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Sample records for addition dft calculations

  1. Theoretical study of ignition reactions of linear symmetrical monoethers as potential diesel fuel additives: DFT calculations

    NASA Astrophysics Data System (ADS)

    Marrouni, Karim El; Abou-Rachid, Hakima; Kaliaguine, Serge

    This work investigates the chemical reactivity of four linear symmetrical monoethers with molecular oxygen. Such oxygenated compounds may be considered as potential diesel fuel additives in order to reduce the ignition delay in diesel fuel engines. For this purpose, a kinetic study is proposed to clarify the relation between the molecular structure of the fuel molecule and its ignition properties. To this end, DFT calculations were performed for these reactions using B3LYP/6-311G(d,p) and BH&HLYP/6-311G(d,p) to determine structures, energies, and vibrational frequencies of stationary points as well as activated complexes involved in each gas-phase combustion initiation reaction of the monoethers CH3OCH3, C2H5OC2H5, C3H7OC3H7, or C4H9OC4H9 with molecular oxygen. This theoretical kinetic study was carried out using electronic structure results and the transition state theory, to assess the rate constants for all studied combustion reactions. As it has been shown in our previous work [Abou-Rachid et al., J Mol Struct (Theochem) 2003, 621, 293], the cetane number (CN) of a pure organic molecule depends on the initiation rate of its homogeneous gas-phase reaction with molecular oxygen. Indeed, the calculated initiation rate constants of the H-abstraction process of linear monoethers with O2 show a very good correlation with experimental CN data of these pure compounds at T D 1,000 K. This temperature is representative of the operating conditions of a diesel fuel engine.0

  2. DFT calculations with the exact functional

    NASA Astrophysics Data System (ADS)

    Burke, Kieron

    2014-03-01

    I will discuss several works in which we calculate the exact exchange-correlation functional of density functional theory, mostly using the density-matrix renormalization group method invented by Steve White, our collaborator. We demonstrate that a Mott-Hubard insulator is a band metal. We also perform Kohn-Sham DFT calculations with the exact functional and prove that a simple algoritm always converges. But we find convergence becomes harder as correlations get stronger. An example from transport through molecular wires may also be discussed. Work supported by DOE grant DE-SC008696.

  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. Oxidative addition of Pd to C-H, C-C and C-Cl bonds: Importance of relativistic effects in DFT calculations

    NASA Astrophysics Data System (ADS)

    Diefenbach, Axel; Bickelhaupt, F. Matthias

    2001-09-01

    To assess the importance of relativistic effects for the quantum chemical description of oxidative addition reactions of palladium to C-H, C-C and C-Cl bonds, we have carried out a systematic study of the corresponding reactions of CH4, C2H6 and CH3Cl with Pd-d10 using nonrelativistic (NR), quasirelativistic (QR), and zeroth-order regularly approximated (ZORA) relativistic density functional theory (DFT) at the BP86/TZ(2)P level. Relativistic effects are important according to both QR and ZORA, the former yielding similar but somewhat more pronounced effects than the latter, more reliable method: activation barriers are reduced by 6-14 kcal/mol and reaction enthalpies become 15-20 kcal/mol more exothermic if one goes from NR to ZORA. This yields, for example, 298 K activation enthalpies ΔH298≠ of -5.0 (C-H), 9.6 (C-C) and -6.0 kcal/mol (C-Cl) relative to the separate reactants at ZORA-BP86/TZ(2)P. In accordance with gas-phase experiments on reactions of Pd with alkanes, we find reaction profiles with pronounced potential wells for reactant complexes (collisionally stabilized and observed in experiments for alkanes larger than CH4) at -11.4 (CH4), -11.6 (C2H6) and -15.6 kcal/mol (CH3Cl) relative to separated reactants [ZORA-BP86/TZ(2)P]. Furthermore, we analyze the height of and the relativistic effects on the activation energies ΔE≠ in terms of the activation strain ΔEstrain≠ of and the transition-state interaction ΔEint≠ between the reactants in the activated complex, with ΔE≠=ΔEstrain≠+ΔEint≠.

  5. Exchange interactions and Tc in rhenium-doped silicon: DFT, DFT + U and Monte Carlo calculations.

    PubMed

    Wierzbowska, Małgorzata

    2012-03-28

    Interactions between rhenium impurities in silicon are investigated by means of the density functional theory (DFT) and the DFT + U scheme. All couplings between impurities are ferromagnetic except the Re-Re dimers which in the DFT method are nonmagnetic, due to the formation of the chemical bond supported by substantial relaxation of the geometry. The critical temperature is calculated by means of classical Monte Carlo (MC) simulations with the Heisenberg Hamiltonian. The uniform ferromagnetic phase is obtained with the DFT exchange interactions at room temperature for the impurities concentration of 7%. With the DFT + U exchange interactions, the ferromagnetic clusters form above room temperature in MC samples containing only 3% Re.

  6. 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

  7. Dispersion-corrected DFT calculations on C(60)-porphyrin complexes.

    PubMed

    Liao, Meng-Sheng; Watts, John D; Huang, Ming-Ju

    2009-06-07

    The quality of the newly added, empirical dispersion correction in density functional theory (DFT) calculations is examined for several supramolecular complexes of fullerene (C(60)) with free-base and metal porphyrins (Por). The benzene dimer (C(6)H(6))(2), naphthalene dimer (C(10)H(8))(2), and anthracene dimer (C(14)H(10))(2) were also included in the study for comparison. Three density functionals, two damping functions, and two types of basis sets were employed in the computations. The estimated dispersion energies in the fullerene-porphyrin systems are rather large, ranging from 0.5 eV in C(60).ZnP to 1 eV in C(60).H(2)TPP. Any dispersion-corrected DFT (DFT + E(disp)) method is shown to perform well for C(60).H(2)TPP, C(60).ZnTPP, and C(60).ZnP, where the intermolecular distances are relatively large. But large basis sets, e.g. TZP (triple-zeta + one polarization function), are required in order to obtain reliable results with DFT + E(disp). In the case of C(60).FeP, where the intermolecular distance R is short, the DFT + E(disp) calculated R depends on the damping function as well as on the DFT method, and all the DFT + E(disp) calculations lead to significant changes in the relative energies of the various spin states. The quality of the DFT + E(disp) calculated results on C(60).FeP is hard to judge here without detailed experimental data on a C(60).FePor complex. Owing to error cancellation, the pure DFT calculations with a smaller DZP (double-zeta + one polarization function) basis set without any correction are shown to give quite accurate results.

  8. 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

  9. 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.

  10. 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.

  11. Calculators and Computers: Graphical Addition.

    ERIC Educational Resources Information Center

    Spero, Samuel W.

    1978-01-01

    A computer program is presented that generates problem sets involving sketching graphs of trigonometric functions using graphical addition. The students use calculators to sketch the graphs and a computer solution is used to check it. (MP)

  12. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values.

    PubMed

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-07

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or "flavors" of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (-6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (-15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  13. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

    NASA Astrophysics Data System (ADS)

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-01

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or "flavors" of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (-6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (-15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  14. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

    SciTech Connect

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-07

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  15. 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.

  16. Accurate and efficient linear scaling DFT calculations with universal applicability.

    PubMed

    Mohr, Stephan; Ratcliff, Laura E; Genovese, Luigi; Caliste, Damien; Boulanger, Paul; Goedecker, Stefan; Deutsch, Thierry

    2015-12-21

    Density functional theory calculations are computationally extremely expensive for systems containing many atoms due to their intrinsic cubic scaling. This fact has led to the development of so-called linear scaling algorithms during the last few decades. In this way it becomes possible to perform ab initio calculations for several tens of thousands of atoms within reasonable walltimes. However, even though the use of linear scaling algorithms is physically well justified, their implementation often introduces some small errors. Consequently most implementations offering such a linear complexity either yield only a limited accuracy or, if one wants to go beyond this restriction, require a tedious fine tuning of many parameters. In our linear scaling approach within the BigDFT package, we were able to overcome this restriction. Using an ansatz based on localized support functions expressed in an underlying Daubechies wavelet basis - which offers ideal properties for accurate linear scaling calculations - we obtain an amazingly high accuracy and a universal applicability while still keeping the possibility of simulating large system with linear scaling walltimes requiring only a moderate demand of computing resources. We prove the effectiveness of our method on a wide variety of systems with different boundary conditions, for single-point calculations as well as for geometry optimizations and molecular dynamics.

  17. 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.

  18. Intermolecular interactions in AST zeolites through (14)N NMR and DFT calculations.

    PubMed

    Dib, Eddy; Freire, Mélanie; Pralong, Valérie; Mineva, Tzonka; Alonso, Bruno

    2017-03-01

    The structure of the silica AST zeolites (octadecasil) synthesized in fluoride medium using tetramethylammonium (TMA) as the organic structure-directing agent has been reinvestigated using (14)N NMR quadrupolar parameters and DFT calculations. The value of the experimental (14)N quadrupolar coupling constant (CQ = 27 kHz) is larger than expected for a TMA cation possessing a high degree of motion. The analysis of a DFT-optimized octadecasil cluster along with the comparison between measured and calculated (14)N NMR parameters demonstrate the presence of weak C-H...O hydrogen bonds between the TMA in the [4(6)6(12)] cages and the silica skeleton. These intermolecular interactions can be related to the presence of Si...F tetrel bonds within the [4(6)] cages. These new results provide additional information with regard to the formation mechanisms and structure of the octadecasil zeolites.

  19. Vibrational spectroscopy and DFT calculations of flavonoid derriobtusone A

    NASA Astrophysics Data System (ADS)

    Marques, A. N. L.; Mendes Filho, J.; Freire, P. T. C.; Santos, H. S.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Leite, R. V.; Braz-Filho, R.; Gusmão, G. O. M.; Nogueira, C. E. S.; Teixeira, A. M. R.

    2017-02-01

    Flavonoids are secondary metabolites of plants which perform various functions. One subclass of flavonoid is auronol that can present immunostimulating activity. In this work Fourier-Transform Infrared with Attenuated Total Reflectance (FTIR-ATR) and Fourier-Transform Raman (FT-Raman) spectra of an auronol, derriobtusone A (C18H12O4), were obtained at room temperature. Theoretical calculations using Density Functional Theory (DFT) were performed in order to assign the normal modes and to interpret the spectra of the derriobtusone A molecule. The FTIR-ATR and FT-Raman spectra of the crystal, were recorded at room temperature in the regions 600 cm-1 to 4000 cm-1 and 40 cm-1 to 4000 cm-1, respectively. The normal modes of vibrations were obtained using Density Functional Theory with B3LYP functional and 6-31G+ (d,p) basis set. The calculated frequencies are in good agreement with those obtained experimentally. Detailed assignments of the normal modes present in both the Fourier-Transform infrared and the Fourier-Transform Raman spectra of the crystal are given.

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

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

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

  1. 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

    2015-01-01

    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.

  2. Organocatalyzed asymmetric Michael addition by an efficient bifunctional carbohydrate-thiourea hybrid with mechanistic DFT analysis.

    PubMed

    Azad, Chandra S; Khan, Imran A; Narula, Anudeep K

    2016-12-28

    A series of thiourea based bifunctional organocatalysts having d-glucose as a core scaffold were synthesized and examined as catalysts for the asymmetric Michael addition reaction of aryl/alkyl trans-β-nitrostyrenes over cyclohexanone and other Michael donors having active methylene. Excellent enantioselectivities (<95%), diastereoselectivities (<99%), and yields (<99%) were attained under solvent free conditions using 10 mol% of 1d0. The obtained results were explained through DFT calculations using the B3LYP/6-311G(d,p)//B3LYP/6-31G(d) basic set. The QM/MM calculations revealed the role of cyclohexanone as a solvent as well as reactant in the rate determining step imparting 31.91 kcal mol(-1) of energy towards the product formation.

  3. 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

  4. DFT Calculations on Mössbauer Parameters of Nonheme Iron Nitrosyls

    PubMed Central

    Hopmann, Kathrin H.; Ghosh, Abhik; Noodleman, Louis

    2009-01-01

    DFT calculations on transition metal nitrosyls often reveal unusual spin density profiles, involving substantial spatial separation of majority and minority spin densities. Against this context, there is a significant lack of studies where DFT calculations have been quantitatively calibrated against experimental spectroscopic properties. Reported herein are DFT calculations of Mössbauer isomer shifts and quadrupole splittings for 21 nonheme iron complexes (26 distinct iron sites) including 9 iron nitrosyls. Low- (S = 1/2) and high-spin (S = 3/2) {FeNO}7 complexes, S = 1/2 {Fe(NO)2}9 species, and polynuclear iron nitrosyls are all represented within the set of compounds examined. The general conclusion with respect to isomer shifts is that DFT (OLYP/STO-TZP) performs comparably well for iron nitrosyls and for iron complexes in general. However, quadrupole splittings are less accurately reproduced for nitrosyl complexes. PMID:19780615

  5. 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.

  6. Assessment of Functionals for TD-DFT Calculations of Singlet-Triplet Transitions.

    PubMed

    Jacquemin, Denis; Perpète, Eric A; Ciofini, Ilaria; Adamo, Carlo

    2010-05-11

    The calculation of transition energies for electronically excited states remains a challenge in quantum chemistry, for which time-dependent density functional theory (TD-DFT) is often viewed as a balanced (computational effort/obtained accuracy) technique. In this study, we benchmark 34 DFT functionals in the specific framework of TD-DFT calculations for singlet-triplet transitions. The results are compared to accurate wave function data reported for the same set of 63 excited-states, and it turns out that, within the selected TD-DFT framework, BMK and M06-2X emerge as the most efficient hybrids. This investigation clearly illustrates that the conclusions drawn for singlet excited states do not necessarily hold for triplet states, even for similar molecular structures.

  7. 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.

  8. Benchmarking the DFT+U method for thermochemical calculations of uranium molecular compounds and solids.

    PubMed

    Beridze, George; Kowalski, Piotr M

    2014-12-18

    Ability to perform a feasible and reliable computation of thermochemical properties of chemically complex actinide-bearing materials would be of great importance for nuclear engineering. Unfortunately, density functional theory (DFT), which on many instances is the only affordable ab initio method, often fails for actinides. Among various shortcomings, it leads to the wrong estimate of enthalpies of reactions between actinide-bearing compounds, putting the applicability of the DFT approach to the modeling of thermochemical properties of actinide-bearing materials into question. Here we test the performance of DFT+U method--a computationally affordable extension of DFT that explicitly accounts for the correlations between f-electrons - for prediction of the thermochemical properties of simple uranium-bearing molecular compounds and solids. We demonstrate that the DFT+U approach significantly improves the description of reaction enthalpies for the uranium-bearing gas-phase molecular compounds and solids and the deviations from the experimental values are comparable to those obtained with much more computationally demanding methods. Good results are obtained with the Hubbard U parameter values derived using the linear response method of Cococcioni and de Gironcoli. We found that the value of Coulomb on-site repulsion, represented by the Hubbard U parameter, strongly depends on the oxidation state of uranium atom. Last, but not least, we demonstrate that the thermochemistry data can be successfully used to estimate the value of the Hubbard U parameter needed for DFT+U calculations.

  9. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    PubMed

    Fouda, Adam; Ryde, Ulf

    2016-11-08

    We have examined how the self-interaction error in density-functional theory (DFT) calculations affects energies calculated on large systems (600-1000 atoms) involving several charged groups. We employ 18 different quantum mechanical (QM) methods, including Hartree-Fock, as well as pure, hybrid, and range-separated DFT methods. They are used to calculate reaction and activation energies for three different protein models in vacuum, in a point-charge surrounding, or with a continuum-solvent model. We show that pure DFT functionals give rise to a significant delocalization of the charges in charged groups in the protein, typically by ∼0.1 e, as evidenced from the Mulliken charges. This has a clear effect on how the surroundings affect calculated reaction and activation energies, indicating that these methods should be avoided for DFT calculations on large systems. Fortunately, methods such as CAM-B3LYP, BHLYP, and M06-2X give results that agree within a few kilojoules per mole, especially when the calculations are performed in a point-charge surrounding. Therefore, we recommend these methods to estimate the effect of the surroundings with large QM systems (but other QM methods may be used to study the intrinsic reaction and activation energies).

  10. Daubechies wavelets for high performance electronic structure calculations: The BigDFT project

    NASA Astrophysics Data System (ADS)

    Genovese, Luigi; Videau, Brice; Ospici, Matthieu; Deutsch, Thierry; Goedecker, Stefan; Méhaut, Jean-François

    2011-02-01

    In this contribution we will describe in detail a Density Functional Theory method based on a Daubechies wavelets basis set, named BigDFT. We will see that, thanks to wavelet properties, this code shows high systematic convergence properties, very good performances and an excellent efficiency for parallel calculations. BigDFT code operation are also well-suited for GPU acceleration. We will discuss how the problematic of fruitfully benefit of this new technology can be match with the needs of robustness and flexibility of a complex code like BigDFT. This work may be of interest not only for expert in electronic structure calculations, but may also provide feedback to the wider community of high performance scientific computing.

  11. Synthesis, spectroscopic characterization and DFT calculations of β-O-4 type lignin model compounds

    NASA Astrophysics Data System (ADS)

    Mostaghni, Fatemeh; Teimouri, Abbas; Mirshokraei, Seyed Ahmad

    2013-06-01

    β-O-4 type lignin model compounds with the title of Erythro-2-(2-methoxyphenoxy)-1-(3,4,5-trimethoxyphenyl)-1,3-propanediol and Erythro-2-(2-methoxyphenoxy)-1-(4-Hydroxy-3,5-dimethoxyphenyl)-1,3-propanediol were synthesised and some modifications and improvements on them were introduced. These compounds were characterized by IR, Mass and NMR spectroscopy. Density functional theory (DFT) calculations were performed for the title compounds using the standard 6-31G* basis set. IR, 13C and 1H NMR of the title compounds were calculated at the DFT-B3LYP level of theory using the 6-31G* basis set. In this work comparison between the experimental and the theoretical results indicates that the DFT-B3LYP method is able to provide satisfactory results for predicting the properties of the considered compounds.

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

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

    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.

  13. Vibrational Frequencies of Fractionally Charged Molecular Species: Benchmarking DFT Results against ab Initio Calculations.

    PubMed

    Bâldea, Ioan

    2017-03-23

    Recent advances in nano/molecular electronics and electrochemistry made it possible to continuously tune the fractional charge q of single molecules and to use vibrational spectroscopic methods to monitor such changes. Approaches to compute vibrational frequencies ω(q) of fractionally charged species based on the density functional theory (DFT) are faced with an important issue: the basic quantity used in these calculations, the total energy, should exhibit piecewise linearity with respect to the fractional charge, but approximate, commonly utilized exchange correlation functionals do not obey this condition. In this paper, with the aid of a simple and representative example, we benchmark results for ω(q) obtained within the DFT against ab initio methods, namely, coupled cluster singles and doubles and also second- and third-order Møller-Plesset perturbation) expansions. These results indicate that, in spite of missing the aforementioned piecewise linearity, DFT-based values ω(q) can reasonably be trusted.

  14. 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.

  15. Rate Constants of Hydroperoxyl Radical Addition to Cyclic Nitrones: A DFT Study

    PubMed Central

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

    2008-01-01

    Nitrones are potential synthetic antioxidants against the reduction of radical-mediated oxidative damage in cells, and as analytical reagent 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 towards 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

  16. Crystal and molecular structure, conformational, vibrational properties and DFT calculations of melaminium bis (hydrogen oxalate)

    NASA Astrophysics Data System (ADS)

    Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Gunasekaran, S.; Rajakumar, P. R.; Anbalagan, G.

    2014-06-01

    Single crystals of melaminium bis (hydrogen oxalate) (MOX) were grown by slow evaporation method. X-ray powder diffraction analysis indicates that MOX crystallizes in monoclinic system (space group C2/c) and the calculated lattice constants are a = 20.075 ± 0.123 Ǻ, b = 8.477 ± 0.045 Ǻ, c = 6.983 ± 0.015, α = γ 90° and β = 102.6 ± 0.33°. Thermal analysis confirms that MOX is thermally stable up to 250 °C. A detailed interpretation of the FT-IR, FT-Raman and NMR spectra were reported. The equilibrium geometry, bonding features, and harmonic vibrational frequencies have been investigated with the help of PM6, HF and DFT/B3LYP methods. The potential energy curve shows that MOX molecule has two stable structures and the computational results diagnose that Rot I is the most stable conformer. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge-Invariant Atomic Orbital (GIAO) method. Stability of the molecule, arising from hyperconjugative interactions and charge delocalization, has been analyzed using Natural Bond Orbital (NBO) analysis. The electronic properties, such as HOMO and LUMO energies, were calculated by Time-Dependent DFT (TD-DFT) approach. To estimate chemical reactivity of the molecule, the molecular electrostatic potential (MEP) surface map is calculated for the optimized geometry of the molecule.

  17. 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.

  18. Stereochemical and conformational study on fenoterol by ECD spectroscopy and TD-DFT calculations.

    PubMed

    Tedesco, Daniele; Zanasi, Riccardo; Wainer, Irving W; Bertucci, Carlo

    2014-03-01

    Fenoterol and its derivatives are selective β2-adrenergic receptor (β2-AR) agonists whose stereoselective biological activities have been extensively investigated in the past decade; a complete stereochemical characterization of fenoterol derivatives is therefore crucial for a better understanding of the effects of stereochemistry on β2-AR binding. In the present project, the relationship between chiroptical properties and absolute stereochemistry of the stereoisomers of fenoterol (1) was investigated by experimental ECD spectroscopy and time-dependent density functional theory (TD-DFT). DFT geometry optimizations were carried out at the RI-B97D/TZVP/IEFPCM(MeOH) level and subsequent TD-DFT calculations were performed using the PBE0 hybrid functional. Despite the large pool of equilibrium conformers found for the investigated compounds and the known limitations of the level of theory employed, the computational protocol was able to reproduce the experimental ECD spectra of the stereoisomers of 1. The main contribution to the overall chiroptical properties was found to arise from the absolute configuration of the chiral center in α-position to the resorcinol moiety. Based on this evidence, a thorough conformational analysis was performed on the optimized DFT conformers, which revealed the occurrence of a different equilibrium between conformational patterns for the diastereomers of fenoterol: the (R,R')/(S,S') enantiomeric pair showed a higher population of folded conformations than the (R,S')/(S,R') pair.

  19. Spectroscopic investigations of 2,5-Difluoronitrobenzene using Hartree-Fock (HF) and density functional theory (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Saravanan, S. P.; Sankar, A.; Parimala, K.

