agreement with the experimental data, however neither model accurately predicts the TDCS over all geometries and energies.

  12. Communication: Systematic shifts of the lowest unoccupied molecular orbital peak in x-ray absorption for a series of 3d metal porphyrins.

    PubMed

    García-Lastra, J M; Cook, P L; Himpsel, F J; Rubio, A

    2010-10-21

    Porphyrins are widely used as dye molecules in solar cells. Knowing the energies of their frontier orbitals is crucial for optimizing the energy level structure of solar cells. We use near edge x-ray absorption fine structure (NEXAFS) spectroscopy to obtain the energy of the lowest unoccupied molecular orbital (LUMO) with respect to the N(1s) core level of the molecule. A systematic energy shift of the N(1s) to LUMO transition is found along a series of 3d metal octaethylporphyrins and explained by density functional theory. It is mainly due to a shift of the N(1s) level rather than a shift of the LUMO or a change in the electron-hole interaction of the core exciton.

  13. 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.

  14. Fragment molecular orbital calculation using the RI-MP2 method

    NASA Astrophysics Data System (ADS)

    Ishikawa, Takeshi; Kuwata, Kazuo

    2009-05-01

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

  15. 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

  16. Beyond the molecular orbital conception of electronically excited states through the quantum theory of atoms in molecules.

    PubMed

    Ferro-Costas, David; Pendás, Angel Martín; González, Leticia; Mosquera, Ricardo A

    2014-05-28

    We show that the use of the quantum theory of atoms in molecules (QTAIM) in electronically excited states allows expanding the knowledge that the molecular orbital (MO) framework provides about electronic rearrangements. Despite that historical prejudice seemed to preclude the use of QTAIM beyond the electronic ground state, this paper evidences that QTAIM is versatile enough to deal with excited states. As an example, the paradigmatic n → π* electronic transition of formaldehyde is analyzed. Using QTAIM, an energy partition of excited state energies into atomic and diatomic energies is carried out for the first time. This partition shows that upon electronic excitation the atoms of the CO bond experience a stabilization in their net energies, accompanied by a destabilization in their interaction, a fact which is in accordance with the idea of populating an antibonding π* MO. The associated C-O bond elongation in the nπ* state does not involve a change in the π atomic populations - as one would expect from a π* orbital - but in the σ ones. Moreover, it is also found that the nπ* state is characterized by a weaker C-O interaction energy in comparison to that in the electronic ground state. In order to strengthen this interaction, the electron-electron repulsion between C and O is reduced via a symmetry-breaking of the electron density, causing the C pyramidalization. A topological analysis based on the Laplacian of the electron density and on the electron localization function (ELF) reveals that the n → π* transition can be visualized as a rotation of 90° of the oxygen lone pairs.

  17. 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.

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

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-05-01

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

  19. 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.

  20. Direct study of eos mixing laws through an orbital-free-molecular-dynamics point of view

    NASA Astrophysics Data System (ADS)

    Lambert, Flavien; Danel, Jean-Francois; Kazandjian, Luc; Clerouin, Jean

    2008-04-01

    We have investigated eos mixing rules by an approach coupling consistently molecular dynamics for the nuclei and orbital free density functional theory for the electronic fluid. This framework allowed us to study, without mixing approximation, mixtures in the hot and dense regime -- ie a plasma strongly coupled and partially degenerated --, regime relevant for inertial confinement fusion. Several mixtures borrowed from this field have been examined in order to both present the method and check the validity of eos mixing rules commonly used in hydrodynamics simulations. [1] F. Lambert, J. Clerouin, J.-F. Danel, L. Kazandjian, and G. Zerah. Direct verification of mixing rules in the hot and dense regime. Phys. Rev. E, 2007. Submitted. [2] F. Lambert, J. Clerouin, and S. Mazevet. Structural and dynamical properties of hot dense matter by a Thomas-Fermi-Dirac molecular dynamics. Europhysics Lett., 75(5):681--687, 2006.

  1. 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.

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    PubMed

    Hitaoka, Seiji; Chuman, Hiroshi; Yoshizawa, Kazunari

    2015-01-21

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

  4. 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.

  5. On the performance of energy-consistent spin orbit pseudopotentials: (111)H revisited

    NASA Astrophysics Data System (ADS)

    Dolg, Michael; Stoll, Hermann; Seth, Michael; Schwerdtfeger, Peter

    2001-09-01

    A new two-component relativistic pseudopotential (PP) of the energy-consistent (EC) variety, adjusted to multi-configuration Dirac-Hartree-Fock (MCDHF) data, is presented for the superheavy element 111 and is applied in correlated valence ab initio calculations, with and without inclusion of spin-orbit (SO) coupling, to the determination of spectroscopic constants of the element 111 monohydride. Good agreement with a recent study by Han and Hirao [Chem. Phys. Lett. 328 (2000) 453] is found, and it is concluded that a direct two-component PP fit is superior to a previously practiced two-step (scalar-relativistic/SO) adjustment procedure. We estimate the molecular constants of element 111 monohydride to be Re=1.529 Å, D e=2.83 eV and ω e=2642 cm-1.

  6. The Z dependence of the total energy, energy components, orbital energy, and MO coefficients for mononuclear, isoelectronic species

    NASA Astrophysics Data System (ADS)

    Murdoch, Joseph R.; Magnoli, Douglas E.

    1982-11-01

    Previous workers have shown that in the limit Z→∞, the total energies, Vne, T, and total orbital energies (E0) of a series of isoelectronic, mononuclear structures are quadratic functions of Z, while Vee is a linear function of Z. In the present paper, a new perturbational treatment is presented which is based on a zero-order solution corresponding to Z=Z0, where Z0 is arbitrary. For first-order corrections to Hartree-Fock wave functions, the same limiting behavior (E,Vne, T, E0≡quadratic functions of Z; Vee≡linear function of Z) is seen as for the high-Z limit (Z→∞). For higher-order corrections, a completely different pattern of behavior emerges. For the ten-electron series (Z=9,18), E and T remain highly quadratic with respect to Z (to within 7 kcal), but Vne, Vee, E 0 exhibit large oscillations (˜60 kcal) around a quadratic function. This behavior is analyzed by applying the virial and Hellmann-Feynman theorems to the total energy, the Hellmann-Feynman theorem to Hartree-Fock orbital energies, and by expressing perturbation expansions for Vne and E in terms of Cheybshev polynomials. The results provide a demonstration of the fact that the total energy and orbital energy may show a different pattern of behavior with respect to substituent effects. The present work has important implications for perturbational treatments, such as Walsh's rules, frontier orbital theory and orbital symmetry correlations, which are based on the behavior of the orbital energy rather than the total energy.

  7. 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

  8. 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.

  9. 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.

  10. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-01

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  11. 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.

  12. 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.

  13. 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.

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

    SciTech Connect

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

    2014-04-14

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

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

    PubMed

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

    2014-04-14

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

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

    NASA Technical Reports Server (NTRS)

    Anderson, A. B.

    1985-01-01

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

  17. A proposal for an extended dual descriptor: a possible solution when Frontier Molecular Orbital Theory fails.

    PubMed

    Tognetti, Vincent; Morell, Christophe; Ayers, Paul W; Joubert, Laurent; Chermette, Henry

    2013-09-14

    In this paper, we introduce new local descriptors in the framework of Conceptual Density Functional Theory. They can be considered as an extension of the dual descriptor [Morell et al., J. Phys. Chem. A, 2005, 109, 205]. These indices are particularly suited for the discrimination between electrophilic and nucleophilic sites inside a molecule. They are computed using the densities of the electronic excited states, giving a picture of the polarization of the electron density induced by the approach of a reactant. Links with the linear-response function are discussed, and the first examples of applications are given, highlighting how these new descriptors can be used in practice for reactivity studies. It has been found that this extension of the dual descriptor can handle tricky cases, such as nitrobenzene or isoquinoline, for which Frontier Molecular Orbital Theory fails.

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  19. 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.

  20. Ab initio molecular orbital calculations of the vibrational frequencies of XY4/sup -n/ anions

    NASA Astrophysics Data System (ADS)

    Curtiss, L. A.; Nichols, R.

    The vibrational frequencies of a seris of XY4/sup -n/ anions (BeF4(-2), BF4(-), AlF4(-), MgCl4(-2), and AlCl4(-)) have been calculated by ab initio molecular orbital theory using the 3-21G and 6-31G* basis sets. The predicted harmonic frequencies are for the most part in good agreement with the observed frequencies of these anions in molten alkali halide mixtures. At the 3-21G basis set level the average difference between the observed and predicted frequencies is 12% while at the 6-31G* basis set level the average difference is 6%. Calculations of this type may be helpful in predicting the vibrational frequencies of other anions in molten salts.

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

    PubMed

    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

  2. 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

  3. Nonlinear dielectric effect (NDE) and molecular orbital study of the conformational equilibrium in 1,4-dimethoxybenzene in benzene solution

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, Maria; Małecki, Jerzy

    1997-10-01

    The conformational equilibrium in 1,4-dimethoxybenzene (1,4-DMB) in benzene solutions has been studied. On the basis of experimental values of the nonlinear dielectric effect (NDE) parameter, electric permittivity and density, determined in this work, and applying the general statistical theory of NDE, the contributions of the syn-anti and syn-syn conformers and the electric dipole moment of the polar syn-syn conformer were calculated. The molecular orbital method (PM3) has also been applied for calculation of the dipole moments and energies of particular conformers. The results of the NDE study and PM3 calculations are consistent and they reveal the existence of two conformers ( syn-anti and syn-syn) of comparable energy values, but different values of dipole moments, and the predominance of the polar form ( syn-syn) of the mole fraction in benzene. Moreover, the energies of intermolecular interactions have been determined from the concentration dependence of linear and nonlinear polarisability.

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

    PubMed

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

    2016-05-13

    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.

  5. 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.

  6. 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.

  7. 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.

    2016-11-01

    LS 5039 is so far the best-studied γ-ray binary system at multiwavelength 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 International Gamma-Ray Astrophysics Laboratory (INTEGRAL)/INTEGRAL on-board Imager/INTEGRAL Soft Gamma-Ray Imager 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-Large Area Telescope (LAT) data between 30 MeV and 10 GeV in five 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 anticlockwise 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 0.45-0.9) and from the superior conjunction phase region (orbital phase 0.9-0.45) 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.

  8. X-ray structural studies and molecular orbital calculations (CNDO/2) in a series of cyclopenta[a]phenanthrenes: attempts at correlation with carcinogenicity.

