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Sample records for addition dft calculations

  1. Spectroscopic analysis and DFT calculations of a food additive Carmoisine

    NASA Astrophysics Data System (ADS)

    Snehalatha, M.; Ravikumar, C.; Hubert Joe, I.; Sekar, N.; Jayakumar, V. S.

    2009-04-01

    FT-IR and Raman techniques were employed for the vibrational characterization of the food additive Carmoisine (E122). The equilibrium geometry, various bonding features, and harmonic vibrational wavenumbers have been investigated with the help of density functional theory (DFT) calculations. A good correlation was found between the computed and experimental wavenumbers. Azo stretching wavenumbers have been lowered due to conjugation and π-electron delocalization. Predicted electronic absorption spectra from TD-DFT calculation have been analysed comparing with the UV-vis spectrum. The first hyperpolarizability of the molecule is calculated. Intramolecular charge transfer (ICT) responsible for the optical nonlinearity of the dye molecule has been discussed theoretically and experimentally. Stability of the molecule arising from hyperconjugative interactions, charge delocalization and C-H⋯O, improper, blue shifted hydrogen bonds have been analysed using natural bond orbital (NBO) analysis.

  2. Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.

    PubMed

    Zgarbová, Marie; Otyepka, Michal; Sponer, Jirí; Hobza, Pavel; Jurecka, Petr

    2010-09-21

    The intermolecular interaction energy components for several molecular complexes were calculated using force fields available in the AMBER suite of programs and compared with Density Functional Theory-Symmetry Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such comparison is meaningful is discussed. The comparability is shown to depend strongly on the intermolecular distance, which means that comparisons made at one distance only are of limited value. At large distances the coulombic and van der Waals 1/r(6) empirical terms correspond fairly well with the DFT-SAPT electrostatics and dispersion terms, respectively. At the onset of electronic overlap the empirical values deviate from the reference values considerably. However, the errors in the force fields tend to cancel out in a systematic manner at equilibrium distances. Thus, the overall performance of the force fields displays errors an order of magnitude smaller than those of the individual interaction energy components. The repulsive 1/r(12) component of the van der Waals expression seems to be responsible for a significant part of the deviation of the force field results from the reference values. We suggest that further improvement of the force fields for intermolecular interactions would require replacement of the nonphysical 1/r(12) term by an exponential function. Dispersion anisotropy and its effects are discussed. Our analysis is intended to show that although comparing the empirical and non-empirical interaction energy components is in general problematic, it might bring insights useful for the construction of new force fields. Our results are relevant to often performed force-field-based interaction energy decompositions.

  3. How do strain and steric interactions affect the reactions of aromatic compounds with free radicals? Characterization of the radicals formed by muonium addition to p-xylene and [2.2]paracyclophane by DFT calculations and muon spin spectroscopy.

    PubMed

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil

    2012-07-26

    Muoniated radicals were produced by the addition of muonium (Mu) to the aromatic compound p-xylene (1) in the solid and liquid states and to the strained aromatic compound [2.2]paracyclophane (2) in the solid state. The radicals were characterized by avoided level crossing muon spin resonance spectroscopy and identified by comparing the experimentally determined muon hyperfine coupling constants with values obtained from DFT calculations. Mu was observed to add to both the secondary and tertiary carbons of 1, with the relative yield of the Mu adduct of the tertiary carbons estimated to be ∼10% in the liquid phase. The relative yield of the tertiary adduct is much higher in the solid state although this cannot be calculated exactly due to the overlap of resonances and the apparent nonuniform distribution of the radical orientations. There are three possible addition sites in 2 due to the lower symmetry of the six-membered ring compared with 1. Mu can add to the secondary carbons either from the outside of 2, generating the "exo" adduct, or from the inside, generating the "endo" adduct. The relative yields of the exo, endo, and tertiary carbon adducts are 67.1(1), 21.8(1), and 11.1(1)%, respectively. The barriers to Mu addition at the different sites of isolated molecules were determined from DFT calculations. The barriers for Mu addition to 2 are lower than the barriers for Mu addition to 1, except for addition to the "endo" position, where the unfavorable steric interactions with the second ring of 2 raise the addition barrier considerably. The measured relative yields do not reflect the distribution of products calculated using the activation energies obtained from the DFT calculations due to strong steric interactions with neighboring molecules.

  4. Advantages of GPU technology in DFT calculations of intercalated graphene

    NASA Astrophysics Data System (ADS)

    Pešić, J.; Gajić, R.

    2014-09-01

    Over the past few years, the expansion of general-purpose graphic-processing unit (GPGPU) technology has had a great impact on computational science. GPGPU is the utilization of a graphics-processing unit (GPU) to perform calculations in applications usually handled by the central processing unit (CPU). Use of GPGPUs as a way to increase computational power in the material sciences has significantly decreased computational costs in already highly demanding calculations. A level of the acceleration and parallelization depends on the problem itself. Some problems can benefit from GPU acceleration and parallelization, such as the finite-difference time-domain algorithm (FTDT) and density-functional theory (DFT), while others cannot take advantage of these modern technologies. A number of GPU-supported applications had emerged in the past several years (www.nvidia.com/object/gpu-applications.html). Quantum Espresso (QE) is reported as an integrated suite of open source computer codes for electronic-structure calculations and materials modeling at the nano-scale. It is based on DFT, the use of a plane-waves basis and a pseudopotential approach. Since the QE 5.0 version, it has been implemented as a plug-in component for standard QE packages that allows exploiting the capabilities of Nvidia GPU graphic cards (www.qe-forge.org/gf/proj). In this study, we have examined the impact of the usage of GPU acceleration and parallelization on the numerical performance of DFT calculations. Graphene has been attracting attention worldwide and has already shown some remarkable properties. We have studied an intercalated graphene, using the QE package PHonon, which employs GPU. The term ‘intercalation’ refers to a process whereby foreign adatoms are inserted onto a graphene lattice. In addition, by intercalating different atoms between graphene layers, it is possible to tune their physical properties. Our experiments have shown there are benefits from using GPUs, and we reached an

  5. Modelling Catalyst Surfaces Using DFT Cluster Calculations

    PubMed Central

    Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

    2009-01-01

    We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO2, γ-Al2O3, V2O5-WO3-TiO2 and Ni/Al2O3. Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies. PMID:20057947

  6. Modelling catalyst surfaces using DFT cluster calculations.

    PubMed

    Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

    2009-11-20

    We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO(2), gamma-Al(2)O(3), V(2)O(5)-WO(3)-TiO(2) and Ni/Al(2)O(3). Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

  7. Vibrational spectroscopic studies and DFT calculations of 4-aminoantipyrine

    NASA Astrophysics Data System (ADS)

    Swaminathan, J.; Ramalingam, M.; Sethuraman, V.; Sundaraganesan, N.; Sebastian, S.

    2009-08-01

    The pyrazole derivative, 4-aminoantipyrine (4AAP), used as an intermediate for the synthesis of pharmaceuticals especially antipyretic and analgesic drugs has been analyzed experimentally and theoretically for its vibrational frequencies. The FTIR and FT Raman spectra of the title compound have been compared with the theoretically computed frequencies invoking the standard 6-311g(d,p) and cc-pVDZ basis sets at DFT level of theory (B3LYP). The harmonic vibrational frequencies at B3LYP/cc-pVDZ after appropriate scaling method seem to coincide satisfactorily with the experimental observations rather than B3LYP/6-311g(d,p) results. The theoretical spectrograms for FT-IR and FT-Raman spectra of 4AAP have been also constructed and compared with the experimental spectra. Additionally, thermodynamic data have also been calculated and discussed.

  8. Predicting the properties of the lead alloys from DFT calculations

    SciTech Connect

    Buimaga-Iarinca, L. Calborean, A.

    2015-12-23

    We provide qualitative results for the physical properties of the lead alloys at atomic scale by using DFT calculations. Our approach is based on the two assumptions: (i) the geometric structure of lead atoms provides a matrix where the alloying elements can take their positions in the structure as substitutions and (ii) there is a small probability of a direct interaction between the alloying elements, thus the interactions of each alloying element may be approximated by the interactions to the lead matrix. DFT calculations are used to investigate the interaction between several types of impurities and the lead matrix for low concentrations of the alloying element. We report results such as the enthalpy of formation, charge transfer and mechanical stress induced by the impurities in the lead matrix; these results can be used as qualitative guide in tuning the physico-chemical properties of the lead alloys.

  9. BH-DFTB/DFT calculations for iron clusters

    NASA Astrophysics Data System (ADS)

    Aktürk, Abdurrahman; Sebetci, Ali

    2016-05-01

    We present a study on the structural, electronic, and magnetic properties of Fen(n = 2 - 20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima have been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe9-13), centered hexagonal antiprism (Fe14-17, Fe20), and truncated decahedral (Fe17(2), Fe18-19). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fen(n = 2 - 20) clusters is between 2.4 and 3.6 μB for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe13 icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.

  10. Vibrational spectra and DFT calculations of sonderianin diterpene

    NASA Astrophysics Data System (ADS)

    Oliveira, I. M. M.; Santos, H. S.; Sena, D. M.; Cruz, B. G.; Teixeira, A. M. R.; Freire, P. T. C.; Braz-Filho, R.; Sousa, J. W.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Bernardino, A. C. S. S.; Gusmão, G. O. M.; Bento, R. R. F.

    2015-11-01

    In the present study, the natural product sonderianin diterpene (C21H26O4), a diterpenoid isolated from Croton blanchetianus, with potential application in the drug industry, was characterized by nuclear magnetic resonance, infrared and Raman spectroscopy. Vibrational spectra were supported by Density Functional Theory calculations. Infrared and Raman spectra of sonderianin were recorded at ambient temperature in the regions from 400 cm-1 to 3600 cm-1 and from 40 cm-1 to 3500 cm-1, respectively. DFT calculations with the hybrid functional B3LYP and the basis set 6-31 G(d,p) were performed with the purpose of obtaining information on the structural and vibrational properties of this organic compound. A comparison with experimental spectra allowed us to assign all of the normal modes of the crystal. The assignment of the normal modes was carried out by means of potential energy distribution.

  11. Architectures and DFT calculations of polyrotaxane MOFs with nanoscale macrocycles.

    PubMed

    Zhang, Ming-Dao; Zheng, Bao-Hui; Chen, Liang; Chen, Min-Dong; Tao, Tao; Chen, Kai; Cao, Hui

    2016-02-28

    Polyrotaxane metal-organic frameworks (PMOFs) have attracted considerable attention due to their aesthetic topologies and potential biological applications. In this paper, we synthesized two kinds of hcb networks with nanoscale macrocycles. The hcb networks interlocked with each other in inclined and parallel interlocking modes respectively, giving rise to two new PMOFs, {[Ni(DPDBT)(bdc)]·(H2O)2}n (1) and {[Zn(DPDBT)(fuma)]}n (2). DFT calculations are used to elucidate why the inclined interlocking mode is preferential for 1 while the parallel interlocking mode is preferential for 2. The networks of 1 with a parallel interlocking mode, as well as 2 with an inclined interlocking mode, were simulated. The total energies of the parallel and inclined structures proved that the as-synthesized interlocking modes of 1and 2 are more stable. Moreover, photophysical properties and thermal analyses of related ligands and complexes are investigated and discussed in detail.

  12. The Dirac equation in electronic structure calculations: Accurate evaluation of DFT predictions for actinides

    SciTech Connect

    Wills, John M; Mattsson, Ann E

    2012-06-06

    Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.

  13. Structural Investigation of Layered Niobates by DFT Calculations

    NASA Astrophysics Data System (ADS)

    Adhikari Subin, Jhashanath

    Layered forms of inorganic niobates have been used for various applications, such as charge transport and storage, photo-catalysis, solid acids, magnetic materials, superconductors, magneto-resistors and photo-luminescence devices. The layered niobates exists in different geometrical forms and composition with variation in the packing of oxide lattice by the constituting monovalent, divalent/trivalent and pentavalent cations. Four different types of lamellar niobates are studied in this research by theoretical methods, namely the all-electron full-potential DFT method using plane wave and periodic boundary conditions. A common feature of all the layered niobates is that the basic building block, NbO6 octahedral units are shared with each other at the corners and edges forming a covalent network and that the sharing is terminated in a particular direction. These octahedral units get modulated along with the geometry of interlayer interface with the change in the composition of the material. The macroscopic structure change is reflected by the alteration of the unit cell axes whereas the local change at various sites in the structure is revealed by the variation of the atomic distances and angles/tilt. The different properties of the layered compounds are a function of these structural variations and thus understanding the mechanism and the characteristics requires atomic level analysis. Calculations reveal the local bonding details and the bulk geometry of a material and can be compared to that obtained from powder diffraction methods. The EFG tensor which is a sensitive probe of the electronic environment around a quadrupolar nucleus can be used to monitor the minor changes in the bond lengths and angles in various structures. Among the configurations lying in the minima of the potential energy surfaces, the one representing the real material would be the one matching with the EFG tensor calculated from DFT methods with that determined from the SSNMR experiments

  14. Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.

    PubMed

    Chain, Fernando E; Romano, Elida; Leyton, Patricio; Paipa, Carolina; Catalán, César A N; Fortuna, Mario; Brandán, Silvia Antonia

    2015-11-01

    In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings. PMID:26057092

  15. Additional calculations of triton moments

    NASA Astrophysics Data System (ADS)

    Lally, D. F.; Levinger, J. S.

    1982-02-01

    The formalism of hyperspherical harmonics is used to calculate several moments of the triton photoeffect for a Volkov potential with Serber exchange. The accuracy of Clare's calculations of moments σ0 and σ1 is improved by including more terms in the hyperspherical harmonic expansion of the potential and of the ground state wave function. The moment σ2=8.9×104 MeV3 mb is calculated using one term in the hyperspherical harmonic expansions of the potential and wave function. We invert four moments and find reasonable agreement with Gorbunov's measurements of the 3He photoeffect. NUCLEAR REACTIONS Triton photoeffect, hyperspherical harmonics, moments of photoeffect, inversion of moments.

  16. Systematic pseudopotentials from reference eigenvalue sets for DFT calculations: Pseudopotential files

    PubMed Central

    Rivero, Pablo; Manuel García-Suárez, Víctor; Pereñiguez, David; Utt, Kainen; Yang, Yurong; Bellaiche, Laurent; Park, Kyungwha; Ferrer, Jaime; Barraza-Lopez, Salvador

    2015-01-01

    We present in this article a pseudopotential (PP) database for DFT calculations in the context of the SIESTA code [1–3]. Comprehensive optimized PPs in two formats (psf files and input files for ATM program) are provided for 20 chemical elements for LDA and GGA exchange-correlation potentials. Our data represents a validated database of PPs for SIESTA DFT calculations. Extensive transferability tests guarantee the usefulness of these PPs. PMID:26217711

  17. Using Density Functional Theory (DFT) for the Calculation of Atomization Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.

  18. Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

    NASA Astrophysics Data System (ADS)

    Beni, Alireza Salimi; Zarandi, Maryam

    2016-02-01

    Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G( d, p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.

  19. Hexakis(4-phormylphenoxy)cyclotriphosphazene: X-ray and DFT-calculated structures

    SciTech Connect

    Albayrak, Cigdem Kosar, Basak; Odabasoglu, Mustafa; Bueyuekguengoer, Orhan

    2010-12-15

    The crystal structure of hexakis(4-phormylphenoxy)cyclotriphosphazene is determined by using X-ray diffraction and then the molecular structure is investigated with density functional theory (DFT). X-Ray study shows that the title compound has C-H-{pi} interaction with phosphazene ring. The molecules in the unit cell are packed with Van der Waals and dipole-dipole interactions and the molecules are packed in zigzag shaped. Optimized molecular geometry is calculated with DFT at B3LYP/6-311G(d,p) level. The results from both experimental and theoretical calculations are compared in this study.

  20. Molecular structure and vibrational and chemical shift assignments of 3'-chloro-4-dimethylamino azobenzene by DFT calculations.

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3'-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400cm(-1) for solid state. The (1)H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory. PMID:25468435

  1. Molecular structure and vibrational and chemical shift assignments of 3‧-chloro-4-dimethylamino azobenzene by DFT calculations

    NASA Astrophysics Data System (ADS)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3‧-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. The 1H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  2. DFT calculations for the structure and properties of polychlorodibenzo-para-dioxine anion-radicals

    SciTech Connect

    Borisov, Yurii A.; Garrett, Bruce C.; Mazunov, V. A.; Nekrasov, Yu S.

    2005-07-31

    Borisov, YA., BC. Garrett, VA. Mazunov, and YS. Nekrasov. 2005. “ DFT calculations for the structure and properties of polychlorodibenzo-para-dioxine anion-radicals,” Journal of Structural Chemistry 46 (4): 591-595. http://www.springerlink.com/content/d361t549815667u7/fulltext.pdf

  3. Performance of DFT Methods in the Calculation of Optical Spectra of Chromophores

    SciTech Connect

    Andzelm, Jan; Rawlett, Adam M.; Dougherty, Joseph; Govind, Niranjan

    2008-07-17

    Organic chromophores possessing a high degree of π -conjugation are ideal materials for advanced electronic and photonic applications including optical information processing, photovoltaic cells, photodynamic therapy agents, and many other applications. These properties are due to the stable macrocyclic conjugated network of π -electrons leading to high electrical polarizability and rapid nonlinear optical response (NLO) of the charge density to the applied intense electromagnetic fields. Changing the substitutional groups and substitution pattern, conjugation and molecular electronic structure can conveniently modify the optical spectra and NLO properties of chromophores. Due to almost limitless optimization space of chromophore structures computational tools are increasingly being used to assist experimental efforts in designing the optimal chromophores. By far the most often used computational approaches are semi-empirical and DFT methods. The semiempirical computational methods, such as ZINDO/CIS are fast and accurate for chromophores similar to systems for which the method was parameterized. DFT, on the other hand, offers the best compromise between accuracy and computational performance for typical chromophores of about 100 atoms. The accuracy of the methods depends strongly on the type of chromophores. For example, the ZINDO/CIS method is excellent for polyphenylacetylene dyes, but fails for many cyano-based acceptors of chromophores; DFT may be better suited for tricyanofuranyl complexes but leads to large errors in spectra of the polyphenylacetylene dyes. The failure of DFT calculations has been associated with the incorrect asymptotic behavior of the typical exchange-correlation (XC) potential. The approximate XC potential does not posses the correct 1/r asymptotic behavior, which leads to the self-interaction error (SIE). As a result, the excited states of dyes, in particular the charge-transfer (CT) chromophores are poorly described. A variety of

  4. Polymer Optical Constants from Long-Range Corrected DFT Calculations.

    PubMed

    Maekawa, Shintaro; Moorthi, Krzysztof

    2016-03-10

    A methodology to calculate refractive indices of plastics based on the Lorentz-Lorenz equation has been proposed. The polarizability of the nonconjugated polymer repeat units is predicted using the long-range corrected functionals. The end effect corrections in repeat unit models are essential to achieve accuracy similar to that observed for molecular liquids (ca. 1% in mean absolute deviation). The functionals with 100% Hartree-Fock (HF) exchange in the long-range limit perform best for aromatic and other hydrogen-deficient compounds; the Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP) performs very well for hydrogen-rich (usually, fully saturated) compounds. Exceptionally good agreement is observed for the sets of wavelength-dependent refractive index data for polystyrene, poly(methyl methacrylate), and for poly(perfluoro-4-vinyloxy-1-butene) (CYTOP), for which the root-mean-square deviations are 0.004, 0.002, and 0.004, respectively.

  5. Theoretical calculation (DFT), Raman and surface-enhanced Raman scattering (SERS) study of ponceau 4R

    NASA Astrophysics Data System (ADS)

    Xie, Yunfei; Li, Yan; Sun, Yingying; Wang, Heya; Qian, He; Yao, Weirong

    2012-10-01

    Ponceau 4R is used as a coloring agent in many different products, such as food, drinks, medicines, cosmetics and tobacco. However, ponceau 4R also shows carcinogenic, teratogenic and mutagenic behavior in high doses. In this work, standard Raman, theoretical Raman and surface-enhanced Raman scattering (SERS) spectra have been used to investigate ponceau 4R. More specifically, density functional theory (DFT) calculations have been used to calculate the optimized Raman spectrum of ponceau 4R at the B3LYP/6-31G(d) level. This has provided a better understanding of the optimized geometry and vibrational frequencies of this dye. In addition, the experimental spectrum of ponceau 4R has been compared with the theoretical spectrum; good agreement was obtained. Finally, it has shown that using SERS the detection limit of the ponceau 4R solution can be as low as 5 μg/mL. This has been achieved by SERS measurements of ponceau 4R on a substrate of gold nanoparticles. The SERS peaks at 1030, 1236, 1356 and 1502 cm-1 were chosen as index for semi-quantitative analysis, showing that the SERS technique provided a useful ultrasensitive method for the detection of ponceau 4R.

  6. Rate constants of hydroperoxyl radical addition to cyclic nitrones: a DFT study.

    PubMed

    Villamena, Frederick A; Merle, John K; Hadad, Christopher M; Zweier, Jay L

    2007-10-01

    Nitrones are potential synthetic antioxidants against the reduction of radical-mediated oxidative damage in cells and as analytical reagents for the identification of HO2* and other such transient species. In this work, the PCM/B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) and PCM/mPW1K/6-31+G(d,p) density functional theory (DFT) methods were employed to predict the reactivity of HO2* with various functionalized nitrones as spin traps. The calculated second-order rate constants and free energies of reaction at both levels of theory were in the range of 100-103 M-1 s-1 and 1 to -12 kcal mol-1, respectively, and the rate constants for some nitrones are on the same order of magnitude as those observed experimentally. The trend in HO2* reactivity to nitrones could not be explained solely on the basis of the relationship of the theoretical positive charge densities on the nitronyl-C, with their respective ionization potentials, electron affinities, rate constants, or free energies of reaction. However, various modes of intramolecular H-bonding interaction were observed at the transition state (TS) structures of HO2* addition to nitrones. The presence of intramolecular H-bonding interactions in the transition states were predicted and may play a significant role toward a facile addition of HO2* to nitrones. In general, HO2* addition to ethoxycarbonyl- and spirolactam-substituted nitrones, as well as those nitrones without electron-withdrawing substituents, such as 5,5-dimethyl-pyrroline N-oxide (DMPO) and 5-spirocyclopentyl-pyrroline N-oxide (CPPO), are most preferred compared to the methylcarbamoyl-substituted nitrones. This study suggests that the use of specific spin traps for efficient trapping of HO2* could pave the way toward improved radical detection and antioxidant protection. PMID:17845014

  7. Structural, electronic, thermodynamical and charge transfer properties of Chloramphenicol Palmitate using vibrational spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mishra, Rashmi; Srivastava, Anubha; Sharma, Anamika; Tandon, Poonam; Baraldi, Cecilia; Gamberini, Maria Christina

    2013-01-01

    The global problem of advancing bacterial resistance to newer drugs has led to renewed interest in the use of Chloramphenicol Palmitate (C27H42Cl2N2O6) [Palmitic acid alpha ester with D-threo-(-),2-dichloro-N-(beta-hydroxy-alpha-(hydroxymethyl)-p-nitrophenethyl)acetamide also known as Detereopal]. The characterization of the three polymorphic forms of Chloramphenicol Palmitate (CPP) was done spectroscopically by employing FT-IR and FT-Raman techniques. The equilibrium geometry, various bonding features, and harmonic wavenumbers have been investigated for most stable form A with the help of DFT calculations and a good correlation was found between experimental data and theoretical values. Electronic properties have been analyzed employing TD-DFT for both gaseous and solvent phase. The theoretical calculation of thermodynamical properties along with NBO analysis has also been performed to have a deep insight into the molecule for further applications.

  8. Enantiomerization of Allylic Trifluoromethyl Sulfoxides Studied by HPLC Analysis and DFT Calculations.

    PubMed

    Bailly, Laetitia; Petit, Emilie; Maeno, Mayaka; Shibata, Norio; Trapp, Oliver; Cardinael, Pascal; Chataigner, Isabelle; Cahard, Dominique

    2016-02-01

    Enantiomerization of allylic trifluoromethyl sulfoxides occurs spontaneously at room temperature through the corresponding allylic trifluoromethanesulfenates via a [2,3]-sigmatropic rearrangement. Dynamic enantioselective high-performance liquid chromatography (HPLC) analysis revealed the stereodynamics of these sulfoxides ranging from chromatographic resolution to peak coalescence at temperatures between 5 and 53 °C. The rate constant of enantiomerization and activation parameters were determined and compared with Density Functional Theory (DFT) calculations.

  9. DFT calculations on nitrodiborane compounds as new potential high energy materials.

    PubMed

    Abdelmalik, John; Ball, David W

    2010-05-01

    We have used DFT methods to determine the structures and thermochemistry of several nitro-substituted diborane molecules in an attempt to rate their potential as high energy materials. The properties of nitrodiborane, three isomers of dinitrodiborane, trinitrodiborane, and tetranitrodiborane were calculated using the B3LYP density functional method. Our results indicate that the absolute enthalpy of combustion decreases with increasing nitro content, in contrast with other nitro-substituted systems that have been studied previously.

  10. Ferrocenyl-substituted dinuclear Cu(II) complex: Synthesis, spectroscopy, electrochemistry, DFT calculations and catecholase activity

    NASA Astrophysics Data System (ADS)

    Emirik, Mustafa; Karaoğlu, Kaan; Serbest, Kerim; Menteşe, Emre; Yilmaz, Ismail

    2016-02-01

    A new ferrocenyl-substituted heterocyclic hydrazide ligand and its Cu(II) complex were prepared. The DFT calculations were performed to determine the electronic and molecular structures of the title compounds. The electronic spectra were calculated by using time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the compounds. The bands assignments of IR spectra were achieved in the light of the theoretical vibrational spectral data and total energy distribution values calculated at DFT/B3LYP/6-311++G(d,p) level. The redox behaviors of the ferrocene derivatives were investigated by cyclic voltammetry. The compounds show reversible redox couple assignable to Fc+/Fc couple. The copper(II) complex behaves as an effective catalyst towards oxidation of 3,5-di-tert-butylcatechol to its corresponding quinone derivative in DMF saturated with O2. The reaction follows Michaelis-Menten enzymatic reaction kinetics with turnover numbers 2.32 × 103.

  11. Ferrocenyl-substituted dinuclear Cu(II) complex: Synthesis, spectroscopy, electrochemistry, DFT calculations and catecholase activity

    NASA Astrophysics Data System (ADS)

    Emirik, Mustafa; Karaoğlu, Kaan; Serbest, Kerim; Menteşe, Emre; Yilmaz, Ismail

    2016-02-01

    A new ferrocenyl-substituted heterocyclic hydrazide ligand and its Cu(II) complex were prepared. The DFT calculations were performed to determine the electronic and molecular structures of the title compounds. The electronic spectra were calculated by using time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the compounds. The bands assignments of IR spectra were achieved in the light of the theoretical vibrational spectral data and total energy distribution values calculated at DFT/B3LYP/6-311++G(d,p) level. The redox behaviors of the ferrocene derivatives were investigated by cyclic voltammetry. The compounds show reversible redox couple assignable to Fc+/Fc couple. The copper(II) complex behaves as an effective catalyst towards oxidation of 3,5-di-tert-butylcatechol to its corresponding quinone derivative in DMF saturated with O2. The reaction follows Michaelis-Menten enzymatic reaction kinetics with turnover numbers 2.32 × 103.

  12. Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.

    PubMed

    Bielecki, Jakub; Lipiec, Ewelina

    2016-02-01

    Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.

  13. Hybrid DFT calculation of Fe57 NMR resonances and orbital order in magnetite

    NASA Astrophysics Data System (ADS)

    Patterson, C. H.

    2014-08-01

    The crystal structure and charge and orbital order of magnetite below the Verwey temperature are calculated using a first-principles hybrid density functional theory (DFT) method. The initial atomic positions in the crystal-structure calculation are those recently refined from x-ray diffraction data for the Cc space-group unit cell [Senn, Wright, and Attfield, Nature (London) 481, 173 (2012), 10.1038/nature10704]. Fermi contact and magnetic dipolar contributions to hyperfine fields at Fe57 nuclei obtained from hybrid DFT calculations are used to obtain NMR resonance frequencies for magnetite for a range of external magnetic field directions in a relatively weak field. NMR frequencies from hybrid density functional theory calculations are compared to NMR data [M. Mizoguchi, J. Phys. Soc. Jpn. 70, 2333 (2001), 10.1143/JPSJ.70.2333] for a range of applied magnetic field directions. NMR resonance frequencies of B-site Fe ions show large relative variations with applied field direction owing to anisotropic hyperfine fields from charge and orbital ordered Fe 3d minority-spin electrons at those sites. Good agreement between computed and measured NMR resonance frequencies confirms the pattern of charge and orbital order obtained from calculations. The charge and orbital order of magne-tite in its low-temperature phase obtained from hybrid DFT calculations is analyzed in terms of one-electron bonds between Fe ions. The Verwey transition in magnetite therefore resembles Mott-Peierls transitions in vanadium oxides which undergo symmetry-breaking transitions owing to electron-pair bond formation.

  14. Modern battery electrolytes: ion-ion interactions in Li+/Na+ conductors from DFT calculations.

    PubMed

    Jónsson, Erlendur; Johansson, Patrik

    2012-08-14

    Sodium-ion batteries, the sodium counterpart of the ubiquitous lithium-ion batteries, are currently being developed as a complementary technology to assure resource availability. As battery electrolytes tend to be one of the more limiting parts of any battery for both performance and life-length, chemical and physical data on sodium-ion battery electrolytes are important for rational development. Here the cation-anion interaction, a key property of any salt used in an electrolyte, of a number of salts is probed using numerous DFT methods via the ion-pair dissociation reaction: AlkAn ⇌ Alk(+) + An(-), where An(-) is any anion and Alk(+) is Na(+) or Li(+), the latter used here for a straight-forward literature and methodology comparison. Furthermore, the applicability of different DFT functionals for these types of calculations is benchmarked vs. a robust higher accuracy method (G4MP2). PMID:22751486

  15. Comparison of DFT methods for molecular structure and vibration spectra of ofloxacin calculations

    NASA Astrophysics Data System (ADS)

    Yang, Yue; Gao, Hongwei

    2012-01-01

    Comparison of the performance of different density functional theory (DFT) methods at various basis sets in predicting molecular and vibration spectra of ofloxacin was reported. The methods employed in this study comprise six functionals, namely, mPW1PW91, HCTH, LSDA, PBEPBE, B3PW91 and B3LYP. Different basis sets including LANL2DZ, SDD, LANL2MB, 6-31g, 6-311g and 3-21g were also examined. Comparison between the calculated and experimental data indicates that the mPW1PW91/6-311g level afford the best quality to predict the structure of ofloxacin. The results also indicate that B3LYP/LANL2DZ level show better performance in the vibration spectra prediction of ofloxacin than other DFT methods.

  16. Coordination chemistry, thermodynamics and DFT calculations of copper(II) NNOS Schiff base complexes.

    PubMed

    Esmaielzadeh, Sheida; Azimian, Leila; Shekoohi, Khadijeh; Mohammadi, Khosro

    2014-12-10

    Synthesis, magnetic and spectroscopy techniques are described for five copper(II) containing tetradentate Schiff bases are synthesized from methyl-2-(N-2'-aminoethane), (1-methyl-2'-aminoethane), (3-aminopropylamino)cyclopentenedithiocarboxylate. Molar conductance and infrared spectral evidences indicate that the complexes are four-coordinate in which the Schiff bases are coordinated as NNOS ligands. Room temperature μeff values for the complexes are 1.71-1.80B.M. corresponding to one unpaired electron respectively. The formation constants and free energies were measured spectrophotometrically, at constant ionic strength 0.1M (NaClO4), at 25˚C in DMF solvent. Also, the DFT calculations were carried out to determine the structural and the geometrical properties of the complexes. The DFT results are further supported by the experimental formation constants of these complexes.

  17. High-pressure behavior of solid nitrobenzene: Combined Raman spectroscopy and DFT-D calculations study

    NASA Astrophysics Data System (ADS)

    Wang, Wen-Peng; Liu, Fu-Sheng; Liu, Qi-Jun; Zhang, Lin-Ji; Wang, Yi-Gao; Liu, Zheng-Tang

    2016-09-01

    Nitrobenzene (NB), a simplest structure of the aromatic nitro compounds, was investigated as a model for understanding structural properties in nitro derivatives of benzene and anilines. Using the Raman spectroscopic technique, the vibrational modes of solid NB were examined under hydrostatic compression up to 10 GPa. The Raman spectra indicated that a subtle phase transition occurred around 5 GPa. Also, the dispersion corrected density functional theory (DFT-D) calculations were performed to provide further insight into pressure effects on the molecular geometry. The calculated data suggested that NB molecules were distorted, and molecular conformation was readjusted when the phase transition with vibrational changes took place under high-pressure.

  18. DFT calculation and vibrational spectroscopic studies of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine.

    PubMed

    Premkumar, S; Jawahar, A; Mathavan, T; Kumara Dhas, M; Sathe, V G; Milton Franklin Benial, A

    2014-08-14

    The molecular structure of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) was optimized by the DFT/B3LYP method with 6-311G (d,p), 6-311++G (d,p) and cc-pVTZ basis sets using the Gaussian 09 program. The most stable optimized structure of the molecule was predicted by the DFT/B3LYP method with cc-pVTZ basis set. The vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals and thermodynamical parameters were calculated. These calculations were done at the ground state energy level of BABP without applying any constraint on the potential energy surface. The vibrational spectra were experimentally recorded using Fourier Transform-Infrared (FT-IR) and micro-Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of Potential Energy Distribution (PED) calculation using the VEDA 4.0 program. The vibrational modes assignments were performed by using the animation option of GaussView 05 graphical interface for Gaussian program. The Mulliken atomic charge distribution was calculated for BABP molecule. The molecular reactivity and stability of BABP were also studied by frontier molecular orbitals (FMOs) analysis. PMID:24727165

  19. DFT calculation and vibrational spectroscopic studies of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine

    NASA Astrophysics Data System (ADS)

    Premkumar, S.; Jawahar, A.; Mathavan, T.; Kumara Dhas, M.; Sathe, V. G.; Milton Franklin Benial, A.

    2014-08-01

    The molecular structure of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) was optimized by the DFT/B3LYP method with 6-311G (d,p), 6-311++G (d,p) and cc-pVTZ basis sets using the Gaussian 09 program. The most stable optimized structure of the molecule was predicted by the DFT/B3LYP method with cc-pVTZ basis set. The vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals and thermodynamical parameters were calculated. These calculations were done at the ground state energy level of BABP without applying any constraint on the potential energy surface. The vibrational spectra were experimentally recorded using Fourier Transform-Infrared (FT-IR) and micro-Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of Potential Energy Distribution (PED) calculation using the VEDA 4.0 program. The vibrational modes assignments were performed by using the animation option of GaussView 05 graphical interface for Gaussian program. The Mulliken atomic charge distribution was calculated for BABP molecule. The molecular reactivity and stability of BABP were also studied by frontier molecular orbitals (FMOs) analysis.

  20. 13C CPMAS NMR studies and DFT calculations of triterpene xylosides isolated from Actaea racemosa

    NASA Astrophysics Data System (ADS)

    Jamróz, Marta K.; Paradowska, Katarzyna; Gliński, Jan A.; Wawer, Iwona

    2011-05-01

    13C CPMAS NMR spectra of four triterpene glycosides: cimigenol xyloside ( 1), 26-deoxyactein ( 2), cimicifugoside H-1 ( 3) and 24-acethylhydroshengmanol xyloside ( 4) were recorded and analyzed to characterize their solid-state structure. Experimental data were supported by theoretical calculations of NMR shielding constants with the GIAO/6-31G**-su1 approach. A number of methods for the conformational search and a number of functionals for the DFT calculations were applied to ( 1). The best method was proven to be MMFF or MMFFAQ for the conformational search and the PBE1PBE functional for the DFT calculations. Extra calculations simulating C16 dbnd O⋯HOH hydrogen bond yield the isotropic shielding closer to the experimental solid-state value. For all the compounds CP kinetics parameters were calculated using either the I-S or the I-I*-S model. The analysis of CP kinetics data for methyl groups revealed differences in the T2 time constant for two methyl groups (C29 and C30) linked at C4.

  1. Ab initio/DFT calculations of butyl ammonium salt of O,O'-dibornyl dithiophosphate.

    PubMed

    Kart, H H; Ozdemir Kart, S; Karakuş, M; Kurt, M

    2014-08-14

    O,O'-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other. PMID:24747929

  2. Ab initio/DFT calculations of butyl ammonium salt of O,O‧-dibornyl dithiophosphate

    NASA Astrophysics Data System (ADS)

    Kart, H. H.; Özdemir Kart, S.; Karakuş, M.; Kurt, M.

    2014-08-01

    O,O‧-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other.

  3. An Automatic K-Point Grid Generation Scheme for Enhanced Efficiency and Accuracy in DFT Calculations

    NASA Astrophysics Data System (ADS)

    Mohr, Jennifer A.-F.; Shepherd, James J.; Alavi, Ali

    2013-03-01

    We seek to create an automatic k-point grid generation scheme for density functional theory (DFT) calculations that improves the efficiency and accuracy of the calculations and is suitable for use in high-throughput computations. Current automated k-point generation schemes often result in calculations with insufficient k-points, which reduces the reliability of the results, or too many k-points, which can significantly increase computational cost. By controlling a wider range of k-point grid densities for the Brillouin zone based upon factors of conductivity and symmetry, a scalable k-point grid generation scheme can lower calculation runtimes and improve the accuracy of energy convergence. Johns Hopkins University

  4. Molecular structure and spectroscopic properties of 4-nitrocatechol at different pH: UV visible, Raman, DFT and TD-DFT calculations

    NASA Astrophysics Data System (ADS)

    Cornard, Jean-Paul; Rasmiwetti; Merlin, Jean-Claude

    2005-03-01

    We investigated theoretically, by density functional theoretical calculations and by vibrational and electronic spectroscopies, the structure and the molecular spectroscopic properties of the 4-nitrocatechol molecule with varying pH. The lower energy stable structures of the neutral, monoanion and dianion forms were compared, and influence of water solvation was examined. The Raman and UV-visible spectra of 4-nitrocatechol and of its singly deprotonated form were recorded by varying the pH from 2 to 9. A calculation of the vibrational frequencies has allowed a complete assignment of the Raman spectra of the two forms of 4-nitrocatechol, and has permitted to investigate the evolution of vibrational normal modes upon deprotonation. Based on the molecular orbital analysis and the time dependent DFT (TD-DFT) calculations, we discussed the electronic structure and the assignment of the absorption bands in the electronic spectra of 4-nitrocatechol and mono-deprotonated 4-nitrocatechol.

  5. Advances in structural analysis of fluoroaluminates using DFT calculations of 27Al electric field gradients.

    PubMed

    Body, M; Legein, C; Buzaré, J-Y; Silly, G; Blaha, P; Martineau, C; Calvayrac, F

    2007-11-22

    Based on the analysis of 23 aluminum sites from 16 fluoroaluminates, the present work demonstrates the strong potential of combining accurate NMR quadrupolar parameter measurements, density functional theory (DFT)-based calculations of electric field gradients (EFG), and structure optimizations as implemented in the WIEN2k package for the structural and electronic characterizations of crystalline inorganic materials. Structure optimizations are essential for compounds whose structure was refined from usually less accurate powder diffraction data and provide a reliable assignment of the 27Al quadrupolar parameters to the aluminum sites in the studied compounds. The correlation between experimental and calculated EFG tensor elements leads to the proposition of a new value of the 27Al nuclear quadrupole moment Q(27Al) = 1.616 (+/-0.024) x 10(-29) m2. The DFT calculations provide the orientation of the 27Al EFG tensors in the crystal frame. Electron density maps support that the magnitude and orientation of the 27Al EFG tensors in fluoroaluminates mainly result from the asymmetric distribution of the Al 3p orbital valence electrons. In most cases, the definition of relevant radial and angular distortion indices, relying on EFG orientation, allows correlations between these distortions and magnitude and sign of the Vii. PMID:17973463

  6. 2-Substituted-1H-perimidines: Synthesis, crystal structure and DFT calculations

    NASA Astrophysics Data System (ADS)

    Sović, Irena; Pavlović, Gordana; Papadopoulos, Anastasios G.; Šišak, Dubravka; Karminski-Zamola, Grace

    2013-06-01

    Perimidines or 1H-perimidines represent an important class of heterocyclic compounds built up of a dihydropyrimidine ring peri-fused to a naphthalene moiety. They exhibit 1,3-annular tautomerism due to two possible hydrogen positions at one or the other endocyclic nitrogen atoms or both resulting in the imine or enamine forms, respectively. The imine forms of 2-substituted-1H-perimidines can exhibit cis or trans orientation of 2-substituent in respect of the double Cdbnd N bond. Here we report synthesis of four 2-substituted perimidine derivatives: 2-hydroxymethyl-perimidine 2, ethyl-1H-perimidine-2-carboxylate 3, perimidine-2-carboxylic acid 4 and 2-cyanomethyl-perimidine 5. The compounds are characterized by MS, IR spectroscopy, single-crystal X-ray diffraction (SCXRD) (2), and powder X-ray diffraction (PXRD) (5), as well as DFT calculations (3, 4 and 5) and by the NMR spectroscopy in the solution (2-5). Single-crystal X-ray diffraction proved that the compound 2 exists in the solid state as imine tautomer. The molecular structure that compound 5 adopt in its crystalline state could not be determined reliably. The results from the PXRD structural analysis cannot univocally indicate which of the forms is more likely to be present in the solid state. On the contrary, DFT calculation shows that the enamine form of 5 is more stable than imine form.

  7. DFT calculations and experimental FT-IR, FT-Raman, NMR, UV-Vis spectral studies of 3-fluorophenylboronic acid.

    PubMed

    Karabacak, M; Kose, E; Sas, E B; Kurt, M; Asiri, A M; Atac, A

    2015-02-01

    The spectroscopic (FT-IR, FT-Raman, (1)H and (13)C NMR, UV-Vis), structural, electronic and thermodynamical properties of 3-fluorophenylboronic acid (C6H4FB(OH)2), 3FPBA) were submitted by using both experimental techniques and theoretical methods (quantum chemical calculations) in this work. The experimental infrared and Raman spectra were obtained in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The equilibrium geometry and vibrational spectra were calculated by using DFT (B3LYP) with 6-311++G(d,p) basis set. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. The total energy distributions (TED) of the vibrational modes were performed for the assignments of the title molecule by using scaled quantum mechanics (SQM) method. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The (1)H and (13)C NMR spectra were computed by using the gauge-invariant atomic orbital (GIAO) method, showing a good agreement with the experimental ones. The last one UV-Vis absorption spectra were analyzed in two solvents (ethanol and water), saved in the range of 200-400 nm. In addition these, HOMO and LUMO energies, the excitation energies, density of states (DOS) diagrams, thermodynamical properties and molecular electrostatic potential surface (MEPs) were presented. Nonlinear optical (NLO) properties and thermodynamic features were performed. The experimental results are combined with the theoretical calculations using DFT calculations to fortification of the paper. At the end of this work, the results were proved our paper had been indispensable for the literature backing. PMID:25448934

  8. DFT calculations and experimental FT-IR, FT-Raman, NMR, UV-Vis spectral studies of 3-fluorophenylboronic acid

    NASA Astrophysics Data System (ADS)

    Karabacak, M.; Kose, E.; Sas, E. B.; Kurt, M.; Asiri, A. M.; Atac, A.

    2015-02-01

    The spectroscopic (FT-IR, FT-Raman, 1H and 13C NMR, UV-Vis), structural, electronic and thermodynamical properties of 3-fluorophenylboronic acid (C6H4FB(OH)2), 3FPBA) were submitted by using both experimental techniques and theoretical methods (quantum chemical calculations) in this work. The experimental infrared and Raman spectra were obtained in the region 4000-400 cm-1 and 3500-10 cm-1, respectively. The equilibrium geometry and vibrational spectra were calculated by using DFT (B3LYP) with 6-311++G(d,p) basis set. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. The total energy distributions (TED) of the vibrational modes were performed for the assignments of the title molecule by using scaled quantum mechanics (SQM) method. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The 1H and 13C NMR spectra were computed by using the gauge-invariant atomic orbital (GIAO) method, showing a good agreement with the experimental ones. The last one UV-Vis absorption spectra were analyzed in two solvents (ethanol and water), saved in the range of 200-400 nm. In addition these, HOMO and LUMO energies, the excitation energies, density of states (DOS) diagrams, thermodynamical properties and molecular electrostatic potential surface (MEPs) were presented. Nonlinear optical (NLO) properties and thermodynamic features were performed. The experimental results are combined with the theoretical calculations using DFT calculations to fortification of the paper. At the end of this work, the results were proved our paper had been indispensable for the literature backing.

  9. New Development of Self-Interaction Corrected DFT for Extended Systems Applied to the Calculation of Native Defects in 3C-SiC

    SciTech Connect

    Bylaska, Eric J.; Tsemekhman, Kiril L.; Gao, Fei

    2006-05-01

    We recently have developed a framework for implementing a scaled self-interaction corrected density functional theory (DFT-SIC) into pseudopotential plane-wave DFT. The technique implements the original method due to Perdew and Zunger by direct minimization of the DFT-SIC total energy functional. By using maximally localized Wannier functions, DFT-SIC calculation can be carried out efficiently even for extended systems. Using this new development the formation energies of defects in 3C-SiC were calculated and compared to more standard DFT calculations. Differences of up to 1eV were seen between DFT and DFT-SIC calculations of the formation energies. When compared to DFT, DFT-SIC produced less stable vacancies and silicon interstials, more stable antisites and carbon interstitials. The most favorable interstitials were found to be C interstitials in a C+-C<100> dumbbell configuration, with the formation energy of 5.91eV with DFT and 5.65 eV with DFT-SIC. Si interstitials were not as stable as C interstitials. The most favorable Si interstitial was found to be Si tetrahedral surrounded by four C atoms, with a formation energy of 7.65eV with DFT and 8.71eV with DFT-SIC.

  10. FT-IR, Raman, RRS measurements and DFT calculation for doxorubicin.

    PubMed

    Das, Gobind; Nicastri, Annalisa; Coluccio, Maria Laura; Gentile, Francesco; Candeloro, Patrizio; Cojoc, Gheorghe; Liberale, Carlo; De Angelis, Francesco; Di Fabrizio, Enzo

    2010-10-01

    Doxorubicin (DOXO) is a powerful anthracycline antibiotic used to treat many human neoplasms, including acute leukemias, lymphomas, stomach, breast and ovarian cancer, and bone tumors, yet causing cardiotoxicity at the same time. For this reason, there is a great interest in medical field to gain deep insight and knowledge of this molecule. Raman, Fourier Transform Infrared (FT-IR) absorption spectroscopy, and Resonance Raman scattering were performed for the vibrational characterization of DOXO molecule. Density function theorem (DFT) modeling of Raman and FT-IR spectra were used for the assignment of the vibrational frequencies. The optimized molecular structured was obtained, first, on the basis of potential energy distribution. The simulation for vibrational bands is based on the calculations for internal force constants and potential energy distribution matrices. The calculated DOXO vibrational bands show qualitative agreement with the experimental observations (FT-IR absorption and Raman scattering). PMID:20232462

  11. FT-IR, Raman, RRS measurements and DFT calculation for doxorubicin.

    PubMed

    Das, Gobind; Nicastri, Annalisa; Coluccio, Maria Laura; Gentile, Francesco; Candeloro, Patrizio; Cojoc, Gheorghe; Liberale, Carlo; De Angelis, Francesco; Di Fabrizio, Enzo

    2010-10-01

    Doxorubicin (DOXO) is a powerful anthracycline antibiotic used to treat many human neoplasms, including acute leukemias, lymphomas, stomach, breast and ovarian cancer, and bone tumors, yet causing cardiotoxicity at the same time. For this reason, there is a great interest in medical field to gain deep insight and knowledge of this molecule. Raman, Fourier Transform Infrared (FT-IR) absorption spectroscopy, and Resonance Raman scattering were performed for the vibrational characterization of DOXO molecule. Density function theorem (DFT) modeling of Raman and FT-IR spectra were used for the assignment of the vibrational frequencies. The optimized molecular structured was obtained, first, on the basis of potential energy distribution. The simulation for vibrational bands is based on the calculations for internal force constants and potential energy distribution matrices. The calculated DOXO vibrational bands show qualitative agreement with the experimental observations (FT-IR absorption and Raman scattering).

  12. Synthesis and DFT calculation on novel derivatives of Bis (indolyl) methanes

    NASA Astrophysics Data System (ADS)

    Zarandi, Maryam; Salimi Beni, Alireza

    2016-09-01

    Bis (indolyl) methane derivatives are an important class of biomolecules and heterocyclic scaffold of organic compounds. To extension novel Bis (indolyl) methane derivatives, two new aldehydes have been applied. In order to structural investigation, the optimized geometry, total energy, potential energy surface and vibrational wavenumbers of Bis (indolyl) methanes have been determined using DFT/B3LYP method with 6-31G (d) basis set. A complete vibrational assignment is provided for the observed IR spectra of Bis (indolyl) methanes. These methods are proposed as a tool to be applied in the structural characterization of Bis (indolyl) methanes. The isotropic chemical shift computed by 1H and 13C NMR chemical shifts of the Bis (indolyl) methanes, calculated using the GIAO method, shows good agreement with experimental observations. The calculated HOMO and LUMO with frontier orbital gap are presented in order to predict antibacterial properties.

  13. A DFT-based model for calculating solvolytic reactivity. The nucleofugality of aliphatic carboxylates in terms of Nf parameters.

    PubMed

    Denegri, Bernard; Matić, Mirela; Kronja, Olga

    2014-08-14

    The most comprehensive nucleofugality scale, based on the correlation and solvolytic rate constants of benzhydrylium derivatives, has recently been proposed by Mayr and co-workers (Acc. Chem. Res., 2010, 43, 1537-1549). In this work, the possibility of employing quantum chemical calculations in further determination of nucleofugality (Nf) parameters of leaving groups is explored. Whereas the heterolytic transition state of benzhydryl carboxylate cannot be optimized by quantum chemical calculations, the possibility of an alternative model reaction is examined in order to obtain nucleofugality parameters of various aliphatic carboxylates, which can properly be included in the current nucleofugality scale. For that purpose, ground and transition state structures have been optimized for the proposed model reaction, which includes anchimerically assisted heterolytic dissociation of cis-2,3-dihydroxycyclopropyl trans-carboxylates. The validity of the model reaction as well as of applied DFT methods in the presence of the IEFPCM solvation model is verified by correlating calculated free energies of activation of the model reaction with literature experimental data for solvolysis of reference dianisylmethyl carboxylates. For this purpose the ability of several functionals (including popular B3LYP) is examined, among which the M06-2X gives the best results. The very good correlation indicates acceptable accurate relative reactivities of aliphatic carboxylates, and enables the estimation of rate constants for solvolysis of other dianisylmethyl carboxylates in aqueous ethanol mixtures, from which the corresponding Nf parameters are determined using mentioned Mayr's equation. In addition, DFT calculations confirm the previous experimental observation that the abilities of aliphatic carboxylate leaving groups in solution are governed by the inductive effect of substituents attached to the carboxyl group. PMID:24964919

  14. Formation of a 6FDA-based ring polyimide with nanoscale cavity evaluated by DFT calculations

    NASA Astrophysics Data System (ADS)

    Fukuda, Mitsuhiro; Takao, Yoshimi; Tamai, Yoshinori

    2005-04-01

    The computer-aided molecular design of a rigid ring molecule has been performed. As a candidate molecule, the polyimide derived from 2,2-bis(3,4-carboxylphenyl) hexafluoropropane dianhydride (6FDA) with m-phenylenediamine (MDA) has been used. The optimized structures of the 6FDA-MDA model compounds including a precursor type amic acid model were investigated using the density functional theory (DFT) at the B3LYP/6-311G(d,p) level. Using the optimized structures of the model compounds, the probable combinations to form a flat ring polyimide are considered by taking the spatial angles between the respective aromatic groups into consideration. We selected several combinations with different conformations and the number of monomer units. We showed that the dimer, trimer and tetramer of not only the 6FDA-based ring imide but also the corresponding ring amic acid can have a stable geometry. Each of them contains a cavity of sub-nanometer size and characteristic shape. Among them, the interaction energy with some guest molecules are evaluated for the smallest ring imide constructed from two units of 6FDA-MDA using the DFT calculations.

  15. Ion-radical mechanism of enzymatic ATP synthesis: DFT calculations and experimental control.

    PubMed

    Buchachenko, Anatoly L; Kuznetsov, Dmitry A; Breslavskaya, Natalia N

    2010-02-18

    A new, ion-radical mechanism of enzymatic ATP synthesis was recently discovered by using magnesium isotopes. It functions at a high concentration of MgCl(2) and includes electron transfer from the Mg(H(2)O)(m)(2+)(ADP(3-)) complex (m = 0-4) to the Mg(H(2)O)(n)(2+) complex as a primary reaction of ATP synthesis in catalytic sites of ATP synthase and kinases. Here, the structures and electron transfer reaction energies of magnesium complexes related to ATP synthesis are calculated in terms of DFT. ADP is modeled by pyrophosphate anions, protonated (HP(2)O(7)H(2-), HP(2)O(7)CH(3)(2-)) and deprotonated (HP(2)O(7)(3-), CH(3)P(2)O(7)(3-)). The reaction generates an ion-radical pair, composed of Mg(H(2)O)(n)(+) ion and pyrophosphate anion-radical coordinated to Mg(2+) ion. The addition of the latter to the substrate P=O bond results in ATP formation. Populations of the singlet and triplet states and singlet-triplet spin conversion in the pair are controlled by hyperfine coupling of unpaired electrons with magnetic (25)Mg and (31)P nuclei and by Zeeman interaction. Due to these two interactions, the yield of ATP is a function of nuclear magnetic moment and magnetic field; both of these effects were experimentally detected. Electron transfer reaction does not depend on m but strongly depends on n. It is exoergic and energy allowed at 0 < or = n < infinity for the deprotonated pyrophosphate anions and at 0 < or = n < 4 for the protonated ones; for other values of n, the reaction is energy deficient and forbidden. The boundary between exoergic and endoergic regimes corresponds to the trigger magnitude n* (n* = 4 for protonated anions and 6 < n* < infinity for deprotonated ones). These results explain why ATP synthesis occurs only in special devices, molecular enzymatic machines, but not in water (n = infinity). Biomedical consequences of the ion-radical enzymatic ATP synthesis are also discussed.

  16. A 45Sc-NMR and DFT calculation study of crystalline scandium compounds

    NASA Astrophysics Data System (ADS)

    Bräuniger, Thomas; Hofmann, Andreas J.; Moudrakovski, Igor L.; Hoch, Constantin; Schnick, Wolfgang

    2016-01-01

    A series of scandium compounds, namely ScPO4, ScOF, Li3Sc(BO3)2, and CaSc2O4, were prepared according to procedures described in the literature, and then characterised by powder X-ray diffraction and solid-state 45Sc-NMR spectroscopy. By computer fitting, the quadrupolar interaction parameters χ and η, as well as the isotropic chemical shifts δiso were extracted from the NMR spectra. For comparison and site assignment of 45Sc, density functional theory (DFT) calculations of the EFG tensor were carried out with the CASTEP code. For the compounds with a well-defined formal coordination number (CN), a convincing linear correlation between CN and isotropic chemical shift could be established.

  17. Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Wolniak, Michał; Tomczyk, Michał; Gudej, Jan; Wawer, Iwona

    2006-12-01

    Methyl brevifolincarboxylate isolated from the herb of Potentilla argentea L. (Rosaceae) is a representative of the naturally occurring polyphenols. The compound is of pharmaceutical interest mainly because of its antiviral and antioxidant properties. 13C NMR spectra were recorded for solution and solid phase. 13C CPMAS spectra were assigned by comparison with solution data, dipolar dephasing and short contact time experiments. The correctness of assignments was verified by GIAO DFT calculations of shielding constants. The differences between the solution and solid state chemical shift values were explained in terms of orientation of OH groups and intramolecular hydrogen bonds. The splitting of the C1 dbnd O resonance shows that there exists a polymorphism in the solid phase, which might be due to the formation of intramolecular hydrogen bond involving carbonyl or methoxy oxygen (i.e. C10 sbnd OH⋯O dbnd C or C10 sbnd OH⋯OCH 3).

  18. Cis-trans isomerisation of azobenzenes studied by laser-coupled NMR spectroscopy and DFT calculations.

    PubMed

    Wazzan, Nuha A; Richardson, Patricia R; Jones, Anita C

    2010-07-30

    In a combined experimental and computational study of a group of para-substituted azobenzenes, the effects of substituents and solvent on the kinetics of thermal cis-to-trans isomerisation have been examined and the success of DFT calculations in predicting kinetic parameters assessed. Mono-substituted species are predicted to isomerise by inversion in both non-polar and polar solvent, whereas for push-pull azobenzenes the mechanism is predicted to change from inversion to rotation on going from non-polar to polar solvent. Computed free energies of activation qualitatively reproduce experimental trends but do not quantitatively predict the kinetics of cis-trans isomerisation. The polarisable continuum model of solvation fails to predict the experimentally observed influence of solvent on the entropy of activation.

  19. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    NASA Astrophysics Data System (ADS)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  20. MCD spectroscopy and TD-DFT calculations of low symmetry subnaphthalocyanine analogs.

    PubMed

    Mack, John; Otaki, Tatsuya; Durfee, William S; Kobayashi, Nagao; Stillman, Martin J

    2014-07-01

    Magnetic circular dichroism (MCD) spectroscopy and time-dependent density functional theory (TD-DFT) calculations are used to analyze the electronic structure and optical properties of low-symmetry subnaphthalocyanine analogs with AAB and ABB structures formed during mixed condensations of tetrafluorophthalonitrile and 2,3-naphthalenedicarbonitrile. The results demonstrate that trends observed in the properties of phthalocyanine analogs can be used to fine tune the optical properties so that the Q(0,0) bands lie in the red region, in a manner that does not significantly destabilize the highest occupied molecular orbital (HOMO) energy relative to that of the parent subphthalocyanine ligand. Attempts to study the spectroscopy of anion radical species proved unsuccessful, since they proved to be unstable. PMID:24507929

  1. Vibrational spectra, DFT calculations, conformational stabilities and assignments of the fundamentals of the 1-butylpiperazine

    NASA Astrophysics Data System (ADS)

    Bağlayan, Özge; Kaya, Mehmet Fatih; Güneş, Esma; Şenyel, Mustafa

    2016-10-01

    FT-IR and FT-Raman spectra of 1-butylpiperazine (1bpa) were experimentally recorded in the region of 4000-10 cm-1 and 4000-100 cm-1, respectively. The optimized geometric parameters, conformational equilibria, normal mode frequencies and corresponding vibrational assignments of 1bpa (C8H18N2) are theoretically examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-31++G(d,p) basis set. Also, reliable conformational investigation and vibrational assignments have been performed by the potential energy surface (PES) and potential energy distribution (PED) analysis, respectively. Calculations are made for four possible conformations. According to the experimental and theoretical data, density functional B3LYP method provides reliable results for predicting vibrational wavenumbers and equatorial-equatorial conformer is considered to be the most stable form of 1bpa.

  2. Study of cerium solubility in Gd2Zr2O7 by DFT + U calculations

    SciTech Connect

    Wang, X. J.; Xiao, H. Y.; Zu, X. T.; Weber, W. J.

    2011-01-01

    The pyrochlore Gd₂Zr₂O₇ has been proposed as a favorable structure for the immobilization of actinide nuclear waste, due to its high radiation resistance. Because CeO2 exhibits similar properties and radiation response to many actinide dioxides, it is often used as a surrogate for actinide dioxides in both experimental and computational studies. In the present work, we investigate the solubility of Ce in Gd₂Zr₂O₇, as well as the energetic and electronic properties of Gd2-yCeyZr₂O₇, based on density functional theory plus Hubbard U correction (DFT + U). Our calculations show that Gd₂Zr₂O₇and Ce₂Zr₂O₇ form a solid solution over the entire range of Ce content, in excellent agreement with experiments. The increased stability of the ordered pyrochlore structure with increasing Ce content may affect radiation resistance.

  3. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  4. Challenges and advances in large-scale DFT calculations on GPUs

    NASA Astrophysics Data System (ADS)

    Kulik, Heather

    2014-03-01

    Recent advances in reformulating electronic structure algorithms for stream processors such as graphical processing units have made DFT calculations on systems comprising up to O(103) atoms feasible. Simulations on such systems that previously required half a week on traditional processors can now be completed in only half an hour. Here, we leverage these GPU-accelerated quantum chemistry methods to investigate large-scale quantum mechanical features in protein structure, mechanochemical depolymerization, and the nucleation and growth of heterogeneous nanoparticle structures. In each case, large-scale and rapid evaluation of electronic structure properties is critical for unearthing previously poorly understood properties and mechanistic features of these systems. We will also discuss outstanding challenges in the use of Gaussian localized-basis-set codes on GPUs pertaining to limitations in basis set size and how we circumvent such challenges to computational efficiency with systematic, physics-based error corrections to basis set incompleteness.

  5. NO Chemisorption on Cu/SSZ-13: a Comparative Study from Infrared Spectroscopy and DFT Calculations

    SciTech Connect

    Zhang, Renqin; McEwen, Jean-Sabin; Kollar, Marton; Gao, Feng; Wang, Yilin; Szanyi, Janos; Peden, Charles HF

    2014-11-07

    The locations and energies of Cu ions in a Cu/SSZ-13 zeolite catalyst were investigated by density functional theory (DFT) calculations. For 'naked' Cu2+ ions (i.e., Cu2+ ions with no ligands in their coordination spheres other than zeolite lattice oxygen atoms), the more energetically favorable sites are within a 6-membered ring. However, with the presence of various adsorbates, the energy difference between 6- and 8-membered ring locations greatly diminishes. Specifically, Cu2+ ions are substantially stabilized by -OH ligands (as [CuII(OH)]+), making the extra-framework sites in an 8-membered ring energetically more favorable than 6-membered ring sites. Under fully dehydrated high vacuum conditions with different Si/Al and Cu/Al ratios, three chemisorbed NO species coexist upon exposure of NO to Cu/SSZ-13: NO+, Cu2+-NO and Cu+-NO. The relative signal intensities for these bands vary greatly with Si/Al ratios. The vibrational frequency of chemisorbed NO was found to be very sensitive to the location of Cu2+ ions. On the one hand, with the aid from DFT calculations, the nature for these vibrations can be assigned in detail. On the other hand, the relative intensities for various Cu2+-NO species provide a good measure of the nature of Cu2+ ions as functions of Si/Al and Cu/Al ratios and the presence of humidity. These new findings cast doubt on the generally accepted proposal that only Cu2+ ions located in 6-membered rings are catalytically active for NH3-SCR.

  6. DFT calculation of vibrational frequencies of clusters in GaAs and the Raman spectra

    NASA Astrophysics Data System (ADS)

    Radhika Devi, V.; Shrivastava, Keshav N.

    2012-09-01

    We have calculated the vibrational frequencies of clusters of Ga and As atoms from the first principles using the density-functional theory (DFT) method and the local-density approximation (LDA). We find that the calculated value of 286.2 cm-1 for a linear cluster of Ga2As2 is very near the experimental value of 292 ± 4 cm-1. The calculated value of 289.4 cm-1 for Ga2As6 (dumb bell) cluster is indeed very near the experimental value. There are strong phonon correlations so that the cluster frequency is within the dispersion relation of the crystal LO value. There is a weak line in the experimental Raman spectrum at 268 cm-1 which is very near the value of 267.3 cm-1 calculated for the Ga2As (triangular) cluster. The weak lines corresponding to the linear bonds provide the strength to the amorphous samples. There are clusters of atoms in the glassy state of GaAs.

  7. FT-IR, FT-Raman spectra and DFT calculations of melaminium perchlorate monohydrate

    NASA Astrophysics Data System (ADS)

    Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Renganathan, N. G.; Gunasekaran, S.; Anbalagan, G.

    2013-08-01

    Melaminium perchlorate monohydrate (MPM), an organic material has been synthesized by slow solvent evaporation method at room temperature. Powder X-ray diffraction analysis confirms that MPM crystal belongs to triclinic system with space group P-1. FTIR and FT Raman spectra are recorded at room temperature. Functional group assignment has been made for the melaminium cations and perchlorate anions. Vibrational spectra have also been discussed on the basis of quantum chemical density functional theory (DFT) calculations using Firefly (PC GAMESS) version 7.1 G. Vibrational frequencies are calculated and scaled values are compared with experimental values. The assignment of the bands has been made on the basis of the calculated PED. The Mulliken charges, HOMO-LUMO orbital energies are analyzed directly from Firefly program log files and graphically illustrated. HOMO-LUMO energy gap and other related molecular properties are also calculated. The theoretically constructed FT-IR and FT-Raman spectra of MPM coincide with the experimental one. The chemical structure of the compound has been established by 1H and 13C NMR spectra. No detectable signal was observed during powder test for second harmonic generation.

  8. DFT calculation of vibrational frequencies of clusters in GaAs and the Raman spectra.

    PubMed

    Radhika Devi, V; Shrivastava, Keshav N

    2012-09-01

    We have calculated the vibrational frequencies of clusters of Ga and As atoms from the first principles using the density-functional theory (DFT) method and the local-density approximation (LDA). We find that the calculated value of 286.2 cm(-1) for a linear cluster of Ga(2)As(2) is very near the experimental value of 292 ± 4 cm(-1). The calculated value of 289.4 cm(-1) for Ga(2)As(6) (dumb bell) cluster is indeed very near the experimental value. There are strong phonon correlations so that the cluster frequency is within the dispersion relation of the crystal LO value. There is a weak line in the experimental Raman spectrum at 268 cm(-1) which is very near the value of 267.3 cm(-1) calculated for the Ga(2)As (triangular) cluster. The weak lines corresponding to the linear bonds provide the strength to the amorphous samples. There are clusters of atoms in the glassy state of GaAs.

  9. A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations.

    PubMed

    Akkaya, Yasemin; Balci, Kubilay; Goren, Yeliz; Akyuz, Sevim

    2015-08-01

    In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed "potential energy surface scan" carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their possible dimer structures were obtained through "geometry optimisation" and "frequency" calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretation of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted. PMID:25854610

  10. A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations

    NASA Astrophysics Data System (ADS)

    Akkaya, Yasemin; Balci, Kubilay; Goren, Yeliz; Akyuz, Sevim

    2015-08-01

    In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed "potential energy surface scan" carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their possible dimer structures were obtained through "geometry optimisation" and "frequency" calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretation of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted.

  11. DFT calculations of magnetic parameters for molybdenum complexes and hydroxymethyl intermediates trapped on silica surface

    NASA Astrophysics Data System (ADS)

    Sojka, Zbigniew; Pietrzyk, Piotr

    2006-03-01

    Density functional theory (DFT) calculations of EPR parameters and their structure sensitivity for selected surface paramagnetic species involved in oxidative dehydrogenation of methanol over silica grafted molybdenum catalyst were investigated. Two surface complexes, Mo 4 c/SiO 2 and {O -sbnd Mo 4 c}/SiO 2, as well as rad CH 2OH radical trapped on the SiO 2 matrix were taken as the examples. The spin-restricted zeroth order regular approximation (ZORA) implemented in the Amsterdam Density Functional suite was used to calculate the electronic g tensor for those species. The predicted values were in satisfactory agreement with experimental EPR results. Five different coordination modes of the rad CH 2OH radical on the silica surface were considered and the isotropic 13C, 17O, and 1H hyperfine coupling constants (HFCC) of the resultant surface complexes were calculated. Structure sensitivity of the HFCC values was discussed in terms of the angular deformations caused by hydrogen bonding with the silica surface.

  12. DFT calculations of magnetic parameters for molybdenum complexes and hydroxymethyl intermediates trapped on silica surface.