    2017-01-01

    The complete structural and vibrational analysis of the 2,5-Difluoronitrobenzene (DNB) was carried out by Hartree-Fock (HF) and density functional theory (DFT) method (B3LYP) with 6-311++G (d,p) basis set. The fundamental vibrations are assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. Using the time-dependent density functional theory (TD-DFT) method, electronic absorption spectra of the title compound have been predicted and a good agreement with the experimental ones is determined. 13C and 1H NMR spectra were recorded and chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The hyperconjugative interaction energy (E(2)) and electron densities of donor (i) and acceptor (j) bonds were calculated using natural bond orbital (NBO) analysis. In addition, molecular electrostatic potential (MEP) and atomic charges were calculated using B3LYP/6-311++G (d,p) level of theory. Moreover, thermodynamic properties (heat capacities, entropy, enthalpy and Gibb's free energy) of the title compound at different temperatures were calculated.

  20. DFT calculations on spectroscopic and structural properties of a NLO chromophore

    NASA Astrophysics Data System (ADS)

    Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

    2016-03-01

    The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

  1. Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations.

    PubMed

    Wang, Xinye; Huang, Yaji; Pan, Zhigang; Wang, Yongxing; Liu, Changqi

    2015-09-15

    Kaolinite can be used as the in-furnace sorbent/additive to adsorb lead (Pb) vapor at high temperature. In this paper, the adsorptions of Pb atom, PbO molecule and PbCl2 molecule on kaolinie surfaces were investigated by density functional theory (DFT) calculation. Si surface is inert to Pb vapor adsorption while Al surfaces with dehydroxylation are active for the unsaturated Al atoms and the O atoms losing H atoms. The adsorption energy of PbO is much higher than that of Pb atom and PbCl2. Considering the energy barriers, it is easy for PbO and PbCl2 to adsorb on Al surfaces but difficult to escape. The high energy barriers of de-HCl process cause the difficulties of PbCl2 to form PbO·Al2O3·2SiO2 with kaolinite. Considering the inertia of Si atoms and the activity of Al atoms after dehydroxylation, calcination, acid/alkali treatment and some other treatment aiming at amorphous silica producing and Al activity enhancement can be used as the modification measures to improve the performance of kaolinite as the in-furnace metal capture sorbent.

  2. 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.

  3. 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.

  4. CO2 adsorption and separation from natural gason phosphorene surface: Combining DFT and GCMC calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Yayun; Liu, Chao; Hao, Feng; Xiao, Hang; Zhang, Shiwei; Chen, Xi

    2017-03-01

    We have examined the performance of phosphorene-based material, phosphorene slit pores (PSP), in CO2 adsorption and separation from natural gas by using Density Function Theory (DFT) calculation and Grand Canonical Monte Carlo (GCMC) simulations. First, the adsorption of CH4 and CO2molecules on phosphorene sheet were conducted by DFT study. Then, adsorption performances of natural gas components as well as their binary CO2/CH4 gas mixture were investigated at 300 K with the pressure up to 3.0 MPa. The effects of slit pore width, H, and mole ratio of CO2/CH4in the gas phase on the separation of CO2 from mixtures of CO2/CH4 were also investigated. Our DFT calculation results show that the CO2 moleculehas higher adsorption energy than that of CH4, which implies that it can be easily adsorbed to the phosphorene surface than CH4. Detailed GCMC simulations reveal that the phosphorene slit pore has a high performance in separating CO2fromnature gas and achieves the highest gas selectivity at H = 1.0 nm at pressures lower than 0.1 MPa. Moreover, the selectivity of CO2 overCO2/CH4gas mixture increases with increasing the mole ratio of CO2/CH4due to the enhanced adsorbate-adsorbent interactions for the favorable component. Therefore, it is suggested that the phosphorene is a promising candidate for natural gas purification and possessing practical potential applications in gas adsorption.

  5. Vibrational, structural and electronic study of a pyridinium salt assisted by SXRD studies and DFT calculations

    NASA Astrophysics Data System (ADS)

    Labra-Vázquez, Pablo; Palma-Contreras, Miguel; Santillan, Rosa; Farfán, Norberto

    2017-03-01

    The molecular structure of 1-[2-oxo-2-(2-pyridinyl)ethyl]pyridinium iodide (C12H11IN2O) is discussed using an experimental (FT-IR/ATR, NMR, SXRD) and theoretical (DFT, B3LYP/6-311G**) approach. Compound 2 crystallized in the monoclinic P21/c space group with 4 molecules per unit cell and unit cell dimensions a = 7.5629 Å (3), b = 21.5694 Å (7), c = 7.8166 Å (3). The crystal packing is governed by ion-dipole contacts and π-π stacking. High electrostatic potential at the ethanone hydrogens was derived from DFT calculations, further explaining the acidity and reactivity of the molecule as a Michael donor.

  6. 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.

  7. Chemisorption of Hydroxide on 2D Materials From DFT Calculations: Graphene Versus Hexagonal Boron Nitride

    PubMed Central

    Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lyderic; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

    2017-01-01

    Recent nanofluidic measurements revealed strongly different surface charge measurements for boron-nitride and graphitic nanotubes when in contact with saline and alkaline water. 1,2 These observations contrast with the similar reactivity of a graphene layer and its boron nitride counterpart, using Density Functional Theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here, we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials – chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values resulting in a favorable (non-favorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echoes the weaker surface charge measurements, but points to an alternative scenario. PMID:27809540

  8. DFT calculations of magnetic anisotropy energy of Ge(1-x)Mn(x)Te ferromagnetic semiconductor.

    PubMed

    Łusakowski, A; Bogusławski, P; Story, T

    2015-06-10

    Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge(1-x)Mn(x)Te were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge(1-x)Mn(x)Te (1 1 1) thin layers.

  9. DFT calculations of magnetic anisotropy energy of Ge1-xMnxTe ferromagnetic semiconductor

    NASA Astrophysics Data System (ADS)

    Łusakowski, A.; Bogusławski, P.; Story, T.

    2015-06-01

    Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge1-xMnxTe were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge1-xMnxTe (1 1 1) thin layers.

  10. Raman spectroscopic study of the Chromobacterium violaceum pigment violacein using multiwavelength excitation and DFT calculations.

    PubMed

    Jehlička, Jan; Edwards, Howell G M; Němec, Ivan; Oren, Aharon

    2015-01-01

    Violacein is a bisindole pigment occurring as a biosynthetic product of Chromobacterium violaceum and Janthinobacterium lividum. It has some structural similarities to the cyanobacterial UV-protective pigment scytonemin, which has been the subject of comprehensive spectroscopic and structural studies. A detailed experimental Raman spectroscopic study with visible and near-infrared excitation of violacein produced by C. violaceum has been undertaken and supported using theoretical DFT calculations. Raman spectra with 514 and 785 nm excitation of cultivated cells as well as extracts and Gaussian (B3LYP/6-311++G(d,p)) calculations with proposed molecular vibrational assignments are reported here.

  11. 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.

  12. 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.

  13. 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.

  14. Water adsorption in SAPO-34: elucidating the role of local heterogeneities and defects using dispersion-corrected DFT calculations.

    PubMed

    Fischer, Michael

    2015-10-14

    The chabazite-type silicoaluminophosphate SAPO-34 is a promising adsorbent for applications in thermal energy storage using water adsorption-desorption cycles. In order to develop a microscopic understanding of the impact of local heterogeneities and defects on the water adsorption properties, the interaction of different models of SAPO-34 with water was studied using dispersion-corrected density-functional theory (DFT-D) calculations. In addition to SAPO-34 with isolated silicon atoms, the calculations considered models incorporating two types of heterogeneities (silicon islands, aluminosilicate domains), and two defect-containing (partially and fully desilicated) systems. DFT-D optimisations were performed for systems with small amounts of adsorbed water, in which all H2O molecules can interact with framework protons, and systems with large amounts of adsorbed water (30 H2O molecules per unit cell). At low loadings, the host-guest interaction energy calculated for SAPO-34 with isolated Si atoms amounts to approximately -90 kJ mol(-1). While the presence of local heterogeneities leads to the creation of some adsorption sites that are energetically slightly more favourable, the interaction strength is drastically reduced in systems with defects. At high water loadings, energies in the range of -70 kJ mol(-1) are obtained for all models. The DFT-D interaction energies are in good agreement with experimentally measured heats of water adsorption. A detailed analysis of the equilibrium structures was used to gain insights into the binding modes at low coverages, and to assess the extent of framework deprotonation and changes in the coordination environment of aluminium atoms at high water loadings.

  15. A group additivity algorithm for polychlorinated dibenzofurans derived from selected DFT analyses.

    PubMed

    Thompson, Dennis; Ewan, Bruce C R

    2007-06-14

    The difficulty in measuring the heats of combustion of polychlorinated dibenzofurans (PCDFs) has resulted in a shortage of data on their heats of formation, required for the purpose of developing an understanding of the role of thermodynamics and kinetics in their production via industrial processes. B3LYP density functional theory calculations have been carried out on a number of PCDFs using 6-31G(d) and 6-311+G(3df,p) basis sets to estimate their heats of formation based on the known experimental values for dibenzofuran, benzene and chlorobenzene. By examining the interactions among chlorine substituents, it is shown that energy contributions arising from successive chlorination can be interpreted in a predictable way, based on a small number of key energy parameters associated with ring position and chlorine atom repulsions. These parameters have been presented as the basis for a simplified prediction algorithm, which can be used to reproduce the predicted DFT heat of formation to within a few kJ/mol, avoiding the need to carry out extensive DFT calculations on the possible 135 isomers of the dibenzofuran group.

  16. Understanding the interfacial properties of graphene-based materials/BiOI heterostructures by DFT calculations

    NASA Astrophysics Data System (ADS)

    Dai, Wen-Wu; Zhao, Zong-Yan

    2017-06-01

    Heterostructure constructing is a feasible and powerful strategy to enhance the performance of photocatalysts, because they can be tailored to have desirable photo-electronics properties and couple distinct advantageous of components. As a novel layered photocatalyst, the main drawback of BiOI is the low edge position of the conduction band. To address this problem, it is meaningful to find materials that possess suitable band gap, proper band edge position, and high mobility of carrier to combine with BiOI to form hetertrostructure. In this study, graphene-based materials (including: graphene, graphene oxide, and g-C3N4) were chosen as candidates to achieve this purpose. The charge transfer, interface interaction, and band offsets are focused on and analyzed in detail by DFT calculations. Results indicated that graphene-based materials and BiOI were in contact and formed van der Waals heterostructures. The valence and conduction band edge positions of graphene oxide, g-C3N4 and BiOI changed with the Fermi level and formed the standard type-II heterojunction. In addition, the overall analysis of charge density difference, Mulliken population, and band offsets indicated that the internal electric field is facilitate for the separation of photo-generated electron-hole pairs, which means these heterostructures can enhance the photocatalytic efficiency of BiOI. Thus, BiOI combines with 2D materials to construct heterostructure not only make use of the unique high electron mobility, but also can adjust the position of energy bands and promote the separation of photo-generated carriers, which provide useful hints for the applications in photocatalysis.

  17. Combination of EPR measurements and DFT calculations to study nitrate impurities in the carbonated nanohydroxyapatite.

    PubMed

    Biktagirov, Timur; Gafurov, Marat; Mamin, Georgy; Klimashina, Elena; Putlayev, Valery; Orlinskii, Sergei

    2014-02-27

    We demonstrate the application of the combined experimental-computational approach for studying the anionic impurities in hydroxyapatite (HAp). Influence of the carbonation level (x) on the concentration of the NO3(2-) radicals in the HAp nanocrystals of Ca10-xNax(PO4)6-x(CO3)x(OH)2 with x in the range 0 < x < 2 and average sizes of 30 nm is investigated by different analytical methods including electron paramagnetic resonance (EPR). Stable NO3(2-) radicals are formed under X-ray irradiation of nano-HAp samples from NO3(-) ions incorporated in trace amounts during the wet synthesis process. Density functional theory (DFT) based calculations show energetic preference for the PO4 group substitution by NO3(-) ions. Comparison of the calculated and experimental spectroscopic parameters (g and hyperfine tensors) reveals that EPR detects the NO3(2-) radicals located in the positions of the PO4 group only. It is shown that with the increase in x, the carbonate ions substitute the NO3(2-)/NO3(-) ions. DFT calculations confirm that carbonate incorporation in HAp structure is energetically more favorable than the formation of the nitrate defect.

  18. Detailed structural study of β-artemether: Density functional theory (DFT) calculations of Infrared, Raman spectroscopy, and vibrational circular dichroism

    NASA Astrophysics Data System (ADS)

    Wang, Zhiqiang; Chen, Jianchao; Li, Linwei; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2015-10-01

    In this study, the experimental and theoretical studies on the structure of β-artemether are presented. The optimized molecular structure, Mulliken atomic charges, vibrational spectra (IR, Raman and vibrational circular dichroism), and molecular electrostatic potential have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (2d, p) basis set. Reliable vibrational assignments for Artemether have been made on the basis of potential energy distribution (PED). The vibrational circular dichroism (VCD) has been explored by ab initio calculations, and then was used to compare with the experimental VCD. The consistence between them confirmed the absolute configuration of Artemether. In addition, HOMO-LUMO of the title compound as well as thermo-dynamical parameters has illustrated the stability of β-artemether.

  19. Structural studies of PCU-hydrazones: NMR spectroscopy, X-ray diffractions, and DFT calculations

    NASA Astrophysics Data System (ADS)

    Veljković, Jelena; Šekutor, Marina; Molčanov, Krešimir; Lo, Rabindranath; Ganguly, Bishwajit; Mlinarić-Majerski, Kata

    2011-06-01

    In this article we present a detailed structural investigation for the configurational isomers of PCU-hydrazones. The structural characterization of these hydrazones was performed using NMR spectroscopy, X-ray diffraction analysis and theoretical calculations. The single crystal X-ray structures of PCU-hydrazones 6B and 6C have been solved and used to conclusively confirm the characterization obtained via NMR spectra of a particular isomer. Nuclear magnetic shielding values calculated for 6A-C using DFT calculations were correlated with the experimentally determined chemical shifts. The computed results were found to be in good agreement with the observed 13C NMR values. The computed NMR results helped to ascertain the isomers of PCU-hydrazones 4A-C.

  20. 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

    2015-02-05

    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.

  1. Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.

    PubMed

    Siiskonen, Antti; Priimagi, Arri

    2017-02-01

    In recent years, halogen bonding has become an important design tool in crystal engineering, supramolecular chemistry and biosciences. The fundamentals of halogen bonding have been studied extensively with high-accuracy computational methods. Due to its non-covalency, the use of triple-zeta (or larger) basis sets is often recommended when studying halogen bonding. However, in the large systems often encountered in supramolecular chemistry and biosciences, large basis sets can make the calculations far too slow. Therefore, small basis sets, which would combine high computational speed and high accuracy, are in great demand. This study focuses on comparing how well density functional theory (DFT) methods employing small, double-zeta basis sets can estimate halogen-bond strengths. Several methods with triple-zeta basis sets are included for comparison. Altogether, 46 DFT methods were tested using two data sets of 18 and 33 halogen-bonded complexes for which the complexation energies have been previously calculated with the high-accuracy CCSD(T)/CBS method. The DGDZVP basis set performed far better than other double-zeta basis sets, and it even outperformed the triple-zeta basis sets. Due to its small size, it is well-suited to studying halogen bonding in large systems.

  2. DFT Calculations of the Electronic Structure and Interlayer Interaction in the Li-INTERCALATED Graphene Bilayer

    NASA Astrophysics Data System (ADS)

    Petrova, N. V.; Yakovkin, I. N.

    The electronic band structure, density of states (DOS) and interlayer interaction in Li-intercalated graphene bilayers are studied by means of density functional theory (DFT) calculations. It has been found that for a pristine bilayer, the relative shift of graphene layers from AB stacking configuration, pertinent to a bulk graphite, to AA configuration results in the opening of the bandgap at Fermi level, so that the bilayer becomes a semiconductor. The Li intercalation of the graphene bilayer significantly increases the density of states at Fermi level, which can be considered as an increased metallicity. The electronic density in the space between graphene layers also substantially increases and leads to related increase of the interlayer interaction. We hope that the obtained results of calculations will be useful for various applications of Li-intercalated graphene layers in nanoelectronics.

  3. Structural and elastic properties characterization of Be and Mg doped boron nitride nanotubes using DFT calculations

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Malakpour, S.

    2015-06-01

    Through doping boron nitride nanotubes, their band gaps could be controlled which results in extending the range of their applications particularly in nanosensors. In this article, the structural and elastic properties of Be and Mg doped boron nitride nanotubes with various chiralities are studied based on ab initio density functional calculations. In order to perform the density functional theory (DFT) calculations, the exchange correlation of Perdew-Burke-Ernzerhof within the generalized gradient approximation (GGA) framework is employed. It is observed that doping Be and Mg atoms increases the equilibrium strain energy of boron nitride nanotubes. Furthermore, it is found that among all of the considered nanotubes, an increase in the value of Young's modulus of (4, 4) armchair boron nitride nanotube through doping Be atom instead of boron atom is so considerable.

  4. A first-principles DFT study of UN bulk and (001) surface: comparative LCAO and PW calculations.

    PubMed

    Evarestov, R A; Bandura, A V; Losev, M V; Kotomin, E A; Zhukovskii, Yu F; Bocharov, D

    2008-10-01

    LCAO and PW DFT calculations of the lattice constant, bulk modulus, cohesive energy, charge distribution, band structure, and DOS for UN single crystal are analyzed. It is demonstrated that a choice of the uranium atom relativistic effective core potentials considerably affects the band structure and magnetic structure at low temperatures. All calculations indicate mixed metallic-covalent chemical bonding in UN crystal with U5f states near the Fermi level. On the basis of the experience accumulated in UN bulk simulations, we compare the atomic and electronic structure as well as the formation energy for UN(001) surface calculated on slabs of different thickness using both DFT approaches.

  5. Molecular and supramolecular properties of nitroaromatic thiosemicarbazones: Synthesis, spectroscopy, X-ray structure elucidation and DFT calculations

    NASA Astrophysics Data System (ADS)

    Dias, L. C.; de Lima, G. M.; Pinheiro, C. B.; Nascimento, M. A. C.; Bitzer, R. S.

    2017-03-01

    The reactions of 6-nitropiperonal with H2Nsbnd NHsbnd C(S)sbnd NHR, R = Me, Et, Ph or H, afforded four nitroaromatic thiosemicarbazones 1-4, respectively. 1-4 were characterized by elemental analysis (CHN), FTIR, and 1H and 13C{1H} NMR spectroscopy. In addition, the crystal structures of 2 and 3 were determined by single-crystal X-ray diffraction. Our X-ray structural results have shown that the nitropiperonal and thiosemicarbazone moieties exhibit an almost coplanar arrangement for both 2 and 3. Moreover, they establish 2-D networks along the [111] base vector by means of classical and nonclassical hydrogen bonds. Electronic and spectroscopic properties of 1-4 were investigated at the DFT B3LYP/6-311G** level of calculation. The Cdbnd S group of 1-4 constitutes a nucleophilic region, whereas the NO2 group defines an electrophilic centre, as expected. Furthermore, a DFT vibrational analysis of 4 allowed a reliable assignment of the thiosemicarbazone-based vibrations. Also, a good agreement between theoretical and experimental 13C chemical shift values was obtained for 1-4.

  6. Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride.

    PubMed

    Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lydéric; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

    2016-11-17

    Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials-chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario.

  7. 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).

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate.

    PubMed

    Chen, Yi; Zhang, Hui; Liu, Qing

    2014-05-21

    The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G(*) level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The C=O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the CC group in VAc. The calculated and experimental C=O stretching vibration frequencies of VAc (νcal(C=O) and νexp(C=O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two C=O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

  15. FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Zhang, Hui; Liu, Qing

    The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G* level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The Cdbnd O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the Cdbnd C group in VAc. The calculated and experimental Cdbnd O stretching vibration frequencies of VAc (νcal(Cdbnd O) and νexp(Cdbnd O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two Cdbnd O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

  16. Structural analysis of N,N-diacyl-1,4-dihydropyrazine by variable-temperature NMR and DFT calculation

    NASA Astrophysics Data System (ADS)

    Song, Xiu-qing; Tan, Hong-bo; Yan, Hong; Chang, Yu

    2017-04-01

    N,N-diacyl-1,4-dihydropyrazine derivatives (1) were prepared via an efficient microwave-assisted synthesis. 1 was isolated and unambiguously confirmed by NMR spectra and high-resolution mass spectrometry. The NMR spectra of 1 showed complicated rather than conventional spectroscopy. Variable-temperature experiments and DFT calculation (PES) were used to investigate this phenomenon. DFT calculations confirmed that the structures of the two rotamers of 1 correspond to those determined by NMR in solution, and gave the syn-anti interconversion barriers of rotamers. The results showed that two isomers exist in solution (deuterated solvent) at room temperature, resulting in complicated NMR spectra.

  17. First-principles study of terpyrrole as a potential hydrogen cyanide sensor: DFT calculations.

    PubMed

    Shokuhi Rad, Ali; Zardoost, Mohammad Reza; Abedini, Ehsan

    2015-10-01

    The sensitivity of terpyrrole (TPy; used as a polypyrrole model) to toxic hydrogen cyanide (HCN) adsorption was studied by using DFT to perform geometry optimization and to calculate the adsorption energy of HCN on TPy as well as orbital properties. The interaction of terpyrrole with HCN was studied for different relative orientations of the molecules. The adsorption energy, charge analysis, and the density of states were used to evaluate the ability of TPy to sense HCN in these different relative orientations. The adsorption energy was calculated to be -3.9 and -3.1 kcal mol(-1) for two possible relative orientations. Frontier molecular orbitals and energies indicated that some hybridization occurs during the adsorption of HCN on TPy when the molecules have appropriate relative orientations, resulting in an increase in conductivity. Considering the changes in the HOMO-LUMO energy gap that were calculated to occur during HCN adsorption, it is clear that TPy is sensitive to HCN adsorption, suggesting that TPy has the potential to act as an HCN sensor. Graphical abstract HCN adsorption on TPy.

  18. Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

    2015-04-01

    A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of Carbamazepine.

  19. Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations.

    PubMed

    Suhasini, M; Sailatha, E; Gunasekaran, S; Ramkumaar, G R

    2015-04-15

    A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the (13)C and (1)H NMR chemical shifts of Carbamazepine.

  20. 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.

  1. Electronic structure and excitations in oxygen deficient CeO2-δ from DFT calculations

    NASA Astrophysics Data System (ADS)

    Jarlborg, T.; Barbiellini, B.; Lane, C.; Wang, Yung Jui; Markiewicz, R. S.; Liu, Zhi; Hussain, Zahid; Bansil, A.