    PubMed

    Clayton, A F; Coombs, M M; Henrick, K; McPartlin, M; Trotter, J

    1983-12-01

    Comparative X-ray crystallographic structure analyses have been carried out on seven cyclopenta[a]phenanthrenes, namely 15,16-dihydocyclopenta[a]phenanthren-17-one and its 2-, 6- and 12-methyl homologues (non-carcinogens) and the 7-and 11-methyl and 1,11-methano derivatives (carcinogens). All-valence-electron molecular-orbital calculations by the CNDO/2 method, using the crystallographic parameters, have also been executed. Charge distribution and the energies of the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) have been calculated. With one exception all the molecules show only small deviations from planarity, the exception being the strongly carcinogenic 11-methyl-17-ketone in which the bay-region methyl group causes out-of-plane deformation of the benzo rings of 12.5 degrees. Among the other six compounds the two carcinogens are readily differentiated by high angle strain induced by a 7-methyl group or a 1,11-methano bridge. As expected, the HOMO's of these molecules to some extent reflect their ease of chemical oxidation at the 6,7-double bond; biological oxidation is less easy to correlate probably due to spatial restrictions at the active site within the mono-oxygenase.

  9. Linearity condition for orbital energies in density functional theory (V): Extension to excited state calculations

    NASA Astrophysics Data System (ADS)

    Imamura, Yutaka; Suzuki, Kensei; Iizuka, Takeshi; Nakai, Hiromi

    2015-01-01

    A new scheme is proposed for constructing an orbital-specific (OS) exchange-correlation functional that satisfies multiple linearity conditions for orbital energies (LCOEs). The Hartree-Fock exchange portions in the OS exchange-correlation functional, based on a multiply range-separated functional, are set so as to satisfy the multiple LCOEs. The current scheme has also been extended to calculations of core, valence, and Rydberg excitations. Numerical assessments on ionization potentials, electron affinities and excitation energies have confirmed accurate descriptions of core, valence, and Rydberg orbitals by the OS hybrid functional.

  10. 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.

  11. 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.

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

    PubMed

    Ewen, Pascal R; Sanning, Jan; Koch, Tobias; Doltsinis, Nikos L; Strassert, Cristian A; Wegner, Daniel

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  14. 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…

  15. Low-energy backscattering quantum orbits in above-threshold ionization

    NASA Astrophysics Data System (ADS)

    Milošević, D. B.

    2016-09-01

    Using the quantum–orbit formalism we consider the influence of the backward-scattering quantum orbits on the low-energy above-threshold ionization spectra. It is shown that the corresponding ionization rate exhibits sharp peaks for electron energies ≲ 0.1 {U}{{P}} ({U}{{P}} is the electron ponderomotive energy) at the same places where the forward-scattering-induced low-energy structures appear. The corresponding incident rescattering electron velocities are very small. Semiclassical expressions for the positions of these peaks as functions of {U}{{P}} and the ionization potential are derived.

  16. Charge-transfer mechanism for electrophilic aromatic nitration and nitrosation via the convergence of (ab initio) molecular-orbital and Marcus-Hush theories with experiments.

    PubMed

    Gwaltney, Steven R; Rosokha, Sergiy V; Head-Gordon, Martin; Kochi, Jay K

    2003-03-19

    The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.

  17. 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.

  18. 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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

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

    2015-03-14

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

  5. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    PubMed

    Ferenczy, György G

    2013-04-01

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.

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

    PubMed

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

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

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

    Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12-20). Selected geometric isomers include those predicted by Ho et al. [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding/genetic algorithm, as well as those found by Rata et al. [Phys. Rev. Lett. 85, 546 (2000)] based on density-functional tight-binding/single-parent evolution algorithm. These geometric isomers are optimized at the Møller-Plesset (MP2) MP2/6-31G(d) level. The single-point energy at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level for several low-lying isomers are further computed. Harmonic vibrational frequency analysis at the MP2/6-31G(d) level of theory is also undertaken to assure that the optimized geometries are stable. For Si12-Si17 and Si19 the isomer with the lowest-energy at the CCSD(T)/6-31G(d) level is the same as that predicted by Ho et al., whereas for Si18 and Si20, the same as predicted by Rata et al. However, for Si14 and Si15, the vibrational frequency analysis indicates that the isomer with the lowest CCSD(T)/6-31G(d) single-point energy gives rise to imaginary frequencies. Small structural perturbation onto the Si14 and Si15 isomers can remove the imaginary frequencies and results in new isomers with slightly lower MP2/6-31G(d) energy; however the new isomers have a higher single-point energy at the CCSD(T)/6-31G(d) level. For most Sin (n=12-18,20) the low-lying isomers are prolate in shape, whereas for Si19 a spherical-like isomer is slightly lower in energy at the CCSD(T)/6-31G(d) level than low-lying prolate isomers.

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

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar

    2001-06-01

    The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25°C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G-). The symbols refer to anti (A) with a torsion angle Φ2(X 8-C 2-C 3-C 4) of about 180° and gauche (G+ and G-) with torsion angles Φ2(X 8-C 2-C 3-C 4) of about +60° and 300°(-60°), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G-) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G- 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G- 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G- 17%). The results for the principal distances ( rg) and angles ∠ α for the G+ conformer of 2-chlorobutane, with estimated 2 σ uncertainties, obtained from the combined GED/ab initio study are: r( C1- C2)=1.524(3) Å, r( C2- C3)=1.528(3) Å, r( C3- C4)=1.539(3) Å, r( C- Cl)=1.812(3) Å, r( C- H) ave=1.098(4) Å, ∠C 1C 2C 3=111.5(16)°, ∠C 2C 3C 4=113.3(5)°, ∠C 1C 2C1=110.4(9)°. The results for the G+ conformer of 2-bromobutane are: r( C1- C2)=1.526(4) Å, r( C2- C3)=1.530(4) Å, r( C3- C4)=1.540(4) Å, r( C- Br)=1.982(5) Å, r( C- H) ave=1.111(8) Å, ∠C 1C 2C 3=112.5(16)°, ∠C 2C 3C 4=114.6(15)°, ∠C 1C 2Br=110.1(16)°. Only average values for r(C-C), r(C-H), ∠CCC, and ∠CCH could be determined in the

  13. 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

  14. Effect of the orbital debris environment on the high-energy Van Allen proton belt

    NASA Technical Reports Server (NTRS)

    Konradi, Andrei

    1988-01-01

    The lifetimes of high-energy (greater than 55 MeV) protons in the Van Allen radiation belt are calculated, assuming that in time the protons will collide with and be absorbed by particulate orbiting material. The calculations are based on the NASA/DoD Civil Needs Database for orbital debris (Gaines, 1966) and moderate assumptions of future space traffic. It is found that the lifetimes of high-energy protons below 1500 km will decrease, leading to a noticeable redution in their fluxes.

  15. 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.

  16. 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.

  17. 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…

  18. Furanose ring conformation: the application of ab initio molecular orbital calculations to the structure and dynamics of erythrofuranose and threofuranose rings

    SciTech Connect

    Serianni, A.S.; Chipman, D.M.

    1987-09-02

    Ab initiao molecular orbital calculations have been conducted on four tetrofuranose anomers, ..cap alpha..- and ..beta..-D-erythrofuranose and ..cap alpha..- and ..beta..-D-threofuranose, to study the effect of ring conformation on molecular parameters (bond lengths, bond angles, bond torsions) and on total energies. Geometric optimizations of envelope and planar conformers were conducted using the STO-3G basis set; single-point calculations were also performed with the 3-21G basis set. Preferred solution conformations deduced from previous NMR studies are in good agreement with those predicted by calculation, indicating that the intrinsic structures of these furanoses dictate their preferred geometries, and that solvation by water (/sup 2/H/sub 2/O) does not appear to be a major conformational determinant. The ..beta..-D-erythro configuration, which is structurally related to the ..beta..-D-ribo configuration found in RNA, was found to have significantly different conformational behavior from the other three configurations.

  19. Earth-to-Moon low energy transfers targeting L1 hyperbolic transit orbits.

    PubMed

    Topputo, Francesco; Vasile, Massimiliano; Bernelli-Zazzera, Franco

    2005-12-01

    In the frame of the lunar exploration, numerous future space missions will require maximization of payload mass, and simultaneously achieving reasonable transfer times. To fulfill this request, low energy non-Keplerian orbits could be used to reach the Moon instead of high energetic transfers. The low energy solutions can be separated into two main categories depending on the nature of the trajectory approaching the Moon: low energy transit orbits that approach the Moon from the interior equilibrium point L(1) and weak stability boundary transfers that reach the Moon after passing through L(2). This paper proposes an alternative way to exploit the opportunities offered by L(1) transit orbits for the design of Earth-Moon transfers. First, in a neighborhood of the L(1) point, the three-body dynamics is linearized and written in normal form; then the entire family of nonlinear transit orbits is obtained by selecting the appropriate nontrivial amplitudes associated with the hyperbolic part. The L(1)-Earth arc is close to a 5:2 resonant orbit with the Moon, whose perturbations cause the apogee to rise. In a second step, two selected low altitude parking orbits around the Earth and the Moon are linked with the transit orbit by means of two three-body Lambert arcs, solutions of two two-point boundary value problems. The resulting Earth-to-Moon trajectories prove to be very efficient in the Moon captured arc and save approximately 100 m/sec in Deltav cost when compared to the Hohmann transfer. Furthermore, such solutions demonstrate that Moon capture could be obtained in the frame of the Earth-Moon R3BP neglecting the presence of the Sun.

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

  1. 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.

  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. 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)

  4. Energy transfer, orbital angular momentum, and discrete current in a double-ring fiber array

    SciTech Connect

    Alexeyev, C. N.; Volyar, A. V.; Yavorsky, M. A.

    2011-12-15

    We study energy transfer and orbital angular momentum of supermodes in a double-ring array of evanescently coupled monomode optical fibers. The structure of supermodes and the spectra of their propagation constants are obtained. The geometrical parameters of the array, at which the energy is mostly confined within the layers, are determined. The developed method for finding the supermodes of concentric arrays is generalized for the case of multiring arrays. The orbital angular momentum carried by a supermode of a double-ring array is calculated. The discrete lattice current is introduced. It is shown that the sum of discrete currents over the array is a conserved quantity. The connection of the total discrete current with orbital angular momentum of discrete optical vortices is made.

  5. 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.

  6. 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.

  7. Effect of the orbital debris environment on the high-energy van allen proton belt.

    PubMed

    Konradi, A

    1988-12-01

    Orbital debris in the near-Earth environment has reached a number density sufficient for a significant collisional interaction with some of the long-lived high-energy protons in the radiation belt. As a result of a continuing buildup of a shell of man-made debris, the lifetimes of high-energy protons whose trajectories remain below 1500 kilometers will decrease to the point where in the next decades we can expect a noticeable reduction in their fluxes.