    PubMed

    Sojka, Zbigniew; Pietrzyk, Piotr

    2006-03-13

    Density functional theory (DFT) calculations of EPR parameters and their structure sensitivity for selected surface paramagnetic species involved in oxidative dehydrogenation of methanol over silica grafted molybdenum catalyst were investigated. Two surface complexes, Mo(4c)/SiO2 and {O(-)-Mo(4c)}/SiO2, as well as *CH2OH radical trapped on the SiO2 matrix were taken as the examples. The spin-restricted zeroth order regular approximation (ZORA) implemented in the Amsterdam Density Functional suite was used to calculate the electronic g tensor for those species. The predicted values were in satisfactory agreement with experimental EPR results. Five different coordination modes of the *CH2OH radical on the silica surface were considered and the isotropic 13C, 17O, and 1H hyperfine coupling constants (HFCC) of the resultant surface complexes were calculated. Structure sensitivity of the HFCC values was discussed in terms of the angular deformations caused by hydrogen bonding with the silica surface.

  13. A strategy of integrating ultraviolet absorption and crosslinking in a single molecule: DFT calculation and experimental

    NASA Astrophysics Data System (ADS)

    Shan, Mingli; Liu, Yujing; Xia, Shuwei; Tang, Qunwei; Yu, Liangmin

    2016-03-01

    Creation of advanced ultraviolet light absorbers having crosslinking ability has been persistent objective for anti-ultraviolent aging polymers. We present here the integration of 2, 4-dihydroxybenzophenone (UV-0) and N-methylol acrylamide (NMA) for novel ultraviolet absorber namely (3,5-dimethacrylamide-2,4-dihydroxyphenyl) (phenyl)methanone (UV-CA), which is subsequently utilized as a crosslinking agent after suffering Friedel-Crafts reaction. The preliminary results demonstrate that quantum chemical calculations (DFT) is a promising avenue in demonstrating the optimized geometry, charges, energy levels and UV electronic absorption bands of the UV-CA in the singlet (steady and excited states). The structure parameters and natural band orbital (NBO) calculations suggest that the intramolecular hydrogen bond (IMHB) in the UV-0 group is significantly enhanced in comparison to that between UV-0 and NMA groups. The acrylic acid polymers functionalized with UV-CA yield high crosslinking degree and robust UV absorbing performance. The impressive results demonstrate that quantum chemical calculations are promising in organic synthesis to develop advanced compounds.

  14. DFT calculations on the structural stability and infrared spectroscopy of endohedral metallofullerenes

    NASA Astrophysics Data System (ADS)

    Peng, Sheng; Zhang, Yan; Li, Xiao Jun; Ren, Yan; Zhang, Deng Xin

    2009-10-01

    Endohedral metallofullerenes M@C 24 (M = Li 0/+, Na 0/+, K 0/+, Be 0/2+, Mg 0/2+ and Ca 0/2+) with different spin configurations have been systematically investigated using the hybrid DFT-B3PW91 functional in conjunction with 6-31G(d) basis sets. Our theoretical studies show that Li@C 24, Be@C 24, Be 2+@C 24, and Mg 2+@C 24 are energetically favorable. In these endohedral metallofullerenes, only the encapsulated Be and Ca atoms can donate the electrons to the cage. With exception of Be 2+@C 24, the energy gaps of other charged compounds are larger than that of corresponding neutral compounds. We also find that some endohedral metallofullerenes have high energy gaps, but they are unlikely to show high thermodynamic stability. Additionally, the vibrational frequencies and active infrared intensities are also used as evidence to identify these endohedral metallofullerenes.

  15. DFT calculations on the structural stability and infrared spectroscopy of endohedral metallofullerenes.

    PubMed

    Peng, Sheng; Zhang, Yan; Li, Xiao Jun; Ren, Yan; Zhang, Deng Xin

    2009-10-01

    Endohedral metallofullerenes M@C(24) (M = Li(0/+), Na(0/+), K(0/+), Be(0/2+), Mg(0/2+) and Ca(0/2+)) with different spin configurations have been systematically investigated using the hybrid DFT-B3PW91 functional in conjunction with 6-31 G(d) basis sets. Our theoretical studies show that Li@C(24), Be@C(24), Be(2+)@C(24), and Mg(2+)@C(24) are energetically favorable. In these endohedral metallofullerenes, only the encapsulated Be and Ca atoms can donate the electrons to the cage. With exception of Be(2+)@C(24), the energy gaps of other charged compounds are larger than that of corresponding neutral compounds. We also find that some endohedral metallofullerenes have high energy gaps, but they are unlikely to show high thermodynamic stability. Additionally, the vibrational frequencies and active infrared intensities are also used as evidence to identify these endohedral metallofullerenes.

  16. DFT calculations, spectroscopy and antioxidant activity studies on (E)-2-nitro-4-[(phenylimino)methyl]phenol

    NASA Astrophysics Data System (ADS)

    Temel, Ersin; Alaşalvar, Can; Gökçe, Halil; Güder, Aytaç; Albayrak, Çiğdem; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan; Dilek, Nefise

    2015-02-01

    We have reported synthesis and characterization of (E)-2-nitro-4-[(phenylimino)methyl]phenol by using X-ray crystallographic method, FT-IR and UV-vis spectroscopies and density functional theory (DFT). Optimized geometry and vibrational frequencies of the title compound in the ground state have been computed by using B3LYP with the 6-311G+(d,p) basis set. HOMO-LUMO energy gap, Non-linear optical properties and NBO analysis of the compound are performed at B3LYP/6-311G+(d,p) level. Additionally, as remarkable properties, antioxidant activity of the title compound (CMPD) has been determined by using different antioxidant test methods i.e. ferric reducing antioxidant power (FRAP), hydrogen peroxide scavenging (HPSA), free radical scavenging (FRSA) and ferrous ion chelating activities (FICA). When compared with standards (BHA, BHT, and α-tocopherol), we have concluded that CPMD has effective FRAP, HPSA, FRSA and FICA.

  17. DFT electronic structure calculations, spectroscopic studies, and normal coordinate analysis of 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate.

    PubMed

    Muthu, S; Elamuruguporchelvi, E; Varghese, Anitha

    2015-03-01

    The solid phase FTIR and FT-Raman spectra of 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate (25N2LCPA) have been recorded 450-4000cm(-1) and 100-4000cm(-1) respectively. The normal coordinate analysis was carried out to confirm the precision of the assignments. DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies and IR intensities. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31+G(d,p) basis set. 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 Vibrational frequencies are calculated in the above method and are compared with experimental frequencies which yield good agreement between observed and calculated frequencies. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In addition, Frontiers molecular orbital and molecular electrostatic potential were computed by using Density Functional Theory (DFT) B3LYP/6-31+G(d,p) basis set. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule.

  18. A DFT study of addition reaction between fragment ion (CH₂) units and fullerene (C₆₀) molecule.

    PubMed

    Zaragoza, Irineo Pedro; Vergara, Jaime; Pérez-Manríquez, Liliana; Salcedo, Roberto

    2011-05-01

    The theoretical study of the interaction between CH(2) and fullerene (C(60)) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH(2) into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH(2) group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C(60)) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH(2) fragment to attack the CC (6, 5) bond. PMID:20658255

  19. Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H4B's role in nitric oxide synthase

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We suggest a possible mechanism of how 8-aminoquinolines (8-AQ's) cause hemotoxicity by oxidizing hemoglobin to methemoglobin. In our DFT calculations, we found that 5-hydroxyprimaquine is able to donate an electron to O2 to facilitate its conversion to H2O2. Meanwhile, Fe(II) is oxidized to Fe(III)...

  20. IR, Raman and SERS spectral analysis and DFT calculations on the Herbicide O,S-Dimethyl phosphoramidothioate, metamidophos.

    PubMed

    Fleming, Guillermo Diaz; Villagrán, Joao; Koch, Rainer

    2013-10-01

    Infrared, Raman and SERS spectra of O,S-Dimethyl phosphoramidothioate, metamidophos, MAP, have been recorded. Density Functional Theory, DFT, with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of this molecule. Calculated geometrical parameters fit very well with the experimental ones. Combining the recorded data, the DFT results and a Normal Coordinate Analysis based on a scaled quantum mechanical (SQM) force field approach, a complete vibrational assignment was made for the first time. The comparison of SERS spectra obtained by using colloidal silver nanoparticles, with the corresponding Raman spectrum reveals enhancement and shifts in bands as well as information about the orientation of MAP on the nm-sized metal structures and the importance of the S atom on the SERS effect. DFT modelling of the SERS effect and Molecular Electrostatic Potentials (MEP) confirms the experimental information. PMID:23756261

  1. IR, Raman and SERS spectral analysis and DFT calculations on the Herbicide O,S-Dimethyl phosphoramidothioate, metamidophos

    NASA Astrophysics Data System (ADS)

    Fleming, Guillermo Diaz; Villagrán, Joao; Koch, Rainer

    2013-10-01

    Infrared, Raman and SERS spectra of O,S-Dimethyl phosphoramidothioate, metamidophos, MAP, have been recorded. Density Functional Theory, DFT, with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of this molecule. Calculated geometrical parameters fit very well with the experimental ones. Combining the recorded data, the DFT results and a Normal Coordinate Analysis based on a scaled quantum mechanical (SQM) force field approach, a complete vibrational assignment was made for the first time. The comparison of SERS spectra obtained by using colloidal silver nanoparticles, with the corresponding Raman spectrum reveals enhancement and shifts in bands as well as information about the orientation of MAP on the nm-sized metal structures and the importance of the S atom on the SERS effect. DFT modelling of the SERS effect and Molecular Electrostatic Potentials (MEP) confirms the experimental information.

  2. FT-IR spectroscopy and DFT calculation study on the solvent effects of benzaldehyde in organic solvents.

    PubMed

    Li, Yi; Zhang, Hui; Liu, Qing

    2012-02-01

    FT-IR spectra of benzaldehyde in 11 different organic solvents were recorded and analyzed. The density functional theory (DFT) B3LYP/6-31G* method was chosen to calculate the infrared spectrum of benzaldehyde in gaseous state. The electrostatic effects of different solvents in benzaldehyde solutions were calculated using DFT with the self-consistent isodensity polarizable continuum model (SCI-PCM). Two remarkable carbonyl (C=O) peaks of benzaldehyde were observed by FT-IR in alcohol solvents, which were caused by different hydrogen bond species and explained by ab initio calculation. The results showed that the combination of SCI-PCM model and ab initio calculation could give excellent agreements with FT-IR spectra of title compound in solutions.

  3. DFT calculations on atom-specific electronic properties of G/SiC(0001)

    NASA Astrophysics Data System (ADS)

    Kajihara, M.; Suzuki, T.; Shahed, S. M. F.; Komeda, T.; Minamitani, E.; Watanabe, S.

    2016-05-01

    We investigate the atom-specific interfacial electronic properties of the epitaxial graphene on Si-terminated SiC substrate using density functional theory (DFT) calculation with van der Waals interaction correction, focusing on the dependency of the local electronic state on the chemical environment. The band structure projected on the respective atomic orbitals of the carbon atoms in the buffer layer and uppermost Si atoms demonstrates that the dangling bonds of these atoms form band structures around the Fermi level. The contribution of each atom to the dangling bond states strongly depends on the chemical environment, i.e., the presence/absence of the interlayer Si-C covalent bond. This difference also affects the atom-specific local density of states of the top-layer graphene through its interaction with the substrate/buffer layer. We demonstrate that the bias voltage dependency of the scanning tunneling spectroscopy (STS) mapping image clearly reflects the presence of the dangling bonds of the buffer layer carbon or uppermost Si atom in the substrate, which would enable the detection of the buried dangling bond with an atomic spatial resolution via STS.

  4. Performance of DFT Methods in the Calculation of Optical Spectra of TCF-Chromophores

    SciTech Connect

    Andzelm, Jan; Rinderspacher, Berend C.; Rawlett, Adam M.; Dougherty, Joseph; Baer, Roi; Govind, Niranjan

    2009-10-01

    We present electronic structure calculations of the ultraviolet/visible (UV-Vis) spectra of highly active push-pull chromophores containing tricyanofuran (TCF) acceptor group. In particular, we have applied the recently developed long-range corrected Baer-Neuhauser-Livshits (BNL) exchange-correlation functional. The performance of this functional compares favorably with other density functional theory (DFT) approaches, including the CAM-B3LYP functional. The accuracy of UV-Vis results for these molecules is best at low values of attenuation parameters (γ) for both BNL and CAM-B3LYP functionals. The optimal value of γ is different for the charge-transfer (CT) and π-π* excitations. The BNL and PBE0 exchange correlation functionals capture the CT states particularly well while the π-π* excitations are less accurate and system dependent. Chromophore conformations, which considerably affect the molecular hyperpolarizability, do not significantly influence the UV-Vis spectra on average. As expected, the color of chromophores is a sensitive function of modifications to its conjugated framework, and is not significantly affected by increasing aliphatic chain length linking a chromophore to a polymer. For selected push-pull aryl-chromophores, we find a significant dependence of absorption spectra on the strength of diphenylaminophenyl donors.

  5. Cobalt-mediated radical polymerization of acrylonitrile: kinetics investigations and DFT calculations.

    PubMed

    Debuigne, Antoine; Michaux, Catherine; Jérôme, Christine; Jérôme, Robert; Poli, Rinaldo; Detrembleur, Christophe

    2008-01-01

    The successful controlled homopolymerization of acrylonitrile (AN) by cobalt-mediated radical polymerization (CMRP) is reported for the first time. As a rule, initiation of the polymerization was carried out starting from a conventional azo-initiator (V-70) in the presence of bis(acetylacetonato)cobalt(II) ([Co(acac)(2)]) but also by using organocobalt(III) adducts. Molar concentration ratios of the reactants, the temperature, and the solvent were tuned, and the effect of these parameters on the course of the polymerization is discussed in detail. The best level of control was observed when the AN polymerization was initiated by an organocobalt(III) adduct at 0 degrees C in dimethyl sulfoxide. Under these conditions, poly(acrylonitrile) with a predictable molar mass and molar mass distribution as low as 1.1 was prepared. A combination of kinetic data, X-ray analyses, and DFT calculations were used to rationalize the results and to draw conclusions on the key role played by the solvent molecules in the process. These important mechanistic insights also permit an explanation of the unexpected "solvent effect" that allows the preparation of well-defined poly(vinyl acetate)-b-poly(acrylonitrile) by CMRP.

  6. A silver complex with ibuprofen: Synthesis, solid state characterization, DFT calculations and antibacterial assays

    NASA Astrophysics Data System (ADS)

    Silva, Irlene Maria Pereira e.; Profirio, Daniel de Moraes; de Paiva, Raphael Enoque Ferraz; Lancellotti, Marcelo; Formiga, André Luiz Barboza; Corbi, Pedro Paulo

    2013-10-01

    The present work describes the synthesis of a silver(I) complex with the non-steroidal anti-inflammatory ibuprofen, Ag-ibu. Elemental and thermal analyses indicate a 1:1 metal/ligand composition. Thermogravimetric analysis shows that Ag-ibu decomposition starts at 180 °C, and ends at 400 °C (mass loss 64.6%; calcd. 65.5%). UV/Vis kinetic measurements suggest the decomposition of Ag-ibu in dimethyl sulfoxide, with the appearance of a broad band in the spectrum of the complex in the range 300-500 nm. Infrared and solid state 13C NMR spectra show the coordination of ibuprofen to silver through the carboxylate group. The DFT calculations led us to propose a dimeric silver bridging structure for the complex. Biological studies show the antibacterial activity of the Ag-ibu complex against Gram-positive and Gram-negative bacterial strains, with MIC values ranging from 6.25 to 12.5 μg mL-1.

  7. DFT calculation and experimental investigation of Mn doping effect in Fe16N2

    NASA Astrophysics Data System (ADS)

    Jiang, Yanfeng; Himmetoglu, Burak; Cococcioni, Matteo; Wang, Jian-Ping

    2016-05-01

    An effective dopant to improve the thermal stability of a Fe16N2 permanent magnet is proposed in this paper. It is demonstrated both theoretically and experimentally that manganese is a promising candidate as dopant in Fe16N2 magnet to improve the thermal stability. Firstly, the atomic moments of the Fe ions with respect to N is investigated by using first-principles DFT calculation. Two possible candidates of elements, including Co and Mn, are compared in terms of its preferred position and magnetic coupling mode. It is found that Mn prefers Fe1 position and ferromagnetic coupling in the Fe16N2 lattice. So Mn is considered as a promising dopant in Fe16N2 magnet to improve its thermal stability. Based on theoretical results, experiments are conducted by a cold-crucible method to prepare (Fe1-xMnx) N bulk samples. The samples are thermal treated at different temperatures to observe their thermal stabilities. X-ray diffraction (XRD) and vibrating sample magnetometer (VSM) are characterized on the samples.

  8. Interaction evaluation of silver and dithizone complexes using DFT calculations and NMR analysis.

    PubMed

    Wasukan, Nootcharin; Srisung, Sujittra; Kuno, Mayuso; Kulthong, Kornphimol; Maniratanachote, Rawiwan

    2015-10-01

    Silver has distinct antibacterial properties and has been used as a component of commercial products with many applications. An increasing number of commercial products cause risks of silver effects for human and environment such as the symptoms of Argyria and the release of silver to the environment. Therefore, the detection of silver in the aquatic environment is important. The colorimetric chemosensor is designed by the basic of ligand interactions with metal ion, leading to the change of signals for the naked-eyes which is very useful method to this application. Dithizone ligand is considered as one of the effective chelating reagents for metal ions due to its high selectivity and sensitivity of a photochromic reaction for silver as well as the linear backbone of dithizone affords the rotation of various isomeric forms. The present study is focused on the conformation and interaction of dithizone with silver using density functional theory (DFT). The interaction parameters were determined in term of binding energy of complexes and the geometry optimization, frequency of the structures and calculation of binding energies using density functional approaches B3LYP and the 6-31G(d,p) basis set. Moreover, the interaction of silver-dithizone complexes was supported by UV-Vis spectroscopy, FT-IR spectrum that were simulated by using B3LYP/6-31G(d,p) and (1)H NMR spectra calculation using B3LYP/6-311+G(2d,p) method compared with the experimental data. The results showed the ion exchange interaction between hydrogen of dithizone and silver atom with minimized binding energies of silver-dithizone interaction. Therefore, the results can be the useful information for determination of complex interaction using the analysis of computer simulations. PMID:26001102

  9. Vibrational spectroscopic studies and DFT calculations on tribromoacetate and tribromoacetic acid in aqueous solution.

    PubMed

    Rudolph, Wolfram W; Irmer, Gert

    2011-09-01

    Aqueous solutions of sodium tribromoacetate (NaCBr3CO2) and its corresponding acid (CBr3COOH) have been studied using Raman and infrared spectroscopy. The spectra of the species in solution were assigned according to symmetry Cs. Characteristic bands of CBr3CO2-(aq) and the tribromoacetic acid, CBr3COOH(aq), are discussed. For the hydrated anion, the CO2 group, the symmetric CO2 stretching mode at 1332 cm(-1) and the asymmetric stretching mode at 1651 cm(-1) are characteristic while the CO mode at 1730 cm(-1) is characteristic for the spectra of the acid. The stretching mode, νC-C at 912cm(-1) for CBr3CO2-(aq) is 10 cm(-1) lower in the anion compared with that of the acid. These characteristic modes are compared to those in acetate, CH3CO2-(aq). Coupling of the modes are fairly extensive and therefore DFT calculations have been carried out in order to compare the measured spectra with the calculated ones. The geometrical parameters such as bond length and bond angles of the tribromoacetate, and tribromoacetic acid have been obtained and may be compared with the ones published for other acetates and their conjugated acids. CBr3COOH(aq) is a moderately strong acid and the pKa value derived from quantitative Raman measurements is equal to -0.23 at 23°C. The deuterated acid CBr3COOD in heavy water has been measured as well and the assignments were given.

  10. Characterizing the Solvated Structure of Photoexcited [Os(terpy)₂](2+) with X-ray Transient Absorption Spectroscopy and DFT Calculations.

    PubMed

    Zhang, Xiaoyi; Pápai, Mátyás; Møller, Klaus B; Zhang, Jianxin; Canton, Sophie E

    2016-01-01

    Characterizing the geometric and electronic structures of individual photoexcited dye molecules in solution is an important step towards understanding the interfacial properties of photo-active electrodes. The broad family of "red sensitizers" based on osmium(II) polypyridyl compounds often undergoes small photo-induced structural changes which are challenging to characterize. In this work, X-ray transient absorption spectroscopy with picosecond temporal resolution is employed to determine the geometric and electronic structures of the photoexcited triplet state of [Os(terpy)₂](2+) (terpy: 2,2':6',2″-terpyridine) solvated in methanol. From the EXAFS analysis, the structural changes can be characterized by a slight overall expansion of the first coordination shell [OsN₆]. DFT calculations supports the XTA results. They also provide additional information about the nature of the molecular orbitals that contribute to the optical spectrum (with TD-DFT) and the near-edge region of the X-ray spectra. PMID:26907233

  11. Characterization of the species-dependent ketoprofen/albumin binding modes by induced CD spectroscopy and TD-DFT calculations.

    PubMed

    Tedesco, Daniele; Pistolozzi, Marco; Zanasi, Riccardo; Bertucci, Carlo

    2015-08-10

    The stereospecificity of high-affinity biorecognition phenomena at the basis of the activity of drugs is an important topic of active research in medicinal chemistry. The binding of drugs to their targets or to carrier proteins may lead to the onset of an induced circular dichroism (ICD) signal, which can be detected experimentally. Quantum mechanical (QM) calculations based on density functional theory (DFT) and its time-dependent formulation (TD-DFT) can be used to determine the theoretical chiroptical response of all the possible conformations of drugs bound to their hosts; by comparison with the experimental ICD spectra of drug-host complexes, this approach can lead to the identification of possible binding modes in the absence of X-ray crystallography or NMR data. The present article reports the application of experimental electronic circular dichroism (ECD) spectroscopy, DFT conformational analysis and TD-DFT calculations to the investigation of the binding modes of (S)-ketoprofen to serum albumins. The peculiar species-dependent ICD spectra observed for the binding of (S)-ketoprofen to different serum albumins can be explained by the selection of different mutual arrangements of the phenyl moieties inside the binding pocket. Such structural elucidations contribute to a better understanding of the changes in the pharmacokinetic and pharmacodynamic profiles of drugs among different species.

  12. (E)-2-[(2-Bromophenylimino)methyl]-5-methoxyphenol: X-ray and DFT-calculated structures

    SciTech Connect

    Kosar, B. Albayrak, C.; Odabasoglu, M.; Bueyuekguengoer, O.

    2010-12-15

    The crystal structure of (E)-2-[(2-Bromophenylimino)methyl]-5-methoxyphenol is determined by using X-ray diffraction and then the molecular structure is investigated with density functional theory (DFT). X-Ray study shows that the title compound has a strong intramolecular O-H-N hydrogen bond and three dimensional crystal structure is primarily determined by C-H-{pi} and weak van der Waals interactions. The strong O-H-N bond is an evidence of the preference for the phenol-imine tautomeric form in the solid state. Optimized molecular geometry is calculated with DFT at the B3LYP/6-31G(d,p) level. The IR spectra of compound were recorded experimentally and calculated to compare with each other. The results from both experiment and theoretical calculations are compared in this study.

  13. Molecular structure, spectroscopic properties (FT-IR, Micro-Raman, and UV-vis), and DFT calculations of minaprine

    NASA Astrophysics Data System (ADS)

    Gökce, H.; Bahçeli, S.

    2014-07-01

    Molecular geometry, experimental vibrational wavenumbers, electronic properties, and quantum chemical calculations of minaprine (C17H22N4O · 2HCl), (with synonym, dihydrochloride salt of N-(4-methyl-6-phenyl-3-pyridazinyl)-4-morpholineethamine) which is widely used as a psychotropic drug at medicinal treatment, in the ground state by using density functional theory (DFT/B3LYP) method with 6-31++G(d,p) basis set have been presented for the first time. The comparison of the observed fundamental vibrational frequencies were in a very good agreement with the experimental data. Furthermore, UV-vis TD-DFT calculations, the highest occupied molecular orbitals (HOMO-1, HOMO), lowest unoccupied molecular orbitals (LUMO, LUMO + 1), molecular electrostatic potential (MEP) surface, atomic charges and thermodynamic properties of minaprine molecule have been theoretically calculated and simulated at the mentioned level.

  14. A cobalt (II) complex with 6-methylpicolinate: Synthesis, characterization, second- and third-order nonlinear optical properties, and DFT calculations

    NASA Astrophysics Data System (ADS)

    Altürk, Sümeyye; Avcı, Davut; Tamer, Ömer; Atalay, Yusuf; Şahin, Onur

    2016-11-01

    A cobalt(II) complex of 6-methylpicolinic acid, [Co(6-Mepic)2(H2O)2]·2H2O, was prepared and fully determined by single crystal X-ray crystal structure analysis as well as FT-IR, FT-Raman. UV-vis spectra were recorded within different solvents, to illustrate electronic transitions and molecular charge transfer within complex 1. The coordination sphere of complex 1 is a distorted octahedron according to single crystal X-ray results. Moreover, DFT (density functional theory) calculations with HSEH1PBE/6-311 G(d,p) level were carried out to back up the experimental results, and form base for future work in advanced level. Hyperconjugative interactions, intramolecular charge transfer (ICT), molecular stability and bond strength were researched by the using natural bond orbital (NBO) analysis. X-ray and NBO analysis results demonsrate that O-H···O hydrogen bonds between the water molecules and carboxylate oxygen atoms form a 2D supramolecular network, and also adjacent 2D networks connected by C-H···π and π···π interactions to form a 3D supramolecular network. Additionally, the second- and third-order nonlinear optical parameters of complex 1 were computed at DFT/HSEH1PBE/6-311 G(d,p) level. The refractive index (n) was calculated by using the Lorentz-Lorenz equation in order to investigate polarization behavior of complex 1 in different solvent polarities. The first-order static hyperpolarizability (β) value is found to be lower than pNA value because of the inversion symmetry around Co (II). But the second-order static hyperpolarizability (γ) value is 2.45 times greater than pNA value (15×10-30 esu). According to these results, Co(II) complex can be considered as a candidate to NLO material. Lastly molecular electrostatic potential (MEP), frontier molecular orbital energies and related molecular parameters for complex 1 were evaluated.

  15. Identification of tert-Butyl Cations in Zeolite H-ZSM-5: Evidence from NMR Spectroscopy and DFT Calculations.

    PubMed

    Dai, Weili; Wang, Chuanming; Yi, Xianfeng; Zheng, Anmin; Li, Landong; Wu, Guangjun; Guan, Naijia; Xie, Zaiku; Dyballa, Michael; Hunger, Michael

    2015-07-20

    Experimental evidence for the presence of tert-butyl cations, which are important intermediates in acid-catalyzed heterogeneous reactions, on solid acids has still not been provided to date. By combining density functional theory (DFT) calculations with (1)H/(13)C magic-angle-spinning NMR spectroscopy, the tert-butyl cation was successfully identified on zeolite H-ZSM-5 upon conversion of isobutene by capturing this intermediate with ammonia. PMID:26096840

  16. Mechanism of Formation of Copper(II) Chloro Complexes Revealed by Transient Absorption Spectroscopy and DFT/TDDFT Calculations.

    PubMed

    Mereshchenko, Andrey S; Olshin, Pavel K; Karabaeva, Kanykey E; Panov, Maxim S; Wilson, R Marshall; Kochemirovsky, Vladimir A; Skripkin, Mikhail Yu; Tveryanovich, Yury S; Tarnovsky, Alexander N

    2015-07-16

    Copper(II) complexes are extremely labile with typical ligand exchange rate constants on the order of 10(6)-10(9) M(-1) s(-1). As a result, it is often difficult to identify the actual formation mechanism of these complexes. In this work, using UV-vis transient absorption when probing in a broad time range (20 ps to 8 μs) in conjunction with DFT/TDDFT calculations, we studied the dynamics and underlying reaction mechanisms of the formation of extremely labile copper(II) CuCl4(2-) chloro complexes from copper(II) CuCl3(-) trichloro complexes and chloride ions. These two species, produced via photochemical dissociation of CuCl4(2-) upon 420 nm excitation into the ligand-to-metal-charge-transfer electronic state, are found to recombine into parent complexes with bimolecular rate constants of (9.0 ± 0.1) × 10(7) and (5.3 ± 0.4) × 10(8) M(-1) s(-1) in acetonitrile and dichloromethane, respectively. In dichloromethane, recombination occurs via a simple one-step addition. In acetonitrile, where [CuCl3](-) reacts with the solvent to form a [CuCl3CH3CN](-) complex in less than 20 ps, recombination takes place via ligand exchange described by the associative interchange mechanism that involves a [CuCl4CH3CN](2-) intermediate. In both solvents, the recombination reaction is potential energy controlled. PMID:26079181

  17. 47 CFR 36.605 - Calculation of safety net additive.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Calculation of safety net additive. 36.605... § 36.605 Calculation of safety net additive. (a) “Safety net additive support.” A rural incumbent local exchange carrier shall receive safety net additive support if it satisfies the conditions set forth...

  18. Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...

  19. p-Tolylimido rhenium(V) complexes - synthesis, X-ray studies, spectroscopic characterization, DFT calculations and catalytic activity.

    PubMed

    Machura, Barbara; Gryca, Izabela; Małecki, Jan Grzegorz; Alonso, Francisco; Moglie, Yanina

    2014-02-14

    Novel p-tolylimido rhenium(V) complexes trans-(Cl,Cl)-[Re(p-NC6H4CH3)Cl2(py-2-COO)(PPh3)]·MeCN (1a), trans-(Cl,Cl)-[Re(p-NC6H4CH3)Cl2(py-2-COO)(PPh3)] (1b), trans-(Br,Br)-[Re(p-NC6H4CH3)Br2(py-2-COO)(PPh3)] (2), cis-(Cl,Cl)-[Re(p-NC6H4CH3)Cl2(py-2-COO)(PPh3)] (3), cis-(Br,Br)-[Re(p-NC6H4CH3)Br2(py-2-COO)(PPh3)]·H2O (4), trans-(Cl,Cl)-[Re(p-NC6H4CH3)Cl2(OMe)] (5) and trans-(Br,Br)-[Re(p-NC6H4CH3)Br2(OMe)(PPh3)2]·1/2H2O (6) were synthesized. The compounds were identified by elemental analysis, IR, NMR ((1)H, (13)C and (31)P), UV-Vis spectroscopy and X-ray crystallography. Calculations at the DFT level were undertaken in order to elucidate the structural, spectroscopic and bonding properties of the trans-(Cl,Cl) and cis-(Cl,Cl) isomers of [Re(p-NC6H4CH3)Cl2(py-2-COO)(PPh3)]. In the first step, extended tests of the ability of different DFT methods (B3LYP, BP86, and PBE1PBE) were performed to find the best overall performer in describing the geometry of the imido Re(v) complexes; then, the electronic spectra of the trans and cis isomers of [Re(p-NC6H4CH3)Cl2(py-2-COO)(PPh3)] were investigated at the TDDFT level employing the PBE1PBE functional. Additional information about bonding in the compounds [Re(p-NC6H4CH3)Cl2(py-2-COO)(PPh3)] was obtained by NBO analysis. The catalytic activity of the complexes incorporating the picolinate ligand was studied and compared in the synthesis of N-substituted ethyl glycine esters from ethyl diazoacetate and amines.

  20. Molecular structure (monomeric and dimeric) and hydrogen bonds in 5-benzyl 2-thiohydantoin studied by FT-IR and FT-Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Deval, Vipin; Kumar, Amit; Gupta, Vineet; Sharma, Anamika; Gupta, Archana; Tandon, Poonam; Kunimoto, Ko-Ki

    2014-11-01

    In the present work the structural and spectral characteristics of 5-benzyl-2-thiohydantoin (5-BTH) have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G++(d,p) basis set. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-vis spectrum of the compound was recorded in methanol solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using PCM and 6-311++G(d,p) basis set. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied.

  1. Anti-inflammatory drugs interacting with Zn (II) metal ion based on thiocyanate and azide ligands: Synthesis, spectroscopic studies, DFT calculations and antibacterial assays

    NASA Astrophysics Data System (ADS)

    Chiniforoshan, Hossein; Tabrizi, Leila; Hadizade, Morteza; Sabzalian, Mohammad R.; Chermahini, Alireza Najafi; Rezapour, Mehdi

    2014-07-01

    Zinc (II) complexes with non-steroidal anti-inflammatory drugs (NSAIDs) naproxen (nap) and ibuprofen (ibu) were synthesized in the presence of nitrogen donor ligands (thiocyanate or azide). The complexes were characterized by elemental analysis, FT-IR, 1H NMR and UV-Vis spectroscopes. The binding modes of the ligands in complexes were established by means of molecular modeling of the complexes, and calculation of their IR, NMR and absorption spectra at DFT (TDDFT)/B3LYP level were studied. The experimental and calculated data verified monodentate binding through the carboxylic oxygen atoms of anti-inflammatory drugs in the zinc complexes. The calculated 1H, FT-IR and UV-Vis data are in better agreement with the experimental results, and confirm the predicted tetrahedral structures for the Zn (II) complexes. In addition to DFT calculations of complexes, natural bond orbital (NBO) was performed at B3LYP/6-31+G(d,p) level of theory. Biological studies showed the antibacterial activity of zinc complexes against Gram-positive and Gram-negative bacterial strains.

  2. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase

    PubMed Central

    Li, Yanwei; Zhang, Ruiming; Du, Likai; Zhang, Qingzhu; Wang, Wenxing

    2016-01-01

    The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study “multiple” conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case. PMID:27556449

  3. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase.

    PubMed

    Li, Yanwei; Zhang, Ruiming; Du, Likai; Zhang, Qingzhu; Wang, Wenxing

    2016-01-01

    The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case. PMID:27556449

  4. Experimental approach to the anion problem in DFT calculation of the partial charge transfer during adsorption at electrochemical interfaces

    NASA Astrophysics Data System (ADS)

    Marichev, V. A.

    2005-08-01

    In DFT calculation of the charge transfer (Δ N), anions pose a special problem since their electron affinities are unknown. There is no method for calculating reasonable values of the absolute electronegativity ( χA) and chemical hardness ( ηA) for ions from data of species themselves. We propose a new approach to the experimental measurement of χA at the condition: Δ N = 0 at which η values may be neglected and χA = χMe. Electrochemical parameters corresponding to this condition may be obtained by the contact electric resistance method during in situ investigation of anion adsorption in the particular system anion-metal.

  5. Computational calculation of equilibrium constants: addition to carbonyl compounds.

    PubMed

    Gómez-Bombarelli, Rafael; González-Pérez, Marina; Pérez-Prior, María Teresa; Calle, Emilio; Casado, Julio

    2009-10-22

    Hydration reactions are relevant for understanding many organic mechanisms. Since the experimental determination of hydration and hemiacetalization equilibrium constants is fairly complex, computational calculations now offer a useful alternative to experimental measurements. In this work, carbonyl hydration and hemiacetalization constants were calculated from the free energy differences between compounds in solution, using absolute and relative approaches. The following conclusions can be drawn: (i) The use of a relative approach in the calculation of hydration and hemiacetalization constants allows compensation of systematic errors in the solvation energies. (ii) On average, the methodology proposed here can predict hydration constants within +/- 0.5 log K(hyd) units for aldehydes. (iii) Hydration constants can be calculated for ketones and carboxylic acid derivatives within less than +/- 1.0 log K(hyd), on average, at the CBS-Q level of theory. (iv) The proposed methodology can predict hemiacetal formation constants accurately at the MP2 6-31++G(d,p) level using a common reference. If group references are used, the results obtained using the much cheaper DFT-B3LYP 6-31++G(d,p) level are almost as accurate. (v) In general, the best results are obtained if a common reference for all compounds is used. The use of group references improves the results at the lower levels of theory, but at higher levels, this becomes unnecessary. PMID:19761202

  6. Computational Calculation of Equilibrium Constants: Addition to Carbonyl Compounds

    NASA Astrophysics Data System (ADS)

    Gómez-Bombarelli, Rafael; González-Pérez, Marina; Pérez-Prior, María Teresa; Calle, Emilio; Casado, Julio

    2009-09-01

    Hydration reactions are relevant for understanding many organic mechanisms. Since the experimental determination of hydration and hemiacetalization equilibrium constants is fairly complex, computational calculations now offer a useful alternative to experimental measurements. In this work, carbonyl hydration and hemiacetalization constants were calculated from the free energy differences between compounds in solution, using absolute and relative approaches. The following conclusions can be drawn: (i) The use of a relative approach in the calculation of hydration and hemiacetalization constants allows compensation of systematic errors in the solvation energies. (ii) On average, the methodology proposed here can predict hydration constants within ± 0.5 log Khyd units for aldehydes. (iii) Hydration constants can be calculated for ketones and carboxylic acid derivatives within less than ± 1.0 log Khyd, on average, at the CBS-Q level of theory. (iv) The proposed methodology can predict hemiacetal formation constants accurately at the MP2 6-31++G(d,p) level using a common reference. If group references are used, the results obtained using the much cheaper DFT-B3LYP 6-31++G(d,p) level are almost as accurate. (v) In general, the best results are obtained if a common reference for all compounds is used. The use of group references improves the results at the lower levels of theory, but at higher levels, this becomes unnecessary.

  7. DFT calculations of electronic and optical properties of SrS with LDA, GGA and mGGA functionals

    NASA Astrophysics Data System (ADS)

    Sharma, Shatendra; Sharma, Jyotsna; Sharma, Yogita

    2016-05-01

    The theoretical investigations of electronic and optical properties of SrS are made using the first principle DFT calculations. The calculations are performed for the local-density approximation (LDA), generalized gradient approximation (GGA) and for an alternative form of GGA i.e. metaGGA for both rock salt type (B1, Fm3m) and cesium chloride (B2, Pm3m) structures. The band structure, density of states and optical spectra are calculated under various available functional. The calculations with LDA and GGA functional underestimate the values of band gaps with all functional, however the values with mGGA show reasonably good agreement with experimental and those calculated by using other methods.

  8. Calculation of low bandgap homopolymers: Comparison of TD-DFT methods with experimental oligomer series

    NASA Astrophysics Data System (ADS)

    Oliveira, Eliezer Fernando; Roldao, Juan Carlos; Milián-Medina, Begoña; Lavarda, Francisco Carlos; Gierschner, Johannes

    2016-02-01

    The performance of different DFT functionals (B3LYP, BHLYP, CAM-B3LYP, M06HF) on the prediction of vertical transition energies Evert of low bandgap homopolymers is tested against the experimentally available oligomer series (thienopyrazines and thienothiophenes). This allows for a detailed and accurate comparison on the consistency of DFT methods for chainlength evolution and polymer limit prediction, and for an understanding of geometry and time-dependent contributions to Evert by combinatorial analysis. Together with former studies on wide/medium bandgap polymers and low bandgap co-polymers, our results on low bandgap homopolymers suggest offset-corrected M06HF as the most viable method for time inexpensive and reliable prediction of semiconducting polymers at the moment.

  9. Correction: Unexpected higher stabilisation of two classical antiaromatic frameworks with a ruthenium fragment compared to the osmium counterpart: origin probed by DFT calculations.

    PubMed

    Wu, Jingjing; Hao, Yulei; An, Ke; Zhu, Jun

    2016-01-25

    Correction for 'Unexpected higher stabilisation of two classical antiaromatic frameworks with a ruthenium fragment compared to the osmium counterpart: origin probed by DFT calculations' by Jingjing Wu et al., Chem. Commun., 2016, 52, 272-275. PMID:26699929

  10. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

    2015-02-01

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  11. A systematic study on hydrogen bond interactions in sulfabenzamide: DFT calculations of the N-14, O-17, and H-2 NQR parameters.

    PubMed

    Nozad, Ahmad G; Najafi, Hamidreza; Meftah, Sakineh; Aghazadeh, Mustafa

    2009-02-01

    A systematic computational study was carried out to characterize the hydrogen bond, HB, interactions of sulfabenzamide crystal structure by DFT calculations of electric field gradient, EFG, tensors at the sites of 14N, 17O, and 2H nuclei. The computations were performed with the B3LYP and B3PW91 DFT methods and 6-311+G and 6-311++G* standard basis sets using the Gaussian 98 package. To perform the calculations, a hydrogen-bonded heptameric cluster of sulfabenzamide was created by X-ray coordinates where the hydrogen atom positions were optimized and the EFG tensors were calculated for the target molecule. Additional optimization and EFG calculations were also performed for crystalline monomer and an isolated gas-phase sulfabenzamide. The calculated EFG tensors were converted to the experimentally measurable nuclear quadrupole resonance, NQR, parameters: quadrupole coupling constant, C(Q), and asymmetry parameter, eta(Q). The results reveal that the geometrical and NQR parameters of the optimized isolated gas-phase and crystalline phase are different. In addition, the difference between the calculated NQR parameters of the monomer and the target molecule shows how much H-bonding interactions affect the EFG tensors of each nucleus. The evaluated NQR parameters reveal that due to the contribution of the target molecule to N-H...O and C-H...O hydrogen bond interactions, the EFG tensors at the sites of N1, O3 and H1 undergo significant changes from monomer to the target molecule in cluster. These features reveal the major role of N-H...O type intermolecular HBs in cluster model of sulfabenzamide which the presence of these interactions can lead to polymorphism directly related to the drug activity and related properties.

  12. The spectroscopic properties of anticancer drug Apigenin investigated by using DFT calculations, FT-IR, FT-Raman and NMR analysis

    NASA Astrophysics Data System (ADS)

    Mariappan, G.; Sundaraganesan, N.; Manoharan, S.

    2012-09-01

    The FT-Raman and FT-Infrared spectra of solid Apigenin sample were measured in order to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm-1 and 4000-400 cm-1, respectively. The recorded FT-IR and FT-Raman spectral measurements favor the calculated (by B3LYP/6-31G(d,p) method) structural parameters which are further supported by spectral simulation. Additional support is given by the collected 1H and 13C NMR spectra recorded with the sample dissolved in DMSO. The predicted chemical shifts at the B3LYP/6-31G(d) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. The UV-visible absorption spectra of the compound that dissolved in Ethanol, Methanol and DMSO were recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and atomic charges of the title compound were investigated using theoretical calculations. The results are discussed herein and compared with similar molecules whenever appropriate.

  13. FT-IR and Raman spectra and vibrational investigation of bis (4-acetylanilinium) hexachlorostannate using DFT (B3LYP) calculation

    NASA Astrophysics Data System (ADS)

    Tarchouna, S.; Chaabane, I.; Rahaiem, A. Ben

    2016-09-01

    4-acetylanilinium was used as a ligand for the synthesis of the organic/inorganic compound bis (4-acetylanilinium) hexachlorostannate. Vibrational study in the solid state was performed by FT-Raman of the free 4-acetylanilinium ligand C8H9ON+ and by FT-IR and FT-Raman spectroscopies of the [C8H10NO]2 SnCl6 compound. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was discussed. The structure of the [C8H10NO]2SnCl6 was optimized by density functional theory (DFT) using B3LYP method and shows that the calculated values obtained by B3LYP/LanL2DZ basis are in a better agreement with the experimental data reported by Song et al. (2011) [1] than those obtained by B3LYP/LanL2MB basis. The vibrational frequencies are calculated using density functional theory (DFT) with the B3LYP/LanL2DZ basis, and scaled by various factors. Root mean square (RMS) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal.

  14. Synthesis, mass spectral characterization, NMR analyses, and DFT calculations of 1-desoxymaquindox and 4-desoxymaquindox

    NASA Astrophysics Data System (ADS)

    Zhang, Jiaheng; Peng, Qingrong; Zhang, Suxia; Li, Yubo; Li, Songqing; Gao, Haixiang; Zhou, Zhiqiang

    2011-02-01

    Maquindox, 3-methyl-2-acetylquinoxaline-1,4-dioxide, is a quinoxaline-N,N-dioxide used in veterinary medicine as a feed additive. 1-Desoxymaquindox and 4-desoxymaquindox, two novel deoxidized metabolites of maquindox are synthesized from their parent drug. This study deals with the structural and spectral properties of the maquindox metabolites by employing experimental and theoretical methods. The investigation, using ultra-performance liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry, shows independent proof of the structures. Gauge-including atomic orbital NMR chemical shifts are calculated for isomeric quinoxaline metabolite pairs and several different parameters (correlation coefficient, mean absolute error, and corrected mean absolute error) are investigated. Comparison of the experimental and calculated 1H and 13C NMR chemical shifts allows the reliable assignment of the isomeric quinoxaline compound pairs.

  15. Electronic structure of interstitial hydrogen in lutetium oxide from DFT+U calculations and comparison study with μ SR spectroscopy

    NASA Astrophysics Data System (ADS)

    da Silva, E. Lora; Marinopoulos, A. G.; Vieira, R. B. L.; Vilão, R. C.; Alberto, H. V.; Gil, J. M.; Lichti, R. L.; Mengyan, P. W.; Baker, B. B.

    2016-07-01

    The electronic structure of hydrogen impurity in Lu2O3 was studied by first-principles calculations and muonium spectroscopy. The computational scheme was based on two methods which are well suited to treat defect calculations in f -electron systems: first, a semilocal functional of conventional density-functional theory (DFT) and secondly a DFT+U approach which accounts for the on-site correlation of the 4 f electrons via an effective Hubbard-type interaction. Three different types of stable configurations were found for hydrogen depending upon its charge state. In its negatively charged and neutral states, hydrogen favors interstitial configurations residing either at the unoccupied sites of the oxygen sublattice or at the empty cube centers surrounded by the lanthanide ions. In contrast, the positively charged state stabilized only as a bond configuration, where hydrogen binds to oxygen ions. Overall, the results between the two methods agree in the ordering of the formation energies of the different impurity configurations, though within DFT+U the charge-transition (electrical) levels are found at Fermi-level positions with higher energies. Both methods predict that hydrogen is an amphoteric defect in Lu2O3 if the lowest-energy configurations are used to obtain the charge-transition, thermodynamic levels. The calculations of hyperfine constants for the neutral interstitial configurations show a predominantly isotropic hyperfine interaction with two distinct values of 926 MHz and 1061 MHz for the Fermi-contact term originating from the two corresponding interstitial positions of hydrogen in the lattice. These high values are consistent with the muonium spectroscopy measurements which also reveal a strongly isotropic hyperfine signature for the neutral muonium fraction with a magnitude slightly larger (1130 MHz) from the ab initio results (after scaling with the magnetic moments of the respective nuclei).

  16. Chiral Dodecanuclear Palladium(II) Thio Cluster: Synthesis, Structure, and Formation Mechanism Explored by ESI-MS and DFT Calculations.

    PubMed

    Lin, Zheng-Guo; Fan, Lin-Yuan; Kondinski, Aleksandar; Vankova, Nina; Heine, Thomas; Chen, Bao-Kuan; Haider, Ali; Wang, Bo; Kortz, Ulrich; Hu, Chang-Wen

    2016-08-15

    The chiral dodecanuclear palladium(II) thio cluster LaPd12(C3H5NO2S)3(C3H6NO2S)21 (1) was prepared by reacting l-cysteine (l-Cys) with PdCl2 and La2O3 in aqueous solution under carefully controlled conditions. Compound 1 was structurally characterized by single-crystal XRD, TGA, IR, UV-vis, (13)C NMR, and CD spectroscopy. Insight into the dimerization process of 1 was obtained by ESI-MS and DFT calculations. PMID:27454534

  17. Crystal structure, vibrational studies, optical properties and DFT calculations of 2-amino-5-diethyl-aminopentanium tetrachlorocadmate (II).

    PubMed

    Baklouti, Yosra; chaari, Najla; Feki, Habib; Chniba-Boudjada, Nassira; Zouari, Fatma

    2015-02-01

    Single crystals of a new organic-inorganic compound (C9H24N2) CdCl4 were grown by the slow evaporation technique and characterized by X-ray diffraction, infrared absorption Raman spectroscopy scattering, optical absorption, differential scanning calorimetry (DSC) analysis and dielectric measurements. The title compound belongs to the orthorhombic space group Pbca with the following unit cell parameters: a=11.397(7), b=13.843(4), c=22.678(5)Å and Z=8. In crystal structure, the tetrachlorocadmate anion is connected to organic cations through N-H⋯Cl hydrogen bonds. Theoretical calculations were performed using density functional theory (DFT) with the B3LYP/LanL2DZ level of theory for studying the molecular structure and vibrational spectra of the title compound. Good consistency is found between the calculated results and the experimental structure, IR, and Raman spectra. The detailed interpretation of the vibrational modes was carried out on the basis on our DFT calculations as primary source of assignment and by comparison with spectroscopic studies of similar compounds. The optical properties were investigated by optical absorption and show three bands at 300, 329 and 513 nm. PMID:25311521

  18. Synthesis, spectroscopic characterization and DFT calculations of N-Methyl-2-(2ʹ-hydroxyphenyl)benzimidazole derivatives

    NASA Astrophysics Data System (ADS)

    Saral, Hasan; Özdamar, Özgür; Uçar, İbrahim; Bekdemir, Yunus; Aygün, Muhittin

    2016-01-01

    1-Methyl-2-(2ʹ-hydroxyphenyl)benzimidazole (1) and 1-Methyl-2-(2ʹ-hydroxy-4ʹ-methylphenyl)benzimidazole (2) compounds have been synthesized and characterized by XRD, IE-MS, FT-IR, UV-Vis and 1H, 13C NMR techniques. The crystal structure of both compounds is stabilized with very strong O-H … N hydrogen-bond and π-π interactions. In the compound 1, an infinite chain structure with a trans-zigzag type was formed along the crystallographic [101] direction. Quantum mechanical calculations of energies, geometries, vibrational wavenumbers, NMR and electronic transitions were carried out by DFT using B3LYP functional combined with 6.31G(d,p) basis set. Calculated bond lengths, bond angles and dihedral angles were only slightly different from the experimental ones. The vibrational study was interpreted by means of potential energy distribution (PED). The electronic absorption spectra of the both compounds were predicted by using the time-dependent DFT methods and good agreement was found between the computational and the experimental values. The chemical shifts (1H and 13C NMR) and isotropic shielding values were calculated by using the gauge-invariant atomic orbital (GIAO) method. The analyses of HOMO and LUMO have been used to explain the charge transfer within the molecule.

  19. Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

    PubMed

    Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

    2013-11-14

    We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

  20. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  1. Combination study of DFT calculation and experiment for photocatalytic properties of S-doped anatase TiO2

    NASA Astrophysics Data System (ADS)

    Liu, Rujun; Zhou, Xiaosong; Yang, Fan; Yu, Ying

    2014-11-01

    Although there are many publications about S-doped TiO2, the related mechanism is still not well elucidated. In order to investigate the origin and trend of S substituting for O in TiO2 crystal lattice with proper dopant concentration, a combination of DFT calculation and experiment was used. Bader charge and electronic location function analysis indicate that the largely ionic character between Ti and S bonding in titanium dioxide decreases and there is free electron gas like behavior around S and neighbor Ti for the S-doped anatase TiO2. From DFT calculation, ST2.78 model is found to stabilize the structure of S substitution for lattice O with lower formation energy and its absorbance in visible light increases. Experiment results demonstrate that the sulfur doping results in the shift of the absorption edge for TiO2 to lower energy region, which leads to the nanoparticles active within the wavelength range of 650 nm.

  2. Vibrational spectra, optical properties, NBO and HOMO-LUMO analysis of L-Phenylalanine L-Phenylalaninium Perchlorate: DFT calculations.

    PubMed

    Elleuch, Nabil; Ben Ahmed, Ali; Feki, Habib; Abid, Younes; Minot, Christian

    2014-01-01

    In this work, we report a combined experimental and theoretical study of a nonlinear optical material, L-Phenylalanine L-Phenylalaninium Perchlorate. Single crystals of the title compound have been grown by slow evaporation of an aqueous solution at room temperature. Theoretical calculations were preceded by redetermination of the crystal X-ray structure. The compound crystallizes in the non-centro symmetric space group P2(1)2(1)2(1) of the orthorhombic system. The FT-IR and Raman spectra of the crystal were recorded and analyzed. The density functional theory (DFT) computations have been performed at B3LYP/6-31G(d) level to derive equilibrium geometry, vibrational wavenumbers, intensity and NLO properties. All observed vibrational bands have been discussed and assigned to normal mode or to combinations on the basis of our DFT calculations as a primary source of attribution and also by comparison with the previous results for similar compounds. Natural bond orbital analysis was carried out to demonstrate the various inter-and intramolecular interaction that are responsible of the stabilization of the compound. The lowering of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gap appears to be the cause of its enhanced charge transfer interaction leading to high NLO activity.

  3. Structure, spectroscopy and DFT calculations of 1,2-di(3-hydroxymethylpyridinium)ethane dibromide

    NASA Astrophysics Data System (ADS)

    Komasa, Anna; Barczyński, Piotr; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Dega-Szafran, Zofia; Szafran, Mirosław

    2016-09-01

    The molecular structure of 1,2-di(3-hydroxymethylpyridinium)ethane dibromide (1) has been characterized by X-ray diffraction, B3LYP/6-311++G(d,p) calculations, FTIR, Raman and NMR spectra. The crystals are monoclinic, space group C2/c. 1,2-Di(3-hydroxymethylpyridinium)ethane dication and hydrogen-bonded bromide anions in crystals are located at the inversion center. The both CH2OH groups are engaged in two equal length hydrogen bonds with bromide anions. Two structures (2) and (3) were optimized at the B3LYP/6-311++G(d,p) level of theory. The optimized complex (2) resembles the crystal structure, while complex (3) is preferred energetically. The O⋯Br- hydrogen bonds distances are: 3.289(2) Å in crystals (1), but in the optimized structures (2) and (3) they are 3.303 Å and 3.461 Å, respectively. The investigated complex is additionally stabilized by the N+⋯Br- electrostatic attractions. The potential energy distributions (PED) were used for the assignments of IR and Raman frequencies in the experimental and calculated spectra of the title compound. The FTIR spectrum of (1) is consistent with the X-ray results. Interpretation of the 1H and 13C NMR spectra in DMSO-d6 has been based on 2D experiments. The calculated GIAO/B3LYP/6-311++G(d,p) magnetic shielding constants have been used to predict 1H and 13C chemical shifts for the optimized structures of (2) and (3).

  4. 1-Pentamethylbenzyl-3-nbuthylbenzimidazolesilver(I)bromide complex: Synthesis, characterization and DFT calculations

    NASA Astrophysics Data System (ADS)

    Kunduracıoğlu, Ahmet; Tamer, Ömer; Avcı, Davut; Kani, İbrahim; Atalay, Yusuf; Çetinkaya, Bekir

    2014-03-01

    A novel NHC complex of silver(I) ion, 1-pentamethylbenzyl-3-nbuthylbenzimidazolesilver(I)bromide, was prepared and fully characterized by single crystal X-ray structure determination. FT-IR, NMR and UV-vis spectroscopies were employed to investigate the electronic transition behaviors of the complex. Additionally, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) 1H and 13C chemical shift and electronic transition values of silver(I) complex were calculated by using density functional theory levels (B3LYP and PBE1PBE) with LANL2DZ basis set. Also, the vibrational frequencies were supported on the basis of the potential energy distribution (PED) analysis calculated for PBE1PBE level. We were also investigated total static dipole moment (μ), the mean polarizability (<α>), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (<β>) of the title complex. Natural bond orbital (NBO) analysis was performed to determine the presence of hyperconjugative interactions, and charge distributions.

  5. 1-Pentamethylbenzyl-3-(n)buthylbenzimidazolesilver(I)bromide complex: synthesis, characterization and DFT calculations.

    PubMed

    Kunduracıoğlu, Ahmet; Tamer, Ömer; Avcı, Davut; Kani, Ibrahim; Atalay, Yusuf; Cetinkaya, Bekir

    2014-01-01

    A novel NHC complex of silver(I) ion, 1-pentamethylbenzyl-3-(n)buthylbenzimidazolesilver(I)bromide, was prepared and fully characterized by single crystal X-ray structure determination. FT-IR, NMR and UV-vis spectroscopies were employed to investigate the electronic transition behaviors of the complex. Additionally, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) (1)H and (13)C chemical shift and electronic transition values of silver(I) complex were calculated by using density functional theory levels (B3LYP and PBE1PBE) with LANL2DZ basis set. Also, the vibrational frequencies were supported on the basis of the potential energy distribution (PED) analysis calculated for PBE1PBE level. We were also investigated total static dipole moment (μ), the mean polarizability (〈α〉), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (〈β〉) of the title complex. Natural bond orbital (NBO) analysis was performed to determine the presence of hyperconjugative interactions, and charge distributions. PMID:24220668

  6. Understanding the difference in cohesive energies between alpha and beta tin in DFT calculations

    NASA Astrophysics Data System (ADS)

    Legrain, Fleur; Manzhos, Sergei

    2016-04-01

    The transition temperature between the low-temperature alpha phase of tin to beta tin is close to the room temperature (Tαβ = 130C), and the difference in cohesive energy of the two phases at 0 K of about ΔEcoh =0.02 eV/atom is at the limit of the accuracy of DFT (density functional theory) with available exchange-correlation functionals. It is however critically important to model the relative phase energies correctly for any reasonable description of phenomena and technologies involving these phases, for example, the performance of tin electrodes in electrochemical batteries. Here, we show that several commonly used and converged DFT setups using the most practical and widely used PBE functional result in ΔEcoh ≈0.04 eV/atom, with different types of basis sets and with different models of core electrons (all-electron or pseudopotentials of different types), which leads to a significant overestimation of Tαβ. We show that this is due to the errors in relative positions of s and p -like bands, which, combined with different populations of these bands in α and β Sn, leads to overstabilization of alpha tin. We show that this error can be effectively corrected by applying a Hubbard +U correction to s -like states, whereby correct cohesive energies of both α and β Sn can be obtained with the same computational scheme. We quantify for the first time the effects of anharmonicity on ΔEcoh and find that it is negligible.

  7. Optical properties of alkali halide crystals from all-electron hybrid TD-DFT calculations

    SciTech Connect

    Webster, R. Harrison, N. M.; Bernasconi, L.

    2015-06-07

    We present a study of the electronic and optical properties of a series of alkali halide crystals AX, with A = Li, Na, K, Rb and X = F, Cl, Br based on a recent implementation of hybrid-exchange time-dependent density functional theory (TD-DFT) (TD-B3LYP) in the all-electron Gaussian basis set code CRYSTAL. We examine, in particular, the impact of basis set size and quality on the prediction of the optical gap and exciton binding energy. The formation of bound excitons by photoexcitation is observed in all the studied systems and this is shown to be correlated to specific features of the Hartree-Fock exchange component of the TD-DFT response kernel. All computed optical gaps and exciton binding energies are however markedly below estimated experimental and, where available, 2-particle Green’s function (GW-Bethe-Salpeter equation, GW-BSE) values. We attribute this reduced exciton binding to the incorrect asymptotics of the B3LYP exchange correlation ground state functional and of the TD-B3LYP response kernel, which lead to a large underestimation of the Coulomb interaction between the excited electron and hole wavefunctions. Considering LiF as an example, we correlate the asymptotic behaviour of the TD-B3LYP kernel to the fraction of Fock exchange admixed in the ground state functional c{sub HF} and show that there exists one value of c{sub HF} (∼0.32) that reproduces at least semi-quantitatively the optical gap of this material.

  8. Optical properties of alkali halide crystals from all-electron hybrid TD-DFT calculations

    NASA Astrophysics Data System (ADS)

    Webster, R.; Bernasconi, L.; Harrison, N. M.

    2015-06-01

    We present a study of the electronic and optical properties of a series of alkali halide crystals AX, with A = Li, Na, K, Rb and X = F, Cl, Br based on a recent implementation of hybrid-exchange time-dependent density functional theory (TD-DFT) (TD-B3LYP) in the all-electron Gaussian basis set code CRYSTAL. We examine, in particular, the impact of basis set size and quality on the prediction of the optical gap and exciton binding energy. The formation of bound excitons by photoexcitation is observed in all the studied systems and this is shown to be correlated to specific features of the Hartree-Fock exchange component of the TD-DFT response kernel. All computed optical gaps and exciton binding energies are however markedly below estimated experimental and, where available, 2-particle Green's function (GW-Bethe-Salpeter equation, GW-BSE) values. We attribute this reduced exciton binding to the incorrect asymptotics of the B3LYP exchange correlation ground state functional and of the TD-B3LYP response kernel, which lead to a large underestimation of the Coulomb interaction between the excited electron and hole wavefunctions. Considering LiF as an example, we correlate the asymptotic behaviour of the TD-B3LYP kernel to the fraction of Fock exchange admixed in the ground state functional cHF and show that there exists one value of cHF (˜0.32) that reproduces at least semi-quantitatively the optical gap of this material.

  9. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    SciTech Connect

    Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  10. Nuclear magnetic resonance, vibrational spectroscopic studies, physico-chemical properties and computational calculations on (nitrophenyl) octahydroquinolindiones by DFT method.

    PubMed

    Pasha, M A; Siddekha, Aisha; Mishra, Soni; Azzam, Sadeq Hamood Saleh; Umapathy, S

    2015-02-01

    In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated.

  11. Electronic structure and optical properties of Cs2HgCl4: DFT calculations and X-ray photoelectron spectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Parasyuk, O. V.; Fedorchuk, A. O.; Khyzhun, O. Y.

    2016-10-01

    A high-quality single crystal of cesium mercury tetrabromide, Cs2HgCl4, was synthesized by using the vertical Bridgman-Stockbarger method and its electronic structure was studied from both experimental and theoretical viewpoints. In particular, X-ray photoelectron spectra were measured for both pristine and Ar+ ion-bombarded Cs2HgCl4 single crystal surfaces. The present XPS measurements indicate that the Cs2HgCl4 single crystal surface is sensitive with respect to Ar+ ion-bombardment: such a treatment changes substantially its elemental stoichiometry. With the aim of exploring total and partial densities of states within the valence band and conduction band regions of the Cs2HgCl4 compound, band-structure calculations based on density functional theory (DFT) using the augmented plane wave + local orbitals (APW + lo) method as incorporated within the WIEN2k package are performed. The calculations indicate that the Cl 3p states are the principal contributors in the upper portion of the valence band, while the Hg 5d and Cs 5p states dominate in its lower portion. In addition, the calculations allow for concluding that the unoccupied Cl p and Hg s states are the main contributors to the bottom of the conduction band. Furthermore, main optical characteristics of Cs2HgCl4, namely dispersion of the absorption coefficient, real and imaginary parts of dielectric function, electron energy-loss spectrum, refractive index, extinction coefficient and optical reflectivity, are elucidated based on the DFT calculations.

  12. Molecular structure, vibrational spectral assignments (FT-IR and FT-RAMAN), NMR, NBO, HOMO-LUMO and NLO properties of O-methoxybenzaldehyde based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.

    2016-05-01

    Fourier transform - Infra red (FT-IR) and Fourier transform - Raman (FT-Raman) spectroscopic techniques have been carried out to analyze O-methoxy benzaldehyde (OMB) molecule. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT). The vibrational analysis of stable isomer of OMB has been carried out by FT-IR and FT-Raman in combination with theoretical method simultaneously. The first-order hyperpolarizability and the anisotropy polarizability invariant were computed by DFT method. The atomic charges, hardness, softness, ionization potential, electronegativity, HOMO-LUMO energies, and electrophilicity index have been calculated. The 13C and 1H Nuclear magnetic resonance (NMR) have also been obtained by GIAO method. Molecular electronic potential (MEP) has been calculated by the DFT calculation method. Electronic excitation energies, oscillator strength and excited states characteristics were computed by the closed-shell singlet calculation method.

  13. (13)C, (15)N CPMAS NMR and GIAO DFT calculations of stereoisomeric oxindole alkaloids from Cat's Claw (Uncaria tomentosa).

    PubMed

    Paradowska, Katarzyna; Wolniak, Michał; Pisklak, Maciej; Gliński, Jan A; Davey, Matthew H; Wawer, Iwona

    2008-11-01

    Oxindole alkaloids, isolated from the bark of Uncaria tomentosa [Willd. ex Schult.] Rubiaceae, are considered to be responsible for the biological activity of this herb. Five pentacyclic and two tetracyclic alkaloids were studied by solid-state NMR and theoretical GIAO DFT methods. The (13)C and (15)N CPMAS NMR spectra were recorded for mitraphylline, isomitraphylline, pteropodine (uncarine C), isopteropodine (uncarine E), speciophylline (uncarine D), rhynchophylline and isorhynchophylline. Theoretical GIAO DFT calculations of shielding constants provide arguments for identification of asymmetric centers and proper assignment of NMR spectra. These alkaloids are 7R/7S and 20R/20S stereoisomeric pairs. Based on the (13)C CP MAS chemical shifts the 7S alkaloids (delta C3 70-71ppm) can be easily and conveniently distinguished from 7R (deltaC3 74.5-74.9ppm), also 20R (deltaC20 41.3-41.7ppm) from the 20S (deltaC20 36.3-38.3ppm). The epiallo-type isomer (3R, 20S) of speciophylline is characterized by a larger (15)N MAS chemical shift of N4 (64.6ppm) than the allo-type (3S, 20S) of isopteropodine (deltaN4 53.3ppm). (15)N MAS chemical shifts of N1-H in pentacyclic alkaloids are within 131.9-140.4ppm.

  14. Anisotropic lattice thermal expansion of PbFeBO4: A study by X-ray and neutron diffraction, Raman spectroscopy and DFT calculations

    SciTech Connect

    Murshed, M. Mangir; Mendive, Cecilia B.; Curti, Mariano; Nénert, Gwilherm; Kalita, Patricia E.; Lipinska, Kris; Cornelius, Andrew L.; Huq, Ashfia; Gesing, Thorsten M.

    2014-11-01

    We present the lattice thermal expansion of mullite-type PbFeBO4 in this study. The thermal expansion coefficients of the metric parameters were obtained from composite data collected from temperature-dependent neutron and X-ray powder diffraction between 10 K and 700 K. The volume thermal expansion was modeled using extended Grüneisen first-order approximation to the zero-pressure equation of state. The additive frame of the model includes harmonic, quasi-harmonic and intrinsic anharmonic potentials to describe the change of the internal energy as a function of temperature. Moreover, the unit-cell volume at zero-pressure and 0 K was optimized during the DFT simulations. Harmonic frequencies of the optical Raman modes at the Γ-point of the Brillouin zone at 0 K were also calculated by DFT, which help to assign and crosscheck the experimental frequencies. The low-temperature Raman spectra showed significant anomaly in the antiferromagnetic regions, leading to softening or hardening of some phonons. Selected modes were analyzed using a modified Klemens model. The shift of the frequencies and the broadening of the line-widths helped to understand the anharmonic vibrational behaviors of the PbO4, FeO6 and BO3 polyhedra as a function of temperature.

  15. Anisotropic lattice thermal expansion of PbFeBO4: A study by X-ray and neutron diffraction, Raman spectroscopy and DFT calculations

    DOE PAGES

    Murshed, M. Mangir; Mendive, Cecilia B.; Curti, Mariano; Nénert, Gwilherm; Kalita, Patricia E.; Lipinska, Kris; Cornelius, Andrew L.; Huq, Ashfia; Gesing, Thorsten M.

    2014-11-01

    We present the lattice thermal expansion of mullite-type PbFeBO4 in this study. The thermal expansion coefficients of the metric parameters were obtained from composite data collected from temperature-dependent neutron and X-ray powder diffraction between 10 K and 700 K. The volume thermal expansion was modeled using extended Grüneisen first-order approximation to the zero-pressure equation of state. The additive frame of the model includes harmonic, quasi-harmonic and intrinsic anharmonic potentials to describe the change of the internal energy as a function of temperature. Moreover, the unit-cell volume at zero-pressure and 0 K was optimized during the DFT simulations. Harmonic frequencies ofmore » the optical Raman modes at the Γ-point of the Brillouin zone at 0 K were also calculated by DFT, which help to assign and crosscheck the experimental frequencies. The low-temperature Raman spectra showed significant anomaly in the antiferromagnetic regions, leading to softening or hardening of some phonons. Selected modes were analyzed using a modified Klemens model. The shift of the frequencies and the broadening of the line-widths helped to understand the anharmonic vibrational behaviors of the PbO4, FeO6 and BO3 polyhedra as a function of temperature.« less

  16. Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: mechanistic insights from DFT calculations.