    2014-04-01

    The electronic structures of supercells of CeO2-δ have been calculated within the density functional theory (DFT). The equilibrium properties such as lattice constants, bulk moduli, and magnetic moments are well reproduced by the generalized gradient approximation (GGA). Electronic excitations are simulated by robust total-energy calculations for constrained states with atomic core holes or valence holes. Pristine ceria CeO2 is found to be a nonmagnetic insulator with magnetism setting in as soon as oxygens are removed from the structure. In the ground state of defective ceria, the Ce-f majority band resides near the Fermi level but appears at about 2 eV below the Fermi level in photoemission spectroscopy experiments due to final-state effects. We also tested our computational method by calculating threshold energies in Ce-M5 and O-K x-ray absorption spectroscopy and comparing theoretical predictions with the corresponding measurements. Our result that f electrons reside near the Fermi level in the ground state of oxygen-deficient ceria is crucial for understanding the catalytic properties of CeO2 and related materials.

  2. Electronic and optical properties of AlN under pressure: DFT calculations

    NASA Astrophysics Data System (ADS)

    Javaheri, Sahar; Boochani, Arash; Babaeipour, Manuchehr; Naderi, Sirvan

    2017-01-01

    Structural, elastic, optical, and electronic properties of wurtzite (WZ), zinc-blende (ZB), and rocksalt (RS) structures of AlN are investigated using the first-principles method and within the framework of density functional theory (DFT). Lattice parameters, bulk modulus, shear modulus, Young’s modulus, and elastic constants are calculated at zero pressure and compared with other experimental and theoretical results. The wurtzite and zinc-blende structures have a transition to rocksalt phase at the pressures of 12.7 GPa and 14 GPa, respectively. The electronic properties are calculated using both GGA and EV-GGA approximations; the obtained results by EV-GGA approximation are in much better agreement with the available experimental data. The RS phase has the largest bandgap with an amount of 4.98 eV; by increasing pressure, this amount is also increased. The optical properties like dielectric function, energy loss function, refractive index, and extinction coefficient are calculated under pressure using GGA approximation. Inter-band transitions are investigated using the peaks of imaginary part of the dielectric function and these transitions mainly occur from N-2p to Al-3p levels. The results show that the RS structure has more different properties than the WZ and ZB structures.

  3. Lipophilicity Assessment of Ruthenium(II)-Arene Complexes by the Means of Reversed-Phase Thin-Layer Chromatography and DFT Calculations

    PubMed Central

    Shweshein, Khalil Salem A. M.; Andrić, Filip; Radoičić, Aleksandra; Gruden-Pavlović, Maja; Tešić, Živoslav; Milojković-Opsenica, Dušanka

    2014-01-01

    The lipophilicity of ten ruthenium(II)-arene complexes was assessed by reversed-phase thin-layer chromatography (RP-TLC) on octadecyl silica stationary phase. The binary solvent systems composed of water and acetonitrile were used as mobile phase in order to determine chromatographic descriptors for lipophilicity estimation. Octanol-water partition coefficient, logKOW, of tested complexes was experimentally determined using twenty-eight standard solutes which were analyzed under the same chromatographic conditions as target substances. In addition, ab initio density functional theory (DFT) computational approach was employed to calculate logKOW values from the differences in Gibbs' free solvation energies of the solute transfer from n-octanol to water. A good overall agreement between DFT calculated and experimentally determined logKOW values was established (R2 = 0.8024–0.9658). PMID:24587761

  4. Lipophilicity assessment of ruthenium(II)-arene complexes by the means of reversed-phase thin-layer chromatography and DFT calculations.

    PubMed

    Shweshein, Khalil Salem A M; Andrić, Filip; Radoičić, Aleksandra; Zlatar, Matija; Gruden-Pavlović, Maja; Tešić, Zivoslav; Milojković-Opsenica, Dušanka

    2014-01-01

    The lipophilicity of ten ruthenium(II)-arene complexes was assessed by reversed-phase thin-layer chromatography (RP-TLC) on octadecyl silica stationary phase. The binary solvent systems composed of water and acetonitrile were used as mobile phase in order to determine chromatographic descriptors for lipophilicity estimation. Octanol-water partition coefficient, logK(OW), of tested complexes was experimentally determined using twenty-eight standard solutes which were analyzed under the same chromatographic conditions as target substances. In addition, ab initio density functional theory (DFT) computational approach was employed to calculate logK(OW) values from the differences in Gibbs' free solvation energies of the solute transfer from n-octanol to water. A good overall agreement between DFT calculated and experimentally determined logK(OW) values was established (R(2) = 0.8024-0.9658).

  5. Copper(II) complexes with pyrazole derivatives - Synthesis, crystal structure, DFT calculations and cytotoxic activity

    NASA Astrophysics Data System (ADS)

    Kupcewicz, Bogumiła; Ciolkowski, Michal; Karwowski, Boleslaw T.; Rozalski, Marek; Krajewska, Urszula; Lorenz, Ingo-Peter; Mayer, Peter; Budzisz, Elzbieta

    2013-11-01

    The series of pyrazole derivatives (1a-4a) were used as bidentate N,N' ligands to obtain neutral Cu(II) complexes of ML2Cl2 type (1b-4b). The molecular structures of ligand 1a and Cu(II) complex 4b were determined by X-ray crystallography and theoretical DFT calculations. In this study, three functionals B3LYP, BP86 and mPW1PW91 with different basis sets and two effective core potentials Los Alamos and Stuttgart/Dresden were performed. The DFT study disclosed the usefulness of BP86 functional with SDD-ECP for Cu(II) ion and dedicated D95 basis set for other non-transition metal atoms, with the exclusion of Cl for which 6-31++G(2df,2pd) were used. The structural analysis shows that the presence of phenyl substituent in a pyrazole ring contributed to Cu-N bond elongation, which can result in different reactivity of complexes 1b and 3b. The cytotoxicity of the obtained compounds was evaluated on three cancer cells lines: HL-60, NALM-6 and WM-115. The complexes have exhibited similar moderate antiproliferative activity. All the complexes, except for 1b, were found to be more active against three cancer cell lines than uncomplexed pyrazoles. The lipophilicity and electrochemical properties of ligands and complexes was also studied. For complexes with ligand 1a and 3a only one reduction process at the metal centre occurs (Cu(II) → Cu(I)) with oxidization of Cu(I)-Cu(II) in the backward step.

  6. 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

    2015-03-05

    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.

  7. 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)...

  8. Electronic structure and thermoelectricity of filled skutterudite EuRu4As12: a DFT calculation

    NASA Astrophysics Data System (ADS)

    Shankar, A.; Rai, D. P.; Sandeep; Ghimire, M. P.; Thapa, R. K.

    2017-01-01

    On the basis of the first-principles density functional theory (DFT), we have investigated the electronic structure, elastic and magnetic properties of the filled skutterudite EuRu4As12 using the full-potential linearized augmented plane wave (FP-LAPW) method. The calculations presented here are carried out within the framework of the local spin density approximation (LSDA) approach. The effects of the localized electrons are treated by including Hubbard's U term in the calculation. The study of the elastic properties suggests the brittle nature of the material with covalent contribution in the atomic bonding. EuRu4As12 is a semi-metal with the presence of the bands originating from the bottom of the conduction region crossing the Fermi energy level (EF) more than twice. The existence of the high density of states at EF implies the large thermopower of the material and likely to be an effective candidate for the thermoelectric application. The exchange-splitting of Eu- f states are analyzed to explain the ferromagnetic ground state of the material. The analysis of the thermal transport properties suggests the high value of Seebeck coefficient of the material with figure of merit ( ZT) value of 0.55, which is consistent with the values obtained for the analogous compounds.

  9. Basis set convergence of electric properties in HF and DFT calculations of nucleic acid bases

    NASA Astrophysics Data System (ADS)

    Campos, C. T.; Jorge, F. E.

    Recently, a hierarchical sequence of augmented basis sets of double, triple, and quadruple zeta valence quality plus polarization functions (AXZP, X = D, T, and Q) for the atoms from H to Ar were presented by Jorge et al. We report a systematic study of basis sets required to obtain accurate values of several electric properties for benzene, pyridine, the five common nucleic acid bases (uracil, cytosine, thymine, guanine, and adenine), and three related bases (fluorouracil, 5-methylcytosine, and hypoxanthine) at their full optimized geometries. Two methods were examined: Hartree-Fock (HF) and density functional theory (DFT). Including electron correlation decreases the magnitude of the dipole moment and increases the mean polarizability and also the polarizability anisotropy for every molecule. Calculated B3LYP/ADZP dipole moments and dipole polarizabilities show good agreement with both experimental and ab initio results based on second-order Møller-Plesset perturbation theory calculations. We have also showed that a basis set of double zeta quality is enough to obtain reliable and accurate electric property results for this kind of compounds.

  10. Elucidating ozonation mechanisms of organic micropollutants based on DFT calculations: Taking sulfamethoxazole as a case.

    PubMed

    Zhang, Siyu; Yu, Gang; Chen, Jingwen; Zhao, Qing; Zhang, Xuejiao; Wang, Bin; Huang, Jun; Deng, Shubo; Wang, Yujue

    2017-01-01

    Ozonation is widely used in wastewater treatment plants to remove diverse organic micropollutants. As molecular structures of organic micropollutants contain multiple ozone-preferred reaction sites, and moreover intermediate products can react with ozone again, ozonation mechanism is complex. A fast increasing number of organic micropollutants and a great demand of ecological risk assessments call for an in silico method to provide insights into the ozonation mechanism of organic micropollutants. Here, an in silico model was developed to unveil ozonation mechanisms of organic micropollutants. Sulfamethoxazole was taken as a case. The model enumerates elementary reactions following well-accepted ozonation patterns and secondary transformation reactions established for intermediates by experiments. Density functional theory (DFT) calculations were employed for evaluating thermodynamic feasibilities of reaction pathways. By calculating Gibbs free energies, ozonation products of SMX were predicted. The predicted products are consistent with those detected in experiments. This method is advanced in revealing all possible reaction pathways including minor pathways that produce toxic byproducts but are difficult to be observed by experiments. Accordingly, water treatment engineers can setup necessary treatment technology to ensure water safety.

  11. Surface study of gallium- and aluminum- doped graphenes upon adsorption of cytosine: DFT calculations

    NASA Astrophysics Data System (ADS)

    Shokuhi Rad, Ali; Zareyee, Daryoush; Peyravi, Majid; Jahanshahi, Mohsen

    2016-12-01

    The adsorption of cytosine molecule on Al- and Ga- doped graphenes is studied using first-principles density functional theory (DFT) calculations. The energetically most stable geometries of cytosine on both Al- and Ga- doped graphenes are determined and the adsorption energies are calculated. The net charge of transfer as well as local charge of doped atoms upon adsorption of cytosine are studied by natural bond orbitals (NBO) analysis. Orbital hybridizing of complexes was searched by frontier molecular orbital theory (FMO), and density of states (DOS). Depending on the side of cytosine, there are four possible sites for its adsorption on doped graphene; denoted as P1, P2, P3, and P4, respectively. The order of binding energy in the case of Al-doped graphene is found as P1 ˃ P4 ˃ P3 ˃ P2. Interestingly, the order in the case of Ga-doped graphene changes to: P4 ∼ P1˃ P3˃ P2. Both surfaces show superior adsorbent property, resulting chemisorption of cytosine, especially at P1 and P4 position configurations. The NBO charge analysis reveals that the charge transfers from Al- and Ga- doped graphene sheets to cytosine. The electronic properties of both surfaces undertake important changes after cytosine adsorption, which indicates notable change in its electrical conductivity.

  12. Study of conformational stability, structural, electronic and charge transfer properties of cladrin using vibrational spectroscopy and DFT calculations.

    PubMed

    Singh, Swapnil; Singh, Harshita; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Bharti, Purnima; Kumar, Sudhir; Kumar, Padam; Maurya, Rakesh

    2014-11-11

    In the present work, a detailed conformational study of cladrin (3-(3,4-dimethoxy phenyl)-7-hydroxychromen-4-one) has been done by using spectroscopic techniques (FT-IR/FT-Raman/UV-Vis/NMR) and quantum chemical calculations. The optimized geometry, wavenumber and intensity of the vibrational bands of the cladrin in ground state were calculated by density functional theory (DFT) employing 6-311++G(d,p) basis sets. The study has been focused on the two most stable conformers that are selected after the full geometry optimization of the molecule. A detailed assignment of the FT-IR and FT-Raman spectra has been done for both the conformers along with potential energy distribution for each vibrational mode. The observed and scaled wavenumber of most of the bands has been found to be in good agreement. The UV-Vis spectrum has been recorded and compared with calculated spectrum. In addition, 1H and 13C nuclear magnetic resonance spectra have been also recorded and compared with the calculated data that shows the inter or intramolecular hydrogen bonding. The electronic properties such as HOMO-LUMO energies were calculated by using time-dependent density functional theory. Molecular electrostatic potential has been plotted to elucidate the reactive part of the molecule. Natural bond orbital analysis was performed to investigate the molecular stability. Non linear optical property of the molecule have been studied by calculating the electric dipole moment (μ) and the first hyperpolarizability (β) that results in the nonlinearity of the molecule.

  13. Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations.

    PubMed

    Manin, Alex N; Voronin, Alexander P; Manin, Nikolay G; Vener, Mikhail V; Shishkina, Anastasia V; Lermontov, Anatoly S; Perlovich, German L

    2014-06-19

    A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.

  14. Geometrical Characterization of Adenine And Guanine on Cu(110) By NEXAFS, XPS, And DFT Calculation

    SciTech Connect

    Furukawa, M.; Yamada, T.; Katano, S.; Kawai, M.; Ogasawara, H.; Nilsson, A.; /SLAC, SSRL /Stockholm U.

    2009-04-30

    Adsorption of purine DNA bases (guanine and adenine) on Cu(1 1 0) was studied by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine-structure spectroscopy (NEXAFS), and density-functional theory (DFT) calculation. At coverages near 0.2 monolayers, Angular-resolved NEXAFS analysis revealed that adenine adsorbates lie almost flat and that guanine adsorbates are tilted up on the surface with the purine ring parallel to the atom rows of Cu(1 1 0). Referring to the previous studies on pyrimidine DNA bases [M. Furukawa, H. Fujisawa, S. Katano, H. Ogasawara, Y. Kim, T. Komeda, A. Nilsson, M. Kawai, Surf. Sci. 532-535 (2003) 261], the isomerization of DNA bases on Cu(1 1 0) was found to play an important role in the adsorption geometry. Guanine, thymine and cytosine adsorption have an amine-type nitrogen next to a carbonyl group, which is dehydrogenated into imine nitrogen on Cu(1 1 0). These bases are bonded by the inherent portion of - NH-CO - altered by conversion into enolic form and dehydrogenation. Adenine contains no CO group and is bonded to Cu(1 1 0) by participation of the inherent amine parts, resulting in nearly flatly-lying position.

  15. 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.

  16. 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.

  17. Theoretical study of atomic oxygen on gold surface by Hückel theory and DFT calculations.

    PubMed

    Sun, Keju; Kohyama, Masanori; Tanaka, Shingo; Takeda, Seiji

    2012-09-27

    It is fundamental to understand the behavior of atomic oxygen on gold surfaces so as to elucidate the mechanism of nano gold catalysts for low-temperature CO oxidation reactions since the atomic oxygen on gold system is an important intermediate involved in both the processes of O(2) dissociation and CO oxidation. We performed theoretical analysis of atomic oxygen adsorption on gold by using Hückel theory. It is found that formation of linear O-Au-O structure on Au surfaces greatly stabilizes the atomic oxygen adsorption due to stronger bond energy and bond order, which is confirmed subsequently by density functional theory (DFT) calculations. The linear O-Au-O structure may explain the surprising first order kinetics behavior of O(2) desorption from gold surfaces. This view of the linear O-Au-O structure as the natural adsorption status is quite different from the conventional view, which may lead to new understanding toward the reaction mechanism of low-temperature CO oxidation reaction on nano gold catalysts.

  18. Modelling the matrix shift on the vibrational frequency of ThO by DFT-D3 calculations

    NASA Astrophysics Data System (ADS)

    Kovács, Attila; Rode, Joanna E.

    2017-03-01

    Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯ Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ω PBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.

  19. 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...

  20. The screened pseudo-charge repulsive potential in perturbed orbitals for band calculations by DFT+U.

    PubMed

    Huang, Bolong

    2017-03-06

    The conventional linear response overestimates the U in DFT+U calculations for solids with fully occupied orbitals. Here, we demonstrate that the challenge arises from the incomplete cancellation of the electron-electron Coulomb repulsion energy under external perturbation. We applied the second charge response, denoted as the "pseudo-charge" model, to offset such residue effects. Counteracting between these two charge response-induced Coulomb potentials, the U parameters are self-consistently obtained by fulfilling the conditions for minimizing the non-Koopmans energy. Moreover, the pseudo-charge-induced repulsive potential shows a screening behavior related to the orbital occupation and is potentially in compliance with the screened exact exchange-correlation of electrons. The resultant U parameters are self-consistent solutions for improved band structure calculations by the DFT+U method. This work extends the validity of the linear response method to both partially and fully occupied orbitals and gives a reference for estimating the Hubbard U parameter prior to other advanced methods. The U parameters were determined in a transferability test using both PBE and hybrid density functional methods, and the results showed that this method is independent of the functional. The electronic structures determined from the hybrid-DFT+U(hybrid) approach are provided. Comparisons are also made with the recently developed self-consistent hybrid-DFT+Uw method.

  1. (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.

  2. 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.

  3. Electronic structure of O-doped SiGe calculated by DFT + U method

    NASA Astrophysics Data System (ADS)

    Zhao, Zong-Yan; Yang, Wen; Yang, Pei-Zhi

    2016-12-01

    To more in depth understand the doping effects of oxygen on SiGe alloys, both the micro-structure and properties of O-doped SiGe (including: bulk, (001) surface, and (110) surface) are calculated by DFT + U method in the present work. The calculated results are as follows. (i) The (110) surface is the main exposing surface of SiGe, in which O impurity prefers to occupy the surface vacancy sites. (ii) For O interstitial doping on SiGe (110) surface, the existences of energy states caused by O doping in the band gap not only enhance the infrared light absorption, but also improve the behaviors of photo-generated carriers. (iii) The finding about decreased surface work function of O-doped SiGe (110) surface can confirm previous experimental observations. (iv) In all cases, O doing mainly induces the electronic structures near the band gap to vary, but is not directly involved in these variations. Therefore, these findings in the present work not only can provide further explanation and analysis for the corresponding underlying mechanism for some of the experimental findings reported in the literature, but also conduce to the development of μc-SiGe-based solar cells in the future. Project supported by the Natural Science Foundation of Yunnan Province, China (Grant No. 2015FB123), the 18th Yunnan Province Young Academic and Technical Leaders Reserve Talent Project, China (Grant No. 2015HB015), and the National Natural Science Foundation of China (Grant No. U1037604).

  4. 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.

  5. 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.

  6. Self-Consistent Constricted Variational Theory RSCF-CV(∞)-DFT and Its Restrictions To Obtain a Numerically Stable ΔSCF-DFT-like Method: Theory and Calculations for Triplet States.

    PubMed

    Park, Young Choon; Senn, Florian; Krykunov, Mykhaylo; Ziegler, Tom

    2016-11-08

    In this paper, the relaxed self-consistent field infinite order constricted variational density functional theory (RSCF-CV(∞)-DFT) for triplet calculations is presented. Here, we focus on two main features of our implementation. First, as an extension of our previous work by Krykunov and Ziegler ( J. Chem. Theory Comput. 2013 , 9 , 2761 ), the optimization of the transition matrix representing the orbital transition is implemented and applied for vertical triplet excitations. Second, restricting the transition matrix, we introduce RSCF-CV(∞)-DFT-based numerically stable ΔSCF-DFT-like methods, the most general of them being SVD-RSCF-CV(∞)-DFT. The reliability of the different methods, RSCF-CV(∞)-DFT and its restricted versions, is examined using the benchmark test set of Silva-Junior et al. ( J. Chem. Phys. 2008 , 129 , 104103 ). The obtained excitation energies validate our approach and implementation for RSCF-CV(∞)-DFT and also show that SVD-RSCF-CV(∞)-DFT mimics very well ΔSCF-DFT, as the root-mean-square deviations between these methods are less than 0.1 eV for all functionals examined.

  7. Study of the thermal stability of studtite by in situ Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Colmenero, Francisco; Bonales, Laura J.; Cobos, Joaquín; Timón, Vicente

    2017-03-01

    The design of a safe spent nuclear fuel repository requires the knowledge of the stability of the secondary phases which precipitate when water reaches the fuel surface. Studtite is recognized as one of the secondary phases that play a key-role in the mobilization of the radionuclides contained in the spent fuel. Thereby, it has been identified as a product formed under oxidation conditions at the surface of the fuel, and recently found as a corrosion product in the Fukushima-Daiichi nuclear plant accident. Thermal stability is one of the properties that should be determined due to the high temperature of the fuel. In this work we report a detailed analysis of the structure and thermal stability of studtite. The structure has been studied both by experimental techniques (SEM, TGA, XRD and Raman spectroscopy) and theoretical DFT electronic structure and spectroscopic calculations. The comparison of the results allows us to perform for the first time the Raman bands assignment of the whole spectrum. The thermal stability of studtite has been analyzed by in situ Raman spectroscopy, with the aim of studying the effect of the heating rate and the presence of water. For this purpose, a new cell has been designed. The results show that studtite is stable under dry conditions only at temperatures below 30 °C, in contrast with the higher temperatures published up to date ( 130 °C). Opposite behaviour has been found when studtite is in contact with water; under these conditions studtite is stable up to 90 °C, what is consistent with the encounter of this phase after the Fukushima-Daiichi accident.

  8. Study of the thermal stability of studtite by in situ Raman spectroscopy and DFT calculations.

    PubMed

    Colmenero, Francisco; Bonales, Laura J; Cobos, Joaquín; Timón, Vicente

    2017-03-05

    The design of a safe spent nuclear fuel repository requires the knowledge of the stability of the secondary phases which precipitate when water reaches the fuel surface. Studtite is recognized as one of the secondary phases that play a key-role in the mobilization of the radionuclides contained in the spent fuel. Thereby, it has been identified as a product formed under oxidation conditions at the surface of the fuel, and recently found as a corrosion product in the Fukushima-Daiichi nuclear plant accident. Thermal stability is one of the properties that should be determined due to the high temperature of the fuel. In this work we report a detailed analysis of the structure and thermal stability of studtite. The structure has been studied both by experimental techniques (SEM, TGA, XRD and Raman spectroscopy) and theoretical DFT electronic structure and spectroscopic calculations. The comparison of the results allows us to perform for the first time the Raman bands assignment of the whole spectrum. The thermal stability of studtite has been analyzed by in situ Raman spectroscopy, with the aim of studying the effect of the heating rate and the presence of water. For this purpose, a new cell has been designed. The results show that studtite is stable under dry conditions only at temperatures below 30°C, in contrast with the higher temperatures published up to date (~130°C). Opposite behaviour has been found when studtite is in contact with water; under these conditions studtite is stable up to 90°C, what is consistent with the encounter of this phase after the Fukushima-Daiichi accident.