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

    NASA Astrophysics Data System (ADS)

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

    This review article is a first attempt to give a systematic and comprehensive description (in the framework of the unified theoretical approach) of the exchange interactions in polynuclear systems based on orbitally degenerate metal ions in the context of their relevance to the modern molecular magnetism. Interest in these systems is related to the fundamental problems of magnetism and at the same time steered by a number of impressive potential applications of molecular magnets, like high-density memory storage units, nanoscale qubits, spintronics and photoswitchable devices. In the presence of orbital degeneracy, the conventional spin Hamiltonian (Heisenberg-Dirac-van Vleck model) becomes inapplicable even as an approximation. The central component of this review article constitutes the concept of orbitally-dependent exchange interaction between metal ions possessing unquenched orbital angular momenta. We present a rigorous procedure of derivation of the kinetic exchange Hamiltonian for a pair of orbitally degenerate transition metal ions that is expressed in terms of the orbital matrices and spin operators. The microscopic background reveals the interrelations between the parameters of the Hamiltonian and the internal parameters of the system including all relevant transfer integrals and fundamental intracenter interactions. The developed formalism integrated with the irreducible tensor operator (ITO) technique makes it possible to describe the exchange coupling and all relevant interactions (crystal fields, spin-orbit (SO) and Zeeman couplings) in terms of the ITOs of the full spherical group, and in this way to develop anunified and efficient computational tool. The orbitally-dependent exchange was shown to lead to an anomalously strong magnetic anisotropy that can be considered as a main physical manifestation of the unquenched orbital angular momentum in metal clusters of orbitally-degenerate ions. The theoretical background is illustrated by the following

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

    PubMed

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

    2014-09-28

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

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

    PubMed

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

    2016-01-25

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

  11. 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.

  12. Molecular Recognition and Free Energy Simulations

    NASA Astrophysics Data System (ADS)

    Cannon, William Robert

    This dissertation describes the study of molecular recognition processes by free energy computer simulations. The introductory chapter briefly outlines the scientific development and significance of molecular recognition, and then describes statistical thermodynamic approaches to computer simulations. Chapter 1 analyzes the relationship of small guest molecules to a synthetic host in which one guest molecule is preorganized to be structurally complementary to the host while the second guest molecule must organize itself in order to obtain the same complementarity. The preferential recognition of imidazolidone over N,N^' -dimethylurea to the host is described in terms of the energetic cost of preorganizing the N,N^' -dimethylurea which can exist in several rotationally isomeric states. Chapter 2 describes the development of potential functions for molecular simulations and analyzes the structural, dynamic and thermodynamic aspects of sulfate anion solvation. Finally, chapter 3 describes the binding of sulfate anion to a periplasmic receptor and analyzes three mutants that have anomalous binding affinities for sulfate. Two of the mutants that have a greater than expected affinity for the anion are proposed to recognize and bind a water-anion complex rather than the anion alone, and the third mutant is proposed to have a dramatically decreased affinity for the anion due to steric and polarization effects.

  13. Modified virtual orbitals for CI calculations of energy splitting in organic diradicals.

    PubMed

    Barone, Vincenzo; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo

    2009-05-28

    We have investigated the possible computational advantages of using modified virtual orbitals in CI calculations of singlet-triplet energy gaps in diradical systems, where the magnetic moieties are bridged by organic unsaturated fragments. The addition to the Fock operator of supplementary positive point charges onto the atoms sharing the unpaired electron in each of the two moieties provides a simple yet very effective recipe for the construction of modified virtual orbitals (MVOs) with significantly improved convergence to the limiting value of the singlet-triplet splitting. This is verified for all the systems investigated in the present study and paves the route towards the fully ab initio computation of magnetic couplings in large systems of current technological and/or biological relevance by supplementary/charge MVOs coupled to the localization and removal of orbitals centered far apart the active moieties, as proposed in a previous study.

  14. 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.

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

    PubMed

    Saravanan, S; Balachandran, V; Vishwanathan, K

    2014-04-24

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

  16. 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

  17. 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.

  18. 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.

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

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-01

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

  20. 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.

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

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  3. Molecular orbital assistance in the design of intramolecular and photoinduced electron transfer systems

    NASA Astrophysics Data System (ADS)

    Petsalakis, Ioannis D.; Theodorakopoulos, Giannoula

    2012-02-01

    A theoretical approach is described for the design of donor-acceptor intramolecular charge transfer (ICT) systems and for photoinduced electron transfer (PET) hybrids of fullerene, based on orbital level diagrams of the separate donor and acceptor moieties. Minimization of the HOMO-LUMO (highest occupied-lowest unoccupied orbital) gap in ICT systems, translates to a requirement for near degeneracy of the HOMO of the donor and LUMO of the acceptor, determined separately for the two moieties by density functional theory calculations. Similarly, near degeneracy of the LUMO of the donor and LUMO of the acceptor moieties would indicate the possibility of PET in the combined hybrid.

  4. 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.

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

    ERIC Educational Resources Information Center

    Gillespie, Ronald J.; And Others

    1996-01-01

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

  6. 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.

  7. 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.

  8. Electronic structure of metal clusters. 4. Photoelectron spectra and molecular orbital calculations on cobalt, iron, ruthenium, and osmium sulfide nonacarbonyl clusters

    SciTech Connect

    Chesky, P.T.; Hall, M.B.

    1983-10-01

    Gas-phase, ultraviolet photoelectron (PE) spectra and molecular orbital (MO) calculations are reported for SCo/sub 3/(CO)/sub 9/, SH/sub n-//sub 1/Fe/sub n/Co/sub 3//sub -n/(CO)/sub 9/ (n = 1-3), S/sub 2/Fe/sub 3/(CO)/sub 9/, and SH/sub 2/M/sub 3/(CO)/sub 9/ (M = Fe, Ru, Os). The first PE spectra reported for mixed-metal clusters are included in this series. As Co atoms are replaced by the isoelectronic FeH unit, the spectra show the loss of a Co band and the appearance of an Fe band. This phenomenon suggests that the d bands localize upon ionization. In a comparison with the PE spectrum of M/sub 3/(CO)/sub 12/ (M = Fe, Ru, Os), the major spectral changes for SH/sub 2/M/sub 3/(CO)/sub 9/ (M = Fe, Ru, Os) are the loss of a band corresponding to direct M-M interactions and the appearance of bands due to a mixture of energy-equivalent M-H-M and M-S interactions. The spectra also show a substantial rearrangement of the bands due to the t/sub 2g/-like electrons, which are usually considered M-CO ..pi.. bonding. An antibonding interaction between a S orbital and the t/sub 2g/-like orbitals is responsible for a unique band in the spectra which occurs at high ionization energy between the M-M bonding band and the main t/sub 2//sub g/-like band. 12 figures, 9 tables

  9. The frozen orbital approximation for calculating ionization energies with application to propane

    NASA Astrophysics Data System (ADS)

    Müller, Wolfgang; Nager, Christoph; Rosmus, Pavel

    1980-09-01

    In the frozen orbital approximation (FOA), the influence of reorganization on correlation contributions to ionization energies is neglected. It is particularly useful in calculations for large molecules because of the advantage that only one integral transformation is required for the calculation of all ionic states. In connection with the concept of independent orbital correlation contributions, the dimensions of the CI matrices can be drastically reduced. The method is applied to the calculation of the valence ionization energies of propane, and compared to more rigorous ab initio results and a recent calculation in which inner valence shell contributions to electron correlation are neglected. The ordering of the first three ionizations in the photoelectron spectrum of propane, which has not been definitively assigned, is shown to be 2B1(2b1),2A1(6a1) and 2B2(4b2), in agreement with Koopmans' theorem.

  10. Electro-magnetic free energy transduction by molecular motors

    NASA Astrophysics Data System (ADS)

    Yakovlev, V. V.

    2009-02-01

    It is generally accepted that molecular motors are utilizing the chemical energy of adenosine triphosphate (ATP) hydrolysis to convert it to the mechanical energy. A set of preliminary data demonstrates that the periodic electric field can induce transport as well, thus providing the energy to the molecular system.

  11. 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

  12. 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.

  13. 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

  14. A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

    PubMed

    Hirano, Toshiyuki; Sato, Fumitoshi

    2014-07-28

    We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules. PMID:24622472

  15. 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.

  16. A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

    PubMed

    Hirano, Toshiyuki; Sato, Fumitoshi

    2014-07-28

    We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

  17. 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.

  18. 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.

  19. 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

  20. An Overview of Electron-Proton and High Energy Telescopes of Solar Orbiter

    NASA Astrophysics Data System (ADS)

    Kulkarni, S. R.; Grunau, J.; Boden, S.; Steinhagen, J.; Martin, C.; Wimmer-Schweingruber, R. F.; Boettcher, S.; Seimetz, L.; Ravanbakhsh, A.; Elftmann, R.; Rodriguez-Pacheco, J.; Prieto, M.; Gomez-Herrero, R.

    2013-12-01

    The Energetic Particle Detector (EPD) suite for ESA's Solar Orbiter will provide key measurements to address particle acceleration at and near the Sun. The EPD suite consists of five sensors (STEP, SIS, EPT, and HET). The University of Kiel in Germany is also responsible for the design, development, and build of EPT and HET which are presented here. The Electron Proton Telescope (EPT) is designed to cleanly separate and measure electrons in the energy range from 20 - 400 keV and protons from 20 - 7000 keV. The Solar Orbiter EPT electron measurements from 20 - 400 keV will cover the gap with some overlap between suprathermal electrons measured by STEP and high energy electrons measured by HET. The proton measurements from 20 -7000 keV will partially cover the gap between STEP and HET. The Electron and Proton Telescope relies on the magnet/foil-technique. The High-Energy Telescope (HET) on ESA's Solar Orbiter mission, will measure electrons from 300 keV up to about 30 MeV, protons from 10 -100 MeV, and heavy ions from ~20 to 200 MeV/nuc. Thus, HET covers the energy range which is of specific interest for studies of the space environment and will perform the measurements needed to understand the origin of high-energy events at the Sun which occasionally accelerate particles to such high energies that they can penetrate the Earth's atmosphere and be measured at ground level. Here we present the current development status of EPT-HET units and calibration results of demonstration models and present plans for future activities.

  1. 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

  2. Molecular orbital studies (hardness, chemical potential, electrophilicity, and first electron excitation), vibrational investigation and theoretical NBO analysis of 2-hydroxy-5-bromobenzaldehyde by density functional method

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    In this work, the vibrational spectral analysis was carried out using Raman and infrared spectroscopy in the range 4000-400 cm-1 and 3500-100 cm-1, respectively, for the 2-hydroxy-5-bromobenzaldehyde (HBB). The experimental spectra were recorded in the solid phase. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-311G++(d,p) method and basis set. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of related compound. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), electrophilicity index (ω), hardness (η), chemical potential (μ), and first electron excitation (τ) are all correlated with the HOMO and LUMO energies with their molecular properties. These show that charge transfer occurs within the molecule. Furthermore, molecular electrostatic potential maps (MESP) of the molecule have been calculated.

  3. 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).

  4. Periodic orbits, damped transitions and targeted energy transfers in oscillators with vibro-impact attachments

    NASA Astrophysics Data System (ADS)

    Lee, Young S.; Nucera, Francesco; Vakakis, Alexander F.; McFarland, D. Michael; Bergman, Lawrence A.