    PubMed

    Liao, Rong-Zhen; Himo, Fahmi; Yu, Jian-Guo; Liu, Ruo-Zhuang

    2010-01-01

    The reaction mechanism of the dinuclear zinc enzyme human renal dipeptidase is investigated using hybrid density functional theory. This enzyme catalyzes the hydrolysis of dipeptides and beta-lactam antibiotics. Two different protonation states in which the important active site residue Asp288 is either neutral or ionized were considered. In both cases, the bridging hydroxide is shown to be capable of performing the nucleophilic attack on the substrate carbonyl carbon from its bridging position, resulting in the formation of a tetrahedral intermediate. This step is followed by protonation of the dipeptide nitrogen, coupled with C-N bond cleavage. The calculations establish that both cases have quite feasible energy barriers. When the Asp288 is neutral, the hydrolytic reaction occurs with a large exothermicity. However, the reaction becomes very close to thermoneutral with an ionized Asp288. The two zinc ions are shown to play different roles in the reaction. Zn1 binds the amino group of the substrate, and Zn2 interacts with the carboxylate group of the substrate, helping in orienting it for the nucleophilic attack. In addition, Zn2 stabilizes the oxyanion of the tetrahedral intermediate, thereby facilitating the nucleophilic attack.

  17. Crystal structure, vibrational studies, optical properties and DFT calculation of bis 2-aminobenzothiazolium tetrachloridocuprate.

    PubMed

    Kessentini, A; Belhouchet, M; Abid, Y; Minot, C; Mhiri, T

    2014-03-25

    The zero dimensional organic-inorganic hybrid compound (C7H7N2S)2CuCl4 was synthesized and characterized by X-ray diffraction, infrared absorption, Raman spectroscopy scattering and optical transmission measurements. The title compound crystallizes in the monoclinic system with P21/c space group. The unit cell parameters are a=7.060 (5) Å, b=9.748 (5) Å, c=14.037 (5) Å, β=98.520 (5)° and Z=2. The copper (II) ion has square planar coordination environment and the structure is built up from isolated [CuCl4](2)(-) anion surrounded by organic cations connected together via N-H⋯Cl hydrogen bonding. Room temperature IR and Raman spectra of the title compound were recorded and analyzed. The theoretical geometrical parameters in the ground state have been investigated by density functional theory (DFT) with the B3LYP/LanL2DZ level of theory. The organic-inorganic hybrid crystal thin film can be easily prepared by spin-coating method from the ethanol solution of the (C7H7N2S)2CuCl4 compound and it showed characteristic absorptions of Cu-Cl based layered perovskite centered at 288 and 400 nm. PMID:24326264

  18. First principles study of Al-doped graphene as nanostructure adsorbent for NO2 and N2O: DFT calculations

    NASA Astrophysics Data System (ADS)

    Rad, Ali Shokuhi

    2015-12-01

    We studied the first principles adsorption phenomena of nitrogen dioxide (NO2) and nitrous oxide (N2O) molecules on the surface of pristine graphene and Al-doped graphene using density functional theory (DFT) calculations. The adsorption energies have been calculated for different possible configurations of the molecules on the surface of pristine and Al-doped graphene. Our calculations reveal that the Al-doped graphene has significant adsorption energy, elevated net charge transferring values and smaller bond distances to gases than that of pristine graphene because of the chemical interaction of the mentioned molecules. Furthermore, the calculated density of states (DOS) show the existing of noteworthy orbital hybridization between NO2 as well as N2O and Al-doped graphene during adsorption process which is proving to strong interaction while there is no evidence for hybridization between the those molecules and the pristine graphene. Our calculated adsorption energies for the most stable states for NO2 and N2O was -62.2 kJ mol-1 (-48.5 kJ mol-1 BSSE corrected energy) and -33.9 kJ mol-1 (-22.7 kJ mol-1 corrected energy), which are correspond to chemisorption process. These results point to the suitability of Al-doped graphene as a powerful sensor for practical applications.

  19. Spectroscopy (FT-IR, FT-Raman), hydrogen bonding, electrostatic potential and HOMO-LUMO analysis of tioxolone based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Tao, Yaping; Li, Xiaofeng; Han, Ligang; Zhang, Weiying; Liu, Zhaojun

    2016-10-01

    Tioxolone possess antipsoriatic and antibacterial properties. Therefore, it has been used in treating various skin and scalp disorders for many years. Spectroscopic analysis of tioxolone was presented by using density functional theory (DFT) calculations and experiments (FT-IR, FT-Raman and UV-Vis). Molecular geometry and vibrational wavenumbers of tioxolone were investigated by using B3LYP method with aug-cc-pVTZ basis set. A complete vibrational spectra was made to analyze the potential energy distributions (PED). In addition, analysis of frontier molecular orbitals, electrostatic potential (ESP) and thermodynamic properties (heat capacity, entropy, enthalpy and Gibbs free energy) was presented with the same basis-set. Furthermore, the nature of molecular association through hydrogen bonding were discussed using atoms in molecules (AIM) and reduced density gradient (RDG) methods.

  20. Synthesis, electronic structure investigation of 3-pentyl-2,6-di(furan-2-yl)piperidin-4-one by FT-IR, FT-Raman and UV-Visible spectral studies and ab initio/DFT calculations.

    PubMed

    Arockia Doss, M; Savithiri, S; Rajarajan, G; Thanikachalam, V; Anbuselvan, C

    2015-12-01

    FT-IR and FT-Raman spectra of 3-pentyl-2,6-di(furan-2-yl) piperidin-4-one (3-PFPO) were recorded in the solid phase. The structural and spectroscopic analyses of 3-PFPO were made by using B3LYP/HF level with 6-311++G(d, p) basis set. The fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Comparison of the observed fundamental vibrational frequencies of 3-PFPO with calculated results by HF and DFT methods indicates that B3LYP is superior to HF method for molecular vibrational problems. The electronic properties such as excitation energies, oscillator strength, wavelengths and HOMO-LUMO energies were obtained by time-dependent DFT (TD-DFT) approach. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The hyperconjugative interaction energy (E((2))) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. In addition, MEP and atomic charges of carbon, nitrogen, oxygen and hydrogen were calculated using B3LYP/6-311++G(d, p) level theory. Moreover, thermodynamic properties (heat capacities, entropy and enthalpy) of the title compound at different temperatures were calculated in gas phase. PMID:26172464

  1. Infrared-induced rotational isomerization of 1,2-ethanediamine in argon matrices and conformational analysis by DFT calculation

    NASA Astrophysics Data System (ADS)

    Kudoh, Satoshi; Takayanagi, Masao; Nakata, Munetaka; Ishibashi, Takaaki; Tasumi, Mitsuo

    1999-04-01

    Infrared spectra of 1,2-ethanediamine and its two deuterated species, ND 2CH 2CH 2ND 2 and NH 2CD 2CD 2NH 2, were measured by matrix-isolation FTIR spectroscopy. Isomerization around the central C-C axis from two gauche conformers to one trans conformer was found to occur upon infrared irradiation. With an aid of density functional theory, DFT, calculations, where the 6-31++G** basis set was used to optimize geometrical structures, the gauche conformers were assigned to G +G +G - and TG +G -, and the trans conformer to TTT. Wavelength dependence of the isomerization rates was examined using a tunable narrow band pass filter. It was found that relative quantum yields depend on excitation energy but not on the type of vibrational modes which absorb infrared rays.

  2. Tripeptides on Gold Nanoparticles: Structural Differences between Two Reverse Sequences as Determined by Solid-State NMR and DFT Calculations.

    PubMed

    Karki, Ichhuk; Wang, Hong; Geise, Natalie R; Wilson, Brendan W; Lewis, James P; Gullion, Terry

    2015-09-10

    The reverse-sequence peptides CysAlaAla and AlaAlaCys may attach to gold nanoparticles through the thiol group, and they differ primarily by whether the charged amino or the carboxylate group is proximal to the sulfur. Alanine residues in these peptides are not expected to interact significantly with the gold surface and serve to place a large separation between the amino and carboxylate groups. Solid-state NMR experiments and DFT calculations were performed to explore the structural differences between CysAlaAla on gold nanoparticles and AlaAlaCys on gold nanoparticles. It is found that the relative positions between the thiol, amino, and carboxylate groups strongly influences the structures of the peptide-gold systems. CysAlaAla orients parallel to the gold surface in a monolayer fashion, whereas AlaAlaCys forms an interdigitating bilayer-like structure that is oriented upright relative to the gold surface.

  3. Vibrational spectroscopic, first-order hyperpolarizability and HOMO, LUMO studies of 4-chloro-2-(trifluoromethyl) aniline based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Arivazhagan, M.; Subhasini, V. P.; Austine, A.

    2012-02-01

    The Fourier-transform infrared and FT-Raman spectra of 4-chloro-2-(trifluoromethyl) aniline (4C2TFA) were recorded in the region 4000-400 cm -1 and 3500-50 cm -1 respectively. Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of 4C2TFA were carried out by density functional theory (DFT/B3LYP) method with 6-311+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The values of the total dipole moment ( μ) and the first order hyperpolarizability ( β) of the investigated compound were computed using B3LYP/6-311++G(d,p) calculations. The calculated results also show that 4C2TFA might have microscopic non-linear optical (NLO) behavior with non-zero values. A detailed interpretation of infrared and Raman spectra of 4C2TFA is also reported. The calculated HOMO-LUMO energy gap shows that charge transfer occurs within the molecule.

  4. Infrared and Raman spectra, DFT-calculations and spectral assignments of germacyclohexane

    SciTech Connect

    Aleksa, V. Ozerenskis, D.; Pucetaite, M.; Sablinskas, V.; Cotter, C.; Guirgis, G. A.

    2015-03-30

    Raman spectra of germacyclohexane in liquid and solid states were recorded and depolarization data obtained. Infrared absorption spectra of the vapor and liquid have been studied. The wavenumbers of the vibrational modes were derived in the harmonic and anharmonic approximation in B3LYP/ccpVTZ calculations. According to the calculations, germacyclohexane exists in the stable chair conformation, whereas a possible twist form should have more than 15 kJ·mol{sup -1} higher enthalpy of formation what makes this conformer experimentally not observable. The 27 A' and 21 A'' fundamentals were assigned on the basis of the calculations and infrared and Raman band intensities, contours of gas phase infrared spectral bands and Raman depolarization measurements. An average discrepancy of ca. 0.77 % was found between the observed and the calculated anharmonic wavenumbers for the 48 modes. Substitution of carbon atom with Ge atom in the cyclohexane ring is reasoning flattening of the ring.

  5. 47 CFR 36.605 - Calculation of safety net additive.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... from the difference between the uncapped expense adjustment for the study area in the qualifying year... receive safety net additive support as calculated in paragraph (b) of this section, if in any study area, the rural incumbent local exchange carrier realizes growth in end of period Telecommunications...

  6. Vibrational spectroscopic and DFT calculation studies of a new organic-inorganic compound of bis (4-acetylanilinium) tetrachlorocadmiate (II)

    NASA Astrophysics Data System (ADS)

    Jellibi, A.; Chaabane, I.; Guidara, K.

    2016-10-01

    The FT-IR and Raman vibrational spectra of bis (4-acetylanilinium) tetrachlorocadmiate (II) compound have been measured at room temperature by FT-infrared spectroscopy (4000-400 cm-1) on polycrystalline samples, and by Raman spectroscopy (3600-30 cm-1) on monocrystals. The structure of the [C8H10NO] 2CdCl4 formed by two cations [C8H10NO]+ of same type and one type of anion [CdCl4]2- was optimized by density functional theory (DFT) using the B3LYP method. The theoretical wavenumbers spectra were scaled by multiple scaling factors, yielding a good agreement between the experimentally recorded and the theoretically calculated values. Root mean square (rms) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal. The comparison between the [C8H9NO] ligand and the [C8H10NO]2[CdCl4] compound of the Raman spectra showed a decrease in the wavenumber of the bands assigned to the stretching vibration of (NH3) group in the compound due to the effect of the protonation of the nitrogen.

  7. Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

    NASA Astrophysics Data System (ADS)

    Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

    2013-01-01

    The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

  8. Interpretation of the resonance Raman spectra of linear tetrapyrroles based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Kneip, Christa; Hildebrandt, Peter; Németh, Károly; Mark, Franz; Schaffner, Kurt

    1999-10-01

    Raman spectra of linear methine-bridged tetrapyrroles in different conformational and protonation states were calculated on the basis of scaled force fields obtained by density functional theory. Results are reported for protonated phycocyanobilin in the extended ZZZasa configuration, as it is found in C-phycocyanin of cyanobacteria. The calculated spectra are in good agreement with experimental spectra of the protein-bound chromophore in the α-subunit of C-phycocyanin and allow a plausible and consistent assignment of most of the observed resonance Raman bands in the region between 1000 and 1700 cm -1.

  9. A novel supramolecular compound of cadmium(II): Synthesis, characterization, crystal structure, ab initio HF, DFT calculations and solution study

    NASA Astrophysics Data System (ADS)

    Aghabozorg, Hossein; Manteghi, Faranak; Ghadermazi, Mohammad; Mirzaei, Masoud; Salimi, Ali R.; Shokrollahi, Ardeshir; Derki, Somayyeh; Eshtiagh-Hosseini, Hossein

    2009-02-01

    A novel compound with formula unit (pipzH 2)[Cd(pydc) 2]·6H 2O, was synthesized and characterized by IR, 1H NMR and 13C NMR spectroscopy, elemental analysis, single crystal X-ray diffractometry. Moreover, the solution behavior was studied, and ab initio HF, DFT calculations were carried out. The compound belongs to a great family of supramolecular metal complexes derived from a proton transfer ion pair i.e. (pipzH 2)(pydc), where pipz is piperazine and pydcH 2 is pyridine-2,6-dicarboxylic acid. The compound shows a distorted octahedral geometry around the six-coordinated Cd II atom. A variety of intermolecular O sbnd H···O, N sbnd H···O and C sbnd H···O hydrogen bonds are responsible to extend the supramolecular network of the compound. The geometry parameters of [Cd(pydc) 2] 2- complex and free (pydc) 2- ligand have been optimized with the B3LYP method of density functional theory (DFT) and ab initio Hartree-Fock (HF) methods for comparison. The effect of basis sets has been investigated using four combination basis sets. The electronic properties of the Cd II compound and free (pydc) 2- ligand have been investigated based on the natural bond orbital (NBO) analysis at the B3LYP/A level of theory which verifies that the synergistic effect have been occurred in the compound. In solution study, the protonation constants of pipz and pydc, the equilibrium constants for pydc/pipz proton transfer system and the stoichiometry and stability of the system with Cd 2+ ion in aqueous solution were investigated by potentiometric pH titrations. The stoichiometry of one of the most abundant complexed species in solution was found to be the same as that of the crystalline cadmium complex.

  10. Infrared and Raman spectroscopic features of the self-interstitial defect in diamond from exact-exchange hybrid DFT calculations.

    PubMed

    Salustro, Simone; Erba, Alessandro; Zicovich-Wilson, Claudio M; Nöel, Yves; Maschio, Lorenzo; Dovesi, Roberto

    2016-08-01

    Quantum-mechanical calculations are performed to investigate the structural, electronic, and infrared (IR) and Raman spectroscopic features of one of the most common radiation-induced defects in diamond: the "dumb-bell" 〈100〉 split self-interstitial. A periodic super-cell approach is used in combination with all-electron basis sets and hybrid functionals of density-functional-theory (DFT), which include a fraction of exact non-local exchange and are known to provide a correct description of the electronic spin localization at the defect, at variance with simpler formulations of the DFT. The effects of both defect concentration and spin state are explicitly addressed. Geometrical constraints are found to prevent the formation of a double bond between the two three-fold coordinated carbon atoms. In contrast, two unpaired electrons are fully localized on each of the carbon atoms involved in the defect. The open-shell singlet state is slightly more stable than the triplet (the energy difference being just 30 meV, as the unpaired electrons occupy orthogonal orbitals) while the closed-shell solution is less stable by about 1.55 eV. The formation energy of the defect from pristine diamond is about 12 eV. The Raman spectrum presents only two peaks of low intensity at wave-numbers higher than the pristine diamond peak (characterized by normal modes extremely localized on the defect), whose positions strongly depend on defect concentration as they blue shift up to 1550 and 1927 cm(-1) at infinite defect dilution. The first of these peaks, also IR active, is characterized by a very high IR intensity, and might then be related to the strong experimental feature of the IR spectrum occurring at 1570 cm(-1). A second very intense IR peak appears at about 500 cm(-1), which, despite being originated from a "wagging" motion of the self-interstitial defect, exhibits a more collective, less localized character.

  11. FT-Raman and FTIR-ATR spectroscopies and DFT calculations of triterpene acetyl aleuritolic acid

    NASA Astrophysics Data System (ADS)

    Melo, I. R. S.; Teixeira, A. M. R.; Sena Junior, D. M.; Santos, H. S.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Rodrigues, A. S.; Braz-Filho, R.; Gusmão, G. O. M.; Silva, J. H.; Faria, J. L. B.; Bento, R. R. F.

    2014-01-01

    Triterpenoids comprise an important class of compounds presenting a wide range of biologically important properties. Acetyl aleutitolic acid (AAA) is a triterpenoid isolated from Croton zehntneri, with molecular formula C32H50O4. Its structure has been characterized by NMR spectroscopy, however, there are no papers available regarding its vibrational properties. The Fourier-Transform Infrared with Attenuated Total Reflectance and Fourier-Transform Raman spectra, together with Density Functional Theory calculations of AAA are reported. Vibrational spectra were recorded at 300 K in the regions 600 cm-1 to 4000 cm-1 and 40 cm-1 to 4000 cm-1, for IR and Raman, respectively. Vibrational wavenumbers were predicted using Density Functional Theory calculations with the hybrid functional B3LYP and the basis set 6-31 G(d,p). A complete assignment of vibrational modes is given.

  12. Predicting the spin state of paramagnetic iron complexes by DFT calculation of proton NMR spectra.

    PubMed

    Borgogno, Andrea; Rastrelli, Federico; Bagno, Alessandro

    2014-07-01

    Many transition-metal complexes easily change their spin state S in response to external perturbations (spin crossover). Determining such states and their dynamics can play a central role in the understanding of useful properties such as molecular magnetism or catalytic behavior, but is often far from straightforward. In this work we demonstrate that, at a moderate computational cost, density functional calculations can predict the correct ground spin state of Fe(ii) and Fe(iii) complexes and can then be used to determine the (1)H NMR spectra of all spin states. Since the spectral features are remarkably different according to the spin state, calculated (1)H NMR resonances can be used to infer the correct spin state, along with supporting the structure elucidation of numerous paramagnetic complexes.

  13. Obtaining the magnetic susceptibility of the heme complex from DFT calculations

    NASA Astrophysics Data System (ADS)

    Pereira, L. M. O.; Resende, S. M.; Leite Alves, H. W.

    2016-09-01

    Magnetic field interactions with particles, as observed in magnetophoresis, are becoming important tool to understand the nature of the iron role in heme molecular complex, besides other useful applications. Accurate estimations of some macroscopic magnetic properties from quantum mechanical calculations, such as the magnetic susceptibility, can also check the reliability of the heme microscopic models. In this work we report, by using the Stoner criterion, a simple way to obtain the magnetic susceptibility of the heme complex from Density Functional Theory calculations. Some of our calculated structural properties and electronic structure show good agreement with both the available experimental and theoretical data, and the results show that its groundstate is a triplet 3A state. From the obtained results, we have evaluated the exchange interaction energy, J = 0.98 eV, the associated magnetic energy gain, Δ EM =-0.68 eV, and the magnetic susceptibility, χ0=1.73 ×10-6 cm3/mol for the heme alone (with uncompleted Fe ligands). If we consider the heme complex with the two histidine residues (completing the Fe ligands), we have then obtained χ0=5.27 ×10-12 cm3/g, which is in good agreement with experimental magnetophoresis data.

  14. Al-doped graphene as a new nanostructure adsorbent for some halomethane compounds: DFT calculations

    NASA Astrophysics Data System (ADS)

    Rad, Ali Shokuhi

    2016-03-01

    We have studied the electronic structure and property of pristine as well as Al-doped graphene sheets towards adsorption of some halomethane compounds (trichloromethane, dichloromethane, and difluoromethane) using density functional theory (DFhsT) calculations. The adsorption energies have been calculated for each adsorbed-adsorbent system. Based on our results, compared to pristine graphene, the Al-doped graphene causes significant adsorption energy, higher charge transferring, and smaller bond distances to halomethane compounds. Our calculated adsorption energies of trichloromethane, dichloromethane, and difluoromethane on Al-doped graphene were - 54.1, - 68.3, and - 123.2 kJ mol- 1, respectively, which are categorized in the chemisorption region while the adsorption of these molecules on pristine graphene release insignificant energies which correspond to very weak adsorption on it. Furthermore, we used charge transfer analysis to search the amount of electron allocation. Orbital analysis including the density of states (DOS) was done to find the possible orbital hybridization between adsorbates and two graphene sheets. These results imply the suitability of Al-doped graphene as a good adsorbent/sensor for halomethane compounds.

  15. FTIR and FTRaman spectroscopic investigation of 2-bromo-4-methylaniline using ab initio HF and DFT calculations

    NASA Astrophysics Data System (ADS)

    Ramalingam, S.; Periandy, S.; Narayanan, B.; Mohan, S.

    2010-06-01

    The FTIR and FTRaman spectra of 2-bromo-4-methyl aniline (2-B-4-MA) molecule have been recorded using Brucker IFS 66 V spectrometer in the range of 4000-100 cm -1. The molecular geometry and vibrational frequencies in the ground state are calculated using the Hartree-Fock (HF) and B3LYP with 6-31+G*(d, p), 6-311+G*(d, p) and 6-311++G* (d, p) basis sets. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The isotropic HF and DFT analysis showed good agreement with experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by HF and B3LYP methods indicates that B3LYP/6-311++G* (d, p) is superior to HF/6-31+G* for molecular vibrational problems. The complete data of this title compound provide the information for future development of substituted aniline. The influences of bromine atom, methyl group and amine group on the geometry of benzene and its normal modes of vibrations have also been discussed.

  16. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations.

    PubMed

    Mishra, Sandeep Kumar; Suryaprakash, N

    2015-06-21

    The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

  17. Calculation of laser absorption by metal powders in additive manufacturing.

    PubMed

    Boley, C D; Khairallah, S A; Rubenchik, A M

    2015-03-20

    We have calculated the absorption of laser light by a powder of metal spheres, typical of the powder employed in laser powder-bed fusion additive manufacturing. Using ray-trace simulations, we show that the absorption is significantly larger than its value for normal incidence on a flat surface, due to multiple scattering. We investigate the dependence of absorption on powder content (material, size distribution, and geometry) and on beam size.

  18. A conformational study of hydroxyflavones by vibrational spectroscopy coupled to DFT calculations

    NASA Astrophysics Data System (ADS)

    Machado, N. F. L.; Batista de Carvalho, L. A. E.; Otero, J. C.; Marques, M. P. M.

    2013-05-01

    The conformational preferences of a series of hydroxyflavones were studied by Raman and FTIR spectroscopies, coupled to Density Functional Theory calculations. Special attention was paid to the effect of hydroxyl substitution, due to its importance on the biological activity of these compounds. Their conformational preferences were found to be determined mainly by the orientation of the hydroxylic groups at C7 and within the catechol moiety, leading to the occurrence of distinct conformers in the solid state. A complete assignment of the experimental spectra was carried out for these molecules, in the light of their most stable conformers and the corresponding predicted vibrational pattern.

  19. Unexpected higher stabilisation of two classical antiaromatic frameworks with a ruthenium fragment compared to the osmium counterpart: origin probed by DFT calculations.

    PubMed

    Wu, Jingjing; Hao, Yulei; An, Ke; Zhu, Jun

    2016-01-01

    Density functional theory (DFT) calculations were carried out to investigate the stability and aromaticity of metallapentalocyclobutadienes. The results reveal unexpected higher stabilisation achieved with a 4d ruthenium fragment compared to the 5d [corrected] osmium counterpart. Moreover, direct 1-3 metal-carbon bonding in the metallabutadiene unit of these two complexes is negligible. PMID:26505956

  20. Electronic structures of halogen-doped Cu2O based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Zhao, Zong-Yan; Yi, Juan; Zhou, Da-Cheng

    2014-01-01

    In order to construct p—n homojunction of Cu2O-based thin film solar cells that may increase its conversion efficiency, to synthesize n-type Cu2O with high conductivity is extremely crucial, and considered as a challenge in the near future. The doping effects of halogen on electronic structure of Cu2O have been investigated by density function theory calculations in the present work. Halogen dopants form donor levels below the bottom of conduction band through gaining or losing electrons, suggesting that halogen doping could make Cu2O have n-type conductivity. The lattice distortion, the impurity formation energy, the position, and the band width of donor level of Cu2O1-xHx (H = F, Cl, Br, I) increase with the halogen atomic number. Based on the calculated results, chlorine doping is an effective n-type dopant for Cu2O, owing to the lower impurity formation energy and suitable donor level.

  1. Combined hybrid functional and DFT+U calculations for metal chalcogenides

    SciTech Connect

    Aras, Mehmet; Kılıç, Çetin

    2014-07-28

    In the density-functional studies of materials with localized electronic states, the local/semilocal exchange-correlation functionals are often either combined with a Hubbard parameter U as in the LDA+U method or mixed with a fraction of exactly computed (Fock) exchange energy yielding a hybrid functional. Although some inaccuracies of the semilocal density approximations are thus fixed to a certain extent, the improvements are not sufficient to make the predictions agree with the experimental data. Here, we put forward the perspective that the hybrid functional scheme and the LDA+U method should be treated as complementary, and propose to combine the range-separated Heyd-Scuseria-Ernzerhof (HSE) hybrid functional with the Hubbard U. We thus present a variety of HSE+U calculations for a set of II-VI semiconductors, consisting of zinc and cadmium monochalcogenides, along with comparison to the experimental data. Our findings imply that an optimal value U{sup *} of the Hubbard parameter could be determined, which ensures that the HSE+U{sup *} calculation reproduces the experimental band gap. It is shown that an improved description not only of the electronic structure but also of the crystal structure and energetics is obtained by adding the U{sup *} term to the HSE functional, proving the utility of HSE+U{sup *} approach in modeling semiconductors with localized electronic states.

  2. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    PubMed

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

  3. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    PubMed

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

  4. Synthesis, characterization and DFT calculations of electronic and optical properties of CaMoO4

    NASA Astrophysics Data System (ADS)

    Bouzidi, Chaker; Horchani-Naifer, Karima; Khadraoui, Zied; Elhouichet, Habib; Ferid, Mokhtar

    2016-09-01

    The electronic and optical properties of calcium molybdate (CaMoO4) have been determined by X-ray diffraction, spectroscopic measurements and calculations of energy-band structures, density of states, and optical response functions by density functional theory. The chemical bonding analysis indicates that Mo-O bonds exhibit more covalent character than the Ca-O bond. The linear photon-energy-dependent dielectric functions, conductivity, refractive index, reflectivity and extinction coefficients were investigated and analyzed. The results are in agreement with previous theoretical works and the experimental data. Reflectivity spectra revealed that the CaMoO4 promises as good coating materials in the energy region of 9.3-11.6 eV with reflectivity larger than 75%.

  5. Growth of Silicon Nanoclusters: Elucidation by gas-phase experiments and DFT calculations

    SciTech Connect

    Shvartsburg, Alexandre A.; Horoi, Mihai; Jackson, Koblar A.

    2004-10-01

    Semiconductor nanostructures are of great interest from both fundamental and applied perspectives. They are intriguing scientifically because their bonding and properties deviate strongly from those of their bulk solids and relevant industrially since nanodevices now approach the scale of large clusters. Understanding the behavior of any molecular system starts from ascertaining its structure. So a colossal effort was expended over the last two decades on characterizing semiconductor cluster geometries. As silicon is the most critical semiconductor, that effort largely focused on Si clusters. Structures of small Si clusters were elucidated early on by ab initio calculations, vibrationally resolved spectroscopy, and optical spectroscopies of matrix-isolated species. Progress for larger systems was enabled in late 1990s by an integrated suite of new tools. It includes ion mobility spectrometry, photoelectron spectroscopy, collisional dissociation, and threshold ionization on the side of experiment, and novel molecular optimization algorithms based on evolution paradigm and fast, but accurate semiempirical protocols for energy evaluation on the theory side. Coherent application of these methods has characterized Si clusters up to the region of radical transition from prolate to spherical growth at ~ 25 atoms.

  6. Electronic spectra and DFT calculations of some pyrimido[1,2-a]benzimidazole derivatives

    NASA Astrophysics Data System (ADS)

    Elshakre, Mohamed E.; Moustafa, H.; Hassaneen, Huwaida. M. E.; Moussa, Abdelrahim. Z.

    2015-06-01

    Ground state properties of 2,4-diphenyl-1,4-dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine, compound 1, and its derivatives are investigated experimentally and theoretically in Dioxane and DMF. The calculations show that all the studied compounds (1-7) are non-planar, resulting in a significant impact on the electronic and structural properties. The ground state properties of compounds 1-7 at B3LYP/6-311G (d, p) show that compound 5 has the lowest EHOMO, ELUMO, and ΔE indicating highest reactivity. Compound 7 is found to have the highest polarity. The observed UV spectra in Dioxane and DMF of compounds 1-4 show 2 bands, while compounds 5-7 show 4 bands in both solvents. Band maxima (λmax) and intensities of the spectra are found to have solvent dependence reflected as blue and red shifts. The theoretical spectra computed at TD-B3LYP/6-311G (d, p) in gas phase, Dioxane and DMF indicate a good agreement with the observed spectra.

  7. Direct comparison between two {gamma}-alumina structural models by DFT calculations

    SciTech Connect

    Ferreira, Ary R.; Martins, Mateus J.F.; Konstantinova, Elena; Capaz, Rodrigo B.; Souza, Wladmir F.; Chiaro, Sandra Shirley X.; Leitao, Alexandre A.

    2011-05-15

    We selected two important {gamma}-alumina models proposed in literature, a spinel-like one and a nonspinel one, to perform a theoretical comparison. Using ab initio calculations, the models were compared regarding their thermodynamic stability, lattice vibrational modes, and bulk electronic properties. The spinel-like model is thermodynamically more stable by 4.55 kcal/mol per formula unit on average from 0 to 1000 K. The main difference between the models is in their simulated infrared spectra, with the spinel-like model showing the best agreement with experimental data. Analysis of the electronic density of states and charge transfer between atoms reveal the similarity on the electronic structure of the two models, despite some minor differences. -- Graphical abstract: Two {gamma}-Alumina bulk models selected in this work for a comparison focusing in the electronic structure and thermodynamics of the systems. (a) The nonspinel model and (b) the spinel-like model. Display Omitted Highlights: {yields} There is still a debate about the {gamma}-Alumina structure in the literature. {yields} Models of surfaces are constructed from different bulk structural models. {yields} Two models commonly used in the literate were selected and compared. {yields} One model reproduce better the experimental data. {yields} Both presented a similar electronic structure.

  8. Characterizing Oxygen Local Environments in Paramagnetic Battery Materials via (17)O NMR and DFT Calculations.

    PubMed

    Seymour, Ieuan D; Middlemiss, Derek S; Halat, David M; Trease, Nicole M; Pell, Andrew J; Grey, Clare P

    2016-08-01

    Experimental techniques that probe the local environment around O in paramagnetic Li-ion cathode materials are essential in order to understand the complex phase transformations and O redox processes that can occur during electrochemical delithiation. While Li NMR is a well-established technique for studying the local environment of Li ions in paramagnetic battery materials, the use of (17)O NMR in the same materials has not yet been reported. In this work, we present a combined (17)O NMR and hybrid density functional theory study of the local O environments in Li2MnO3, a model compound for layered Li-ion batteries. After a simple (17)O enrichment procedure, we observed five resonances with large (17)O shifts ascribed to the Fermi contact interaction with directly bonded Mn(4+) ions. The five peaks were separated into two groups with shifts at 1600 to 1950 ppm and 2100 to 2450 ppm, which, with the aid of first-principles calculations, were assigned to the (17)O shifts of environments similar to the 4i and 8j sites in pristine Li2MnO3, respectively. The multiple O environments in each region were ascribed to the presence of stacking faults within the Li2MnO3 structure. From the ratio of the intensities of the different (17)O environments, the percentage of stacking faults was found to be ca. 10%. The methodology for studying (17)O shifts in paramagnetic solids described in this work will be useful for studying the local environments of O in a range of technologically interesting transition metal oxides. PMID:27404908

  9. Fluoridonitrosyl complexes of technetium(I) and technetium(II). Synthesis, characterization, reactions, and DFT calculations.

    PubMed

    Balasekaran, Samundeeswari Mariappan; Spandl, Johann; Hagenbach, Adelheid; Köhler, Klaus; Drees, Markus; Abram, Ulrich

    2014-05-19

    A mixture of [Tc(NO)F5](2-) and [Tc(NO)(NH3)4F](+) is formed during the reaction of pertechnetate with acetohydroxamic acid (Haha) in aqueous HF. The blue pentafluoridonitrosyltechnetate(II) has been isolated in crystalline form as potassium and rubidium salts, while the orange-red ammine complex crystallizes as bifluoride or PF6(-) salts. Reactions of [Tc(NO)F5](2-) salts with HCl give the corresponding [Tc(NO)Cl4/5](-/2-) complexes, while reflux in neat pyridine (py) results in the formation of the technetium(I) cation [Tc(NO)(py)4F](+), which can be crystallized as hexafluoridophosphate. The same compound can be synthesized directly from pertechnetate, Haha, HF, and py or by a ligand-exchange procedure starting from [Tc(NO)(NH3)4F](HF2). The technetium(I) cation [Tc(NO)(NH3)4F](+) can be oxidized electrochemically or by the reaction with Ce(SO4)2 to give the corresponding Tc(II) compound [Tc(NO)(NH3)4F](2+). The fluorido ligand in [Tc(NO)(NH3)4F](+) can be replaced by CF3COO(-), leaving the "[Tc(NO)(NH3)4](2+) core" untouched. The experimental results are confirmed by density functional theory calculations on [Tc(NO)F5](2-), [Tc(NO)(py)4F](+), [Tc(NO)(NH3)4F](+), and [Tc(NO)(NH3)4F](2+).

  10. Synthesis, spectroscopy, X-ray crystallography, DFT calculations, DNA binding and molecular docking of a propargyl arms containing Schiff base.

    PubMed

    Balakrishnan, C; Subha, L; Neelakantan, M A; Mariappan, S S

    2015-11-01

    A propargyl arms containing Schiff base (L) was synthesized by the condensation of 1-[2-hydroxy-4-(prop-2-yn-1-yloxy)phenyl]ethanone with trans-1,2-diaminocyclohexane. The structure of L was characterized by IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by single crystal X-ray diffraction analysis. The UV-Visible spectral behavior of L in different solvents exhibits positive solvatochromism. Density functional calculation of the L in gas phase was performed by using DFT (B3LYP) method with 6-31G basis set. The computed vibrational frequencies and NMR signals of L were compared with the experimental data. Tautomeric stability study inferred that the enolimine is more stable than the ketoamine form. The charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Electronic absorption and emission spectral studies were used to study the binding of L with CT-DNA. The molecular docking was done to identify the interaction of L with A-DNA and B-DNA.

  11. One new and six known triterpene xylosides from Cimicifuga racemosa: FT-IR, Raman and NMR studies and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jamróz, Marta K.; Jamróz, Michał H.; Cz. Dobrowolski, Jan; Gliński, Jan A.; Gleńsk, Michał

    One new and six known triterpene xylosides were isolated from Cimicifuga racemosa (black cohosh, Actaea racemosa). The structure of a new compound, designated as isocimipodocarpaside (1), was established to be (24S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10-seco-9,19-cyclolanost-1(10),7(8),9(11)-trien 3-O-β-D-xylopyranoside, by means of 1H and 13C NMR, IR and Raman spectroscopies and Mass Spectrometry. The six known compounds are: 23-epi-26-deoxycimicifugoside (2), 23-epi-26-deoxyactein (3), 25-anhydrocimigenol xyloside (4), 23-O-acetylshengmanol xyloside (5), 25-O-acetylcimigenol xyloside (6) and 3'-O-acetylcimicifugoside H-1 (7). On the basis of NMR data supported by DFT calculations of NMR shielding constants of (2), its structure, previously described as 26-deoxycimicifugoside was corrected and determined as 23-epi-26-deoxycimicifugoside. The 13C CPMAS NMR spectra of the studied compounds (1)-(7) provided data on their solid-state interactions. The IR and Raman spectra in the Cdbnd O, Cdbnd C, and Csbnd H stretching vibration regions clearly discriminate different triterpenes found in C. racemosa.

  12. The lifetime of CFC substitutes studied by a network trained with chaotic mapping modified genetic algorithm and DFT calculations.

    PubMed

    Lü, Q; Wu, H; Yu, R; Shen, G

    2004-08-01

    The hydrohaloalkanes have attracted much attention as potential substitutes of chlorofluorocarbons (CFCs) that deplete the ozone layer and lead to great high global warming. Having a short atmospheric lifetime is very important for the potential substitutes that may also induce ozone depletion and yield high global warming gases to be put in use. Quantitative structure-activity relationship (QSAR) studies were presented for their lifetimes aided by the quantum chemistry parameters including net charges, Mulliken overlaps, E(HOMO) and E(LUMO) based on the density functional theory (DFT) at B3PW91 level, and the C-H bond dissociation energy based on AM1 calculations. Outstanding features of the logistic mapping, a simple chaotic system, especially the inherent ability to search the space of interest exhaustively have been utilized. The chaotic mapping aided genetic algorithm artificial neural network training scheme (CGANN) showed better performance than the conventional genetic algorithm ANN training when the structure of the data set was not favorable. The lifetimes of HFCs and HCs appeared to be greatly dependent on their energies of the highest occupied molecular orbitals. The perference of the RMSRE comparing to RMSE as objective function of ANN training was better for the samples of interest with relatively short lifetimes. C(2)H(6) and C(3)H(8) as potential green substitutes of CFCs present relatively short lifetimes.

  13. Synthesis, spectroscopic, DFT calculations and biological activity studies of ruthenium carbonyl complexes with 2-picolinic acid and a secondary ligand

    NASA Astrophysics Data System (ADS)

    Shohayeb, Shahera M.; Mohamed, Rania G.; Moustafa, H.; El-Medani, Samir M.

    2016-09-01

    Thermal reaction of [Ru3(CO)12] with 2-picolinic acid (Hpic) in the absence and presence of a secondary ligand (pyridine, Py, bipyridine, Bipy, or thiourea, Tu) was investigated. Four complexes with molecular formulae: [Ru(CO)3(Hpic)], 1, [Ru2(CO)5(Hpic)(Py)], 2, [Ru2(CO)5(Hpic)(Tu)], 3 and [Ru2(CO)4(Hpic)(Bipy)], 4, were isolated. All complexes were characterized based on elemental analyses, IR, 1H NMR, magnetic studies, mass spectrometry and thermal analysis. The ligand and its complexes have been screened for antibacterial activities. Density Functional Theory (DFT) calculations at the B3LYP/6-311G (d,p)_ level of theory have been carried out to investigate the equilibrium geometry of the ligands. The optimized geometry parameters of the complexes were evaluated using B3LYP method and LANL2DZ basis set. The extent of natural charge population (core, valence and rydberg), exact electronic configuration, total Lewis and total non-Lewis are estimated and discussed in terms of natural bond orbitals (NBO) analysis.

  14. Infrared and Raman spectroscopic features of the self-interstitial defect in diamond from exact-exchange hybrid DFT calculations.

    PubMed

    Salustro, Simone; Erba, Alessandro; Zicovich-Wilson, Claudio M; Nöel, Yves; Maschio, Lorenzo; Dovesi, Roberto

    2016-08-01

    Quantum-mechanical calculations are performed to investigate the structural, electronic, and infrared (IR) and Raman spectroscopic features of one of the most common radiation-induced defects in diamond: the "dumb-bell" 〈100〉 split self-interstitial. A periodic super-cell approach is used in combination with all-electron basis sets and hybrid functionals of density-functional-theory (DFT), which include a fraction of exact non-local exchange and are known to provide a correct description of the electronic spin localization at the defect, at variance with simpler formulations of the DFT. The effects of both defect concentration and spin state are explicitly addressed. Geometrical constraints are found to prevent the formation of a double bond between the two three-fold coordinated carbon atoms. In contrast, two unpaired electrons are fully localized on each of the carbon atoms involved in the defect. The open-shell singlet state is slightly more stable than the triplet (the energy difference being just 30 meV, as the unpaired electrons occupy orthogonal orbitals) while the closed-shell solution is less stable by about 1.55 eV. The formation energy of the defect from pristine diamond is about 12 eV. The Raman spectrum presents only two peaks of low intensity at wave-numbers higher than the pristine diamond peak (characterized by normal modes extremely localized on the defect), whose positions strongly depend on defect concentration as they blue shift up to 1550 and 1927 cm(-1) at infinite defect dilution. The first of these peaks, also IR active, is characterized by a very high IR intensity, and might then be related to the strong experimental feature of the IR spectrum occurring at 1570 cm(-1). A second very intense IR peak appears at about 500 cm(-1), which, despite being originated from a "wagging" motion of the self-interstitial defect, exhibits a more collective, less localized character. PMID:27326546

  15. DFT Calculations on the Mechanism of Transition-Metal-Catalyzed Reaction of Diazo Compounds with Phenols: O-H Insertion versus C-H Insertion.

    PubMed

    Liu, Yuan; Luo, Zhoujie; Zhang, John Zenghui; Xia, Fei

    2016-08-18

    The reaction of diazo compounds with transition-metal carbenes is an efficient way to achieve the functionalization of chemical bonds in organic molecules, especially for the C-H and O-H bonds. However, the selective mechanisms of C-H and O-H bond insertions by various metal carbenes such as Rh and Cu complexes are not quite clear. In this work, we performed a comprehensively theoretical investigation of the phenol C-H and O-H bonds inserted by Rh and Cu carbenes by using DFT calculations. The calculated results reveal that the nucleophilic additions of phenols to the Rh and Cu carbenes in the C-H bond insertions are the rate-determining steps of whole reactions, which are higher than the barriers in the O-H insertions. In the process of intramolecular [1,3]-H transfer, the Rh and Cu ligands in their carbenes tend to dissociate into solution rather than the intramolecular migration due to their weak metal-carbon bonds. A deeply theoretical analysis of the electronic structures of Rh, Cu, and Au carbenes as well as their complexes elucidated their differences in the chemoselectivity of C-H and O-H insertion products, which agrees with the experimental observations well. PMID:27472439

  16. Emission property and DFT calculation for the 3MLCT luminescence of Ru(bpy)2(L)2+ complex

    NASA Astrophysics Data System (ADS)

    Yoshikawa, Naokazu; Kimura, Hiroko; Yamabe, Shinichi; Kanehisa, Nobuko; Inoue, Tsuyoshi; Takashima, Hiroshi

    2016-08-01

    Electronic structures of ruthenium complexes [Ru(bpy)2(L)]2+ were studied by DFT calculations, where bpy is 2,2‧-bipyridine and L's are its derivatives. They are parent (1) and five complexes with L = 4,4‧-dimethyl-2,2‧-bipyridine (2), 6,6‧-dimethyl-2,2‧-bipyridine (3), biquinoline (4), 5-nitro-1,10-phenanthroline (5) and two acetonitrile molecules (6). These complexes were characterized by ESI-MS, 1H NMR, UV-vis spectroscopy and elementary analysis. The crystal structures of 3·(PF6)2, 4·(PF6)2, 5·(PF6)2 and 6·(PF6)2 were also determined. Spin densities were analyzed to characterize the excited triplet states in those complexes. It was found that the complexes have three triplet (called here 3MLCT, 3MC1 and 3MC2) states. The 3MC1 and 3MC2 states have elongated Rusbnd N bonds and large spin densities on Ru2+. Those states are stable and would lead to the nonradiative relaxation to the ground state. In particular, those of 3, 5 and 6 are very stable, which results in their poor quantum yields (Φ < 0.01) of the emissions. In contrast, both 1 and 2 showed the 3MLCT states. Energy gaps between triplet and ground states were compared with energies corresponding to wavelengths of emission spectra of 1-5. Good agreement between the calculated and the experimental energies was found. Moreover, dual emission which depends on the excitation wavelength was observed in complex 4.

  17. Structural Rearrangement of Niobium Oxides from Lamellar Phases to Discrete Nanosheets and Nanoscrolls Probed by DFT Calculations

    NASA Astrophysics Data System (ADS)

    Adhikari, Jhashanath; Smith, Luis J.

    2012-02-01

    Inorganic niobates ACa2Nb3O10 (A= H and K) with layered structures are good photocatalytic materials due to their high surface areas accommodating a larger number of active sites and ease of processing through soft chemical techniques like exfoliation and restacking. Alkali metal phases can be ion-exchanged to the acid phase, which in turn can be easily exfoliated to individual nanosheets. The nanosheets can change their form to nanoscrolls with a curled geometry instead of a flat surface. During these morphological transformations, the local structure at the Nb-atom, H-atom and the interface may undergo rearrangement which is responsible for the alteration of properties of the materials. This presentation highlights the preliminary results on these structural modifications (interface variation, stacking of layers, lattice contraction and space group settings) and the possible positions of the proton. Our calculations show that the protons in the acid form are non-bridging and bonded to the same layer oxygen atoms unlike the K-atoms in its parent compound. The Electric field gradient (EFG) is a parameter very sensitive to the electron density around a quadrupolar nucleus ^2H and ^93Nb that can be detected using NMR. Changes in its magnitude/sign can be correlated to the change in the local environment (bond lengths and angles) around the sites of interest. EFG values from DFT calculations based on the proposed structural models will be used for the characterization of surface O-H bond lengths, H-bonding and Nb-O bond lengths and can be used to interpret NMR studies.

  18. Conformational studies on 2-substituted ethanesulfonates in aqueous solution by 1H NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Musio, Roberta; Sciacovelli, Oronzo

    2009-09-01

    The conformation of some 2-substituted sodium ethanesulfonates exerting biological functions, XCH 2CH 2SO 3Na (X = S -, Br, Cl, OH, NH 2, SH), has been investigated in aqueous solution by 1H NMR spectroscopy. Potential energy curves for rotation about the C-C bond have been calculated at DFT level of theory (B3LYP/6-311++G(2d,p)) in vacuum and in water (by IEF-PCM method). As concerning dianionic coenzyme M (X = S -), 2-bromo- and 2-chloroethanesulfonate, in vacuum the torsional potential curves and the variations of atomic charges and geometric parameters suggest that electrostatic and steric repulsions between the substituent X and -SO3- moiety determine the preference for anti conformer. In isethionate (X = OH), anionic taurine (X = NH 2), and coenzyme M (X = SH), the formation of an intramolecular hydrogen bond stabilizes also gauche-like conformers and the torsional potential curves exhibit two minima. According to Natural Bond Orbital analysis, hydrogen bond can be ascribed to electron transfer from two oxygen lone-pairs of the -SO3- moiety to the antibonding Y-H orbital of the substituent X. In all the compounds examined, hyperconjugative interactions tend to stabilize the gauche conformers with respect to the anti one. This means that conformational preferences in vacuum are determined by a counterbalancing of electrostatic, steric, and hyperconjugative interactions. Calculations in vacuum are not in agreement with the experimental conformational behaviour of the compounds examined. In order to reproduce the experimental results at least qualitatively, solvent effect must be introduced.

  19. Extinction coefficients of CC and CC bands in ethyne and ethene molecules interacting with Cu+ and Ag+ in zeolites--IR studies and quantumchemical DFT calculations.

    PubMed

    Kozyra, Paweł; Góra-Marek, Kinga; Datka, Jerzy

    2015-02-01

    The values of extinction coefficients of CC and CC IR bands of ethyne and ethene interacting with Cu+ and Ag+ in zeolites were determined in quantitative IR experiments and also by quantumchemical DFT calculations with QM/MM method. Both experimental and calculated values were in very good agreement validating the reliability of calculations. The values of extinction coefficients of ethyne and ethene interacting with bare cations and cations embedded in zeolite-like clusters were calculated. The interaction of organic molecules with Cu+ and Ag+ in zeolites ZSM-5 and especially charge transfers between molecule, cation and zeolite framework was also discussed in relation to the values of extinction coefficients.

  20. Mechanism and Site Selectivity in Visible-Light Photocatalyzed C-H Functionalization: Insights from DFT Calculations.

    PubMed

    Demissie, Taye B; Hansen, Jørn H

    2016-08-19

    Visible-light photocatalyzed (VLPC) late-stage C-H functionalization is a powerful addition to the chemical synthesis toolkit. VLPC has a demonstrated potential for discovery of elusive and valuable transformations, particularly in functionalization of bioactive heterocycles. In order to fully harvest the potential of VLPC in the context of complex molecule synthesis, a thorough understanding of the elementary processes involved is crucial. This would enable more rational design of suitable reagents and catalysts, as well as prediction of activated C-H sites for functionalization. Such knowledge is essential when VLPC is to be employed in retrosynthetic analysis of complex molecules. Herein, we present a density functional theory (DFT) study of mechanistic details in the C-H functionalization of bioactive heterocycles exemplified by the methylation of the antifungal agent voriconazole. Moreover, we show that readily computed atomic charges can predict major site-selectivity in good agreement with experimental studies and thus be informative tools for the identification of active C-H functionalization sites in synthetic planning. PMID:27347684

  1. Additional muon calculations for the SLC positron source

    SciTech Connect

    Nelson, W.R.; McCall, R.C.

    1985-04-23

    This note is an update to the muon calculations presented in CN-221 and takes into account: (1) a more complete muon production and transport model, including an estimate of wide angle production based on experimental data, (2) additional earth shielding that will be added on top and both sides of the 2/3 tunnel areas, and (3) a detailed analysis of the earth profile as it pertains to shielding in the direction of the SLAC site boundary. The highest annual dose at the SLAC boundary is found to be 13 mrem/year (4000 hours of operation at 50 kW), and this occurs at a horizontal angle of 0 degrees and a vertical angle of 3.6 degrees relative to the incident beam direction. Although the shielding criteria is 10 mrem/year at the site boundary, the radiation transport model becomes somewhat conservative at large distances from the shield, which should bring the 13 mrem/year number actually well below the criteria. This point is also about 28 feet above the roadway. Extension of this line may strike the ground in the Christmas tree farm beyond the SLAC boundary but there will be additional attenuation due to distance. We do not recommend that any additional shielding be added at this time. 4 refs., 1 fig.

  2. Specific features of the electronic structure and optical properties of KPb2Br5: DFT calculations and X-ray spectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Denysyuk, N. M.; Shkumat, P. N.; Tarasova, A. Y.; Isaenko, L. I.; Khyzhun, O. Y.

    2016-03-01

    Density functional theory (DFT) calculations are made in order to explore the total and partial densities of states of potassium dilead pentabromide, KPb2Br5, by using the augmented plane wave + local orbitals (APW + lo) method as incorporated in the WIEN2k package. The present calculations reveal that the principle contributors to the valence band of KPb2Br5 are the Pb 6s and Br 4p states contributing predominantly at the bottom and at the top of the band, respectively, while the bottom of the conduction band is formed mainly from contributions of the unoccupied Pb 6p states. The curves of total density of states derived by the present DFT calculations of KPb2Br5 are found to be in agreement with the experimental X-ray photoelectron valence-band spectrum of the compound studied. Comparison on a common energy scale of the X-ray emission bands representing the energy distribution of the valence Br p and K s states and the X-ray photoelectron valence-band spectrum of the KPb2Br5 single crystal indicate that the Br 4p and K 4s states contribute mainly at the top and in the upper portion of the valence band, respectively, being in agreement with data of the present DFT band-structure calculations of this compound. Principal optical characteristics of KPb2Br5, namely dispersion of the absorption coefficient, real and imaginary parts of dielectric function, electron energy-loss spectrum, refractive index, extinction coefficient and optical reflectivity are also studied by the DFT calculations.

  3. Ruthenium(II) bipyridine complexes bearing new keto-enol azoimine ligands: Synthesis, structure, electrochemistry and DFT calculations

    NASA Astrophysics Data System (ADS)

    Al-Noaimi, Mousa; Awwadi, Firas F.; Mansi, Ahmad; Abdel-Rahman, Obadah S.; Hammoudeh, Ayman; Warad, Ismail

    2015-01-01

    The novel azoimine ligand, Phsbnd NHsbnd Ndbnd C(COCH3)sbnd NHPh(Ctbnd CH) (H2L), was synthesized and its molecular structure was determined by X-ray crystallography. Catalytic hydration of the terminal acetylene of H2L in the presence of RuCl3·3H2O in ethanol at reflux temperature yielded a ketone (L1 = Phsbnd Ndbnd Nsbnd C(COCH3)dbnd Nsbnd Ph(COCH3) and an enol (L2 = Phsbnd Ndbnd Nsbnd C(COCH3)dbnd Nsbnd PhC(OH)dbnd CH2) by Markovnikov addition of water. Two mixed-ligand ruthenium complexes having general formula, trans-[Ru(bpy)(Y)Cl2] (1-2) (where Y = L1 (1) and Y = L2 (2), bpy is 2.2‧-bipyrdine) were achieved by the stepwise addition of equimolar amounts of (H2L) and bpy ligands to RuCl3·3H2O in absolute ethanol. Theses complexes were characterized by elemental analyses and spectroscopic (IR, UV-Vis, and NMR (1D 1H NMR, 13C NMR, (DEPT-135), (DEPT-90), 2D 1H-1H and 13C-1H correlation (HMQC) spectroscopy)). The two complexes exhibit a quasi-reversible one electron Ru(II)/Ru(III) oxidation couple at 604 mV vs. ferrocene/ferrocenium (Cp2Fe0/+) couple along with one electron ligand reduction at -1010 mV. The crystal structure of complex 1 showed that the bidentate ligand L1 coordinates to Ru(II) by the azo- and imine-nitrogen donor atoms. The complex adopts a distorted trans octahedral coordination geometry of chloride ligands. The electronic spectra of 1 and 1+ in dichloromethane have been modeled by time-dependent density functional theory (TD-DFT).

  4. Ruthenium(II) bipyridine complexes bearing new keto-enol azoimine ligands: synthesis, structure, electrochemistry and DFT calculations.

    PubMed

    Al-Noaimi, Mousa; Awwadi, Firas F; Mansi, Ahmad; Abdel-Rahman, Obadah S; Hammoudeh, Ayman; Warad, Ismail

    2015-01-25

    The novel azoimine ligand, Ph-NH-N=C(COCH3)-NHPh(C≡CH) (H2L), was synthesized and its molecular structure was determined by X-ray crystallography. Catalytic hydration of the terminal acetylene of H2L in the presence of RuCl3·3H2O in ethanol at reflux temperature yielded a ketone (L1=Ph-N=N-C(COCH3)=N-Ph(COCH3) and an enol (L2=Ph-N=N-C(COCH3)=N-PhC(OH)=CH2) by Markovnikov addition of water. Two mixed-ligand ruthenium complexes having general formula, trans-[Ru(bpy)(Y)Cl2] (1-2) (where Y=L1 (1) and Y=L2 (2), bpy is 2.2'-bipyrdine) were achieved by the stepwise addition of equimolar amounts of (H2L) and bpy ligands to RuCl3·3H2O in absolute ethanol. Theses complexes were characterized by elemental analyses and spectroscopic (IR, UV-Vis, and NMR (1D (1)H NMR, (13)C NMR, (DEPT-135), (DEPT-90), 2D (1)H-(1)H and (13)C-(1)H correlation (HMQC) spectroscopy)). The two complexes exhibit a quasi-reversible one electron Ru(II)/Ru(III) oxidation couple at 604 mV vs. ferrocene/ferrocenium (Cp2Fe(0/+)) couple along with one electron ligand reduction at -1010 mV. The crystal structure of complex 1 showed that the bidentate ligand L1 coordinates to Ru(II) by the azo- and imine-nitrogen donor atoms. The complex adopts a distorted trans octahedral coordination geometry of chloride ligands. The electronic spectra of 1 and 1+ in dichloromethane have been modeled by time-dependent density functional theory (TD-DFT).

  5. Structure, photophysical properties, and DFT calculations of selenide-centered pentacapped trigonal prismatic silver(I) clusters.

    PubMed

    Liu, C W; Feng, Ching-Shiang; Fu, Rei-Jen; Chang, Hao-Wei; Saillard, Jean-Yves; Kahlal, Samia; Wang, Ju-Chun; Chang, I-Jy

    2010-06-01

    Undecanuclear silver clusters [Ag(11)(mu(9)-Se)(mu(3)-Br)(3){Se(2)P(OR)(2)}(6)] (R = Et, (i)Pr, (2)Bu) were isolated from the reaction of [Ag(CH(3)CN)(4)](PF(6)), NH(4)[Se(2)P(OR)(2)], and Bu(4)NBr in a molar ratio of 4:3:1 in CH(2)Cl(2) at -20 degrees C. Clusters were characterized by elemental analysis, NMR spectroscopy ((1)H, (31)P, and (77)Se), positive FAB mass spectrometry, and X-ray crystallography of the isopropyl derivative. Structural elucidations revealed that the Ag(11)Se core geometry of clusters is a selenide-centered, slightly distorted 3,3,4,4,4-pentacapped trigonal prism surrounded by six diselenophosphato ligands, each in a tetrametallic tetraconnective (mu(2), mu(2)) coordination mode, and three mu(3)-bromide anions. All compounds exhibited orange luminescence both as a solid and in solution. The electronic structure of these clusters was studied by DFT calculations, and their optical properties were rationalized through a TDDFT investigation. The computed metrical parameters of the clusters were consistent with the corresponding X-ray data of [Ag(11)(mu(9)-Se)(mu(3)-Br)(3){Se(2)P(O(i)Pr)(2)}(6)] . The theoretical investigations affirmed that the low-energy absorptions as well as emissions were due to transitions from an orbital mostly of a selenophosphate ligand/central Se atom character to an orbital of metal character. PMID:20459139

  6. Synthesis, characterization, electrochemical studies and DFT calculations of amino acids ternary complexes of copper (II) with isonitrosoacetophenone. Biological activities

    NASA Astrophysics Data System (ADS)

    Tidjani-Rahmouni, Nabila; Bensiradj, Nour el Houda; Djebbar, Safia; Benali-Baitich, Ouassini

    2014-10-01

    Three mixed complexes having formula [Cu(INAP)L(H2O)2] where INAP = deprotonated isonitrosoacetophenone and L = deprotonated amino acid such as histidine, phenylalanine and tryptophan have been synthesized. They have also been characterized using elemental analyses, molar conductance, UV-Vis, IR and ESR spectra. The value of molar conductance indicates them to be non-electrolytes. The spectral studies support the binding of the ligands with two N and two O donor sites to the copper (II) ion, giving an arrangement of N2O2 donor groups. Density Functional Theory (DFT) calculations were applied to evaluate the cis and trans coordination modes of the two water molecules. The trans form was shown to be energetically more stable than the cis one. The ESR data indicate that the covalent character of the metal-ligand bonding in the copper (II) complexes increases on going from histidine to phenylalanine to tryptophan. The electrochemical behavior of the copper (II) complexes was determined by cyclic voltammetry which shows that the chelate structure and electron donating effects of the ligands substituent are among the factors influencing the redox potentials of the complexes. The antimicrobial activities of the complexes were evaluated against several pathogenic microorganisms to assess their antimicrobial potentials. The copper complexes were found to be more active against Gram-positive than Gram-negative bacteria. Furthermore, the antioxidant efficiencies of the metal complexes were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. The antioxidant activity of the complexes indicates their moderate scavenging activity against the radical DPPH.

  7. Enhancement of antioxidant activity of green tea epicatechins in β-cyclodextrin cavity: Single-crystal X-ray analysis, DFT calculation and DPPH assay.

    PubMed

    Aree, Thammarat; Jongrungruangchok, Suchada

    2016-10-20

    Green tea catechins are potent antioxidant for prevention of various free radical-related diseases. Their antioxidant properties can be improved by encapsulation in cyclodextrins (CDs). Four inclusion complexes of β-CD with (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECG) and (-)-epigallocatechin gallate (EGCG) have been investigated using single-crystal X-ray diffraction analysis combined with full geometry optimization by DFT/B3LYP calculation and the DPPH assay, aiming to deepen the understanding on their structure-antioxidant activity relationship. Scrutinizing the inclusion structures and conformational changes of the four encapsulated epicatechins reveals the common host-guest stabilization scheme and the epicatechin conformational flexibility facilitating the enhancement of activity. Thermodynamic stability order derived from DFT calculation in vacuum fairly agrees with the order of improved antioxidant capacity deduced from the DPPH assay, β-CD-EGCG>β-CD-ECG>β-CD-EGC≈β-CD-EC. PMID:27474665

  8. X-ray Single Crystal Structure, DFT Calculations and Biological Activity of 2-(3-Methyl-5-(pyridin-2'-yl)-1H-pyrazol-1-yl) Ethanol.

    PubMed

    Radi, Smaail; Attayibat, Ahmed; El-Massaoudi, Mohamed; Salhi, Amin; Eddike, Driss; Tillard, Monique; Mabkhot, Yahia N

    2016-01-01

    A pyridylpyrazole bearing a hydroxyethyl substituent group has been synthesized by condensation of (Z)-4-hydroxy-4-(pyridin-2-yl)but-3-en-2-one with 2-hydroxyethylhydrazine. The compound was well characterized and its structure confirmed by single crystal X-ray diffraction. Density functional calculations have been performed using DFT method with 6-31G* basis set. The HOMO-LUMO energy gap, binding energies and electron deformation densities are calculated at the DFT (BLYP, PW91, PWC) level. The electrophilic f(-) and nucleophilic f(+) Fukui functions and also the electrophilic and nucleophilic Parr functions are well adapted to find the electrophile and nucleophile centers in the molecule. The title compound has been tested for its DPPH radical scavenging activity which is involved in aging processes, anti-inflammatory, anticancer and wound healing activity. Compound is also found with a significant antioxidant activity, probably due to the ability to donate a hydrogen atom to the DPPH radical. PMID:27527141

  9. 2-[(1H-Benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester: Crystal structure, DFT calculations and biological activity evaluation

    NASA Astrophysics Data System (ADS)

    Ghani, Nour T. Abdel; Mansour, Ahmed M.

    2011-10-01

    In the present study, structural properties of 2-[(1H-benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester have been studied extensively by spectral methods and X-ray crystallography. Quantum mechanical calculations of energies, geometries, vibrational wavenumbers, NMR and electronic transitions were carried out by DFT using B3LYP functional combined with 6-31G(d) basis set. Natural bond orbitals (NBO) analysis and frontier molecular orbitals were performed at the same level of theory. DFT calculations showed good agreement between the theoretical and experimental values of optimized and X-ray structure as well as between the vibrational and NMR spectroscopy. The title compound was screened for its antibacterial activity referring to Tetracycline as standard antibacterial agent.

  10. Enhancement of antioxidant activity of green tea epicatechins in β-cyclodextrin cavity: Single-crystal X-ray analysis, DFT calculation and DPPH assay.

    PubMed

    Aree, Thammarat; Jongrungruangchok, Suchada

    2016-10-20

    Green tea catechins are potent antioxidant for prevention of various free radical-related diseases. Their antioxidant properties can be improved by encapsulation in cyclodextrins (CDs). Four inclusion complexes of β-CD with (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECG) and (-)-epigallocatechin gallate (EGCG) have been investigated using single-crystal X-ray diffraction analysis combined with full geometry optimization by DFT/B3LYP calculation and the DPPH assay, aiming to deepen the understanding on their structure-antioxidant activity relationship. Scrutinizing the inclusion structures and conformational changes of the four encapsulated epicatechins reveals the common host-guest stabilization scheme and the epicatechin conformational flexibility facilitating the enhancement of activity. Thermodynamic stability order derived from DFT calculation in vacuum fairly agrees with the order of improved antioxidant capacity deduced from the DPPH assay, β-CD-EGCG>β-CD-ECG>β-CD-EGC≈β-CD-EC.

  11. X-ray Single Crystal Structure, DFT Calculations and Biological Activity of 2-(3-Methyl-5-(pyridin-2'-yl)-1H-pyrazol-1-yl) Ethanol.

    PubMed

    Radi, Smaail; Attayibat, Ahmed; El-Massaoudi, Mohamed; Salhi, Amin; Eddike, Driss; Tillard, Monique; Mabkhot, Yahia N

    2016-08-05

    A pyridylpyrazole bearing a hydroxyethyl substituent group has been synthesized by condensation of (Z)-4-hydroxy-4-(pyridin-2-yl)but-3-en-2-one with 2-hydroxyethylhydrazine. The compound was well characterized and its structure confirmed by single crystal X-ray diffraction. Density functional calculations have been performed using DFT method with 6-31G* basis set. The HOMO-LUMO energy gap, binding energies and electron deformation densities are calculated at the DFT (BLYP, PW91, PWC) level. The electrophilic f(-) and nucleophilic f(+) Fukui functions and also the electrophilic and nucleophilic Parr functions are well adapted to find the electrophile and nucleophile centers in the molecule. The title compound has been tested for its DPPH radical scavenging activity which is involved in aging processes, anti-inflammatory, anticancer and wound healing activity. Compound is also found with a significant antioxidant activity, probably due to the ability to donate a hydrogen atom to the DPPH radical.

  12. Vibrational spectroscopy and DFT calculations of the di-amino acid peptide L-aspartyl-L-glutamic acid in the zwitterionic state.

    PubMed

    Kausar, Nighat; Dines, Trevor J; Chowdhry, Babur Z; Alexander, Bruce D

    2009-08-14

    Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the linear di-amino acid peptide L-aspartyl-L-glutamic acid (L-Asp-L-Glu); the solution state Raman spectrum has also been obtained for the N,O-deuterated derivative. SCF-DFT calculations at the B3-LYP/cc-pVDZ level established that the structure and vibrational spectra of L-Asp-L-Glu can be interpreted using a model of the peptide with ten hydrogen-bonded water molecules, in conjunction with the conductor-like polarizable continuum solvation method. The DFT calculations resulted in the computation of a stable zwitterionic structure, which displays trans-amide conformation. The vibrational spectra were computed at the optimised molecular geometry, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.

  13. A new mixed-ligand copper(II) complex of (E)-N";-(2-hydroxybenzylidene) acetohydrazide: Synthesis, characterization, NLO behavior, DFT calculation and biological activities

    NASA Astrophysics Data System (ADS)

    Yousef Ebrahimipour, S.; Sheikhshoaie, Iran; Crochet, Aurelien; Khaleghi, Moj; Fromm, Katharina M.

    2014-08-01

    A tridentate hydrazone Schiff base ligand, (E)-N";-(2-hydroxybenzylidene)acetohydrazide [HL], and its mixed-ligand Cu(II) complex [CuL(phen)], have been synthesized and characterized by elemental analyses, FT-IR, molar conductivity, UV-Vis spectroscopy. The structure of the complex has been determined by X-ray diffraction. This complex has square pyramidal geometry and the positions around central atom are occupied with donor atoms of Schiff base ligand and two nitrogens of 1,10-phenanthroline. Computational studies of compounds were performed by using DFT calculations. The linear polarizabilities and first hyperpolarizabilities of the studied molecules indicate that these compounds can be good candidates of nonlinear optical materials. It is in accordance with experimental data. In addition, invitro antimicrobial results show that these compounds specially [CuL(phen)] have great potential of antibacterial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Listeria monocytogenes bacteria and antifungal activity against Candida Albicans in comparison to some standard drugs.

  14. Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion.

    PubMed

    Singh, R; Yadav, R A

    2014-09-15

    Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5C6 bond length increases and loses its double bond character while the C4C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled NH stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

  15. Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site.