  9. Segregation formation, thermal and electronic properties of ternary cubic CdZnTe clusters: MD simulations and DFT calculations

    NASA Astrophysics Data System (ADS)

    Kurban, Mustafa; Erkoç, Şakir

    2017-04-01

    Surface and core formation, thermal and electronic properties of ternary cubic CdZnTe clusters are investigated by using classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations. In this work, MD simulations of the CdZnTe clusters are performed by means of LAMMPS by using bond order potential (BOP). MD simulations are carried out at different temperatures to study the segregation phenomena of Cd, Zn and Te atoms, and deviation of clusters and heat capacity. After that, using optimized geometries obtained, excess charge on atoms, dipole moments, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, HOMO-LUMO gaps (Eg) , total energies, spin density and the density of states (DOS) have been calculated with DFT. Simulation results such as heat capacity and segregation formation are compared with experimental bulk and theoretical results.

  10. Oxidative addition of methane and benzene C--H bonds to rhodium center: A DFT study

    NASA Astrophysics Data System (ADS)

    Bi, Siwei; Zhang, Zhenwei; Zhu, Shufen

    2006-11-01

    A density functional theory study on mechanisms of the oxidative addition of methane and benzene C-H bonds to the rhodium center containing Cp and PMe 3 ligands has been performed. Our calculated results confirm that the C-H bond cleavage from a sigma complex to a hydride alkyl complex is the rate-determining step. Compared with the case of methane C-H bond, the oxidative addition of benzene C-H bond is more favorable kinetically and thermodynamically. Stronger backdonation from metal center to the σ ∗ antibonding orbital of benzene C-H bond is responsible for the observations.

  11. Study of wetting on chemically soften interfaces by using combined solution thermodynamics and DFT calculations: forecasting effective softening elements.

    PubMed

    Shu, Guo Gang; Xu, Qiang; Wu, Ping

    2015-04-15

    Despite recent progress in understanding the wetting principles on soft solids, the roles of chemical bonding in the formation of interfaces have been largely ignored, because most of these studies are conducted at room temperatures. Here we propose a universal wetting principle from solution thermodynamics to account for the softening of both the solid and liquid surfaces (stable or metastable). Density functional theory (DFT) calculations are applied to evaluate the stability and electron transportation across the interfaces. We find that wetting is dominated by the system entropy changes involving not only the stable liquid alloy phase but also the metastable liquid oxide phases. The state-of-art multicomponent solution thermodynamic models and databases are applied to describe the entropy changes and predict the wetting behaviors. Our results show that by chemically softening either the liquid or the solid phase, the wetting angle reduces. And an effective soften agent/additive (either in the form of chemical elements or molecules) will weaken the bonds within the liquid (or solid) phase and promote new bonds at the interfaces, thus increasing the interface entropy. Subsequently, as an example, Ti and Zr are proposed as effective softening elements to improve the wetting of aluminum liquid on B6Si(s). This approach provides a concept and tool to advance research in catalytic chemistry, nucleation (growth), elastowetting, and cell-substrate interactions.

  12. 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.

  13. DFT calculations of 2,6-dimethylpyrazine (26DMP) and its complex with chloranilic acid (CLA): Comparison to INS, IR and Raman vibration spectra

    NASA Astrophysics Data System (ADS)

    Pawlukojć, A.; Sobczyk, L.; Prager, M.; Bator, G.; Grech, E.; Nowicka-Scheibe, J.

    2008-12-01

    The inelastic neutron scattering (INS), infrared and Raman spectra of crystalline 2,6-dimethylpyrazine (26DMP) and its complex with chloranilic acid (26DMP·CLA) were measured. Simultaneously the DFT calculations of the molecular structures and frequencies of the normal vibrations were performed by using various functionals. The INS spectra were simulated in the energy range up to 1200 cm -1, on the basis of the calculated frequencies. A very good conformity was obtained between experimental and calculated data with respect to the structure as well as to frequencies, with exception, however, of the CH 3 torsional modes. The structural analysis based on the deviation from the sum of the van der Waals radii showed that the packing of the methyl groups in the 26DMP·CLA complex was markedly stronger than that in the neat 26DMP. However, the DFT calculations overestimated the role of this effect that may be due to a limitation of the applied methods. In addition the anharmonicity of the rotational potential led to the librational energies different from those obtained using a harmonic potential.

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

    PubMed

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

    2014-11-11

    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.

  15. 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.

  16. 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.

  17. 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...

  18. Unbiased QM/MM approach using accurate multipoles from a linear scaling DFT calculation with a systematic basis set

    NASA Astrophysics Data System (ADS)

    Mohr, Stephan; Genovese, Luigi; Ratcliff, Laura; Masella, Michel

    The quantum mechanics/molecular mechanis (QM/MM) method is a popular approach that allows to perform atomistic simulations using different levels of accuracy. Since only the essential part of the simulation domain is treated using a highly precise (but also expensive) QM method, whereas the remaining parts are handled using a less accurate level of theory, this approach allows to considerably extend the total system size that can be simulated without a notable loss of accuracy. In order to couple the QM and MM regions we use an approximation of the electrostatic potential based on a multipole expansion. The multipoles of the QM region are determined based on the results of a linear scaling Density Functional Theory (DFT) calculation using a set of adaptive, localized basis functions, as implemented within the BigDFT software package. As this determination comes at virtually no extra cost compared to the QM calculation, the coupling between QM and MM region can be done very efficiently. In this presentation I will demonstrate the accuracy of both the linear scaling DFT approach itself as well as of the approximation of the electrostatic potential based on the multipole expansion, and show some first QM/MM applications using the aforementioned approach.

  19. 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

  20. 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.

  1. Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches

    PubMed Central

    2015-01-01

    Quantum mechanical (QM) calculations of noncovalent interactions are uniquely useful as tools to test and improve molecular mechanics force fields and to model the forces involved in biomolecular binding and folding. Because the more computationally tractable QM methods necessarily include approximations, which risk degrading accuracy, it is essential to evaluate such methods by comparison with high-level reference calculations. Here, we use the extensive Benchmark Energy and Geometry Database (BEGDB) of CCSD(T)/CBS reference results to evaluate the accuracy and speed of widely used QM methods for over 1200 chemically varied gas-phase dimers. In particular, we study the semiempirical PM6 and PM7 methods; density functional theory (DFT) approaches B3LYP, B97-D, M062X, and ωB97X-D; and symmetry-adapted perturbation theory (SAPT) approach. For the PM6 and DFT methods, we also examine the effects of post hoc corrections for hydrogen bonding (PM6-DH+, PM6-DH2), halogen atoms (PM6-DH2X), and dispersion (DFT-D3 with zero and Becke–Johnson damping). Several orders of the SAPT expansion are also compared, ranging from SAPT0 up to SAPT2+3, where computationally feasible. We find that all DFT methods with dispersion corrections, as well as SAPT at orders above SAPT2, consistently provide dimer interaction energies within 1.0 kcal/mol RMSE across all systems. We also show that a linear scaling of the perturbative energy terms provided by the fast SAPT0 method yields similar high accuracy, at particularly low computational cost. The energies of all the dimer systems from the various QM approaches are included in the Supporting Information, as are the full SAPT2+(3) energy decomposition for a subset of over 1000 systems. The latter can be used to guide the parametrization of molecular mechanics force fields on a term-by-term basis. PMID:24803867

  2. Electronic structure and optical properties of noncentrosymmetric LiGaSe2: Experimental measurements and DFT band structure calculations

    NASA Astrophysics Data System (ADS)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Ananchenko, L. N.; Isaenko, L. I.; Yelisseyev, A. P.; Khyzhun, O. Y.

    2017-04-01

    We report on measurements of X-ray photoelectron (XP) spectra for pristine and Ar+ ion-irradiated surfaces of LiGaSe2 single crystal grown by Bridgman-Stockbarger method. Electronic structure of the LiGaSe2 compound is studied from a theoretical and experimental viewpoint. In particular, total and partial densities of states of LiGaSe2 are investigated by density functional theory (DFT) calculations employing the augmented plane wave + local orbitals (APW + lo) method and they are verified by data of X-ray spectroscopy measurements. The DFT calculations indicate that the main contributors to the valence band of LiGaSe2 are the Se 4p states, which contribute mainly at the top and in the upper portion of the valence band, with also essential contributions of these states in the lower portion of the band. Other substantial contributions to the valence band of LiGaSe2 emerge from the Ga 4s and Ga 4p states contributing mainly at the lower ant upper portions of the valence band, respectively. With respect to the conduction band, the calculations indicate that its bottom is composed mainly from contributions of the unoccupied Ga s and Se p states. The present calculations are confirmed experimentally when comparing the XP valence-band spectrum of the LiGaS2 single crystal on a common energy scale with the X-ray emission bands representing the energy distribution of the Ga 4p and Se 4p states. Measurements of the fundamental absorption edges at room temperature reveal that bandgap value, Eg, of LiGaSe2 is equal to 3.47 eV and the Eg value increases up to 3.66 eV when decreasing temperature to 80 K. The main optical characteristics of the LiGaSe2 compound are clarified by the DFT calculations.

  3. 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.

  4. 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.

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

    PubMed

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

    2015-02-25

    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)-H(7A)-O(2), N(7)-H(7B)-O(3), N(1)-H(1)-N(2), C(5)-H(5)-O(3)-S(1) and N(7)-(H7A)-O(2)-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 4.37×10(4)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.

  6. Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car-Parrinello calculations

    NASA Astrophysics Data System (ADS)

    Varini, Nicola; Ceresoli, Davide; Martin-Samos, Layla; Girotto, Ivan; Cavazzoni, Carlo

    2013-08-01

    One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO (Giannozzi et al., 2009 [3]) for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over electronic bands, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car-Parrinello routines (Car-Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange-correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.

  7. 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.

  8. To address surface reaction network complexity using scaling relations machine learning and DFT calculations.

    PubMed

    Ulissi, Zachary W; Medford, Andrew J; Bligaard, Thomas; Nørskov, Jens K

    2017-03-06

    Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.

  9. To address surface reaction network complexity using scaling relations machine learning and DFT calculations

    PubMed Central

    Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.

    2017-01-01

    Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations. PMID:28262694

  10. To address surface reaction network complexity using scaling relations machine learning and DFT calculations

    NASA Astrophysics Data System (ADS)

    Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.

    2017-03-01

    Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.

  11. 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).

  12. Structural determination of stable MoOx monolayers on O/Cu3Au(1 0 0): DFT calculations

    NASA Astrophysics Data System (ADS)

    Valadares, George C. S.; Mendes, F. M. T.; Dionízio Moreira, M.; Leitão, A. A.; Niehus, H.; Capaz, Rodrigo B.; Achete, C. A.

    2012-10-01

    Using ab initio calculations based on density functional theory (DFT), we propose a geometrical structure for MoOx monolayers recently grown on O/Cu3Au(1 0 0) substrates. The proposed structure reproduces the p(2 × 2) symmetry found by scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED), as well as the intermediate oxidation state between Mo(IV) and Mo(VI) identified by X-ray photoelectron spectroscopy (XPS). Simulated STM images assign the bright spots in the experimental images to oxygen 2p states.

  13. 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.

  14. 47 CFR 54.1304 - Calculation of safety net additive.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... additive unless the carrier's realized total growth in Telecommunications Plant in Service (TPIS) was more... (CONTINUED) UNIVERSAL SERVICE High Cost Loop Support for Rate-of-Return Carriers § 54.1304 Calculation of..., a rate-of-return incumbent local exchange carrier shall receive safety net additive support...

  15. Infrared absorption spectroscopic and DFT calculation studies on the adsorption structures of nitromethane on the single crystals of Cu and Ag

    NASA Astrophysics Data System (ADS)

    Itoh, K.; Iwa, A.; Uriu, Y.; Kadokura, K.

    2008-07-01

    The adsorption structures of nitromethane on Ag(1 1 0), Ag(1 1 1), Cu(1 1 0) and Cu(1 1 1) at 80 K were studied by using infrared reflection absorption spectroscopy (IRAS) and non-local density functional theory (DFT) calculation performed on nitromethane/Cu(1 1 0) and nitromethane/Cu(1 1 1) cluster models. Upon increasing exposure levels, the adsorbate on each substrate exhibits discrete spectral changes, characterizing sub-monolayer and/or monolayer, amorphous and multilayer (crystalline) states. The DFT calculation successively simulated the IRA spectra of nitromethane on the copper substrates, suggesting that nitromethane adsorbs on Cu(1 1 0) through an on-top coordination with one of the oxygen atom of the NO 2 group to the Cu atom and that nitromethane adsorbs on Cu(1 1 1) through a bridging coordination of the oxygen atom. In both states nitromethane takes an eclipsed form with the molecular plane perpendicular to the substrates surface and the hydrogen atom pointing to the surface in the molecular plane plays an important role in stabilizing the adsorption states in addition to the coordination interaction.

  16. FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach

    NASA Astrophysics Data System (ADS)

    Sert, Yusuf; Sreenivasa, S.; Doğan, H.; Manojkumar, K. E.; Suchetan, P. A.; Ucun, Fatih

    2014-06-01

    In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400 cm-1) and Laser-Raman spectra (4000-100 cm-1) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

  17. FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach.

    PubMed

    Sert, Yusuf; Sreenivasa, S; Doğan, H; Manojkumar, K E; Suchetan, P A; Ucun, Fatih

    2014-06-05

    In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

  18. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals

    PubMed Central

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-01-01

    Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly. PMID:28361050

  19. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals.

    PubMed

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-01-01

    Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly.

  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. Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of 3,3'-diaminobenzidine with DFT quantum chemical calculations.

    PubMed

    Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

    2015-11-05

    In this work, infrared, Raman and UV spectra of 3,3'-diaminobenzidine (3,3-DAB) were carried out by using density functional theory (DFT)/B3LYP method with 6-311G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the region 4000-400 and 4000-50 cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and fundamental vibrations were assigned on the basis of the potential energy distribution (PED) of the vibrational modes. The UV spectrum of the investigated compound was recorded in the range of 200-400 nm in ethanol and water solutions. 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. Thermodynamic properties, Mulliken atomic charges and molecular electrostatic potential (MEP) were calculated for the title molecule. Also the nonlinear optical properties of 3,3-DAB molecule were explored theoretically. As a result, the calculated results were compared with the observed values and generally found to be in good agreement.

  2. Molecular structures and electronic properties of isonicotinic acid (3-methoxy-4-hydroxy-benzylidene)-hydrazide: Ab initio and DFT calculation

    NASA Astrophysics Data System (ADS)

    Uǧurlu, Güventürk

    2017-02-01

    The molecular structure and conformational analysis of isonicotinic acid (3-methoxy-4-hydroxy-benzylidene)- hydrazide were investigated by Ab initio and density functional theory DFT/B3LYP levels of theory with complete relaxation in the potential energy surface using varied basis set. The four stable conformers of the studied molecule (C1, C2, C3 and C4) were computed. The computational results diagnose the most stable conformer of (3-methoxy-4-hydroxy-benzylidene)-hydrazide as the C1 form. Molecular structure, dipole moment, polarizability and first static hyperpolarizability of the four stable conformers have been calculated by using 6-311++G (d, p) basis set for both models. Besides, EHOMO (the highest occupied molecular orbital energy), ELUMO (the lowest unoccupied molecular orbital energy) and HOMO-LUMO energy gap (ΔEg) are investigated. The dipole moment for C1, C2, C3 and C4 conformers are calculated at 2.44, 7.74, 7.75 and 6.58 with DFT/B3LYP level of the theory 6-311++G (d, p) basis set and at the HF/6-311++ G (d, p) 2.60, 7.42, 7.41 and 6.36 Debye, respectively. The structural parameters of the studied molecule compared with data in the literature.

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

    PubMed

    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 (13)C 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.

  4. 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).

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

    PubMed

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

    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.

  6. 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.

  7. DFT calculations on spectroscopic, structural and NLO properties of silver (I) complex with picolinamide

    NASA Astrophysics Data System (ADS)

    Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

    2017-02-01

    The molecular geometry optimization, vibrational frequencies, the molecular static polarizability (α), first-order static hyperpolarizability (β), second-order static hyperpolarizability (γ) and frontier molecular orbital (FMO) energies of silver (I) complex with picolinamide, [Ag(C6H6N2O)2](NO3).H2O, were investigated using density functional theory (DFT) HSEh1PBE and B3LYP methods with LANL2DZ basis set. The molecular hardness (η) and electronegativity (χ) parameters were also obtained by using FMO energies. The NLO parameters of the complex were compared with those of para-Nitroaniline (pNA) and urea which are typical NLO materials. Obtained data showed that there is an agreement between the predicted and experimental data.

  8. Anharmonic vibrational studies of L-aspartic acid using HF and DFT calculations

    NASA Astrophysics Data System (ADS)

    Alam, Mohammad Jane; Ahmad, Shabbir

    2012-10-01

    The experimental and theoretical studies on the structure, molecular properties and vibrational spectra of L-aspartic acid are presented. The molecular structure, harmonic and anharmonic vibrational frequencies, molecular properties, MEP mapping, NBO analysis and electronic spectra of L-aspartic acid have been reported. Computed geometrical parameters and anharmonic frequencies of fundamental, combination and overtone transitions were found in satisfactory agreement with the experimental data. The UV-Vis spectrum of present molecule has been recorded and the electronic properties such as HOMO and LUMO energies and few low lying excited states were carried out by using time dependent density functional theory (TD-DFT) approach. Natural Bond Orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Molecular electrostatic potential map has also been used for quantitative measure of the chemical activities of various sites of the molecule.

  9. 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.

  10. 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.

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

    PubMed

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

    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 cHF and show that there exists one value of cHF (∼0.32) that reproduces at least semi-quantitatively the optical gap of this material.

  12. 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.

  13. 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

    2015-02-05

    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.

  14. Ab initio/DFT electronic structure calculations, spectroscopic studies of 5-bromo-2-pyridinecarbonitrile - A comparative study

    NASA Astrophysics Data System (ADS)

    Kandasamy, M.; Velraj, G.

    2012-08-01

    Fourier transform infrared (FTIR) and FT-Raman spectra have been recorded and extensive spectroscopic investigations have been carried out on 5-bromo-2-pyridinecarbonitrile (5B2PC). The optimized geometries, wavenumber and intensity of the vibrational bands of (5B2PC) have been calculated using density functional level of theory (DFT/B3LYP) employing 6-311G(d,p) basis set. On the basis of the comparison between calculated and experimental results, assignments of the fundamental vibrational modes are examined. The molecular stability and bond strength were investigated by applying the natural bond orbital (NBO) analysis. The electronic properties like HOMO-LUMO analysis of (5B2PC) have been reported.

  15. Structural, optoelectronic, infrared and Raman spectra of orthorhombic SrSnO{sub 3} from DFT calculations

    SciTech Connect

    Moreira, E.; Henriques, J.M.; Azevedo, D.L.; Caetano, E.W.S.; Freire, V.N.; Albuquerque, E.L.

    2011-04-15

    Orthorhombic SrSnO{sub 3} was investigated using density functional theory (DFT) considering both the local density and generalized gradient approximations, LDA and GGA, respectively. The electronic band structure, density of states, complex dielectric function, optical absorption, and the infrared and Raman spectra were computed. Calculated lattice parameters are close to the experimental measurements, and an indirect band gap E(S{yields}{Gamma})=1.97eV (2.27 eV) was obtained within the GGA (LDA) level of calculation. Effective masses for holes and electrons were estimated, being very anisotropic in comparison with similar results for orthorhombic CaSnO{sub 3}. The complex dielectric function and the optical absorption of SrSnO{sub 3} were shown to be sensitive to the plane of polarization of the incident light. The infrared spectrum between 100 and 600 cm{sup -1} was obtained, with its main peaks being assigned, and a nice agreement between experimental and theoretical peaks of the Raman spectrum of orthorhombic SrSnO{sub 3} was achieved. -- Graphical abstract: Orthorhombic SrSnO{sub 3}: a view of the unit cell (left) and plots showing the calculated and experimental Raman spectra (right). Display Omitted Research highlights: {yields} We have performed DFT calculations on orthorhombic SrSnO{sub 3} crystals, obtaining their structural, electronical and optical properties. {yields} An indirect band gap was obtained, and anisotropic effective masses were found for both electrons and holes. {yields} The complex dielectric function and the optical absorption of SrSnO{sub 3} were shown to be very sensitive to the plane of polarization of the incident light. {yields} The infrared spectrum between 100 and 600 cm{sup -1} was obtained, with its main peaks being assigned, and a nice agreement between experimental and theoretical peaks of the Raman spectrum was achieved.

  16. 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.

  17. 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; ...

    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

  18. 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.

  19. UV-Vis spectroscopic study and DFT calculation on the solvent effect of trimethoprim in neat solvents and aqueous mixtures

    NASA Astrophysics Data System (ADS)

    Almandoz, M. C.; Sancho, M. I.; Duchowicz, P. R.; Blanco, S. E.

    2014-08-01

    The solvatochromic behavior of trimethoprim (TMP) was analyzed using UV-Vis spectroscopy and DFT methods in neat and binary aqueous solvent mixtures. The effects of solvent dipolarity/polarizability and solvent-solute hydrogen bonding interactions on the absorption maxima were evaluated by means of the linear solvation energy relationship concept of Kamlet and Taft. This analysis indicated that both interactions play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra of TMP and TMP:(solvent)n complexes in ACN and H2O using TD-DFT methods were in agreement with the experimental ones. Binary aqueous mixtures containing as co-solvents DMSO, ACN and EtOH were studied. Preferential solvation was detected as a nonideal behavior of the wavenumber curve respective to the analytical mole fraction of co-solvent in all binary systems. TMP molecules were preferentially solvated by the organic solvent over the whole composition range. Index of preferential solvation, as well as the influence of solvent parameters were calculated as a function of solvent composition.

  20. UV-Vis spectroscopic study and DFT calculation on the solvent effect of trimethoprim in neat solvents and aqueous mixtures.

    PubMed

    Almandoz, M C; Sancho, M I; Duchowicz, P R; Blanco, S E

    2014-08-14

    The solvatochromic behavior of trimethoprim (TMP) was analyzed using UV-Vis spectroscopy and DFT methods in neat and binary aqueous solvent mixtures. The effects of solvent dipolarity/polarizability and solvent-solute hydrogen bonding interactions on the absorption maxima were evaluated by means of the linear solvation energy relationship concept of Kamlet and Taft. This analysis indicated that both interactions play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra of TMP and TMP:(solvent)n complexes in ACN and H2O using TD-DFT methods were in agreement with the experimental ones. Binary aqueous mixtures containing as co-solvents DMSO, ACN and EtOH were studied. Preferential solvation was detected as a nonideal behavior of the wavenumber curve respective to the analytical mole fraction of co-solvent in all binary systems. TMP molecules were preferentially solvated by the organic solvent over the whole composition range. Index of preferential solvation, as well as the influence of solvent parameters were calculated as a function of solvent composition.