    2009-09-01

    We study complex damped and undamped dynamics and targeted energy transfers (TETs) in systems of coupled oscillators, consisting of single-degree-of-freedom primary linear oscillators (LOs) with vibro-impact attachments, acting, in essence, as vibro-impact nonlinear energy sinks (VI NESs). First, the complicated dynamics of such VI systems is demonstrated by computing the VI periodic orbits of underlying Hamiltonian systems and depicting them in appropriate frequency-energy plots (FEPs). Then, VI damped transitions and distinct ways of passive TETs from the linear oscillators to the VI attachments for various parameter ranges and initial conditions are investigated. As in the case of smooth stiffness nonlinearity [Y. Lee, G. Kerschen, A. Vakakis, P. Panagopoulos, L. Bergman, D.M. McFarland, Complicated dynamics of a linear oscillator with a light, essentially nonlinear attachment, Physica D 204 (1-2) (2005) 41-69], both fundamental and subharmonic TET can be realized in the VI systems under consideration. It is found that the most efficient mechanism for VI TET is through the excitation of highly energetic VI impulsive orbits (IOs), i.e., of periodic or quasiperiodic orbits corresponding to zero initial conditions except for the initial velocities of the linear oscillators. In contrast to NESs with smooth essential nonlinearities considered in previous works, VI NESs are capable of passively absorbing and locally dissipating significant portions of the energies of the primary systems to which they are attached, at fast time scale. This renders such devices suitable for applications, like seismic mitigation, where dissipation of vibration energy in the early, highly energetic regime of the motion is a critical requirement.

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

    PubMed

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

    1998-08-24

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

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

    PubMed

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

    2008-08-14

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

  7. 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.

  8. 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.

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

    PubMed

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-11-11

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

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

    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.

  11. Molecular orbital calculation of proton shielding tensors for the interpretation of solid state NMR data

    NASA Astrophysics Data System (ADS)

    Sternberg, U.; Rosenberger, H.

    1981-02-01

    We give a short review of the gauge-invariant calculation of shielding constants and susceptibilities from the ground state wvefunction. Since the method is well suited for localizad orbitals, PC ILO bond orbitals are used for the shielding calculation of glycine and its hydrogen bonded dimer (and for testing the theory also CH 4 and C 2H 6). From these values the 1H shielding tensors are constructed in an incrementary way. The calculated data are compared with experimental results and the NH…O hydrogen bond is investigated in detail. The theory gives an anisotropy of a NH…O hydrogen bonded proton of Δσ = 28.3 ppm and a value of a NH proton without hydrogen bond of Δσ = 18.8 ppm and for the CH proton Δσ = 12.5 ppm results. When taking into account the rotation of the NH θ3 groups we find that the qualitative features of the experiment are correctly represented. For the anisotropy Δσ = -6.55 ppm and for the asymmetry η = 0.588 are obtained. The experimental values are -5.63 ppm and 0.805, respectively.

  12. Solitary fibrous tumor of the orbit: morphological, cytogenetic and molecular features.

    PubMed

    Cerdá-Nicolás, Miguel; Löpez-Gines, Concha; Gil-Benso, Rosario; Benito, Rafael; Pellin, Antonio; Ruiz-Saurí, Amparo; Sanchos-Garcia, Juan; Roldan, Pedro; Talamantes, Fernando; Barberá, José

    2006-12-01

    Solitary fibrous tumor (SFT), a benign neoplasm arising in mesenchymal structures, was initially described in the pleura but subsequently has also been documented in other locations. It is uncommon in the orbit, where it closely resembles other benign spindle-shaped mesenchymal tumors of this area such as schwannoma, meningioma or hemangiopericytoma. We present a case of orbital SFT in a 34-year-old woman. The radiological study showed the presence of an enhanced uptake lesion measuring 2 cm in major diameter. The histopathological evaluation revealed alternating cellular and hypocellular areas with spindle-shaped cells. The cellular organization displayed a broad variety of irregular morphological patterns. The neoplastic cells were intensely positive for CD34 and vimentin, while S100, epithelial membrane antigen (EMA), Caldesmon, Calretinin and WT-1 proved negative. The pericellular matrix exhibited strong positivity for CD44 and collagen IV. Scarce mitotic figures, a Ki-67 nuclear labeling index of <5%, and focal expression of p53 were also observed. Measurement of DNA content revealed a DNA index of 1, indicating a diploid peak in 95% of the tumor cells. A normal 46,XX karyotype was present. No TP53 (exons 5-8) mutations or MDM2 and CDK4 amplifications were observed. No p14(ARF), p15(INK4B) and p16(INK4A) deletions or hypermethylation were observed in this benign tumor. Following surgical resection and radiotherapy, the patient showed no tumor relapse after one year of follow-up.

  13. 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.

  14. Advanced Potential Energy Surfaces for Molecular Simulation.

    PubMed

    Albaugh, Alex; Boateng, Henry A; Bradshaw, Richard T; Demerdash, Omar N; Dziedzic, Jacek; Mao, Yuezhi; Margul, Daniel T; Swails, Jason; Zeng, Qiao; Case, David A; Eastman, Peter; Wang, Lee-Ping; Essex, Jonathan W; Head-Gordon, Martin; Pande, Vijay S; Ponder, Jay W; Shao, Yihan; Skylaris, Chris-Kriton; Todorov, Ilian T; Tuckerman, Mark E; Head-Gordon, Teresa

    2016-09-22

    Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

  15. Computing molecular correlation energies with guaranteed precision

    NASA Astrophysics Data System (ADS)

    Bischoff, Florian A.; Valeev, Edward F.

    2013-09-01

    We present an approach to compute accurate correlation energies for atoms and molecules in the framework of multiresolution analysis (MRA), using an adaptive discontinuous multiresolution spectral-element representation for the six-dimensional (two-electron) pair function. The key features of our approach that make it feasible, namely (1) low-rank tensor approximations of functions and operators and (2) analytic elimination of operator singularities via explicit correlation, were retained from the previous work [F. A. Bischoff, R. J. Harrison, and E. F. Valeev, J. Chem. Phys. 137, 104103 (2012)]. Here we generalized the working equations to handle general (non-symmetric) many-electron systems at the MP2 level. The numerical performance is shown for the beryllium atom and the water molecule where literature data for the basis set limits could be reproduced to a few tens of μEh. The key advantages of molecular MRA-MP2 are the absence of bias and arbitrariness in the choice of the basis set, high accuracy, and low scaling with respect to the system size.

  16. 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.

  17. Advanced Potential Energy Surfaces for Molecular Simulation.

    PubMed

    Albaugh, Alex; Boateng, Henry A; Bradshaw, Richard T; Demerdash, Omar N; Dziedzic, Jacek; Mao, Yuezhi; Margul, Daniel T; Swails, Jason; Zeng, Qiao; Case, David A; Eastman, Peter; Wang, Lee-Ping; Essex, Jonathan W; Head-Gordon, Martin; Pande, Vijay S; Ponder, Jay W; Shao, Yihan; Skylaris, Chris-Kriton; Todorov, Ilian T; Tuckerman, Mark E; Head-Gordon, Teresa

    2016-09-22

    Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields. PMID:27513316

  18. 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

  19. Metal-sulfur valence orbital interaction energies in metal-dithiolene complexes: determination of charge and overlap interaction energies by comparison of core and valence ionization energy shifts.

    PubMed

    Wiebelhaus, Nicholas J; Cranswick, Matthew A; Klein, Eric L; Lockett, L Tori; Lichtenberger, Dennis L; Enemark, John H

    2011-11-01

    The electronic interactions between metals and dithiolenes are important in the biological processes of many metalloenzymes as well as in diverse chemical and material applications. Of special note is the ability of the dithiolene ligand to support metal centers in multiple coordination environments and oxidation states. To better understand the nature of metal-dithiolene electronic interactions, new capabilities in gas-phase core photoelectron spectroscopy for molecules with high sublimation temperatures have been developed and applied to a series of molecules of the type Cp(2)M(bdt) (Cp = η(5)-cyclopentadienyl, M = Ti, V, Mo, and bdt = benzenedithiolato). Comparison of the gas-phase core and valence ionization energy shifts provides a unique quantitative energy measure of valence orbital overlap interactions between the metal and the sulfur orbitals that is separated from the effects of charge redistribution. The results explain the large amount of sulfur character in the redox-active orbitals and the 'leveling' of oxidation state energies in metal-dithiolene systems. The experimentally determined orbital interaction energies reveal a previously unidentified overlap interaction of the predominantly sulfur HOMO of the bdt ligand with filled π orbitals of the Cp ligands, suggesting that direct dithiolene interactions with other ligands bound to the metal could be significant for other metal-dithiolene systems in chemistry and biology.

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Kalfaoğlu, Emel; Karabulut, Bünyamin

    2011-03-01

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

  4. 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.

  5. 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)].

  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. 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.

  8. 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.

  9. 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.

  10. The IMOMM (Integrated Molecular Orbitals/Molecular Mechanics) Approach for Ligand-Stabilized Metal Clusters. Comparison to Full Density Functional Calculations for the Model Thiolate Cluster Cu13(SCH2CH3)8.

    PubMed

    Genest, Alexander; Woiterski, André; Krüger, Sven; Shor, Aleksey M; Rösch, Notker

    2006-01-01

    To validate the IMOMM (integrated molecular orbitals/molecular mechanics) method for ligand-stabilized transition metal clusters, we compare results of this combined quantum mechanical and molecular mechanical (QM/MM) approach, as implemented in the program ParaGauss (Kerdcharoen, T.; Birkenheuer, U.; Krüger, S.; Woiterski, A.; Rösch, N. Theor. Chem. Acc. 2003, 109, 285), to a full density functional (DF) treatment. For this purpose, we have chosen a model copper ethylthiolate cluster, Cu13(SCH2CH3)8 in D4h symmetry. The evaluation is based on 16 conformers of the cluster which exhibit single and bridging coordination of the ligands at the Cu13 cluster as well as various ligand orientations. For corresponding isomers, we obtained moderate deviations between QM and QM/MM results:  0.01-0.06 Å for pertinent bond lengths and up to ∼15° for bond angles. Ligand binding energies of the two approaches deviated less than 6 kcal/mol. The largest discrepancies between full DF and IMOMM results were found for isomers exhibiting short Cu-H and H-H contacts. We traced this back to the localization of different minima, reflecting the unequal performance of the DF and the force-field methods for nonbonding interactions. Thus, QM/MM results can be considered as more reliable because of the well-known limitations of standard exchange-correlation functionals for the description of nonbonding interactions for this class of systems.

  11. 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.