    PubMed

    Dey, Abhishek; Chow, Marina; Taniguchi, Kayoko; Lugo-Mas, Priscilla; Davin, Steven; Maeda, Mizuo; Kovacs, Julie A; Odaka, Masafumi; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

    2006-01-18

    The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO. PMID:16402841

  16. New heterocyclic green, blue and orange dyes from indazole: Synthesis, tautomerism, alkylation studies, spectroscopic characterization and DFT/TD-DFT calculations

    NASA Astrophysics Data System (ADS)

    Poorhaji, Soodabeh; Pordel, Mehdi; Ramezani, Shirin

    2016-09-01

    Tautomerism and alkylation studies on the green intermediate 2-(5-hydroxyimino-1-methyl-4,5-dihydro-1H-4-indazolyliden)-2-phenylacetonitrile led to the synthesis of new heterocyclic green, blue and orange dyes in high yields. The structures of all newly synthesized compounds were confirmed by spectral and analytical data. The optical properties of the dyes were spectrally characterized by using a UV-vis spectrophotometer and results show that they exhibited interesting photophysical properties. Solvent effects on the absorption spectra of these dyes have been studied and the absorption band in polar solvents undergoes a red shift. Density functional theory calculations of the dyes were performed to provide the optimized geometries and relevant frontier orbitals. Calculated electronic absorption spectra were also obtained by time-dependent density functional theory method.

  17. Pyrazinamide drug interacting with Co(III) and Zn(II) metal ions based on 2,2‧-bipyridine and 1,10-phenanthroline ligands: Synthesis, studies and crystal structure, DFT calculations and antibacterial assays

    NASA Astrophysics Data System (ADS)

    Chiniforoshan, Hossein; Radani, Zahra Sadeghian; Tabrizi, Leila; Tavakol, Hossein; Sabzalian, Mohammad R.; Mohammadnezhad, Gholamhossein; Görls, Helmar; Plass, Winfried

    2015-02-01

    Three novel compounds, [Co(PZAH)(bipy)2](ClO4)2 (1), [Zn(PZAH)(bipy)2]ClO4 (2), [Zn(PZAH)(phen)2]ClO4 (3), which PZAH2 = pyrazinamide, bipy = 2,2‧-bipyridine, phen = 1,10-phenanthroline, were synthesized and characterized by elemental analysis, IR, 1H NMR and electronic absorption spectroscopies. The crystal structure of 1 has been determined in an orthorhombic Pbca space group. The binding modes of the ligands in complex 1 were established by means of molecular modeling of the complex, and calculation of their IR and absorption spectra DFT calculations. The calculated FT-IR and UV-Vis data are in good agreement with the experimental results, and confirmed the experimental one. In addition to DFT calculations of the complex 1, natural bond orbital (NBO) was performed to obtain atomic charges. Biological studies also showed the antibacterial activity of complexes 1-3 against Gram-positive and Gram-negative bacterial strains.

  18. Comparison of the performance of different DFT methods in the calculations of the molecular structure and vibration spectra of serotonin (5-hydroxytryptamine, 5-HT)

    NASA Astrophysics Data System (ADS)

    Yang, Yue; Gao, Hongwei

    2012-04-01

    Serotonin (5-hydroxytryptamine, 5-HT) is a monoamine neurotransmitter which plays an important role in treating acute or clinical stress. The comparative performance of different density functional theory (DFT) methods at various basis sets in predicting the molecular structure and vibration spectra of serotonin was reported. The calculation results of different methods including mPW1PW91, HCTH, SVWN, PBEPBE, B3PW91 and B3LYP with various basis sets including LANL2DZ, SDD, LANL2MB, 6-31G, 6-311++G and 6-311+G* were compared with the experimental data. It is remarkable that the SVWN/6-311++G and SVWN/6-311+G* levels afford the best quality to predict the structure of serotonin. The results also indicate that PBEPBE/LANL2DZ level show better performance in the vibration spectra prediction of serotonin than other DFT methods.

  19. Molecular structure, vibrational analysis (FT-IR, FT-Raman), NMR, UV, NBO and HOMO-LUMO analysis of N,N-Diphenyl Formamide based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Mathammal, R.; Monisha, N. R.; Yasaswini, S.; Krishnakumar, V.

    2015-03-01

    In this work, the vibrational spectral analysis is carried out by using Raman and infrared spectroscopy in the range 4000-400 cm-1 and 4000-50 cm-1 respectively for N,N-Diphenyl Formamide (DPF) molecule. The optimized molecular structures, vibrational frequencies and corresponding vibrational assignments, nuclear magnetic resonance (NMR) and ultraviolet-visible (UV-VIS) spectra of the title molecule are evaluated using density functional theory (DFT) with standard B3LYP/6-31G(d, p) basis set. The harmonic vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed using natural bond (NBO) analysis. The possible electronic transitions are determined by HOMO-LUMO orbital shapes and their energies. Thermodynamic properties (heat capacity, entropy and enthalpy) and the first hyperpolarizability of the title compound are calculated. The Mulliken charges and electric dipole moment of the molecule are computed using DFT calculations. The 1H and 13C nuclear magnetic resonance (NMR) chemical shift of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

  20. Analysis of valence XPS and AES of C, N, O, and F-containing substances by DFT calculations using the model molecules

    NASA Astrophysics Data System (ADS)

    Endo, Kazunaka; Hyodo, Kenji; Takaoka, Kazuchiyo; Ida, Tomonori; Shimada, Shingo; Takagi, Yusuke; Kurmaev, Ernst Z.

    2015-05-01

    Experimental valence X-ray photoelectron spectra (VXPS) and Auger electron spectra (AES) of (Li, C, N, O, F) elements of four solid substances [graphite, GaN, SiO2, LiF] are analyzed by density-functional theory calculations using the model molecules of the unit cell. For the calculations, we use deMon density functional theory (DFT) program to estimate VXPS, core-electron binding energies, and (Li, C, N, O, F)-KVV AES of the solid substances. In the AES simulations, we evaluate theoretical kinetic energies of the AES with our modified calculation method. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. Experimental KVV AES of the (Li, C, N, O) atoms in the substances agree considerably well to simulation of AES obtained with the maximum kinetic energies of the atoms, while, the experimental F KVV AES of LiF is almost in accordance with the spectra from the transition-state kinetic energy calculations.

  1. Electron transfer within a reaction path model calibrated by constrained DFT calculations: application to mixed-valence organic compounds.

    PubMed

    Mangaud, E; de la Lande, A; Meier, C; Desouter-Lecomte, M

    2015-12-14

    The quantum dynamics of electron transfer in mixed-valence organic compounds is investigated using a reaction path model calibrated by constrained density functional theory (cDFT). Constrained DFT is used to define diabatic states relevant for describing the electron transfer, to obtain equilibrium structures for each of these states and to estimate the electronic coupling between them. The harmonic analysis at the diabatic minima yields normal modes forming the dissipative bath coupled to the electronic states. In order to decrease the system-bath coupling, an effective one dimensional vibronic Hamiltonian is constructed by partitioning the modes into a linear reaction path which connects both equilibrium positions and a set of secondary vibrational modes, coupled to this reaction coordinate. Using this vibronic model Hamiltonian, dissipative quantum dynamics is carried out using Redfield theory, based on a spectral density which is determined from the cDFT results. In a first benchmark case, the model is applied to a series of mixed-valence organic compounds formed by two 1,4-dimethoxy-3-methylphenylene fragments linked by an increasing number of phenylene bridges. This allows us to examine the coherent electron transfer in extreme situations leading to a ground adiabatic state with or without a barrier and therefore to the trapping of the charge or to an easy delocalization.

  2. FTIR, FT-RAMAN, NMR, spectra, normal co-ordinate analysis, NBO, NLO and DFT calculation of N,N-diethyl-4-methylpiperazine-1-carboxamide molecule.

    PubMed

    Muthu, S; Elamurugu Porchelvi, E

    2013-11-01

    The Fourier Transform Infrared (FT-IR) and FT-Raman of N,N-diethyl-4-methylpiperazine-1-carboxamide (NND4MC) have been recorded and analyzed. The structure of the compound was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d,p) and 6-311G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. 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. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) antibonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using Density Functional Theory (DFT/B3LYP) with 6-31G(d,p) and 6-311G(d,p) basis sets. The calculated results also show that the NND4MC molecule may have microscopy nonlinear optical (NLO) behavior with non zero values. Mulliken atomic charges of NND4MC were calculated. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. The UV-Vis spectrum of the compound was recorded. The theoretical electronic absorption spectra have been calculated by using CIS, TD-DFT methods. A study on the electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) were also performed.

  3. 37 CFR 1.776 - Calculation of patent term extension for a food additive or color additive.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... extension for a food additive or color additive. 1.776 Section 1.776 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a food additive or color additive. (a) If a determination is made pursuant to § 1.750 that a patent for a food additive or color additive is eligible for extension, the...

  4. 37 CFR 1.776 - Calculation of patent term extension for a food additive or color additive.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... extension for a food additive or color additive. 1.776 Section 1.776 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a food additive or color additive. (a) If a determination is made pursuant to § 1.750 that a patent for a food additive or color additive is eligible for extension, the...

  5. 37 CFR 1.776 - Calculation of patent term extension for a food additive or color additive.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... extension for a food additive or color additive. 1.776 Section 1.776 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a food additive or color additive. (a) If a determination is made pursuant to § 1.750 that a patent for a food additive or color additive is eligible for extension, the...

  6. 37 CFR 1.776 - Calculation of patent term extension for a food additive or color additive.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... extension for a food additive or color additive. 1.776 Section 1.776 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a food additive or color additive. (a) If a determination is made pursuant to § 1.750 that a patent for a food additive or color additive is eligible for extension, the...

  7. 37 CFR 1.776 - Calculation of patent term extension for a food additive or color additive.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... extension for a food additive or color additive. 1.776 Section 1.776 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a food additive or color additive. (a) If a determination is made pursuant to § 1.750 that a patent for a food additive or color additive is eligible for extension, the...

  8. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde.

    PubMed

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M; Ben Altabef, Aída

    2015-02-01

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C.

  9. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde

    NASA Astrophysics Data System (ADS)

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M.; Altabef, Aída Ben

    2015-02-01

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34 °C and decomposes at temperatures higher than 193 °C.

  10. Analysis of valence XPS and AES of (PP, P4VP, PVME, PPS, PTFE) polymers by DFT calculations using the model molecules

    NASA Astrophysics Data System (ADS)

    Endo, Kazunaka; Shimada, Shingo; Kato, Nobuhiko; Ida, Tomonori

    2016-10-01

    We simulated valence X-ray photoelectron spectra (VXPS) of five [(CH2CH(CH3))n {poly(propyrene) PP}, ((CH2CH(C5NH4))n {poly(4-vinyl-pyridine) P4VP}, (CH2CHO(CH3))n {poly(vinyl methyl ether) PVME}, (C6H4S)n {poly(phenylene) sulphide PPS}, (CF2CF2)n {poly(tetrafluoroethylene) PTFE}] polymers by density-functional theory (DFT) calculations using the model oligomers. The spectra reflect the differences in the chemical structures between each polymer, since the peak intensities of valence band spectra are seen to be due to photo-ionization cross-section of (C, N, O, S, F) atoms by considering the orbital energies and cross-section values of the polymer models, individually. In the Auger electron spectra (AES) simulations, theoretical kinetic energies of the AES are obtained with our modified calculation method. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. Experimental peaks of (C, N, O)- KVV, and S L2,3VV AES for each polymer are discussed in detail by our modified calculation method.

  11. Comparative vibrational spectroscopic studies, HOMO-LUMO, NBO analyses and thermodynamic functions of p-cresol and 2-methyl-p-cresol based on DFT calculations.

    PubMed

    Balachandran, V; Murugan, M; Nataraj, A; Karnan, M; Ilango, G

    2014-11-11

    In the present study structural properties of p-cresol, and 2-methoxy-p-cresol have been studied by using B3LYP/cc-pvdz and B3PW91/cc-pvdz of Density Functional Theory (DFT) utilizing Becke three exchange functional and Lee Yang Paar correlation functional. The Fourier transform infrared and Fourier transform Raman spectra of title molecules were recorded (solid phase). Optimized geometry, harmonic vibrational frequencies and various thermodynamic parameters of the title compounds were calculated with B3LYP/cc-pvdz, and B3PW91/cc-pvdz basis sets. Non-linear optical (NLO) behavior of the p-cresol and 2-methoxy-p-cresol were investigated by determining of electric dipole moment, polarizability α, and hyperpolarizability β using the above mentioned basis sets. The molecular properties such as ionization potential, electronegativity, chemical potential, electrophilicity have been deduced from HOMO-LUMO analysis employing the same basis sets. A detailed interpretation of the infrared and Raman spectra of title molecules were reported. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecules have also been constructed.

  12. Comparative vibrational spectroscopic studies, HOMO-LUMO, NBO analyses and thermodynamic functions of p-cresol and 2-methyl-p-cresol based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Balachandran, V.; Murugan, M.; Nataraj, A.; Karnan, M.; Ilango, G.

    2014-11-01

    In the present study structural properties of p-cresol, and 2-methoxy-p-cresol have been studied by using B3LYP/cc-pvdz and B3PW91/cc-pvdz of Density Functional Theory (DFT) utilizing Becke three exchange functional and Lee Yang Paar correlation functional. The Fourier transform infrared and Fourier transform Raman spectra of title molecules were recorded (solid phase). Optimized geometry, harmonic vibrational frequencies and various thermodynamic parameters of the title compounds were calculated with B3LYP/cc-pvdz, and B3PW91/cc-pvdz basis sets. Non-linear optical (NLO) behavior of the p-cresol and 2-methoxy-p-cresol were investigated by determining of electric dipole moment, polarizability α, and hyperpolarizability β using the above mentioned basis sets. The molecular properties such as ionization potential, electronegativity, chemical potential, electrophilicity have been deduced from HOMO-LUMO analysis employing the same basis sets. A detailed interpretation of the infrared and Raman spectra of title molecules were reported. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecules have also been constructed.

  13. 47 CFR 36.605 - Calculation of safety net additive.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... exchange carriers shall not receive safety net additive for growth of Telecommunications Plant in Service... longer receive safety net additive after January 1, 2012 unless the carrier's realized total growth in Telecommunications Plant in Service was more than 14 percent during the qualifying period, defined as 2010 or...

  14. 47 CFR 36.605 - Calculation of safety net additive.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... exchange carriers shall not receive safety net additive for growth of Telecommunications Plant in Service... longer receive safety net additive after January 1, 2012 unless the carrier's realized total growth in Telecommunications Plant in Service was more than 14 percent during the qualifying period, defined as 2010 or...

  15. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV-Vis spectroscopies combined with DFT calculations.

    PubMed

    Rajesh, P; Gunasekaran, S; Gnanasambandan, T; Seshadri, S

    2015-02-25

    The complete vibrational assignment and analysis of the fundamental vibrational modes of Trifluoperazine (TFZ) was carried out using the experimental FT-IR, FT-Raman and UV-Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-31G (d,p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. The HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as first hyperpolarizability of TFZ have been computed using B3LYP quantum chemical calculation.

  16. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV-Vis spectroscopies combined with DFT calculations

    NASA Astrophysics Data System (ADS)

    Rajesh, P.; Gunasekaran, S.; Gnanasambandan, T.; Seshadri, S.

    2015-02-01

    The complete vibrational assignment and analysis of the fundamental vibrational modes of Trifluoperazine (TFZ) was carried out using the experimental FT-IR, FT-Raman and UV-Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-31G (d,p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. The HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as first hyperpolarizability of TFZ have been computed using B3LYP quantum chemical calculation.

  17. Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion

    NASA Astrophysics Data System (ADS)

    Singh, R.; Yadav, R. A.

    2014-09-01

    Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5sbnd C6 bond length increases and loses its double bond character while the C4sbnd C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled Nsbnd H stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

  18. Spin-transfer pathways in paramagnetic lithium transition-metal phosphates from combined broadband isotropic solid-state MAS NMR spectroscopy and DFT calculations.

    PubMed

    Clément, Raphaële J; Pell, Andrew J; Middlemiss, Derek S; Strobridge, Fiona C; Miller, Joel K; Whittingham, M Stanley; Emsley, Lyndon; Grey, Clare P; Pintacuda, Guido

    2012-10-17

    Substituted lithium transition-metal (TM) phosphate LiFe(x)Mn(1-x)PO(4) materials with olivine-type structures are among the most promising next generation lithium ion battery cathodes. However, a complete atomic-level description of the structure of such phases is not yet available. Here, a combined experimental and theoretical approach to the detailed assignment of the (31)P NMR spectra of the LiFe(x)Mn(1-x)PO(4) (x = 0, 0.25, 0.5, 0.75, 1) pure and mixed TM phosphates is developed and applied. Key to the present work is the development of a new NMR experiment enabling the characterization of complex paramagnetic materials via the complete separation of the individual isotropic chemical shifts, along with solid-state hybrid DFT calculations providing the separate hyperfine contributions of all distinct Mn-O-P and Fe-O-P bond pathways. The NMR experiment, referred to as aMAT, makes use of short high-powered adiabatic pulses (SHAPs), which can achieve 100% inversion over a range of isotropic shifts on the order of 1 MHz and with anisotropies greater than 100 kHz. In addition to complete spectral assignments of the mixed phases, the present study provides a detailed insight into the differences in electronic structure driving the variations in hyperfine parameters across the range of materials. A simple model delimiting the effects of distortions due to Mn/Fe substitution is also proposed and applied. The combined approach has clear future applications to TM-bearing battery cathode phases in particular and for the understanding of complex paramagnetic phases in general.

  19. Sulfur K-Edge XAS and DFT Calculations on NitrileHydratase: Geometric and Electronic Structure of the Non-heme Iron Active Site

    SciTech Connect

    Dey, Abhishek; Chow, Marina; Taniguchi, Kayoko; Lugo-Mas, Priscilla; Davin, Steven; Maeda, Mizuo; Kovacs, Julie A.; Odaka, Masafumi; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.; /SLAC, SSRL

    2006-09-28

    The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS{sup -})-, sulfenate (RSO{sup -})-, and sulfinate (RSO{sub 2}{sup -})-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO- species changes upon protonation as the S-O bond is elongated (by {approx}0.1 {angstrom}). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe{sup III} in the active site of NHase as CysS{sup -}, CysSOH, and CysSO{sub 2}{sup -} both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z{sub eff} of the Fe and reveals that the Fe in [FeNO]{sup 6} NHase species has a Z{sub eff} very similar to that of its photolyzed Fe{sup III} counterpart. DFT calculations reveal that this results from the strong {pi} back-bonding into the {pi}* antibonding orbital of NO, which shifts significant charge from the formally t{sub 2}{sup 6} low-spin metal to the coordinated NO.

  20. A dissociation between addition and subtraction with written calculation.

    PubMed

    McNeil, J E; Warrington, E K

    1994-06-01

    A patient with a severe dyscalculia and a mild arabic number dyslexia is described. He could perform simple addition and subtraction sums with oral presentation. However with written arabic number sums he was impaired with addition but not with subtraction. These findings require modifications to current models of arithmetic processing which have suggested that numerical inputs are converted into abstract internal representations before arithmetical processing can occur. PMID:8084426

  1. Highly Phosphorescent Crystals of Square-Planar Platinum Complexes with Chiral Organometallic Linkers: Homochiral versus Heterochiral Arrangements, Induced Circular Dichroism, and TD-DFT Calculations.

    PubMed

    Sesolis, Hugo; Dubarle-Offner, Julien; Chan, Carmen K M; Puig, Emmanuel; Gontard, Geoffrey; Winter, Pierre; Cooksy, Andrew L; Yam, Vivian W W; Amouri, Hani

    2016-06-01

    A novel class of chiral luminescent square-planar platinum complexes with a π-bonded chiral thioquinonoid ligand is described. Remarkably the presence of this chiral organometallic ligand controls the aggregation of this square planar luminophor and imposes a homo- or hetero-chiral arrangement at the supramolecular level, displaying non-covalent Pt-Pt and π-π interactions. Interestingly these complexes are highly luminescent in the crystalline state and their photophysical properties can be traced to their aggregation in the solid state. A TD-DFT calculation is obtained to rationalize this unique behavior. PMID:27142245

  2. Insight into the formation of the tert-butyl cation confined inside H-ZSM-5 zeolite from NMR spectroscopy and DFT calculations.

    PubMed

    Huang, Mengdi; Wang, Qiang; Yi, Xianfeng; Chu, Yueying; Dai, Weili; Li, Landong; Zheng, Anmin; Deng, Feng

    2016-08-23

    Solid-state NMR experiments and DFT calculations have been carried out to determine the complex structures of coadsorbed (13)C-labeled tert-butanol and NH3 in acidic H-ZSM-5 zeolite. It is found, besides the physically adsorbed tert-butanol/NH4(+) complex on Brønsted acid sites, the tert-butylamine cation is formed as well, confirming the presence of the tert-butyl cation confined in zeolite channels. Furthermore, (13)C-(27)Al double-resonance solid-state NMR spectroscopy is adopted to determine the host/guest interaction between the carbocation and the zeolite framework. PMID:27400892

  3. Rh-Catalyzed Decarbonylation of Conjugated Ynones via Carbon–Alkyne Bond Activation: Reaction Scope and Mechanistic Exploration via DFT Calculations

    PubMed Central

    Dermenci, Alpay; Whittaker, Rachel E.; Gao, Yang; Cruz, Faben A.; Yu, Zhi-Xiang; Dong, Guangbin

    2015-01-01

    In this full article, detailed development of a catalytic decarbonylation of conjugated monoynones to synthesize disubstituted alkynes is described. The reaction scope and limitation has been thoroughly investigated, and a broad range of functional groups including heterocycles were compatible under the catalytic conditions. Mechanistic exploration via DFT calculations has also been executed. Through the computational study, a proposed catalytic mechanism has been carefully evaluated. These efforts are expected to serve as an important exploratory study for developing catalytic alkyne-transfer reactions via carbon−alkyne bond activation. PMID:26229587

  4. Chiral vanadium(V) complexes with 2-aminoglucose Schiff-base ligands and their solution configurations: synthesis, structures, and DFT calculations.

    PubMed

    Mohammadnezhad, Gholamhossein; Böhme, Michael; Geibig, Daniel; Burkhardt, Anja; Görls, Helmar; Plass, Winfried

    2013-09-01

    two diastereomers are observed for the carbon atoms C2 (2 ppm) and C3 (4 ppm). DFT calculations of the NMR chemical shift parameters have been performed which are in good agreement with the experimental data. Moreover, the isomerization mechanism between the diastereomers is analysed on the basis of DFT calculations which indicate the required presence of methanol molecules as protic donors.

  5. Benchmarking dispersion and geometrical counterpoise corrections for cost-effective large-scale DFT calculations of water adsorption on graphene.

    PubMed

    Lorenz, Marco; Civalleri, Bartolomeo; Maschio, Lorenzo; Sgroi, Mauro; Pullini, Daniele

    2014-09-15

    The physisorption of water on graphene is investigated with the hybrid density functional theory (DFT)-functional B3LYP combined with empirical corrections, using moderate-sized basis sets such as 6-31G(d). This setup allows to model the interaction of water with graphene going beyond the quality of classical or semiclassical simulations, while still keeping the computational costs under control. Good agreement with respect to Coupled Cluster with singles and doubles excitations and perturbative triples (CCSD(T)) results is achieved for the adsorption of a single water molecule in a benchmark with two DFT-functionals (Perdew/Burke/Ernzerhof (PBE), B3LYP) and Grimme's empirical dispersion and counterpoise corrections. We apply the same setting to graphene supported by epitaxial hexagonal boron nitride (h-BN), leading to an increased interaction energy. To further demonstrate the achievement of the empirical corrections, we model, entirely from first principles, the electronic properties of graphene and graphene supported by h-BN covered with different amounts of water (one, 10 water molecules per cell and full coverage). The effect of h-BN on these properties turns out to be negligibly small, making it a good candidate for a substrate to grow graphene on. PMID:25056422

  6. Molecular structure and vibrational assignment of 1-[N-(2-pyridyl) aminomethylidene}-2(1H)-Naphtalenone by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations.

    PubMed

    Tanak, Hasan; Toy, Mehmet

    2016-01-01

    The molecular geometry and vibrational frequencies of 1-[N-(2-pyridyl)aminomethylidene}-2(1H)-Naphtalenone in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311++G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. In addition, calculated results are related to the linear correlation plot of computed data versus experimental geometric parameters and IR data. From the results it was concluded that the B3LYP method is superior to the HF method for the vibrational frequencies. Using the time-dependent density functional theory (TD-DFT) and Hartree-Fock (TD-HF) methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and experimental ones is determined. PMID:25468437

  7. Assignment of IR bands of isolated and protein-bound Peridinin in its fundamental and triplet state by static FTIR, time-resolved step-scan FTIR and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mezzetti, Alberto; Kish, Elizabeth; Robert, Bruno; Spezia, Riccardo

    2015-06-01

    The vibrational properties of Peridinin in its fundamental state and in the excited triplet state have been investigated by DFT calculations and static and time-resolved FTIR spectroscopy. The infrared spectrum of Peridinin in its fundamental state has been explored in the whole 2000-600 cm-1 range, and interpreted in term of molecular vibrations. In particular, new infrared bands have been identified and assigned to specific molecular vibrations. 3Peridinin molecular vibrations have also been investigated by DFT calculations. In addition, putative IR bands belonging to Peridinin and 3Peridinin have been identified in the step-scan FTIR difference spectrum of the Peridinin-Chlorophyll a-Protein from Amphidinium carterae, where light induce formation of a triplet state localized on one or more Peridinins. The exact nature of the triplet state formed in Peridinin-Chlorophyll a-Protein from dinoflagellates, in particular the possible involvement in this triplet state of 3Chlorophyll a, has been largely debated in the last few years (see Carbonera et al., 2014 [3]); time-resolved differential FTIR experiments have played a key role in this debate. Identification of IR marker bands for the main molecule (Peridinin) implicated in this photophysical process is therefore particularly important and makes this study a significant step towards the full understanding of Peridinin-Chlorophyll-a-Proteins photophysics.

  8. Molecular structure and vibrational assignment of 1-[N-(2-pyridyl) aminomethylidene}-2(1H)-Naphtalenone by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

    NASA Astrophysics Data System (ADS)

    Tanak, Hasan; Toy, Mehmet

    2016-01-01

    The molecular geometry and vibrational frequencies of 1-[N-(2-pyridyl)aminomethylidene}-2(1H)-Naphtalenone in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311++G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. In addition, calculated results are related to the linear correlation plot of computed data versus experimental geometric parameters and IR data. From the results it was concluded that the B3LYP method is superior to the HF method for the vibrational frequencies. Using the time-dependent density functional theory (TD-DFT) and Hartree-Fock (TD-HF) methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and experimental ones is determined.

  9. X-ray Crystallography, DFT Calculations and Molecular Docking of Indole-Arylpiperazine Derivatives as α1A-Adrenoceptor Antagonists.

    PubMed

    Xu, Wei; Huang, Jun-Jun; Shao, Bin-Hao; Xu, Xing-Jie; Jiang, Ren-Wang; Yuan, Mu

    2015-10-30

    Indole-arylpiperazine derivatives have exhibited good selectivity for the α1A-adrenoceptor, but the structure-activity-binding mechanism relationship remains unclear. In the current study, three compounds (1, 2 and 3) were investigated through single-crystal X-ray diffraction analysis, density functional theory (DFT) calculations and molecular docking using a homology model of the α1A receptor. Compounds 1 and 3 form H-bonds networks to stabilize their three-dimensional structures, while C-H···π interactions play a significant role in the packing of 2. Based on DFT-optimized conformations, the HOMO-LUMO energy gaps and molecular electrostatic potential (MEP) were theoretically calculated at the B3LYP/6-311G (d, p) level of theory. Chemical reactivity increases in the order of 3 < 2 < 1, and the maximum positive region of the MEP maps is mainly localized over the NH group. The binding mechanisms of ligand-α1A-adrenoceptor complexes were illustrated by molecular docking. Binding to Gln177 of the second extracellular loop region via hydrogen bonds is likely to be essential for α1A-selective antagonists. The present work sheds light on the studies of structure-activity-binding mechanism and aids in the design of α1A antagonists with high selectivity.

  10. 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.

  11. Ti{sub 3}GaC{sub 2} and Ti{sub 3}InC{sub 2}: First bulk synthesis, DFT stability calculations and structural systematics

    SciTech Connect

    Cuskelly, Dylan T.; Richards, Erin R.; Kisi, Erich H.; Keast, Vicki J.

    2015-10-15

    A simple methodology for identifying possible higher order M{sub n+1}AX{sub n} phases (n≥2) from the chemical characteristics of known phases was developed. The method was used to identify two potential M{sub 3}AC{sub 2} phases Ti{sub 3}GaC{sub 2} and Ti{sub 3}InC{sub 2}. After verifying that the n=1 MAX phases in these systems could be synthesised in bulk using a simple pressureless reactive sintering process, the new phases were synthesised using the same method. DFT calculations were used to test the thermodynamic stability of the new phases against the known competing phases within the same ternary systems. Both were found to be stable although Ti{sub 3}InC{sub 2} only marginally so. Crystal structure refinements and comparison to other MAX phases revealed a linear increase in the c-axis length as a function of the atomic radius of the A element. - Highlights: • Chemical systematics were used to highlight a search window for new MAX phases. • Two new higher order MAX phases, Ti{sub 3}InC{sub 2} and Ti{sub 3}GaC{sub 2}, were synthesised. • Pressureless reactive sintering was effective in producing bulk material. • DFT calculations indicate that the new phases are stable.

  12. Analysis of electronic structure and optical properties of N-doped SiO2 based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Sui-Shuan; Zhao, Zong-Yan; Yang, Pei-Zhi

    2015-07-01

    The crystal structure, electronic structure and optical properties of N-doped SiO2 with different N impurity concentrations were calculated by density function theory within GGA+U method. The crystal distortion, impurity formation energy, band gap, band width and optical parameter of N-doped SiO2 are closely related with N impurity concentration. Based on the calculated results, there are three new impurity energy levels emerging in the band gap of N-doped SiO2, which determine the electronic structure and optical properties. The variations of optical properties induced by N doping are predominately determined by the unsaturated impurity states, which are more obvious at higher N impurity concentration. In addition, all the doping effects of N in both α-quartz SiO2 and β-quartz SiO2 are very similar. According to these findings, one could understand the relationship between nitrogen concentration and optical parameter of SiOxNy materials, and design new optoelectrionic Si-O-N compounds.

  13. Unveiling self-sensitized photodegradation pathways by DFT calculations: A case of sunscreen p-aminobenzoic acid.

    PubMed

    Zhang, Siyu; Chen, Jingwen; Zhao, Qing; Xie, Qing; Wei, Xiaoxuan

    2016-11-01

    Self-sensitized photodegradation has been observed for diverse aquatic organic pollutants. However, photodegradation pathways have not been clarified in previous experimental studies. Here, we attempted to probe self-sensitized photodegradation pathways of organic pollutants employing both photolytic experiments and density functional theory calculations. By performing photolytic experiments, we found that singlet state oxygen ((1)O2) play an essential role in photodegradation of a sunscreen p-aminobenzoic acid (PABA). PABA can photogenerate (1)O2 and react fast with (1)O2. We hypothesized that PABA underwent (1)O2 induced self-sensitized photodegradation. By calculating transition states, intermediates and reaction barriers, we found that (1)O2 can oxidize PABA through electrophilic attacks on the benzene ring to abstract one H atom of the amino group following a 1,3-addition mechanism or to induce decarboxylation. Either pathway produces a hydroperoxide. O-O bond cleavage of the hydroperoxides occurring at ground states or the lowest triplet excited states can produce phenoxyl radical precursors of 4-amino-3-hydroxybenzoic acid and 4-aminophenol, which are photodegradation products detected in experiments. Thus, a viable (1)O2 self-sensitized photodegradation mechanism was unveiled for PABA. PMID:27529387

  14. DFT calculations of isomer shifts and quadrupole splitting parameters in synthetic iron-oxo complexes: applications to methane monooxygenase and ribonucleotide reductase.

    PubMed

    Liu, Tiqing; Lovell, Timothy; Han, Wen-Ge; Noodleman, Louis

    2003-08-25

    To predict isomer shifts and quadrupole splitting parameters of Fe atoms in the protein active sites of methane monooxygenase and ribonucleotide reductase, a correlation between experimental isomer shifts ranging 0.1-1.5 mm s(-)(1) for Fe atoms in a training set with the corresponding density functional theory (DFT) calculated electron densities at the Fe nuclei in those complexes is established. The geometries of the species in the training set, consisting of synthetic polar monomeric and dimeric iron complexes, are taken from the Cambridge structural database. A comparison of calculated Mössbauer parameters for Fe atoms from complexes in the training set with their corresponding experimental values shows very good agreement (standard deviation of 0.11 mm/s, correlation coefficient of -0.94). However, for the Fe atoms in the active sites of the structurally characterized proteins of methane monooxygenase and ribonucleotide reductase, the calculated Mössbauer parameters deviate more from their experimentally measured values. The high correlation that exists between calculated and observed quadrupole splitting and isomer shift parameters for the synthetic complexes leads us to conclude that the main source of the error arising for the protein active sites is due to the differing degrees of atomic-level resolution for the protein structural data, compared to the synthetic complexes in the training set. Much lower X-ray resolutions associated with the former introduce uncertainty in the accuracy of several bond lengths. This is ultimately reflected in the calculated isomer shifts and quadrupole splitting parameters of the Fe sites in the proteins. For the proteins, the closest correspondence between predicted and observed Mössbauer isomer shifts follows the order MMOH(red), RNR(red), MMOH(ox), and RNR(ox), with average deviations from experiment of 0.17, 0.17, 0.17-0.20, and 0.32 mm/s, but this requires DFT geometry optimization of the iron-oxo dimer complexes.

  15. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures).

    PubMed

    Sas, E B; Kose, E; Kurt, M; Karabacak, M

    2015-02-25

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

  16. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures).

    PubMed

    Sas, E B; Kose, E; Kurt, M; Karabacak, M

    2015-02-25

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule. PMID:25305625

  17. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures)

    NASA Astrophysics Data System (ADS)

    Sas, E. B.; Kose, E.; Kurt, M.; Karabacak, M.

    2015-02-01

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm-1 and 3500-10 cm-1, respectively. The 1H, 13C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The 1H and 13C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

  18. Synthesis, structure, spectral, thermal analyses and DFT calculation of a hydrogen bonded crystal: 2-Aminopyrimidinium dihydrogenphosphate monohydrate

    NASA Astrophysics Data System (ADS)

    Thangarasu, S.; Suresh Kumar, S.; Athimoolam, S.; Sridhar, B.; Asath Bahadur, S.; Shanmugam, R.; Thamaraichelvan, A.

    2014-09-01

    A proton transfer complex of 2-aminopyrimidine with phosphoric acid was synthesized and crystallized. Single crystal X-ray studies, the vibrational spectral analysis using Laser Raman and FT-IR spectroscopy in the range of 4000-400 cm-1, UV-Vis-NIR studies and thermogravimetric analyses were carried out in the solid crystalline form. The single crystal X-ray studies shows that the crystal packing is dominated by Nsbnd H⋯O and Osbnd H⋯O hydrogen bonds leading to a hydrogen bonded ensemble. The two dimensional cationic layers, connected through the centrosymmetric anionic dimer of R22(8) motif, is extending along ab plane of the crystal leading to zig-zag infinite chain C21(6) and C22(6) motifs. To investigate the strength of the hydrogen bonds, vibrational spectral studies were adopted and the shifting of bands due to the intermolecular interactions were analyzed. Density Functional Theory (DFT) using the B3LYP function with the 6-311++G(d,p) basis set was applied to the solid state molecular geometry obtained from single crystal X-ray studies. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which shows appreciable agreement. NBO analysis has been carried out by DFT level. In this study explains charge delocalization of the present molecule which shows the possible biological/pharmaceutical activity of the molecule. The number of normal modes were also attempted by the factor group analysis method. It is evident that the influence of extensive intermolecular hydrogen bonds reduces the Td symmetry of the phosphate anion to the lower C2v symmetry. The existence of exothermic peaks in DTA iterate the breaking of intermolecular hydrogen bonds and the phase change of the crystal. The presence of water molecule is also confirmed in the thermal analyses.

  19. Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10(1)0).

    PubMed

    Hellström, Matti; Spångberg, Daniel; Hermansson, Kersti

    2015-12-15

    We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10(1)0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10(1)0), as long as care is taken to account for the effects of CT. PMID:26525161

  20. Influence of the chemical functionalities of a molecularly imprinted conducting polymer on its sensing properties: electrochemical measurements and semiempirical DFT calculations.

    PubMed

    Lattach, Youssef; Archirel, Pierre; Remita, Samy

    2012-02-01

    Starting from thiophene-based functional monomers (FM), namely, TMA, TAA, TMeOH, EDOT, and Th, bonded to atrazine (ATZ) target molecules into FM/ATZ prepolymerization dimers in acetonitrile solutions, differently functionalized molecularly imprinted conducting polymers (FM-MICP) are electrosynthesized and then washed and used as sensitive layers for ATZ recognition. Sensitivity of these layers toward ATZ, which is quantified by cyclic voltammetric measurements, decreases in the following order of functional monomers: TMA, TAA, TMeOH, EDOT, and Th. Absolute values of the FM-ATZ dimerization free energies are calculated with the help of DFT/PCM calculations and of an empirical correction of the entropy effects, using a modified Wertz formula. A strong correlation is found between FM-MICP sensitivity and the amount of FM/ATZ prepolymerization complexes. PMID:22206269

  1. On the nature of lithium biphenyl in ethereal solvents. A critical analysis unifying DFT calculations, physicochemical data in solution, and a X-ray structure.

    PubMed

    de la Viuda, Mónica; Yus, Miguel; Guijarro, Albert

    2011-12-15

    The lithium ion is an important type of electrolyte that has technological applications in the manufacture of lithium ion cells; therefore, a better understanding of the nature of its solutions is desirable. When associated to the radical anion of biphenyl in an organic solvent, it forms conducting solutions comparable to strong electrolytes such as lithium perchlorate. We have studied the lithium biphenyl solution in dimethoxyethane using DFT calculations. The nature of these ionic solutions is described in terms of a dynamic equilibrium between different types of ionic associations, the composition of which depends on the solvent and the temperature. The X-ray structure of [Li(+)·4C(5)H(10)O][C(12)H(10)(•-)], a solvent-separated ion pair of lithium biphenyl complexed with tetrahydropyran, is reported. Its main structural characteristics coincide with the calculated one, which we think is the dominant species at room temperature, in agreement with the available physicochemical data.

  2. Main chemical species and molecular structure of deep eutectic solvent studied by experiments with DFT calculation: a case of choline chloride and magnesium chloride hexahydrate.

    PubMed

    Zhang, Chao; Jia, Yongzhong; Jing, Yan; Wang, Huaiyou; Hong, Kai

    2014-08-01

    The infrared spectrum of deep eutectic solvent of choline chloride and magnesium chloride hexahydrate was measured by the FTIR spectroscopy and analyzed with the aid of DFT calculations. The main chemical species and molecular structure in deep eutectic solvent of [MgClm(H2O)6-m]2-m and [ChxCly]x+y complexes were mainly identified and the active ion of magnesium complex during the electrochemical process was obtained. The mechanism of the electrochemical process of deep eutectic solvent of choline chloride and magnesium chloride hexahydrate was well explained by combination theoretical calculations and experimental. Besides, based on our results we proposed a new system for the dehydration study of magnesium chloride hexahydrate.

  3. Research of the structural and electronic properties of VN/AlN/VN and AlN/VN/AlN based on DFT calculation

    NASA Astrophysics Data System (ADS)

    Díaz F, J. H.; Espitia R, M. J.; Rodriguez Martínez, J. A.

    2016-08-01

    We investigated the structural, electronic, and magnetic properties of AlN/VN/AlN and VN/AlN/VN interlayers in the wurtzite structure, via first-principles calculations using the psuedopotential method within density functional theory (DFT) as implemented in the Quantum ESPRESSO code. The total energy calculation showed that the VN/AlN/VN interlayer is energetically more favorable than the AlN/VN/AlN one. Analysis of the density of states showed that the interlayers exhibit a metallic behavior that essentially comes from the hybridization and polarization of states V-d and N-p across the Fermi level. The interlayers exhibit magnetic properties, with a magnetic moment of 4μβ/cell. Due to these properties, the superlattices can potentially be used in the field of spintronics.

  4. Phase Transformation in Sm{sub 2}O{sub 3} at High Pressure: in Situ Synchrotron X-Ray Diffraction Study And Ab Initio DFT Calculation

    SciTech Connect

    Guo, Q.X.; Zhao, Y.S.; Jiang, C.; Mao, W.L.; Wang, Z.W.; /Cornell U., CHESS

    2009-06-09

    Sm{sub 2}O{sub 3} was compressed at room temperature up to 44.0 GPa and then decompressed back to ambient pressure. In situ X-ray diffraction was used to monitor the structural changes in the sample. A cubic to hexagonal phase transformation was observed in Sm{sub 2}O{sub 3} for the first time. After decompression back to ambient pressure, the hexagonal phase was not quenchable and transformed to a monoclinic phase. Ab initio Density-Functional-Theory (DFT) calculations were performed to obtain theoretical data for comparison with the experimental results and elucidation of the transformation mechanism. A possible phase transformation mechanism that is consistent with the experimental results and theoretical calculations is proposed.

  5. First-principles DFT+DMFT calculations of structural properties of actinides: Role of Hund's exchange, spin-orbit coupling, and crystal structure

    NASA Astrophysics Data System (ADS)

    Amadon, Bernard

    2016-09-01

    We utilize a combination of an ab initio calculation of effective Coulomb interactions and a DFT+DMFT calculation of total energy to study the structural properties of pure actinides. We first show that the effective direct Coulomb interactions in plutonium and americium are much smaller than usually expected. Secondly, we emphasize the key role of Hund's exchange in combination with the spin-orbit coupling in determining the structural parameters of δ -plutonium and americium. Thirdly, using this ab initio description, we reproduce the experimental transition from low volume early actinides (uranium, neptunium, α -plutonium) to high-volume late actinides (δ -plutonium, americium, and curium) without the need of an artificial magnetism. Finally, we compare the energies and structural properties of α , γ , ɛ , and δ phases of plutonium to experimental data.

  6. Comparative vibrational spectroscopic studies, HOMO-LUMO, NBO analyses and thermodynamic functions of p-cresol and 2-methyl-p-cresol based on DFT calculations.

    PubMed

    Balachandran, V; Murugan, M; Nataraj, A; Karnan, M; Ilango, G

    2014-11-11

    In the present study structural properties of p-cresol, and 2-methoxy-p-cresol have been studied by using B3LYP/cc-pvdz and B3PW91/cc-pvdz of Density Functional Theory (DFT) utilizing Becke three exchange functional and Lee Yang Paar correlation functional. The Fourier transform infrared and Fourier transform Raman spectra of title molecules were recorded (solid phase). Optimized geometry, harmonic vibrational frequencies and various thermodynamic parameters of the title compounds were calculated with B3LYP/cc-pvdz, and B3PW91/cc-pvdz basis sets. Non-linear optical (NLO) behavior of the p-cresol and 2-methoxy-p-cresol were investigated by determining of electric dipole moment, polarizability α, and hyperpolarizability β using the above mentioned basis sets. The molecular properties such as ionization potential, electronegativity, chemical potential, electrophilicity have been deduced from HOMO-LUMO analysis employing the same basis sets. A detailed interpretation of the infrared and Raman spectra of title molecules were reported. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecules have also been constructed. PMID:24892532

  7. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations.

    PubMed

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400cm(-1) and 3500-50cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The (1)H, (13)C and HMQC ((1)H-(13)C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement. PMID:23886506

  8. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400 cm-1 and 3500-50 cm-1, respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The 1H, 13C and HMQC (1H-13C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400 nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.

  9. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation.

  10. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation. PMID:27264846

  11. A new nano-scale manganese (II) coordination polymer constructed from semicarbazone Schiff base and dicyanamide ligands: Synthesis, crystal structure and DFT calculations

    NASA Astrophysics Data System (ADS)

    Farhadi, Saeed; Mahmoudi, Farzaneh; Simpson, Jim

    2016-03-01

    A new nano-structured Mn(II) coordination polymer [Mn(HL)(dca)(Cl)]n(1), [HL= Pyridine-2-carbaldehyde semicarbazone, dca= dicyanamide] has been synthesized by a sonochemical method and has been characterized by scanning electron microscopy, X-ray powder diffraction elemental analysis and IR spectroscopy. Single crystals of compound 1 was synthesized by slow evaporation method and was structurally characterised by single crystal X-ray diffraction. The single crystal structure shows one dimensional zig-zag chains with end-to-end dicyanamide-bridged ligand. A distorted octahedral geometry around the Mn2+centers was achieved by NNO atoms from HL, two nitrogen atoms of dicyanamide and one chlorine atom. Also for more details, the structure of 1, has been optimized by density functional theory (DFT calculations).

  12. Structural studies of pyrido[1,2- c]pyrimidine derivatives by 13C CPMAS NMR, X-ray diffraction and GIAO/DFT calculations

    NASA Astrophysics Data System (ADS)

    Pisklak, Maciej; Król, Marek; Herold, Franciszek; Wolska, Irena; Wawer, Iwona

    2008-12-01

    New 1-aryl- or 1-heteroaryl-piperazinylbutyl derivatives with pyrido[1,2- c]pyrimidine imide moiety, with the expected higher selectivity to 5-HT 1A receptors, have been synthesized. Five hydrochlorides and one base were studied by solid-state 13C CPMAS NMR spectroscopy. 13C chemical shifts indicated that the piperazine ring nitrogen N-1 was protonated. The crystal structure of the base (with 4'F, 3″-CF 3 substituents) was determined by X-ray crystallography. The pyridopyrimidine fragment is essentially planar, and aromatic substituent at C4 is twisted by 59.0°. The crystals are stabilized mainly by the C dbnd O…H sbnd C interactions. The analysis was completed by theoretical calculations of the shielding constants at the GIAO/DFT (B3LYP/6-311+G ∗∗) level.

  13. Electron density distribution in cladribine (2-chloro-2‧-deoxyadenosine) - A drug against leukemia and multiple sclerosis - Studied by multinuclear NQR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Latosińska, J. N.; Latosińska, M.; Seliger, J.; Žagar, V.; Kazimierczuk, Z.

    2009-07-01

    2-Chloro-2'-deoxyadenosine (Cladribine) chemotherapeutic drug has been studied experimentally in solid state by 35Cl NQR and NMR-NQR double resonance and theoretically by the Density Functional Theory. Fifteen resonance frequencies on 14N have been detected and assigned to particular nitrogen sites in the 2-CdA molecule. The effects of tautomerism, regioisomerism, conformations and molecular aggregations, related to intermolecular hydrogen bond formation, on the NQR parameters have been analysed within the DFT and AIM ( Atoms in Molecules) formalism. The properties of the whole molecule, the so-called global reactivity descriptors, have been calculated for a comparison of both syn and anti conformations of 2-CdA molecule to check the effect of crystal packing on molecular conformation.

  14. Novel oxorhenium complex of 2-(2-pyridyl)-4-methylthiazole-5-carboxylic acid - Synthesis, spectroscopic characterization, X-ray structure and DFT calculations

    NASA Astrophysics Data System (ADS)

    Machura, B.; Wolff, M.; Świtlicka, A.; Palion, J.; Kruszynski, R.

    2011-05-01

    The reaction of the complex [ReOBr 3(AsPh 3) 2] with 2-(2-pyridyl)-4-methylthiazole-5-carboxylic acid (pmtca) has been examined and novel dinuclear rhenium oxocomplex - [{ReOBr 2(pmtca) 2} 2(μ-O)]·Me 2CO·2H 2O with a linear O dbnd Re sbnd O sbnd Re dbnd O backbone - has been obtained. The complex has been studied by IR, UV-Vis spectroscopy and X-ray crystallography. The electronic structure of [{ReOBr 2(pmtca) 2} 2(μ-O)] has been calculated with the density functional theory (DFT) method, and the electronic spectrum of the complex was investigated at the TDDFT level employing B3LYP functional in combination with LANL2DZ.

  15. Synthesis, structural characterization and DFT calculation on a square-planar Ni(II) complex of a compartmental Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Biswas, Surajit; Dolai, Malay; Dutta, Arpan; Ali, Mahammad

    2016-12-01

    Reaction of a symmetric compartmental Schiff-base ligand, (H2L) with nickel(II) perchlorate hexahydrate in 1:1 M ratio in methanol gives rise to a mononuclear nickel(II) compound, NiL (1). The compound has been characterized by C, H, N microanalyses and UV-Vis spectra. The single crystal X-ray diffraction studies reveal a square planar geometry around the Ni(II) center. The compound crystallizes in monoclinic system with space group C2/c with a = 21.6425(6), b = 9.9481(3), c = 13.1958(4) Å, β = 107.728(2)°, V = 2706.16(14) Å3 and Z = 4. Ground state DFT optimization and TDDFT calculations on the ligand and complex were performed to get their UV-Vis spectral pattern.

  16. The stereoselectivities of tributyltin hydride-mediated reductions of 5-bromo-D-glucuronides to L-iduronides are dependent on the anomeric substituent: syntheses and DFT calculations.

    PubMed

    Mohamed, Shifaza; Krenske, Elizabeth H; Ferro, Vito

    2016-03-14

    One of the shortest synthetic routes to L-iduronic acid derivatives is via free radical reduction of the C-5 bromide of the corresponding protected D-glucuronic acid derivative. The epimerization of such C-5 bromides to the L-ido derivatives via reaction with tributyltin hydride was investigated. It was found that the stereoselectivity of the reaction was dependent on the anomeric substituent. If the substituent was fluoride the L-ido product was obtained exclusively in 65-72% yield whereas the O-methyl or O-acetyl derivatives led to isomeric mixtures of both the L-ido and D-gluco products in different ratios depending on the reaction conditions. DFT calculations were performed to determine the stereoelectronic factors that favour formation of the L-ido isomer from the fluoride and suggest the selectivity is due to a transition state gauche effect and an Sn-F interaction. PMID:26878700

  17. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by 35Cl NQR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Bronisz, K.; Ostafin, M.; Poleshchuk, O. Kh.; Mielcarek, J.; Nogaj, B.

    2006-11-01

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by 35Cl NQR method in order to find the correlation between electronic structure and biological activity. The 35Cl NQR resonance frequencies ( νQ) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period ( t0.5), affinity to benzodiazepine receptor (IC 50) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of 35Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  18. Density functional computational thermochemistry: Accurate determination of the enthalpy of formation of perfluoropropane from DFT and ab initio calculations on isodesmic reactions

    NASA Astrophysics Data System (ADS)

    Ventura, Oscar N.; Segovia, Marc

    2005-02-01

    The experimental enthalpy of formation of perfluoropropane (C 3F 8), reported originally as -1729 kJ/mol and latter corrected to -1784.7 kJ/mol, is reexamined at the light of density functional and model chemistry (G3, CBS-4, CBS-Q) calculations of several isodesmic reactions relating C 3F 8 to smaller fluoroalkanes. The average enthalpy of formation of C 3F 8 obtained from all reactions studied was -1739 ± 12 kJ/mol at the DFT level and -1748 ± 12 kJ/mol at the ab initio level, thus ruling out the larger experimental value. A value of -1732 ± 5 kJ/mol is recommended from careful analysis of the theoretical results.

  19. Heterotrimetallic Ru(II)/Pd(II)/Ru(II) complexes: synthesis, crystalstructure, spectral characterization, DFT calculation and antimicrobial study.

    PubMed

    Al-Noaimi, Mousa; Nafady, Ayman; Warad, Ismail; Alshwafy, Rwaida; Husein, Ahmad; Talib, Wamidh H; Hadda, Taibi Ben

    2014-03-25

    New ruthenium(II) mononuclear complexes of the type [RuCl2(PPh3)2(η(2)-triamine)] (2) [RuCl(PPh3)2(η(3)-triamine)]Cl (5) (triemine=N(1)-(2-aminoethyl)-1,2-ethanediamine) have been synthesized by reacting [RuCl2(PPh3)3] (1) with one mole equivalent of N(1)-(2-aminoethyl)-1,2-ethanediamine in dichloromethane. Reaction of (2) with half-equivalent of (PhCN)2PdCl2 or Pd(OAc)2 in dichloromethane as a solvent afforded two novel heterotrimetallic Ru(II)-Pd(II)-Ru(II) complexes, [Ru(II)Cl2(PPh3)2(triamine)]2[Pd(II)X2](X=Cl, OAc) (3 and 4), bearing bioactive ligand. The progress of the undertaken reactions was monitored by (31)P{1H} NMR and FTIR. Crystal structure of complex 2 was confirmed by X-ray diffraction. The absorption spectrum of 2 in dichloromethane was modeled by time-dependent density functional theory (TD-DFT). The in vitro antimicrobial studies of complex 2-5 against an array of microorganisms (bacteria and fungi) were conducted. Complexes 3 and 4 exhibit high dual antibacterial and antifungal activity inhibiting microorganisms possibly via hydrolytic pathway which further evidenced by electrochemical analyses. The complexes 3 and 4 show a high inhibitory activity at 200 μg/ml concentration, suggesting that complexes 3 and 4 are two efficient catalytic inhibitor of microorganisms and further, they should be tested against cancer strains.

  20. Synthesis, physicochemical characterization, DFT calculation and biological activities of Fe(III) and Co(II)-omeprazole complexes. Potential application in the Helicobacter pylori eradication

    NASA Astrophysics Data System (ADS)

    Russo, Marcos G.; Vega Hissi, Esteban G.; Rizzi, Alberto C.; Brondino, Carlos D.; Salinas Ibañez, Ángel G.; Vega, Alba E.; Silva, Humberto J.; Mercader, Roberto; Narda, Griselda E.

    2014-03-01

    The reaction between the antiulcer agent omeprazole (OMZ) with Fe(III) and Co(II) ions was studied, observing a high ability to form metal complexes. The isolated microcrystalline solid complexes were characterized by elemental analysis, X-ray powder diffraction (XRPD), Scanning Electron Microscopy (SEM), magnetic measurements, thermal study, FTIR, UV-Visible, Mössbauer, electronic paramagnetic resonance (EPR), and DFT calculations. The metal-ligand ratio for both complexes was 1:2 determined by elemental and thermal analysis. FTIR spectroscopy showed that OMZ acts as a neutral bidentate ligand through the pyridinic nitrogen of the benzimidazole ring and the oxygen atom of the sulfoxide group, forming a five-membered ring chelate. Electronic, Mössbauer, and EPR spectra together with magnetic measurements indicate a distorted octahedral geometry around the metal ions, where the coordination sphere is completed by two water molecules. SEM and XRPD were used to characterize the morphology and the crystal nature of the complexes. The most favorable conformation for the Fe(III)-OMZ and Co(II)-OMZ complexes was obtained by DFT calculations by using B3LYP/6-31G(d)&LanL2DZ//B3LYP/3-21G(d)&LanL2DZ basis set. Studies of solubility along with the antibacterial activity against Helicobacter pylori for OMZ and its Co(II) and Fe(III) complexes are also reported. Free OMZ and both metal complexes showed antibacterial activity against H. pylori. Co(II)-OMZ presented a minimal inhibitory concentration ˜32 times lower than that of OMZ and ˜65 lower than Fe(III)-OMZ, revealing its promising potential use for the treatment of gastric pathologies associated with the Gram negative bacteria. The morphological changes observed in the cell membrane of the bacteria after the incubation with the metal-complexes were also analyzed by SEM microscopy. The antimicrobial activity of the complexes was proved by the viability test.

  1. 40 CFR 75.75 - Additional ozone season calculation procedures for special circumstances.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Additional ozone season calculation... § 75.75 Additional ozone season calculation procedures for special circumstances. (a) The owner or operator of a unit that is required to calculate ozone season heat input for purposes of providing...

  2. 40 CFR 75.75 - Additional ozone season calculation procedures for special circumstances.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Additional ozone season calculation... § 75.75 Additional ozone season calculation procedures for special circumstances. (a) The owner or operator of a unit that is required to calculate ozone season heat input for purposes of providing...

  3. 40 CFR 75.75 - Additional ozone season calculation procedures for special circumstances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Additional ozone season calculation... § 75.75 Additional ozone season calculation procedures for special circumstances. (a) The owner or operator of a unit that is required to calculate ozone season heat input for purposes of providing...

  4. 40 CFR 75.75 - Additional ozone season calculation procedures for special circumstances.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 17 2014-07-01 2014-07-01 false Additional ozone season calculation... § 75.75 Additional ozone season calculation procedures for special circumstances. (a) The owner or operator of a unit that is required to calculate ozone season heat input for purposes of providing...

  5. 40 CFR 75.75 - Additional ozone season calculation procedures for special circumstances.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Additional ozone season calculation... § 75.75 Additional ozone season calculation procedures for special circumstances. (a) The owner or operator of a unit that is required to calculate ozone season heat input for purposes of providing...

  6. Combined EXAFS and DFT structure calculations provide structural insights into the 1:1 multi-histidine complexes of Cu(II) , Cu(I) , and Zn(II) with the tandem octarepeats of the mammalian prion protein.

    PubMed

    Pushie, M Jake; Nienaber, Kurt H; McDonald, Alex; Millhauser, Glenn L; George, Graham N

    2014-07-28

    The metal-coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of its interaction with copper just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, but structural details of the various metal coordination modes have not been fully elucidated in some cases. In the present study, we have employed X-ray absorption near-edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for Cu(II) , Cu(I) , and Zn(II) with an N-terminal fragment of PrP. The PrP fragment corresponds to four tandem repeats representative of the mammalian octarepeat domain, designated as OR4 , which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations have provided additional structural and thermodynamic data, and candidate structures have been used to inform EXAFS data analysis. The optimized geometries from DFT calculations have been used to identify potential coordination complexes for multi-histidine coordination of Cu(II) , Cu(I) , and Zn(II) in an aqueous medium, modelled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve-fitting, using full multiple scattering on candidate structures derived from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of Cu(II) , Cu(I) , and Zn(II) with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as square-planar [Cu(II) (His)4 ](2+) , digonal [Cu(I) (His)2 ](+) , and tetrahedral [Zn(II) (His)3 (OH2 )](2+) , respectively.

  7. Molecular vibrational investigation [FT-IR, FT-Raman, UV-Visible and NMR] on Bis(thiourea) Nickel chloride using HF and DFT calculations

    NASA Astrophysics Data System (ADS)

    Anand, S.; Sundararajan, R. S.; Ramachandraraja, C.; Ramalingam, S.; Durga, R.

    2015-03-01

    In the present research work, the FT-IR, FT-Raman spectra of the Bis(thiourea) Nickel chloride (BTNC) were recorded and analyzed. The observed fundamental frequencies in finger print and functional group regions were assigned according to their uniqueness region. The computational calculations were carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The present organo-metallic compound was made up of covalent and coordination covalent bonds. The modified vibrational pattern of the complex molecule associated with ligand group was analyzed. Furthermore, the 13C NMR and 1H NMR spectral data were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP/6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A investigation on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed.

  8. Spectroscopic [FT-IR and FT-Raman] and theoretical [UV-Visible and NMR] analysis on α-Methylstyrene by DFT calculations

    NASA Astrophysics Data System (ADS)

    Karthikeyan, N.; Joseph Prince, J.; Ramalingam, S.; Periandy, S.

    2015-05-01

    In the present research work, the FT-IR, FT-Raman and 13C and 1H NMR spectra of the α-Methylstyrene were recorded. The observed fundamental frequencies in finger print as well as functional group regions were assigned according to their uniqueness region. The Gaussian computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The impact of the presence of vinyl group in phenyl structure of the compound is investigated. The modified vibrational pattern of the molecule associated vinyl group was analyzed. Moreover, 13C NMR and 1H NMR were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed.

  9. FT-IR, FT-Raman, UV/Vis spectra and fluorescence imaging studies on 2-(bromoacetyl)benzo(b)furan by ab initio DFT calculations.

    PubMed

    Veeraiah, A

    2015-08-01

    The vibrational and electronic properties of 2-(bromoacetyl)benzo(b)furan have been studied in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-31G(d,p) basis set. The theoretically calculated optimized parameters, vibrational frequencies etc., were compared with the experimental values, which yield good agreement between the observed and calculated values. The complete assignments of fundamental modes were performed on the basis of the potential energy distribution (PED). UV-visible spectrum of the compound was recorded in the region 300-600 nm and compared with the theoretical spectrum obtained from SAC-CI calculations. A good agreement is observed between the experimental and theoretical spectra. Fluorescence microscopic imaging studies proved that the compound can be used as one of the potential light sources in the yellow region with suitable excitation. Further, the predicted electronic transitions between the MOs 47→64, 52→62, 56→65, 56→72, 56→77 of the compound show a strong line at 569.8 nm.

  10. Crystal structures, spectra properties and DFT calculations studies on 4-phenyl-1-(3-phenylallylidene)thiosemicarbazide and its Ni(II) complex.

    PubMed

    Song, Jie; Zhu, Fengxia; Wang, Hongyan; Zhao, Pusu

    2014-08-14

    4-Phenyl-1-(3-phenylallylidene)thiosemicarbazide (HL) and its metal complex of NiL2 have been synthesized. For them, elemental analysis, IR and X-ray single crystal diffraction have been carried out. In complex NiL2, the central Ni(2+) ion coordinates with two deprotonated ligands of L(-) and adopts a distorted square planar configuration with the Ni(2+) ion being located at the inversion center. The thermal analyses result shows that complex NiL2 undergoes two decomposition processes. For the title compounds, DFT calculations of the structures and natural population analysis (NPA) have been performed at B3LYP/LANL2DZ level of theory. The predicted geometric parameters are compared with the experimental values and they are supported each other. By using TD-DFT method, electron spectra of ligand HL and complex NiL2 have been predicted, which suggest the B3LYP/LANL2DZ method can approximately simulate the electron spectra for the system presented here. The NPA results indicate that, for ligand HL, the electronic absorption spectra are mainly assigned to n-π(∗) and π-π(∗) electron transitions, while for the complex NiL2, the electronic transitions are mainly derived from the contribution of an intra-ligand (IL) transition, a metal-to-ligand charge transfer (MLCT) transition and a d-d transition. Based on vibrational analysis, thermodynamic properties for ligand HL and complex NiL2 at different temperatures have been obtained. PMID:24735780

  11. The electronic spectrum of AgBr 2: Ab initio benchmark vs. DFT calculations on the lowest ligand-field states including spin-orbit effects

    NASA Astrophysics Data System (ADS)

    Santoyo-Castillo, I.; Ramírez-Solís, A.

    2010-10-01

    The X 2Π g, 2Σ g+ and 2Δ g states of AgBr 2 have been studied through benchmark ab initio CASSCF + Averaged Coupled Pair Functional (ACPF) and DFT calculations using especially developed valence basis sets to study the transition energies, geometries, vibrational frequencies, Mulliken charges and spin densities. The spin-orbit (SO) effects were included through the effective hamiltonian formalism using the |ΛSΣ> ACPF energies as diagonal elements. At the ACPF level, the ground state is 2Π g, in contradiction with ligand-field theory and Hartree-Fock results. The ACPF adiabatic excitation energies of the 2Σ g+ and 2Δ g states are 3825 and 20 152 cm -1, respectively. The inclusion of the SO effects leads to a pure Ω = 3/2 ( 2Π g) ground state, a Ω = 1/2 (97% 2Π g + 3% 2Σ g+) A state, a Ω = 1/2 (3% 2Π g + 97% 2Σ g+) B state, a Ω = 5/2 ( 2Δ g) C state and a Ω = 3/2 (99% 2Δ g) D state. The B97, B3LYP and PBE0 functionals, which were shown to yield accurate transition energies for CuCl 2, overestimate the X 2Π g- 2Σ g+ T e by around 25% but provide a qualitative energetic ordering in agreement with CASSCF and ACPF results. The nature of the bonding in the X 2Π g ground state is different from that of AgCl 2 since the Mulliken charge on the metal is 0.95 while the spin density is only 0.39. DFT strongly delocalizes the spin density providing even smaller values of around 0.13 on Ag not only for the ground state, but also for the 2Σ g+ state.

  12. Multichromophoric bimetallic Ru(II) terpyridine complexes based on pyrenyl-bis-phenylimidazole spacer: synthesis, photophysics, spectroelectrochemistry, and TD-DFT calculations.

    PubMed

    Karmakar, Srikanta; Maity, Dinesh; Mardanya, Sourav; Baitalik, Sujoy

    2014-11-17

    A symmetrical bridging ligand, 5,11-bis(4-([2,2':6',2″-terpyridine]-4'-yl)phenyl)-4,12-dihydropyreno[4,5-d:9,10-d']diimidazole (tpy-H2PhImzPy-tpy), containing terpyridyl coordinating units connected via a pyrenyl-bis-phenylimidazole spacer have been designed to synthesize a new class of light harvesting bimetallic Ru(II) complexes. The electronic properties of this complexes can be fine-tuned by varying tridentate terminal ligands. Full characterization of the compounds has been done with the help of (1)H NMR spectroscopy, high-resolution mass spectrometry, and elemental analysis. Geometry optimization of the complexes was also carried out with density functional theory (DFT). Electronic absorption spectra exhibit a number of very intense π-π* and n-π* transitions in the UV and moderately intense MLCT and ILCT transitions in the visible region. Interestingly, the present bimetallic complexes exhibit moderately strong luminescence in the range between 657 and 703 nm and lifetimes (long component) between 5.8 and 67.0 ns at room temperature showing the dependence of the emission characteristics upon the type of terminal ligand and solvent. Detailed temperature-dependent emission measurements showed that an overall enhancement of photoluminescence intensity and lifetime occur in all three cases upon lowering of temperature. The redox behavior of the compounds is characterized by a single reversible anodic wave corresponding to two closely spaced one-electron processes. The appearance of intervalence charge transfer transition (IVCT) bands in the NIR region on electrochemical generation of Ru(II)Ru(II)/Ru(II)Ru(III) species indicates the presence of substantial electronic communication among the two ruthenium centers in the bimetallic complexes. DFT and TDDFT calculations were also done for better understanding of the absorption and emission spectral characteristics of the complexes. PMID:25376014

  13. First principles (DFT) characterization of Rh(I) /dppp-catalyzed C-H activation by tandem 1,2-addition/1,4-Rh shift reactions of norbornene to phenylboronic acid.

    PubMed

    Kantchev, Eric Assen B; Pangestu, Surya R; Zhou, Feng; Sullivan, Michael B; Su, Hai-Bin

    2014-11-17

    The C-H activation in the tandem, "merry-go-round", [(dppp)Rh]-catalyzed (dppp=1,3-bis(diphenylphosphino)propane), four-fold addition of norborene to PhB(OH)2 has been postulated to occur by a C(alkyl)H oxidative addition to square-pyramidal Rh(III) -H species, which in turn undergoes a C(aryl)-H reductive elimination. Our DFT calculations confirm the Rh(I) /Rh(III) mechanism. At the IEFPCM(toluene, 373.15 K)/PBE0/DGDZVP level of theory, the oxidative addition barrier was calculated to be 12.9 kcal mol(-1) , and that of reductive elimination was 5.0 kcal mol(-1) . The observed selectivity of the reaction correlates well with the relative energy barriers of the cycle steps. The higher barrier (20.9 kcal mol(-1) ) for norbornyl-Rh protonation ensures that the reaction is steered towards the 1,4-shift (total barrier of 16.3 kcal mol(-1) ), acting as an equilibration shuttle. The carborhodation (13.2 kcal mol(-1) ) proceeds through a lower barrier than the protonation (16.7 kcal mol(-1) ) of the rearranged aryl-Rh species in the absence of o- or m-substituents, ensuring multiple carborhodations take place. However, for 2,5-dimethylphenyl, which was used as a model substrate, the barrier for carborhodation is increased to 19.4 kcal mol(-1) , explaining the observed termination of the reaction at 1,2,3,4-tetra(exo-norborn-2-yl)benzene. Finally, calculations with (Z)-2-butene gave a carborhodation barrier of 20.2 kcal mol(-1) , suggesting that carborhodation of non-strained, open-chain substrates would be disfavored relative to protonation.

  14. Structure of 3-aminopyridine betaine hydrochloride studied by X-ray diffraction, DFT calculations, FTIR and NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kowalczyk, I.; Katrusiak, A.; Szafran, M.