  1. Spin states of FeOOH at high pressure using x-ray emission spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mao, W. L.; Gleason, A. E.; Pentcheva, R.; Otte, K.; Suzuki, A.

    2011-12-01

    Electronic spin transitions in alpha-FeOOH (goethite) and high-pressure phase epsilon-FeOOH were monitored using high pressure x-ray emission spectroscopy. A high- to low-spin transition in trivalent iron was found in synthesized epsilon-FeOOH on compression at 56.8 GPa, which returned to high-spin on decompression at 20 GPa. This corroborates density-functional theory (DFT) calculations with an on-site Coulomb repulsion term (GGA+U) predict the transition to occur at 56.6 GPa. Compression of alpha-FeOOH to 60 GPa did not show any high- to low-spin transition consistent with the DFT results. Monitoring the spin states of iron-oxy-hydroxides as a function of pressure gives insight into the relationship between electronic spin transitions and structural transitions - which has previously been studied in other key mantle minerals, including iron-bearing perovskites and ferropericlase. Furthermore, this may help uncover a connection between water content (presence of hydroxyl) in a mineral and Fe3+ spin-transition pressure at mid- to lower-mantle conditions in the Earth.

  2. 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

    2015-12-05

    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.

  3. 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.

  4. Oxidation induced decomposition of ethylene carbonate from DFT calculations--importance of explicitly treating surrounding solvent.

    PubMed

    Xing, Lidan; Borodin, Oleg

    2012-10-05

    The oxidation induced reactions of the common lithium battery electrolyte solvent ethylene carbonate (EC) have been investigated for EC(2) using density functional theory and for selected reaction paths using Møller-Plesset perturbation theory (MP4). The importance of explicitly treating at least one solvent molecule interacting with EC during oxidation (removal of an electron) on the EC oxidation potential and decomposition reactions was shown by comparing oxidation of EC and EC(2). Accuracy of DFT results was evaluated by comparing with MP4 and G4 values for oxidation of EC. The polarized continuum model (PCM) was used to implicitly include the rest of the surrounding solvent. The oxidation potentials of EC(2) and EC(4) were found to be significantly lower than the intrinsic oxidation potential of an isolated EC and also lower than the oxidation potential of EC-BF(4)(-). The exothermic proton abstraction from the ethylene group of EC by the carbonyl group of another EC was responsible for the decreased oxidative stability of EC(2) and EC(4) compared to EC. The most exothermic path with the smallest barrier for EC(2) oxidation yielded CO(2) and an ethanol radical cation. The reaction paths with the higher barrier yielded oligo(ethylene carbonate) suggesting a pathway for the experimentally observed poly(ethylene carbonate) formation of EC-based electrolytes at cathode surfaces.

  5. An investigation of solute-solvent interactions in binary liquid mixtures of 3'-methoxyacetophenone: using Raman spectroscopy and DFT calculations.

    PubMed

    Yamini, D; Ramakrishnan, V

    2013-07-01

    Raman spectral measurements have been carried out for neat 3'-methoxy acetophenone (3'-MAP) and binary liquid mixtures of 3'-MAP in three solvents of different polarity. Also Density Functional Theory (DFT) geometry optimization and vibrational wavenumber calculation have been performed on monomer and dimer structures of 3'-MAP to analyze the experimentally observed Raman spectrum. Mulliken charge analysis has also been made on optimized geometries of 3'-MAP with solvents. The changes associated with the observed peak position, intensity and linewidth in the carbonyl stretching mode of 3'-MAP are explained as a consequence of intermolecular interactions between solute-solute and solute-solvent molecules. This analysis reports that the solute-solvent interaction is dominant in the case of binary liquid mixtures of 3'-MAP with ethanol compared to DMF and benzene.

  6. 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.

  7. 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.

  8. DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline.

    PubMed

    Gowda, Vasantha; Laitinen, Risto S; Telkki, Ville-Veikko; Larsson, Anna-Carin; Antzutkin, Oleg N; Lantto, Perttu

    2016-12-06

    The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state (13)C and (15)N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and (13)C and (15)N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P21/n. Both (13)C and (15)N CP-MAS NMR revealed the presence of six structurally different dithiocarbamate groups in the asymmetric unit cell, implying a non-centrosymmetric packing arrangement of molecules. This was supported by single-crystal X-ray crystallography showing that the title compound crystallised in the triclinic space group P1[combining macron]. In addition, the crystal structure also revealed that one of the dithiocarbamate ligands has a conformational disorder. NMR chemical shift calculations employing the periodic gauge including projector augmented wave (GIPAW) approach supported the assignment of the experimental (13)C and (15)N NMR spectra. However, the best correspondences were obtained with the structure where the atomic positions in the X-ray unit cell were optimised at the DFT level. The roles of the scalar and spin-orbit relativistic effects on NMR shielding were investigated using the zeroth-order regular approximation (ZORA) method with the outcome that already the scalar relativistic level qualitatively reproduces the experimental chemical shifts. The electronic properties of the complex were evaluated based on the results of the natural bond orbital (NBO) and topology of the electron density analyses. Overall, we apply a multidisciplinary approach acquiring comprehensive information about the solid-state structure and the

  9. Substituent effects on axle binding in amide pseudorotaxanes: comparison of NMR titration and ITC data with DFT calculations.

    PubMed

    Kaufmann, Lena; Dzyuba, Egor V; Malberg, Friedrich; Löw, Nora L; Groschke, Matthias; Brusilowskij, Boris; Huuskonen, Juhani; Rissanen, Kari; Kirchner, Barbara; Schalley, Christoph A

    2012-08-14

    The binding behaviour of differently substituted diamide axle molecules to Hunter/Vögtle tetralactam macrocycles was studied with a combination of NMR titration, isothermal titration calorimetry (ITC) experiments and calculations employing density functional theory (DFT), along with dispersion-corrected exchange-correlation functionals. Guests with alkyl or alkenyl chains attached to the diamide carbonyl groups have a significantly higher binding affinity to the macrocycle than guests with benzoyl amides and their substituted analogues. While the binding of the benzoyl and alkenyl substituted axles is enthalpically driven, the alkyl-substituted guest binds mainly because of a positive binding entropy. The electronic effects of para-substituents at the benzoyl moieties have an influence on the binding affinities. Electron donating substituents increase, while electron-withdrawing substituents decrease the binding energies. The binding affinities obtained from both NMR titration and ITC experiments correlate well with each other. The substituent effects observed in the experimental data are reflected in adiabatic interaction energies calculated with density functional methods. The calculated structures also agree well with pseudorotaxane crystal structures.

  10. Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations.

    PubMed

    Ramos, Javier; Cruz, Victor L

    2016-11-01

    Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PPII and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ1), along with the computation of (3)J(H(α)H(β)), revealed a preference for the g - and g + rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PPII and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.

  11. Electronic band structure and specific features of Sm2NiMnO6 compound: DFT calculation

    NASA Astrophysics Data System (ADS)

    Reshak, A. H.; Azam, Sikander

    2013-09-01

    The band structure, density of states, electronic charge density, Fermi surface and optical properties of Sm2NiMnO6 compound have been investigated with the support of density functional theory (DFT). The atomic positions of Sm2NiMnO6 compound were optimized by minimizing the forces acting on the atoms, using the full potential linear augmented plane wave method. We employed the local density approximation (LDA), generalized gradient approximation (GGA) and Engel-Vosko GGA (EVGGA) to treat the exchange correlation potential by solving Kohn-Sham equations. The calculation shows that the compound is metallic with strong hybridization near the Fermi energy level (EF). The calculated density of states at the EF is about 21.60, 24.52 and 26.21 states/eV, and the bare linear low-temperature electronic specific heat coefficient (γ) is found to be 3.74, 4.25 and 4.54 mJ/mol K2 for EVGGA, GGA and LDA, respectively. The Fermi surface is composed of two sheets. The bonding features of the compounds are analyzed using the electronic charge density in the (011) crystallographic plane. The dispersion of the optical constants was calculated and discussed.

  12. 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.

  13. 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.

  14. Vibrational Spectra, DFT Calculations, and Assignments of the syn and the gauche Forms of Vinylphosphine.

    PubMed

    Benidar, A.; Le Doucen, R.; Guillemin, J. C.; Mó, O.; Yáñez, M.

    2001-02-01

    Infrared spectra (3500-600 cm(-1)) of vinylphosphine and its P-dideuterated derivative in the gas phase were recorded at 1 cm(-1) resolution. Both the infrared absorption bands of the syn and gauche conformers of the vinylphosphine were observed and assigned. The assignment was based on density functional theory calculations performed at the B3LYP/6-311G(d) level. The agreement between calculated and observed frequencies for both CH(2)&dbond;CHPH(2) and CH(2)&dbond;CHPD(2) was fairly good. The integrated intensities of isolated and overlapping vibrational bands were determined experimentally. Copyright 2001 Academic Press.

  15. Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

    PubMed Central

    Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

    2009-01-01

    Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can

  16. Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST.

    PubMed

    Nakata, Ayako; Bowler, David R; Miyazaki, Tsuyoshi

    2014-11-11

    Multisite local orbitals, which are formed from linear combinations of pseudoatomic orbitals from a target atom and its neighbor atoms, have been introduced in the large-scale density functional theory calculation code CONQUEST. Multisite local orbitals correspond to local molecular orbitals so that the number of required local orbitals can be minimal. The multisite support functions are determined by using the localized filter diagonalization (LFD) method [ Phys. Rev. B 2009 , 80 , 205104 ]. Two new methods, the double cutoff method and the smoothing method, are introduced to the LFD method to improve efficiency and stability. The Hamiltonian and overlap matrices with multisite local orbitals are constructed by efficient sparse-matrix multiplications in CONQUEST. The investigation of the calculated energetic and geometrical properties and band structures of bulk Si, Al, and DNA systems demonstrate the accuracy and the computational efficiency of the present method. The representability of both occupied and unoccupied band structures with the present method has been also confirmed.

  17. 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.

  18. Quantitative analysis of weak interactions by Lattice energy calculation, Hirshfeld surface and DFT studies of sulfamonomethoxine

    NASA Astrophysics Data System (ADS)

    Patel, Kinjal D.; Patel, Urmila H.

    2017-01-01

    Sulfamonomethoxine, 4-Amino-N-(6-methoxy-4-pyrimidinyl) benzenesulfonamide (C11H12N4O3S), is investigated by single crystal X-ray diffraction technique. Pair of N-H⋯N and C-H⋯O intermolecular interactions along with π···π interaction are responsible for the stability of the molecular packing of the structure. In order to understand the nature of the interactions and their quantitative contributions towards the crystal packing, the 3D Hirshfeld surface and 2D fingerprint plot analysis are carried out. PIXEL calculations are performed to determine the lattice energies correspond to intermolecular interactions in the crystal structure. Ab initio quantum chemical calculations of sulfamonomethoxine (SMM) have been performed by B3LYP method, using 6-31G** basis set with the help of Schrodinger software. The computed geometrical parameters are in good agreement with the experimental data. The Mulliken charge distribution, calculated using B3LYP method to confirm the presence of electron acceptor and electron donor atoms, responsible for intermolecular hydrogen bond interactions hence the molecular stability.

  19. 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.

  20. Structural, electronic and optical properties of ilmenite and perovskite CdSnO3 from DFT calculations.

    PubMed

    Sesion, P D; Henriques, J M; Barboza, C A; Albuquerque, E L; Freire, V N; Caetano, E W S

    2010-11-03

    CdSnO(3) ilmenite and perovskite crystals were investigated using both the local density and generalized gradient approximations, LDA and GGA, respectively, of the density functional theory (DFT). The electronic band structures, densities of states, dielectric functions, optical absorption and reflectivity spectra related to electronic transitions were obtained, as well as the infrared absorption spectra after computing the vibrational modes of the crystals at q = 0. Dielectric optical permittivities and polarizabilities at ω = 0 and ∞ were also calculated. The results show that GGA-optimized geometries are more accurate than LDA ones, and the Kohn-Sham band structures obtained for the CdSnO(3) polymorphs confirm that ilmenite has an indirect band gap, while perovskite has a direct band gap, both being semiconductors. Effective masses for both crystals are obtained for the first time, being highly isotropic for electrons and anisotropic for holes. The optical properties reveal a very small degree of anisotropy of both crystals with respect to different polarization planes of incident light. The phonon calculation at q = 0 for perovskite CdSnO(3) does not show any imaginary frequencies, in contrast to a previous report suggesting the existence of a more stable crystal of perovskite CdSnO(3) with ferroelectric properties.

  1. Experimental study on the structure and vibrational, thermal and dielectric properties of bis(2-methylanilinium) selenate accomplished with DFT calculation

    NASA Astrophysics Data System (ADS)

    Ben hassen, C.; Boujelbene, M.; Bahri, M.; Zouari, N.; Mhiri, T.

    2014-09-01

    The present paper undertakes the study of a new hybrid compound [2-CH3C6H4NH3]2SeO4 characterized by the X-ray diffraction, IR, DFT calculation, TG-DTA, DSC and electrical conductivity. This new organic-inorganic hybrid compound crystallizes in the monoclinic system with P21/c space group and the following parameters a = 14.821 (5) Å; b = 16.245 (5) Å; c = 6.713 (5) Å; ß = 102.844 (5)°, Z = 4 and V = 1575.8 (14) Å3. The atomic arrangement can be described as isolated tetrahedral SeO42- connected with the organic groups by means of Nsbnd H⋯O hydrogen bonds to form infinite sinusoidal chains in the c-direction. BHHLYP/6-311g** method was used to determine the harmonic frequencies for two optimized cluster structures. The calculated modes were animated using the Molden graphical package to give tentative assignments of the observed IR spectra. Thermal analysis of the title compound does not indicate the occurrence of a phase transition in the temperature range of 300-650 K. Dielectric study of this compound has been measured, in order to determine the conductivity. The conductivity relaxation parameters associated with some H+ conduction have been determined from an analysis of the M″/M″max spectrum measured in a wide temperature range.

  2. 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.

  3. Molecular structure and vibrational study of diprotonated guanazolium using DFT calculations and FT-IR and FT-Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Guennoun, L.; Zaydoun, S.; El jastimi, J.; Marakchi, K.; Komiha, N.; Kabbaj, O. K.; El Hajji, A.; Guédira, F.

    2012-11-01

    The purpose of this manuscript is to discuss our investigations of diprotonated guanazolium chloride using vibrational spectroscopy and quantum chemical methods. The solid phase FT-IR and FT-Raman spectra were recorded in the regions 4000-400 cm-1 and 3600-50 cm-1 respectively, and the band assignments were supported by deuteration effects. Different sites of diprotonation have been theoretically examined at the B3LYP/6-31G∗ level. The results of energy calculations show that the diprotonation process occurs with the two pyridine-like nitrogen N2 and N4 of the triazole ring. The molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated for this form by DFT/B3LYP methods, using a 6-31G∗ basis set. Both the optimized geometries and the theoretical and experimental spectra for diprotonated guanazolium under a stable form are compared with theoretical and experimental data of the neutral molecule reported in our previous work. This comparison reveals that the diprotonation occurs on the triazolic nucleus, and provide information about the hydrogen bonding in the crystal. The scaled vibrational wave number values of the diprotonated form are in close agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PED) using the VEDA 4 program.

  4. Molecular structure and vibrational study of diprotonated guanazolium using DFT calculations and FT-IR and FT-Raman spectroscopies.

    PubMed

    Guennoun, L; Zaydoun, S; El Jastimi, J; Marakchi, K; Komiha, N; Kabbaj, O K; El Hajji, A; Guédira, F

    2012-11-01

    The purpose of this manuscript is to discuss our investigations of diprotonated guanazolium chloride using vibrational spectroscopy and quantum chemical methods. The solid phase FT-IR and FT-Raman spectra were recorded in the regions 4000-400cm(-1) and 3600-50cm(-1) respectively, and the band assignments were supported by deuteration effects. Different sites of diprotonation have been theoretically examined at the B3LYP/6-31G level. The results of energy calculations show that the diprotonation process occurs with the two pyridine-like nitrogen N2 and N4 of the triazole ring. The molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated for this form by DFT/B3LYP methods, using a 6-31G basis set. Both the optimized geometries and the theoretical and experimental spectra for diprotonated guanazolium under a stable form are compared with theoretical and experimental data of the neutral molecule reported in our previous work. This comparison reveals that the diprotonation occurs on the triazolic nucleus, and provide information about the hydrogen bonding in the crystal. The scaled vibrational wave number values of the diprotonated form are in close agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PED) using the VEDA 4 program.

  5. Complementarity of DFT Calculations, NMR Anisotropy, and ECD for the Configurational Analysis of Brevipolides K-O from Hyptis brevipes.

    PubMed

    Suárez-Ortiz, G Alejandra; Cerda-García-Rojas, Carlos M; Fragoso-Serrano, Mabel; Pereda-Miranda, Rogelio

    2017-01-27

    Brevipolides K-O (1-5), five new cytotoxic 6-(6'-cinnamoyloxy-2',5'-epoxy-1'-hydroxyheptyl)-5,6-dihydro-2H-pyran-2-ones (IC50 values against six cancer cell lines, 1.7-10 μM), were purified by recycling HPLC from Hyptis brevipes. The structures, containing a distinctive tetrahydrofuran ring, were established by comprehensive quantum mechanical calculations and experimental spectroscopic analysis of their NMR and ECD data. Detailed analysis of the experimental NMR (1)H-(1)H vicinal coupling constants in comparison with the corresponding DFT-calculated values at the B3LYP/DGDZVP level confirmed the absolute configuration of 3 and revealed its conformational preferences, which were further strengthened by NOESY correlations. NMR anisotropy experiments by the application of Mosher's ester methodology and chemical correlations were also used to conclude that this novel brevipolide series (1-5) share the same absolute configuration corresponding to C-6(R), C-1'(S), C-2'(R), C-5'(S), and C-6'(S).

  6. The conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, followed by IR spectra, ab initio and DFT force field calculations

    NASA Astrophysics Data System (ADS)

    Binev, Yuri I.; Georgieva, Miglena K.; Novkova, Snezhana I.

    2003-11-01

    The spectral and structural changes, caused by the conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, have been followed by IR spectra, ab initio HF, MP2 and DFT BLYP force field calculations. In agreement between theory and experiment, the conversion is accompanied with strong frequency decreases (with 114 cm -1, mean value) of the cyano stretching bands νCN, dramatic increases in the corresponding integrated intensities (136-fold, total value), strong enhancement of the νCN vibrational coupling and other essential spectral changes. According to the calculations, the strongest structural changes take place at the carbanionic center: (i) shortenings of the CPh and CCN bonds with 0.064-0.092 Å, and increases in the corresponding bond orders with 0.14-0.21 U; (ii) simultaneous enlargements of the bond angles at the same carbon atom with 7.6°-9.7°, as from tetrahedral its configuration becomes trigonal. The carbanionic charge is distributed between the two cyano groups (0.44-0.52 e -), phenyl ring (0.31-0.34 e -) and carbanionic center (0.14-0.25 e -). The formation of moderately strong (CH 3) 2SO⋯HC(CN) 2C 6H 5 hydrogen bonds has been found experimentally.

  7. 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.

  8. Ruthenium tetraoxide oxidations of alkanes: DFT calculations of barrier heights and kinetic isotope effects.

    PubMed

    Drees, Markus; Strassner, Thomas

    2006-03-03

    The oxidation of C-H and C-C bonds by metal-oxo compounds is of general interest. We studied the RuO4-mediated catalytic oxidation of several cycloalkanes such as adamantane and cis- and trans-decalin as well as methane. B3LYP/6-31G(d) calculations on the experimentally proposed (3+2) mechanism are in good agreement with known experimental results. Comparison of experimental and theoretical kinetic isotope effects confirms the proposed mechanism. Besides RuO4, we also looked at RuO4(OH)- as a potential active species to account for ruthenium tetraoxide oxidations under strong basic conditions.

  9. Intermolecular associations in an equimolar formamide-water solution based on neutron scattering and DFT calculations.

    PubMed

    Abdelmoulahi, Hafedh; Ghalla, Houcine; Nasr, Salah; Darpentigny, Jacques; Bellissent-Funel, Marie-Claire

    2016-10-07

    In the present work, we have investigated the intermolecular associations of formamide with water in an equimolar formamide-water solution (FA-Water) by means of neutron scattering in combination with density functional theory calculations. The neutron scattering data were analyzed to deduce the structure factor SM(q) and the intermolecular pair correlation function gL(r). By considering different hydrogen bonded FA-Water associations, it has been shown that some of them describe well the local order in the solution. Natural bond orbital and atoms in molecules analyses have been performed to give more insight into the properties of hydrogen bonds involved in the more probable models.

  10. Gas phase infrared spectra and corresponding DFT calculations of α, ω-diphenylpolyenes

    NASA Astrophysics Data System (ADS)

    Biemann, Lars; Braun, Michaela; Kleinermanns, Karl

    2010-01-01

    We present gas phase Fourier Transform Infrared (FTIR) spectra of the homologue series of α, ω-diphenylpolyenes consisting of trans- and cis-stilbene, diphenylbutadiene (DPB) and diphenylhexatriene (DPH) obtained by a fast thermal heating technique that enables vaporization without decomposition. Infrared marker bands for the cis-isomers of the polyenes have been identified by density functional calculations at the B3LYP/TZVP level of theory. The all trans isomers of DPB and DPH do not interconvert to the cis-isomers in the gas phase at 200 °C.

  11. A structural study of fentanyl by DFT calculations, NMR and IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Asadi, Zahra; Esrafili, Mehdi D.; Vessally, Esmail; Asnaashariisfahani, Manzarbanou; Yahyaei, Saeideh; Khani, Ali

    2017-01-01

    N-(1-(2-phenethyl)-4-piperidinyl-N-phenyl-propanamide (fentanyl) is synthesized and characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy and elemental analyses. The geometry optimization is performed using the B3LYP and M06 density functionals with 6-311 + G(d) and 6-311++G(d,p) basis sets. The complete assignments are performed on the basis of the potential energy distribution (PED) of the all vibrational modes. Almost a nice correlation is found between the calculated 13C chemical shifts and experimental data. The frontier molecular orbitals and molecular electrostatic potential of fentanyl are also obtained.

  12. 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.