  12. An Overview of the Electron-Proton and High Energy Telescopes for Solar Orbiter

    NASA Astrophysics Data System (ADS)

    Boden, Sebastian; Kulkarni, Shrinivasrao R.; Tammen, Jan; Steinhagen, Jan; Martin, César; Wimmer-Schweingruber, Robert F.; Böttcher, Stephan I.; Seimetz, Lars; Ravanbakhsh, Ali; Elftmann, Robert; Rodriguez-Pacheco, Javier; Prieto Mateo, Manuel; Gomez Herrero, Rául

    2014-05-01

    The Energetic Particle Detector (EPD) suite for ESA's Solar Orbiter will provide key measurements to address particle acceleration at and near the Sun. The EPD suite consists of four sensors (STEP, SIS, EPT, and HET). The University of Kiel in Germany is responsible for the design, development, and building of STEP, EPT and HET. This poster will focus on the last two. The Electron Proton Telescope (EPT) is designed to cleanly separate and measure electrons in the energy range from 20 - 400 keV and protons from 20 - 7000 keV. To separate electrons and protons EPT relies on the magnet/foil-technique. EPT is intended to close the gap between the supra-thermal particles measured by STEP and the high energy range covered by HET. The High-Energy Telescope (HET) will measure electrons from 300 keV up to about 30 MeV, protons from 10 to 100 MeV, and heavy ions from ~20 to 200 MeV/nuc. To achieve this performance HET consists of a series of silicon detectors in a telescope configuration with a scintillator calorimeter to stop high energy protons and ions. It uses the dE/dx vs. total E technique . In this way HET covers an energy range which is of interest for studies of the space radiation environment and will perform measurements needed to understand the origin of high-energy particle events at the Sun. EPT and HET share a common Electronics Box, there are two EPT-HET sensors on Solar Orbiter to allow rudimentary pitch-angle coverage. Here we present the current development status of EPT-HET units and calibration results of demonstration models as well as plans for future activities.

  13. Molecular structure, Mulliken charge, frontier molecular orbital and first hyperpolarizability analysis on 2-nitroaniline and 4-methoxy-2-nitroaniline using density functional theory.

    PubMed

    Azhagiri, S; Jayakumar, S; Gunasekaran, S; Srinivasan, S

    2014-04-24

    In the present study, we made an attempt to calculate the energy gap, molecular dipole moment and first hyperpolarizability of 2-nitroaniline (2NA) and 4-methoxy-2-nitroaniline (4M2N) with a basis set 6-31G (d, p) function has been employed at density functional theory (DFT) methods. Geometry optimizations was carried out with DFT-B3LYP/6-31G (d, p), the results have revealed that intramolecular hydrogen bonding present in both the molecular system. We analyzed the energy gap, molecular dipole moment and hyperpolarizability changes due to substitution effect of the methoxy group in 2NA molecule. It is confirmed that strong electron acceptor and donor groups in a material yield higher NLO response.

  14. Molecular Structures of Isomeric Ortho, Meta, and Para Bromo-Substituted α-Methylsulfonyl-α-diethoxyphosphoryl Acetophenones by X-ray and DFT Molecular Orbital Calculations.

    PubMed

    Rodrigues, Alessandro; Olivato, Paulo R; Zukerman-Schpector, Julio; Maganhi, Stella H; Reis, Adriana K C A; Tiekink, Edward R T

    2015-08-13

    The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.

  15. 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.

  16. 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

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

    PubMed

    Conradie, Jeanet; Ghosh, Abhik

    2014-05-19

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  19. 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.

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

    PubMed

    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.

  1. 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.

  2. 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.

  3. Urea's effect on the ribonuclease A catalytic efficiency: a kinetic, 1H NMR and molecular orbital study.

    PubMed

    Almarza, Jorge; Rincón, Luis; Bahsas, Alí; Pinto, María Angela; Brito, Francisco

    2013-02-01

    Understanding of protein-urea interactions is one of the greatest challenges to modern structural protein chemistry. Based in enzyme kinetics experiments and (1)H NMR spectroscopic analysis we proposed that urea, at low concentrations, directly interacts with the protonated histidines of the active center of RNase A, following a simple model of competitive inhibition. These results were supported by theoretical analysis based on the frontier molecular orbital theory and suggest that urea might establish a favorable interaction with the cationic amino acids. Our experimental evidence and theoretical analysis indicate that the initials steps of the molecular mechanism of Urea-RNase A interaction passes through the establishment of a three center four electron adduct. Also, our results would explain the observed disruption of the (1)H NMR signals corresponding to H12 and H119 (involved in catalysis) of the RNase A studied in the presence of urea. Our interaction model of urea-amino acids (cationic) can be extended to explain the inactivation of other enzymes with cationic amino acids at the active site.

  4. 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.

  5. Energy Band and Josephson Dynamics of Spin-Orbit Coupled Bose-Einstein Condensates

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Yu, Zi-Fa; Xue, Ju-Kui

    2015-10-01

    We theoretically investigate the energy band structure and Josephson dynamics of a spin-orbit coupled Bose-Einstein condensate in a double-well potential. We study the energy band structure and the corresponding tunneling dynamics of the system by properly adjusting the SO coupling, Raman coupling, Zeeman field and atomic interactions. The coupled effects of SO coupling, Raman coupling, Zeeman field and atomic interactions lead to the appearance of complex energy band structure including the loop structure. Particularly, the emergence of the loop structure in energy band also depends on SO coupling, Raman coupling, Zeeman field and atomic interactions. Correspondingly, the Josephson dynamics of the system are strongly related to the energy band structure. Especially, the emergence of the loop structure results in complex tunneling dynamics, including suppression-revival transitions and self-trapping of atoms transfer between two spin states and two wells. This engineering provides a possible means for studying energy level and corresponding dynamics of two-species SO coupled BECs. Supported by the National Natural Science Foundation of China under Grant Nos. 11274255 and 11305132, by Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20136203110001, by the Natural Science Foundation of Gansu province under Grant No. 2011GS04358, and by Creation of Science and Technology of Northwest Normal University under Grant Nos. NWNU-KJCXGC-03-48, NWNU-LKQN-12-12

  6. 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.

  7. 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.

  8. 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.

  9. Interactions between 1alpha,25(OH)2D3 and residues in the ligand-binding pocket of the vitamin D receptor: a correlated fragment molecular orbital study.

    PubMed

    Yamagishi, Kenji; Tokiwa, Hiroaki; Makishima, Makoto; Yamada, Sachiko

    2010-07-01

    To provide physicochemical insight into the role of each residue in the ligand-binding pocket (LBP) of the vitamin D receptor (VDR), we evaluated the energies of the interactions between the LBP residues and 1alpha,25(OH)2D3 by using an ab initio fragment molecular orbital (FMO) method at the Møller-Plesset second-order perturbation (MP2) level. This FMO-MP2 method can be used to correctly evaluate both electrostatic and van der Waals dispersion interactions, and it affords these interaction energies separately. We deduced the nature of each interaction and determined the importance of all the LBP residues involved in ligand recognition by the VDR. We previously reported the results of alanine-scanning mutational analysis (ASMA) of all 34 non-alanine residues lining the LBP of the human VDR. The theoretical results in combination with the ASMA results enabled us to assign the role of each LBP residue. We concluded that electrostatic interactions are the major determinant of the ligand-binding activity and ligand recognition specificity and that van der Waals interactions are important for protein folding and, in turn, for cofactor binding.

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Lablanquie, P.; Penent, F.; Hikosaka, Y.

    2016-09-01

    The interest of molecular double core holes was predicted in 1986 by Cederbaum et al who showed that their spectroscopy can be more informative than that of single core holes, especially when the holes are located at different sites in the molecule (Cederbaum et al 1986 J. Chem. Phys. 85 6513). Their experimental study of single photon formation had to wait until 2009-2010 with progress in synchrotron sources and the development of efficient multi-electron coincidence experiments based on a magnetic bottle time-of-flight spectrometer. At the same time the advent of x-ray free electron lasers opened the possibilty of creating them in a two-photon process, and motivated new theoretical studies of their properties. We will illustrate here the progress made recently in the field with a few examples, including the formation of double core holes by double core photoionization, their spectroscopy and decay paths, and the related process of simultaneous core ionization and core excitation.

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

    NASA Astrophysics Data System (ADS)

    Lablanquie, P.; Penent, F.; Hikosaka, Y.

    2016-09-01

    The interest of molecular double core holes was predicted in 1986 by Cederbaum et al who showed that their spectroscopy can be more informative than that of single core holes, especially when the holes are located at different sites in the molecule (Cederbaum et al 1986 J. Chem. Phys. 85 6513). Their experimental study of single photon formation had to wait until 2009–2010 with progress in synchrotron sources and the development of efficient multi-electron coincidence experiments based on a magnetic bottle time-of-flight spectrometer. At the same time the advent of x-ray free electron lasers opened the possibilty of creating them in a two-photon process, and motivated new theoretical studies of their properties. We will illustrate here the progress made recently in the field with a few examples, including the formation of double core holes by double core photoionization, their spectroscopy and decay paths, and the related process of simultaneous core ionization and core excitation.

  14. Orbital Feshbach resonances with a small energy gap between open and closed channels

    NASA Astrophysics Data System (ADS)

    Cheng, Yanting; Zhang, Ren; Zhang, Peng

    2016-04-01

    Recently, a new type of Feshbach resonance, i.e., orbital Feshbach resonance (OFR), was proposed for the ultracold alkaline-earth-metal-like atoms and was experimentally observed in the ultracold gases of 173Yb atoms. Unlike most of the magnetic Feshbach resonances of ultracold alkali atoms, when the OFR of 173Yb atoms appears, the energy gap between the thresholds of the open channel (OC) and the closed channel (CC) is much smaller than the characteristic energy of the interatomic interaction, i.e., the van der Waals energy. In this paper we study the OFR in systems with a small CC-OC threshold gap. We show that in these systems the OFR can be induced by the coupling between the OC and either an isolated bound state of the CC or the scattering states of the CC. Moreover, we also show that in each case the two-channel Huang-Yang pesudopotential is always applicable for the approximate calculation of the low-energy scattering amplitude. Our results imply that in the two-channel theoretical calculations for these systems it is appropriate to take into account the contributions from the scattering states of the CC.

  15. 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

  16. 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.

  17. 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.

  18. Antihydrogen-hydrogen elastic scattering at thermal energies using an atomic-orbital technique

    SciTech Connect

    Sinha, Prabal K.; Chaudhuri, Puspitapallab; Ghosh, A.S.

    2003-05-01

    In view of the recent interest in the trapping of antihydrogen atom H(bar sign), at very low temperatures, H-bar-H scattering has been investigated at low incident energies using a close-coupling model with the basis set H-bar(1s,2s,2p-bar)+H(1s,2s,2p-bar). The predicted s-wave elastic phase shifts, scattering length, and effective range are in a good agreement with the other recent predictions of Jonsell et al. and of Armour and Chamberlain. The results indicate that the atomic orbital expansion model is suitable to study the H-bar-H scattering at ultracold temperatures.

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

    PubMed

    Dudkin, V E; Potapov YuV; 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%. PMID:11537519

  20. 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%.