    2010-08-01

    The structure of 3-aminopyridine betaine hydrochloride (1-carboxymethyl-3-aminopyridinium chloride), 3-NH 2PBH·Cl, has been studied by X-ray diffraction, B3LYP/6-311G(d,p) calculations, FTIR and NMR spectra. The compound crystallized in monoclinic, space group P2 1/c in the crystal, the Cl - anion is connected with protonated betaine via the hydrogen bond O-H⋯Cl of 2.946(3) Å. Both protons of the NH 2 group are engaged in hydrogen bonds with the neighboring molecules: N(2)-H(2B)⋯O(2) of 2.905(6) Å and N(2)-H(2B)⋯Cl(1) of 3.324(3) Å. The Cl - ion interacts electrostatically with three neighboring molecules. The probable assignments of the anharmonic experimental solid state vibrational frequencies of the investigated compound, based on the calculated frequencies in vacuum at the same level of theory for optimized structure, have been made. Correlations between the experimental 13C and 1H NMR chemical shifts ( δexp) and the GIAO/B3LYP/6-311G(d,p) calculated magnetic isotropic shielding ( σcal) in DMSO and D 2O, δexp = a + b · σcalc, are reported.

  15. Structure of 1-methyl-6-oxyquinolinium betaine dihydrate studied by X-ray diffraction, DFT calculations, vibrational and NMR spectra

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Ratajczak-Sitarz, M.; Katrusiak, A.; Szafran, M.

    2010-07-01

    The crystals of 1-methyl-6-oxyquinolinium betaine dihydrate, 6QB·2H 2O, are triclinic, space group P1¯. The oxygen atom of 6QB exhibits an extremely rare capability of accepting four hydrogen bonds. It is engaged in four hydrogen bonds to water molecules of the 2.823, 2.825, 2.833 and 2.849 Å; each water molecule interacts with two neighbouring 6QB molecules linking them into infinite sheets. Differences in geometrical parameters between the X-ray and calculated molecules reflect changes in their structures between zwitterion and quinonoid forms. The probable assignments of the experimental FTIR solid spectrum have been made on the basis of B3LYP/6-311G(d,p) calculated frequencies in vacuum. Both 1H and 13C chemical shifts are solvent dependent. Linear correlations between the experimental 1H and 13C NMR chemical shifts of 6QB·2H 2O in solutions and the GIAO/B3LYP/6-311G(d,p) calculated magnetic isotropic shielding tensors ( σcal) using the screening solvation model, δexp = a + bσcal, are reported.

  16. Molecular structure, spectroscopic characterization and DFT calculations of a novel (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one

    NASA Astrophysics Data System (ADS)

    Alpaslan, Yelda Bingöl; Gökce, Halil; Macit, Mustafa; Alpaslan, Gökhan; Özdemir, Namık

    2015-09-01

    A novel Schiff base compound (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 2-ethylaniline. The structural properties of the compound have been characterized by using FT-IR, 1H and 13C NMR, UV-vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the keto-amine tautomeric form. The molecular geometry, vibrational frequencies, electronic absorption spectra and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the title compound in the ground state have been calculated by using density functional theory (DFT/B3LYP) method with 6-311G++(d,p) basis set, and compared with the experimental data. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The theoretical values are in good agreement with the experimental ones. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the 6-311G++(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the compound decreases with increasing polarity of the solvent. The molecular electrostatic potential (MEP), HOMO-LUMO energy gap and non-linear optical (NLO) properties of the compound were investigated using theoretical calculations.

  17. Glyphosate complexation to aluminium(III). An equilibrium and structural study in solution using potentiometry, multinuclear NMR, ATR-FTIR, ESI-MS and DFT calculations.

    PubMed

    Purgel, Mihály; Takács, Zoltán; Jonsson, Caroline M; Nagy, Lajos; Andersson, Ingegärd; Bányai, István; Pápai, Imre; Persson, Per; Sjöberg, Staffan; Tóth, Imre

    2009-11-01

    The stoichiometries and stability constants of a series of Al(3+)-N-phosponomethyl glycine (PMG/H(3)L) complexes have been determined in acidic aqueous solution using a combination of precise potentiometric titration data, quantitative (27)Al and (31)P NMR spectra, ATR-FTIR spectrum and ESI-MS measurements (0.6M NaCl, 25 degrees C). Besides the mononuclear AlH(2)L(2+), Al(H(2)L)(HL), Al(HL)(2)(-) and Al(HL)L(2-), dimeric Al(2)(HL)L(+) and trinuclear Al(3)H(5)L(4)(2+) complexes have been postulated. (1)H and (31)P NMR data show that different isomers co-exist in solution and the isomerization reactions are slow on the (31)P NMR time scale. The geometries of monomeric and dimeric complexes likely double hydroxo bridged and double phosphonate bridged isomers have been optimized using DFT ab initio calculations starting from rational structural proposals. Energy calculations using the PCM solvation method also support the co-existence of isomers in solutions.

  18. Spectroscopic investigation, natural bond orbital analysis, HOMO-LUMO and thermodynamic functions of 2-tert-butyl-5-methyl anisole using DFT (B3LYP) calculations.

    PubMed

    Balachandran, V; Santhi, G; Karpagam, V; Revathi, B; Karabacak, M

    2015-02-01

    The optimized molecular structure and corresponding vibrational assignments of 2-tert-butyl-5-methyl anisole (TBMA) have been investigated using density functional theory (DFT)/B3LYP with 6-31G(d,p) and 6-311++G(d,p) basis sets investigation of the relative orientation of the methoxy group has shown two conformers (O-cis) and (O-trans) exist. The vibrational analysis of the stable conformer of the title compound is performed by means of infrared absorption and Raman spectroscopy in combination with theoretical simultaneously. The natural bond orbital (NBO) analysis is useful to understand the intra-molecular hyper conjugative interaction lone pair and π(∗)(C-C), σ(∗)(C-H) bond orbital. HOMO and LUMO energies show that charge transfer occurs in the molecule, therefore; HOMO, LUMO and molecular electrostatic potential (MEP) were calculated and analyzed. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data. The thermodynamic functions of TBMA were calculated by B3LYP/6-311+G(d,p) basis set.

  19. Synthesis, DFT calculations and cytotoxic investigation of platinum complexes with 3-thiolanespiro-5‧-hydantoin and 4-thio-1H-tetrahydropyranespiro-5‧-hydantoin

    NASA Astrophysics Data System (ADS)

    Bakalova, Adriana; Buyukliev, Rossen; Momekov, Georgi

    2015-07-01

    Two organic compounds - 3-thiolanespiro-5‧-hydantoin, 4-thio-1H-tetrahydropyranespiro-5‧-hydantoin and four new Pt(II) and Pt(IV) complexes with general formulas cis-[Pt(L)2Cl2] and cis-[Pt(L)2Cl4] were synthesized. The obtained compounds were characterized by elemental analysis, IR, 1H, 13C NMR spectroscopy. The hybrid DFT calculations were used for optimization of the structure geometries of the ligand (L1) and its Pt(II) complex (1). The calculated structural parameters such as bond lengths and angles are in good agreement with the experimental data for similar hydantoins and their platinum complexes. The obtained results showed that the geometry of the complex (1) is plane square and the bounding of the L1 with platinum ion is realized by sulfur atom from thiolane ring. The complexes were tested for cytotoxicity in vitro on four human tumor cell lines. The tested compounds exerted concentration-dependent cytotoxic effects against some of the tumor cell lines.

  20. A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis.

    PubMed

    Astani, Elahe K; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L

    2016-07-01

    A theoretical study at the level of density functional theory (DFT) was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond interactions, in the active site of enzyme human androsterone sulphotransferase (SULT2A1/ADT). Geometry optimization, interaction energy, (2)H, (14)N, and (17)O electric field gradient (EFG) tensors, (1)H, (13)C, (17)O, and (15)N chemical shielding (CS) tensors, Natural Bonding Orbital (NBO) analysis, and quantum theory of atoms in molecules (QTAIM) analysis of this active site were investigated. It was found that androsterone (ADT) is able to form hydrogen bonds with residues Ser80, Ile82, and His99 of the active site. The interaction energy calculations and NBO analysis revealed that the ADT molecule forms the strongest hydrogen bond with Ser80. Results revealed that ADT interacts with the other residues through electrostatic and Van der Waals interactions. Results showed that these hydrogen bonds influence on the calculated (2)H, (14)N, and (17)O quadrupole coupling constants (QCCs), as well as (1)H, (13)C, (17)O, and (15)N CS tensors. The magnitude of the QCC and CS changes at each nucleus depends directly on its amount of contribution to the hydrogen bond interaction. PMID:27337388

  1. Spectroscopic (FTIR, FT-Raman), molecular electrostatic potential, NBO and HOMO-LUMO analysis of P-bromobenzene sulfonyl chloride based on DFT calculations.

    PubMed

    Jeyavijayan, S

    2015-02-01

    The FTIR and FT-Raman spectra of P-bromobenzene sulfonyl chloride (P-BBSC) have been recorded in the regions 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method. A good agreement between experimental and calculated normal modes of vibrations has been observed. A detailed interpretation of the infrared and Raman spectra of P-BBSC is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms. The UV-vis spectral analysis of P-BBSC has also been done which confirms the charge transfer of the molecule.

  2. Crystal structures, DFT calculations and Hirshfeld surface analyses of three new cobalt(III) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

    NASA Astrophysics Data System (ADS)

    Masoudi, Mohaddeseh; Behzad, Mahdi; Arab, Ali; Tarahhomi, Atekeh; Rudbari, Hadi Amiri; Bruno, Giuseppe

    2016-10-01

    Three new Cobalt(III) Schiff base complexes were synthesized and characterized by spectroscopic methods and x-ray crystallography. The DFT optimized structures of the complexes agreed well with the corresponding x-ray structures. According to the calculated vibrational normal modes, the observed signals in the IR spectra of the complexes were assigned. The experimental UV-Vis spectra of the complexes were also discussed considering the calculated excited states and molecular orbitals. Hirshfeld surface analysis was carried out to study the inter-contact interactions in these complexes. These studies provided comprehensive description of such inter-contact interactions by means of an appealing graphical approach using 3D Hirshfeld surfaces and 2D fingerprint plots derived from the surfaces. It indicated the dominant role of various hydrogen intermolecular interactions such as H⋯H (above 60%), C⋯H/H⋯C (near 15%-20%), O⋯H/H⋯O (about 16% or 17% for structures with counter ion ClO4-) and H⋯F (17% for structure with counter ion PF6-) contacts into the crystal packing which are discussed in details.

  3. EPR spectrum of the Y@C82 metallofullerene isolated in solid argon matrix: hyperfine structure from EPR spectroscopy and relativistic DFT calculations.

    PubMed

    Misochko, Eugenii Ya; Akimov, Alexander V; Belov, Vasilii A; Tyurin, Daniil A; Bubnov, Vyacheslav P; Kareev, Ivan E; Yagubskii, Eduard B

    2010-08-21

    The EPR spectrum of the Y@C(82) molecules isolated in solid argon matrix was recorded for the first time at a temperature of 5 K. The isotropic hyperfine coupling constant (hfcc) A(iso) = 0.12 +/- 0.02 mT on the nucleus (89)Y as derived from the EPR spectrum is found in more than two times greater than that obtained in previous EPR measurements in liquid solutions. Comparison of the measured hfcc on a metal atom with that predicted by density-functional theory calculations (PBE/L22) indicate that relativistic method provides good agreement between experiment in solid argon and theory. Analysis of the DFT calculated dipole-dipole hf-interaction tensor and electron spin distribution in the endometallofullerenes with encaged group 3 metal atoms Sc, Y and La has been performed. It shows that spin density on the scandium atom represents the Sc d(yz) orbital lying in the symmetry plane of the C(2v) fullerene isomer and interacting with two carbon atoms located in the para-position on the fullerene hexagon. In contrast, the configuration of electron spin density on the heavier atoms, Y and La, is associated with the hybridized orbital formed by interaction of the metal d(yz) and p(y) electronic orbitals.

  4. Effect of doping β-NiOOH with Co on the catalytic oxidation of water: DFT+U calculations.

    PubMed

    Costanzo, Francesca

    2016-03-14

    Electrocatalytic water splitting using energy from sunlight represents a promising strategy for clean, low-cost, and environmentally friendly production of H2. Unfortunately, the oxygen evolution reaction (OER) at the anode is kinetically slow and represents the bottleneck of this process. Transition metal oxides are good candidates for the anode in electrochemical water splitting. Inspired by recent computational work on β-NiOOH, which is considered the active phase during the charging and discharging process in alkaline batteries, we performed density functional theory calculations with the inclusion of the Hubbard-U correction on selected surfaces of pure and Co-doped β-NiOOH to calculate the energetics of the OER. The goal of the paper is to investigate theoretically whether doping a NiOOH surface with Co might change the mechanism and lower the overpotential of the OER on a specific NiOOH surface, and to what extent the choice of the surface unit cell may affect the results. Our results indicate that the most likely reaction mechanism depends on the amount of Co doping. We find that doping the β-NiOOH surface with only 25% Co decreases the overpotential from 0.28 to 0.18 V. We also find that the theoretical overpotential, and which step is the potential limiting step, depends on the size of the surface unit cell selected in the calculations. This work highlights how optimizing the binding energies of the various intermediates (O, OH and H2O) on the Ni and Co surface sites, may be key to reducing the overpotential. PMID:26902752

  5. Characterization of peroxide-based explosives using Raman spectroscopy: isotopic analysis and DFT calculations of triacetone triperoxide (TATP)

    NASA Astrophysics Data System (ADS)

    Brauer, Carolyn S.; Barber, Jeffrey; Weatherall, James C.; Smith, Barry T.; Tomlinson-Phillips, Jill; Wooten, Alfred

    2011-06-01

    The Raman spectra of triacetone triperoxide (TATP) and its fully deuterated isotopologue (d18-TATP) have been measured. Density functional theory calculations were performed using the EDF2/6-311++G** and B3LYP/6-311++G** methods/basis set to predict the Raman spectra of both the parent and deuterated isotopologues. The predicted isotopic shifts were used to identify frequency shifts in the experimental results and tentative assignments have been made for 10 fundamental vibrational modes of d18-TATP.

  6. Electronic structures and optical properties of rutile TiO2 with different point defects from DFT + U calculations

    NASA Astrophysics Data System (ADS)

    Zhu, H. X.; Zhou, P. X.; Li, X.; Liu, J.-M.

    2014-07-01

    The electronic states and formation energies of four types of lattice point defects in rutile TiO2 are studied using the first-principles calculations. The existence of oxygen vacancy leads to a deep donor defect level in the forbidden band, while the Ti interstitial forms two local states. It is predicted that oxygen vacancy prefers to combine with Ti-interstitial to form VO-Tii dimer by a partial 3d electron transfer from the Tii to its neighboring VO. The charge distribution between a Ti interstitial and its neighboring Ti ions partially shields the Coulomb interactions. Lastly, optical properties of these defective lattices are discussed.

  7. DFT calculations of 15N NMR shielding constants, chemical shifts and complexation shifts in complexes of rhodium(II) tetraformate with some nitrogenous organic ligands

    NASA Astrophysics Data System (ADS)

    Leniak, Arkadiusz; Jaźwiński, Jarosław

    2015-03-01

    Benchmark calculations of 15N NMR shielding constants for a set of model complexes of rhodium(II) tetraformate with nine organic ligands using the Density Functional Theory (DFT) methods have been carried out. The calculations were performed by means of several methods: the non-relativistic, relativistic scalar ZORA, and spin-orbit ZORA approaches at the CGA-PBE/QZ4P theory level, and the GIAO NMR method using the B3PW91 functional with the 6-311++G(2d,p) basis set for C, H, N, O atoms and the Stuttgart basis set for the Rh atom. The geometry of compounds was optimised either by the same basis set as for the NMR calculations or applying the B3LYP functional with the 6-31G(2d) basis set for C, H, N, O atoms and LANL2DZ for the Rh atom. Computed 15N NMR shielding constants σ were compatible with experimental 15N chemical shifts δ of complexes exhibiting similar structure and fulfil the linear equation δ = aσ + b. The a and b parameters for all data sets have been estimated by means of linear regression analysis. In contrast to the correlation method giving "scaled" chemical shifts, the conversion of shielding constants to chemical shifts with respect to the reference shielding of CH3NO2 provided very inaccurate "raw" δ values. The application of the former to the calculation of complexation shifts Δδ (Δδ = δcompl - δlig) reproduced experimental values qualitatively or semi-quantitatively. The non-relativistic B3PW91/[6-311++G(2d,p), Stuttgart] theory level reproduced the NMR parameters as good as the more expensive relativistic CGA-PBE//QZ4P ZORA approaches.

  8. Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate.

    PubMed

    Zanuy, David; Hamley, Ian W; Alemán, Carlos

    2011-07-21

    The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helical-like arrangements. Furthermore, calculations indicate that backbone···side chain interactions involving the N-H of the amide groups and the π clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand, MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.

  9. Non-covalent interactions between ATP and RecA DNA-repairing proteins: DFT and semiempirical calculations

    NASA Astrophysics Data System (ADS)

    Rodriguez, Jorge

    2015-03-01

    The role of Bacterial RecA in the structural maintenance of genomes and the genetic information they carry has been established. In particular, the RecA DNA-repairing protein from D. Radiodurans, a radiation-resistant bacteria, is crucial for the repair of double strand breaks (DSBs). We have performed semi-empirical free-energy calculations and QM/MM calculations to study their non-covalent interactions with ATP and ADP. Such studies provide insight into the mechanisms of ATP/ADP --> RecA energy transfer and, therefore, about specific functional uses of incoming energy for DNA repairing mechanisms. We present a detailed analysis of the non-covalent interactions which minimize the interaction Gibbs free energies leading to the most stable non-covalent binding sites. Van der Waal, hydrogen bonding and electrostatic interactions has been quantified which provides a detailed insight into the mechanisms of ATP-RecA interaction. Further, possible chemical interactions and functional roles of RecA proteins are explored based on the previously mentioned studies. Acknowledgements: Funded, in part, by DTRA award 106339 (JHR). Dr. Mark C. Palenik and Mrs. Lora Beard are gratefully acknowledged Supported in part by DTRA Award 106339.

  10. Structure of 6-hydroxy-1-methylquinolinium chloride hydrate studied by X-ray, DFT calculations, FTIR and NMR spectroscopes

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Komasa, A.; Ratajczak-Sitarz, M.; Katrusiak, A.; Koput, J.; Dega-Szafran, Z.; Szafran, M.

    2010-12-01

    The crystal structure of 6-hydroxy-1-methylquinolinium chloride hydrate ( 1), 6QBWHCl, is monoclinic, space group P2 1/ n and Z = 4. 1-Methyl-6-oxyquinolinium betaine, 6QB, is protonated and its OH group participates in a moderate hydrogen bond with water molecule (O(1)-H⋯O(W1) = 2.636(2) Å). The water molecule is further connected by a hydrogen bond to chloride ion (O(W1)-H(W2)⋯Cl(1) = 3.090(3) Å). Structures of five complexes ( 2- 6) have been optimized by the B3LYP/6-311G(d, p) level of theory and the results have been compared with the X-ray data of 1. Linear correlations between the experimental 1H and 13C NMR chemical shifts ( δexp) of complexes 2- 5 and the magnetic isotropic shielding constants ( σcal) calculated by the GIAO/B3LYP/6-311G(d, p) approach, using the screening solvation model (COSMO), δexp = a + bσcal, are reported. The probable assignments of the anharmonic experimental solid state vibrational frequencies of anhydrous complex, 6QBHCl, based on the calculated B3LYP/6-311G(d, p) harmonic frequencies have been proposed.

  11. TD-DFT calculations and thermal effects on conformers of calmagite in protic solvents varying the degree of protonation.

    PubMed

    Cisneros-García, Z N; Mara Non-Ruiz, V F; Rodríguez-Zavala, J G

    2016-08-01

    The main absorption peaks were obtained for 1-(1-hydroxy-4-methyl-2-phenylazo)-2-naphthol-4-sulfonic acid. Generalized gradient approximation, hybrid, semi-empirical, and Coulomb attenuating methods were utilized to compare theoretical electronic transitions and experimental absorption spectra at different pH. The main peaks and shoulders observed in experimental spectra were assigned to its correct conformer. In order to find the most populated conformer, thermal effects on stability calculations were investigated to obtain molar fractions of possible isomers present at room and higher temperature. Theoretical electronic transitions at distinct pH could be obtained varying the protonation a deprotonation degree. It was found that generalized gradient approximation performs very well the first transition peak at neutral pH. For higher pH, all methodologies got a bathochromic shift in agreement with experiment and finally, from these theoretical results, it was obtained that this azo dye is hardly protonated in experiments since results presented here, predict a variation of absorption spectra for all proposed methodologies when the molecule is protonated, which is different to experimental results. Graphical Abstract Calculated electronic transitions of azo and hydrazone tautomers in water implicit solvent (BLYP/6-311G(2d,p) methodology). PMID:27460921

  12. A nonacoordinated bridging selenide in a tricapped trigonal prismatic geometry identified in undecanuclear copper clusters: syntheses, structures, and DFT calculations.

    PubMed

    Liu, C W; Hung, Chiu-Mine; Santra, Bidyut Kumar; Chu, Yi-Hua; Wang, Ju-Chun; Lin, Zhenyang

    2004-07-12

    Undecanuclear copper clusters, [Cu(11)(micro(9)-Se)(micro(3)-Br)(3)[Se(2)P(OR)(2)](6)] (R = Et, Pr, (i)Pr) (1a-c), were isolated along with closed-shell ion-centered cubes, [Cu(8)(micro(8)-Br)[Se(2)P(OR)(2)](6)] (PF(6)) (2a-c) and [Cu(8)(micro(8)-Se)[Se(2)P(OR)(2)](6)] (3a-c), from the reaction of [Cu(CH(3)CN)(4)](PF(6)), NH(4)[Se(2)P(OR)(2)], and Bu(4)NBr in a molar ratio of 2:3:2 in CH(2)Br(2). The molecular formulations of these clusters were confirmed by elemental analysis, positive FAB mass spectrometry, and multinuclear NMR ((1)H, (31)P, and (77)Se). (77)Se NMR spectra of Cu(11) clusters (1a-c) are of special interest as two inequivalent selenium nuclei of the diselenophosphate (dsep) ligand exhibit different scalar coupling patterns with the adjacent phosphorus nuclei. X-ray analysis of 1c reveals a Cu(11)Se core stabilized by three bromide and six dsep ligands. The central core adopts the geometry of a 3,3,4,4,4-pentacapped trigonal prism with a selenium atom in the center. The coordination geometry for the nonacoordinate selenium atom is tricapped trigonal prismatic. The X-ray structure 2a or 2c consists of a cationic cluster in which eight copper ions are linked by six diselenophosphate ligands with a central micro(8)-Br ion. The shape of the molecule is a bromide-centered distorted Cu(8) cube. Each diselenophosphate ligand occupies square faces of the cube and adopts a tetrametallic tetraconnective coordination pattern. Each copper atom of the cube is coordinated by three selenium atoms with a strong interaction with the central bromide ion. Molecular orbital calculations at the B3LYP level of the density functional theory have been carried out to study the Cu-micro(9)-Se interactions for clusters [Cu(11)(micro(9)-Se)(micro(3)-X)(3)[Se(2)P(OR)(2)](6)] (X = Br, I). Calculations show that the formal bond order of each Cu-micro(9)-Se bond is slightly smaller than half of those calculated for the terminal Cu-micro(2)-Se bonds.

  13. Determination of the hyperfine magnetic field in magnetic carbon-based materials: DFT calculations and NMR experiments

    PubMed Central

    Freitas, Jair C. C.; Scopel, Wanderlã L.; Paz, Wendel S.; Bernardes, Leandro V.; Cunha-Filho, Francisco E.; Speglich, Carlos; Araújo-Moreira, Fernando M.; Pelc, Damjan; Cvitanić, Tonči; Požek, Miroslav

    2015-01-01

    The prospect of carbon-based magnetic materials is of immense fundamental and practical importance, and information on atomic-scale features is required for a better understanding of the mechanisms leading to carbon magnetism. Here we report the first direct detection of the microscopic magnetic field produced at 13C nuclei in a ferromagnetic carbon material by zero-field nuclear magnetic resonance (NMR). Electronic structure calculations carried out in nanosized model systems with different classes of structural defects show a similar range of magnetic field values (18–21 T) for all investigated systems, in agreement with the NMR experiments. Our results are strong evidence of the intrinsic nature of defect-induced magnetism in magnetic carbons and establish the magnitude of the hyperfine magnetic field created in the neighbourhood of the defects that lead to magnetic order in these materials. PMID:26434597

  14. Synthesis, crystal structure, property research, and DFT calculation of 2,3-diphenylfuro[3,2-b]quinoxaline

    NASA Astrophysics Data System (ADS)

    Yao, Qi-Chao; Wu, Ding-Er; Xia, Min

    2013-06-01

    The title compound is obtained via the intramolecular condensation of 3-(2-oxo-1,2-diphenylethyl)quinoxalin-2(1H)-one in the presence of excessive boron trifluoride etherate and characterized by 1H NMR, 13C NMR, IR, and EI-MS. The solution-based and solid-state fluorescence along with the electrochemical property are studied in detail. The unique herring-bone arrangement which is revealed by the X-ray crystallography should account for the intense solid-state fluorescence. The theoretic calculations are employed to clarify the origin of the large Stokes shift and the positive solvatochromism in view of the geometric relaxation and the transition feature.

  15. ANALYSIS OF OH STRETCHING FREQUENCIES IN GLUCOSE AND GLUCOSE MONOHYDRATES CALCULATED BY DFT: ROTOMER AND WATER PLACEMENT EFFECTS ON THE CALCULATED SPECTRUM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infrared spectra were calculated for glucose molecules and glucose monohydrate complexes, based on geometry optimization at the B3LYP/6-311++G** level of theory. Alpha and Beta anomers were considered, with all possible combinations of hydroxymethyl rotamer (gg,gt, or tg) and hydroxyl orientation (...

  16. Temperature and pressure effects on GFP mutants: explaining spectral changes by molecular dynamics simulations and TD-DFT calculations.

    PubMed

    Jacchetti, Emanuela; Gabellieri, Edi; Cioni, Patrizia; Bizzarri, Ranieri; Nifosì, Riccardo

    2016-05-14

    By combining spectroscopic measurements under high pressure with molecular dynamics simulations and quantum mechanics calculations we investigate how sub-angstrom structural perturbations are able to tune protein function. We monitored the variations in fluorescence output of two green fluorescent protein mutants (termed Mut2 and Mut2Y, the latter containing the key T203Y mutation) subjected to pressures up to 600 MPa, at various temperatures in the 280-320 K range. By performing 150 ns molecular dynamics simulations of the protein structures at various pressures, we evidenced subtle changes in conformation and dynamics around the light-absorbing chromophore. Such changes explain the measured spectral tuning in the case of the sizable 120 cm(-1) red-shift observed for pressurized Mut2Y, but absent in Mut2. Previous work [Barstow et al., Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 13362] on pressure effects on GFP also involved a T203Y mutant. On the basis of cryocooling X-ray crystallography, the pressure-induced fluorescence blue shift at low temperature (77 K) was attributed to key changes in relative conformation of the chromophore and Tyr203 phenol ring. At room temperature, however, a red shift was observed at high pressure, analogous to the one we observe in Mut2Y. Our investigation of structural variations in compressed Mut2Y also explains their result, bridging the gap between low-temperature and room-temperature high-pressure effects. PMID:27102429

  17. Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

    PubMed

    Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

    2015-08-01

    Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. PMID:25829160

  18. Overlooked difference between hydrogen bonds of equal strength formed between catechol and an oxygen or nitrogen base. Experiments and DFT calculations.

    PubMed

    Foti, Mario C; DiLabio, Gino A; Ingold, K U

    2003-11-26

    The IR spectrum of catechol in CCl(4) shows two fairly sharp O-H stretching bands of roughly equal absorbance at 3615.0 and 3569.6 cm(-1) due, respectively, to the "free" OH and the intramolecularly H-bonded OH groups. Intermolecular H-bond formation between the "free" OH and a hydrogen bond acceptor (HBA) decreases its stretching frequency by several hundred wavenumbers and simultaneously decreases the frequency of the intramolecularly H-bonded OH by a few tens of wavenumbers. The magnitude of these frequency shifts, Deltaupsilon(inter) and Deltaupsilon(intra), respectively, are very well reproduced by DFT calculations. As would be expected, the magnitudes of Deltaupsilon(inter) and Deltaupsilon(intra) increase as the HB accepting ability of the HBA increases as quantified, on a relative scale, by the HBA's values (Abraham et al. J. Chem. Soc. Perkin Trans. 2 1990, 521). However, plots of experimental, or calculated, frequency shifts versus reveal that Deltaupsilon(inter) and Deltaupsilon(intra) are ca. 40% larger for a nitrogen atom HBA than for an oxygen atom HBA having equal HBA activity. We hypothesize that for HBAs of equal strength, i.e., of equal, the H-bond in (O-H- - -O)(inter) is shorter and, hence, intrinsically stronger than the H-bond in the (O-H- - -N)(inter). However, we further hypothesize that there is more charge separation in the H-bond to N because N is a better proton acceptor than O. Hence, it is the greater Coulombic attraction in (O-H- - -N)(inter) which strengthens this H-bond and compensates for its greater length. Theoretical calculations lend support to these hypotheses. PMID:14624616

  19. Tuning electronic and magnetic properties of blue phosphorene by doping Al, Si, As and Sb atom: A DFT calculation

    NASA Astrophysics Data System (ADS)

    Sun, Minglei; Hao, Yitong; Ren, Qingqiang; Zhao, Yiming; Du, Yanhui; Tang, Wencheng

    2016-09-01

    Using density functional theory computations, we systematically investigated the structural, electronic and magnetic properties of Al, Si, As and Sb doped blue phosphorene. The electronic properties of blue phosphorene can be effectively turned by substitutional doping. Especially, Al and Sb lead to an indirect-to-direct-gap transition. The interaction between the impurity and P atoms should be responsible for the transition. In addition, blue phosphorene can exhibit dilute magnetic semiconductor property with doping of Si impurity. The magnetic moment in Si-substituted blue phosphorene predominantly originates from the hybridization of Si-s pz and P-pz orbitals. These results provide many useful applications of blue phosphorene in electronics, optoelectronics and spintronics.

  20. Hydrogen bonding and molecular association in 2-(quinuclidinium)-butyric acid bromide hydrate studied by X-ray diffraction, DFT calculations, FTIR and NMR spectroscopy, and potentiometric titration

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.; Barczyński, P.

    2010-06-01

    The structure of 2-(quinuclidinium)-butyric acid bromide hydrate (QNBu·H 2O·HBr, 3) has been determined by X-ray diffraction, DFT calculations and characterized by FTIR and NMR spectroscopy. Crystals of 3 are monoclinic, space group P2 1. The water molecule interacts with the carboxylic group of 2-(quinuclidinium)-butyric acid and with the bromide anion by the COOH⋯OH 2 and HOH⋯Br hydrogen bonds of 2.575(3) and 3.293(2) Å, respectively. The structures of monomer ( 4) and dimeric cation ( 5) of the title complex have been optimized by the B3LYP/6-31G(d,p) approach, yielding conformations consistent with this in the crystal. The solid-state FTIR spectra of 3 and its deuterated analogue have been measured and compared with the theoretical spectrum of 4. The assignments of the observed and predicted bands have been proposed. The molecule of 3 has a chiral center at the C(9) atom, which is responsible for the non-magnetically equivalence of the α-ring and C(11)H 2 methylene protons in 1H NMR spectrum. The values of p Ka of quinuclidinium-acetate (quinuclidine betaine), 2-(quinuclidinium)-propionate and 2-(quinuclidinium)-butyrate have been determined by the potentiometric titration of their hydrohalides.

  1. Synthesis, DFT Calculation, and Antimicrobial Studies of Novel Zn(II), Co(II), Cu(II), and Mn(II) Heteroleptic Complexes Containing Benzoylacetone and Dithiocarbamate

    PubMed Central

    Ekennia, Anthony C.; Onwudiwe, Damian C.; Olasunkanmi, Lukman O.; Osowole, Aderoju A.; Ebenso, Eno E.

    2015-01-01

    Heteroleptic complexes of zinc(II), copper(II), manganese(II), and cobalt(II) of the types [MLL′(H2O)2]·nH2O and [MLL′]·nH2O have been synthesized using sodium N-methyl-N-phenyldithiocarbamate (L) and benzoylacetone (L′). The metal complexes were characterized by elemental analysis, electrical conductance, magnetic susceptibility, infrared (IR), and UV-visible spectroscopic studies. The electrical conductance measurements revealed the nonelectrolytic nature of the synthesized complexes. The results of the elemental analyses, magnetic susceptibility measurements, and electronic spectra inferred that the Zn(II) complex adopted a four-coordinate geometry while the Co(II), Cu(II), and Mn(II) complexes assumed octahedral geometries. The IR spectra showed that the metal ions coordinated with the ligands via the S- and O-donor atoms. The geometry, electronic, and thermodynamic parameters of the complexes were obtained from density functional theory (DFT) calculations. The spin density distributions, relative strength of H–bonds, and thermodynamic parameters revealed that the order of stability of the metal complexes is Mn < Co < Cu > Zn. The agar diffusion methods were used to study the antimicrobial activity of the complexes against two Gram positive bacteria (S. aureus and S. pneumoniae), one Gram negative bacterium (E. coli), and two fungi organisms (A. niger and A. candida) and the complexes showed a broad spectrum of activities against the microbes. PMID:26681931

  2. Synthesis, growth, optical and DFT calculation of 2-naphthol derived Mannich base organic non linear optical single crystal for frequency conversion applications

    NASA Astrophysics Data System (ADS)

    Raj, A. Dennis; Jeeva, M.; Shankar, M.; Purusothaman, R.; Prabhu, G. Venkatesa; Potheher, I. Vetha

    2016-11-01

    2-naphthol derived Mannich base 1-((4-methylpiperazin-1-yl) (phenyl) methyl) naphthalen-2-ol (MPN) - a nonlinear optical single crystal was synthesized and successfully grown by slow evaporation technique at room temperature. The molecular structure was confirmed by single crystal XRD, FT-IR, 1H NMR and 13C NMR spectral studies. The single crystal X-ray diffraction analysis reveals that the crystal belongs to orthorhombic crystal system with non-centrosymmetric space group Pna21. The chemical shift of 5.34 ppm (singlet methine CH proton) in 1H NMR and signal for the CH carbon around δ70.169 ppm in 13C NMR confirms the formation of the title compound. The crystal growth pattern and dislocations of crystal are analyzed using chemical etching technique. UV cut off wavelength of the material was found to be 212 nm. The second harmonic generation (SHG) of MPN was determined from Kurtz Perry powder technique and the efficiency is almost equal to that of standard KDP crystal. The laser damage threshold was measured by passing Nd: YAG laser beam through the sample and it was found to be 1.1974 GW/cm2. The material was thermally stable up to 142 °C. The relationship between the molecular structure and the optical properties was also studied from quantum chemical calculations using Density Functional Theory (DFT) and reported for the first time.

  3. Effect of the components' interface on the synthesis of methanol over Cu/ZnO from CO2/H2: a microkinetic analysis based on DFT + U calculations.

    PubMed

    Tang, Qian-Lin; Zou, Wen-Tian; Huang, Run-Kun; Wang, Qi; Duan, Xiao-Xuan

    2015-03-21

    The elucidation of chemical reactions occurring on composite systems (e.g., copper (Cu)/zincite (ZnO)) from first principles is a challenging task because of their very large sizes and complicated equilibrium geometries. By combining the density functional theory plus U (DFT + U) method with microkinetic modeling, the present study has investigated the role of the phase boundary in CO2 hydrogenation to methanol over Cu/ZnO. The absence of hydrogenation locations created by the interface between the two catalyst components was revealed based on the calculated turnover frequency under realistic conditions, in which the importance of interfacial copper to provide spillover hydrogen for remote Cu(111) sites was stressed. Coupled with the fact that methanol production on the binary catalyst was recently believed to predominantly involve the bulk metallic surface, the spillover of interface hydrogen atoms onto Cu(111) facets facilitates the production process. The cooperative influence of the two different kinds of copper sites can be rationalized applying the Brönsted-Evans-Polanyi (BEP) relationship and allows us to find that the catalytic activity of ZnO-supported Cu catalysts is of volcano type with decrease in the particle size. Our results here may have useful implications in the future design of new Cu/ZnO-based materials for CO2 transformation to methanol.

  4. Study of morphology effects on magnetic interactions and band gap variations for 3d late transition metal bi-doped ZnO nanostructures by hybrid DFT calculations

    NASA Astrophysics Data System (ADS)

    Datta, Soumendu; Kaphle, Gopi Chandra; Baral, Sayan; Mookerjee, Abhijit

    2015-08-01

    Using density functional theory (DFT) based electronic structure calculations, the effects of morphology of semiconducting nanostructures on the magnetic interaction between two magnetic dopant atoms as well as a possibility of tuning band gaps have been studied in the case of the bi-doped (ZnO)24 nanostructures with the impurity dopant atoms of the 3d late transition metals—Mn, Fe, Co, Ni, and Cu. To explore the morphology effect, three different structures of the host (ZnO)24 nano-system, having different degrees of spatial confinement, have been considered: a two dimensional nanosheet, a one dimensional nanotube, and a finite cage-shaped nanocluster. The present study employs hybrid density functional theory to accurately describe the electronic structure of all the systems. It is shown here that the magnetic coupling between the two dopant atoms remains mostly anti-ferromagnetic in the course of changing the morphology from the sheet geometry to the cage-shaped geometry of the host systems, except for the case of energetically most stable bi-Mn doping, which shows a transition from ferromagnetic to anti-ferromagnetic coupling with decreasing aspect ratio of the host system. The effect of the shape change, however, has a significant effect on the overall band gap variations of both the pristine as well as all the bi-doped systems, irrespective of the nature of the dopant atoms and provides a means for easy tunability of their optoelectronic properties.

  5. Study of morphology effects on magnetic interactions and band gap variations for 3d late transition metal bi-doped ZnO nanostructures by hybrid DFT calculations.

    PubMed

    Datta, Soumendu; Kaphle, Gopi Chandra; Baral, Sayan; Mookerjee, Abhijit

    2015-08-28

    Using density functional theory (DFT) based electronic structure calculations, the effects of morphology of semiconducting nanostructures on the magnetic interaction between two magnetic dopant atoms as well as a possibility of tuning band gaps have been studied in the case of the bi-doped (ZnO)24 nanostructures with the impurity dopant atoms of the 3d late transition metals-Mn, Fe, Co, Ni, and Cu. To explore the morphology effect, three different structures of the host (ZnO)24 nano-system, having different degrees of spatial confinement, have been considered: a two dimensional nanosheet, a one dimensional nanotube, and a finite cage-shaped nanocluster. The present study employs hybrid density functional theory to accurately describe the electronic structure of all the systems. It is shown here that the magnetic coupling between the two dopant atoms remains mostly anti-ferromagnetic in the course of changing the morphology from the sheet geometry to the cage-shaped geometry of the host systems, except for the case of energetically most stable bi-Mn doping, which shows a transition from ferromagnetic to anti-ferromagnetic coupling with decreasing aspect ratio of the host system. The effect of the shape change, however, has a significant effect on the overall band gap variations of both the pristine as well as all the bi-doped systems, irrespective of the nature of the dopant atoms and provides a means for easy tunability of their optoelectronic properties.

  6. Tip enhanced Raman spectroscopy, DFT and PED calculations of 4″-trimethylsilylethylsulfanyl-4,4‧-di(phenyleneethynylene)benzene thiol adsorbed on silver

    NASA Astrophysics Data System (ADS)

    Fletcher, Melissa C.; Alexson, Dimitri M.; Moore, Martin M.; Prokes, S. M.; Glembocki, Orest; Vivoni, Alberto; McCoy, Rhonda; Mishra, Soni; Tandon, Poonam; Hosten, Charles M.

    2015-11-01

    Monolayers of α,ω-dithiol oligo(phenyleneethynlene) molecules are critical to the field of molecular electronics because of their abilities to form bonds with many metallic surfaces and rectify current. In this study Fourier Transformation-Raman, surface-enhanced Raman scattering (SERS) spectroscopy and Tip-enhanced Raman Spectroscopy (TERS) were used to characterize a selectively oriented self-assembled monolayer of 4″-trimethylsilylethylsulfanyl-4,4‧-bis-(phenyleneethynylene)benzenethiol (OPE‧) on silver coated nanospheres. Selective orientation was achieved by synthesizing 4″-trimethylsilylethylsulfanyl-4,4‧-bis-(phenyleneethynylene)benzene disulfide, which undergoes oxidative dissociation and covalently bonds to the metal surface. The Ag coated nanosphere surfaces were characterized by scanning electron microscopy (SEM), which showed a large area of surface charging. The SERS and TERS spectra show similar results; however, a greater enhancement was achieved with the TERS relative to the SERS spectra. Assignments of vibrational bands were based on DFT calculations performed at the B3LYP level with good agreement between theoretical and experimental values. An average percent difference of 2.5 cm-1 was obtained for the non-CH stretching frequencies and a scaling factor was not applied to theoretically generated frequencies. A red shift of the ν(C-S) peak at 1087 cm-1 was observed when OPE‧ was adsorbed on a Ag surface. Vibrations specific to the trimethylsilylethyl (TMSE) group were visible in the TERS spectra, and disappear upon deprotection.

  7. Molecular structure of mercury(II) thiocyanate complexes based on DFT calculations and experimental UV-electron spectroscopy and Raman studies

    NASA Astrophysics Data System (ADS)

    Elijošiutė, Erika; Eicher-Lorka, Olegas; Griškonis, Egidijus; Matulaitienė, Ieva; Jankūnaitė, Dalia; Denafas, Gintaras

    2013-11-01

    In this work, we report a combined experimental and theoretical study on molecular structure, vibrational and electronic spectra of [Hg(SCN)n]2-n complexes (where n = 2, 3, 4) in the aqueous solution. Molecular modeling of the mercury(II) complexes were done by the density functional theory (DFT) method using B3LYP functional with Stuttgart relativistic ECP 78MWB basis set for Hg and 6-311++G(d,p) basis set for all other atoms. The effect of different solvation models with explicit (ligand) and/or implicit water environment upon its geometry, vibrational frequencies and UV spectrum have been studied. The influence of H2O/D2O exchange on the experimental and calculated vibrational frequencies of studied complexes has been established. The double-peak character of the νHgsbnd S vibrational mode of the all analyzed mercury complexes and νCtbnd N mode of [Hg(SCN)3H2O]- complex, respectively, were proposed here for the first time. The formation of four-coordinated Hg(II) complexes with thiocyanate and (or) water ligands was verified.

  8. Direct Detection and Characterization of Chloride in the Active Site of the Low-pH Form of Sulfite Oxidase Using ESEEM Spectroscopy, Isotopic Labeling, and DFT Calculations

    PubMed Central

    Klein, Eric L.; Astashkin, Andrei V.; Ganyushin, Dmitry; Riplinger, Christoph; Johnson-Winters, Kayunta; Neese, Frank; Enemark, John H.

    2009-01-01

    Electron spin echo envelope modulation (ESEEM) investigations were carried out on samples of the low-pH (lpH) form of vertebrate sulfite oxidase (SO) prepared with 35Cl- and 37Cl-enriched buffers as well as with buffer containing the natural abundance of Cl isotopes. The isotope-related changes observed in the ESEEM spectra provide direct and unequivocal evidence that Cl− is located in close proximity to the Mo(V) center of lpH SO. The measured isotropic hyperfine interaction constant of about 4 MHz (35Cl) suggests that the Cl− ion is either weakly coordinated to Mo(V) at its otherwise vacant axial position, trans to the oxo ligand, or is hydrogen-bonded to the equatorial exchangeable OH ligand. Scalar relativistic all-electron density functional theory (DFT) calculations of the hyperfine and nuclear quadrupole interaction parameters, along with steric and energetic arguments, strongly support the possibility that Cl− is hydrogen-bonded to the equatorial OH ligand rather than being directly coordinated to the Mo(V). PMID:19402624

  9. Study of morphology effects on magnetic interactions and band gap variations for 3d late transition metal bi-doped ZnO nanostructures by hybrid DFT calculations

    SciTech Connect

    Datta, Soumendu Baral, Sayan; Mookerjee, Abhijit; Kaphle, Gopi Chandra

    2015-08-28

    Using density functional theory (DFT) based electronic structure calculations, the effects of morphology of semiconducting nanostructures on the magnetic interaction between two magnetic dopant atoms as well as a possibility of tuning band gaps have been studied in the case of the bi-doped (ZnO){sub 24} nanostructures with the impurity dopant atoms of the 3d late transition metals—Mn, Fe, Co, Ni, and Cu. To explore the morphology effect, three different structures of the host (ZnO){sub 24} nano-system, having different degrees of spatial confinement, have been considered: a two dimensional nanosheet, a one dimensional nanotube, and a finite cage-shaped nanocluster. The present study employs hybrid density functional theory to accurately describe the electronic structure of all the systems. It is shown here that the magnetic coupling between the two dopant atoms remains mostly anti-ferromagnetic in the course of changing the morphology from the sheet geometry to the cage-shaped geometry of the host systems, except for the case of energetically most stable bi-Mn doping, which shows a transition from ferromagnetic to anti-ferromagnetic coupling with decreasing aspect ratio of the host system. The effect of the shape change, however, has a significant effect on the overall band gap variations of both the pristine as well as all the bi-doped systems, irrespective of the nature of the dopant atoms and provides a means for easy tunability of their optoelectronic properties.

  10. A real-time fluorescent sensor specific to Mg2+: crystallographic evidence, DFT calculation and its use for quantitative determination of magnesium in drinking water.

    PubMed

    Men, Guangwen; Chen, Chunrong; Zhang, Shitong; Liang, Chunshuang; Wang, Ying; Deng, Mengyu; Shang, Hongxing; Yang, Bing; Jiang, Shimei

    2015-02-14

    An "off-the-shelf" fluorescence "turn-on" Mg(2+) chemosensor 3,5-dichlorosalicylaldehyde (BCSA) was rationally designed and developed. This proposed sensor works based on Mg(2+)-induced formation of the 2 : 1 BCSA-Mg(2+) complex. The coordination of BSCA to Mg(2+) increases its structural rigidity generating a chelation-enhanced fluorescence (CHEF) effect which was confirmed by single crystal XRD studies of the BSCA-Mg(2+) complex and TD/DFT calculations. This sensor exhibits high sensitivity and selectivity for the quantitative monitoring of Mg(2+) with a wide detection range (0-40 μM), a low detection limit (2.89 × 10(-7) mol L(-1)) and a short response time (<0.5 s). It can also resist the interference from the other co-existing metal ions, especially Ca(2+). Consequently, this fluorescent sensor can be utilized to monitor Mg(2+) in real time within actual samples from drinking water.

  11. Ammonia-Containing Species Formed in Cu-Chabazite As Per In Situ EPR, Solid-State NMR, and DFT Calculations.

    PubMed

    Moreno-González, Marta; Hueso, Beatriz; Boronat, Mercedes; Blasco, Teresa; Corma, Avelino

    2015-03-19

    Nowadays, the most attractive technology for the elimination of nitric oxides from the exhaust gas of diesel vehicles is the selective catalytic reduction with ammonia (NH3-SCR-NOx) using Cu zeolite with the chabazite structure as the catalyst. Isolated copper species are the active sites, but the reaction intermediates and the overall reaction mechanism are still under debate. Here, we study the interaction of ammonia with zeolite Cu-SSZ-13 (CHA topology) with a uniform distribution of Cu(2+) sites prepared in one pot and a conventional Cu-ZSM-5 (MFI topology) for comparison. In situ EPR and solid-state NMR spectroscopies combined with DFT calculations have allowed the identification of NH4(+), [Cu(NH3)5](2+), [Cu(Of)2(NH3)2](2+), [Cu(Of)3NH3](2+), [Cu(NH3)2](+), and [CuOf(NH3)](+) (Of being framework oxygen) under different conditions. The results demonstrate that ammonia is able to reduce Cu(2+) to Cu(+) and provide new information on the species formed in Cu-SSZ-13, which have important implications for the elucidation of the SCR reaction mechanism. PMID:26262861

  12. Spectroscopic, analytical and DFT calculation studies of two novel Al3+ complexes derived from 2,4,6-tri-(2-pyridyl)-1,3,5-triazine (TPTZ).

    PubMed

    Azahari, Shaker J; Abdel Rhman, Mohamed H; Mostafa, Mohsen M

    2014-11-11

    In this study TPTZ is used exclusively as an analytical reagent for the determination of micro amounts of Al3+ ions with high accuracy and lower detection limit, which reach 2.7 ppm. The developed blue color of Al3+-TPTZ complex was used selectivity to determine the concentration and the geometry of the Al3+ complex using continuous variation and molar ratio methods. Also, the novel Al3+ complexes derived from the reaction of TPTZ were synthesized. The solid complexes were characterized by elemental analyses, spectral (IR, UV-vis., 1H NMR, mass) and magnetic measurements. The isolated complexes have the general formulae, [Al(TPTZ)Cl3]·H2O·1½EtOH (1:1; M:L) and [Al2(TPTZ)Cl6(EtOH)2] (2:1; M:L). IR spectra indicate that TPTZ behaves in a bidentate manner in case of 1:1 and 2:1 (M:L). Elemental analyses and mass spectra of the complexes suggest the existence of an octahedral structure around the Al3+ ions. DFT calculations were used to determine the geometry of complexes. PMID:24858358

  13. Synthesis, spectral, X-ray single structure, DFT calculations and antimicrobial activities of [Co(II)X2 (dmphen)] (X = Br and SCN-)

    NASA Astrophysics Data System (ADS)

    Al-Noaimi, Mousa; Awwadi, Firas F.; Haddad, Salim F.; Talib, Wamidh H.; Jodeh, Shehdeh; Radi, Smaail; Ben Hadda, Taibi; Abdoh, Muneer; Naveen, S.; Lokanath, N. K.; Warad, Ismail

    2015-04-01

    Two tetrahedral mononuclear complexes with a general formula [CoX2(dmphen)](1-2) (where dmphen is 2,9-dimethyl-1,10-phenanthroline and 1 (X = Br), 2 (X = NCS)) have been synthesized. These complexes are characterized by elemental analysis, IR, UV-visible, TG/DTA and by X-ray diffraction. The calculated electrostatic potential surface of 2 has shown that the electrostatic potential values around sulfur atom is anistropically distributed; the potential values along C-S bond is less negative than the corresponding values in the π-region of S atom. This agrees with the observed geometrical arrangement of C-H⋯S-C hydrogen bonding interactions, the avg. of H⋯S-C angle is 81°. Antimicrobial properties of cobalt(II) complexes was also assessed. Cobalt complexes exhibited significant antibacterial activity against different gram negative and positive human pathogens. The absorption spectrum of these complexes in acetone was modeled by time-dependent density functional theory (TD-DFT).

  14. Supramolecular clusters and chains of 2,6-dimethylpyridine on Cu(110): Observation of dynamic configuration change with real-space surface science techniques and DFT calculations

    NASA Astrophysics Data System (ADS)

    Lee, Junseok; Sorescu, Dan C.; Lee, Jae-Gook; Dougherty, Dan

    2016-10-01

    The adsorption of 2,6-dimethylpyridine (2,6-DMP) on Cu(110) has been studied using low temperature scanning tunneling microscopy (LT-STM), time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD), and density functional theory (DFT) calculations. At low temperatures (T < ~ 150 K), the 2,6-DMP adsorbs in a flat configuration on Cu(110) producing clusters and extended domains via weak hydrogen bonding (C-H···N) with the molecular symmetry axis aligned along the < 001 > surface direction. At near-saturation coverage, a c(6 × 2) long-range ordered structure was observed. Upon annealing to T = 200 K, the 2,6-DMP molecules adopt an upright configuration with their pyridine ring plane oriented parallel to the < 1 1 ̅ 0 > azimuth. These upright 2,6-DMP molecules produce extended molecular chains where the repulsive interactions between the molecular chains give rise to coverage-dependent interchain distances.

  15. Effect of the components' interface on the synthesis of methanol over Cu/ZnO from CO2/H2: a microkinetic analysis based on DFT + U calculations.

    PubMed

    Tang, Qian-Lin; Zou, Wen-Tian; Huang, Run-Kun; Wang, Qi; Duan, Xiao-Xuan

    2015-03-21

    The elucidation of chemical reactions occurring on composite systems (e.g., copper (Cu)/zincite (ZnO)) from first principles is a challenging task because of their very large sizes and complicated equilibrium geometries. By combining the density functional theory plus U (DFT + U) method with microkinetic modeling, the present study has investigated the role of the phase boundary in CO2 hydrogenation to methanol over Cu/ZnO. The absence of hydrogenation locations created by the interface between the two catalyst components was revealed based on the calculated turnover frequency under realistic conditions, in which the importance of interfacial copper to provide spillover hydrogen for remote Cu(111) sites was stressed. Coupled with the fact that methanol production on the binary catalyst was recently believed to predominantly involve the bulk metallic surface, the spillover of interface hydrogen atoms onto Cu(111) facets facilitates the production process. The cooperative influence of the two different kinds of copper sites can be rationalized applying the Brönsted-Evans-Polanyi (BEP) relationship and allows us to find that the catalytic activity of ZnO-supported Cu catalysts is of volcano type with decrease in the particle size. Our results here may have useful implications in the future design of new Cu/ZnO-based materials for CO2 transformation to methanol. PMID:25697118

  16. Study of morphology effects on magnetic interactions and band gap variations for 3d late transition metal bi-doped ZnO nanostructures by hybrid DFT calculations.

    PubMed

    Datta, Soumendu; Kaphle, Gopi Chandra; Baral, Sayan; Mookerjee, Abhijit

    2015-08-28

    Using density functional theory (DFT) based electronic structure calculations, the effects of morphology of semiconducting nanostructures on the magnetic interaction between two magnetic dopant atoms as well as a possibility of tuning band gaps have been studied in the case of the bi-doped (ZnO)24 nanostructures with the impurity dopant atoms of the 3d late transition metals-Mn, Fe, Co, Ni, and Cu. To explore the morphology effect, three different structures of the host (ZnO)24 nano-system, having different degrees of spatial confinement, have been considered: a two dimensional nanosheet, a one dimensional nanotube, and a finite cage-shaped nanocluster. The present study employs hybrid density functional theory to accurately describe the electronic structure of all the systems. It is shown here that the magnetic coupling between the two dopant atoms remains mostly anti-ferromagnetic in the course of changing the morphology from the sheet geometry to the cage-shaped geometry of the host systems, except for the case of energetically most stable bi-Mn doping, which shows a transition from ferromagnetic to anti-ferromagnetic coupling with decreasing aspect ratio of the host system. The effect of the shape change, however, has a significant effect on the overall band gap variations of both the pristine as well as all the bi-doped systems, irrespective of the nature of the dopant atoms and provides a means for easy tunability of their optoelectronic properties. PMID:26328845

  17. Synthesis, DFT Calculation, and Antimicrobial Studies of Novel Zn(II), Co(II), Cu(II), and Mn(II) Heteroleptic Complexes Containing Benzoylacetone and Dithiocarbamate.

    PubMed

    Ekennia, Anthony C; Onwudiwe, Damian C; Olasunkanmi, Lukman O; Osowole, Aderoju A; Ebenso, Eno E

    2015-01-01

    Heteroleptic complexes of zinc(II), copper(II), manganese(II), and cobalt(II) of the types [MLL'(H2O)2]·nH2O and [MLL']·nH2O have been synthesized using sodium N-methyl-N-phenyldithiocarbamate (L) and benzoylacetone (L'). The metal complexes were characterized by elemental analysis, electrical conductance, magnetic susceptibility, infrared (IR), and UV-visible spectroscopic studies. The electrical conductance measurements revealed the nonelectrolytic nature of the synthesized complexes. The results of the elemental analyses, magnetic susceptibility measurements, and electronic spectra inferred that the Zn(II) complex adopted a four-coordinate geometry while the Co(II), Cu(II), and Mn(II) complexes assumed octahedral geometries. The IR spectra showed that the metal ions coordinated with the ligands via the S- and O-donor atoms. The geometry, electronic, and thermodynamic parameters of the complexes were obtained from density functional theory (DFT) calculations. The spin density distributions, relative strength of H-bonds, and thermodynamic parameters revealed that the order of stability of the metal complexes is Mn < Co < Cu > Zn. The agar diffusion methods were used to study the antimicrobial activity of the complexes against two Gram positive bacteria (S. aureus and S. pneumoniae), one Gram negative bacterium (E. coli), and two fungi organisms (A. niger and A. candida) and the complexes showed a broad spectrum of activities against the microbes. PMID:26681931

  18. Merging Kohn-Sham and Orbital-Free DFT Calculations to Extend the LiH Hugoniot to Very High Pressures

    NASA Astrophysics Data System (ADS)

    Kress, Joel

    2013-06-01

    Large-scale hydrodynamic simulations of fluids and plasmas under extreme conditions require knowledge of various properties such as the equation of state (EOS), mass diffusion, and shear viscosity. While many approaches exist for the determination of these properties, one of the most accurate employs quantum molecular dynamics (QMD) simulations on large samples of atoms of the various species. Examples include the shock compression of metal hydrides and the mixing of deuterium/tritium (DT) fuel with ablator materials (such as C/H plastics and Be) in inertial confinement fusion capsules. The quantum nature of the electrons is described with two flavors of finite-temperature density functional theory (DFT), namely orbital-based Kohn-Sham (KS) and Orbital Free (OF). EOSs for Lithium Hydride and Lithium 6 Deuteride (Li6D) have been calculated with both KSMD and with OFMD. The shock Hugoniot for Li6D has been determined for temperatures up to 25 eV (5000 GPa) using a KSMD based EOS, and for T = 5 eV and above (up to 10,000 GPa) using an OFMD based EOS. KSMD simulations here have a practical upper limit of T = 25 eV due to the scaling of the computational work. The OFMD simulations have a lower limit of T = 5 eV since the OF DFT yields a poor description at low temperatures. The KSMD and OFMD Hugoniots agree well in the region of overlap (T = 5 to 25 eV). Comparisons will be presented with experimental data and with shock Hugoniots constructed from both existing EOS tables and from a new, improved SESAME table. By utilizing the KSMD and OFMD results to guide the parameter choices, the new EOS overall is a better match to melt and shock experimental data. This work was performed in collaboration with L. A. Collins, S. Crockett, M. P. Desjarlais, and F. Lambert and under the auspices of an agreement between CEA/DAM and NNSA/DP on cooperation on fundamental science. LANL is operated by LANS, LLC for the NNSA of the USDoE under contract no. DE-AC52-06NA25396.

  19. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations.

    PubMed

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-01

    The vibrational and reorientational motions of NH3 ligands and ClO4(-) anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385cm(-1), associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR≈10(-12)-10(-13)s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5kJmol(-1), in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TC(c)=137.6K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6](2+) cation and ClO4(-) anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models. PMID:25459713

  20. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-01

    The vibrational and reorientational motions of NH3 ligands and ClO4- anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385 cm-1, associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR ≈ 10-12-10-13 s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5 kJ mol-1, in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TCc = 137.6 K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311 + G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6]2+ cation and ClO4- anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models.

  1. ENDOR spectroscopy and DFT calculations: evidence for the hydrogen bond network within α2 in the PCET of E. coli ribonucleotide reductase

    PubMed Central

    Argirević, Tomislav; Riplinger, Christoph; Stubbe, JoAnne; Neese, Frank; Bennati, Marina

    2015-01-01

    E.coli class I ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides and is composed of two subunits: α2 and β2. β2 contains a stable di-iron tyrosyl radical (Y122•) cofactor required to generate a thiyl radical (C439•) in α2 over a distance of 35 Å, which in turn initiates the chemistry of the reduction process. The radical transfer process is proposed to occur by proton-coupled electron transfer (PCET) via a specific pathway: Y122 ⇆ W48[?] ⇆ Y356 in β2, across the subunit interface to Y731⇆ Y730 ⇆ C439 in α2. Within α2 a co-linear PCET model has been proposed. To obtain evidence for this model, 3-amino tyrosine (NH2Y) replaced Y730 in α2 and this mutant was incubated with β2, CDP and ATP to generate a (NH2Y730•) in D2O. [2H]-Electron-nuclear double resonance (ENDOR) spectra at 94 GHz of this intermediate were obtained and together with DFT models of α2 and quantum chemical calculations allowed assignment of the prominent ENDOR features to two hydrogen bonds likely associated with C439 and Y731. A third proton was assigned to a water molecule in close proximity (2.2 Å O-H---O distance) to residue 730. The calculations also suggest that the unusual g-values measured for NH2Y730• are consistent with the combined effect of the hydrogen bonds to Cys439 and Tyr731, both nearly perpendicular to the ring plane of NH2Y730. The results provide the first experimental evidence for the hydrogen bond network between the pathway residues in α2 of the active RNR complex, for which no structural data is available. PMID:23072506

  2. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields.

    PubMed

    Xiao, Yuming; Koutmos, Markos; Case, David A; Coucouvanis, Dimitri; Wang, Hongxin; Cramer, Stephen P

    2006-05-14

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies. The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT

  3. Synthesis, spectral characterization, thermal behaviour, antibacterial activity and DFT calculation on N'-[bis(methylsulfanyl) methylene]-2-hydroxybenzohydrazide and N'-(4-methoxy benzoyl)-hydrazinecarbodithioic acid ethyl ester.

    PubMed

    Bharty, M K; Dani, R K; Kushawaha, S K; Prakash, Om; Singh, Ranjan K; Sharma, V K; Kharwar, R N; Singh, N K

    2015-06-15

    Two new compounds N'-[bis(methylsulfanyl) methylene]-2-hydroxybenzohydrazide {Hbmshb (1)} and N'-(4-methoxy benzoyl)-hydrazinecarbodithioic acid ethyl ester {H2mbhce (2)} have been synthesized and characterized with the aid of elemental analyses, IR, NMR and single crystal X-ray diffraction data. Compounds 1 and 2 crystallize in orthorhombic and monoclinic systems with space group Pna21 and P21/n, respectively. Inter and intra molecular hydrogen bonding link two molecules and provide linear chain structure. In addition to this, compound 2 is stabilized by CH⋯π and NH⋯π interactions. Molecular geometry from X-ray analysis, geometry optimization, charge distribution, bond analysis, frontier molecular orbital (FMO) analysis and non-linear optical (NLO) effects have been performed using the density functional theory (DFT) with the B3LYP functional. The bioefficacy of compounds has been examined against the growth of bacteria to evaluate their anti-microbial potential. Compounds 1 and 2 are thermally stable and show NLO behaviour better than the urea crystal. PMID:25767993

  4. A DFT study on the NHC catalysed Michael addition of enols to α,β-unsaturated acyl-azoliums. A base catalysed C-C bond-formation step.

    PubMed

    Domingo, Luis R; Sáez, José A; Arnó, Manuel

    2014-02-14

    The NHC catalysed nucleophilic additions of enols to α,β-unsaturated acyl-azolium intermediates have been investigated using DFT methods at the MPWB1K/6-31G** computational level. In the direct and the conjugate additions, formation of a hydrogen bond (HB) with the carboxyl oxygen is not sufficient to favour the C-C bond formation as a consequence of the low nucleophilic character of enols. Interestingly, when enols form a HB with the chloride counterion, the activation energies associated with the conjugate addition decrease as a consequence of the increased nucleophilic character of enols and the increased electrophilic character of the 'acyl-azolium + Cl' ion pair. Analysis of the DFT reactivity indices allows establishing a base catalysed C-C bond-formation step promoted by the chloride counterion. PMID:24343422

  5. A DFT study on the NHC catalysed Michael addition of enols to α,β-unsaturated acyl-azoliums. A base catalysed C-C bond-formation step.

    PubMed

    Domingo, Luis R; Sáez, José A; Arnó, Manuel

    2014-02-14

    The NHC catalysed nucleophilic additions of enols to α,β-unsaturated acyl-azolium intermediates have been investigated using DFT methods at the MPWB1K/6-31G** computational level. In the direct and the conjugate additions, formation of a hydrogen bond (HB) with the carboxyl oxygen is not sufficient to favour the C-C bond formation as a consequence of the low nucleophilic character of enols. Interestingly, when enols form a HB with the chloride counterion, the activation energies associated with the conjugate addition decrease as a consequence of the increased nucleophilic character of enols and the increased electrophilic character of the 'acyl-azolium + Cl' ion pair. Analysis of the DFT reactivity indices allows establishing a base catalysed C-C bond-formation step promoted by the chloride counterion.

  6. On the accuracy of the GIAO-DFT calculation of 15N NMR chemical shifts of the nitrogen-containing heterocycles--a gateway to better agreement with experiment at lower computational cost.

    PubMed

    Samultsev, Dmitry O; Semenov, Valentin A; Krivdin, Leonid B

    2014-05-01

    The main factors affecting the accuracy and computational cost of the gauge-independent atomic orbital density functional theory (GIAO-DFT) calculation of (15)N NMR chemical shifts in the representative series of key nitrogen-containing heterocycles--azoles and azines--have been systematically analyzed. In the calculation of (15)N NMR chemical shifts, the best result has been achieved with the KT3 functional used in combination with Jensen's pcS-3 basis set (GIAO-DFT-KT3/pcS-3) resulting in the value of mean absolute error as small as 5 ppm for a range exceeding 270 ppm in a benchmark series of 23 compounds with an overall number of 41 different (15)N NMR chemical shifts. Another essential finding is that basically, the application of the locally dense basis set approach is justified in the calculation of (15)N NMR chemical shifts within the 3-4 ppm error that results in a dramatic decrease in computational cost. Based on the present data, we recommend GIAO-DFT-KT3/pcS-3//pc-2 as one of the most effective locally dense basis set schemes for the calculation of (15)N NMR chemical shifts.

  7. Substituent effects in nitro derivatives of carbazoles investigated by comparison of low-temperature crystallographic studies with density functional theory (DFT) calculations.

    PubMed

    Gajda, Katarzyna; Zarychta, Bartosz; Kopka, Katarzyna; Daszkiewicz, Zdzisław; Ejsmont, Krzysztof

    2014-10-01

    The crystal structure of 9H-carbazole, C12H9N, (I), has been redetermined at low temperature for use as a reference structure in a comparative study with the structures of 1-nitro-9H-carbazole, C12H8N2O2, (II), and 9-nitrocarbazole, C12H8N2O2, (III). The molecule of (I) has crystallographically imposed mirror symmetry (Z' = 0.5). All three solid-state structures are slightly nonplanar, the dihedral angles between the planes of the arene and pyrrole rings ranging from 0.40 (7)° in (III) to 1.82 (18)° in (II). Nevertheless, a density functional theory (DFT) study predicts completely planar conformations for the isolated molecules. To estimate the influence of nitro-group substitution on aromaticity, the HOMA (harmonic oscillator model of aromaticity) descriptor of π-electron delocalization has been calculated in each case. The HOMA indices for the isolated and solid-state molecules are relatively consistent and decrease in value for aromatic rings that are substituted with a π-electron-withdrawing nitro group. Substitution of the arene ring influences the π-electron delocalization in the ring only weakly, showing strong resistance to a perturbation of its geometry, contrary to what is observed for nitro substitution of the five-membered heterocyclic pyrrole ring. In (II), the molecules are arranged in near-planar dimers connected to each other by strong N-H···O hydrogen bonds that stack parallel to the crystallographic b axis. A similar stacking arrangement is observed in (III), although here the stacked structure is formed by stand-alone molecules.

  8. Antioxidant potential of curcumin-related compounds studied by chemiluminescence kinetics, chain-breaking efficiencies, scavenging activity (ORAC) and DFT calculations.