  13. Infrared spectral evidence and DFT calculations of hydrogen-bonding and molecular structures of acetogenins

    NASA Astrophysics Data System (ADS)

    Afonso, Sabrina; Silva, Fabiano B.; Silva, Arnaldo F.; Scarminio, Ieda S.; Bruns, Roy E.

    2017-02-01

    FTIR spectra have been measured for 31 different five component - simplex centroid design solvent mixture extracts of shaded and sun-exposed Annonaceous leaves harvested in all four seasons. The spectral frequencies are characteristic of anonnaceous acetogenins known to be a major component of these leaves. Osbnd H stretching spectral bands in the 3100-3600 cm-1 region provide evidence of notable intensity changes for the shaded and sun-exposed leaves. Chemometric principal component analysis involving 264 spectra show that shaded samples tend to have more intense Osbnd H stretching bands than those grown in the sun. B3LYP density functional calculations indicate significant Osbnd H stretching band changes in this region owing to hydrogen bond formation. Weak Osbnd H intensity enhancements, around 40 km mol-1, occur when an Osbnd H group forms a hydrogen bond with the oxygen atom of an adjacent tetrahydrofuran ring oxygen atom. Much more intense enhancements, 400-500 km mol-1, are predicted to occur for acetogenins with two tetrahydrofuran rings for which the Osbnd H group hydrogen bonds with its fartherest removed tetrahydrofuran ring oxygen. Whereas weak or moderate H-bond stretching intensities are obtained for acetogenins with slightly bent carbon chain structures the strongest hydrogen bond intensities are calculated for molecules with a 45° V-type backbone structure. These important structural modifications as well as significant changes in bond lengths and angles owing to hydrogen bonding are detailed.

  14. 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

  15. Synthesis, structure, spectral properties and DFT quantum chemical calculations of 4-aminoazobenzene dyes. Effect of intramolecular hydrogen bonding on photoisomerization

    NASA Astrophysics Data System (ADS)

    Georgiev, Anton; Bubev, Emil; Dimov, Deyan; Yancheva, Denitsa; Zhivkov, Ivaylo; Krajčovič, Jozef; Vala, Martin; Weiter, Martin; Machkova, Maria

    2017-03-01

    In this paper three different "push-pull" 4-aminoazobenzene dyes have been synthesized in order to characterize their photochromic behavior in different solvents. The molecular geometry was optimized by DFT/B3LYP functional combined with the standard 6-31 + G(d,p) basis set for trans (E) and cis (Z) isomers and the energy levels of HOMO and LUMO frontier orbitals were computed using IEFPCM solvation in CHCl3 and DMF. The calculated results were compared to the experimental optical band gap and HOMO values of cyclic voltammetry. The intramolecular six-membered hydrogen bond was formed in both isomers of the synthesized dyes. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis, ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. The solvatochromic shift was evaluated by UV-VIS spectroscopy in CHCl3 (nonpolar), EtOH (polar protic) and DMF (polar aprotic) solvents to determine the electron withdrawing and donating properties of the substituents on electron transitions energy. Through the increasing solvent polarity a strong bathochromic shift is observed. The photoisomerization experiments have been performed in two solvents CHCl3 (nonpolar) and DMF (polar aprotic) by UV light irradiation with λ = 365 nm at equal concentrations and time of illuminations. The electronic spectra were computed by TD-DFT after geometry optimization using IEFPCM solvation in CHCl3 and DMF. The degree of photoisomerization was calculated for the three azo chromophores in both solvents. By using first derivative of the UV-VIS spectra it was possible to resolve the overlapped

  16. Synthesis, structure, spectral properties and DFT quantum chemical calculations of 4-aminoazobenzene dyes. Effect of intramolecular hydrogen bonding on photoisomerization.

    PubMed

    Georgiev, Anton; Bubev, Emil; Dimov, Deyan; Yancheva, Denitsa; Zhivkov, Ivaylo; Krajčovič, Jozef; Vala, Martin; Weiter, Martin; Machkova, Maria

    2017-03-15

    In this paper three different "push-pull" 4-aminoazobenzene dyes have been synthesized in order to characterize their photochromic behavior in different solvents. The molecular geometry was optimized by DFT/B3LYP functional combined with the standard 6-31+G(d,p) basis set for trans (E) and cis (Z) isomers and the energy levels of HOMO and LUMO frontier orbitals were computed using IEFPCM solvation in CHCl3 and DMF. The calculated results were compared to the experimental optical band gap and HOMO values of cyclic voltammetry. The intramolecular six-membered hydrogen bond was formed in both isomers of the synthesized dyes. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans→cis, Δμtrans→cis, ΔHtrans→cis, ΔGtrans→cis and ΔStrans→cis values. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. The solvatochromic shift was evaluated by UV-VIS spectroscopy in CHCl3 (nonpolar), EtOH (polar protic) and DMF (polar aprotic) solvents to determine the electron withdrawing and donating properties of the substituents on electron transitions energy. Through the increasing solvent polarity a strong bathochromic shift is observed. The photoisomerization experiments have been performed in two solvents CHCl3 (nonpolar) and DMF (polar aprotic) by UV light irradiation with λ=365nm at equal concentrations and time of illuminations. The electronic spectra were computed by TD-DFT after geometry optimization using IEFPCM solvation in CHCl3 and DMF. The degree of photoisomerization was calculated for the three azo chromophores in both solvents. By using first derivative of the UV-VIS spectra it was possible to resolve the overlapped electron

  17. Optical absorption and DFT calculations in L-aspartic acid anhydrous crystals: Charge carrier effective masses point to semiconducting behavior

    NASA Astrophysics Data System (ADS)

    Silva, A. M.; Silva, B. P.; Sales, F. A. M.; Freire, V. N.; Moreira, E.; Fulco, U. L.; Albuquerque, E. L.; Maia, F. F., Jr.; Caetano, E. W. S.

    2012-11-01

    Density functional theory (DFT) computations within the local-density approximation and generalized gradient approximation in pure form and with dispersion correction (GGA+D) were carried out to investigate the structural, electronic, and optical properties of L-aspartic acid anhydrous crystals. The electronic (band structure and density of states) and optical absorption properties were used to interpret the light absorption measurements we have performed in L-aspartic acid anhydrous crystalline powder at room temperature. We show the important role of the layered spatial disposition of L-aspartic acid molecules in anhydrous L-aspartic crystals to explain the observed electronic and optical properties. There is good agreement between the GGA+D calculated and experimental lattice parameters, with (Δa, Δb, Δc) deviations of (0.029,-0.023,-0.024) (units in Å). Mulliken [J. Chem. Phys.JCPSA60021-960610.1063/1.1740588 23, 1833 (1955)] and Hirshfeld [Theor. Chim. ActaTCHAAM0040-574410.1007/BF00549096 44, 129 (1977)] population analyses were also performed to assess the degree of charge polarization in the zwitterion state of the L-aspartic acid molecules in the DFT converged crystal. The lowest-energy optical absorption peaks related to transitions between the top of the valence band and the bottom of the conduction band involve O 2p valence states and C 1p and O 2p conduction states, with the carboxyl and COOH lateral chain group contributing significantly to the energy band gap. Among the calculated band gaps, the lowest GGA+D (4.49-eV) gap is smaller than the experimental estimate of 5.02 eV, as obtained by optical absorption. Such a wide-band-gap energy together with the small carrier effective masses estimated from band curvatures allows us to suggest that an L-aspartic acid anhydrous crystal can behave as a wide-gap semiconductor. A comparison of effective masses among directions parallel and perpendicular to the L-aspartic molecules layers reveals that charge

  18. DABCO mono-betaine hydrate studied by X-ray diffraction, DFT calculations and spectroscopic methods

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Dega-Szafran, Z.; Katrusiak, A.; Perdoch, W.; Szafran, M.

    2009-09-01

    A new DABCO mono-betaine (1-carboxymethyl-1,4-diazabicyclo[2.2.2]octane inner salt) has been synthesized. It crystallizes as monohydrate in orthorhombic space group Pmn2 1. The DABCO mono-betaine and water molecules are located on a mirror plane. The water molecules link DABCO mono-betaine into linear chains through the H-O-H⋯OOC and H-O-H⋯N hydrogen bonds of 2.709(2) and 2.875(2) Å. The structure of the title compound optimized at B3LYP/6-31G(d,p) level of theory is consistent with X-ray diffraction. The absorption bands in the FTIR spectrum have been assigned. The calculated magnetic isotropic shielding tensors confirm the assignments of the 13C NMR resonance signals.

  19. Molecular structure of trans-cinnamaldehyde as determined by gas electron diffraction aided by DFT calculations

    NASA Astrophysics Data System (ADS)

    Egawa, Toru; Matsumoto, Rui; Yamamoto, Daisuke; Takeuchi, Hiroshi

    2008-12-01

    The molecular structure of trans-cinnamaldehyde (( E)-3-phenyl-2-propenal) was determined by means of gas electron diffraction. The nozzle temperature was 165 °C. The results of B3LYP calculations with the 6-31G ∗∗ basis set were used as Supporting information. It was found that this molecule has two stable conformers, s- cis and s- trans, which differ in the orientation of the sbnd CH dbnd O group. Their abundances at 165 °C were determined to be 25 ± 19% and 75%, for the s- cis and s- trans, respectively. This conformational composition is consistent with the prediction by the theoretical calculations. The determined structural parameters ( rg and ∠ α) of the more abundant conformer, s- trans, of trans-cinnamaldehyde are as follows: < r(C sbnd C) ring> = 1.398(1) Å; r(C dbnd C) = 1.348 (←) Å; r(C 1sbnd C) = 1.470(8) Å; r(C sbnd C( dbnd O)) = 1.473(←) Å; r(C dbnd O) = 1.225(6) Å; < r(C sbnd H)> = 1.116(6) Å; ∠C 6sbnd C 1sbnd C 2 = 118.6(3)°; ∠C 1sbnd C 2sbnd C = 121.0(←)°; ∠C sbnd C 6sbnd C 1 = 121.4(←)°; ∠C 2sbnd C 1sbnd C( dbnd C) = 122.0(26)°; ∠C 1sbnd C dbnd C = 128.3(26)°; ∠C dbnd C sbnd CO = 115.3(27)°; ∠C sbnd C dbnd O = 126.6(19)°. The C 1, C 2 and C 6 atoms are on the ring with the C 1 attached to the sbnd CH dbnd CH sbnd CHO group, and the C 2 and C 6 are on the cis and trans sides to the C dbnd C bond, respectively. Angle brackets denote average values; parenthesized values are the estimated limits of error (3 σ) referring to the last significant digit; left arrows in the parentheses mean that the differences to the preceding parameters are fixed.

  20. 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.

  1. 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.

  2. DFT-Based Electronic Structure Calculations on Hybrid and Massively Parallel Computer Architectures

    NASA Astrophysics Data System (ADS)

    Briggs, Emil; Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry

    2014-03-01

    The latest generation of supercomputers is capable of multi-petaflop peak performance, achieved by using thousands of multi-core CPU's and often coupled with thousands of GPU's. However, efficient utilization of this computing power for electronic structure calculations presents significant challenges. We describe adaptations of the Real-Space Multigrid (RMG) code that enable it to scale well to thousands of nodes. A hybrid technique that uses one MPI process per node, rather than on per core was adopted with OpenMP and POSIX threads used for intra-node parallelization. This reduces the number of MPI process's by an order of magnitude or more and improves individual node memory utilization. GPU accelerators are also becoming common and are capable of extremely high performance for vector workloads. However, they typically have much lower scalar performance than CPU's, so achieving good performance requires that the workload is carefully partitioned and data transfer between CPU and GPU is optimized. We have used a hybrid approach utilizing MPI/OpenMP/POSIX threads and GPU accelerators to reach excellent scaling to over 100,000 cores on a Cray XE6 platform as well as a factor of three performance improvement when using a Cray XK7 system with CPU-GPU nodes.

  3. DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF3Br.

    PubMed

    Lee, Edmond P F; Dyke, John M; Chow, Wan-Ki; Chau, Foo-Tim; Mok, Daniel K W

    2007-07-15

    Reaction enthalpies and barrier heights of the reactions CF3Br+H-->CF3+HBr {reaction (1)} and CF3CHFCF3+H-->CF3CFCF3+H2 {reaction (2)} have been calculated at the near state-of-the-art ab initio level, and also by employing the B3LYP, BH&HLYP, BB1K, MPW1K, MPWB1K and TPSS1KCIS functionals. In addition, the integrated molecular orbital+molecular orbital (IMOMO) method has been used to study reaction (2). The ab initio benchmark values of the reaction enthalpy (298 K) and barrier height (0 K) of reaction (2) are reported for the first time {-(0.7+/-0.7) and 13.3+/-0.5 kcal/mole respectively}. When density functional theory (DFT) results are compared with ab initio benchmarks for both reactions (1) and (2), the MPWB1K functional is found to have the best performance of the six functionals used. The IMOMO method with the RCCSD/aug-cc-pVTZ and/or RCCSD(T)/aug-cc-pVTZ levels, as the high levels of calculation on the model system, gives reaction enthalpies and barrier heights of reaction (2), which agree with ab initio benchmark values to within 1 kcal/mole. Computed key geometrical parameters and imaginary vibrational frequencies of the transition state structures of reactions (1) and (2) obtained at different levels of calculation are compared. The magnitudes of the computed imaginary vibrational frequencies of the transition states of both reactions considered are found to be very sensitive to the levels of calculation used to obtain them. The heat of formation (298 K) of CF3CFCF3 calculated at the near state-of-the-art level has a value of -(318+/-3) kcal/mole.

  4. 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+).

  5. Effect of transition metal-doped Ni(211) for CO dissociation: Insights from DFT calculations

    NASA Astrophysics Data System (ADS)

    Yang, Kuiwei; Zhang, Minhua; Yu, Yingzhe

    2017-03-01

    Density functional theory slab calculations were performed to investigate the adsorption and dissociation of CO over pure and M-doped Ni(211) (M = Fe, Co, Ru and Rh) with the aim to elucidate the effect of transition metal doping for CO activation. Doping the step edge of Ni(211) with Fe, Co and Ru is found to enhance the binding of CO in the initial state (IS) (in the sequence by the improvement degree: Fe > Ru > Co) as well as the co-adsorption of C and O in the final state (FS) (Ru > Fe > Co). In contrast, Rh doping is unfavorable both in the IS and in the FS. Analysis of the overall potential energy surfaces (PES) suggests CO dissociation is facilitated by Fe, Ru and Co doping both kinetically and thermodynamically, wherein Fe and Ru behave extraordinary. Interestingly, Fe substitute is slightly superior to Ru in kinetics whereas the contrary is the case in thermodynamics. Rh doping elevates the energy height from 0.97 eV on Ni(211) to 1.32 eV and releases 0.39 eV less heat relative to Ni(211), again manifesting a negative effect. Besides the classical Brønsted-Evans-Polanyi relationship, we put forward another two neat linear relations, which can well describe the feature of CO dissociation. The differences of CO adsorption and activation in the IS over pure and doped Ni(211) surfaces are rationalized via electronic structure analysis. The findings presented herein are expected to provide theoretical guidance for catalyst design and optimization in relevant processes.

  6. 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

    2015-11-05

    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.

  7. Raman spectra and DFT calculations for tetraterpene hydrocarbons from the L race of the green microalga Botryococcus braunii

    NASA Astrophysics Data System (ADS)

    Chun, Hye Jin; Waqued, Sergio; Thapa, Hem R.; Han, Arum; Yakovlev, Vladislav V.; Laane, Jaan; Devarenne, Timothy P.

    2017-02-01

    The green microalga Botryococcus braunii produces large amounts of liquid hydrocarbons that can be used as a renewable source for producing transportation fuels. In the L race of B. braunii the tetraterpene known as lycopadiene accumulates as the main hydrocarbon. Lycopadiene biosynthesis begins with the production of the eight carbon-carbon double bond (C=C) containing molecule lycopaoctaene, which is reduced to lycopadiene through four intermediates containing less C=C bonds. While the biosynthetic pathway for these hydrocarbons has recently been deciphered, a spectroscopic understanding of the molecular structure for these molecules remains to be reported. Here we describe the vibrational frequency assignments for all six L race hydrocarbons using density functional theory (DFT) calculations, showing that these molecules have between 312 and 348 vibrational frequencies. Experimental Raman spectroscopy analysis shows the regions for ν(C=C) stretch and CH2/CH3 bending vibrations offer unique spectral signatures allowing for the differentiation of several of the hydrocarbons from each other.

  8. 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.

  9. 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.

  10. Vibrational spectroscopic studies and DFT calculations on NaCH3CO2(aq) and CH3COOH(aq).

    PubMed

    Rudolph, Wolfram W; Fischer, Dieter; Irmer, Gert

    2014-02-28

    Aqueous solutions of sodium acetate, NaCH3CO2, and acetic acid, CH3COOH, were studied using Raman and infrared spectroscopy. The spectra were recorded over a large concentration range, in the terahertz region and up to 4000 cm(-1). In the isotropic Raman spectrum in R-format, a polarized band at 189 cm(-1) was assigned to the ν1Na-O stretch of the hydrated Na(+)-ion and a shoulder at 245 cm(-1) to the restricted translation band, νsO-H···O* of the hydrated acetate ion, CH3CO2(-)(aq). The CH3CO2(-)(aq) and the hydrated acetic acid, CH3COOH(aq), possess pseudo Cs symmetry. Geometrical parameters for the species in the gas phase and for CH3CO2(-)(aq) and CH3COOH(aq) are reported. Characteristic bands for CH3CO2(-)(aq) and CH3COOH(aq) were assigned under the guidance of the DFT vibrational frequency calculations and discussed in detail. In aqueous NaCH3CO2 solutions, at high concentrations, no contact ion pairs could be detected, but instead solvent separated ion pairs were found. In LiCH3CO2(aq), however, contact ion pairs are formed which is indicated by the appearance of a shoulder at 939 cm(-1) and the shift of the symmetric stretching mode of the -CO2(-) group to higher wavenumbers.

  11. Pseudopotential and full-electron DFT calculations of thermodynamic properties of electrons in metals and semiempirical equations of state.

    PubMed

    Levashov, P R; Sin'ko, G V; Smirnov, N A; Minakov, D V; Shemyakin, O P; Khishchenko, K V

    2010-12-22

    In the present work, we compare the thermal contribution of electrons to thermodynamic functions of metals in different models at high densities and electron temperatures. One of the theoretical approaches, the full-potential linear-muffin-tin-orbital method, treats all electrons in the framework of density functional theory (DFT). The other approach, VASP, uses projector-augmented-wave pseudopotentials for the core electrons and considers the valent electrons also in the context of DFT. We analyze the limitations of the pseudopotential approach and compare the DFT results with a finite-temperature Thomas-Fermi model and two semiempirical equations of state.

  12. Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations.

    PubMed

    Castro, Maria Eugenia; Percino, M Judith; Chapela, Victor M; Soriano-Moro, Guillermo; Ceron, Margarita; Melendez, Francisco J

    2013-05-01

    This study examined absorption properties of 2-styrylpyridine, trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)]pyridine, and trans-4-(m-cyanostyryl)pyridine compounds based on theoretical UV/Vis spectra, with comparisons between time-dependent density functional theory (TD-DFT) using B3LYP, PBE0, and LC-ωPBE functionals. Basis sets 6-31G(d), 6-31G(d,p), 6-31+G(d,p), and 6-311+G(d,p) were tested to compare molecular orbital energy values, gap energies, and maxima absorption wavelengths. UV/Vis spectra were calculated from fully optimized geometry in B3LYP/6-311+G(d,p) in gas phase and using the IEFPCM model. B3LYP/6-311+G(d,p) provided the most stable form, a planar structure with parameters close to 2-styrylpyridine X-ray data. Isomeric structures were evaluated by full geometry optimization using the same theory level. Similar energetic values were found: ~4.5 kJ mol(-1) for 2-styrylpyridine and ~1 kJ mol(-1) for derivative compound isomers. The 2-styrylpyridine isomeric structure differed at the pyridine group N-atom position; structures considered for the other compounds had the cyano group attached to the phenyl ring m-position equivalent. The energy difference was almost negligible between m-cyano-substituted molecules, but high energy barriers existed for cyano-substituted phenyl ring torsion. TD-DFT appeared to be robust and accurate approach. The B3LYP functional with the 6-31G(d) basis set produced the most reliable λmax values, with mean errors of 0.5 and 12 nm respect to experimental values, in gas and solution, respectively. The present data describes effects on the λmax changes in the UV/Vis absorption spectra of the electron acceptor cyano substituent on the phenyl ring, the electron donor methyl substituent, and the N-atom position on the electron acceptor pyridine ring, causing slight changes respect to the 2-styrylpyridine title compound.

  13. Evidence for Alkene cis-Aminocupration, an Aminooxygenation Case Study: Kinetics, EPR Spectroscopy, and DFT Calculations

    PubMed Central

    Paderes, Monissa C.; Belding, Lee; Fanovic, Branden; Dudding, Travis; Keister, Jerome B.

    2012-01-01

    Alkene difunctionalization reactions are important in organic synthesis. We have recently shown that copper(II) complexes can promote and catalyze intramolecular alkene aminooxygenation, carboamination, and diamination reactions. In this contribution, we report a combined experimental and theoretical examination of the mechanism of the copper(II)-promoted olefin aminooxygenation reaction. Kinetics experiments revealed a mechanistic pathway involving an equilibrium reaction between a copper(II) carboxylate complex and the γ-alkenyl sulfonamide substrate and a rate-limiting intramolecular cis-addition of N–Cu across the olefin. Kinetic isotope effect studies support that the cis-aminocupration is the rate-determining step. UV/Vis spectra support a role for the base in the break-up of copper(II) carboxylate dimer to monomeric species. Electron paramagnetic resonance (EPR) spectra provide evidence for a kinetically competent N–Cu intermediate with a CuII oxidation state. Due to the highly similar stereochemical and reactivity trends among the CuII-promoted and catalyzed alkene difunctionalization reactions we have developed, the cis-aminocupration mechanism can reasonably be generalized across the reaction class. The methods and findings disclosed in this report should also prove valuable to the mechanism analysis and optimization of other copper(-II) carboxylate promoted reactions, especially those that take place in aprotic organic solvents. PMID:22237868

  14. 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.