  1. Dynamics of Finite Energy Airy Beams Carrying Orbital Angular Momentum in Multilevel Atomic Vapors

    NASA Astrophysics Data System (ADS)

    Wu, Zhenkun; Wang, Shun; Hu, Weifei; Gu, Yuzong

    2016-10-01

    We numerically investigate the dynamics of inward circular finite-energy Airy beams carrying different orbital angular momentum (OAM) numbers in a close-Λ three-level atomic vapor with the electromagnetically induced transparency (EIT) window. We report that due to the EIT induced by the microwave field, the transverse intensity distribution properties of Airy beam can be feasibly manipulated and modulated through adjusting OAM numbers l and the frequency detuning, as well as the propagation distance, in the multi-level atomic systems. What's more, the rotation of the beam also can be observed with different positions in atomic ensembles. The investigation may provide a useful tool for studying particle manipulation, signal processing and propagation in graded-index (GRIN) fibers.

  2. 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.

  3. 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.

  4. 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.

  5. The activation strain model and molecular orbital theory: understanding and designing chemical reactions.

    PubMed

    Fernández, Israel; Bickelhaupt, F Matthias

    2014-07-21

    In this Tutorial Review, we make the point that a true understanding of trends in reactivity (as opposed to measuring or simply computing them) requires a causal reactivity model. To this end, we present and discuss the Activation Strain Model (ASM). The ASM establishes the desired causal relationship between reaction barriers, on one hand, and the properties of reactants and characteristics of reaction mechanisms, on the other hand. In the ASM, the potential energy surface ΔE(ζ) along the reaction coordinate ζ is decomposed into the strain ΔEstrain(ζ) of the reactants that become increasingly deformed as the reaction proceeds, plus the interaction ΔEint(ζ) between these deformed reactants, i.e., ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). The ASM can be used in conjunction with any quantum chemical program. An analysis of the method and its application to problems in organic and organometallic chemistry illustrate the power of the ASM as a unifying concept and a tool for rational design of reactants and catalysts.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  7. Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

    PubMed

    Szostak, Roman; Aubé, Jeffrey; Szostak, Michal

    2015-08-21

    Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.

  8. 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.

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

    DOE PAGES

    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

  10. 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.

  11. 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.

  12. A bifurcated molecular pentad capable of sequential electronic energy transfer and intramolecular charge transfer.

    PubMed

    Harriman, Anthony; Stachelek, Patrycja; Sutter, Alexandra; Ziessel, Raymond

    2015-10-21

    An extended molecular array, comprising three distinct types of chromophores and two additional redox-active subunits, that harvests photons over most of the visible spectral range has been synthesized and characterised. The array exhibits a rich variety of electrochemical waves when examined by cyclic voltammetry but assignment can be made on the basis of control compounds and molecular orbital calculations. Stepwise electronic energy transfer occurs along the molecular axis, corresponding to a gradient of excitation energies, to populate the lowest-energy excited state of the ultimate acceptor. The latter species, which absorbs and emits in the far-red region, enters into light-induced charge transfer with a terminal amine group. The array is relatively stable under illumination with white light but degrades slowly via a series of well-defined steps, the first of which is autocatalytic. One of the main attributes of this system is the capability to harvest an unusually high fraction of sunlight while providing protection against exposure to UV light.

  13. Field-dependent molecular ionization and excitation energies: Implications for electrically insulating liquids

    NASA Astrophysics Data System (ADS)

    Davari, N.; Åstrand, P.-O.; Unge, M.; Lundgaard, L. E.; Linhjell, D.

    2014-03-01

    The molecular ionization potential has a relatively strong electric-field dependence as compared to the excitation energies which has implications for electrical insulation since the excited states work as an energy sink emitting light in the UV/VIS region. At some threshold field, all the excited states of the molecule have vanished and the molecule is a two-state system with the ground state and the ionized state, which has been hypothesized as a possible origin of different streamer propagation modes. Constrained density-functional theory is used to calculate the field-dependent ionization potential of different types of molecules relevant for electrically insulating liquids. The low singlet-singlet excitation energies of each molecule have also been calculated using time-dependent density functional theory. It is shown that low-energy singlet-singlet excitation of the type n → π* (lone pair to unoccupied π* orbital) has the ability to survive at higher fields. This type of excitation can for example be found in esters, diketones and many color dyes. For alkanes (as for example n-tridecane and cyclohexane) on the other hand, all the excited states, in particular the σ → σ* excitations vanish in electric fields higher than 10 MV/cm. Further implications for the design of electrically insulating dielectric liquids based on the molecular ionization potential and excitation energies are discussed.

  14. Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

    PubMed

    Moon, Jiwon; Kim, Joonghan

    2016-09-29

    Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

  15. 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.

  16. 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.

  17. 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

    2016-03-28

    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.

  18. 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

  19. 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.

  20. 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.

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

    PubMed

    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.

  2. 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.

  3. Spin-orbit-coupled BEC in a double-well potential: Quantum energy spectrum and flat band

    NASA Astrophysics Data System (ADS)

    Wang, Wen-Yuan; Cao, Hui; Liu, Jie; Fu, Li-Bin

    2015-09-01

    Spin-orbit-coupled Bose-Einstein condensates (BECs) provide a powerful platform for studies on physical problems in various fields. Here we study the energy spectrum of a tunable spin-orbit-coupled BEC in a double-well potential with adjustable Raman laser intensity. We find in the single-particle spectrum there is a highly degenerate flat band in the ground state of the BEC, which remains stable against changes of the Raman strength. Many-body interactions between atoms remove this high degeneracy. Analytical results for particular cases are obtained by using the perturbation theory, which are in good agreement with the numerical results.

  4. 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..

  5. 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.

  6. 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.

  7. Effect of the f-Orbital Delocalization on the Ligand-Field Splitting Energies in Lanthanide-Containing Elpasolites.

    PubMed

    Zbiri, Mohamed; Daul, Claude A; Wesolowski, Tomasz A

    2006-07-01

    The ligand-field induced splitting energies of f-levels in lanthanide-containing elpasolites are derived using the first-principles universal orbital-free embedding formalism [Wesolowski and Warshel, J. Phys. Chem. 1993, 97, 8050]. In our previous work concerning chloroelpasolite lattice (Cs2NaLnCl6), embedded orbitals and their energies were obtained using an additional assumption concerning the localization of embedded orbitals on preselected atoms leading to rather good ligand-field parameters. In this work, the validity of the localization assumption is examined by lifting it. In variational calculations, each component of the total electron density (this of the cation and that of the ligands) spreads over the whole system. It is found that the corresponding electron densities remain localized around the cation and the ligands, respectively. The calculated splitting energies of f-orbitals in chloroelpasolites are not affected noticeably in the whole lanthanide series. The same computational procedure is used also for other elpasolite lattices (Cs2NaLnX6, where X=F, Br, and I) [Formula: see text] materials which have not been fabricated or for which the ligand-field splitting parameters are not available.

  8. Visualization and analysis of the Kohn-Sham kinetic energy density and its orbital-free description in molecules

    NASA Astrophysics Data System (ADS)

    Cancio, Antonio C.; Stewart, Dane; Kuna, Aeryk

    2016-02-01

    We visualize the Kohn-Sham kinetic energy density (KED) and the ingredients — the electron density, its gradient, and Laplacian — used to construct orbital-free models of it, for the AE6 test set of molecules. These are compared to related quantities used in metaGGA's, to characterize two important limits — the gradient expansion and the localized-electron limit typified by the covalent bond. We find the second-order gradient expansion of the KED to be a surprisingly successful predictor of the exact KED, particularly at low densities where this approximation fails for exchange. This contradicts the conjointness conjecture that the optimal enhancement factors for orbital-free kinetic and exchange energy functionals are closely similar in form. In addition we find significant problems with a recent metaGGA-level orbital-free KED, especially for regions of strong electron localization. We define an orbital-free description of electron localization and a revised metaGGA that improves upon atomization energies significantly.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. MP2 energy and density for large molecular systems with internal error control using the Divide-Expand-Consolidate scheme.

    PubMed

    Kristensen, Kasper; Høyvik, Ida-Marie; Jansik, Branislav; Jørgensen, Poul; Kjærgaard, Thomas; Reine, Simen; Jakowski, Jacek

    2012-12-01

    Divide-Expand-Consolidate (DEC) is a local correlation method where the inherent locality of the electron correlation problem is used to express the correlated calculation on a large molecular system in terms of small independent fragment calculations employing small subsets of local HF orbitals. A crucial feature of the DEC scheme is that the sizes of the local orbital spaces are determined in a black box manner during the calculation. In this way it is ensured that the correlation energy has been determined to a predefined precision compared to a conventional calculation. In the present work we apply the DEC scheme to calculate the correlation energy as well as the electron density matrix for the insulin molecule using second order Møller-Plesset (MP2) theory. This is the first DEC calculation on a molecular system which is too large to be treated using a conventional MP2 implementation. The fragmentation errors for the insulin DEC calculation are carefully analyzed using internal consistency checks. It is demonstrated that size-intensive properties are determined to the same precision for small and large molecules. For example, the percentage of correlation energy recovered and the error per electron in the correlated density matrix depend only on the predefined precision and not on the molecular size.

  15. Orbital mapping of energy bands and the truncated spin polarization in three-dimensional Rashba semiconductors

    NASA Astrophysics Data System (ADS)

    Liu, Qihang; Zhang, Xiuwen; Waugh, J. A.; Dessau, D. S.; Zunger, Alex

    2016-09-01

    Associated with spin-orbit coupling (SOC) and inversion symmetry breaking, Rashba spin polarization opens an avenue for spintronic applications that was previously limited to ordinary magnets. However, spin-polarization effects in actual Rashba systems are far more complicated than what conventional single-orbital models would suggest. By studying via density functional theory and a multiorbital k .p model a three-dimensional bulk Rashba system (free of complications by surface effects), BiTeI, we find that the physical origin of the leading spin-polarization effects is SOC-induced hybridization between spin and multiple orbitals, especially those with nonzero orbital angular momenta. In this framework we establish a general understanding of the orbital mapping, common to the surface of topological insulators and the Rashba system. Consequently, the intrinsic mechanism of various spin-polarization effects—which pertain to all Rashba systems, even those with global inversion symmetry—is understood as a manifestation of the orbital textures. This finding suggests a route for designing high-spin-polarization materials by considering the atomic-orbital content.

  16. 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.

  17. Photoswitchable Molecular Rings for Solar-Thermal Energy Storage.

    PubMed

    Durgun, E; Grossman, Jeffrey C

    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.

  18. 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.

  19. 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.

  20. Analysis of canonical molecular orbitals to identify fermi contact coupling pathways. 1. Through-space transmission by overlap of (31)P lone pairs.

    PubMed

    Contreras, Rubén H; Gotelli, Gustavo; Ducati, Lucas C; Barbosa, Thais M; Tormena, Cláudio F

    2010-01-21

    In this work, a new approach to studying coupling pathways for the Fermi contact term of NMR spin-spin coupling constants (SSCCs) is presented. It is based on the known form of propagating the Fermi hole through a canonical molecular orbital (CMO). It requires having an adequate spatial description of the relevant canonical molecular orbitals, which are obtained by expanding CMOs in terms of natural bond orbitals (NBOs). For detecting the relevant contributions of CMOs to a given Fermi contact (FC) pathway, the description of the FC in terms of the triplet polarization propagator (PP) is used. To appreciate the potential of this approach, dubbed FCCP-CMO (Fermi contact coupling pathways-CMO), it is applied to analyze the through-space transmission of the FC term of J(PP) SSCCs by overlap of the P lone pairs. This method can be applied using well-known quantum chemistry software without any further modification, which makes it appealing for use as a complement to SSCC measurements by NMR spectroscopy.