    PubMed

    Slavova-Kazakova, Adriana K; Angelova, Silvia E; Veprintsev, Timur L; Denev, Petko; Fabbri, Davide; Dettori, Maria Antonietta; Kratchanova, Maria; Naumov, Vladimir V; Trofimov, Aleksei V; Vasil'ev, Rostislav F; Delogu, Giovanna; Kancheva, Vessela D

    2015-01-01

    This study compares the ability to scavenge different peroxyl radicals and to act as chain-breaking antioxidants of monomers related to curcumin (1): dehydrozingerone (2), zingerone (3), (2Z,5E)-ethyl 2-hydroxy-6-(4-hydroxy-3-methoxyphenyl)-4-oxohexa-2,5-dienoate (4), ferulic acid (5) and their corresponding C 2-symmetric dimers 6-9. Four models were applied: model 1 - chemiluminescence (CL) of a hydrocarbon substrate used for determination of the rate constants (k A) of the reactions of the antioxidants with peroxyl radicals; model 2 - lipid autoxidation (lipidAO) used for assessing the chain-breaking antioxidant efficiency and reactivity; model 3 - oxygen radical absorbance capacity (ORAC), which yields the activity against peroxyl radicals generated by an azoinitiator; model 4 - density functional theory (DFT) calculations at UB3LYP/6-31+G(d,p) level, applied to explain the structure-activity relationship. Dimers showed 2-2.5-fold higher values of k A than their monomers. Model 2 gives information about the effects of the side chains and revealed much higher antioxidant activity for monomers and dimers with α,β-unsaturated side chains. Curcumin and 6 in fact are dimers of the same monomer 2. We conclude that the type of linkage between the two "halves" by which the molecule is made up does not exert influence on the antioxidant efficiency and reactivity of these two dimers. The dimers and the monomers demonstrated higher activity than Trolox (10) in aqueous medium (model 3). A comparison of the studied compounds with DL-α-tocopherol (11), Trolox and curcumin is made. All dimers are characterized through lower bond dissociation enthalpies (BDEs) than their monomers (model 4), which qualitatively supports the experimental results. PMID:26425195

  9. Antioxidant potential of curcumin-related compounds studied by chemiluminescence kinetics, chain-breaking efficiencies, scavenging activity (ORAC) and DFT calculations

    PubMed Central

    Slavova-Kazakova, Adriana K; Angelova, Silvia E; Veprintsev, Timur L; Denev, Petko; Fabbri, Davide; Dettori, Maria Antonietta; Kratchanova, Maria; Naumov, Vladimir V; Trofimov, Aleksei V; Vasil’ev, Rostislav F

    2015-01-01

    Summary This study compares the ability to scavenge different peroxyl radicals and to act as chain-breaking antioxidants of monomers related to curcumin (1): dehydrozingerone (2), zingerone (3), (2Z,5E)-ethyl 2-hydroxy-6-(4-hydroxy-3-methoxyphenyl)-4-oxohexa-2,5-dienoate (4), ferulic acid (5) and their corresponding C 2-symmetric dimers 6–9. Four models were applied: model 1 – chemiluminescence (CL) of a hydrocarbon substrate used for determination of the rate constants (k A) of the reactions of the antioxidants with peroxyl radicals; model 2 – lipid autoxidation (lipidAO) used for assessing the chain-breaking antioxidant efficiency and reactivity; model 3 – oxygen radical absorbance capacity (ORAC), which yields the activity against peroxyl radicals generated by an azoinitiator; model 4 – density functional theory (DFT) calculations at UB3LYP/6-31+G(d,p) level, applied to explain the structure–activity relationship. Dimers showed 2–2.5-fold higher values of k A than their monomers. Model 2 gives information about the effects of the side chains and revealed much higher antioxidant activity for monomers and dimers with α,β-unsaturated side chains. Curcumin and 6 in fact are dimers of the same monomer 2. We conclude that the type of linkage between the two “halves” by which the molecule is made up does not exert influence on the antioxidant efficiency and reactivity of these two dimers. The dimers and the monomers demonstrated higher activity than Trolox (10) in aqueous medium (model 3). A comparison of the studied compounds with DL-α-tocopherol (11), Trolox and curcumin is made. All dimers are characterized through lower bond dissociation enthalpies (BDEs) than their monomers (model 4), which qualitatively supports the experimental results. PMID:26425195

  10. Molecular structure and hydrogen bonding in liquid cyclohexanol and cyclohexanol/water mixtures studied by FT-NIR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Czarnecki, Mirosław Antoni; Muszyński, Andrzej S.; Troczyńska, Helena

    2010-06-01

    The molecular structure and hydrogen bonding in liquid cyclohexanol and cyclohexanol/water mixtures has been examined by Fourier-transform near-infrared (FT-NIR) spectroscopy. FT-NIR spectra of pure cyclohexanol and binary mixtures with water at selected water mole fractions ( XO) from 30 to 80 °C and the spectra of the mixtures from XO = 0-0.4 at 30 °C were measured. Besides, FT-IR and FT-NIR spectra of cyclohexanol in CCl 4 and cyclohexane solutions were recorded. The experimental spectra were analyzed by two-dimensional (2D) correlation approach and chemometrics methods. Interpretation of the spectra was guided by DFT calculations. It has been shown that small to moderate water content has a negligible effect on the structure of liquid cyclohexanol at constant temperature. Water molecules predominantly act as double donors to different species of cyclohexanol and this hydrogen bonding is stronger than that in bulk water. At lower water content appears a noticeable amount of singly bonded water molecules, however, population of this species in cyclohexanol is significantly smaller as compared with that in butyl alcohols. This results from much higher viscosity of cyclohexanol that stabilizes the cyclohexanol-water interactions. Increasing water content leads to creation of small clusters of water, where the water-water interaction is much weaker than that in bulk water. The temperature-induced breaking of smaller associates of cyclohexanol occurs easier in the presence of water, while an opposite effect was observed for the higher associates. The hydrophobic interactions in the cyclohexanol/water mixtures are of minor importance.

  11. Solvation structure and thermodynamics for Pr(III), Nd(III) and Dy(III) complexes in ionic liquids evaluated by Raman spectroscopy and DFT calculation

    NASA Astrophysics Data System (ADS)

    Kuribara, Keita; Matsumiya, Masahiko; Tsunashima, Katsuhiko

    2016-12-01

    The coordination states of trivalent praseodymium, neodymium, and dysprosium complexes in the ionic liquid, triethyl-n-pentylphosphonium bis(trifluoromethyl-sulfonyl) amide ([P2225][TFSA]) were investigated by Raman spectroscopy. The effect of the concentration of rare earth ions on the Raman spectra was investigated, ranging from 0.23 to 0.45 mol kg-1 of Pr(III), Nd(III), and Dy(III) in [P2225][TFSA]. Based on a conventional analysis, the solvation numbers, n, of Pr(III), Nd(III), and Dy(III) in [P2225][TFSA] were determined to be 4.99, 5.01, and 5.00 at 298 K and 5.04, 5.06, and 5.07 at 373 K, respectively. Thermodynamic properties such as ΔisoG, ΔisoH, and ΔisoS for the isomerism of [TFSA]- from trans- to cis-coordinated isomer in the bulk and the first solvation sphere of the central RE3+ (RE = Pr, Nd, and Dy) cation in [P2225][TFSA] were evaluated from the temperature dependence of the Raman bands, measured at temperatures ranging from 298 to 398 K. Regarding the bulk properties, ΔisoG(bulk), ΔisoH(bulk), and TΔisoS(bulk) at 298 K were found to be -1.06, 6.86, and 7.92 kJ mol-1, respectively. The trans-[TFSA]- was a dominant contributor to the enthalpy, as shown by the positive value of ΔisoH(bulk). The value of TΔisoS(bulk) was slightly larger than that of ΔisoH(bulk), and cis-[TFSA]- was, therefore, entropy-controlled in [P2225][TFSA]. In contrast, in the first solvation sphere of the RE3+ cation, ΔisoH(RE) became remarkably negative, suggesting that cis-[TFSA]- isomers were stabilized by enthalpic contributions. Furthermore, ΔisoH(RE) contributed to the remarkable decrease in ΔisoG(RE), and this result clearly indicates that cis-[TFSA]- conformers bound to RE3+ cations are the preferred coordination state of [RE(III)(cis-TFSA)5]2- in [P2225][TFSA]. Moreover, optimized geometries and binding energies of [Pr(III)(cis-TFSA)5]2-, [Nd(III)(cis-TFSA)5]2-, and [Dy(III)(cis-TFSA)5]2- clusters were also investigated by DFT calculations using the ADF

  12. Calculation of vibrational and electronic excited state absorption spectra of arsenic-water complexes using density functional theory

    NASA Astrophysics Data System (ADS)

    Huang, L.; Lambrakos, S. G.; Shabaev, A.; Massa, L.

    2016-05-01

    Calculations are presented of vibrational and electronic excited-state absorption spectra for As-H2O complexes using density function theory (DFT) and time-dependent density functional theory (TD-DFT). DFT and TD-DFT can provide interpretation of absorption spectra with respect to molecular structure for excitation by electromagnetic waves at frequencies within the IR and UV-visible ranges. The absorption spectrum corresponding to excitation states of As-H2O complexes consisting of relatively small numbers of water molecules should be associated with response features that are intermediate between that of isolated molecules and that of a bulk system. DFT and TD-DFT calculated absorption spectra represent quantitative estimates that can be correlated with additional information obtained from laboratory measurements and other types of theory based calculations. The DFT software GAUSSIAN was used for the calculations of excitation states presented here.

  13. Gas-phase ion-molecule reactions of metal-carbide cations MCn+ (M=Y and La; n=2, 4, and 6) with benzene and cyclohexane investigated by FTICR mass spectrometry and DFT calculations.

    PubMed

    Zhang, Rui; Dinca, Adriana; Fisher, Keith J; Smith, Derek R; Willett, Gary D

    2005-01-13

    Yttrium- and lanthanum-carbide cluster cations YC(n)(+) and LaC(n)(+) (n = 2, 4, and 6) are generated by laser ablation of carbonaceous material containing Y(2)O(3) or La(2)O(3). YC(2)(+), YC(4)(+), LaC(2)(+), LaC(4)(+), and LaC(6)(+) are selected to undergo gas-phase ion-molecule reactions with benzene and cyclohexane. The FTICR mass spectrometry study shows that the reactions of YC(2)(+) and LaC(2)(+) with benzene produce three main series of cluster ions. They are in the form of M(C(6)H(4))(C(6)H(6))(n)(+), M(C(8)H(4))(C(6)H(6))(n)(+), and M(C(8)H(6))(C(6)H(6))(m)(+) (M = Y and La; n = 0-3; m = 0-2). For YC(4)(+), LaC(4)(+), and LaC(6)(+), benzene addition products in the form of MC(n)(C(6)H(6))(m)(+) (M = Y and La; n = 4, 6; m = 1, 2) are observed. In the reaction with cyclohexane, all the metal-carbide cluster ions are observed to form metal-benzene complexes M(C(6)H(6))(n)(+) (M = Y and La; n= 1-3). Collision-induced-dissociation experiments were performed on the major reaction product ions, and the different levels of energy required for the fragmentation suggest that both covalent bonding and weak electrostatic interaction exist in these organometallic complexes. Several major product ions were calculated using DFT theory, and their ground-state geometries and energies were obtained.

  14. Graph model for calculating the properties of saturated monoalcohols based on the additivity of energy terms

    NASA Astrophysics Data System (ADS)

    Grebeshkov, V. V.; Smolyakov, V. M.

    2012-05-01

    A 16-constant additive scheme was derived for calculating the physicochemical properties of saturated monoalcohols CH4O-C9H20O and decomposing the triangular numbers of the Pascal triangle based on the similarity of subgraphs in the molecular graphs (MGs) of the homologous series of these alcohols. It was shown, using this scheme for calculation of properties of saturated monoalcohols as an example, that each coefficient of the scheme (in other words, the number of methods to impose a chain of a definite length i 1, i 2, … on a molecular graph) is the result of the decomposition of the triangular numbers of the Pascal triangle. A linear dependence was found within the adopted classification of structural elements. Sixteen parameters of the schemes were recorded as linear combinations of 17 parameters. The enthalpies of vaporization L {298/K 0} of the saturated monoalcohols CH4O-C9H20O, for which there were no experimental data, were calculated. It was shown that the parameters are not chosen randomly when using the given procedure for constructing an additive scheme by decomposing the triangular numbers of the Pascal triangle.

  15. Ni(II) and Pd(II) complexes with new N,O donor thiophene appended Schiff base ligand: Synthesis, electrochemistry, X-ray structure and DFT calculation

    NASA Astrophysics Data System (ADS)

    Kundu, Subhankar; Pramanik, Ajoy Kumar; Mondal, Apurba Sau; Mondal, Tapan Kumar

    2016-07-01

    The thiophene appended Schiff's base ligand, 1-(2-(thiophen-2-yl)ethylimino)methyl)naphthalene-2-ol (HL) with N,O donor sites has been synthesized by the condensation between 2-hydroxy-1-naphthaldehyde and thiophene-2-ethylamine. The square planar 1:2 complexes of HL having general formula [M(L)2] (M = Ni(1) and Pd(2)) with nickel(II) and palladium(II) have been synthesized and characterized by several spectroscopic techniques. The geometry has been confirmed by single crystal X-ray study for complex 1. The electronic structure and spectral properties of the complexes are interpreted by DFT and TDDFT studies.

  16. Synthesis, crystal structure, thermal analysis and vibrational spectroscopy accomplished with DFT calculation of new hybrid compound [2-CH3C6H4NH3]HSO4.H2O

    NASA Astrophysics Data System (ADS)

    Ben Hassen, C.; Boujelbene, M.; Marweni, S.; Bahri, M.; Mhiri, T.

    2015-10-01

    The present paper undertakes the study of a new organic/inorganic hybrid compound [2-CH3C6H4NH3]HSO4.H2O characterized by the X-ray diffraction, TG-DTA, IR and Raman spectroscopy accomplished with DFT calculation. It is crystallized in the monoclinic system with the centrosymmetric space group P 21/c, with a = 9.445 (5) Å, b = 10.499 Å, c = 10.073 Å, β = 90.627 (5)° and Z = 4. The atomic arrangement can be described as inorganic layers built by infinite chains, parallel to the (a c) planes between which the organic cations are inserted. In this atomic arrangement, hydrogen bonds and π-π interactions between the different species have an important role in the tri-dimensional network cohesion. Besides, the X-ray powder diffraction of the title compound confirms the existence of only one phase at room temperature. The thermal decomposition of precursors studied by thermo gravimetric analysis (TGA), the differential thermal analysis (DTA) and the temperature-dependent X-ray diffraction, show crystalline anhydrous compounds upon dehydration. DFT/BHHLYP calculations were performed, using the DZV (d,p) basis set, to determine the harmonic frequencies of the vibrational modes of an optimized cluster structure. The calculated modes were animated using the Molden graphical package to give tentative assignments of the observed IR and Raman spectra.

  17. New insight into the hydrocarbon-pool chemistry of the methanol-to-olefins conversion over zeolite H-ZSM-5 from GC-MS, solid-state NMR spectroscopy, and DFT calculations.

    PubMed

    Wang, Chao; Chu, Yueying; Zheng, Anmin; Xu, Jun; Wang, Qiang; Gao, Pan; Qi, Guodong; Gong, Yanjun; Deng, Feng

    2014-09-22

    Over zeolite H-ZSM-5, the aromatics-based hydrocarbon-pool mechanism of methanol-to-olefins (MTO) reaction was studied by GC-MS, solid-state NMR spectroscopy, and theoretical calculations. Isotopic-labeling experimental results demonstrated that polymethylbenzenes (MBs) are intimately correlated with the formation of olefin products in the initial stage. More importantly, three types of cyclopentenyl cations (1,3-dimethylcyclopentenyl, 1,2,3-trimethylcyclopentenyl, and 1,3,4-trimethylcyclopentenyl cations) and a pentamethylbenzenium ion were for the first time identified by solid-state NMR spectroscopy and DFT calculations under both co-feeding ([(13) C6 ]benzene and methanol) conditions and typical MTO working (feeding [(13) C]methanol alone) conditions. The comparable reactivity of the MBs (from xylene to tetramethylbenzene) and the carbocations (trimethylcyclopentenyl and pentamethylbenzium ions) in the MTO reaction was revealed by (13) C-labeling experiments, evidencing that they work together through a paring mechanism to produce propene. The paring route in a full aromatics-based catalytic cycle was also supported by theoretical DFT calculations.

  18. Studies on the synthesis, spectroscopic analysis and DFT calculations on (E)-4,6-dichloro-2-[(2-chlorophenylimino)methyl]-3methoxyphenol as a novel Schiff's base

    NASA Astrophysics Data System (ADS)

    Yıldırım, Arzu Özek; Yıldırım, M. Hakkı; Kaştaş, Çiğdem Albayrak

    2016-06-01

    In this study, we report synthesis, single crystal X-ray diffraction, FT-IR and Uv-Vis. characterizations and computational investigations of the (E)-4,6-dichloro-2-[(2-chlorophenylimino)methyl]-3-methoxyphenol. The tautomeric equilibrium between enol, keto and transition state (TS) forms of (E)-4,6-dichloro-2-[(2-chlorophenylimino)methyl]-3-methoxyphenol have been investigated by considering the presence of the compound in vacuum and various solvents. Experimental studies clearly reveal that the title compound has enol form in solid state and ethanol solution. In addition, the enol, keto and TS structures of the compound have been investigated computationally. Intramolecular proton transfer process on the O-H⋯N hydrogen bond and transition state structure during the transfer process have been studied by scan calculations for vacuum and solvent media. Moreover, the stabilization energies of the title compound were computed by using second-order perturbation theory to have insight on the intra- and intermolecular interactions, interaction among bonds, conjugative interactions. To find out most reactive sites of the title molecule, condensed Fukui functions have been calculated by means of natural population analysis. Nonlinear optical property calculations of the compound indicate that the compound can be used as a NLO material.

  19. Evaluation of a combination of local hybrid functionals with DFT-D3 corrections for the calculation of thermochemical and kinetic data.

    PubMed

    Theilacker, Kolja; Arbuznikov, Alexei V; Bahmann, Hilke; Kaupp, Martin

    2011-08-18

    Due to their position-dependent exact exchange admixture, local hybrid functionals offer a higher flexibility and thus the potential for more universal and accurate exchange correlation functionals compared to global hybrids with a constant admixture, as has been demonstrated in previous work. Yet, the local hybrid constructions used so far do not account for the inclusion of dispersion-type interactions. As a first exploratory step toward a more general approach that includes van der Waals-type interactions with local hybrids, the present work has added DFT-D3-type corrections to a number of simple local hybrid functionals. Optimization of only the s(8) and s(r,6) parameters for the S22 set provides good results for weak interaction energies but deteriorates the excellent performance of the local hybrids for G3 atomization energies and for classical reaction barriers. A combined optimization of the two DFT-D3 parameters with one of the two parameters of the spin-polarized local mixing function (LMF) of a local hybrid for a more general optimization set provides simultaneously accurate dispersion energies, improved atomization energies, and accurate reaction barriers, as well as excellent alkane protobranching ratios. For other LMFs, the improvements of such a combined optimization for the S22 energies have been less satisfactory. The most notable advantage of the dispersion-corrected local hybrids over, for example, a B3LYP-D3 approach, is in the much more accurate reaction barriers.

  20. Performance on paced serial addition tasks indicates an associative network for calculation.

    PubMed

    Hiscock, M; Caroselli, J S; Kimball, L E; Panwar, N

    2001-06-01

    Although paced serial addition (PSA) tasks are considered to be tests of general information-processing capacity, recent work suggests that performance on such tasks is influenced by arithmetic-specific variables. We designed two visual PSA experiments to determine whether the performance of normal adults would support predictions derived from the cognitive psychology of calculation. Experiment 1 showed that mixing familiar (Arabic numeral) and less familiar (Roman numeral) stimulus formats reduced scores below the averaged scores for pure Arabic and Roman lists. The Roman-Arabic order of addends was more difficult than the Arabic-Roman order. Experiment 2, which involved only Arabic numerals as addends, showed that performance could be impaired by constraining the trial-to-trial variability of sums. The results of both experiments confirm the importance of arithmetic-specific variables in PSA and provide support for an associative network model of calculation. In addition, the findings implicate interference from extraneous addends and responses as the performance-limiting factor. PMID:11404809

  1. Evaluation of additive element to improve PZT piezoelectricity by using first-principles calculation

    NASA Astrophysics Data System (ADS)

    Yasoda, Yutaka; Uetsuji, Yasutomo; Tsuchiya, Kazuyoshi

    2015-12-01

    Recently, piezoelectric material has a very important potential for functional material which configure Bio-MEMS (Biological Micro Electro Mechanical Systems) actuator and sensor. Specifically, in implementation of piezoelectric material for Bio-MEMS, thin film fabrication by sputtering method is made from the viewpoint of miniaturization. Furthermore, in piezoelectric material, perovskite type material composed of ABO3 has a high piezoelectricity. Then, PZT (Lead Zirconate Titanate) as the perovskite type piezoelectric material is widely used since it is easy to produce and has high piezoelectricity. PZT has zirconium or titanium in the B site of ABO3 structure. PZT has the features such as physical properties to greatly change by change in the B site composition ratio of zirconium and titanium. Thus, the B site greatly influences physical properties and therefore function improvement by additive element is tried widely. However, experimental method to lack in economy and quantitativeness is mainstream. Therefore, application of the result is difficult and new evaluation method of B site additive element for sputtering fabrication is necessary. Accordingly, in this research, search of an additive element at low cost and quantitative from the viewpoint of energy by first-principles calculation. First of all, the additive elements which capable of substituting for a B site of PZT were searched. Next, change of piezoelectricity was evaluated by change of crystal structure in a PZT system was introduced an additive element that substitution of the B site was possible. As a result, additive elements for the PZT B site capable of improving piezoelectricity were determined.

  2. Hydrogen and halogen bonding patterns and π-π aromatic interactions of some 6,7-disubstituted 1,3-benzothiazoles studied by X-ray diffraction and DFT calculations

    NASA Astrophysics Data System (ADS)

    Čičak, Helena; Đaković, Marijana; Mihalić, Zlatko; Pavlović, Gordana; Racané, Livio; Tralić-Kulenović, Vesna

    2010-06-01

    The structures of five 6,7-disubstituted 1,3-benzothiazole (1,3-benzothiazole = bta) derivatives: 6-chloro-7-nitro-bta ( 3), 6-iodo-7-nitro-bta ( 5), 6-amino-7-iodo-bta ( 6), 6-acetylamino-7-iodo-bta ( 7) and 6-amino-7-bromo-bta ( 8) are reported and investigated by X-ray crystallography and DFT calculations. The crystal structures of 3 and 5- 8 are characterized by: (i) relatively weak C sbnd H⋯O/N/Br and N sbnd H⋯O/N/S hydrogen bonds, (ii) C sbnd Cl⋯O and C sbnd I⋯O/N halogen bonds and Br⋯Br interactions and (iii) π-π interactions. DFT optimized structures of 3, 5, 6 and 8 are in a good agreement with the corresponding X-ray molecular data. Calculated structure of 7 deviates from the experimental geometry because of more favourable intermolecular hydrogen bonding in crystal phase compared to the weak intramolecular hydrogen bond in the gas phase. The molecular electrostatic potential maps were used for predicting possible hydrogen and halogen bonding sites in structures of 3, 5, 6 and 8, and AIM analysis in order to characterize the nature and strength of intermolecular interactions in all of the examined crystal structures. Experimental results agree well with AIM analysis suggesting that the detected hydrogen and halogen bonds are weak and mostly of electrostatic origin.

  3. Dicarboxylate assisted synthesis of the monoclinic heterometallic tetrathiocyanato bridged copper(II) and mercury(II) coordination polymer {Cu[Hg(SCN) 4]} n: Synthesis, structural, vibration, luminescence, EPR studies and DFT calculations

    NASA Astrophysics Data System (ADS)

    Khandar, Ali Akbar; Klein, Axel; Bakhtiari, Akbar; Mahjoub, Ali Reza; Pohl, Roland W. H.

    2011-02-01

    The synthesis of the monoclinic polymorph of {Cu[Hg(SCN) 4]} n is reported. The compound, as determined by X-ray diffraction of a twinned crystal, consists of mercury and copper atoms linked by μ1,3-SCN bridges. The crystal packing shows a highly porous infinite 3D structure. Diagnostic resonances for the SCN - ligand and metal-ligand bonds in the IR, far-IR and Raman spectra are assigned and discussed. The electronic band structure along with density of states (DOS) calculated by the DFT method indicates that the compound is an indirect band gap semiconductor. The DFT calculations show that the observed luminescence of the compound arises mainly from an excited LLCT state with small MLCT contributions (from the copper to unoccupied π* orbital of the thiocyanate groups). The X-band EPR spectrum of the powdered sample at room temperature reveals an axial signal with anisotropic g factors consistent with the unpaired electron of Cu(II) ion in the dx2- y2 orbital.

  4. Synthesis, crystal structures, spectroscopic analysis and DFT calculations of 2-ethoxy-1-naphtaldehyde and (E)-N-((2-ethoxynaphthalen-1-yl)methylene)-3-methylaniline

    NASA Astrophysics Data System (ADS)

    Yıldırım, M. Hakkı; Yıldırım, Arzu Özek; Macit, Mustafa; Ağar, Ayşen Alaman; Paşaoğlu, Hümeyra; Soylu, M. Serkan

    2016-08-01

    (E)-N-((2-ethoxynaphthalen-1-yl)methylene)-3-methylaniline has been synthesized and characterized by using single-crystal X-ray diffraction, FT-IR, UV-Visible spectroscopy and computational methods. By using the same techniques, also for the first time, the 2-ethoxy-1-naphtaldehyde has been characterized. The molecular geometries, intra- and inter-molecular interactions of the compounds have been found by using X-ray crystallography. Characteristic infrared bands and the electronic bands have been discovered by experimental and theoretical IR and UV-Vis. spectroscopy. The geometry optimizations and the calculations of IR frequencies have been performed by using the Gaussian type orbitals at Gaussian 09W and the Slater type orbitals at ADF2009.01 software. In addition, the Fukui functions have been calculated to reveal active sites of the compounds. Furthermore, non-linear optical properties and thermodynamic correlation functions have been theoretically found for a further study of the titled compounds.

  5. Structural and spectroscopic study of a pectin isolated from citrus peel by using FTIR and FT-Raman spectra and DFT calculations

    NASA Astrophysics Data System (ADS)

    Bichara, Laura C.; Alvarez, Patricia E.; Fiori Bimbi, María V.; Vaca, Hugo; Gervasi, Claudio; Brandán, Silvia Antonia

    2016-05-01

    In this work, pectin isolated from citrus peel with a degree of esterification of 76% was characterized by Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectroscopies. Structural studies were carried out taking into account their partial degree of esterification and considering the polygalacturonic acid chain as formed by two different subunits, one with both COOH and COOsbnd CH3 groups (Ac) and the other one as constituted by two subunits with two COOsbnd CH3 groups (Es). Their structural properties, harmonic frequencies, force fields and force constants in gas and aqueous solution phases were calculated by using the hybrid B3LYP/6-31G∗ method. Then, their complete vibrational analyses were performed by using the IR and Raman spectra accomplished with the scaled quantum mechanical (SQM) methodology. Reactivities and behaviors in both media were predicted for Ac and Es by using natural bond orbital (NBO), atoms in molecules (AIM), and frontier orbitals calculations. We report for first time the complete assignments of those two different units of polygalacturonic acid chain which are the 132 normal vibration modes of Ac and the 141 normal vibration modes of Es, combining the normal internal coordinates with the SQM methodology. In addition, three subunits were also studied. Reasonable correlations between the experimental and theoretical spectra were obtained. Thus, this work would allow the quick identification of pectin by using infrared and Raman spectroscopies and also provides new insight into the interactions that exist between subunits of a large pectin chain.

  6. Study on the adsorption properties of O3, SO2, and SO3 on B-doped graphene using DFT calculations

    NASA Astrophysics Data System (ADS)

    Rad, Ali Shokuhi; Shabestari, Sahand Sadeghi; Mohseni, Soheil; Aghouzi, Samaneh Alijantabar

    2016-05-01

    We investigated the structure, adsorption, electronic states, and charge transfer of O3, SO2 and SO3 molecules on the surface of a B-doped graphene using density functional theory (DFT). We found weak physisorption of SO2 (-10.9 kJ/mole, using B3LYP-D) and SO3 (-15.7 kJ/mole, using B3LYP-D) on the surface of B-doped graphene while there is strong chemisorption for O3 (-96.3 kJ/mole, using B3LYP-D) on this surface. Our results suggest the potential of B-doped graphene as a selective sensor/adsorbent for O3 molecule. We noticed some change in hybridizing of boron from sp2 to sp3 upon adsorption of O3 which cases transformation of the adsorbent from 2D to 3D.

  7. Montecrinanes A-C: Triterpenes with an Unprecedented Rearranged Tetracyclic Skeleton from Celastrus vulcanicola. Insights into Triterpenoid Biosynthesis Based on DFT Calculations.

    PubMed

    Purino, Martín; Ardiles, Alejandro E; Callies, Oliver; Jiménez, Ignacio A; Bazzocchi, Isabel L

    2016-05-23

    Three new triterpenoids with an unprecedented 6/6/6/6-fused tetracyclic carbon skeleton, montecrinanes A-C (1-3), were isolated from the root bark of Celastrus vulcanicola, along with known D:B-friedobaccharanes (4-6), and lupane-type triterpenes (7-12). The stereostructures of the new metabolites were elucidated based on spectroscopic (1D and 2D NMR) and spectrometric (HR-EIMS and HR-ESIMS) techniques. Their absolute configurations were determined by both NMR spectroscopy, with (R)-(-)-α-methoxyphenylacetic acid as a chiral derivatizing agent, and biogenetic considerations. Biogenetic pathways for montecrinane and D:B-friedobaccharane skeletons were proposed and studied by DFT methods. The theoretical results support the energetic feasibility of the putative biogenetic pathways, in which the 1,2-methyl shift from the secondary baccharenyl cation represents a novel and key reaction step for a new montecrinane skeleton.

  8. Doping-induced stability in vanadium-doped ZnO quantum well wires (QWW): Combination of DFT calculations within experimental measurements

    NASA Astrophysics Data System (ADS)

    Yumak, A.; Goumri-Said, Souraya; Khan, Wilayat; Boubaker, Karem; Petkova, P.

    2016-07-01

    ZnO quantum well wires (QWW) have grown on glass substrates by an inexpensive, simplified and enhanced spray pyrolysis technique then doped by Vanadium. The effects of V-doping on the structural, morphological and optical properties of the QWW were investigated experimentally and theoretically. The accuracy of control can be achieved on functional performance by adjusting vanadium doping extent. The incorporation of Vanadium in ZnO-QWW induced the formation of band tailing in states. The interactions with phonons and the presence of a tail absorption profile are following the empirical Urbach law. The electronic structure using density functional theory have shown the changes induced by vanadium doping in ZnO-QWW, where the phonon band structure and density of states were reported. The DFT results showed a good agreement with the lattice compatibility theory as well as with the experimental results.

  9. Magnetic property, DFT calculation, and biological activity of bis[(μ(2)-chloro)chloro(1,10-phenanthroline)copper(II)] complex.

    PubMed

    Mroueh, Mohammad; Daher, Costantine; Hariri, Essa; Demirdjian, Sally; Isber, Samih; Choi, Eun Sang; Mirtamizdoust, Babak; Hammud, Hassan H

    2015-04-25

    The dinuclear complex bis[(μ(2)-chloro)chloro(1,10-phenanthroline)copper(II)] (1) was synthesized, and characterized by X-ray, FTIR and thermal analysis. The fitting of magnetic susceptibility and magnetization curve of (1) indicates the occurrence of weak antiferromagnetic exchange interaction between copper(II) ions. The electronic structure has been also determined by density functional theory (DFT) method. Complex (1) displayed potent anticancer activity against B16 (Melanoma), MDA-MB-32 (Breast Adenocarcinoma), A549 (Lung Adenocarcinoma), HT-29 (Colon Adenocarcinoma) and SF (Astrocytoma) cell lines with an average IC50 value of 0.726 μg/ml compared to 4.88 μg/ml for cisplatin. Complex (1) has a better therapeutic index and toxicological profile than cisplatin, and has demonstrated a potential chemotherapeutic property.

  10. Free energy calculation of water addition coupled to reduction of aqueous RuO4-

    NASA Astrophysics Data System (ADS)

    Tateyama, Yoshitaka; Blumberger, Jochen; Ohno, Takahisa; Sprik, Michiel

    2007-05-01

    Free energy calculations were carried out for water addition coupled reduction of aqueous ruthenate, RuO4-+H2O +e-→[RuO3(OH)2]2-, using Car-Parrinello molecular dynamics simulations. The full reaction is divided into the reduction of the tetrahedral monoanion, RuO4-+e-→RuO42-, followed by water addition, RuO42-+H2O →[RuO3(OH)2]2-. The free energy of reduction is computed from the fluctuations of the vertical energy gap using the MnO4-+e -→MnO42- reaction as reference. The free energy for water addition is estimated using constrained molecular dynamics methods. While the description of this complex reaction, in principle, involves multiple reaction coordinates, we found that reversible transformation of the reactant into the product can be achieved by control of a single reaction coordinate consisting of a suitable linear combination of atomic distances. The free energy difference of the full reaction is computed to be -0.62eV relative to the normal hydrogen electrode. This is in good agreement with the experimental value of -0.59eV, lending further support to the hypothesis that, contrary to the ruthenate monoanion, the dianion is not tetrahedral but forms a trigonal-bipyramidal dihydroxo complex in aqueous solution. We construct an approximate two-dimensional free energy surface using the coupling parameter for reduction and the mechanical constraint for water addition as variables. Analyzing this surface we find that in the most favorable reaction pathway the reduction reaction precedes water addition. The latter takes place via the protonated complex [RuO3(OH)]- and subsequent transport of the created hydroxide ion to the fifth coordination site of Ru.

  11. The effect of Cu(2+) chelation on the direct photolysis of oxytetracycline: A study assisted by spectroscopy analysis and DFT calculation.

    PubMed

    Jin, Xin; Qiu, Shanshan; Wu, Ke; Jia, Mingyun; Wang, Fang; Gu, Chenggang; Zhang, Aiqian; Jiang, Xin

    2016-07-01

    The extensive usage of OTC and Cu(2+) in livestock and poultry industry caused high residues in natural environment. Co-contamination of OTC and Cu(2+) was a considerable environmental problem in surface waters. In this study, Cu(2+) mediated direct photolysis of OTC was studied. Cu(2+) chelating with OTC was found to greatly inhibit OTC photodegradation. To reveal the chelation mechanism of OTC-Cu complexes, multiple methods including UV-Vis absorption spectra, Infrared (IR) spectra, mass spectroscopy, and density functional theoretical (DFT) modeling were performed. Four OTC-Cu complexes were proposed. Cu(2+) preferably bond to O11O12 site with the binding constants logK = 8.19 and 7.86 for CuHL+ and CuL±, respectively. The second chelating site was suggested to be O2O3 with the binding constants of logK = 4.41 and 4.62 for Cu2HL3+ and Cu2L2+, respectively. The suppressed quantum yield of OTC by Cu2+ chelation was accused for their intra-/inter-molecular electron transfer, by which the energy in activated states was distributed. The occurrence of electron transfer between BCD ring and A ring also from BCD ring to Cu was evidenced by the TD-DFT result only for the OTC-Cu complexes. Besides, the cyclic voltammetry measurement also suggested one OTC-Cu(II)/OTC-Cu(I) redox couple. These results suggested that the persistence of OTC in environmental surface waters will probably be underestimated for neglecting the chelating effect of Cu2+. The photolysis quantum yield of OTC-Cu complexes, as well as the specific molar absorption constants, the equilibrium binding constants of Cu2+ with OTC could contribute to more accurate kinetic models of OTC.

  12. Synthesis, structure, DFT calculations, electrochemistry, fluorescence, DNA binding and molecular docking aspects of a novel oxime based ligand and its palladium(II) complex.

    PubMed

    Bandyopadhyay, Nirmalya; Pradhan, Ankur Bikash; Das, Suman; Lu, Liping; Zhu, Miaoli; Chowdhury, Shubhamoy; Naskar, Jnan Prakash

    2016-07-01

    A novel oxime based ligand, phenyl-(pyridine-2-yl-hydrazono)-acetaldehyde oxime (LH), and its palladium(II) complex (1) have been synthesised and spectroscopically characterised. The ligand crystallizes in the monoclinic space group (P21/c). The X-ray crystal structure of the ligand shows that it forms a hydrogen bonded helical network. The ligand has been characterised by C, H and N microanalyses, (1)H and (13)C NMR, ESI-MS, FT-IR and UV-Vis spectral measurements. Geometry optimizations at the level of DFT show that the Pd(II) centre is nested in a square-planar 'N3Cl' coordination chromophore. The diamagnetic palladium complex has been characterised by C, H and N microanalyses, FAB-MS, FT-IR, UV-Vis spectra and molar electrical conductivity measurements. The observed electronic spectrum of 1 correlates with our theoretical findings as evaluated through TD-DFT. 1 displays quasi-reversible Pd(II)/Pd(III) and Pd(III)/Pd(IV) redox couples in its CV in acetonitrile. 1 is nine-fold more emissive with respect to the binding ligand. Biophysical studies have been carried out to show the DNA binding aspects of both the ligand and complex. The binding constants for the ligand and complex were found to be 3.93×10(4) and 1.38×10(3)M(-1) respectively. To have an insight into the mode of binding of LH and 1 with CT DNA a hydrodynamic study was also undertaken. The mode of binding has also been substantiated through molecular docking. A promising groove binding efficacy has been revealed for the ligand. PMID:27179300

  13. Can approximate mental calculation account for operational momentum in addition and subtraction?

    PubMed

    Knops, André; Dehaene, Stanislas; Berteletti, Ilaria; Zorzi, Marco

    2014-01-01

    The operational momentum (OM) effect describes a cognitive bias whereby we overestimate the results of mental addition problems while underestimating for subtraction. To test whether the OM emerges from psychophysical characteristics of the mental magnitude representation we measured two basic parameters (Weber fraction and numerical estimation accuracy) characterizing the mental magnitude representation and participants' performance in cross-notational addition and subtraction problems. Although participants were able to solve the cross-notational problems, they consistently chose relatively larger results in addition problems than in subtraction problems, thus replicating and extending previous results. Combining the above measures in a psychophysical model allowed us to partially predict the chosen results. Most crucially, however, we were not able to fully model the OM bias on the basis of these psychophysical parameters. Our results speak against the idea that the OM is due to basic characteristics of the mental magnitude representation. In turn, this might be interpreted as evidence for the assumption that the OM effect is better explained by attentional shifts along the mental magnitude representation during mental calculation. PMID:24499435

  14. Synthesis, characterization, X-ray crystal structure, DFT calculations, and catalytic properties of a dioxidovanadium(V) complex derived from oxamohydrazide and pyridoxal: a model complex of vanadate-dependent bromoperoxidase.

    PubMed

    Das, Chandrima; Adak, Piyali; Mondal, Satyajit; Sekiya, Ryo; Kuroda, Reiko; Gorelsky, Serge I; Chattopadhyay, Shyamal Kumar

    2014-11-01

    A vanadium(V) complex with the formula [Et3NH][V(V)O2(sox-pydx)] with a new tridentate ligand 2-[2-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methylene]hydrazinyl]-2-oxoacetamide (soxH-pydxH), obtained by condensation of oxamohydrazide and pyridoxal (one of the forms of vitamin B6), has been synthesized. The compound was characterized by various analytical and spectroscopic methods, and its structure was determined by single-crystal X-ray diffraction technique. Density functional theory (DFT) and time-dependent DFT calculations were used to understand the electronic structure of the complex and nature of the electronic transitions observed in UV-vis spectra. In the complex, vanadium(V) is found to be pentacoordinated with two oxido ligands and a bianionic tridentate ONO-donor ligand. The vanadium center has square-pyramidal geometry with an axial oxido ligand, and the equatorial positions are occupied by another oxido ligand and a phenolato oxygen, an imine nitrogen, and a deprotonated amide oxygen of the hydrazone ligand. A DFT-optimized structure of the complex shows very similar metrical parameters as determined by X-ray crystallography. The O4N coordination environment of vanadium and the hydrogen-bonding abilities of the pendant amide moiety have a strong resemblance with the vanadium center in bromoperoxidase enzyme. Bromination experiments using H2O2 as the oxidizing agent, with model substrate phenol red, and the vanadium complex as a catalyst show a remarkably high value of kcat equal to 26,340 h(-1). The vanadium compound also efficiently catalyzes bromination of phenol and salicylaldehyde as well as oxidation of benzene to phenol by H2O2. PMID:25321493

  15. Glaucoma Surgery Calculator: Limited Additive Effect of Phacoemulsification on Intraocular Pressure in Ab Interno Trabeculectomy

    PubMed Central

    Schuman, Joel S.; Brown, Eric N.

    2016-01-01

    Purpose To compare intraocular pressure (IOP) reduction and to develop a predictive surgery calculator based on the results between trabectome-mediated ab interno trabeculectomy in pseudophakic patients versus phacoemulsification combined with trabectome-mediated ab interno trabeculectomy in phakic patients. Methods This observational surgical cohort study analyzed pseudophakic patients who received trabectome-mediated ab interno trabeculectomy (AIT) or phacoemulsification combined with AIT (phaco-AIT). Follow up for less than 12 months or neovascular glaucoma led to exclusion. Missing data was imputed by generating 5 similar but non-identical datasets. Groups were matched using Coarsened Exact Matching based on age, gender, type of glaucoma, race, preoperative number of glaucoma medications and baseline intraocular pressure (IOP). Linear regression was used to examine the outcome measures consisting of IOP and medications. Results Of 949 cases, 587 were included consisting of 235 AIT and 352 phaco-AIT. Baseline IOP between groups was statistically significant (p≤0.01) in linear regression models and was minimized after Coarsened Exact Matching. An increment of 1 mmHg in baseline IOP was associated with a 0.73±0.03 mmHg IOP reduction. Phaco-AIT had an IOP reduction that was only 0.73±0.32 mmHg greater than that of AIT. The resulting calculator to determine IOP reduction consisted of the formula -13.54+0.73 × (phacoemulsification yes:1, no:0) + 0.73 × (baseline IOP) + 0.59 × (secondary open angle glaucoma yes:1, no:0) + 0.03 × (age) + 0.09 × (medications). Conclusions This predictive calculator for minimally invasive glaucoma surgery can assist clinical decision making. Only a small additional IOP reduction was observed when phacoemulsification was added to AIT. Patients with a higher baseline IOP had a greater IOP reduction. PMID:27077914

  16. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  17. Structural investigation of a high-affinity MnII binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding.

    PubMed

    Schiemann, Olav; Fritscher, Jörg; Kisseleva, Natalja; Sigurdsson, Snorri Th; Prisner, Thomas F

    2003-10-01

    Electron paramagnetic resonance spectroscopy and density functional theory methods were used to study the structure of a single, high-affinity Mn(II) binding site in the hammerhead ribozyme. This binding site exhibits a dissociation constant Ke of 4.4 microM in buffer solutions containing 1 M NaCl, as shown by titrations monitored by continuous wave (cw) EPR. A combination of electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) experiments revealed that the paramagnetic manganese(II) ion in this binding site is coupled to a single nitrogen atom with a quadrupole coupling constant kappa of 0.7 MHz, an asymmetry parameter eta of 0.4, and an isotropic hyperfine coupling constant of Aiso(14N)=2.3 MHz. All three EPR parameters are sensitive to the arrangement of the Mn(II) ligand sphere and can therefore be used to determine the structure of the binding site. A possible location for this binding site may be at the G10.1, A9 site found to be occupied by Mn(II) in crystals (MacKay et al., Nature 1994, 372, 68 and Scott et al., Science 1996, 274, 2065). To determine whether the structure of the binding site is the same in frozen solution, we performed DFT calculations for the EPR parameters, based on the structure of the Mn(II) site in the crystal. Computations with the BHPW91 density function in combination with a 9s7p4d basis set for the manganese(II) center and the Iglo-II basis set for all other atoms yielded values of kappa(14N)=+0.80 MHz, eta=0.324, and Aiso(14N)=+2.7 MHz, in excellent agreement with the experimentally obtained EPR parameters, which suggests that the binding site found in the crystal and in frozen solution are the same. In addition, we demonstrated by EPR that Mn(II) is released from this site upon binding of the aminoglycoside antibiotic neomycin B (Kd=1.2 microM) to the hammerhead ribozyme. Neomycin B has previously been shown to inhibit the catalytic activity of this ribozyme (Uhlenbeck et al., Biochemistry

  18. Understanding the Adsorption of PFOA on MIL-101(Cr)-Based Anionic-Exchange Metal-Organic Frameworks: Comparing DFT Calculations with Aqueous Sorption Experiments.

    PubMed

    Liu, Kai; Zhang, Siyu; Hu, Xiyue; Zhang, Kunyang; Roy, Ajay; Yu, Gang

    2015-07-21

    To examine the effects of different functionalization methods on adsorption behavior, anionic-exchange MIL-101(Cr) metal-organic frameworks (MOFs) were synthesized using preassembled modification (PAM) and postsynthetic modification (PSM) methods. Perfluorooctanoic acid (PFOA) adsorption results indicated that the maximum PFOA adsorption capacity was 1.19 and 1.89 mmol g(-1) for anionic-exchange MIL-101(Cr) prepared by PAM and PSM, respectively. The sorption equilibrium was rapidly reached within 60 min. Our results indicated that PSM is a better modification technique for introducing functional groups onto MOFs for adsorptive removal because PAM places functional groups onto the aperture of the nanopore, which hinders the entrance of organic contaminants. Our experimental results and the results of complementary density functional theory calculations revealed that in addition to the anion-exchange mechanism, the major PFOA adsorption mechanism is a combination of Lewis acid/base complexation between PFOA and Cr(III) and electrostatic interaction between PFOA and the protonated carboxyl groups of the bdc (terephthalic acid) linker. PMID:26066631

  19. Understanding the Adsorption of PFOA on MIL-101(Cr)-Based Anionic-Exchange Metal-Organic Frameworks: Comparing DFT Calculations with Aqueous Sorption Experiments.

    PubMed

    Liu, Kai; Zhang, Siyu; Hu, Xiyue; Zhang, Kunyang; Roy, Ajay; Yu, Gang

    2015-07-21

    To examine the effects of different functionalization methods on adsorption behavior, anionic-exchange MIL-101(Cr) metal-organic frameworks (MOFs) were synthesized using preassembled modification (PAM) and postsynthetic modification (PSM) methods. Perfluorooctanoic acid (PFOA) adsorption results indicated that the maximum PFOA adsorption capacity was 1.19 and 1.89 mmol g(-1) for anionic-exchange MIL-101(Cr) prepared by PAM and PSM, respectively. The sorption equilibrium was rapidly reached within 60 min. Our results indicated that PSM is a better modification technique for introducing functional groups onto MOFs for adsorptive removal because PAM places functional groups onto the aperture of the nanopore, which hinders the entrance of organic contaminants. Our experimental results and the results of complementary density functional theory calculations revealed that in addition to the anion-exchange mechanism, the major PFOA adsorption mechanism is a combination of Lewis acid/base complexation between PFOA and Cr(III) and electrostatic interaction between PFOA and the protonated carboxyl groups of the bdc (terephthalic acid) linker.

  20. Comparative spectroscopic and DFT calculations of binary and ternary complexes derived from 4-allyl-1-(2-hydroxybenzoyl) thiosemicarbazide (L1) and 2,2‧-dipyridyl

    NASA Astrophysics Data System (ADS)

    Mlahi, Mossad R.; Azhari, Shaker J.; El-Asmy, Ahmed A.; Mostafa, Mohsen M.

    2015-01-01

    Five metal complexes derived the reactions of 4-allyl-1-(2-hydroxybenzoyl) thiosemicarbazide (L1) with MX2 (M = Co2+, Cu2+ and Zn2+ ions; X = Cl- in case of Co2+ and Cu2+ ions and Cl- and Ac- in case of Zn2+ ion) in EtOH were synthesized and characterized. The results suggested that the binary and ternary complexes have the general formulae, [Cu(L1-2H)(EtOH)], [Co(L1-2H)(H2O)2]ṡH2O and [Zn(L1-2H) (H2O)1/2]ṡ½EtOH, [Cu2(dipy)(L1-2H)(OH)2(H2O)], [Co(dipy)(L1-2H)]ṡ4H2O and [Zn(dipy)(L1-2H)]. The binary and ternary complexes were characterized by elemental analyses, molar conductivities, spectral (IR, UV-vis; 1H NMR, mass), thermal (TGA, DTG) and magnetic moments measurements. The mode of chelation is suggested using spectral data. The existence of OH group in the ternary complexes is confirmed from the results of IR, mass and 1H NMR spectra. All the geometries of the ligands and the complexes are confirmed using DFT method from DMOL3. The biological activity for the L1 and two metal complexes were tested against DNA.

  1. Synthesis, crystal structures HOMO-LUMO analysis and DFT calculation of new complexes of p-substituted dibenzyltin chlorides and 1,10-phenanthroline.

    PubMed

    Chandrasekar, S; Balachandran, V; Evans, Helen-Stoeckli; Latha, A

    2015-05-15

    In the present work, the complex formation of p-substituted dibenzyltin dichlorides with 1,10-phenanthroline. The reaction of (p-MeBz)2SnCl2 with 1,10-phenanthroline results (p-MeBz)2SnCl2-1,10-phenanthroline complex, (2a). Likewise (p-ClBz)2SnCl2 with 1,10-phenanthroline results (p-ClBz)2SnCl2-1,10-phenanthroline complex, (2b), in the similar reaction conditions. The IR, (1)H NMR, (13)C NMR, (119)Sn NMR spectral analyses indicate that the formation of hexacoordinated tin(IV) complexes in 1:1 ratio. The crystal structures of complexes 2a and 2b show that the tin atom is in regular octahedral geometry with the benzyl groups in the equidirectional positions. A comparison was made with the structural data of other R2SnX2-1,10-phenathroline derivatives. Fourier transforms infrared and Raman spectral studies were performed for analyzing and assigning the vibrations and to identify the functional groups. Optimized geometrical parameters, harmonic vibrational frequencies, frontier molecular orbitals were obtained by DFT/B3LYP method combined with LanL2DZ basis set. PMID:25725209

  2. Co(II), Ni(II) and Cu(II) complexes of methyl-5-(Phenylthio) benzimidazole-2-carbamate: Molecular structures, spectral and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mansour, Ahmed M.; El Bakry, Eslam M.; Abdel-Ghani, Nour T.

    2016-05-01

    [Co(FBZ)2(H2O)]·2NO3·0.5H2O (1), [Ni(FBZ)2X2]·zH2O (X = Cl​-, z = 0.5 (2) and X = CH3COO-, z = 1 (3)) and [Cu(FBZ)2(H2O) (NO3)]·NO3·1.5H2O (4) (FBZ = methyl-5-(Phenylthio) benzimidazole-2-carbamate; Fenbendazole) complexes were synthesized and characterized by elemental analysis, thermal, IR, EPR, UV-Vis, magnetic and conductance measurements. Geometry optimization, molecular electrostatic potential maps and natural bond orbital analysis were carried out at DFT/B3LYP/6-31G∗ level of theory. FBZ behaves as a neutral bidentate ligand via the pyridine-type nitrogen of the benzimidazole moiety and the carbamate group. Three-step ionization with pKa values of 3.38, 4.06 and 10.07 were reported for FBZ. The coordination of FBZ to the metal ions led to an increase in the antibacterial activity against the tested Staphylococcus aureus and Escherichia coli bacteria.

  3. Synthesis, characterization of (3E)-1-(6-chloro-2-methyl-4-phenyl quinolin-3-Yl)-3-aryl prop-2-en-1-ones through IR, NMR, single crystal X-ray diffraction and insights into their electronic structure using DFT calculations

    NASA Astrophysics Data System (ADS)

    Sarveswari, S.; Srikanth, A.; Arul Murugan, N.; Vijayakumar, V.; Jasinski, Jerry P.; Beauchesne, Hanna C.; Jarvis, Ethan E.

    2015-02-01

    3E-1-(6-Chloro-2-methyl-4-phenylquinolin-3-yl)-3-arylprop-2-en-1-ones were synthesized and characterized by FTIR, 1H NMR, 13C NMR, HSQC, DEPT-135. In addition the compound 3E-1-(6-chloro-2-methyl-4-phenylquinolin-3-yl)-3-(2,5-dimethoxyphenyl)prop-2-en-1-one was subjected to the single crystal X-ray diffraction studies. Density functional theory calculations were carried out for this chalcone and its derivatives to investigate into their electronic structure, chemical reactivity, linear and non-linear optical properties. The structure predicted from DFT for chalcone is in good agreement with the structure from XRD measurement.

  4. Crystal packing of TCNQ anion pi-radicals governed by intermolecular covalent pi-pi bonding: DFT calculations and statistical analysis of crystal structures.

    PubMed

    Huang, Jingsong; Kingsbury, Stephanie; Kertesz, Miklos

    2008-05-21

    On the basis of a thorough Cambridge Structural Database survey, we present a statistical analysis of the packing of TCNQ anion pi-radicals in TCNQ charge transfer salts, which reveals three packing motifs between neighboring TCNQs: one with a zero longitudinal offset and an approximate 1 A transversal offset, another with an approximate 2 A longitudinal offset and zero transversal offset, and the third with a relatively long sigma-bond in the length of r = 1.6-1.7 A connecting two TCNQ fragments. Along with the statistical analysis of the crystal structures, we also present density functional theory calculations of the total energy, covalent pi-pi bonding interaction energy, and Coulombic repulsion energy for the [TCNQ](2)(2-)pi-dimers with various packing geometries. We find that the interactions between TCNQ anion pi-radicals include contributions from intermolecular covalent pi-pi bonding interaction and local dipole repulsions, in addition to Coulombic repulsion, van der Waals and the attractive electrostatic forces between counter-cations and TCNQ anions pointed out recently by other groups for TCNE anion radicals. We describe an approximate formula for intermolecular interaction energy, E(int) = E(coul) + E(bond) + E(vdW), for systems in vacuum, while in the solid state E(coul) is compensated by the attractive electrostatic forces between counter-cations and TCNQ anions. We conclude that the crystal packing of TCNQ molecules in their charge transfer salts is predominantly determined by the intermolecular covalent pi-pi bonding term, E(bond).

  5. Electronic structures of TiO2-TCNE, -TCNQ, and -2,6-TCNAQ surface complexes studied by ionization potential measurements and DFT calculations: Mechanism of the shift of interfacial charge-transfer bands

    NASA Astrophysics Data System (ADS)

    Fujisawa, Jun-ichi; Hanaya, Minoru

    2016-06-01

    Interfacial charge-transfer (ICT) transitions between inorganic semiconductors and π-conjugated molecules allow direct charge separation without loss of energy. This feature is potentially useful for efficient photovoltaic conversions. Charge-transferred complexes of TiO2 nanoparticles with 7,7,8,8-tetracyanoquinodimethane (TCNQ) and its analogues (TCNX) show strong ICT absorption in the visible region. The ICT band was reported to be significantly red-shifted with extension of the π-conjugated system of TCNX. In order to clarify the mechanism of the red-shift, in this work, we systematically study electronic structures of the TiO2-TCNX surface complexes (TCNX; TCNE, TCNQ, 2,6-TCNAQ) by ionization potential measurements and density functional theory (DFT) calculations.

  6. 2-Amino-3,5-dichlorobenzonitrile: DFT calculations in the monomer and dimer forms, FT-IR and FT-Raman spectra, molecular geometry, atomic charges and thermodynamical parameters.

    PubMed

    Rastogi, V K; Alcolea Palafox, M; Tomar, Rashmi; Singh, Upama

    2013-06-01

    The experimental IR and Raman spectra of 2-amino-3,5-dichlorobenzonitrile molecule were recorded, and the results compared with theoretical values. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated using MP2 and DFT quantum chemical methods. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of vibrations of the molecule. Simulations in the dimer form were carried out to improve the assignment of the bands in the solid state experimental spectra. The error obtained was in general very low. Using PED's were determined the contributions of the different modes to each wavenumber. Several general conclusions were also deduced.

  7. Molecular structure, NLO, MEP, NBO analysis and spectroscopic characterization of 2,5-dimethylanilinium dihydrogen phosphate with experimental (FT-IR and FT-Raman) techniques and DFT calculations.

    PubMed

    Guidara, Sameh; Feki, Habib; Abid, Younes

    2014-12-10

    Single crystals of 2,5-dimethylanilinium dihydrogen phosphate were grown by slow evaporation method at room temperature. The synthesized compound was characterized by powder X-ray diffraction analysis to confirm its crystalline nature. The optimized molecular structure, vibrational spectra and the optical properties were calculated by the density functional theory (DFT) method using the B3LYP function with the 6-31G(d,p) basis set. Theoretical simulation of infrared and Raman spectra led to excellent overall agreement with the observed spectral patterns. The complete assignments of the vibrational spectra were carried out with the aid of potential energy distribution (PED). The stability of the molecule arising from hyperconjugative interaction and charge delocalization has been analyzed using natural bond orbital (NBO) analysis leading to high nonlinear optical (NLO) activity. The lowering in the HOMO and LUMO energy gap explains the eventual charge transfer interactions that take place within the molecules.

  8. Explicitly correlated benchmark calculations on C8H8 isomer energy separations: how accurate are DFT, double-hybrid, and composite ab initio procedures?

    NASA Astrophysics Data System (ADS)

    Karton, Amir; Martin, Jan M. L.

    2012-10-01

    Accurate isomerization energies are obtained for a set of 45 C8H8 isomers by means of the high-level, ab initio W1-F12 thermochemical protocol. The 45 isomers involve a range of hydrocarbon functional groups, including (linear and cyclic) polyacetylene, polyyne, and cumulene moieties, as well as aromatic, anti-aromatic, and highly-strained rings. Performance of a variety of DFT functionals for the isomerization energies is evaluated. This proves to be a challenging test: only six of the 56 tested functionals attain root mean square deviations (RMSDs) below 3 kcal mol-1 (the performance of MP2), namely: 2.9 (B972-D), 2.8 (PW6B95), 2.7 (B3PW91-D), 2.2 (PWPB95-D3), 2.1 (ωB97X-D), and 1.2 (DSD-PBEP86) kcal mol-1. Isomers involving highly-strained fused rings or long cumulenic chains provide a 'torture test' for most functionals. Finally, we evaluate the performance of composite procedures (e.g. G4, G4(MP2), CBS-QB3, and CBS-APNO), as well as that of standard ab initio procedures (e.g. MP2, SCS-MP2, MP4, CCSD, and SCS-CCSD). Both connected triples and post-MP4 singles and doubles are important for accurate results. SCS-MP2 actually outperforms MP4(SDQ) for this problem, while SCS-MP3 yields similar performance as CCSD and slightly bests MP4. All the tested empirical composite procedures show excellent performance with RMSDs below 1 kcal mol-1.

  9. Reaction of phenols with the 2,2-diphenyl-1-picrylhydrazyl radical. Kinetics and DFT calculations applied to determine ArO-H bond dissociation enthalpies and reaction mechanism.

    PubMed

    Foti, Mario C; Daquino, Carmelo; Mackie, Iain D; DiLabio, Gino A; Ingold, K U

    2008-12-01

    The formal H-atom abstraction by the 2,2-diphenyl-1-picrylhydrazyl (dpph(*)) radical from 27 phenols and two unsaturated hydrocarbons has been investigated by a combination of kinetic measurements in apolar solvents and density functional theory (DFT). The computed minimum energy structure of dpph(*) shows that the access to its divalent N is strongly hindered by an ortho H atom on each of the phenyl rings and by the o-NO(2) groups of the picryl ring. Remarkably small Arrhenius pre-exponential factors for the phenols [range (1.3-19) x 10(5) M(-1) s(-1)] are attributed to steric effects. Indeed, the entropy barrier accounts for up to ca. 70% of the free-energy barrier to reaction. Nevertheless, rate differences for different phenols are largely due to differences in the activation energy, E(a,1) (range 2 to 10 kcal/mol). In phenols, electronic effects of the substituents and intramolecular H-bonds have a large influence on the activation energies and on the ArO-H BDEs. There is a linear Evans-Polanyi relationship between E(a,1) and the ArO-H BDEs: E(a,1)/kcal x mol(-1) = 0.918 BDE(ArO-H)/kcal x mol(-1) - 70.273. The proportionality constant, 0.918, is large and implies a "late" or "product-like" transition state (TS), a conclusion that is congruent with the small deuterium kinetic isotope effects (range 1.3-3.3). This Evans-Polanyi relationship, though questionable on theoretical grounds, has profitably been used to estimate several ArO-H BDEs. Experimental ArO-H BDEs are generally in good agreement with the DFT calculations. Significant deviations between experimental and DFT calculated ArO-H BDEs were found, however, when an intramolecular H-bond to the O(*) center was present in the phenoxyl radical, e.g., in ortho semiquinone radicals. In these cases, the coupled cluster with single and double excitations correlated wave function technique with complete basis set extrapolation gave excellent results. The TSs for the reactions of dpph(*) with phenol, 3- and 4

  10. Syntheses, X-ray structures, photochemistry, redox properties, and DFT calculations of interconvertible fac- and mer-[Mn(SPS)(CO)3] isomers containing a flexible SPS-based pincer ligand.

    PubMed

    Doux, Marjolaine; Mézailles, Nicolas; Ricard, Louis; Le Floch, Pascal; Vaz, Pedro D; Calhorda, Maria José; Mahabiersing, Taasje; Hartl, Frantisek

    2005-12-12

    The lithium salt of the anionic SPS pincer ligand composed of a central hypervalent lambda4-phosphinine ring bearing two ortho-positioned diphenylphosphine sulfide side arms reacts with [Mn(CO)5Br] to give fac-[Mn(SPS)(CO)3]. This isomer can be converted photochemically to mer-[Mn(SPS)(CO)3], with a very high quantum yield (0.80+/-0.05). The thermal backreaction is slow (taking ca. 8 h at room temperature), in contrast to rapid electrode-catalyzed mer-to-fac isomerization triggered by electrochemical reduction of mer-[Mn(SPS)(CO)3]. Both geometric isomers of [Mn(SPS)(CO)3] have been characterized by X-ray crystallography. Both isomers show luminescence from a low-lying 3IL (SPS-based) excited state. The light emission of fac-[Mn(SPS)(CO)3] is largely quenched by the efficient photoisomerization occurring probably from a low-lying Mn-CO dissociative excited state. Density functional theory (DFT) and time-dependent DFT calculations describe the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of fac- and mer-[Mn(CO)3(SPS)] as ligand-centered orbitals, largely localized on the phosphinine ring of the SPS pincer ligand. In line with the ligand nature of its frontier orbitals, fac-[Mn(SPS)(CO)3] is electrochemically reversibly oxidized and reduced to the corresponding radical cation and anion, respectively. The spectroscopic (electron paramagnetic resonance, IR, and UV-vis) characterization of the radical species provides other evidence for the localization of the redox steps on the SPS ligand. The smaller HOMO-LUMO energy difference in the case of mer-[Mn(CO)3(SPS)], reflected in the electronic absorption and emission spectra, corresponds with its lower oxidation potential compared to that of the fac isomer. The thermodynamic instability of mer-[Mn(CO)3(SPS)], confirmed by the DFT calculations, increases upon one-electron reduction and oxidation of the complex.

  11. Temperature effects on prevalent structures of hydrated Fe{sup +} complexes: Infrared spectroscopy and DFT calculations of Fe{sup +}(H{sub 2}O){sub n} (n = 3–8)

    SciTech Connect

    Ohashi, Kazuhiko Sekiya, Hiroshi; Sasaki, Jun; Yamamoto, Gun; Judai, Ken; Nishi, Nobuyuki

    2014-12-07

    Hydrated Fe{sup +} ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe{sup +}(H{sub 2}O){sub n} (n = 3–8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe{sup +} is observed already at n = 3, indicating the completion of the first hydration shell with two H{sub 2}O molecules. Size dependent variations in the spectra for n = 5–7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe{sup +}(H{sub 2}O){sub 2} subunit is solvated with four H{sub 2}O molecules. Overall spectral features for n = 3–8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.

  12. Modeling Ti/Ge Distribution in LiTi2-xGex(PO4)3 NASICON Series by (31)P MAS NMR and First-Principles DFT Calculations.

    PubMed

    Diez-Gómez, Virginia; Arbi, Kamel; Sanz, Jesús

    2016-08-01

    Ti/Ge distribution in rhombohedral LiTi2-xGex(PO4)3 NASICON series has been analyzed by (31)P magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and first-principles density functional theory (DFT) calculations. Nuclear magnetic resonance is an excellent probe to follow Ti/Ge disorder, as it is sensitive to the atomic scale environment without long-range periodicity requirements. In the samples considered here, PO4 units are surrounded by four Ti/Ge octahedra, and then, five different components ascribed to P(OTi)4, P(OTi)3(OGe), P(OTi)2(OGe)2, P(OTi)(OGe)3, and P(OGe)4 environments are expected in (31)P MAS NMR spectra of R3̅c NASICON samples. However, (31)P MAS NMR spectra of analyzed series display a higher number of signals, suggesting that, although the overall symmetry remains R3̅c, partial substitution causes a local decrement in symmetry. With the aid of first-principles DFT calculations, 10 detected (31)P NMR signals have been assigned to different Ti4-nGen arrangements in the R3 subgroup symmetry. In this assignment, the influence of octahedra of the same or different R2(PO4)3 structural units has been considered. The influence of bond distances, angles and atom charges on (31)P NMR chemical shieldings has been discussed. Simulation of the LiTi2-xGex(PO4)3 series suggests that detection of 10 P environments is mainly due to the existence of two oxygen types, O1 and O2, whose charges are differently affected by Ge and Ti occupation of octahedra. From the quantitative analysis of detected components, a random Ti/Ge distribution has been deduced in next nearest neighbor (NNN) sites that surround tetrahedral PO4 units. This random distribution was supported by XRD data displaying Vegard's law.

  13. Distance dependence in photoinduced intramolecular electron transfer. Additional remarks and calculations

    NASA Astrophysics Data System (ADS)

    Larsson, Sven; Volosov, Andrey

    1987-12-01

    Rate constants for photoinduced intramolecular electron transfer are calculated for four of the molecules studied by Hush et al. The electronic factor is obtained in quantum chemical calculations using the CNDO/S method. The results agree reasonably well with experiments for the forward reaction. Possible reasons for the disagreement for the charge recombination process are offered.

  14. Vibrational spectroscopy [FTIR and FTRaman] investigation, computed vibrational frequency analysis and IR intensity and Raman activity peak resemblance analysis on 4-chloro 2-methylaniline using HF and DFT [LSDA, B3LYP and B3PW91] calculations

    NASA Astrophysics Data System (ADS)

    Ramalingam, S.; Periandy, S.

    2011-03-01

    In the present study, the FT-IR and FT-Raman spectra of 4-chloro-2-methylaniline (4CH2MA) have been recorded in the range of 4000-100 cm -1. The fundamental modes of vibrational frequencies of 4CH2MA are assigned. All the geometrical parameters have been calculated by HF and DFT (LSDA, B3LYP and B3PW91) methods with 6-31G (d, p) and 6-311G (d, p) basis sets. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for aniline and some substituted aniline. The harmonic and anharmonic vibrational wavenumbers, IR intensities and Raman activities are calculated at the same theory levels used in geometry optimization. The calculated frequencies are scaled and compared with experimental values. The scaled vibrational frequencies at LSDA/B3LYP/6-311G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The impact of substitutions on the benzene structure is investigated. The molecular interactions between the substitutions (Cl, CH 3 and NH 2) are also analyzed.