  15. Spectrum-splitting approach for Fermi-operator expansion in all-electron Kohn-Sham DFT calculations

    NASA Astrophysics Data System (ADS)

    Motamarri, Phani; Gavini, Vikram; Bhattacharya, Kaushik; Ortiz, Michael

    2017-01-01

    We present a spectrum-splitting approach to conduct all-electron Kohn-Sham density functional theory (DFT) calculations by employing Fermi-operator expansion of the Kohn-Sham Hamiltonian. The proposed approach splits the subspace containing the occupied eigenspace into a core subspace, spanned by the core eigenfunctions, and its complement, the valence subspace, and thereby enables an efficient computation of the Fermi-operator expansion by reducing the expansion to the valence-subspace projected Kohn-Sham Hamiltonian. The key ideas used in our approach are as follows: (i) employ Chebyshev filtering to compute a subspace containing the occupied states followed by a localization procedure to generate nonorthogonal localized functions spanning the Chebyshev-filtered subspace; (ii) compute the Kohn-Sham Hamiltonian projected onto the valence subspace; (iii) employ Fermi-operator expansion in terms of the valence-subspace projected Hamiltonian to compute the density matrix, electron density, and band energy. We demonstrate the accuracy and performance of the method on benchmark materials systems involving silicon nanoclusters up to 1330 electrons, a single gold atom, and a six-atom gold nanocluster. The benchmark studies on silicon nanoclusters revealed a staggering fivefold reduction in the Fermi-operator expansion polynomial degree by using the spectrum-splitting approach for accuracies in the ground-state energies of ˜10-4Ha/atom with respect to reference calculations. Further, numerical investigations on gold suggest that spectrum splitting is indispensable to achieve meaningful accuracies, while employing Fermi-operator expansion.

  16. 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

    2015-02-05

    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.

  17. Assessment of Popular DFT and Semiempirical Molecular Orbital Techniques for Calculating Relative Transition State Energies and Kinetic Product Distributions in Enantioselective Organocatalytic Reactions.

    PubMed

    Schenker, Sebastian; Schneider, Christopher; Tsogoeva, Svetlana B; Clark, Timothy

    2011-11-08

    The performance of computationally accessible levels of calculation for the transition states of organocatalytic reaction has been assessed. Reference post-Hartree-Fock single point energy calculations were used as standards for the gas-phase Born-Oppenheimer relative energies of pairs of alternative transition states that lead to the two product enantiomers. We show that semiempirical methods cannot even be relied on to yield qualitatively correct results. The geometries (optimized, for instance, with DFT) have a large impact on the results of high-level post-HF calculations, so that it is essential to use an adequate DFT technique and basis set. DFT can yield quantitatively correct results that are consistent with post-HF calculations if functionals that consider dispersion are used. Geometries for large systems show larger errors than those for smaller ones but are treated better by functionals such as M06-2X and w97Bxd that include dispersion implicitly or explicitly. Local correlation techniques introduce errors of comparable magnitude to those given by different levels of geometry optimization. We recommend RICC2/TZVP//M06-2X/TZVP, RI-MP2/TZVP// M06-2X/TZVP, and M06-2X/TZVP// M06-2X/TZVP calculations in that order, depending on the size of the system.

  18. 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.

  19. Three iodometalate organic-inorganic hybrid materials based on methylene blue cation: Syntheses, structures, properties and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chai, Wen-Xiang; Lin, Jian; Song, Li; Qin, Lai-Shun; Shi, Hong-Sheng; Guo, Jia-Yu; Shu, Kang-Ying

    2012-08-01

    The functional dye of methylene blue (MB) has been employed for seeking new organic-inorganic hybrid photochromic materials. Although the photochromism has not been observed yet, three iodometalate compounds, namely (MB) (PbI3) (DMF) (1), (MB)4(Cu2I4)2 (2), and (MB)3(Bi2I9) (DMF)2 (3), have been synthesized and characterized. The iodometalate anion features as a [PbI3]∞- chain in 1, a dinuclear unit of Cu2I42- in 2, and a dinuclear unit of Bi2I93- in 3. Due to the synergy of cations and anions, the MB+ cations present supramolecular column stacks in 1 and 3, but a novel supramolecular octamer structure in 2. Their thermogravimetric analyses reveal that the polymeric inorganic anion structure is helpful to increase the stability of cation whereas the discrete structure is adverse. For seeking some clues which is significant to searching new photochromic systems, the density functional theory (DFT) studies have been performed on 1, in which the electronic structure analyses suggests that the stacking mode of cations and anions could be also an important factor influencing the charge transfer between them. In addition, dielectric hysteresis loop testing has been performed on 1 due to its polar space group of Cc.

  20. 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).

  1. A coumarin-derived fluorescent chemosensor for selectively detecting Cu²⁺: synthesis, DFT calculations and cell imaging applications.

    PubMed

    Chen, Fengjuan; Liu, Guozhen; Shi, Yanjun; Xi, Pinxian; Cheng, Ju; Hong, Jinpeng; Shen, Rong; Yao, Xiaojun; Bai, Decheng; Zeng, Zhengzhi

    2014-06-01

    A novel coumarin-based fluorescent probe L ((4E)-4-((7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl) methyleneamino)-1,2-dihyydro-2,3-dimethyl-1-phenylpyrazol-5-one) has been developed as a simple and efficient chemosensor which exhibits a significant fluorescence reduction in the presence of metal cations. This sensor exhibits high selectivity and sensitivity toward Cu(2+) over other common cations. The mechanism for detecting copper was evaluated by time-dependent density functional theory (TD-DFT) calculations and the coordination mode was also confirmed by density functional theory (DFT) calculations. Furthermore, results of cell imaging in this study indicate that this new probe may be useful for detection and monitoring of Cu(2+) in biological applications.

  2. 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.

  3. 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.

  4. Versatile and green synthesis, spectroscopic characterizations, crystal structure and DFT calculations of 1,2,3‒triazole‒based sulfonamides

    NASA Astrophysics Data System (ADS)

    Saeidian, Hamid; Sadighian, Hamed; Abdoli, Morteza; Sahandi, Morteza

    2017-03-01

    A green, and practically reliable method for the synthesis of novel 1,2,3‒triazole-based sulfonamides via copper (I)‒catalyzed azide‒alkyne [3 + 2] cycloaddition reaction was reported. The desired products were characterized by CHN analysis, FT-IR, 1H and 13C NMR, ESI-MS spectroscopy, single crystal X-ray diffraction and density functional theory (DFT) geometry optimization and molecular orbital calculations. Mild and green reaction conditions, atom-economic and high yields (61-91%) make this protocol an attractive option for the synthesis of 1,2,3‒triazoles bearing sulfonamide moiety. Geometrical structures, vibrational frequencies, 1H and 13C chemical shift values, Mulliken charge distribution and electrophilicity index (HOMO-LUMO analysis) of the characterized structure of 3f in the ground state have been calculated with the aid of DFT studies. The calculated chemical shifts (NMR) and vibrational frequencies (FT-IR) are in compliance with the experimental findings. The aim of the DFT study was to make a reasonable assignment of vibrational bands and chemical shifts.

  5. Total Energy Calculations using DFT+DMFT: Application to the Pressure-composition Phase Diagram of Rare-earth Element Nickelates

    NASA Astrophysics Data System (ADS)

    Park, Hyowon

    2014-03-01

    Ab-initio total energy calculations have been implemented within the fully self-consistent density functional theory plus dynamical mean field theory (DFT+DMFT) method, using a Wannier orbital basis. The method is used to calculate the structural and metal-insulator transition phase diagrams of the rare-earth element nickelate RNiO3 perovskites as a function of rare-earth ion, pressure and temperature. This phase diagram is of interest because the insulating phase arises from a remarkable site-selective Mott state, in which unusual electronic physics is strongly coupled to a breathing-mode Ni-O bond disproportionation. Conventional DFT fails to stabilize the breathing distortion and thus does not reproduce the insulating phase. DFT+U overpredicts order, in particular finding that La NiO3 is disproportionated, in disagreement with experiment. In contrast to these theories, the DFT+DMFT method can quantitatively reproduce the metal-insulator and structural phase diagram of all RNiO3 perovskites in the plane of pressure and rare-earth elements. The calculated temperature dependence of the energetics of the phase transformation indicates that the thermal transition is driven by phonon entropy effects. This present method can be generally applied to nano-structured or artificially structured strongly correlated materials including heterostructures and thin films, whose electronic phases are strongly coupled to their lattice degrees of freedom. The authors acknowledge funding from the U. S. Army Research Office via grant No. W911NF0910345 56032PH, US Department of Energy under grant DOE-ER-046169, and in part by FAME, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

  6. QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study.

    PubMed

    Sinnecker, Sebastian; Neese, Frank

    2006-09-01

    A detailed study of the influence of the surrounding protein on magnetic and optical spectra of metalloproteins is presented using the quantum-mechanical/molecular mechanical (QM/MM) approach. The well-studied type I copper site in plastocyanin in the cupric oxidation state is taken as a test case because its spectroscopic properties have been extensively studied and are well understood. The calculations have been performed using nonrelativistic and scalar relativistic (at the level of the zeroth order regular approximation, ZORA) calculations (B3LYP functional). Linear response theory has been used to calculate first- and second-order properties, namely the EPR g-tensor, the central metal hyperfine couplings (HFCs), the HFCs of the directly coordinating ligands, as well as superhyperfine couplings (1H, 14N) from remote nuclei, transition energies, and oscillator strengths. Two different model systems have been defined that do not and do include important amino acids from the second coordination sphere, respectively. For comparison, calculations have been carried out in the gas phase and in a dielectric continuum (conductor like screening model, COSMO) with a dielectric constant of four. The best results were obtained at the scalar relativistic ZORA level for the largest model in conjunction with explicit modeling of the protein environment through the QM/MM procedure, which is also considered to be the highest level of theory used in this work. The protein effects beyond the second coordination sphere were found to be quite substantial (up to 30% changes on some properties), and were found to require an explicit treatment of the protein beyond the second coordination sphere. In addition, the embedding water cage was found to have a nonnegligible influence on the calculated spectroscopic data, which is of the same order as the influence of the protein backbone charges. However, while qualitatively satisfactory, the errors in the calculated spectroscopic parameters

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. Ion/molecule reactions of 2-chloro- and 2-bromopropene radical cations with methanol and ethanol--FT-ICR spectrometry and DFT calculations

    NASA Astrophysics Data System (ADS)

    Grützmacher, Hans-Friedrich; Büchner, Michael; Zipse, Hendrik

    2005-02-01

    Continuing the studies of ion/molecule reactions of haloalkene radical cations with nucleophiles, the reactions of the radical cations of 2-chloropropene, 1+, and 2-bromopropene. 2+, with methanol and ethanol, respectively, have been investigated by FT-ICR spectrometry and by computational analysis using DFT calculation (BHLYP/6-311 + G(2d,p)//BHLYP/6-31 + G(d) level). Only slow reactions (reaction efficiency <1%) are observed for 1+/methanol and 2+/methanol. Slow proton transfer is the main process for 1+/methanol besides minor addition of methanol to 1+ followed by loss of HCl or Cl. Addition of methanol accompanied by loss of Br is the exclusive process observed for 2+/methanol. In contrast, both 1+ and 2+ react efficiently with ethanol yielding protonated acetaldehyde as the exclusive (1+) or by far dominant (2+) primary reaction product. The computational analysis of these ion/molecule reactions shows that in the case of 1+/methanol and 2+/methanol all processes are either endothermic or blocked by large activation energies. Nonetheless, addition of methanol to the ionized CC double bond of 1+ or 2+ is exothermic, yielding in each case a pair of isomeric [beta]-distonic methoxonium ions. A new reaction mechanism has been found for the HX (X = Cl, Br) elimination from the less stable isomer of the distonic intermediates. Further, an energetically favorable transition state has been detected for hydrogen atom transfer from the [alpha]-CH2 group of alcohol to the halogenoalkene radical cations. These findings lead to a revised mechanism of the oxidation process and provide a plausible explanation for the excessive H/D exchange between 1+ and CD3OH during their slow reaction.

  12. Synthesis, Characterization, Properties and DFT Calculations of 2-(Benzo[b]thiophen-2-yl)pyridine-based Iridium(III) Complexes with Different Ancillary Ligands.

    PubMed

    Li, Gao-Nan; Zeng, Yong-Pi; Li, Kai-Xiu; Chen, Hao-Hua; Xie, Hui; Zhang, Fu-Lin; Chen, Guang-Ying; Niu, Zhi-Gang

    2016-01-01

    A series of new cyclometalated btp-based iridium(III) complexes with three different ancillary ligands, Ir(btp)2(bozp) (3a), Ir(btp)2(btzp) (3b) and Ir(btp)2(izp) (3c) (btp = 2-(benzo[b]thiophen-2-yl)pyridine, bozp =2-(benzo[d]oxazol-2-yl)phenol, btzp =2-(benzo[d]thiazol-2-yl)phenol, izp = 2-(2 H-indazol-2-yl)phenol), have been synthesized and fully characterized. The crystal structure of 3b has been determined by single crystal X-ray diffraction analysis. A comparative study has been carried out for complexes 3a - 3c by UV-vis absorption spectroscopy, photoluminescence spectroscopy, cyclic voltammetry and DFT calculations. This observation illustrates that the substitution of N or S in ancillary ligand can lead to a marked bathochromic shift of absorption and emission wavelengths. The spectroscopic characterisation of these complexes has been complemented by DFT and TD-DFT calculations, supporting the assignment of (3)MLCT/(3)LC to the lowest energy excited state.

  13. Conformational stability, spectral analysis (infrared, Raman and NMR) and DFT calculations of 2-Amino-5-(ethylthio)-1,3,4-thiadiazole

    NASA Astrophysics Data System (ADS)

    Mohamed, Tarek A.; Hassan, Ahmed E.; Shaaban, Ibrahim A.; Abuelela, Ahmed M.; Zoghaib, Wajdi M.

    2017-02-01

    The infrared (4000-225 cm-1) and Raman (3500-60 cm-1) spectra of 2-Amino-5-(ethylthio)-1,3,4-thiadiazole (AEST; C4H7N3S2) have been recorded in the solid phase. In addition, the 1H and 13C NMR spectra of AEST were obtained in DMSO-d6. We have focused on five staggered conformers (1-5) resulting from rotations of the methyl, ethyl and thioethyl groups around Csbnd C and Csbnd S bonds with the sbnd NH2 group having a non-planar (sp3) geometry. DFT-B3LYP/6-31G(d) calculations proved that only conformers 4 and 5 produce real vibrational frequencies and conformer 5 is the favored one with an energy difference of 124 cm-1 (0.35 kcal/mol) in agreement with the observed ethyl torsion at 92 cm-1. The calculated frequencies, infrared intensities, Raman activities and potential energy distributions were compiled with spectral observations in favor of conformer 5. All vibrational modes were assigned to their corresponding vibrational bands. Applying the observed methyl torsions, the kinetic parameter F number was found to be 5.3263 cm-1 and an average V3 value of 1565 ± 14 cm-1 (4.48 ± 0.04 kcal/mol) was obtained. These values are close to the methyl barriers predicted from B3LYP/6-31G(d) potential surface scans. Moreover, the 1H and 13C NMR chemical shifts were also estimated for conformers 4 and 5 with DMSO as solvent implementing GIAO/PCM approximation utilizing B3LYP method at 6-311++G (d,p) basis set. The results are reported and discussed herein and compared with 2-Amino-5-ethyl-1,3,4-thiadiazole (AET) whenever appropriate.

  14. Insights into the intramolecular donor stabilisation of organostannylene palladium and platinum complexes: syntheses, structures and DFT calculations.

    PubMed

    Wagner, Michael; Deáky, Vajk; Dietz, Christina; Martincová, Jana; Mahieu, Bernard; Jambor, Roman; Herres-Pawlis, Sonja; Jurkschat, Klaus

    2013-05-17

    The syntheses of the transition metal complexes cis-[(4-tBu-2,6-{P(O)(OiPr)2}2C6H2SnCl)2MX2] (1, M = Pd, X = Cl; 2, M = Pd, X = Br; 3, M = Pd, X = I; 4, M = Pt, X = Cl), cis-[{2,6-(Me2NCH2)2C6H3SnCl}2MX2] (5, M = Pd, X = I; 6, M = Pt, X = Cl), trans-[{2,6-(Me2NCH2)2C6H3SnI}2PtI2] (7) and trans-[(4-tBu-2,6-{P(O)(OiPr)2}2C6H2SnCl)PdI2]2 (8) are reported. Also reported is the serendipitous formation of the unprecedented complexes trans-[(4-tBu-2,6-{P(O)(OiPr)2}2C6H2SnCl)2Pt(SnCl3)2] (10) and [(4-tBu-2,6-{P(O)(OiPr)2}2C6H2SnCl)3Pt(SnCl3)2] (11). The compounds were characterised by elemental analyses, (1)H, (13)C, (31)P, (119)Sn and (195)Pt NMR spectroscopy, single-crystal X-ray diffraction analysis, UV/Vis spectroscopy and, in the cases of compounds 1, 3 and 4, also by Mössbauer spectroscopy. All the compounds show the tin atoms in a distorted trigonal-bipyramidal environment. The Mössbauer spectra suggest the tin atoms to be present in the oxidation state III. The kinetic lability of the complexes was studied by redistribution reactions between compounds 1 and 3 as well as between 1 and cis-[{2,6-(Me2 NCH2)2C6H3SnCl}2PdCl2]. DFT calculations provided insights into both the bonding situation of the compounds and the energy difference between the cis and trans isomers. The latter is influenced by the donor strength of the pincer-type ligands.

  15. 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.

  16. DFT calculations on molecular structure, spectral analysis, multiple interactions, reactivity, NLO property and molecular docking study of flavanol-2,4-dinitrophenylhydrazone

    NASA Astrophysics Data System (ADS)

    Singh, Ravindra Kumar; Singh, Ashok Kumar

    2017-02-01

    A new flavanol-2,4-dinitrophenylhydrazone (FDNP) was synthesized and its structure was confirmed by FT-IR, FT-Raman, 1H NMR, mass spectrometry and elemental analysis. All quantum chemical calculations were carried out at level of density functional theory (DFT) with B3LYP functional using 6-311++ G (d,p) basis atomic set. UV-Vis absorption spectra for the singlet-singlet transition computed for fully optimized ground state geometry using Time-Dependent-Density Functional Theory (TD-DFT) with CAM-B3LYP functional was found to be in consistent with that of experimental findings. Analysis of vibrational (FT-IR and FT-Raman) spectrum and their assignments has been done by computing Potential Energy Distribution (PED) using Gar2ped. HOMO-LUMO analysis was performed and reactivity descriptors were calculated. Calculated global electrophilicity index (ω = 7.986 eV) shows molecule to be a strong electrophile. 1H NMR chemical shift calculated with the help of gauge-including atomic orbital (GIAO) approach shows agreement with experimental data. Various intramolecular interactions were analysed by AIM approach. DFT computed total first static hyperpolarizability (β0 = 189.03 × 10-30 esu) indicates that title molecule can be used as attractive future NLO material. Solvent induced effects on the NLO properties studied by using self-consistent reaction field (SCRF) method shows that β0 value increases with increase in solvent polarity. To study the thermal behaviour of title molecule, thermodynamic properties such as heat capacity, entropy and enthalpy change at various temperatures have been calculated and reported. Molecular docking results suggests title molecule to be a potential kinase inhibitor and might be used in future for designing of new anticancer drug.

  17. 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.

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

    PubMed

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

    2015-03-15

    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 (1)H and (13)C nuclear magnetic resonance (NMR) chemical shift of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

  19. 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.

  20. Deep-red phosphorescent iridium(III) complexes containing 1-(benzo[b] thiophen-2-yl) isoquinoline ligand: synthesis, photophysical and electrochemical properties and DFT calculations.

    PubMed

    Li, Gao-Nan; Zou, Ying; Yang, Yi-Ding; Liang, Jiao; Cui, Feng; Zheng, Tao; Xie, Hui; Niu, Zhi-Gang

    2014-09-01

    Four new bis-cyclometalated iridium(III) complexes, [Ir(btq) 2phen] [PF6] (3a), [Ir(btq) 2bpy] [PF6] (3b), [Ir(btq) 2dtbipy] [PF6] (3c) and [Ir(btq) 2pic] (3d) (btq = 1-(benzo[b] thiophen-2-yl) isoquinoline, phen = 1,10-phenanthroline, bpy = 2,2'-bipyridine, dtbipy = 4,4'-di-tert-butyl-2,2'-bipyridine, pic = picolinic acid) have been synthesized and fully characterized. The crystal structure of 3a has been determined by X-ray analysis. The photophysical and electrochemical properties of these new complexes 3a - 3d have been studied. The photoluminescence spectra of all Ir(III) complexes exhibit deep-red emission maxima at 682, 682, 683 and 698 nm, respectively. The most representative molecular orbital energy-level diagrams and the lowest energy electronic transitions of 3a - 3d have been calculated with density functional theory (DFT) and time-dependent DFT (TD - DFT). The results show that the pic ancillary ligand of complex 3d influences the absorption and emission energies with a further red-shift relative to other three complexes 3a - 3c.

  1. 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

    2015-02-05

    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.

  2. Solvent decompositions and physical properties of decomposition compounds in Li-ion battery electrolytes studied by DFT calculations and molecular dynamics simulations.

    PubMed

    Tasaki, Ken

    2005-02-24

    The density functional theory (DFT) calculations have been performed for the reduction decompositions of solvents widely used in Li-ion secondary battery electrolytes, ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonates (DMC), ethyl methyl carbonate (EMC), and diethyl carbonate (DEC), including a typical electrolyte additive, vinylene carbonate (VC), at the level of B3LYP/6-311+G(2d,p), both in the gas phase and solution using the polarizable conductor calculation model. In the gas phase, the first electron reduction for the cyclic carbonates and for the linear carbonates is found to be exothermic and endothermic, respectively, while the second electron reduction is endothermic for all the compounds examined. On the contrary, in solution both first and second electron reductions are exothermic for all the compounds. Among the solvents and the additive examined, the likelihood of undergoing the first electron reduction in solution was found in the order of EC > PC > VC > DMC > EMC > DEC with EC being the most likely reduced. VC, on the other hand, is most likely to undergo the second electron reduction among the compounds, in the order of VC > EC > PC. Based on the results, the experimentally demonstrated effectiveness of VC as an excellent electrolyte additive was discussed. The bulk thermodynamic properties of two dilithium alkylene glycol dicarbonates, dilithium ethylene glycol dicarbonate (Li-EDC) and dilithium 1,2-propylene glycol dicarbonate (Li-PDC), as the major component of solid-electrolyte interface (SEI) films were also examined through molecular dynamics (MD) simulations in order to understand the stability of the SEI film. It was found that film produced from a decomposition of EC, modeled by Li-EDC, has a higher density, more cohesive energy, and less solubility to the solvent than the film produced from decomposition of PC, Li-PDC. Further, MD simulations of the interface between the decomposition compound and graphite suggested

  3. Chemical synthesis, crystal structure, vibrational spectroscopy, non-linear optical properties and DFT calculation of bis (2,6-diaminopyridinium) sulfate monohydrate

    NASA Astrophysics Data System (ADS)

    Ben Hassen, Chaouki; Dammak, Thameur; Chniba-Boudjada, Nassira; Mhiri, Tahar; Boujelbene, Mohamed

    2017-01-01

    Single crystals of a new organic inorganic hybrid compound "bis (2,6-diaminopyridinium) sulfate monohydrate [C5H8N3]2SO4·H2O ([2,6-HDAP]2SO4·H2O)" was synthesized by slow evaporation method at room temperature and characterized by X-ray single crystal diffraction, infrared spectroscopy and DFT calculation. The new hybrid compound crystallizes in the orthorhombic system with the non-centro symmetric space group Pna21 and the following parameters a = 14.759(2) Å, b = 7.076 (2) Å and c = 28.159 (2) Å. The atomic arrangement can be described as inorganic chains following the b axis connected with the organic groups by means of Nsbnd H⋯O hydrogen bonds to form 3D network. Antiparallelly π-π stacked 2,6-HDAP cations form molecular columns in the spaces between the chains. 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 LanL2DV basis set. The wavenumber calculated are in good agreement with the observed frequency values. The calculated hyperpolarizability βtot is about 4.5 times more than that of the reference crystal KDP. Hence, the large β value shows that the title compound is an attractive object for future studies of nonlinear optical properties.