  1. Electron Momentum Distributions for 4a1 Orbitals of CFxCl4-x in Low Momentum Region: a Possible Evidence of Molecular Geometry Distortion

    NASA Astrophysics Data System (ADS)

    Shan, Xu; Xu, Chun-kai; Yin, Xiao-feng; Zhou, Li-xia; Xu, Ke-zun; Chen, Xiang-jun

    2009-12-01

    Electron momentum distributions for 4a1 orbitals of serial freon molecules CF3Cl, CF2Cl2, and CFCl3 (CFxCl4-x, x = 1-3) have been reanalyzed due to the severe discrepancies between theory and experiment in low momentum region. The tentative calculations using equilibrium geometries of molecular ions have exhibited a great improvement in agreement with the experimental data, which suggests that the molecular geometry distortion may be responsible for the observed high intensities at p < 0.5 a.u. Further analyses show that the severe discrepancies at low momentum region mainly arise from the influence of molecular geometry distortion on C-Cl bonding electron density distributions.

  2. 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.

  3. Harnessing Reversible Electronic Energy Transfer: From Molecular Dyads to Molecular Machines.

    PubMed

    Denisov, Sergey A; Yu, Shinlin; Pozzo, Jean-Luc; Jonusauskas, Gediminas; McClenaghan, Nathan D

    2016-06-17

    Reversible electronic energy transfer (REET) may be instilled in bi-/multichromophoric molecule-based systems, following photoexcitation, upon judicious structural integration of matched chromophores. This leads to a new set of photophysical properties for the ensemble, which can be fully characterized by steady-state and time-resolved spectroscopic methods. Herein, we take a comprehensive look at progress in the development of this type of supermolecule in the last five years, which has seen systems evolve from covalently tethered dyads to synthetic molecular machines, exemplified by two different pseudorotaxanes. Indeed, REET holds promise in the control of movement in molecular machines, their assembly/disassembly, as well as in charge separation.

  4. 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.

  5. 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

  6. The properties of gamma-radiation and high-energy neutron fluxes in "MIR" station orbit.

    PubMed

    Bogomolov, A V; Bogomolov, V V; Denisov, Yu I; Logachev, Yu I; Svertilov, S I; Kudryavtsev, M I; Lyagushin, V I; Ershova, T V

    2002-10-01

    The study of radiation background components in the near-Earth space is very important for different branches of space research, in particular for space dosimetry and for the planning of gamma-astronomy experiments. Detailed information on the neutral components (gamma-quanta, neutrons) of background radiation was obtained during the Grif-1 experiment onboard Mir orbital station (OS). The measurements of fluxes of 0.05-50 MeV gamma-quanta and >30 MeV neutrons with a large area instrument (approximately 250 cm2 for gamma-quanta, approximately 30 cm2 for neutrons) as well as corresponding charged particle measurements (0.4-1.5 MeV electrons, 1-200 MeV protons) were made during this experiment. The background components induced by the station's own radiation as well as the albedo gamma-rays from the Earth's atmosphere were revealed as the result of data analysis for about 600 h of observation. A mathematical model describing the latitude and energy dependences of atmospheric albedo gamma-rays as well as of those of gamma-quanta produced in the material of the station due to cosmic ray interactions was developed. An analytical approximation of the spectrum of induced gamma-rays from radioactive isotopes stored in the station and instrument's materials is presented. The dynamics of gamma-quantum background fluxes during the geomagnetic disturbances of January 10-11, 1997 are discussed. An analytical representation of the latitude dependence of the integral flux of neutrons with >30 MeV is given.

  7. The properties of gamma-radiation and high-energy neutron fluxes in "MIR" station orbit.

    PubMed

    Bogomolov, A V; Bogomolov, V V; Denisov, Yu I; Logachev, Yu I; Svertilov, S I; Kudryavtsev, M I; Lyagushin, V I; Ershova, T V

    2002-10-01

    The study of radiation background components in the near-Earth space is very important for different branches of space research, in particular for space dosimetry and for the planning of gamma-astronomy experiments. Detailed information on the neutral components (gamma-quanta, neutrons) of background radiation was obtained during the Grif-1 experiment onboard Mir orbital station (OS). The measurements of fluxes of 0.05-50 MeV gamma-quanta and >30 MeV neutrons with a large area instrument (approximately 250 cm2 for gamma-quanta, approximately 30 cm2 for neutrons) as well as corresponding charged particle measurements (0.4-1.5 MeV electrons, 1-200 MeV protons) were made during this experiment. The background components induced by the station's own radiation as well as the albedo gamma-rays from the Earth's atmosphere were revealed as the result of data analysis for about 600 h of observation. A mathematical model describing the latitude and energy dependences of atmospheric albedo gamma-rays as well as of those of gamma-quanta produced in the material of the station due to cosmic ray interactions was developed. An analytical approximation of the spectrum of induced gamma-rays from radioactive isotopes stored in the station and instrument's materials is presented. The dynamics of gamma-quantum background fluxes during the geomagnetic disturbances of January 10-11, 1997 are discussed. An analytical representation of the latitude dependence of the integral flux of neutrons with >30 MeV is given. PMID:12442742

  8. 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.

  9. 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

  10. 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.

  11. Transport properties of a single-molecular diode with one backbone, and two backbones in parallel: Frontier orbital analysis and NEGF-DFT study

    NASA Astrophysics Data System (ADS)

    Zahedi, Ehsan

    2015-05-01

    The conductance and electronic transport properties of a single-molecular diode with one backbone ( 1), and two backbones in parallel ( 2) have been investigated using frontier orbital analysis, and the NEGF formalism combined with DFT. The frontier orbital analysis results demonstrate that the electron transport from one end of the studied molecules to other end is symmetrically allowed and the conductance of the molecule with two parallel backbones is more than the molecule with a single backbone. Transmission spectra study based on the NEGF-DFT of the selected molecules sandwiched between two gold (1 1 1) electrodes showed that, due to a higher coupling between the two electrodes and the molecule 2, the zero-bias conductance is more than twice that of the other molecular junction. Transmission spectra under different biases showed that the maximum constructive interference exists at the bias voltage 0.2, while in some of the biases destructive effects are observed. I- V curves showed that the rectifying directions of molecular junctions 1 and 2 are opposite.

  12. 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+}.

  13. A computational study on the N-heterocyclic carbene-catalyzed Csp(2)-Csp(3) bond activation/[4+2] cycloaddition cascade reaction of cyclobutenones with imines: a new application of the conservation principle of molecular orbital symmetry.

    PubMed

    Wang, Yang; Wu, Bohua; Zhang, Haoyang; Wei, Donghui; Tang, Mingsheng

    2016-07-20

    A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction.

  14. A computational study on the N-heterocyclic carbene-catalyzed Csp(2)-Csp(3) bond activation/[4+2] cycloaddition cascade reaction of cyclobutenones with imines: a new application of the conservation principle of molecular orbital symmetry.

    PubMed

    Wang, Yang; Wu, Bohua; Zhang, Haoyang; Wei, Donghui; Tang, Mingsheng

    2016-07-20

    A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction. PMID:27400324

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

    NASA Astrophysics Data System (ADS)

    Lee, Sung Keun; Stebbins, Jonathan F.

    2006-08-01

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

  16. 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

  17. 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.

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

    ERIC Educational Resources Information Center

    Magnasco, Valerio

    2008-01-01

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

  19. 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.

  20. 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.

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

    DOE PAGES

    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

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

    PubMed

    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.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Carter, Melvin Keith

    2007-04-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  12. Modification of Earth-satellite orbits using medium-energy pulsed lasers

    NASA Astrophysics Data System (ADS)

    Phipps, Claude R.

    1993-05-01

    Laser impulse space propulsion (LISP) has become an attractive concept, due to recent advances in gas laser technology, high-speed segmented mirrors, and improved coefficients 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 discuss these most immediate applications, leaving LEO-LISP -- the application requiring the longest reach -- for another venue.

  13. 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.

  14. 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.

  15. Modification of Earth-satellite orbits using medium-energy pulsed lasers

    NASA Astrophysics Data System (ADS)

    Phipps, C. R.

    Laser Impulse Space Propulsion (LISP) has become an attractive concept, due to recent advances in gas laser technology, high-speed segmented mirrors and improved coefficients 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.

  16. 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.

  17. 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.

  18. Spin-orbit coupling effect on quantum hall ferromagnets with vanishing zeeman energy

    PubMed

    Fal'ko; Iordanskii

    2000-01-01

    We present the phase diagram of a ferromagnetic nu = 2N+1 quantum Hall liquid in a narrow quantum well with vanishing single-particle Zeeman splitting, varepsilon(Z), and a pronounced spin-orbit coupling. Upon decreasing varepsilon(Z) the spin-polarization field of a liquid takes, first, the easy-axis configuration, followed by the formation of a helical state which affects the transport and NMR properties of a liquid and the form of topological defects in it.

  19. 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.

  20. 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

  1. 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.

  2. Energy levels and redox properties of aqueous Mn(2+/3+) from photoemission spectroscopy and density functional molecular dynamics simulation.

    PubMed

    Moens, Jan; Seidel, Robert; Geerlings, Paul; Faubel, Manfred; Winter, Bernd; Blumberger, Jochen

    2010-07-22

    Energy-resolved photoemission spectroscopy and density functional molecular dynamics simulations are combined to construct an energy level diagram for the Mn(2+/3+) redox reaction in aqueous solution. Two peaks centered at 8.88 and 10.26 eV electron binding energies can be assigned to the Mn2+ hexa-aquo complex with a peak area ratio of 2:2.83. Using the notation of crystal field theory, the peak at lower energies can be interpreted as arising from ionization from the e(g) levels (highest occupied molecular orbital, HOMO), and the peak at higher energies are from ionization of the t(2g) levels. The difference corresponds to the average crystal field splitting, 1.38 eV. From the position of the HOMO level and the absolute redox potential, an experimental value for the reorganization free energy of the aqueous Mn3+ hexa-aquo complex is estimated to be 2.98 eV. Density functional molecular dynamics simulations can reproduce the experimental vertical ionization energy, redox free energy, and reorganization free energies fairly well, provided that the absolute potential shift in periodic boundary conditions, finite size effects, and inaccuracies of the exchange correlation functional are taken into account. Most strikingly, in the simulations, we observe spontaneous and reversible deprotonation of the aqueous Mn3+ hexa-aquo complex to form MnOH(H2O)5(2+) + H+, in line with the low experimental pKa value of this ion. The interconversion between protonation states leads to interesting redox phenomena for aqueous Mn3+, culminating in a bimodal thermal distribution of the electron affinity.