  15. Molecular structure and computational studies on 2-((2-(4-(3-(2,5-dimethylphenyl)-3-methylcyclobutyl)thiazol-2-yl)hydrazono)methyl)phenol monomer and dimer by DFT calculations

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Cukurovali, Alaaddin; Subasi, Nuriye Tuna; Kani, Ibrahim

    2016-12-01

    The title compound, 2-((2-(4-(3-(2,5-Dimethylphenyl)-3-methylcyclobutyl)thiazol-2-yl)hydrazono)methyl)phenol, was characterized by single-crystal X-ray diffraction. In order to calculate molecular geometry along with the infrared, Atoms in Molecules (AIM) analysis and 1H and 13C NMR chemical shift values, the density functional theory (DFT) method with 6-311G++(d,p) basis set was utilized. Experimental data were then used for comparison. While the title crystal structure is photochromic, the molecule is nonplanar. It takes on an enol form including a forceful intramolecular Osbnd H⋯N hydrogen bond as well as a forceful intermolecular Nsbnd H⋯N hydrogen bond. The 6-311G++(d,p) basis function was used to examine the intramolecular tautomerism single proton transfer reaction of the hydrogen-bonded enol-imine and keto-amine monomer in the title crystal structure at the B3LYP theory level. Further, the frontier molecular orbitals (FMO), molecular docking and NLO properties were studied by using theoretical calculations. The calculated NLO properties of title compound are much greater than urea. The title compound generates a stable complex with CDK2 as is distinct from the binding energy values. These results proposed that the compound might exhibit inhibitory effect against CDK2. These are important in development of new antitumor agent.

  16. The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods.

    PubMed

    Pohl, Gabor; Plumley, Joshua A; Dannenberg, J J

    2013-06-28

    We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.

  17. The structure elucidation of mequindox and 1,4-bisdesoxymequindox: NMR analyses, FT-IR spectra, DFT calculations and thermochemical studies

    NASA Astrophysics Data System (ADS)

    Zhang, Jiaheng; He, Xin; Gao, Haixiang

    2011-10-01

    In the current work, we report a combined experimental and theoretical study on the molecular conformation, vibrational spectra, and nuclear magnetic resonance (NMR) spectra of mequindox (MEQ) and 1,4-bisdesoxymequindox (1,4-BDM). The geometric structure and vibrational frequencies of MEQ and 1,4-BDM have been calculated by density functional theory employing the B3LYP functional and 6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts have been calculated by gauge-including atomic orbital method with B3LYP 6-311++G(2df,2pd) approach. The calculation results have been applied to simulate the infrared and NMR spectra of the compounds. The theoretical results agree well with the observed spectra. The bond dissociation enthalpy of MEQ and the heat of formation of MEQ and 1,4-BDM have also been computed.

  18. Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene.

    PubMed

    Bayrakdar, A; Kart, H H; Elcin, S; Deligoz, H; Karabacak, M

    2015-02-01

    In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and (1)H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000-400 cm(-1). (1)H NMR spectrum is recorded for 0.1-0.2 M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for (1)H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO-LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement. PMID:25448961

  19. Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene.

    PubMed

    Bayrakdar, A; Kart, H H; Elcin, S; Deligoz, H; Karabacak, M

    2015-02-01

    In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and (1)H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000-400 cm(-1). (1)H NMR spectrum is recorded for 0.1-0.2 M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for (1)H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO-LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.

  20. Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene

    NASA Astrophysics Data System (ADS)

    Bayrakdar, A.; Kart, H. H.; Elcin, S.; Deligoz, H.; Karabacak, M.

    2015-02-01

    In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and 1H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000-400 cm-1. 1H NMR spectrum is recorded for 0.1-0.2 M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for 1H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO-LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.

  1. Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide using DFT-D calculations and {sup 13}C solid-state NMR

    SciTech Connect

    Li, Xiaozhou; Bond, Andrew D.; Johansson, Kristoffer E.; Van de Streek, Jacco

    2014-08-01

    The crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured {sup 13}C solid-state NMR spectra. The crystal structure of the title compound, C{sub 11}H{sub 13}N{sub 3}O{sub 2}S{sub 2}, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated {sup 13}C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol@@ecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thia@@diazol-2-yl)-p-toluene@@sulfonamide], rather than the correct imine tautomer. The protonation site on the mol@@ecule’s 1,3,4-thia@@diazole ring is indicated by the inter@@molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter molecular inter@@actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu@@anti@@tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the {sup 13}C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured {sup 13}C SS-NMR spectrum.

  2. 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.

  3. PCM/TD-DFT analysis of 1-bromo-2,3-dichlorobenzene - A combined study of experimental (FT-IR and FT-Raman) and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Arivazhagan, M.; Muniappan, P.; Meenakshi, R.; Rajavel, G.

    2013-03-01

    This study represents an integral approach towards understanding the electronic and structural aspects of 1-bromo-2,3-dichlorobenzene (BDCB). The experimental spectral bands were structurally assigned with the theoretical calculation, and the thermodynamic properties of the studied compound were obtained from the theoretically calculated frequencies. The relationship between the structure and absorption spectrum and effects of solvents have been discussed. It turns that the hybrid PBE1PBE functional with 6-311+G(d,p) basis provide reliable λmax when solvent effects are included in the model. The NBO analysis reveals that the studied compound presents a structural characteristic of electron-transfer within the compound. The frontier molecular orbitals (HOMO-LUMO) are responsible for the electron polarization and electron-transfer properties. The reactivity sites are identified by mapping the electron density into electrostatic potential surface (MESP). Besides, 13C and 1H have been calculated using the gauge-invariant atomic orbital (GIAO) method. The thermodynamic properties at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. Furthermore, the studied compound can be used as a good nonlinear optical material due to the higher value of first hyper polarizability (5.7 times greater than that of urea (0.37289 × 10-30 esu)). Finally, it is worth to mentioning that solvent induces a considerable red shift of the absorption maximum going from the gas phase, and a slight blue shift of the transition S0 → S1 going from less polar to more polar solvents.

  4. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH₃)₂)₆](ClO₄)₂ supported by theoretical (DFT) calculations.

    PubMed

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-15

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made. PMID:25795611

  5. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH3)2)6](ClO4)2 supported by theoretical (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-01

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5c = 222.9 K on cooling and at TC5h = 225.4 K on heating) the CH3 groups perform fast (τR ≈ 10-12-10-13 s) reorientational motions. These motions start to slow down below TC5c Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6]2+ cation and ClO4- anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made.

  6. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH₃)₂)₆](ClO₄)₂ supported by theoretical (DFT) calculations.

    PubMed

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-15

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made.

  7. Synthesis, crystal structure analysis, spectral IR, NMR UV-Vis investigations, NBO and NLO of 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide with use of X-ray diffractions studies along with DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Sarioğlu, Ahmet Oral; Güler, Semih; Dege, Necmi; Sönmez, Mehmet

    2016-08-01

    The title compound, 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide compound (C22H16NO3Cl) has been synthesized and characterized by X-ray diffraction, IR, 1H and 13C NMR and UV-Vis spectra. Optimized geometrical structure, harmonic vibrational frequencies and chemical shifts were computed using hybrid-DFT (B3LYP and B3PW91) methods and 6-311G(d,p) as the basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The calculated optimized geometries, vibrational frequencies and 1H NMR chemical shift values are in strong agreement with experimentally measured values. UV-Vis spectrum of the title compound, was also recorded and the electronic properties, such as calculated energies, excitation energies, oscillator strengths, dipole moments and frontier orbital energies and band gap energies were computed with TDDFT-B3LYP methodolgy and using 6-311G(d,p) as the basis set. Furthermore, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), natural bond orbital (NBO) and non linear optical (NLO) properties were performed by using B3LYP/6-311G(d,p) level for the title compound.

  8. Structural, vibrational, electronic, NMR, NLO and reactivity analyses of (3Z)-3-(2-oxo-2-phenylethylidene)-1,3-dihydro-2H-indol-2-one (OPEDI) by ab initio HF and DFT calculations.

    PubMed

    Sridevi, C; Velraj, G

    2013-04-15

    This study represents the vibrational, electronic, NMR, NLO, reactivity and structural aspects of (3Z)-3-(2-oxo-2-phenylethylidene)-1,3-dihydro-2H-indol-2-one (OPEDI). A detailed interpretation of the FT-IR, FT-Raman, UV and NMR spectra were reported. Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. The most preferred Z isomer (cis-configuration) was confirmed through PES scan studies. The vibrational wavenumbers and potential energy distribution (PED) of various normal modes were calculated. The lower frontier orbital energy gap and high dipole moment of OPEDI illustrates the high reactivity. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. OPEDI exhibited good nonlinear optical activity and was 13 times greater than that of urea. Molecular electrostatic potential (MEP) was carried out for predicting the reactive sites. The NMR results indicated that the observed chemical shifts depend not only on the structure of the molecule being studied, but also on the solvent used.

  9. Structural, Electronic, and Optical Properties of BiOX1-xYx (X, Y = F, Cl, Br, and I) Solid Solutions from DFT Calculations.

    PubMed

    Zhao, Zong-Yan; Liu, Qing-Lu; Dai, Wen-Wu

    2016-01-01

    Six BiOX1-xYx (X, Y = F, Cl, Br, and I) solid solutions have been systematically investigated by density functional theory calculations. BiOCl1-xBrx, BiOBr1-xIx, and BiOCl1-xIx solid solutions have very small bowing parameters; as such, some of their properties increase almost linearly with increasing x. For BiOF1-xYx solid solutions, the bowing parameters are very large and it is extremely difficult to fit the related calculated data by a single equation. Consequently, BiOX1-xYx (X, Y = Cl, Br, and I) solid solutions are highly miscible, while BiOF1-xYx (Y = Cl, Br, and I) solid solutions are partially miscible. In other words, BiOF1-xYx solid solutions have miscibility gaps or high miscibility temperature, resulting in phase separation and F/Y inhomogeneity. Comparison and analysis of the calculated results and the related physical-chemical properties with different halogen compositions indicates that the parameters of BiOX1-xYx solid solutions are determined by the differences of the physical-chemical properties of the two halogen compositions. In this way, the large deviation of some BiOX1-xYx solid solutions from Vegard's law observed in experiments can be explained. Moreover, the composition ratio of BiOX1-xYx solid solutions can be measured or monitored using optical measurements.

  10. Structural, Electronic, and Optical Properties of BiOX1-xYx (X, Y = F, Cl, Br, and I) Solid Solutions from DFT Calculations.

    PubMed

    Zhao, Zong-Yan; Liu, Qing-Lu; Dai, Wen-Wu

    2016-01-01

    Six BiOX1-xYx (X, Y = F, Cl, Br, and I) solid solutions have been systematically investigated by density functional theory calculations. BiOCl1-xBrx, BiOBr1-xIx, and BiOCl1-xIx solid solutions have very small bowing parameters; as such, some of their properties increase almost linearly with increasing x. For BiOF1-xYx solid solutions, the bowing parameters are very large and it is extremely difficult to fit the related calculated data by a single equation. Consequently, BiOX1-xYx (X, Y = Cl, Br, and I) solid solutions are highly miscible, while BiOF1-xYx (Y = Cl, Br, and I) solid solutions are partially miscible. In other words, BiOF1-xYx solid solutions have miscibility gaps or high miscibility temperature, resulting in phase separation and F/Y inhomogeneity. Comparison and analysis of the calculated results and the related physical-chemical properties with different halogen compositions indicates that the parameters of BiOX1-xYx solid solutions are determined by the differences of the physical-chemical properties of the two halogen compositions. In this way, the large deviation of some BiOX1-xYx solid solutions from Vegard's law observed in experiments can be explained. Moreover, the composition ratio of BiOX1-xYx solid solutions can be measured or monitored using optical measurements. PMID:27549344

  11. Structural, Electronic, and Optical Properties of BiOX1‑xYx (X, Y = F, Cl, Br, and I) Solid Solutions from DFT Calculations

    NASA Astrophysics Data System (ADS)

    Zhao, Zong-Yan; Liu, Qing-Lu; Dai, Wen-Wu

    2016-08-01

    Six BiOX1‑xYx (X, Y = F, Cl, Br, and I) solid solutions have been systematically investigated by density functional theory calculations. BiOCl1‑xBrx, BiOBr1‑xIx, and BiOCl1‑xIx solid solutions have very small bowing parameters; as such, some of their properties increase almost linearly with increasing x. For BiOF1‑xYx solid solutions, the bowing parameters are very large and it is extremely difficult to fit the related calculated data by a single equation. Consequently, BiOX1‑xYx (X, Y = Cl, Br, and I) solid solutions are highly miscible, while BiOF1‑xYx (Y = Cl, Br, and I) solid solutions are partially miscible. In other words, BiOF1‑xYx solid solutions have miscibility gaps or high miscibility temperature, resulting in phase separation and F/Y inhomogeneity. Comparison and analysis of the calculated results and the related physical–chemical properties with different halogen compositions indicates that the parameters of BiOX1‑xYx solid solutions are determined by the differences of the physical–chemical properties of the two halogen compositions. In this way, the large deviation of some BiOX1‑xYx solid solutions from Vegard’s law observed in experiments can be explained. Moreover, the composition ratio of BiOX1‑xYx solid solutions can be measured or monitored using optical measurements.

  12. Structural, Electronic, and Optical Properties of BiOX1−xYx (X, Y = F, Cl, Br, and I) Solid Solutions from DFT Calculations

    PubMed Central

    Zhao, Zong-Yan; Liu, Qing-Lu; Dai, Wen-Wu

    2016-01-01

    Six BiOX1−xYx (X, Y = F, Cl, Br, and I) solid solutions have been systematically investigated by density functional theory calculations. BiOCl1−xBrx, BiOBr1−xIx, and BiOCl1−xIx solid solutions have very small bowing parameters; as such, some of their properties increase almost linearly with increasing x. For BiOF1−xYx solid solutions, the bowing parameters are very large and it is extremely difficult to fit the related calculated data by a single equation. Consequently, BiOX1−xYx (X, Y = Cl, Br, and I) solid solutions are highly miscible, while BiOF1−xYx (Y = Cl, Br, and I) solid solutions are partially miscible. In other words, BiOF1−xYx solid solutions have miscibility gaps or high miscibility temperature, resulting in phase separation and F/Y inhomogeneity. Comparison and analysis of the calculated results and the related physical–chemical properties with different halogen compositions indicates that the parameters of BiOX1−xYx solid solutions are determined by the differences of the physical–chemical properties of the two halogen compositions. In this way, the large deviation of some BiOX1−xYx solid solutions from Vegard’s law observed in experiments can be explained. Moreover, the composition ratio of BiOX1−xYx solid solutions can be measured or monitored using optical measurements. PMID:27549344

  13. Low-lying electronic structure of EuH, EuOH, and EuO neutrals and anions determined by anion photoelectron spectroscopy and DFT calculations

    SciTech Connect

    Kafader, Jared O.; Ray, Manisha; Jarrold, Caroline Chick

    2015-07-21

    The anion photoelectron (PE) spectra of EuH{sup −} and the PE spectrum of overlapping EuOH{sup −} and EuO{sup −} anions are presented and analyzed with supporting results from density functional theory calculations on the various anions and neutrals. Results point to ionically bound, high-spin species. EuH and EuOH anions and neutrals exhibit analogous electronic structures: Transitions from {sup 8}Σ{sup −} anion ground states arising from the 4f{sup 7}σ{sub 6s}{sup 2} superconfiguration to the close-lying neutral {sup 9}Σ{sup −} and {sup 7}Σ{sup −} states arising from the 4f{sup 7}σ{sub 6s} superconfiguration are observed spaced by an energy interval similar to the free Eu{sup +} [4f{sup 7}6s] {sup 9}S - {sup 7}S splitting. The electron affinities (EAs) of EuH and EuOH are determined to be 0.771 ± 0.009 eV and 0.700 ± 0.011 eV, respectively. Analysis of spectroscopic features attributed to EuO{sup −} photodetachment is complicated by the likely presence of two energetically competitive electronic states of EuO{sup −} populating the ion beam. However, based on the calculated relative energies of the close-lying anion states arising from the 4f{sup 7}σ{sub 6s} and 4f{sup 6}σ{sub 6s}{sup 2} configurations and the relative energies of the one-electron accessible 4f{sup 7} and 4f{sup 6}σ{sub 6s} neutral states based on ligand-field theory [M. Dulick, E. Murad, and R. F. Barrow, J. Chem. Phys. 85, 385 (1986)], the remaining features are consistent with the 4f{sup 6}σ{sub 6s}{sup 2}  {sup 7}Σ{sup −} and 4f{sup 7}σ{sub 6s}{sup 7}Σ{sup −} anion states lying very close in energy (the former was calculated to be 0.15 eV lower in energy than the latter), though the true anion ground state and neutral EA could not be established unambiguously. Calculations on the various EuO anion and neutral states suggest 4f-orbital overlap with 2p orbitals in species with 4f{sup 6} occupancy.

  14. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

    NASA Astrophysics Data System (ADS)

    Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-01

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.

  15. Determination of a solvent hydrogen-bond acidity scale by means of the solvatochromism of pyridinium-N-phenolate betaine dye 30 and PCM-TD-DFT calculations.

    PubMed

    Cerón-Carrasco, José P; Jacquemin, Denis; Laurence, Christian; Planchat, Aurélien; Reichardt, Christian; Sraïdi, Khadija

    2014-05-01

    Empirical parameters of solvents describing their hydrogen-bond (HB) acidity (e.g., the Kamlet-Taft α parameter) are often difficult to determine for new solvents because they are not directly related to a single definition process. Here, we propose a simple method based on one probe, the betaine dye 30, and one reference process, the solvatochromism of this dye, measured by its first electronic transition energy, ET(30). These ET(30) values are calculated within the time-dependent density functional theory framework, using a polarizable continuum solvent model (PCM). The part of ET(30) values that is not included in the PCM calculation is taken as the HB component of the measured ET(30) values, allowing us to deduce a solvent HB acidity parameter α1. The validity of this simple model is assessed by good linear correlations between α1 and a variety of solute properties mainly depending on the solvent's HB acidity. The quality of fit observed with α1 is at least comparable with that obtained by previous solvent HB acidity scales. The simplicity of our method is illustrated by the determination of α1 and of its companion, the electrostatic solvent parameter ES, for some new green solvents derived from glycerol. PMID:24702635

  16. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation.

    PubMed

    Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-28

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals. PMID:27475350

  17. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation.

    PubMed

    Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-28

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.

  18. Modeling Ti/Ge Distribution in LiTi2-xGex(PO4)3 NASICON Series by (31)P MAS NMR and First-Principles DFT Calculations.

    PubMed

    Diez-Gómez, Virginia; Arbi, Kamel; Sanz, Jesús

    2016-08-01

    Ti/Ge distribution in rhombohedral LiTi2-xGex(PO4)3 NASICON series has been analyzed by (31)P magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and first-principles density functional theory (DFT) calculations. Nuclear magnetic resonance is an excellent probe to follow Ti/Ge disorder, as it is sensitive to the atomic scale environment without long-range periodicity requirements. In the samples considered here, PO4 units are surrounded by four Ti/Ge octahedra, and then, five different components ascribed to P(OTi)4, P(OTi)3(OGe), P(OTi)2(OGe)2, P(OTi)(OGe)3, and P(OGe)4 environments are expected in (31)P MAS NMR spectra of R3̅c NASICON samples. However, (31)P MAS NMR spectra of analyzed series display a higher number of signals, suggesting that, although the overall symmetry remains R3̅c, partial substitution causes a local decrement in symmetry. With the aid of first-principles DFT calculations, 10 detected (31)P NMR signals have been assigned to different Ti4-nGen arrangements in the R3 subgroup symmetry. In this assignment, the influence of octahedra of the same or different R2(PO4)3 structural units has been considered. The influence of bond distances, angles and atom charges on (31)P NMR chemical shieldings has been discussed. Simulation of the LiTi2-xGex(PO4)3 series suggests that detection of 10 P environments is mainly due to the existence of two oxygen types, O1 and O2, whose charges are differently affected by Ge and Ti occupation of octahedra. From the quantitative analysis of detected components, a random Ti/Ge distribution has been deduced in next nearest neighbor (NNN) sites that surround tetrahedral PO4 units. This random distribution was supported by XRD data displaying Vegard's law. PMID:27373306

  19. 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.

  20. Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations.

    PubMed

    Tarcan, Erdoğan; Altindağ, Ozgü; Avci, Davut; Atalay, Yusuf

    2008-11-01

    The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C3H7N6+.C8H5O4(-)) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000-100 cm(-1) region where the theoretical evaluation and assignment of all observed bands were made.

  1. F+ tunable laser activity and interaction of atomic halogens (F, Cl and Br) at the low coordinated surface sites of SrOAb initio and DFT calculations.

    PubMed

    Shalabi, Ahmed S

    2002-10-01

    The twofold potential of F+ color centers at the low coordinated surfaces of SrO for providing tunable laser activity and adsorption properties for atomic halogens (F, Cl and Br) has been investigated using ab initio electronic structure calculations. SrO clusters of variable sizes were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces and the nearest neighbor ions to F+ were allowed to relax to equilibrium. Based on Stokes shifted optical transition bands and horizontal shifts along the configuration coordinate diagrams, the F+ laser activity was found to decrease as the coordination number of the surface ions decreases from 5 (flat) to 4 (edge) to 3 (corner). An attempt has been made to explain this result in terms of Madelung potentials and optical-optical conversion efficiencies. All relaxed excited states are deep below the conduction bands of the perfect ground states, implying that F+ is a laser-suitable defect. The most laser active flat surface is the least probable for relaxed excited state orientational destruction of F+. The excited state at the edge has the highest energy, implying exciton (energy) transfer to the flat and edge sites. F+ relaxation and defect-formation energies increase with increasing surface coordination number. The Glasner-Tompkins relation between the fundamental optical absorption of F+ in solids and the fundamental absorption of the host crystals can be generalized to include the low coordinated surfaces of SrO. The F+ color center changes the nature of halogen-surface interaction (adsorption energies) from physical adsorption to chemical adsorption. The halogen-surface interactions increase with increasing electronegativity of the halogen. The calculated adsorption energies can be explained in terms of surface electrostatic potentials, and the covalent spin pairing mechanism plays a dominant role in determining adsorbate-substrate interactions.

  2. Crystal structure, DFT and HF calculations and radical scavenging activities of (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol.

    PubMed

    Alaşalvar, Can; Soylu, Mustafa Serkan; Güder, Aytaç; Albayrak, Çiğdem; Apaydın, Gökhan; Dilek, Nefise

    2014-05-01

    In this study, (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol has been synthesized and characterized by using X-ray technique and FT-IR experimentally and using B3LYP/6-31G(d,p) and HF/6-31G(d,p) methods theoretically. The intermolecular and intramolecular interactions of the title compound have been determined according to X-ray results. The molecular geometry, vibrational frequencies of the title compound in the ground state have been calculated using the density functional B3LYP and HF method with the 6-31G(d,p) basis set and calculated bond parameters and vibrational frequencies values show good agreement with experimental values. Theoretical and experimental results show that tautomeric form of the structure is phenol-imine form. Besides HOMO-LUMO energy gap, molecular electrostatic potential map were performed at B3LYP/6-31G(d,p) level. It is worthy note of that, the free radical scavenging activities of the title compound were assessed using DPPH˙, DMPD˙(+), and ABTS˙(+) assays. The obtained results show that the title compound has effective DPPH˙ (SC50 2.61±0.09 μg/mL), DMPD˙(+) (SC50 2.82±0.14 μg/mL), and ABTS˙(+) (SC50 4.91±0.18 μg/mL) radical scavenging activities when compared with standard antioxidants (BHA, rutin, and trolox). PMID:24566110

  3. [CALCULATION OF RADIATION LOADS ON THE ANTHROPOMORPHIC PHANTOM ONBOARD THE SPACE STATION IN THE CASE OF ADDITIONAL SHIELDING].

    PubMed

    Kartashov, D A; Shurshakov, V A

    2015-01-01

    The paper presents the results of calculating doses from space ionizing radiation for a modeled orbital station cabin outfitted with an additional shield aimed to reduce radiation loads on cosmonaut. The shield is a layer with the mass thickness of -6 g/cm2 (mean density = 0.62 g/cm3) that covers the outer cabin wall and consists of wet tissues and towels used by cosmonauts for hygienic purposes. A tissue-equivalent anthropomorphic phantom imitates human body. Doses were calculated for the standard orbit of the International space station (ISS) with consideration of the longitudinal and transverse phantom orientation relative to the wall with or without the additional shield. Calculation of dose distribution in the human body improves prediction of radiation loads. The additional shield reduces radiation exposure of human critical organs by -20% depending on their depth and body spatial orientation in the ISS compartment.

  4. [CALCULATION OF RADIATION LOADS ON THE ANTHROPOMORPHIC PHANTOM ONBOARD THE SPACE STATION IN THE CASE OF ADDITIONAL SHIELDING].

    PubMed

    Kartashov, D A; Shurshakov, V A

    2015-01-01

    The paper presents the results of calculating doses from space ionizing radiation for a modeled orbital station cabin outfitted with an additional shield aimed to reduce radiation loads on cosmonaut. The shield is a layer with the mass thickness of -6 g/cm2 (mean density = 0.62 g/cm3) that covers the outer cabin wall and consists of wet tissues and towels used by cosmonauts for hygienic purposes. A tissue-equivalent anthropomorphic phantom imitates human body. Doses were calculated for the standard orbit of the International space station (ISS) with consideration of the longitudinal and transverse phantom orientation relative to the wall with or without the additional shield. Calculation of dose distribution in the human body improves prediction of radiation loads. The additional shield reduces radiation exposure of human critical organs by -20% depending on their depth and body spatial orientation in the ISS compartment. PMID:26554132

  5. Structural, magnetic, and redox diversity of first-row transition metal complexes of a pyridine-based macrocycle: well-marked trends supported by theoretical DFT calculations.

    PubMed

    Drahoš, Bohuslav; Herchel, Radovan; Trávníček, Zdeněk

    2015-04-01

    A series of first-row transition metal complexes with 15-membered pyridine-based macrocycle (3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1(18),14,16-triene = L) was prepared ([M(II)(L)Cl2], where M = Mn, Co, Ni, Zn (1, 3, 4, 6); [Fe(III)(L)Cl2]Cl (2), [Cu(II)(L)Cl]Cl (5)) and thoroughly characterized. Depending on the complexated metal atom, the coordination number varies from 7 (Mn, Fe, Co), through 5 + 2 for Ni and 4 + 1 for Cu, to 5 for Zn accompanied by changes in the coordination geometry from the pentagonal bipyramid (1-4) to the square pyramid (5 and 6). Along the series, the metal-oxygen distances were prolonged in such manner that their bonding character was investigated, apart from X-ray structural analysis, also by ab initio calculations (Mayer's bond order, electron localization function), which confirmed that, in 4 and 5, two and one oxygen donor atoms are semicoordinated, respectively, and one and two oxygen atoms are uncoordinated in 5, and 6, respectively. On the basis of the temperature variable magnetic susceptibility measurements, 1 and 2 behave as expected for 3d(5) high-spin configuration with negligible zero-field splitting (ZFS). On the other hand, a large axial ZFS (D(Co) ≈ 40 cm(-1), D(Ni) ≈ -6.0 cm(-1)) was found for 3 and 4, and rhombic ZFS (E/D ≈ 0.15) for 4. Antiferromagnetic exchange coupling was observed for 4 and 5 (J(Ni) = -0.48 cm(-1), and J(Cu) = -2.43 cm(-1), respectively). The obtained results correlate well with ab initio calculations of ZFS parameters as well as J-values, which indicate that the antiferromagnetic exchange is mediated by hydrogen bonds. The complexes were also investigated by cyclic voltammetry in water or acetonitrile. A quasi-reversible couple Mn(II)/Mn(III) at 1.13/0.97 V, an almost reversible couple Fe(II)/Fe(III) at 0.51/0.25 V, and a one-step/multistep reduction/oxidation of Cu(II) complex 5 at -0.33 V/0.06-0.61 V were detected. PMID:25761063

  6. Synthesis, characterization, MCD spectroscopy, and TD-DFT calculations of copper-metalated nonperipherally substituted octaoctyl derivatives of tetrabenzotriazaporphyrin, cis- and trans-tetrabenzodiazaporphyrin, tetrabenzomonoazaporphyrin, and tetrabenzoporphyrin.

    PubMed

    Mack, John; Sosa-Vargas, Lydia; Coles, Simon J; Tizzard, Graham J; Chambrier, Isabelle; Cammidge, Andrew N; Cook, Michael J; Kobayashi, Nagao

    2012-12-01

    Synthesis of the title compounds has been achieved through refinement of a recently reported synthetic protocol whereby varying equivalents of MeMgBr are reacted with 1,4-dioctylphthalonitrile to produce mixtures favoring specific hybrid structures. The initially formed magnesium-metalated compounds are obtained as pure materials and include, for the first time, both isomers (cis and trans) of tetrabenzodiazaporphyrin. The compounds were demetalated to the metal-free analogues, which were then converted into the copper-metalated derivatives. The X-ray structure of the copper tetrabenzotriazaporphyrin derivative is reported. The metal-free and copper-metalated macrocycles exhibit columnar mesophase behavior, and it is found that the mesophase stability is unexpectedly reduced in the diazaporphyrin derivatives compared to the rest of the series. The results of time-dependent density functional theory calculations for the copper complexes are compared to the observed optical properties. Michl's perimeter model was used as a conceptual framework for analyzing the magnetic circular dichroism spectral data, which predicted and accounted for trends in the observed experimental spectra.

  7. Thiazole-based nitrogen mustards: Design, synthesis, spectroscopic studies, DFT calculation, molecular docking, and antiproliferative activity against selected human cancer cell lines

    NASA Astrophysics Data System (ADS)

    Łączkowski, Krzysztof Z.; Świtalska, Marta; Baranowska-Łączkowska, Angelika; Plech, Tomasz; Paneth, Agata; Misiura, Konrad; Wietrzyk, Joanna; Czaplińska, Barbara; Mrozek-Wilczkiewicz, Anna; Malarz, Katarzyna; Musioł, Robert; Grela, Izabela

    2016-09-01

    Synthesis, characterization and investigation of antiproliferative activity of ten thiazole-based nitrogen mustard against human cancer cells lines (MV4-11, A549, MCF-7 and HCT116) and normal mouse fibroblast (BALB/3T3) is presented. The structures of novel compounds were determined using 1H and 13C NMR, FAB(+)-MS, and elemental analyses. Among the derivatives, 5b, 5c, 5e, 5f and 5i were found to exhibit high activity against human leukaemia MV4-11 cells with IC50 values of 2.17-4.26 μg/ml. The cytotoxic activity of compound 5c and 5f against BALB/3T3 cells is up to 20 times lower than against cancer cell lines. Our results also show that compounds 5e and 5i have very strong activity against MCF-7 and HCT116 with IC50 values of 3.02-4.13 μg/ml. Moreover, spectroscopic characterization and cellular localization for selected compound were performed. In order to identify potential drug targets we perform computer simulations with DNA-binding site of hTopoI and hTopoII and quantum chemical calculation of interaction and binding energies in complexes of the five most active compounds with guanine.

  8. Geothermal Economics Calculator (GEC) - additional modifications to final report as per GTP's request.

    SciTech Connect

    Gowda, Varun; Hogue, Michael

    2015-07-17

    This report will discuss the methods and the results from economic impact analysis applied to the development of Enhanced Geothermal Systems (EGS), conventional hydrothermal, low temperature geothermal and coproduced fluid technologies resulting in electric power production. As part of this work, the Energy & Geoscience Institute (EGI) has developed a web-based Geothermal Economics Calculator (Geothermal Economics Calculator (GEC)) tool that is aimed at helping the industry perform geothermal systems analysis and study the associated impacts of specific geothermal investments or technological improvements on employment, energy and environment. It is well-known in the industry that geothermal power projects will generate positive economic impacts for their host regions. Our aim in the assessment of these impacts includes quantification of the increase in overall economic output due to geothermal projects and of the job creation associated with this increase. Such an estimate of economic impacts of geothermal investments on employment, energy and the environment will also help us understand the contributions that the geothermal industry will have in achieving a sustainable path towards energy production.

  9. A method for calculating minimum biodiversity offset multipliers accounting for time discounting, additionality and permanence

    PubMed Central

    Laitila, Jussi; Moilanen, Atte; Pouzols, Federico M

    2014-01-01

    Biodiversity offsetting, which means compensation for ecological and environmental damage caused by development activity, has recently been gaining strong political support around the world. One common criticism levelled at offsets is that they exchange certain and almost immediate losses for uncertain future gains. In the case of restoration offsets, gains may be realized after a time delay of decades, and with considerable uncertainty. Here we focus on offset multipliers, which are ratios between damaged and compensated amounts (areas) of biodiversity. Multipliers have the attraction of being an easily understandable way of deciding the amount of offsetting needed. On the other hand, exact values of multipliers are very difficult to compute in practice if at all possible. We introduce a mathematical method for deriving minimum levels for offset multipliers under the assumption that offsetting gains must compensate for the losses (no net loss offsetting). We calculate absolute minimum multipliers that arise from time discounting and delayed emergence of offsetting gains for a one-dimensional measure of biodiversity. Despite the highly simplified model, we show that even the absolute minimum multipliers may easily be quite large, in the order of dozens, and theoretically arbitrarily large, contradicting the relatively low multipliers found in literature and in practice. While our results inform policy makers about realistic minimal offsetting requirements, they also challenge many current policies and show the importance of rigorous models for computing (minimum) offset multipliers. The strength of the presented method is that it requires minimal underlying information. We include a supplementary spreadsheet tool for calculating multipliers to facilitate application. PMID:25821578

  10. Improved DFT Potential Energy Surfaces via Improved Densities.

    PubMed

    Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron

    2015-10-01

    Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases. PMID:26722874

  11. Metal-organic frameworks in cadmium(II) complexes with 5-methoxyindole-2-carboxylic acid: structure, vibrational spectra and DFT calculations

    NASA Astrophysics Data System (ADS)

    Morzyk-Ociepa, Barbara; Szmigiel, Ksenia; Dysz, Karolina; Turowska-Tyrk, Ilona; Michalska, Danuta

    2016-11-01

    Two new complexes of Cd(II) with an O-deprotonated anion of 5-methoxyindole-2-carboxylic acid (5-MeOI2CA), of the formulas [Cd(5-MeOI2CA)2(H2O)2]n (1) and [Cd3(5-MeOI2CA)6(H2O)4(DMSO)4]ṡ2DMSO (2) were synthesized. In the polymeric complex 1, the 5-MeOI2CA anion acts as a bidentate bridging ligand and the coordination environment around the Cd(II) ion can be described as a distorted octahedron. Single crystal X-ray diffraction analysis of 2 has revealed that this complex is a trimer and it crystallizes in the monoclinic system (space group P21/c with a = 20.3403(4), b = 14.3079(2), c = 15.0603(3) Å, β = 92.4341(17)°, V = 4379.00(14) Å3 and Z = 2). In 2, the 5-MeOI2CA anions act as bidentate bridging and bidentate chelating ligands. The asymmetric unit of 2 contains two crystallographically independent Cd(II) cations. One of the cations is coordinated to six oxygen atoms and shows an octahedral geometry with a rhombic deformation. The other Cd(II) cation adopts a distorted seven-coordinate pentagonal-bipyramidal geometry involving seven oxygen atoms. In 2, the DMSO solvent molecules play a key role in the formation of metal-organic frameworks by filling voids, which are created by the bridging and chelating 5-MeOI2CA anions, the cadmium cations and the other DMSO molecules coordinated to cadmium. Comprehensive theoretical calculations (including the optimized structural parameters, harmonic frequencies and vibrational intensities) were performed for 2 using the B3LYP method with the 6-311++G(d,p)/LanL2DZ basis sets. The infrared and Ramana spectra were measured and a detailed assignment of the experimental spectra of 2 was performed. All cadmium-oxygen stretching vibrations occur in the range below 400 cm-1.

  12. A triple-bridged azido-Cu(II) chain compound fine-tuned by mixed carboxylate/ethanol linkers displays slow-relaxation and ferromagnetic order: synthesis, crystal structure, magnetic properties and DFT calculations.

    PubMed

    Liu, Xiangyu; Chen, Sanping; Grancha, Thais; Pardo, Emilio; Ke, Hongshan; Yin, Bing; Wei, Qing; Xie, Gang; Gao, Shengli

    2014-11-01

    A new azido-Cu(II) compound, [Cu(4-fba)(N3)(C2H5OH)] (4-fba = 4-fluorobenzoic acid) (1), has been synthesized and characterized. The X-ray crystal structure analysis demonstrates that only one crystallographically independent Cu(II) ion in the asymmetric unit of 1 exhibits a stretched octahedral geometry in which two azido N atoms and two carboxylic O atoms locate in the equatorial square, while two ethanol O atoms occupy the apical positions, forming a 1D Cu(II) chain with an alternating triple-bridge of EO-azido, syn,syn-carboxylate, and μ2-ethanol. The title compound consists of ferromagnetically interacting ferromagnetic chains, which exhibit ferromagnetic order (T(c) = 7.0 K). The strong ferromagnetic coupling between adjacent Cu(II) ions within each chain is due to the countercomplementarity of the super-exchange pathways, whereas the ferromagnetic interchain interactions--responsible for the long-range magnetic ordering--are most likely due to the presence of coordinated ethanol molecules establishing hydrogen bonds with neighboring chains. DFT calculations have been performed on compound 1 to offer a qualitative theoretical explanation of the magnetic behavior.

  13. Crystal structure, solvothermal synthesis, thermogravimetric studies and DFT calculations of a five-coordinate cobalt(II) compound based on the N,N-bis­(2-hy­droxy­eth­yl)glycine anion

    PubMed Central

    Zhou, Yanling; Liu, Xianrong; Wang, Qijun; Wang, Lisheng; Song, Baoling

    2016-01-01

    The reaction of CoCl2·6H2O, N,N-bis­(2-hy­droxy­eth­yl)glycine and tri­ethyl­amine (Et3N) in ethanol solution under solvothermal conditions produced crystals of [N,N-bis­(2-hy­droxy­eth­yl)glycinato]chloridocobalt(II), [Co(C6H12NO4)Cl]. The CoII ion is coordinated in a slightly distorted trigonal–bipyramidal environment which is defined by three O atoms occupying the equatorial plane and the N and Cl atoms in the apical sites. In the crystal, two types of O—H⋯O hydrogen bonds connect the mol­ecules, forming a two-dimensional network parallel to (001). The mol­ecular structure of the title compound confirms the findings of FTIR, elemental analysis, ESI–MS analysis and TG analysis. By using the density functional theory (DFT) (B3LYP) method with 6-31G(d) basis set, the molecular structure has been calculated and optimized. PMID:27746942

  14. Crystal structure and DFT calculations of 3,4- seco-lup-20(29)-en-3-oic acid isolated from Wrightia tinctoria: Stacking of supramolecular dimers in the crystal lattice

    NASA Astrophysics Data System (ADS)

    Ghosh, Anindita; Sarkar, Ananda; Mitra, Partha; Banerji, Avijit; Banerji, Julie; Mandal, Suvra; Das, Manosi

    2010-09-01

    3,4- Seco-lup-20(29)-en-3-oic acid ( 1), a rare triterpene, was isolated from Wrightia tinctoria R.Br (Family: Apocyanaceae). It appeared promising to study the structural chemistry of this compound because of its unique bio activity. X-ray diffraction analysis demonstrated that this compound consists of three six membered rings and one five membered ring. The first six membered ring (A) is in the twist boat form while the remaining two six membered rings (B, C) are in the chair form. The crystal of this compound belongs - to the monoclinic crystal system and space group P2 1. Lattice constituents are as follows: a = 13.074(6) Å, b = 11.972(5) Å, c = 17.394(7) Å; α = 90.00°, β = 98.20(13)°, γ = 90.00°; V = 2695(2) Å 3, d = 1.094 Mg/m 3, Z = 4. The optimized geometry of the reported molecule has been calculated with the DFT/B3LYP theory using 6-31G(d,p) basis set.

  15. Rate coefficients of the CF3CHFCF3 + H → CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths.

    PubMed

    Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

    2013-03-15

    The minimum energy path (MEP) of the reaction, CF(3)CHFCF(3) + H → transition state (TS) → CF(3)CFCF(3) + H(2), has been computed at different ab initio levels and with density functional theory (DFT) using different functionals. The computed B3LYP/6-31++G**, BH&HLYP/cc-pVDZ, BMK/6-31++G**, M05/6-31+G**, M05-2X/6-31+G**, UMP2/6-31++G**, PUMP2/6-31++G**//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVDZ//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVTZ(spd,sp)//UMP2//6-31++G**, RCCSD(T)/CBS//M05/6-31+G**, and RCCSD(T)/CBS//UMP2/6-31++G** MEPs, and associated gradients and Hessians, were used in reaction rate coefficient calculations based on the transition state theory (TST). Reaction rate coefficients were computed between 300 and 1500 K at various levels of TST, which include conventional TST, canonical variational TST (CVT) and improved CVT (ICVT), and with different tunneling corrections, namely, Wigner, zero-curvature, and small-curvature (SCT). The computed rate coefficients obtained at different ab initio, DFT and TST levels are compared with experimental values available in the 1000-1200 K temperature range. Based on the rate coefficients computed at the ICVT/SCT level, the highest TST level used in this study, the BH&HLYP functional performs best among all the functionals used, while the RCCSD(T)/CBS//MP2/6-31++G** level is the best among all the ab initio levels used. Comparing computed reaction rate coefficients obtained at different levels of theory shows that, the computed barrier height has the strongest effect on the computed reaction rate coefficients as expected. Variational effects on the computed rate coefficients are found to be negligibly small. Although tunneling effects are relatively small at high temperatures (~1500 K), SCT corrections are significant at low temperatures (~300 K), and both barrier heights and the magnitudes of the imaginary frequencies affect SCT corrections.

  16. Mental Arithmetic in Children with Mathematics Learning Disabilities: The Adaptive Use of Approximate Calculation in an Addition Verification Task

    ERIC Educational Resources Information Center

    Rousselle, Laurence; Noel, Marie-Pascale

    2008-01-01

    The adaptive use of approximate calculation was examined using a verification task with 18 third graders with mathematics learning disabilities, 22 typically achieving third graders, and 21 typically achieving second graders. Participants were asked to make true-false decisions on simple and complex addition problems while the distance between the…

  17. The new Schiff base 4-[(4-Hydroxy-3-fluoro-5-methoxy-benzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one: Experimental, DFT calculational studies and in vitro antimicrobial activity

    NASA Astrophysics Data System (ADS)

    İskeleli, Nazan Ocak; Alpaslan, Yelda Bingöl; Direkel, Şahin; Ertürk, Aliye Gediz; Süleymanoğlu, Nevin; Ustabaş, Reşat

    2015-03-01

    The synthesized Schiff base, 4-[(4-Hydroxy-3-fluoro-5-methoxy-benzylidene)amino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one (I), has been characterized by 13C NMR, 1H NMR, 2D NMR (1H-1H COSY and 13C APT), FT-IR, UV-vis and X-ray single-crystal techniques. Molecular geometry of the compound I in the ground state, vibrational frequencies and chemical shift values have been calculated by using the density functional method (DFT) with 6-311++G(d,p) basis set. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The differences between experimental and calculated results of FT-IR and NMR have supported the existence of intermolecular (O-H⋯O type) and intramolecular (C-H⋯O type) hydrogen bonds in the crystal structure. Molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO) and electronic absorption spectra were carried out at B3LYP/6-311G++(d,p). HOMO-LUMO electronic transition of 3.92 eV is due to contribution of the bands the n → π∗. The antimicrobial activity of the compound I was determined against the selected 11 bacteria and 8 fungi by microdilution broth assay with Alamar Blue. In vitro studies showed that the compound I has no antifungal effect for selected fungal isolates. However, the compound I shows remarkable antibacterial effect for the bacteria; Streptococcus pneumoniae, Haemophilus influenzae and Enterococcus faecalis.

  18. Synthesis, structures and DFT calculations of 2-(4,6-dimethyl pyrimidyl)selenolate complexes of Cu(I), Ag(I) and Au(I) and their conversion into metal selenide nanocrystals.

    PubMed

    Sharma, Rakesh K; Wadawale, Amey; Kedarnath, G; Manna, Debashree; Ghanty, Tapan K; Vishwanadh, B; Jain, Vimal K

    2014-05-01

    The complexes [M{SeC4H(Me-4,6)2N2}]6 (M = Cu (1), Ag (2)) and [Au{SeC4H(Me-4,6)2N2}(PEt3)] (3) have been prepared and characterized by elemental analyses, UV-vis, NMR ((1)H, (13)C, (77)Se) spectroscopy and single crystal X-ray diffraction. The crystal structures of [Cu{SeC4H(Me-4,6)2N2}]6·H2O (1·H2O), [Ag{SeC4H(Me-4,6)2N2}]6·6MeOH·H2O (2·6MeOH·H2O) and [Au{SeC4H(Me-4,6)2N2}(PEt3)] (3) revealed that their metal centers acquire distorted square-pyramidal, trigonal and linear geometries, respectively. DFT calculations have been carried out to rationalize nuclearity in copper(i) chalcogenolate complexes. The calculations suggest that there is hardly any energy difference between the tetrameric and hexameric forms. Thermal behavior of [Cu{SeC4H(Me-4,6)2N2}]6 was studied by thermogravimetric analysis. Thermolysis of [M{SeC4H(Me-4,6)2N2}]6 (M = Cu, Ag) in 1-dodecanethiol (DDT) at 150 °C gave a cubic phase of Cu7Se4 and an orthorhombic phase of Ag2Se, respectively. Copper selenide (Cu7Se4) thin films were deposited on glass and silicon substrates by using [Cu{SeC4H(Me-4,6)2N2}]6 at 400 °C by AACVD. PMID:24623060

  19. Synthesis and spectroscopic characterization on 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid: A DFT approach

    NASA Astrophysics Data System (ADS)

    Kurt, M.; Sas, E. Babur; Can, M.; Okur, S.; Icli, S.; Demic, S.; Karabacak, M.; Jayavarthanan, T.; Sundaraganesan, N.

    2016-01-01

    A complete structural and vibrational analysis of the 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid (TPBA), was carried out by ab initio calculations, at the density functional theory (DFT) method. Molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) 13C NMR and 1H NMR chemical shift values of (TPBA), in the ground state have been calculated by using ab initio density functional theory (DFT/B3LYP) method with 6-311G(d,p) as basis set for the first time. Comparison of the observed fundamental vibrational modes of (TPBA) and calculated results by DFT/B3LYP method indicates that B3LYP level of theory giving yield good results for quantum chemical studies. Vibrational wavenumbers obtained by the DFT/B3LYP method are in good agreement with the experimental data. The study was complemented with a natural bond orbital (NBO) analysis, to evaluate the significance of hyperconjugative interactions and electrostatic effects on such molecular structure. By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals analysis and thermodynamic properties of TPBA were investigated using theoretical calculations.

  20. Mental arithmetic in children with mathematics learning disabilities: the adaptive use of approximate calculation in an addition verification task.

    PubMed

    Rousselle, Laurence; Noël, Marie-Pascale

    2008-01-01

    The adaptive use of approximate calculation was examined using a verification task with 18 third graders with mathematics learning disabilities, 22 typically achieving third graders, and 21 typically achieving second graders. Participants were asked to make true-false decisions on simple and complex addition problems while the distance between the proposed and the correct answer was manipulated. Both typically achieving groups were sensitive to answer plausibility on simple problems, were faster at rejecting extremely incorrect results than at accepting correct answers on complex addition problems, and showed a reduction of the complexity effect on implausible problems, attesting to the use of approximate calculation. Conversely, children with mathematics disabilities were unaffected by answer plausibility on simple addition problems, processed implausible and correct sums with equal speed on complex problems, and exhibited a smaller reduction of the complexity effect on implausible problems. They also made more errors on implausible problems. Different hypotheses are discussed to account for these results. PMID:18443150

  1. EFT for DFT

    NASA Astrophysics Data System (ADS)

    Furnstahl, R. J.

    These lectures give an overview of the ongoing application of effective field theory (EFT) and renormalization group (RG) concepts and methods to density functional theory (DFT), with special emphasis on the nuclear many-body problem. Many of the topics covered are still in their infancy, so rather than a complete review these lectures aim to provide an introduction to the developing literature.

  2. L-edge X-ray Absorption Spectroscopy and DFT Calculations on Cu2O2 Species: Direct Electrophilic Aromatic Attack by Side-on Peroxo Bridged Dicopper(II) Complexes

    PubMed Central

    Qayyum, Munzarin F.; Sarangi, Ritimukta; Fujisawa, Kiyoshi; Stack, T. Daniel P.; Karlin, Kenneth D.; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

    2013-01-01

    The hydroxylation of aromatic substrates catalyzed by coupled binuclear copper enzymes has been observed with side-on-peroxo-dicopper(II) (P) and bis-μ-oxo-dicopper(III) (O) model complexes. The substrate-bound-O intermediate in [Cu(II)2(DBED)2(O)2]2+ (DBED=N,N′-di-tert-butyl-ethylenediamine) was shown to perform aromatic hydroxylation. For the [Cu(II)2(NO2-XYL)(O2)]2+ complex, only a P species was spectroscopically observed. However, it was not clear whether this O-O bond cleaves to proceed through an O-type structure along the reaction coordinate for hydroxylation of the aromatic xylyl linker. Accurate evaluation of these reaction coordinates requires reasonable quantitative descriptions of the electronic structures of the P and O species. We have performed Cu L-edge XAS on two well-characterized P and O species to experimentally quantify the Cu 3d character in their ground state wavefunctions. The lower per-hole Cu character (40±6%) corresponding to higher covalency in the O species compared to the P species (52±4%) reflects a stronger bonding interaction of the bis-μ-oxo core with the Cu(III) centers. DFT calculations show that 10-20% Hartree-Fock (HF) mixing for P and ~38% for O species are required to reproduce the Cu-O bonding; for the P species this HF mixing is also required for an antiferromagnetically coupled description of the two Cu(II) centers. B3LYP (with 20% HF) was, therefore, used to calculate the hydroxylation reaction coordinate of P in [Cu(II)2(NO2-XYL)(O2)]2+. These experimentally calibrated calculations indicate that the electrophilic attack on the aromatic ring does not involve formation of a Cu(III)2(O2−)2 species. Rather, there is direct electron donation from the aromatic ring into the peroxo σ* orbital of the Cu(II)2(O22−) species, leading to concerted C-O bond formation with O-O bond cleavage. Thus, species P is capable of direct hydroxylation of aromatic substrates without the intermediacy of an O-type species. PMID:24102191

  3. A Boron-Fluorinated Tris(pyrazolyl)borate Ligand ((F) Tp*) and Its Mono- and Dinuclear Copper Complexes [Cu((F) Tp*)2 ] and [Cu2 ((F) Tp*)2 ]: Synthesis, Structures, and DFT Calculations.

    PubMed

    Augenstein, Timo; Dorner, Franziska; Reiter, Kevin; Wagner, Hanna E; Garnier, Delphine; Klopper, Wim; Breher, Frank

    2016-06-01

    Reaction of [Si(3,5-Me2 pz)4 ] (1) with [Cu(MeCN)4 ][BF4 ] (2) gave the mono- and dinuclear copper complexes [Cu2 ((F) Tp*)2 ] (3) and [Cu((F) Tp*)2 ] (4). Both complexes contain the so-far unprecedented boron-fluorinated (F) Tp* ligand ([FB(3,5-Me2 pz)3 ](-) with pz=pyrazolyl) originating from 1, acting as a pyrazolyl transfer reagent, and the [BF4 ](-) counter anion of 2, serving as the source of the {BF} entity. The solid-state structures as well as the NMR and EPR spectroscopic characteristics of the complexes were elaborated. Pulsed gradient spin echo (PGSE) experiments revealed that 3 retains (almost entirely) its dimeric structure in benzene, whereas dimer cleavage and formation of acetonitrile adducts, presumably [Cu((F) Tp*)(MeCN)], is observed in acetonitrile. The short Cu⋅⋅⋅Cu distance of 269.16 pm in the solid-state is predicted by DFT calculations to be dictated by dispersion interactions between all atoms in the complex (the Cu-Cu dispersion contribution itself is only very small). As revealed by cyclic voltammetry studies, 3 shows an irreversible (almost quasi-reversible at higher scan rates) oxidation process centred at E(pa) =-0.23 V (E(0) 1/2 =-0.27 V) (vs. Fc/Fc(+) ). Oxidation reactions on a preparative scale with one equivalent of the ferrocenium salt [Fc][BF4 ] (very slow reaction) or air (fast reaction) furnished blue crystals of the mononuclear copper(II) complex [Cu((F) Tp*)2 ] (4). As expected for a Jahn-Teller-active system, the coordination sphere around copper(II) is strongly distorted towards a stretched octahedron, in accordance with EPR spectroscopic findings. PMID:27106294

  4. DFT study on a fullerene doped with Si and N

    NASA Astrophysics Data System (ADS)

    Beigi, Hossein Shirani IL

    2013-09-01

    DFT calculations are applied for some stable C60, C59Si, and C59N hetero fullerenes. Sn and Ge atoms are doped at the same position of C60. Computations are carried out at the B3LYP/cc pVDZ levels. In this work the effects of the heteroatoms, Si and N, on the structural properties of the fullerene have been studied. The structure, energetic and relative stabilities of the compounds were compared and analyzed with each other. In addition, vibrations spectra of proposed stable neutral species, as well as the infrared intensities are calculated. From the data obtained from calculation, we found that there is strong correlation between the stability of pure C60 fullerene molecule and the numbers of different C-C bonds.

  5. Simultaneous presence of (Si3O10)8- and (Si2O7)6- groups in new synthetic mixed sorosilicates: BaY4(Si2O7)(Si3O10) and isotypic compounds, studied by single-crystal X-ray diffraction, Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Wierzbicka-Wieczorek, Maria; Többens, Daniel M.; Kolitsch, Uwe; Tillmanns, Ekkehart

    2013-11-01

    Three new, isotypic silicate compounds, BaY4(Si2O7)(Si3O10), SrYb4(Si2O7)(Si3O10) and SrSc4(Si2O7)(Si3O10), were synthesized using high-temperature flux growth techniques, and their crystal structures were solved from single-crystal X-ray intensity data: monoclinic, P21/m, with a=5.532(1)/5.469(1)/5.278(1), b=19.734(4)/19.447(4)/19.221(4), c=6.868(1)/6.785(1)/6.562(1) Å, β=106.53(3)/106.20(3)/106.50(3)°, V=718.8(2)/693.0(2)/638.3(2) Å3, R(F)=0.0225/0.0204/0.0270, respectively. The topology of the novel structure type contains isolated horseshoe-shaped Si3O10 groups (Si-Si-Si=93.15-95.98°), Si2O7 groups (Si-Obridge-Si=180°, symmetry-restricted) and edge-sharing M(1)O6 and M(2)O6 octahedra. Single-crystal Raman spectra of the title compounds were measured and compared with Raman spectroscopic data of chemically and topologically related disilicates and trisilicates, including BaY2(Si3O10) and SrY2(Si3O10). The band assignments are supported by additional theoretical calculation of Raman vibrations by DFT methods.

  6. A modified additivity rule for the calculation of electron impact ionization cross-section of molecules ABn

    NASA Astrophysics Data System (ADS)

    Deutsch, H.; Becker, K.; Mark, T. D.

    1997-11-01

    This paper describes a modified additivity rule for the calculation of electron impact ionization cross-sections of molecules and radicals of the form ABn(n = 1-6). This additivity rule incorporates weighting factors for the contributions to the molecular ionization cross-sections from the ionization cross-sections of the constituent atoms, which depend explicitly on the atomic radii and the effective number of atomic electrons. In a few special cases (hydrides where the other constituent atom has a radius smaller than the radius of the H atom and species where both constituent atoms have radii smaller than the radius of the H atom), the weighting factors can be simplified, so that they depend only on the atomic radii, i.e. on geometric effects. A comprehensive comparison of the predictions of this new modified additivity rule with available experimental data and with other theoretical predictions is presented.

  7. The solvatochromic, spectral, and geometrical properties of nifenazone: a DFT/TD-DFT and experimental study.

    PubMed

    Bani-Yaseen, Abdulilah Dawoud; Al-Balawi, Mona

    2014-08-01

    The solvatochromic, spectral, and geometrical properties of nifenazone (NIF), a pyrazole-nicotinamide drug, were experimentally and computationally investigated in several neat solvents and in hydro-organic binary systems such as water-acetonitrile and water-dioxane systems. The bathochromic spectral shift observed in NIF absorption spectra when reducing the polarity of the solvent was correlated with the orientation polarizability (Δf). Unlike aprotic solvents, a satisfactory correlation between λ(max) and Δf was determined (linear correlation of regression coefficient, R, equal to 0.93) for polar protic solvents. In addition, the medium-dependent spectral properties were correlated with the Kamlet-Taft solvatochromic parameters (α, β, and π*) by applying a multiple linear regression analysis (MLRA). The results obtained from this analysis were then employed to establish MLRA relationships for NIF in order to estimate the spectral shift in different solvents, which in turn exhibited excellent correlation (R > 0.99) with the experimental values of ν(max). Density functional theory (DFT) and time-dependent DFT theory calculations coupled with the integral equation formalism-polarizable continuum model (IEF-PCM) were performed to investigate the solvent-dependent spectral and geometrical properties of NIF. The calculations showed good and poor agreements with the experimental results using the CAM-B3LYP and B3LYP functionals, respectively. Experimental and theoretical results confirmed that the chemical properties of NIF are strongly dependent on the polarity of the chosen medium and its hydrogen bonding capability. This in turn supports the hypothesis of the delocalization of the electron density within the pyrazole ring of NIF.

  8. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    PubMed

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.

  9. Calculation of enhanced slowing and cooling due to the addition of a traveling wave to an intense optical standing wave

    NASA Astrophysics Data System (ADS)

    Gottesman, D.; Mervis, J.; Prentiss, M.; Bigelow, N. P.

    1992-07-01

    We investigate the force on a two-level atom interacting with intense monochromatic laser fields which are combinations of standing and traveling waves. We present a continued-fraction solution to the optical Bloch equations. Using this solution to calculate the force on an atom, we have examined the slowing and cooling of a thermal Na atomic beam. We find that the addition of a traveling wave to an intense standing wave can significantly improve the slowing rate and simultaneously decrease the final velocity of the cooled beam.

  10. Iodine adsorption on Ni(111): STM and DFT study

    NASA Astrophysics Data System (ADS)

    Komarov, N. S.; Pavlova, T. V.; Andryushechkin, B. V.

    2016-09-01

    Iodine adsorption on the Ni(111) surface has been studied in ultra-high vacuum conditions with scanning tunneling microscopy (STM), Auger electron spectroscopy (AES), low-energy electron diffraction (LEED) and density functional theory (DFT) calculations. At the first stage of adsorption, iodine was found to form a simple commensurate (√{ 3 } ×√{ 3 }) R 30∘ structure at the coverage of 0.33 ML. According to DFT calculations, all iodine atoms in the (√{ 3 } ×√{ 3 }) R 30∘ structure occupy fcc hollow sites. Increase of the coverage in the range of (0.333 ML <θ < 0.364 ML) results in the uniaxial compression of the iodine lattice and the formation of the high-order commensurate structure (11 ×√{ 3 } R 30∘). The mechanism of compression involves the formation and the development of the striped super-heavy domain wall network. Further iodine dosing gives rise to nucleation and growth of flat 2D islands of surface nickel iodide. Atomic resolution STM images of iodide islands, in addition to atomic modulation, exhibit clear visible moiré-like superstructures with a period about 26 Å. The origin of the moiré-patterns was explained by the incommensurability of lattices of the surface nickel iodide and underlying Ni(111).

  11. Calculating slope and ED50 of additive dose-response curves, and application of these tabulated parameter values.

    PubMed

    Pöch, G; Pancheva, S N

    1995-06-01

    Comparing dose-response curves (DRCs) of a compound A in the absence and presence of a fixed dose of an antagonist B is standard in pharmacology and toxicology. When B qualitatively resembles A in its action, it is often useful to construct theoretical DRCs of additive and independent combinations. Theoretical curves are calculated from experimental values by the program ALLFIT, which uses the four parameter logistic equation. DRCs of theoretical, additive DRCs are obtained by using the respective values for slope and ED50, which were taken from tables presented here compiled on the basis of the slope of the DRC of A alone (0.6-14) and of the effect of B alone (1-75%). These tables are unnecessary for the construction of theoretical curves if A acts by an independent mechanism, giving values for slope and ED50 identical to those of the DRC of A alone. Experimental DRCs of antiviral and other effects (the latter taken from data in the literature) are compared with theoretical curves by an F-test analysis provided by ALLFIT. The method can be used successfully for the construction of theoretical curves for additive and independent DRCs and comparison with experimental curves. This comparison may help clarify the mode of interaction of A with B. PMID:7640393

  12. STRMDEPL08 - An Extended Version of STRMDEPL with Additional Analytical Solutions to Calculate Streamflow Depletion by Nearby Pumping Wells

    USGS Publications Warehouse

    Reeves, Howard W.

    2008-01-01

    STRMDEPL, a one-dimensional model using two analytical solutions to calculate streamflow depletion by a nearby pumping well, was extended to account for two additional analytical solutions. The extended program is named STRMDEPL08. The original program incorporated solutions for a stream that fully penetrates the aquifer with and without streambed resistance to ground-water flow. The modified program includes solutions for a partially penetrating stream with streambed resistance and for a stream in an aquitard subjected to pumping from an underlying leaky aquifer. The code also was modified to allow the user to input pumping variations at other than 1-day intervals. The modified code is shown to correctly evaluate the analytical solutions and to provide correct results for half-day time intervals.

  13. Fractional Electron Loss in Approximate DFT and Hartree-Fock Theory.

    PubMed

    Peach, Michael J G; Teale, Andrew M; Helgaker, Trygve; Tozer, David J

    2015-11-10

    Plots of electronic energy vs electron number, determined using approximate density functional theory (DFT) and Hartree-Fock theory, are typically piecewise convex and piecewise concave, respectively. The curves also commonly exhibit a minimum and maximum, respectively, in the neutral → anion segment, which lead to positive DFT anion HOMO energies and positive Hartree-Fock neutral LUMO energies. These minima/maxima are a consequence of using basis sets that are local to the system, preventing fractional electron loss. Ground-state curves are presented that illustrate the idealized behavior that would occur if the basis set were to be modified to enable fractional electron loss without changing the description in the vicinity of the system. The key feature is that the energy cannot increase when the electron number increases, so the slope cannot be anywhere positive, meaning frontier orbital energies cannot be positive. For the convex (DFT) case, the idealized curve is flat beyond a critical electron number such that any additional fraction of an electron added to the system is unbound. The anion HOMO energy is zero. For the concave (Hartree-Fock) case, the idealized curve is flat up to some critical electron number, beyond which it curves down to the anion energy. A minimum fraction of an electron is required before any binding occurs, but beyond that, the full fraction abruptly binds. The neutral LUMO energy is zero. Approximate DFT and Hartree-Fock results are presented for the F → F(-) segment, and results approaching the idealized behavior are recovered for highly diffuse basis sets. It is noted that if a DFT calculation using a highly diffuse basis set yields a negative LUMO energy then a fraction of an electron must bind and the electron affinity must be positive, irrespective of whether an electron binds experimentally. This is illustrated by calculations on Ne → Ne(-).

  14. Hardware efficient implementation of DFT using an improved first-order moments based cyclic convolution structure

    NASA Astrophysics Data System (ADS)

    Xiong, Jun; Liu, J. G.; Cao, Li

    2015-12-01

    This paper presents hardware efficient designs for implementing the one-dimensional (1D) discrete Fourier transform (DFT). Once DFT is formulated as the cyclic convolution form, the improved first-order moments-based cyclic convolution structure can be used as the basic computing unit for the DFT computation, which only contains a control module, a barrel shifter and (N-1)/2 accumulation units. After decomposing and reordering the twiddle factors, all that remains to do is shifting the input data sequence and accumulating them under the control of the statistical results on the twiddle factors. The whole calculation process only contains shift operations and additions with no need for multipliers and large memory. Compared with the previous first-order moments-based structure for DFT, the proposed designs have the advantages of less hardware consumption, lower power consumption and the flexibility to achieve better performance in certain cases. A series of experiments have proven the high performance of the proposed designs in terms of the area time product and power consumption. Similar efficient designs can be obtained for other computations, such as DCT/IDCT, DST/IDST, digital filter and correlation by transforming them into the forms of the first-order moments based cyclic convolution.

  15. Application of the modified additivity rule to the calculation of electron-impact ionization cross sections of complex molecules

    SciTech Connect

    Deutsch, H.; Becker, K.; Basner, R.; Schmidt, M.; Maerk, T.D.

    1998-11-05

    This paper describes the application of the modified additivity rule (MAR) to the calculation of total (counting) electron-impact ionization cross sections of complex molecules with sum formulas of the form A{sub x},B{sub y}, A{sub x},B{sub y},C{sub z}, and A{sub p},B{sub s}C{sub t}D{sub u}. The MAR incorporates weighting factors for the contributions to the molecular ionization cross section from the ionization cross sections of the constituent atoms, which depend explicitly on the atomic radii and the effective number of atomic electrons except for a few special cases (hydrides where the other constituent atom has a radius smaller than the radius of the H atom and species where both constituent atoms have radii smaller than the radius of the H atom), where the weighting factors depend only on the atomic radii, i.e., on geometric effects. A comprehensive comparison of the predictions of the modified additivity rule with available experimental data and with other theoretical predictions is presented.

  16. Resonance scattering and radiation force calculations for an elastic cylinder using the translational addition theorem for cylindrical wave functions

    SciTech Connect

    Mitri, F. G.

    2015-09-15

    The standard Resonance Scattering Theory (RST) of plane waves is extended for the case of any two-dimensional (2D) arbitrarily-shaped monochromatic beam incident upon an elastic cylinder with arbitrary location using an exact methodology based on Graf’s translational addition theorem for the cylindrical wave functions. The analysis is exact as it does not require numerical integration procedures. The formulation is valid for any cylinder of finite size and material that is immersed in a nonviscous fluid. Partial-wave series expansions (PWSEs) for the incident, internal and scattered linear pressure fields are derived, and the analysis is further extended to obtain generalized expressions for the on-axis and off-axis acoustic radiation force components. The wave-fields are expressed using generalized PWSEs involving the beam-shape coefficients (BSCs) and the scattering coefficients of the cylinder. The off-axial BSCs are expressed analytically in terms of an infinite PWSE with emphasis on the translational offset distance d. Numerical computations are considered for a zeroth-order quasi-Gaussian beam chosen as an example to illustrate the analysis. Acoustic resonance scattering directivity diagrams are calculated by subtracting an appropriate background from the expression of the scattered pressure field. In addition, computations for the radiation force exerted on an elastic cylinder centered on the axis of wave propagation of the beam, and shifted off-axially are analyzed and discussed.

  17. Resonance scattering and radiation force calculations for an elastic cylinder using the translational addition theorem for cylindrical wave functions

    NASA Astrophysics Data System (ADS)

    Mitri, F. G.

    2015-09-01

    The standard Resonance Scattering Theory (RST) of plane waves is extended for the case of any two-dimensional (2D) arbitrarily-shaped monochromatic beam incident upon an elastic cylinder with arbitrary location using an exact methodology based on Graf's translational addition theorem for the cylindrical wave functions. The analysis is exact as it does not require numerical integration procedures. The formulation is valid for any cylinder of finite size and material that is immersed in a nonviscous fluid. Partial-wave series expansions (PWSEs) for the incident, internal and scattered linear pressure fields are derived, and the analysis is further extended to obtain generalized expressions for the on-axis and off-axis acoustic radiation force components. The wave-fields are expressed using generalized PWSEs involving the beam-shape coefficients (BSCs) and the scattering coefficients of the cylinder. The off-axial BSCs are expressed analytically in terms of an infinite PWSE with emphasis on the translational offset distance d. Numerical computations are considered for a zeroth-order quasi-Gaussian beam chosen as an example to illustrate the analysis. Acoustic resonance scattering directivity diagrams are calculated by subtracting an appropriate background from the expression of the scattered pressure field. In addition, computations for the radiation force exerted on an elastic cylinder centered on the axis of wave propagation of the beam, and shifted off-axially are analyzed and discussed.

  18. A DFT-D study of structural and energetic properties of TiO2 modifications

    NASA Astrophysics Data System (ADS)

    Moellmann, Jonas; Ehrlich, Stephan; Tonner, Ralf; Grimme, Stefan

    2012-10-01

    The structures and relative energies of the three naturally occurring modifications of titanium dioxide (rutile, brookite and anatase) were investigated. For an accurate description, atom-pairwise dispersion-corrected density functional theory (DFT-D) was applied. The DFT-D3 scheme was extended non-empirically to improve the description of Ti atoms in bulk systems. New dispersion coefficients were derived from TDDFT calculations for electrostatically embedded TiO2 clusters. The dispersion coefficient {C}_{6}^{{TiTi}} is reduced by a factor of 18 compared to the free atom. The three TiO2 modifications were optimized in periodic plane-wave calculations with dispersion-corrected GGA (PBE, revPBE) and hybrid density functionals (PBE0, revPBE0). The calculated lattice parameters are in good agreement with experimental data, in particular the dispersion-corrected PBE0 and revPBE0 hybrid functionals. Although the observed relative stabilities could not be reproduced in all cases, dispersion corrections improve the results. For an accurate description of bulk metal oxides, London dispersion is a prominent force that should not be neglected when energies and structures are computed with DFT. Additionally, the influence of dispersion interactions on the relaxation of the TiO2(110) surface is investigated.

  19. Assessment of DFT methods for computing activation energies of Mo/W-mediated reactions.

    PubMed

    Hu, Lianrui; Chen, Hui

    2015-10-13

    Using high level ab initio coupled cluster calculations as reference, the performances of 15 commonly used density functionals (DFs) on activation energy calculations for typical Mo/W-mediated reactions have been systematically assessed for the first time in this work. The selected representative Mo/W-mediated reactions cover a wide range from enzymatic reactions to organometallic reactions, which include Mo-catalyzed aldehyde oxidation (aldehyde oxidoreductase), Mo-catalyzed dimethyl sulfoxide (DMSO) reduction (DMSO reductase), W-catalyzed acetylene hydration (acetylene hydratase), Mo/W-mediated olefin metathesis, Mo/W-mediated olefin epoxidation, W-mediated alkyne metathesis, and W-mediated C-H bond activation. Covering both Mo- and W-mediated reactions, four DFs of B2GP-PLYP, M06, B2-PLYP, and B3LYP are uniformly recommended with and without DFT empirical dispersion correction. Among these four DFs, B3LYP is notably improved in performance by DFT empirical dispersion correction. In addition to the absolute value of calculation error, if the trend of DFT results is also a consideration, B2GP-PLYP, B2-PLYP, and M06 keep better performance than other functionals tested and constitute our final recommendation of DFs for both Mo- and W-mediated reactions. PMID:26574251

  20. Gamma-point lattice free energy estimates from O1 force calculations.

    PubMed

    Voss, Johannes; Vegge, Tejs

    2008-05-14

    We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum of the phonon eigenvectors obtained from a fast-relative to, e.g., density-functional theory (DFT)-Hessian calculation using interatomic potentials. These potentials are based here on effective charges obtained from a DFT calculation of the ground state electronic charge density but could also be based on other, e.g., empiric approaches.

  1. Using DFT Methods to Study Activators in Optical Materials

    SciTech Connect

    Du, Mao-Hua

    2015-08-17

    Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for new materials. DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn4+ activated red phosphors, scintillators activated by Ce3+, Eu2+, Tl+, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.

  2. Using DFT Methods to Study Activators in Optical Materials

    DOE PAGES

    Du, Mao-Hua

    2015-08-17

    Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for new materials.more » DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn4+ activated red phosphors, scintillators activated by Ce3+, Eu2+, Tl+, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.« less

  3. Adaptive DFT-based Interferometer Fringe Tracking

    NASA Technical Reports Server (NTRS)

    Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

    2004-01-01

    An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) observatory at Mt. Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on off-line data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 2.0 milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse.

  4. Understanding density functional theory (DFT) and completing it in practice

    SciTech Connect

    Bagayoko, Diola

    2014-12-15

    We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.

  5. Semiempirical and DFT Investigations of the Dissociation of Alkyl Halides

    ERIC Educational Resources Information Center

    Waas, Jack R.

    2006-01-01

    Enthalpy changes corresponding to the gas phase heats of dissociation of 12 organic halides were calculated using two semiempirical methods, the Hartree-Fock method, and two DFT methods. These calculated values were compared to experimental values where possible. All five methods agreed generally with the expected empirically known trends in the…

  6. TD-DFT study of the pKa∗ for coumarins

    NASA Astrophysics Data System (ADS)

    Houari, Ymène; Jacquemin, Denis; Laurent, Adèle D.

    2013-09-01

    The excited state acid dissociation constants (pKa∗) of a panel of five coumarins have been studied using several PCM-TD-DFT protocols including both vibrational and state-specific (SS) effects. The pKa∗ have been calculated using the excited state thermodynamical cycle and the Förster cycle. For this set of compounds the addition of explicit water molecules does not improve the computed acidity constants computed with the thermodynamical cycle. However, the addition of explicit water molecules to the PCM model apparently improves the quality of the optical spectra and hence the Förster estimates. State specific effects do not bring significant improvements in this case.

  7. "Additive" cooperativity of hydrogen bonds in complexes of catechol with proton acceptors in the gas phase: FTIR spectroscopy and quantum chemical calculations.

    PubMed

    Varfolomeev, Mikhail A; Klimovitskii, Alexander E; Abaidullina, Dilyara I; Madzhidov, Timur I; Solomonov, Boris N

    2012-06-01

    Experimental study of hydrogen bond cooperativity in hetero-complexes in the gas phase was carried out by IR-spectroscopy method. Stretching vibration frequencies of O-H groups in phenol and catechol molecules as well as of their complexes with nitriles and ethers were determined in the gas phase using a specially designed cell. O-H groups experimental frequency shifts in the complexes of catechol induced by the formation of intermolecular hydrogen bonds are significantly higher than in the complexes of phenol due to the hydrogen bond cooperativity. It was shown that the cooperativity factors of hydrogen bonds in the complexes of catechol with nitriles and ethers in the gas phase are approximately the same. Quantum chemical calculations of the studied systems have been performed using density functional theory (DFT) methods. It was shown, that theoretically obtained cooperativity factors of hydrogen bonds in the complexes of catechol with proton acceptors are in good agreement with experimental values. Cooperative effects lead to a strengthening of intermolecular hydrogen bonds in the complexes of catechol on about 30%, despite the significant difference in the proton acceptor ability of the bases. The analysis within quantum theory of atoms in molecules was carried out for the explanation of this fact.

  8. DFT investigations of structural and electronic properties of gallium arsenide (GaAs)

    NASA Astrophysics Data System (ADS)

    Anua, N. Najwa; Ahmed, R.; Saeed, M. A.; Shaari, A.; Haq, Bakhtiar Ul

    2012-09-01

    First principles calculations for structural and electronic properties of GaAs have been reported using a full potential linearized augmented plane wave (FP-LAPW) scheme of calculations developed within density functional theory (DFT). We use in this study local density approximation (LDA), Perdew-Burke-Ernzerhof parameterized generalized gradient approximation (PBE-GGA), Wu-Cohen parameterized GGA (WC-GGA) executed in WIEN2k code. In addition, to calculate band structure with high accuracy we used modified Becke-Johnson exchange potential (MBJ) + LDA approach. Our calculated lattice constant with GGA-WC is in good agreement to experimental value than LDA and PBE-GGA. Whereas our calculations for the band structure show that MBJ+ LDA approach gives much better results for band gap value as compared to other exchange correlation approaches.

  9. Assessment of DFT functionals with fluorine-fluorine coupling constants

    NASA Astrophysics Data System (ADS)

    García de la Vega, J. M.; San Fabián, J.

    2015-07-01

    Density functional theory (DFT) calculations of nuclear magnetic resonance (NMR) spin-spin coupling constants (SSCCs) provide an important contribution for understanding experimentally observed values. It is known that calculated SSCCs using DFT methods correlate well with those experimentally measured. Unlike most of SSCCs, in fluorine compounds, fluorine-fluorine SSCC JFF shows that the Fermi contact (FC) term is not dominant, particularly for JFF in polyfluorinated organic molecules. In order to devise a DFT approach that would correctly reproduce the variation of SSCCs within a series of fluorine compounds, we test several DFT-based approaches, using different exchange and correlation functionals. Isotropic contributions to NMR fluorine-fluorine coupling constants (FC, spin-dipolar, SD, paramagnetic spin-orbit, PSO, and diamagnetic spin-orbit, DSO) have been calculated. Results show that DFT methods give appropriate values for nJFF (n = 4 to 7), while for geminal and vicinal JFF present large deviations from experimental values. For the latter SSCCs (2JFF and 3JFF), the four contributions (FC, SD, PSO and DSO) are analysed as a function of the local and nonlocal exchange in 1,1- and 1,2-difluoroethylene. Although FC term is not dominant for these SSCCs, the variation of this contribution with exchange is remarkable. On the other hand, SD and PSO contributions can be suitably computed without and with exact exchange, respectively. This article is dedicated to the memory of Prof. N. C. Handy, whose contributions to the development of Theoretical Chemistry have been widely recognized.

  10. Vibrational spectroscopic studies, NMR, HOMO-LUMO, NLO and NBO analysis of 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole with use X-ray diffractions and DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Tinmaz, Feyza; Dege, Necmi; Ilhan, Ilhan Ozer

    2016-03-01

    The crystal and molecular structure of the title compound, 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole, was reported and confirmed by single crystal X-ray diffraction and spectroscopic data. The structure, geometry optimization, vibrational frequencies and nuclear magnetic resonance were also investigated. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (ED) in the σ∗ and π∗ antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. Satisfactory theoretical aspects were made for the stable conformer of the molecule using density functional theory DFT-B3LYP methods with the 6-311G++(d,p) basis set.

  11. Molecular structure and charge transfer contributions to nonlinear optical property of 2-Methyl-4-nitroaniline: A DFT study

    NASA Astrophysics Data System (ADS)

    Jasmine, G. Femina; Amalanathan, M.; Roy, S. Dawn Dharma

    2016-05-01

    The Charge transfer contributions to the second-order nonlinear optical properties of 2-Methyl-4-nitroaniline have been performed by means of DFT computation. The vibrational contribution studies of 2-Methyl-4-nitroaniline have also been performed using FTIR, FT-Raman analysis. More support on the experimental findings were added from the quantum chemical studies performed with DFT (B3LYP) method using 6-311++G(d,p)basis sets. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. The HOMO and LUMO analysis reveals the possibility of charge transfer within the molecule. The first order hyperpolarizability (α0) and related properties (β,α0 and Δα) of 2-Methyl-4-nitroaniline were calculated. In addition, molecular electrostatic potential (MEP), charge analysis also were investigated using theoretical calculations.

  12. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    NASA Astrophysics Data System (ADS)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  13. Simultaneous presence of (Si{sub 3}O{sub 10}){sup 8−} and (Si{sub 2}O{sub 7}){sup 6−} groups in new synthetic mixed sorosilicates: BaY{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}) and isotypic compounds, studied by single-crystal X-ray diffraction, Raman spectroscopy and DFT calculations

    SciTech Connect

    Wierzbicka-Wieczorek, Maria; Többens, Daniel M.; Kolitsch, Uwe; Tillmanns, Ekkehart

    2013-11-15

    Three new, isotypic silicate compounds, BaY{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}), SrYb{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}) and SrSc{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}), were synthesized using high-temperature flux growth techniques, and their crystal structures were solved from single-crystal X-ray intensity data: monoclinic, P2{sub 1}/m, with a=5.532(1)/5.469(1)/5.278(1), b=19.734(4)/19.447(4)/19.221(4), c=6.868(1)/6.785(1)/6.562(1) Å, β=106.53(3)/106.20(3)/106.50(3)°, V=718.8(2)/693.0(2)/638.3(2) Å{sup 3}, R(F)=0.0225/0.0204/0.0270, respectively. The topology of the novel structure type contains isolated horseshoe-shaped Si{sub 3}O{sub 10} groups (Si–Si–Si=93.15–95.98°), Si{sub 2}O{sub 7} groups (Si–O{sub bridge}–Si=180°, symmetry-restricted) and edge-sharing M(1)O{sub 6} and M(2)O{sub 6} octahedra. Single-crystal Raman spectra of the title compounds were measured and compared with Raman spectroscopic data of chemically and topologically related disilicates and trisilicates, including BaY{sub 2}(Si{sub 3}O{sub 10}) and SrY{sub 2}(Si{sub 3}O{sub 10}). The band assignments are supported by additional theoretical calculation of Raman vibrations by DFT methods. - Graphical abstract: View of BaY{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}) along [100], showing zigzag chains and the tri- and disilicate groups. The unit cell is outlined. Display Omitted - Highlights: • We report a novel interesting crystal structure type for mixed sorosilicates containing Y, Yb, and Sc. • Synthesis of such mixed sorosilicates is possible by a high-temperature flux-growth technique. • Calculation of Raman vibrations by advanced DFT methods allows a considerably improved interpretation of measured Raman spectra.

  14. One component metal sintering additive for {beta}-SiC based on thermodynamic calculation and experimental observations

    SciTech Connect

    Noviyanto, Alfian; Yoon, Dang-Hyok

    2011-08-15

    Graphical abstract: . Standard Gibbs formation free energies vs. temperature for various metal carbides. The heavy line represents the standard Gibbs free energy for {beta}-SiC. The hatched area denotes the typical liquid phase hot pressing temperature of {beta}-SiC (1973-2123 K). Highlights: {yields} Various metal elements were examined as a sintering additive for {beta}-SiC. {yields} Al and Mg enhanced the density significantly without decomposing {beta}-SiC, as predicted by thermodynamic simulation. {yields} Cr, Fe, Ta, Ti, V and W additives formed metal carbide and/or silicide compounds by decomposing {beta}-SiC. {yields} This approach would be useful for selecting effective sintering additive for high temperature ceramics. -- Abstract: Various types of metals were examined as sintering additives for {beta}-SiC by considering the standard Gibbs formation free energy and vapor pressure under hot pressing conditions (1973-2123 K), particularly for applications in nuclear reactors. Metallic elements having the low long-term activation under neutron irradiation condition, such as Cr, Fe, Ta, Ti, V and W, as well as widely used elements, Al, Mg and B, were considered. The conclusions drawn from thermodynamic considerations were compared with the experimental observations. Al and Mg were found to be effective sintering additives, whereas the others were not due to the formation of metal carbides or silicides from the decomposition of SiC under hot pressing conditions.

  15. Electronic and mechanical properties of single-walled carbon nanotubes interacting with epoxy: A DFT study

    NASA Astrophysics Data System (ADS)

    Ghorbanzadeh Ahangari, M.; Fereidoon, A.; Jahanshahi, M.; Ganji, M. D.

    2013-02-01

    Carbon nanotubes exhibit extremely high stiffness and strength, and are regarded as perfect reinforcing fibers for developing a new class of nanocomposites. The use of quantum mechanical calculations is more accurate than other atomistic methods for studying the interface and mechanical properties on the nanoscale for such materials. Ab initio calculations based on density functional theory (DFT) are employed to investigate the interaction properties of epoxy on typical zigzag and armchair single-walled carbon nanotubes (SWCNTs). The interaction energies for epoxy monomers with different orientations on SWCNTs are investigated. The results indicate that epoxy is weakly bound to the outer surface of the considered nanotubes and that the obtained interaction energy values are typical for physisorption. In addition, the influence of different defects (Stone-Wale, one- and two-atom vacancies) and functional groups (-NH2 and -OH) on the interaction properties between the epoxy and the respective SWCNTs has been investigated. Our results indicate that the interaction energy between the SWCNT and the epoxy decreased as the number of defects increased. In addition, the strongest interaction was observed for the SWCNT functionalized with the -OH group. Therefore, DFT calculations were performed to investigate the effect of the -OH functional group on the mechanical properties of SWCNTs interacting with epoxy.

  16. Synthesis, crystal structure, spectral analysis and DFT computational studies on a novel isoindoline derivative

    NASA Astrophysics Data System (ADS)

    Evecen, Meryem; Duru, Gülcan; Tanak, Hasan; Ağar, Ayşen Alaman

    2016-08-01

    The isoindoline compound, 2-(3-chloro-4-(4-chlorophenoxy)phenyl)isoindoline-1,3-dione, has been synthesized and characterized by FT-IR, UV-Vis and X-ray single-crystal determination. The compound crystallizes in the monoclinic space group P21/c with a = 20.441 (3) Å, b = 4.0258 (4) Å, c = 23.836 (2) Å, β = 121.918 (7)° and Z = 4. The molecular structure and vibrational frequencies in the ground state were calculated using the density functional theory method (B3LYP) with 6-311++G(d,p) basis set. The results obtained from the optimization and vibrational analyses are agree with the experimental results. Using the TD-DFT method, electronic absorption spectra have been calculated, and they are compatible with the experimental ones. The electric dipole moment (μ), polarizability (α) and the first hyperpolarizability (β) values of the compound were calculated theoretically. The first hyperpolarizability of the molecule shows that the compound can be a good candidate of nonlinear optical material. In addition, DFT calculations of the compound, atomic charges, molecular electrostatic potential and thermodynamic properties were also performed at B3LYP/6-311++G(d,p) level of theory.

  17. Experimental and DFT studies of the conversion of ethanol and acetic acid on PtSn-based catalysts.

    PubMed

    Alcala, Rafael; Shabaker, John W; Huber, George W; Sanchez-Castillo, Marco A; Dumesic, James A

    2005-02-17

    Reaction kinetics studies were conducted for the conversions of ethanol and acetic acid over silica-supported Pt and Pt/Sn catalysts at temperatures from 500 to 600 K. Addition of Sn to Pt catalysts inhibits the decomposition of ethanol to CO, CH4, and C2H6, such that PtSn-based catalysts are active for dehydrogenation of ethanol to acetaldehyde. Furthermore, PtSn-based catalysts are selective for the conversion of acetic acid to ethanol, acetaldehyde, and ethyl acetate, whereas Pt catalysts lead mainly to decomposition products such as CH4 and CO. These results are interpreted using density functional theory (DFT) calculations for various adsorbed species and transition states on Pt(111) and Pt3Sn(111) surfaces. The Pt3Sn alloy slab was selected for DFT studies because results from in situ (119)Sn Mössbauer spectroscopy and CO adsorption microcalorimetry of silica-supported Pt/Sn catalysts indicate that Pt-Sn alloy is the major phase present. Accordingly, results from DFT calculations show that transition-state energies for C-O and C-C bond cleavage in ethanol-derived species increase by 25-60 kJ/mol on Pt3Sn(111) compared to Pt(111), whereas energies of transition states for dehydrogenation reactions increase by only 5-10 kJ/mol. Results from DFT calculations show that transition-state energies for CH3CO-OH bond cleavage increase by only 12 kJ/mol on Pt3Sn(111) compared to Pt(111). The suppression of C-C bond cleavage in ethanol and acetic acid upon addition of Sn to Pt is also confirmed by microcalorimetric and infrared spectroscopic measurements at 300 K of the interactions of ethanol and acetic acid with Pt and PtSn on a silica support that had been silylated to remove silanol groups. PMID:16851198

  18. Identification of mixed bromidochloridotellurate anions in disordered crystal structures of (bdmim)2[TeX2Y4] (X, Y=Br, Cl; bdmim=1-butyl-2,3-dimethylimidazolium) by combined application of Raman spectroscopy and solid-state DFT calculations.

    PubMed

    Närhi, Sari M; Kutuniva, Johanna; Lajunen, Marja K; Lahtinen, Manu K; Tuononen, Heikki M; Karttunen, Antti J; Oilunkaniemi, Raija; Laitinen, Risto S

    2014-01-01

    The discrete mixed [TeBrxCl6-x](2-) anions in their disordered crystal structures have been identified by using the phases prepared by the reaction of 1-butyl-2,3-dimethylimidazolium halogenides (bdmim)X with tellurium tetrahalogenides TeX4 (X=Cl, Br) as examples. Homoleptic (bdmim)2[TeX6] [X=Cl (1), Br (2)] and mixed (bdmim)2[TeBr2Cl4] (3), and (bdmim)2[TeBr4Cl2] (4) are formed depending on the choice of the reagents, and their crystal structures have been determined by single-crystal X-ray diffraction. The coordination environments of tellurium in all hexahalogenidotellurates are almost octahedral. Because of the crystallographic disorder, the mixed [TeBr2Cl4](2-) and [TeBr4Cl2](2-) anions in 3 and 4 cannot be identified in their crystal structures. Pawley refinement of the X-ray powder diffraction patterns of 1-4 indicates the presence of single phases in all four products. The solid state Raman spectra of 1-4 were assigned with help of DFT calculations that were performed both for the discrete anions in vacuum and for the complete crystal structures employing periodic boundary conditions. The fundamental vibrations of the homoleptic [TeX6](2-) (X=Cl, Br) anions could be well reproduced by the solid-state DFT computations and enabled a complete assignment of the Raman spectra. While the presence of cis-isomers in both [TeBr2Cl4](2-) and [TeBr4Cl2](2-) could be inferred by the computed fundamental vibrations, that of trans-isomers among the reaction products is, however, also possible. The pathway of the formation of [TeX4Y2](2-) isomers from TeX4 and Y(-) (X, Y=Cl, Br) was also explored by DFT calculations both in vacuum and in solution and indicated that both reactions afforded 80 mol% of cis-isomers and 20 mol% of trans-isomers.

  19. Assessing clinical outcomes of patients with acute calculous cholecystitis in addition to the Tokyo grading: a retrospective study.

    PubMed

    Cheng, Wei-Chun; Chiu, Yen-Cheng; Chuang, Chiao-Hsiung; Chen, Chiung-Yu

    2014-09-01

    The management of acute cholecystitis is still based on clinical expertise. This study aims to investigate whether the outcome of acute cholecystitis can be related to the severity criteria of the Tokyo guidelines and additional clinical comorbidities. A total of 103 patients with acute cholecystitis were retrospectively enrolled and their medical records were reviewed. They were all classified according to therapeutic modality, including early cholecystectomy and antibiotic treatment with or without percutaneous cholecystostomy. The impact of the Tokyo guidelines and the presence of comorbidities on clinical outcome were assessed by univariate and multivariate regression analyses. According to Tokyo severity grading, 48 patients were Grade I, 31 patients were Grade II, and 24 patients were Grade III. The Grade III patients had a longer hospital stay than Grade II and Grade I patients (15.2 days, 9.2 days, and 7.3 days, respectively, p < 0.05). According to multivariate analysis, patients with Grade III Tokyo severity, higher Charlson's Comorbidity Score, and encountering complications had a longer hospital stay. Based on treatment modality, surgeons selected the patients with less severity and fewer comorbidities for cholecystectomy, and these patients had a shorter hospital stay. In addition to the grading of the Tokyo guidelines, comorbidities had an additional impact on clinical outcomes and should be an important consideration when making therapeutic decisions.

  20. Does DFT-SAPT method provide spectroscopic accuracy?

    SciTech Connect

    Shirkov, Leonid; Makarewicz, Jan

    2015-02-14

    Ground state potential energy curves for homonuclear and heteronuclear dimers consisting of noble gas atoms from He to Kr were calculated within the symmetry adapted perturbation theory based on the density functional theory (DFT-SAPT). These potentials together with spectroscopic data derived from them were compared to previous high-precision coupled cluster with singles and doubles including the connected triples theory calculations (or better if available) as well as to experimental data used as the benchmark. The impact of midbond functions on DFT-SAPT results was tested to study the convergence of the interaction energies. It was shown that, for most of the complexes, DFT-SAPT potential calculated at the complete basis set (CBS) limit is lower than the corresponding benchmark potential in the region near its minimum and hence, spectroscopic accuracy cannot be achieved. The influence of the residual term δ(HF) on the interaction energy was also studied. As a result, we have found that this term improves the agreement with the benchmark in the repulsive region for the dimers considered, but leads to even larger overestimation of potential depth D{sub e}. Although the standard hybrid exchange-correlation (xc) functionals with asymptotic correction within the second order DFT-SAPT do not provide the spectroscopic accuracy at the CBS limit, it is possible to adjust empirically basis sets yielding highly accurate results.

  1. Liquid-liquid extraction of metal ions, DFT and TD-DFT analysis of some 1,2,4-triazole Schiff Bases with high selectivity for Pb(II) and Fe(II)

    NASA Astrophysics Data System (ADS)

    Khoutoul, Mohamed; Lamsayah, Morad; Al-blewi, Fawzia F.; Rezki, Nadjet; Aouad, Mohamed Reda; Mouslim, Messali; Touzani, Rachid

    2016-06-01

    Liquid-liquid extraction of metal ions using some 1,2,4-triazole Schiff base derivatives as new extractants was studied. Fe2+, Zn2+, Cu2+, Co2+, Cd2+ and Pb2+ were extracted from the aqueous phase into the organic phase and the extractability for each metal ion was determined by atomic absorption. Interestingly, a competitive extraction was also investigated and then examined at different pH in order to explore the effect of the different substituent groups on metal extraction. Accordingly, high selectivity towards Fe2+ (90.1%) and Pb2+ (94.3%) provided respectively by the presence of electron withdrawing group and electron donor group was attained. In addition, geometry optimizations of the ground and excited-states of the ligands in order to get better insight into the geometry and the electronic structure were carried out by means of DFT and TD-DFT calculations.

  2. How Well Can Kohn-Sham DFT Describe the HO2 + O3 Reaction?

    PubMed

    Viegas, Luís P; Branco, Adriana; Varandas, António J C

    2010-09-14

    In a previous work (J. Chem. Theory Comput. 2010, 6, 412) we reported an ab initio investigation of the reaction between ozone and the hydroperoxyl radical. The studies on this atmospheric reaction are here continued with an evaluation of different exchange-correlation functionals (all rungs of "Jacob's ladder" of density functional approximations are represented) in Kohn-Sham DFT calculations. We focus on the comparison between the barrier heights of the oxygen- and hydrogen-abstraction mechanisms here calculated with the ones previously obtained at the CASPT2(11,11)/AVTZ level. The comparison is also extended to the remaining stationary points. Additionally, a relation between the fraction of exact exchange of one-parameter hybrid functionals and the imaginary frequency of a saddle point is developed, originating three new functionals that are also used in the present benchmark calculations. PMID:26616077

  3. Applications of DFT to Lanthanides and Precious Metal Complexes

    NASA Astrophysics Data System (ADS)

    Balboa, Alex; Hurley, Margaret; Jenkins, Amanda; None Collaboration; None Collaboration

    2014-03-01

    Density functional theory is widely used for computational characterization of novel materials. While study of materials containing the lighter elements is commonplace, the application of these methods to the bottom of the periodic table, including the lanthanides and the heavier precious metals such as Osmium, requires careful validation. Here we present results of recent quantum mechanical studies to characterize Lanthanide/Graphene Materials and assess the suitability of DFT for these systems. Additionally, we will present recent work on similar application of DFT to characterize Os bipridine complexes.

  4. Design Techniques for Uniform-DFT, Linear Phase Filter Banks

    NASA Technical Reports Server (NTRS)

    Sun, Honglin; DeLeon, Phillip

    1999-01-01

    Uniform-DFT filter banks are an important class of filter banks and their theory is well known. One notable characteristic is their very efficient implementation when using polyphase filters and the FFT. Separately, linear phase filter banks, i.e. filter banks in which the analysis filters have a linear phase are also an important class of filter banks and desired in many applications. Unfortunately, it has been proved that one cannot design critically-sampled, uniform-DFT, linear phase filter banks and achieve perfect reconstruction. In this paper, we present a least-squares solution to this problem and in addition prove that oversampled, uniform-DFT, linear phase filter banks (which are also useful in many applications) can be constructed for perfect reconstruction. Design examples are included illustrate the methods.

  5. Determination of the origin of stereoselectivity in multiple-transition-state reactions using DFT calculations: enantioselective synthesis of homoallylic alcohols from aliphatic methyl ketones via an auxiliary-mediated allylation.

    PubMed

    Tietze, Lutz F; Kinzel, Tom; Schmatz, Stefan

    2008-04-01

    Computational investigations on the highly stereoselective allylation of butanone in the presence of a chiral norpseudoephedrine-derived auxiliary have been performed. They suggest an SN1-type mechanism via the attack of allyltrimethylsilane to an intermediately formed oxocarbenium ion. The identification of preferred transition states (TSs) leads to a straightforward rationalization of the observed selectivity which can be extended to analogues of the auxiliary. A screening process has been devised to select 61 potentially relevant TSs from a total of almost 300 theoretically possible TSs. Final results were obtained from gas-phase calculations employing the B3LYP/6-31+G(d) level of theory as well as in dichloromethane solution using the B3LYP/6-311++G(2d,p)//B3LYP/6-31+G(d) level of theory in combination with polarizable continuum model and the UAKS set of radii. The agreement of theoretically predicted and experimentally observed selectivities is very good in both cases. However, the relative energy differences for several relevant TSs differ significantly when going from gas phase to solution, thus illustrating the necessity of performing calculations in solution to draw correct conclusions. PMID:18331031

  6. The biomolecule of 5-bromocytosine: FT-IR and FT-Raman spectra and DFT calculations. Identification of the tautomers in the isolated state and simulation the spectra in the solid state.

    PubMed

    Alcolea Palafox, M; Rastogi, V K; Kumar, Satendra; Joe, Hubert

    2013-07-01

    An accurate assignment of the IR spectrum in Ar matrix of 5-bromocytosine and of the IR and Raman spectra in the solid state was carried out. For this purpose Density functional calculations (DFTs) were performed to clarify wavenumber assignments of the experimental observed bands. The calculated values were scaled using scaling equations and they were compared with IR and Raman experimental data. Good reproduction of the experimental wavenumbers is obtained and the% error is very small in the majority of cases. In the isolated state all the tautomer forms of 5-bromocytosine were determined and optimized. The wavenumbers corresponding to C1 and C2b tautomers were identified and assigned in the IR experimental spectrum reported in Ar matrix. Our study confirms the existence of at least two tautomers, the amino-oxo and the amino-hydroxy in the isolated state. In the solid state the FT-IR and FT-Raman spectra of 5-bromocytosine in the powder form were recorded in the region 400-4000 cm(-1) and 50-3500 cm(-1), respectively. The unit cell found in the crystal was simulated as a tetramer form in three tautomers. Thus, it has been possible to assign all the 33 normal modes of vibration. The study indicates that the features, that are the characteristic of the vibrational spectra of cytosine, are retained by the spectra of 5-bromocytosine and it exists in the solid phase in the amino-oxo form.

  7. A comparative study of 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under high pressures using Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Zeng, Yangyang; Song, Yunfei; Yu, Guoyang; Zheng, Xianxu; Guo, Wencan; Zhao, Jun; Yang, Yanqiang

    2016-09-01

    High pressure Raman experiment was performed to compare RDX and HMX crystals. Ab initio calculations using B3LYP Density Functional Theory method with Sadlej's medium-sized polarized basis set (SadlejpVTZ) were carried out for Caae RDX and 1,5-diaxial-3,7-diequatorial chair HMX molecules. Our calculations and measured Raman vibrational spectra reveal both molecules have similarities on bonding and vibrational properties at ambient pressure. However, high pressure responses for both molecules aren't the same. For RDX, at pressure near 4 GPa, a number of changes become apparent in the Raman spectra, such as modes splitting, intensity modification, and discontinuity of pressure-dependence of frequency shifts, which are consistent with previous experiment and believed to associate with α-γ phase transition. For HMX, only slight conformational deformation involving NO2 group was observed, and was considered as an onset of β-ε phase transition. It is proposed that the markedly different behavior under high pressure for these two molecules results from different molecular packing in unit cell.

  8. Partial vs. integer electron transfer in molecular assemblies: On the importance of multideterminant theoretical description and the necessity to find a solution within DFT

    NASA Astrophysics Data System (ADS)

    Geskin, Victor; Stadler, Robert; Cornil, Jérôme

    2015-01-01

    Nonequilibrium Green's function techniques (NEGF) combined with density functional theory (DFT) calculations have become a standard tool for the description of electron transport through single molecule nanojunctions in the coherent tunneling (CT) regime. However, the applicability of these methods for transport in the Coulomb blockade (CB) regime is questionable. For a molecular assembly model, with multideterminant calculations as a benchmark, we show how a closed-shell ansatz, the usual ingredient of mean-field methods, fails to properly describe the step like electron-transfer characteristic in weakly coupled systems. Detailed analysis of this misbehavior allows us to propose a practical scheme to extract the addition energies in the CB regime for single-molecule junctions from NEGF DFT within the local-density approximation (closed shell). We show also that electrostatic screening effects are taken into account within this simple approach.

  9. Partial vs. integer electron transfer in molecular assemblies: On the importance of multideterminant theoretical description and the necessity to find a solution within DFT

    SciTech Connect

    Geskin, Victor; Cornil, Jérôme; Stadler, Robert

    2015-01-22

    Nonequilibrium Green's function techniques (NEGF) combined with density functional theory (DFT) calculations have become a standard tool for the description of electron transport through single molecule nanojunctions in the coherent tunneling (CT) regime. However, the applicability of these methods for transport in the Coulomb blockade (CB) regime is questionable. For a molecular assembly model, with multideterminant calculations as a benchmark, we show how a closed-shell ansatz, the usual ingredient of mean-field methods, fails to properly describe the step like electron-transfer characteristic in weakly coupled systems. Detailed analysis of this misbehavior allows us to propose a practical scheme to extract the addition energies in the CB regime for single-molecule junctions from NEGF DFT within the local-density approximation (closed shell). We show also that electrostatic screening effects are taken into account within this simple approach.

  10. Thiourea catalyzed organocatalytic enantioselective Michael addition of diphenyl phosphite to nitroalkenes.

    PubMed

    Alcaine, Ana; Marqués-López, Eugenia; Merino, Pedro; Tejero, Tomás; Herrera, Raquel P

    2011-04-21

    Bifunctional thiourea catalyzes the enantioselective Michael addition reaction of diphenyl phosphite to nitroalkenes. This methodology provides a facile access to enantiomerically enriched β-nitrophosphonates, precursors for the preparation of synthetically and biologically useful β-aminophosphonic acids. DFT level of computational calculations invoke the attack of the diphenyl phosphite to the nitroolefin by the Re face, this give light to this scarcely explored process update in the literature. The computational calculations support the absolute configuration obtained in the final adducts.

  11. Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis.

    PubMed

    Afonin, Andrei V; Ushakov, Igor A; Pavlov, Dmitry V; Ivanov, Andrei V; Mikhaleva, Al'bina I

    2010-09-01

    The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer. PMID:20623827

  12. Structure of 1H-2-oxo-2,3-dihydroimidazo[1,2- a]pyridinium perchlorate studied by X-ray diffraction, DFT calculations and by FTIR and NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kowalczyk, I.; Bartoszak-Adamska, E.; Jaskólski, M.; Dega-Szafran, Z.; Szafran, M.

    2010-07-01

    2-Aminopyridine betaine (1-carboxymethyl-2-aminopyridinium inner salt) forms crystalline complexes with HCl, HBr and HClO 4. These complexes on heating in ethanol cyclize to 1H-2-oxo-2,3-dihydroimidazo[1,2- a]pyridinium chloride ( 1Ax), bromide ( 2Ax) and perchlorate ( 3Ax), respectively. Infrared spectra of the 1H-2-oxo-2,3-dihydroimidazo[1,2- a]pyridinium complexes indicate that the length of the N(1)-H···X - hydrogen bond depends on the counter-ions and increases in the order: Cl - < Br - < ClO 4-. In the crystal structure of 3Ax determined by X-ray diffraction, the ClO 4- anion is disordered and the N(1)-H···OClO 3- distance cannot be determined accurately. Three types of cyclic molecules were optimized by the B3LYP/6-31G(d,p) level of theory: type A with N(1)-H⋯X -, type B with N(1)⋯H-X hydrogen bonds and type C with electrostatic interactions between the positively charged nitrogen atom N +(4) and the counter anion (X - = Cl -, Br - or ClO 4-). Correlations between the experimental 1H and 13C NMR chemical shifts ( δexp) and the GIAO/B3LYP/6-31G(d,p) calculated magnetic isotropic shielding tensors ( σcalc) for 3Ao and 3Co,δexp = a + bσcalc, are reported. Tentative assignments of the experimental anharmonic solid state vibrational frequencies of the perchlorate complex, 3Ax, based on the B3LYP/6-31G(d,p) calculated harmonic frequencies, are presented.

  13. First-principles DFT +GW study of oxygen vacancies in rutile TiO2

    NASA Astrophysics Data System (ADS)

    Malashevich, Andrei; Jain, Manish; Louie, Steven G.

    2014-02-01

    We perform first-principles calculations of the quasiparticle defect states, charge transition levels, and formation energies of oxygen vacancies in rutile titanium dioxide. The calculations are done within the recently developed combined DFT +GW formalism, including the necessary electrostatic corrections for the supercells with charged defects. We find the oxygen vacancy to be a negative U defect, where U is the defect electron addition energy. For Fermi level values below ˜2.8 eV (relative to the valence-band maximum), we find the +2 charge state of the vacancy to be the most stable, while above 2.8 eV we find that the neutral charge state is the most stable.

  14. Physicochemical studies of chemosensor imidazole derivatives: DFT based ESIPT process

    NASA Astrophysics Data System (ADS)

    Jayabharathi, Jayaraman; Thanikachalam, Venugopal; Jayamoorthy, Karunamoorthy

    2012-04-01

    A series of substituted imidazoles have been synthesized in very good yield under a solvent free condition using molecular iodine as the catalyst. An excited state intramolecular proton transfer (ESIPT) process in hydroxy imidazole has been studied using emission spectroscopy. DFT calculations on energy, dipole moment, charge distribution of the rotamers in the ground and excited states of the imidazole derivatives have been performed and discussed. DFT analysis about HOMO, HOMO-1, LUMO and LUMO+1 has been carried out and discussed. The energy barrier for the interconversion of two rotamers is too high in the excited state than the ground state that is shown by PES calculation. The molecular electrostatic potential surface (MEP) has also been employed to show the higher electron density at N(3) nitrogen. Fluorescence enhancement has been found in the presence of transition metal ions and this may result from the suppression of radiationless transitions from the n-π* state in the chemosensors.

  15. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3Thermus thermophilus

    PubMed Central

    2016-01-01

    The Fea33+···CuB2+ dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO’s were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea32+···CuB+ DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779–5783) revealed multiple 57Fea32+ and 57Fea33+ components. Moreover, one of the 57Fea33+ components observed at 4.2 K transformed from a proposed “low-spin” state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin 57Fea33+ component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the 57Fea33+ components, and how the coordination and spin states of the Fea33+/2+ and Cu2+/1+ sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB+ site, and they may become potential proton loading sites during the catalytic cycle

  16. Novel and unusual triterpene from Black Cohosh. Determination of structure of 9,10- seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jamróz, Marta K.; Jamróz, Michał H.; Dobrowolski, Jan Cz.; Gliński, Jan A.; Davey, Matthew H.; Wawer, Iwona

    2011-01-01

    A new triterpene xyloside, designated cimipodocarpaside was isolated from a Black Cohosh ( Actea racemosa L.) extract and its structure was elucidated by means of 1H, 13C NMR, IR and Raman spectroscopy supported by B3LYP/6-31G** calculations. The vibrational spectra were interpreted using the PED analysis of 273 fundamentals. Its structure comprises four condensed rings A-D which are 6, 7, 6, and 5-membered, respectively. An oxiirane ring is located in the side chain and a xylose moiety is attached to the A-ring. Comparison of the experimental 13C NMR data with the theoretical chemical shifts of 24 S- and 24 R-cimipodocarpaside isomers revealed that the isolated compound has the 24 S-configuration. Combined spectroscopic and computational studies enabled the determination of the structure of cimipodocarpaside as (24 S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10- seco-9,19-cyclolanost-7(8),9(11),10(19)-trien-3-O-β- D-xylopyranoside. Triterpenes with 7-membered ring were thus far isolated from only Actea podocarpa DC. plants. This is the first report on the isolation of such a compound from Black Cohosh.

  17. O sbnd H⋯O and O sbnd H⋯N hydrogen bonds in the complex of DABCO mono-betaine with p-hydroxybenzoic acid studied by X-ray diffraction, DFT calculations and spectroscopic methods

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2011-08-01

    DABCO mono-betaine (1,4-diazabicyclo[2.2.2]octane-1-acetate) forms a complex with p-hydroxybenzoic acid (HBA) at the 1:1 ratio. The crystals are monoclinic, space group P2 1/ m. The HBA and DABCO mono-betaine molecules are linked into infinite chains through the COOH⋯OOC and O sbnd H⋯N hydrogen bonds of 2.604(1) and 2.771(2) Å, respectively. The DABCO mono-betaine is located on a mirror plane and the HBA molecule lies on this plane. In the structure of the 1:1 complex optimized by the B3LYP/6-31G(d,p) approach, the DABCO ring has a planar conformation, while in the chains formed by two complexes, the DABCO moieties assume the propeller conformations. The FTIR spectrum shows several bands attributed to the O sbnd H, O sbnd H⋯O, O sbnd H⋯N, C dbnd O and COO stretching vibrations. 1H and 13C chemical shifts assignments were confirmed by the magnetic isotropic shielding constants, calculated by the GIAO/B3LYP/6-31G(d,p) approach.

  18. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    C. F. Melius; M. D. Allendorf

    1999-04-01

    In the 1980's, the authors developed a bond-additivity correction procedure for quantum chemical calculations called BAC-MP4, which has proven reliable in calculating the thermochemical properties of molecular species, including radicals as well as stable closed-shell species. New Bond Additivity Correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid DFT/MP2 method, BAC-Hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method due to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-Hybrid and BAC-MP4. The BAC-Hybrid method should scale well for large molecules. The BAC-Hybrid method uses the differences between the DFT and MP2 as an indicator of the method's accuracy, while the BAC-G2 method uses its internal methods (G1 and G2MP2) to provide an indicator of its accuracy. Indications of the average error as well as worst cases are provided for each of the BAC methods.

  19. On the crystal energy and structure of A{sub 2}Ti{sub n}O{sub 2n+1} (A=Li, Na, K) titanates by DFT calculations and neutron diffraction

    SciTech Connect

    Catti, Michele; Pinus, Ilya; Scherillo, Antonella

    2013-09-15

    First-principles quantum-mechanical calculations (CRYSTAL09 code, B3LYP functional) were performed on alkali titanates A{sub 2}Ti{sub n}O{sub 2n+1} with layered structure (n=3,4,6). Monoclinic structural types with unshifted (P2{sub 1}/m) and with shifted (C2/m) layers were considered. Crystal energies and full structural details were obtained for all Li, Na, and K phases. Neutron diffraction data were collected on powder samples of P2{sub 1}/m-Li{sub 2}Ti{sub 3}O{sub 7} (a=9.3146(3), b=3.7522(1), c=7.5447(3) Å, β=97.611(4)°) and C2/m-K{sub 2}Ti{sub 4}O{sub 9} (a=18.2578(8), b=3.79160(9), c=12.0242(4) Å, β=106.459(4)°) and their structures were Rietveld-refined. Computed energies show the P2{sub 1}/m arrangement as favoured over the C2/m one for n=3, and the opposite holds for n=6. In the n=4 case the P2{sub 1}/m configuration is predicted to be more stable for Li and Na, and the C2/m one for K titanates. Analysis of Li–O and K–O crystal-chemical environments from experiment and theory shows that the alkali atom bonding is stabilized/destabilized in the different phases consistently with the energy trend. - Graphical abstract: Display Omitted - Highlights: • The P2{sub 1}/m structure-type is found to be more stable for A{sub 2}Ti{sub 3}O{sub 7} layer titanates. • The C2/m structure-type is found to be more stable for A{sub 2}Ti{sub 6}O{sub 13} layer titanates. • Tetratitanates are predicted to prefer the P2{sub 1}/m (Li and Na) or C2/m (K) structure. • Li–O and K–O bond distances follow a trend consistent with computed phase energies.

  20. Alkenes as Chelating Groups in Diastereoselective Additions of Organometallics to Ketones

    PubMed Central

    2015-01-01

    Alkenes have been discovered to be chelating groups to Zn(II), enforcing highly stereoselective additions of organozincs to β,γ-unsaturated ketones. 1H NMR studies and DFT calculations provide support for this surprising chelation mode. The results expand the range of coordinating groups for chelation-controlled carbonyl additions from heteroatom Lewis bases to simple C–C double bonds, broadening the 60 year old paradigm. PMID:25328269

  1. The construction of graph models for calculations of the properties of substitution isomers of basis structures on the basis of additivity of energy contributions

    NASA Astrophysics Data System (ADS)

    Nilov, D. Yu.; Smolyakov, V. M.

    2012-05-01

    A method for the construction of additive models for calculations of the properties of substitution isomers of basis structures is described for the example of a series of X-substituted methylsilanes CH3 - k X k -SiH3 - l X l (where X = CH3, F, Cl, …, k, l = 0, 1, 2, 3). The method is based on similarity of subgraphs in graphs of several molecules and the arrangement of polygonal numbers (triangular, tetrahedral) of the Pascal triangle. Parameters taking into account multiple nonvalence interactions (-C-Si<, >C-Si<, …) through two atoms along the molecular chain of an X-substituted methylsilane (X = CH3) were for the first time explicitly included in the calculation scheme. Taking these interactions into account allows us to completely differentiate all the structural isomers of certain molecules and obtain numerical parameter values for predicting properties P under consideration in various approximations. Numerical calculations of Δf H {g,298/K o} were performed for 16 alkylsilanes (as X-substituted methylsilanes), including 7 compounds not studied experimentally.

  2. Synthesis, antimicrobial activity, structural and spectral characterization and DFT calculations of Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile.

    PubMed

    Mohamed, Tarek A; Shaaban, Ibrahim A; Farag, Rabei S; Zoghaib, Wajdi M; Afifi, Mahmoud S

    2015-01-25

    Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile (APC) have been synthesized and characterized using elemental analysis, magnetic susceptibility, mass spectrometry, infrared (4000-200 cm(-1)), UV-Visible (200-1100 nm), (1)H NMR and ESR spectroscopy as well as TGA analysis. The molar conductance measurements in DMSO imply non-electrolytic complexes, formulated as [M(APC)2Cl2] where M=Co(II), Ni(II), Cu(II) and Pd(II). The infrared spectra of Co(II), Ni(II) and Cu(II) complexes indicate a bidentate type of bonding for APC through the exocyclic amino and adjacent pyrimidine nitrogen as donors whereas APC coordinated to Pd(II) ion as a monodentated ligand via a pyrimidine nitrogen donor. The magnetic measurements and the electronic absorption spectra support distorted octahedral geometries for Co(II), Ni(II) and Cu(II) complexes however a square planar complex was favored for the Pd(II) complex (C2h skeleton symmetry). In addition, we carried out B3LYP and ω-B97XD geometry optimization at 6-31G(d) basis set except for Pd(II) where we implemented LanL2DZ/6-31G(d) combined basis set. The computational results favor all trans geometrical isomers where amino N, pyrimidine N and Cl are trans to each other (structure 1). Finally, APC and its divalent metal ion complexes were screened for their antibacterial activity, and the synthesized complexes were found to be more potent antimicrobial agents than APC against one or more microbial species. PMID:25105264

  3. Synthesis, antimicrobial activity, structural and spectral characterization and DFT calculations of Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile.

    PubMed

    Mohamed, Tarek A; Shaaban, Ibrahim A; Farag, Rabei S; Zoghaib, Wajdi M; Afifi, Mahmoud S

    2015-01-25

    Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile (APC) have been synthesized and characterized using elemental analysis, magnetic susceptibility, mass spectrometry, infrared (4000-200 cm(-1)), UV-Visible (200-1100 nm), (1)H NMR and ESR spectroscopy as well as TGA analysis. The molar conductance measurements in DMSO imply non-electrolytic complexes, formulated as [M(APC)2Cl2] where M=Co(II), Ni(II), Cu(II) and Pd(II). The infrared spectra of Co(II), Ni(II) and Cu(II) complexes indicate a bidentate type of bonding for APC through the exocyclic amino and adjacent pyrimidine nitrogen as donors whereas APC coordinated to Pd(II) ion as a monodentated ligand via a pyrimidine nitrogen donor. The magnetic measurements and the electronic absorption spectra support distorted octahedral geometries for Co(II), Ni(II) and Cu(II) complexes however a square planar complex was favored for the Pd(II) complex (C2h skeleton symmetry). In addition, we carried out B3LYP and ω-B97XD geometry optimization at 6-31G(d) basis set except for Pd(II) where we implemented LanL2DZ/6-31G(d) combined basis set. The computational results favor all trans geometrical isomers where amino N, pyrimidine N and Cl are trans to each other (structure 1). Finally, APC and its divalent metal ion complexes were screened for their antibacterial activity, and the synthesized complexes were found to be more potent antimicrobial agents than APC against one or more microbial species.

  4. NMR, DFT and luminescence studies of the complexation of Zn(II) with 8-hydroxyquinoline-5-sulfonate.

    PubMed

    Luísa Ramos, M; Justino, Licínia L G; Branco, Adriana; Duarte, Cláudia M G; Abreu, Paulo E; Fonseca, Sofia M; Burrows, Hugh D

    2011-11-28

    Multinuclear ((1)H, (13)C) magnetic resonance spectroscopy, DFT calculations and luminescence techniques have been used to study 8-hydroxyquinoline-5-sulfonate (8-HQS) and its complexes with Zn(ii), in aqueous solution. The study combines the high sensitivity of luminescence techniques, the selectivity of multinuclear NMR spectroscopy with the structural details accessible through DFT calculations, and aims to obtain a detailed understanding of the complexation between the Zn(2+) ion and 8-HQS. In addition to a complete assignment of the (1)H and (13)C NMR signals of 8-HQS, a full speciation study has been performed. Over the concentration region studied, Zn(2+) metal ion forms only one significant complex species with 8-HQS in aqueous solution in the pH range 6-8. Job's method shows that this species has a 1:2 (metal:ligand) stoichiometry. The geometry around the metal centre, according to structural optimization using DFT calculations, is suggested to be square bipyramidal, with two coordinated water molecules mutually trans, and the remaining positions occupied by the donor groups of the two coordinated 8-HQS ligands. On binding to Zn(ii), 8-HQS shows a marked fluorescence compared with the weakly-luminescent free ligand. In addition, as previously noted, there are marked changes in the absorption spectra, which support the use of 8-HQS as a sensitive fluorescent sensor to detect Zn(2+) metal ion in surface waters, biological fluids, etc. Based on results of the structural studies, suggestions are made of ways for enhancing fluorescence sensitivity.

  5. Time-dependent density functional theory (TD-DFT) study on the excited-state intramolecular proton transfer (ESIPT) in 2-hydroxybenzoyl compounds: Significance of the intramolecular hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Lan, Xin; Yang, Dapeng; Sui, Xiao; Wang, Dandan

    2013-02-01

    The excited-state properties of intramolecular hydrogen bonding (IMHB) in methyl salicylate (MS) and its effects on the excited-state intramolecular proton transfer (ESIPT) have been investigated using theoretical methods. From the geometric optimization and IR spectra in the ground and excited states calculated by density functional theory (DFT) and time-dependent DFT (TD-DFT) methods respectively, the IMHB is demonstrated to be significantly strengthened upon excitation to excited state S1. Thereby, the ESIPT is facilitated by the excited-state IMHB strengthening since ESIPT takes place through IMHB. In addition, the absorption and fluorescence peaks of the S1 state are also calculated using the TD-DFT method. It is noted that the calculated spectra are in good agreement with the experimental results, which has confirmed the ESIPT mechanism of MS first proposed by Weller. Moreover, other four 2-hydroxybenzoyl compounds forming strong IMHB are investigated to understand the effect of substituent R on the ESIPT process. We find that the hydrogen bond strength can be controlled by the inductive field effect of the substituent. Thus it is inferred that the ESIPT reaction can be facilitated by the inductive effect of electron-donating substituent.

  6. Introducing constricted variational density functional theory in its relaxed self-consistent formulation (RSCF-CV-DFT) as an alternative to adiabatic time dependent density functional theory for studies of charge transfer transitions

    SciTech Connect

    Krykunov, Mykhaylo; Seth, Mike; Ziegler, Tom

    2014-05-14

    We have applied the relaxed and self-consistent extension of constricted variational density functional theory (RSCF-CV-DFT) for the calculation of the lowest charge transfer transitions in the molecular complex X-TCNE between X = benzene and TCNE = tetracyanoethylene. Use was made of functionals with a fixed fraction (α) of Hartree-Fock exchange ranging from α = 0 to α = 0.5 as well as functionals with a long range correction (LC) that introduces Hartree-Fock exchange for longer inter-electronic distances. A detailed comparison and analysis is given for each functional between the performance of RSCF-CV-DFT and adiabatic time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation. It is shown that in this particular case, all functionals afford the same reasonable agreement with experiment for RSCF-CV-DFT whereas only the LC-functionals afford a fair agreement with experiment using TDDFT. We have in addition calculated the CT transition energy for X-TCNE with X = toluene, o-xylene, and naphthalene employing the same functionals as for X = benzene. It is shown that the calculated charge transfer excitation energies are in as good agreement with experiment as those obtained from highly optimized LC-functionals using adiabatic TDDFT. We finally discuss the relation between the optimization of length separation parameters and orbital relaxation in the RSCF-CV-DFT scheme.

  7. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    SciTech Connect

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  8. Why Is MP2-Water "Cooler" and "Denser" than DFT-Water?

    PubMed

    Willow, Soohaeng Yoo; Zeng, Xiao Cheng; Xantheas, Sotiris S; Kim, Kwang S; Hirata, So

    2016-02-18

    Density functional theory (DFT) with a dispersionless generalized gradient approximation (GGA) needs much higher temperature and pressure than the ambient conditions to maintain water in the liquid phase at the correct (1 g/cm(3)) density during first-principles simulations. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water require lower temperature and pressure than DFT/GGA to keep water liquid. Here we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the different temperatures and pressures between DFT/GGA and MP2 at which the simulated water displays the experimentally observed liquid structure under the ambient conditions can be largely explained by their differences in polarizability and dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for DFT-water to be liquid. MP2 gives a stronger dispersion interaction and thus shorter intermolecular distances than dispersionless DFT/GGA, which is why MP2-water is denser than DFT-water under the same external pressure.

  9. DFT Study of Optical Properties of Pt-based Complexes

    NASA Astrophysics Data System (ADS)

    Oprea, Corneliu I.; Dumbravǎ, Anca; Moscalu, Florin; Nicolaides, Atnanassios; Gîrţu, Mihai A.

    2010-01-01

    We report Density Functional Theory (DFT) calculations providing the geometrical and electronic structures, as well as the vibrational and optical properties of the homologous series of Pt-pyramidalized olefin complexes (CH2)n-(C8H10)Pt(PH3)2, where n = 0, 1, and 2, in their neutral and oxidized states. All complexes were geometry optimized for the singlet ground state in vacuum using DFT methods with B3LYP exchange-correlation functional and the Effective Core Potential LANL2DZ basis set, within the frame of Gaussian03 quantum chemistry package. We find the coordination geometry of Pt to be distorted square planar, with dihedral angles ranging from 0°, for n = 0 and 1, which have C2V symmetry to 3.4°, for n = 2 with C2 symmetry. The Mulliken charge analysis allows a discussion of the oxidation state of the Pt ion. Electronic transitions were calculated at the same level of theory by means of Time Dependant-DFT. For n = 2 the electronic absorption bands are located in the UV region of the spectrum, the transitions being assigned to metal to ligand charge transfers. The relevance of these Pt-based compounds as possible pigments for dye-sensitized solar cells is discussed.

  10. THz Absorption Spectra of Fe Water Complexes Interacting with O3 Calculated by Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Huang, L.; Lambrakos, S. G.; Shabaev, A.; Massa, L.; Yapijakis, C.

    2013-05-01

    The need for better monitoring of water quality and levels of water contamination implies a need for determining the dielectric response properties of water contaminants with respect to electromagnetic wave excitation. In addition to monitoring contaminants, there is an associated need for monitoring chemical processes that are for deactivation or assistance in the removal of water contaminants. Iron and manganese are two naturally occurring water contaminants, where iron is in general at much higher concentrations. Correspondingly, a process that is highly effective for assisting filtration of water contaminants, including iron and manganese, is the addition in solution of Ozone, i.e., the preozonation process. The present study uses density functional theory (DFT) for the calculation of ground-state resonance structure associated with Fe water complexes interacting with Ozone in solution. The calculations presented are for excitation by electromagnetic waves at frequencies within the THz range. Dielectric response functions can provide for different types of analyses concerning water contaminants. In particular, dielectric response functions can provide quantitative initial estimates of spectral response features for subsequent adjustment with respect to additional information such as laboratory measurements and other types of theory-based calculations. In addition, with respect to qualitative analysis, DFT-calculated absorption spectra provide for molecular level interpretation of response structure. The DFT software GAUSSIAN was used for the calculations of ground-state resonance structure presented in this article.

  11. Temperature dependent Raman and DFT study of creatine.

    PubMed

    Gangopadhyay, Debraj; Sharma, Poornima; Singh, Ranjan K

    2015-01-01

    Temperature dependent Raman spectra of creatine powder have been recorded in the temperature range 420-100K at regular intervals and different clusters of creatine have been optimized using density functional theory (DFT) in order to determine the effect of temperature on the hydrogen bonded network in the crystal structure of creatine. Vibrational assignments of all the 48 normal modes of the zwitterionic form of creatine have been done in terms of potential energy distribution obtained from DFT calculations. Precise analysis gives information about thermal motion and intermolecular interactions with respect to temperature in the crystal lattice. Formation of higher hydrogen bonded aggregates on cooling can be visualized from the spectra through clear signature of phase transition between 200K and 180K. PMID:26010702

  12. Vibrational modes of aminothiophenol: a TERS and DFT study.

    PubMed

    Merlen, A; Chaigneau, M; Coussan, S

    2015-07-15

    We report Tip Enhanced Raman Spectroscopy (TERS) mapping and Density Functional (DFT) calculations of aminothiophenol (ATP) grafted on a gold surface. The TERS mapping has demonstrated Raman modes of (ATP) and its dimerised derivative Dimercaptoazobenzene (DMAB). This feature confirms that the plasmon activated chemical reaction of ATP has occurred during TERS measurements. In some specific part of the samples some unidentified Raman modes are observed. We suggest that they could come from intermediate species formed during the conversion of ATP into DMAB. These modes are compared with calculated Raman spectra of some possible intermediate species. These results confirm the high potentiality of TERS measurements for nanochemistry.

  13. Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2016-09-14

    Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

  14. Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

    PubMed

    Zhang, Changzhe; Bu, Yuxiang

    2016-09-14

    Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems. PMID:27522987

  15. DFT calculations of point defects on UN(001) surface

    NASA Astrophysics Data System (ADS)

    Bocharov, D.; Gryaznov, D.; Zhukovskii, Yu. F.; Kotomin, E. A.

    2011-02-01

    The density functional theory is used in a study of point defects on both UN(001) surface and sub-surface layers. We compare the results for slabs of different thicknesses (both perfect and containing nitrogen or uranium vacancies) with a full geometry, electronic and spin density optimization. The electronic charge density re-distribution, density of states, magnetic moments of U atoms and local atomic displacements around defects are carefully analyzed. It is predicted that the vacancies are formed easier on the surface, whereas the property of sub-surface layer does not differ significantly from the central one in the slab.

  16. NMR, DFT and luminescence studies of the complexation of Al(III) with 8-hydroxyquinoline-5-sulfonate.

    PubMed

    Ramos, M Luísa; Justino, Licínia L G; Salvador, Andreia I N; de Sousa, Andreia R E; Abreu, Paulo E; Fonseca, Sofia M; Burrows, Hugh D

    2012-10-28

    Multinuclear ((1)H, (13)C and (27)Al) magnetic resonance spectroscopy (1D and 2D), DFT calculations and fluorescence have been used to study the complexation of 8-hydroxyquinoline-5-sulfonate (8-HQS) with Al(III). The study combines the high sensitivity of luminescence techniques, the selectivity of multinuclear NMR spectroscopy with the structural details accessible through DFT calculations, and aims to provide a detailed understanding of the complexation between the Al(3+) ion and 8-HQS. A full speciation study has been performed and over the concentration region studied, the Al(3+) ion forms complexes with 8-HQS in an aqueous solution in the pH range 2-6. At higher pH, the extensive hydrolysis of the metal limits complexation. Using Job's method, three complexes were detected, with 1 : 1, 1 : 2 and 1 : 3 (metal : ligand) stoichiometries. These results are in agreement with those previously reported using potentiometric and electrochemical techniques. The geometries of the complexes are proposed based on the combination of NMR results with optimized DFT calculations. All the complexes in aqueous solutions at 25 °C are mononuclear species, and have an approximately octahedral geometry with the metal coordinated to one molecule of 8-HQS and four molecules of water (1 : 1 complex), two molecules of 8-HQS and two molecules of water mutually cis (1 : 2 complex), and to three molecules of 8-HQS in non-symmetrical arrangement (mer-isomer), for the 1 : 3 (metal : ligand) complex. On binding to Al(III), 8-HQS shows a more marked fluorescence than the weakly fluorescent free ligand. In addition, as previously noted, there are marked changes in the absorption spectra, which support the use of 8-HQS as a sensitive optical sensor to detect Al(3+) metal ions in surface waters and biological fluids. These complexes also show potential for applications in organic light emitting diodes (OLEDs).

  17. Syntheses, crystal structure, Hirshfeld surfaces, fluorescence properties, and DFT analysis of benzoic acid hydrazone Schiff bases

    NASA Astrophysics Data System (ADS)

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2015-06-01

    Two hydrazone Schiff base analogues, namely, (E)-N‧-(4-hydroxy-3-methoxybenzylidene)benzohydrazide (3a) and (E)-N‧-(4-methoxybenzylidene)benzohydrazide (3b), were synthesized using a mild, efficient method and characterized by 1H NMR, mass spectrometry, elemental analysis, and single-crystal X-ray diffraction. X-ray analysis of a single crystal of 3a revealed a tetragonal, space group I4(1)/a structure, with an E-configuration around the azomethine (sbnd C8dbnd N2sbnd) double bond. In this structure, the sbnd NHsbnd and sbnd OH groups act as proton donors and the >Cdbnd O and sbnd Ndbnd groups as proton acceptors, and these facilitate hydrogen bond formation in the crystal state. Plausible intermolecular interactions were studied using 3D Hirshfeld surfaces and related 2D fingerprint plots. The optimized geometry, vibrational frequencies, Mulliken charge distribution, molecular electrostatic potential (MEP) maps, frontier molecular orbitals (FMOs), and associated energies of the ground state and the first single excited state were calculated using density functional theory (DFT) and time-dependant DFT calculations using the B3LYP/6-311G method. Vibrational frequencies calculated in the gaseous phase compared with experimental values measured in the solid state and showed good agreement with each other. The chemical reactivities of 3a and 3b were predicted by mapping MEP surface over optimized geometries and comparing these with MEP map generated over crystal structures. Mulliken charge distribution analysis and MEP map of 3a and 3b revealed that N(1), O(1), O(2) and O(3) atoms could act as electron donors and coordinate with metals and that these represented the most suitable sites for electrophilic attack. In fluorescence spectra, the absorption and emission spectra of 3a and 3b were similar in different polar solvents with few exceptions. In addition, both compounds exhibited dual emission spectra in acetone due to keto-enol tautomerism induced by

  18. Syntheses, crystal structure, Hirshfeld surfaces, fluorescence properties, and DFT analysis of benzoic acid hydrazone Schiff bases.

    PubMed

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2015-06-15

    Two hydrazone Schiff base analogues, namely, (E)-N'-(4-hydroxy-3-methoxybenzylidene)benzohydrazide (3a) and (E)-N'-(4-methoxybenzylidene)benzohydrazide (3b), were synthesized using a mild, efficient method and characterized by (1)H NMR, mass spectrometry, elemental analysis, and single-crystal X-ray diffraction. X-ray analysis of a single crystal of 3a revealed a tetragonal, space group I4(1)/a structure, with an E-configuration around the azomethine (C8N2) double bond. In this structure, the NH and OH groups act as proton donors and the >CO and N groups as proton acceptors, and these facilitate hydrogen bond formation in the crystal state. Plausible intermolecular interactions were studied using 3D Hirshfeld surfaces and related 2D fingerprint plots. The optimized geometry, vibrational frequencies, Mulliken charge distribution, molecular electrostatic potential (MEP) maps, frontier molecular orbitals (FMOs), and associated energies of the ground state and the first single excited state were calculated using density functional theory (DFT) and time-dependant DFT calculations using the B3LYP/6-311G method. Vibrational frequencies calculated in the gaseous phase compared with experimental values measured in the solid state and showed good agreement with each other. The chemical reactivities of 3a and 3b were predicted by mapping MEP surface over optimized geometries and comparing these with MEP map generated over crystal structures. Mulliken charge distribution analysis and MEP map of 3a and 3b revealed that N(1), O(1), O(2) and O(3) atoms could act as electron donors and coordinate with metals and that these represented the most suitable sites for electrophilic attack. In fluorescence spectra, the absorption and emission spectra of 3a and 3b were similar in different polar solvents with few exceptions. In addition, both compounds exhibited dual emission spectra in acetone due to keto-enol tautomerism induced by photoexcitation. PMID:25804368

  19. Syntheses, crystal structure, Hirshfeld surfaces, fluorescence properties, and DFT analysis of benzoic acid hydrazone Schiff bases.

    PubMed

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2015-06-15

    Two hydrazone Schiff base analogues, namely, (E)-N'-(4-hydroxy-3-methoxybenzylidene)benzohydrazide (3a) and (E)-N'-(4-methoxybenzylidene)benzohydrazide (3b), were synthesized using a mild, efficient method and characterized by (1)H NMR, mass spectrometry, elemental analysis, and single-crystal X-ray diffraction. X-ray analysis of a single crystal of 3a revealed a tetragonal, space group I4(1)/a structure, with an E-configuration around the azomethine (C8N2) double bond. In this structure, the NH and OH groups act as proton donors and the >CO and N groups as proton acceptors, and these facilitate hydrogen bond formation in the crystal state. Plausible intermolecular interactions were studied using 3D Hirshfeld surfaces and related 2D fingerprint plots. The optimized geometry, vibrational frequencies, Mulliken charge distribution, molecular electrostatic potential (MEP) maps, frontier molecular orbitals (FMOs), and associated energies of the ground state and the first single excited state were calculated using density functional theory (DFT) and time-dependant DFT calculations using the B3LYP/6-311G method. Vibrational frequencies calculated in the gaseous phase compared with experimental values measured in the solid state and showed good agreement with each other. The chemical reactivities of 3a and 3b were predicted by mapping MEP surface over optimized geometries and comparing these with MEP map generated over crystal structures. Mulliken charge distribution analysis and MEP map of 3a and 3b revealed that N(1), O(1), O(2) and O(3) atoms could act as electron donors and coordinate with metals and that these represented the most suitable sites for electrophilic attack. In fluorescence spectra, the absorption and emission spectra of 3a and 3b were similar in different polar solvents with few exceptions. In addition, both compounds exhibited dual emission spectra in acetone due to keto-enol tautomerism induced by photoexcitation.

  20. A general framework for numerical simulation of improvised explosive device (IED)-detection scenarios using density functional theory (DFT) and terahertz (THz) spectra.

    PubMed

    Shabaev, Andrew; Lambrakos, Samuel G; Bernstein, Noam; Jacobs, Verne L; Finkenstadt, Daniel

    2011-04-01

    We have developed a general framework for numerical simulation of various types of scenarios that can occur for the detection of improvised explosive devices (IEDs) through the use of excitation using incident electromagnetic waves. A central component model of this framework is an S-matrix representation of a multilayered composite material system. Each layer of the system is characterized by an average thickness and an effective electric permittivity function. The outputs of this component are the reflectivity and the transmissivity as functions of frequency and angle of the incident electromagnetic wave. The input of the component is a parameterized analytic-function representation of the electric permittivity as a function of frequency, which is provided by another component model of the framework. The permittivity function is constructed by fitting response spectra calculated using density functional theory (DFT) and parameter adjustment according to any additional information that may be available, e.g., experimentally measured spectra or theory-based assumptions concerning spectral features. A prototype simulation is described that considers response characteristics for THz excitation of the high explosive β-HMX. This prototype simulation includes a description of a procedure for calculating response spectra using DFT as input to the Smatrix model. For this purpose, the DFT software NRLMOL was adopted.