  3. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

    PubMed Central

    2011-01-01

    Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations. PMID:22241967

  4. Iron sulfur and iron molybdenum sulfur compounds: Comparison of molecular orbital calculations and spin-Hamiltonian analysis of Mössbauer spectra

    NASA Astrophysics Data System (ADS)

    Trautwein, A. X.; Bill, E.; Bläs, R.; Lauer, S.; Winkler, H.; Kostikas, A.

    1985-04-01

    The electronic structures of mononuclear Fe-S complexes with a FeIIS4 core and of binuclear Fe-Mo-S complexes containing the FeS2Mo core have been calculated by a semiempirical molecular orbital method (iterative extended Hückel theory), followed by a spin-orbit coupling calculation on the five highest occupied iron-like molecular orbitals. Fine structure and hyperfine structure tensors and parameters (g, D, E, A, and electric field gradient) have been calculated and compared with data from spin-Hamiltonian analysis of Mössbauer measurements. For the mononuclear complex anions [Fe(SPh)4]2- and [Fe(dts)2]2- it was found that Vẑẑ is negative, D positive, and that the magnetic anisotropy places the preferred direction of the hyperfine magnetic field perpendicular to the Vẑẑ direction in agreement with spin-Hamiltonian results. The similarity of parameters of [Fe(SPh)4]2- and reduced rubredoxin (Rdred) confirms the suggestion that this anion has a ground electronic state practically identical to Rdred. The complex anion [Fe(dts)2]2- shows smaller anisotropy, and due to the fact that the orbital ground state is energetically not well separated from higher states in this case a strong temperature dependence of the quadrupole splitting is observed. For the binuclear complex anions [(SPh)2FeS2MoS2]2-, [S5FeS2MoS2]2-, and [Cl2FeS2MoS2]2- it was found that d is negative and Vẑẑ is positive. A specific feature of these binuclear Fe-Mo-S complexes is that Vẑẑ is directed perpendicular to the Fe-Mo line. (This theoretical result is confirmed by single crystal Mössbauer studies on [Cl2FeS2MoS2]2-; see the following paper in this journal.) The preferred direction of the magnetic hyperfine field is close to the Vẑẑ axis. The correlation of calculated values of ρ(0) and isomer shifts for mononuclear and binuclear compounds confirms the role of MoS2-4 as a charge withdrawing ligand.

  5. 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.

  6. Molecular Dynamics and Energy Minimization Based on Embedded Atom Method

    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

  7. 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.

  8. 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.

  9. 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.

  10. Molecular orbital imaging of the acetone S2 excited state using time-resolved (e, 2e) electron momentum spectroscopy.

    PubMed

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

    2015-03-13

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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. BMAP dipole magnetic field analysis and orbit tracking/calculations of energy deposition in GaAs WHEBY detectors

    NASA Astrophysics Data System (ADS)

    Humphries, S., Jr.; Baltrusaitis, R. M.; Ekdahl, C.; Young, C.; Warn, C.

    This report contains two separate papers. The first paper discusses BMAP which is a versatile program for field analysis and orbit tracking in dipole magnets. The program was created to aid the design of charged-particle magnetic spectrometers. BMAP is written in Pascal and runs on any IBM-PC computer or compatible. The second paper covers a study on energy deposition in GaAS WHEBY detectors. The study was done for two purposes: (1) to set up a three-dimensional electron-photon transport problem using the ACCEPT computer code; and (2) to calculate energy deposition in GaAs detectors in the WHEBY for a given flux of electrons.

  16. 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).

  17. Efficient orbit integration by orbital longitude methods

    NASA Astrophysics Data System (ADS)

    Fukushima, Toshio

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

  18. Orbital-free ab initio molecular dynamics study of the free liquid surface of Sn. From pseudopotential generation to structural and dynamic properties

    NASA Astrophysics Data System (ADS)

    Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique

    We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface of Sn at 1000 K. A key ingredient in the OF-AIMD method is the local ionic pseudopotential describing the ions-valence electrons interaction. We have developed a force-matching method to derive a local ionic pseudopotential suitable to account for a rapidly varying density system, such as in a free liquid surface. We obtain very good results for several structural properties. We have also studied the evolution of some dynamical properties when going from the central region (where the system behaves like the bulk liquid) towards the free liquid surface. We aknowledge the spanish MSI (Project FIS2012-33126) and the University of Valladolid for the provision of a PhD grant.

  19. 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.

  20. Correlation of observed and model vibrational frequencies for aqueous organic acids: UV resonance Raman spectra and molecular orbital calculations of benzoic, salicylic, and phthalic acids.

    PubMed

    Trout, Chad C; Tambach, T J; Kubicki, James D

    2005-09-01

    The aromatic carboxylic acids benzoic, salicylic and phthalic acid were used to study the interaction of soluble organics compounds with metal cations. To accomplish this, we have developed methods for studying the carboxylic acids using UV resonance Raman (UVRR) combined with molecular orbital density functional theory calculations. The pH values of the acid solutions were based on the pK(a)'s for the different acids to examine the neutral and charged species. Deprotonation of the organic acids was detectable down to 10(-4)M using UVRR (two orders of magnitude lower than previous vibrational spectroscopy studies). Limitations to decreasing the concentration lower using the current UVRR facilities are discussed. Two methods were used to calculate the optimized geometry and frequencies of the acids: explicit and continuum solvation. The frequencies from the experimental spectra were then compared to the theoretical results obtained from the two methods.

  1. Correlation of observed and model vibrational frequencies for aqueous organic acids: UV resonance Raman spectra and molecular orbital calculations of benzoic, salicylic, and phthalic acids

    NASA Astrophysics Data System (ADS)

    Trout, Chad C.; Tambach, T. J.; Kubicki, James D.

    2005-09-01

    The aromatic carboxylic acids benzoic, salicylic and phthalic acid were used to study the interaction of soluble organics compounds with metal cations. To accomplish this, we have developed methods for studying the carboxylic acids using UV resonance Raman (UVRR) combined with molecular orbital density functional theory calculations. The pH values of the acid solutions were based on the p Ka's for the different acids to examine the neutral and charged species. Deprotonation of the organic acids was detectable down to 10 -4 M using UVRR (two orders of magnitude lower than previous vibrational spectroscopy studies). Limitations to decreasing the concentration lower using the current UVRR facilities are discussed. Two methods were used to calculate the optimized geometry and frequencies of the acids: explicit and continuum solvation. The frequencies from the experimental spectra were then compared to the theoretical results obtained from the two methods.

  2. Ab initio molecular-orbital study on electron correlation effects in CuO sub 6 clusters relating to high- Tc superconductivity

    SciTech Connect

    Yamamoto, S. Faculty of Liberal Arts, Chukyo University, Kaizu-cho, Toyota 470-03 ); Yamaguchi, K. ); Nasu, K. )

    1990-07-01

    {ital Ab} {ital initio} molecular-orbital calculations for CuO{sub 6} clusters have been performed to elucidate the electronic structures of undoped and doped copper oxides, which are of current interest in relation to high-{ital T}{sub {ital c}} superconductivity. The electron correlation effects for these species are thoroughly investigated by the full-valence configuration-interaction method and the complete-active-space self-consistent-field method. The electron correlation effect is relatively simple for the {ital A}{sub {ital g}} state ({sigma} hole), whereas pair excitations and spin-flip excitations give sizable contributions to the configuration-interaction wave function for the {ital B} state (in-plane {pi} hole). Implications of these results are discussed in relation to the mechanisms of the high-{Tc} superconductivity.

  3. 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.

  4. 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. 

  5. 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.

  6. Orbit to orbit transportation

    NASA Astrophysics Data System (ADS)

    Bergeron, R. P.

    1980-07-01

    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.

  7. A DFT study on structures, frontier molecular orbitals and UV-vis spectra of RuX(PPh3)(NHCPh2)L (X=Tp and Cp; L=Cl and N3).

    PubMed

    Wang, Tsang-Hsiu; Wang, I-Teng; Huang, Wen-Lin; Huang, Li-Yu

    2014-01-01

    Geometry optimization for RuX(PPh3)(NHCPh2)(L) (X=hydridotris(pyrazolyl)borate (Tp) and cyclopentadiene (Cp); L=Cl and N3) are investigated by using density functional theory (DFT) with DZVP2/DZVP all-electron mixed basis sets and compared with available experimental values, and the calculated structures are in very good agreement with experimental data. The frontier molecular orbitals (FMOs) and electronic transitions have been investigated as well. Our calculations show that the π electron-rich ligand (N3) may increase the energies of occupied orbitals and reduce the energy gap of the HOMO-LUMO (ΔEL-H) in these ruthenium based complexes. The simulated UV-vis spectra of these complexes in methanol have been studied with time-dependent density functional theory (TD-DFT), and conductor-like polarizable continuum model (CPCM) was employed to account for the solvent effects. Our results show that a number of absorption peaks are found in the visible region (400-800 nm) with non-zero oscillator strengths. The strongest adsorption feature is associated to a transition from HOMO-2 to LUMO, which is assigned to metal-to-ligand charge transfer (MLCT) or metal/ligand-to-ligand charge transfer (MLCT/LLCT) depending on co-ligands. In addition, the Cp group increases electron-accept ability and results in red shift due to its π electron-rich and π donor characters. According to our results, these ruthenium based complexes are good candidates for dye-sensitized solar cell owing to their absorption intensities and rich absorption bands in the visible region.

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

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

    From commercial origins as a molybdenum molecular beam nozzle, a ceramic nozzle of silicon carbide (SiC) was developed for space environment simulation. The nozzle is mechanically stable under extreme conditions of temperature and pressure. A heated, continuous, supersonically-expanded hydrogen beam with a 1% argon seed produced an argon beam component of nearly 4 km/s, with an argon flux exceeding 1x1014 /cm2.s. This nozzle was part of a molecular beam machine used in the Atmospheric Experiments Branch at NASA Goddard Space Flight Center to characterize the performance of the University of Texas at Dallas Ram Wind Sensor (RWS) aboard the Air Force Communications/Navigation Outage Forecasting System (C/NOFS) launched in the Spring of 2008.

  9. (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.

  10. Exploring the free energy surface using ab initio molecular dynamics

    DOE PAGES

    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

  11. 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

  12. 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.

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

    PubMed

    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 4000-450cm(-1) and 4000-50cm(-1), respectively. The molecular structure, geometry optimization, intensities, vibrational frequencies were obtained by the ab initio and DFT levels of theory B3LYP with 6-311++G(d,p) standard basis set and a different scaling of the calculated wave numbers. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using vibrational energy distribution analysis (VEDA 4) program. The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman data. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The thermodynamic properties of the title compound at different temperature reveal the correlations between standard heat capacities (C) standard entropies (S) standard enthalpy changes (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.

  14. 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.

  15. 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.

  16. 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.

  17. 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 ...

  18. 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.

  19. 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.

  20. 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.