  4. 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.

  5. 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.

  6. MPW1K Performs Much Better than B3LYP in DFT Calculations on Reactions that Proceed by Proton-Coupled Electron Transfer (PCET)

    PubMed Central

    Lingwood, Mark; Hammond, Jeff R.; Hrovat, David A.; Mayer, James M.; Borden, Weston Thatcher

    2008-01-01

    DFT calculations have been performed with the B3LYP and MPW1K functional on the hydrogen atom abstraction reactions of ethenoxyl with ethenol and of phenoxyl with both phenol and α-naphthol. Comparison with the results of G3 calculations shows that B3LYP seriously underestimates the barrier heights for the reaction of ethenoxyl with ethenol by both proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms. The MPW1K functional also underestimates the barrier heights, but by much less than B3LYP. Similarly, comparison with the results of experiments on the reaction of phenoxyl radical with α-naphthol indicates that the barrier height for the preferred PCET mechanism is calculated more accurately by MPW1K than by B3LYP. These findings indicate that the MPW1K functional is much better suited than B3LYP for calculations on hydrogen abstraction reactions by both HAT and PCET mechanisms. PMID:18725967

  7. 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.

  8. 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.

  9. 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

  10. Solvation chemistry of water-soluble thiol-protected gold nanocluster Au₁₀₂ from DOSY NMR spectroscopy and DFT calculations.

    PubMed

    Salorinne, Kirsi; Lahtinen, Tanja; Malola, Sami; Koivisto, Jaakko; Häkkinen, Hannu

    2014-07-21

    The hydrodynamic diameter of Aum(pMBA)n [(m, n) = (102, 44) and (144, 60)] clusters in aqueous media was determined via DOSY NMR spectroscopy. The apparent size of the same (n, m) cluster depends on the counter ion of the deprotonated pMBA(-) ligand as explained by the competing ion-pair strength and hydrogen bonding interactions studied in DFT calculations. The choice of the counter ion affects the surface chemistry and molecular structure at the organic/water interface, which is relevant for biological applications.

  11. Conformational equilibrium of bis(trifluoromethanesulfonyl) imide anion of a room-temperature ionic liquid: Raman spectroscopic study and DFT calculations.

    PubMed

    Fujii, Kenta; Fujimori, Takao; Takamuku, Toshiyuki; Kanzaki, Ryo; Umebayashi, Yasuhiro; Ishiguro, Shin-Ichi

    2006-04-27

    The structure of bis(trifluoromethanesulfonyl) imide (TFSI-) in the liquid state has been studied by means of Raman spectroscopy and DFT calculations. Raman spectra of 1-ethyl-3-methylimidazolium (EMI+) TFSI- show relatively strong bands arising from TFSI- at about 398 and 407 cm(-1). Interestingly, the 407 cm(-1) band, relative to the 398 cm(-1) one, is appreciably intensified with raising temperature, suggesting that an equilibrium is established between TFSI- conformers in the liquid state. According to DFT calculations followed by normal frequency analyses, two conformers of C2 and C1 symmetry, respectively, constitute global and local minima, with an energy difference 2.2-3.3 kJ mol(-1). The wagging omega-SO2 vibration appears at 396 and 430 cm(-1) for the C1 conformer and at 387 and 402 cm(-1) for the C2 one. Observed Raman spectra over the range 380-440 cm(-1) were deconvoluted to extract intrinsic bands of TFSI- conformers, and the enthalpy of conformational change from C2 to C1 was evaluated. The enthalpy value is in good agreement with that obtained by theoretical calculations. We thus conclude that a conformational equilibrium is established between the C1 and C2 conformers of TFSI- in the liquid EMI+TFSI-, and the C2 conformer is more favorable than the C1 one.

  12. 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

    2013-09-07

    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.

  13. VLSI Architectures for Computing DFT's

    NASA Technical Reports Server (NTRS)

    Truong, T. K.; Chang, J. J.; Hsu, I. S.; Reed, I. S.; Pei, D. Y.

    1986-01-01

    Simplifications result from use of residue Fermat number systems. System of finite arithmetic over residue Fermat number systems enables calculation of discrete Fourier transform (DFT) of series of complex numbers with reduced number of multiplications. Computer architectures based on approach suitable for design of very-large-scale integrated (VLSI) circuits for computing DFT's. General approach not limited to DFT's; Applicable to decoding of error-correcting codes and other transform calculations. System readily implemented in VLSI.

  14. 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.

  15. 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.

  16. 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

    2016-01-05

    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.

  17. Lithium choreography: intramolecular arylations of carbamate-stabilised carbanions and their mechanisms probed by in situ IR spectroscopy and DFT calculations.

    PubMed

    Fournier, Anne M; Nichols, Christopher J; Vincent, Mark A; Hillier, Ian H; Clayden, Jonathan

    2012-12-14

    Deprotonation of O-allyl, O-propargyl or O-benzyl carbamates in the presence of a lithium counterion leads to carbamate-stabilised organolithium compounds that may be quenched with electrophiles. We now report that when the allylic, propargylic or benzylic carbamate bears an N-aryl substituent, an aryl migration takes place, leading to stereochemical inversion and C-arylation of the carbamate α to oxygen. The aryl migration is an intramolecular S(N) Ar reaction, despite the lack of anion-stabilising aryl substituents. Our in situ IR studies reveal a number of intermediates along the rearrangement pathway, including a "pre-lithiation complex," the deprotonated carbamate, the rearranged anion, and the final arylated carbamate. No evidence was obtained for a dearomatised intermediate during the aryl migration. DFT calculations predict that during the reaction the solvated Li cation moves from the carbanion centre, thus freeing its lone pair for nucleophilic attack on the remote phenyl ring. This charge separation leads to several alternative conformations. The one having Li(+) bound to the carbamate oxygen gives rise to the lowest-energy transition structure, and also leads to inversion of the configuration. In agreement with the IR studies, the DFT calculations fail to locate a dearomatised intermediate.

  18. Fourier-transform infrared and Raman spectra of cysteine dichloride cadmium(II) anion DFT: B3LYP/3-21G(d) structural and vibrational calculations.

    PubMed

    Faget, Grisset; Felcman, Judith; Giannerini, Tiago; Téllez, Claudio A

    2005-07-01

    The cysteine dichloride cadmium(II) potassium was synthesized and the structural analysis was carried out through the following methods: determination of the C, H, N, S and O contents, thermogravimetry, infrared and Raman spectra. Assuming Cd-S, Cd-O (O-carboxilate) and Cd-N bonds, several hypothetical structures were calculated by means DFT: B3LYP/3-21G(d) quantum mechanical method. The calculations shows that the Cd-S and Cd-N central bonds are favoured in the anion complex formation [Cd(Cys)Cl2]-, being the stabilization energy 55.52 kcal mol(-1) lower than isotopomers with Cd-S and Cd-O central bonds. Features of the infrared and Raman spectra confirm the theoretical structural prediction. Full assignment of the vibrational spectra is proposed based on the DFT procedure, and in order to confirm the C-H, N-H, C-C, C-N, Cd-N, Cd-S and Cd-Cl stretching and the HNH and HCH bending, a normal coordinate analysis based on local symmetry force field for -SC(H2)C-, -CdN(H2)C- and -SCd(Cl2)N- fragments was carried out.

  19. 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.

  20. 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.

  1. Lithium ion solvation in room-temperature ionic liquids involving bis(trifluoromethanesulfonyl) imide anion studied by Raman spectroscopy and DFT calculations.

    PubMed

    Umebayashi, Yasuhiro; Mitsugi, Takushi; Fukuda, Shuhei; Fujimori, Takao; Fujii, Kenta; Kanzaki, Ryo; Takeuchi, Munetaka; Ishiguro, Shin-Ichi

    2007-11-15

    The solvation structure of the lithium ion in room-temperature ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl) imide (EMI(+)TFSI(-)) and N-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl) imide (BMP(+0TFSI(-)) has been studied by Raman spectroscopy and DFT calculations. Raman spectra of EMI(+)TFSI(-) and BMP(+)TFSI(-) containing Li(+)TFSI(-) over the range 0.144-0.589 and 0.076-0.633 mol dm(-3), respectively, were measured at 298 K. A strong 744 cm-1 band of the free TFSI(-) ion in the bulk weakens with increasing concentration of the lithium ion, and it revealed by analyzing the intensity decrease that the two TFSI(-) ions bind to the metal ion. The lithium ion may be four-coordinated through the O atoms of two bidentate TFSI(-) ions. It has been established in our previous work that the TFSI(-) ion involves two conformers of C(1) (cis) and C(2) (trans) symmetries in equilibrium, and the dipole moment of the C(1) conformer is significantly larger than that of the C(2) conformer. On the basis of these facts, the geometries and SCF energies of possible solvate ion clusters [Li(C(1)-TFSI(-))(2)](-), [Li(C(1)-TFSI(-))(C(2)-TFSI(-))](-), and [Li(C(2)-TFSI(-))(2)](-) were examined using the theoretical DFT calculations. It is concluded that the C(1) conformer is more preferred to the C(2) conformer in the vicinity of the lithium ion.

  2. Structural characterization, vibrational study, NLO and DFT calculations of a novel organic sulfate monohydrate templated with (S)-(-)-2,6-diammonium-4,5,6,7-tetrahydrobenzothiazole

    NASA Astrophysics Data System (ADS)

    Barhoumi, Abir; Mhiri, Tahar; Dammak, Thameur; Suñol, Joan Josep; Belhouchet, Mohamed

    2017-01-01

    A single crystal of (S)-(-)-2,6-diammonium-4,5,6,7-tetrahydrobenzothiazole sulfate monohydrate has been synthesized and grown at room temperature by slow evaporation of aqueous solution. The studied compound crystallizes in the space group P212121 of the orthorhombic system with cell parameters a = 7.0014(12), b = 8.7631(15), c = 19.773(3) Å. We report the molecular structure and the theoretical and experimental vibrational spectra of the synthesized compound. The atomic arrangement, which is an alternation of organic inorganic layers linked together through hydrogen bonds, gives rise to three types of rings formed by the interconnection of organic-inorganic entities. The experimental FT-IR and the Raman spectra the synthesized compound were recorded and analyzed. The peaks assignment has been made unambiguously from the literature. To confirm the assignment, the experimental spectra were compared with theoretical spectra obtained with the Gaussian 98 program by the Density Functional Theory (DFT) method using B3LYP function with the LanL2DZ basis set. Moreover, to study the nonlinear optical (NLO) property of this compound, the hyperpolarizability βtot, the electric dipole μtot and the polarizability αtot were calculated using the DFT. Based on our calculation the synthesized compound has a non-zero hyperpolarizability suggesting that it may be used in some NLO applications.

  3. 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.

  4. Pyrazolo[4,3-a]quinindoline as a new highly fluorescent heterocyclic system: Design, synthesis, spectroscopic characterization and DFT calculations

    NASA Astrophysics Data System (ADS)

    Alikhani, Elaheh; Pordel, Mehdi; Daghigh, Leila Rezaei

    2015-02-01

    After obtaining the desired precursors in several reactions, new N-alkyl-substituted heterocyclic system pyrazolo[4,3-a]quinindolines (pyrazolo[4,3-f]-indolo[2,3-b]quinolines) were synthesized by one-pot reaction of 1-alkyl-5-nitro-1H-indazole with 2-(1-alkyl-1H-3-indolyl)acetonitrile in MeOH/KOH solution via the nucleophilic substitution of hydrogen in excellent yields. Spectral (UV-Vis, FT-IR, NMR and fluorescence) and analytical data allowed the structures of the synthesized compounds to be established. The values of absorption and fluorescence maxima, extinction coefficients and fluorescence quantum yield of these new heterocyclic fluorophores were obtained and they show highlighting interesting photophysical properties. Density functional theory (DFT) calculations of one structure by using the B3LYP hybrid functional and the 6-311 + G(d,p) basis set were performed to provide the optimized geometry, relevant frontier orbitals and the prediction of 1H NMR chemical shifts. Calculated electronic absorption spectrum of one structure was also obtained by time-dependent density functional theory (TD-DFT) method. Solvatochromic properties of these dyes have been discussed and the results showed that the absorption and emission bands in polar solvents undergo a modest red shift.

  5. 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.

  6. 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.

  7. A comparative study between para-aminophenyl and ortho-aminophenyl benzothiazoles using NMR and DFT calculations.

    PubMed

    Pierens, G K; Venkatachalam, T K; Reutens, D

    2014-08-01

    Ortho-substituted and para-substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho-substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho-substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o-aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the (1)H, (13)C and (15)N NMR chemical shifts and density functional theory calculated structures of the compounds are described.

  8. 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.

  9. Synthesis, Characterization, Spectral Studies, Antibacterial Evaluation, Thermodynamics and DFT Calculations of Dimethyltin(IV) Dichloride Schiff Base.

    PubMed

    Esmaielzadeh, Sheida; Shekoohi, Khadijeh; Sharif-Mohammadi, Mohammad; Mashhadiagha, Ghazal; Mohammadi, Khosro

    2015-01-01

    A number of new 1:1 complexes of SnMe(2)Cl(2) with unsymmetrical tetradentate Schiff base ligand with NNOS coordination sphere have been synthesized and fully characterized by a variety of physico-chemical techniques viz. elemental analysis, molar conductivity, (1)H and (119)Sn NMR, IR and mass spectroscopy. IR spectral data show that the fifth coordination position of tin atom is occupied by an oxygen atom of Schiff base ligands. In the light of titled techniques, trigonal bipyramidal geometry around the tin atom is proposed for the synthesized complexes. The in vitro antibacterial activities of the complexes against Staphylococcus aureus and Escherichia Coli have been studied. It was found that they possess significant antibacterial activity. Also, DFT/B3LYP method was used to analyze the electronic structures and study of the geometries. The thermodynamic formation constants of the complexes were determined spectrophotometrically at 25ºC in DMF solvent.

  10. Novel 2-(naphthalen-1-yl)-5-stilbene-1,3,4-oxadiazole molecules: Synthesis, optical properties and DFT calculation

    NASA Astrophysics Data System (ADS)

    Lu, Huixiong; He, Daohang

    2014-02-01

    Six novel 1,3,4-oxadiazole derivatives containing naphthalene and stibene units were synthesized by Wittig-Horner reaction in good yield. Their structures were characterized by FT-IR, 1H NMR, 13C NMR and elemental analysis. The optical properties were investigated by UV-Vis absorption and fluorescence emission spectra in THF solution. Their optimized structures and the electron density distribution of HOMO and LUMO were performed by density functional theory (DFT) at the (B3LYP)/6-31G* level. The compounds exhibit blue fluorescence emission with the fluorescence quantum yield ranged from 0.05 to 0.59. The effects of substituents on the emission spectra of these compounds are interpreted. The HOMO and LUMO levels of target compounds are -5.86 to -5.64 eV and -2.79 to -2.13 eV, respectively.

  11. 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.

  12. 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.

  13. Determination of thermodynamic parameters of tautomerization in gas phase by mass spectrometry and DFT calculations: Keto-enol versus nitrile-ketenimine equilibria.

    PubMed

    Giussi, Juan M; Gastaca, Belen; Albesa, Alberto; Cortizo, M Susana; Allegretti, Patricia E

    2011-02-01

    The study of tautomerics equilibria is really important because the reactivity of each compound with tautomeric capacity can be determined from the proportion of each tautomer. In the present work the tautomeric equilibria in some γ,δ-unsaturated β-hydroxynitriles and γ,δ-unsaturated β-ketonitriles were studied. The first family of compounds presents two possible theoretical tautomers, nitrile and ketenimine, while the second one presents four possible theoretical tautomers, keto-nitrile, enol (E and Z)-nitrile and keto-ketenimine. The equilibrium in gas phase was studied by gas chromatography-mass spectrometry (GC-MS). Tautomerization enthalpies were calculated by this methodology, and results were compared with those obtained by density functional theory (DFT) calculations, observing a good agreement between them. Nitrile tautomers were favored within the first family of compounds, while keto-nitrile tautomers were favored in the second family.

  14. 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

    2012-02-09

    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.

  15. 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.

  16. TD-DFT calculations of the potential energy curves for the trans-cis photo-isomerization of protonated Schiff base of retinal.

    PubMed

    Tachikawa, Hiroto; Iyama, Tetsuji

    2004-10-25

    One-dimensional potential energy curves for the isomerization of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin (bR), i.e., isomerization from all-trans- to 13-cis-forms, have been calculated by means of time-dependent density functional theory (TD-DFT) calculations, in order to elucidate the mechanism of initial step in photo-absorption. The transition state of the isomerization in the first excited state is located at theta(13-14)=58 degrees , where theta(13-14) means twist angle around the C(13)=C(14) double bond of PSBR The potential barrier is formed by the avoided crossing between S(1) (B(u)-like) and S(2) (A(g)-like) states. The mechanism of the isomerization was discussed on the basis of theoretical results.

  17. Second and third-order nonlinear optical and DFT calculations on 2-amino-5-chloro pyridinium-L-tartrate: A phasematchable organic single crystal

    NASA Astrophysics Data System (ADS)

    Krishnakumar, M.; Karthick, S.; Thirupugalmani, K.; Brahadeeswaran, S.

    2017-04-01

    Single crystals of 2-amino-5-chloro pyridinium L-tartrate have been successfully grown by controlled solvent evaporation technique. The crystal system and the lattice parameters of the grown crystals were reconfirmed by Single crystal X-ray diffraction (SXRD) measurements. UV-Vis-NIR spectrum was recorded for the grown crystal and optical band gap was calculated. Fourier transform infrared (FT-IR) spectroscopic studies were also performed for the identification of different modes present in the compound. The relative SHG efficiency of the material was investigated and the phase matching property of the crystal was also studied through the SHG dependence of average particle sizes. Further, the optical birefringence of the grown crystal was determined. The specific heat capacity of the title compound was measured using Differential Scanning Calorimetric studies. The photoconductivity study for the title compound was carried out. The DFT calculations were performed for the first time for this compound.

  18. 13C CP MAS NMR and GIAO-CHF/DFT calculations of flavonoids: Morin, kaempferol, tricin, genistein, formononetin and 3,7-dihydroxyflavone

    NASA Astrophysics Data System (ADS)

    Zielińska, Agnieszka; Paradowska, Katarzyna; Jakowski, Jacek; Wawer, Iwona

    2008-02-01

    13C CP MAS NMR spectra of the flavonoids: morin, kaempferol, 3,7-dihydroxyflavone, tricin and isoflavones: genistein and formononetin were recorded to characterize solid-state conformations. Intramolecular hydrogen bonds forming five-, six- and seven-membered rings are present in the two morin molecules in the crystals - their 13C resonances have been assigned with the aid of the calculated shielding constants. Linear relationships between the calculated shielding constants σDFT (ppm) and chemical shifts ( δCPMAS, ppm) were obtained for all studied compounds. Higher correlation coefficients suggest that the conformation with "clockwise" orientation of both OH groups is more probable in the solid 3,7-dihydroxyflavone, whereas in the solid formononetin the OH and OCH 3 substituents are directed "anticlockwise". The barrier to the rotation of phenyl ring B decreases in the order: morin (2'-OH, 3-OH) > kaempferol (3-OH) > tricin.

  19. 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...

  20. 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...

  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, 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...

  3. 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...

  4. Effects of Fe substitution on B3-B1 phase transition and structural, vibrational, and electronic properties of ZnS from DFT calculations

    NASA Astrophysics Data System (ADS)

    Das, Pratik Kr.; Mandal, Nibir; Arya, A.

    2017-02-01

    Naturally occurring zinc sulfide (ZnS) contains a substantial amount of iron (Fe) in its crystal structure. This study explores the possible effects of such Fe impurity on the physical properties of its two phases: B3 and B1, crystallizing in a cubic system with zinc blend (ZB, space group: F-43m) and rock salt (RS, space group: Fm-3m) structures. We have performed ab-initio calculations within density functional theory (DFT) to determine the equilibrium volumes of B3- and B1-ZnS phases, doped with Fe in varying concentrations (0% to 25%), and their corresponding lattice structures. Using the enthalpy cross-over, we determine the pressure-dependent B3 to B1 transition as a function of Fe concentration. Our DFT calculations suggest an inverse relation of the transition pressure with Fe content. For pure ZnS, the transition occurs at 17 GPa, which drops to ˜12 GPa for 25% Fe. This study also provides a first-hand analysis of the elastic constants (C11, C12, and C44) to show the effects of Fe impurity on the mechanical properties of ZnS phases. Their values generally drop due to Fe and the differences widen with increasing pressure. Fe causes large softening of C44, especially for the B1 phase. We have also performed phonon calculations to characterize the vibrational properties and explain the pressure dependent structural instability of the B3- ZnS. Finally, our calculations of the electronic structures show a transition of semi-conductor to conductor behavior of ZnS with incorporation of Fe impurity.

  5. 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.

  6. 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.

  7. Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: hydroxylamine anion is predicted to be a better antidote with DFT calculations.

    PubMed

    Khan, Md Abdul Shafeeuulla; Lo, Rabindranath; Bandyopadhyay, Tusar; Ganguly, Bishwajit

    2011-08-01

    Inactivation of acetylcholinesterase (AChE) due to inhibition by organophosphorus (OP) compounds is a major threat to human since AChE is a key enzyme in neurotransmission process. Oximes are used as potential reactivators of OP-inhibited AChE due to their α-effect nucleophilic reactivity. In search of more effective reactivating agents, model studies have shown that α-effect is not so important for dephosphylation reactions. We report the importance of α-effect of nucleophilic reactivity towards the reactivation of OP-inhibited AChE with hydroxylamine anion. We have demonstrated with DFT [B3LYP/6-311G(d,p)] calculations that the reactivation process of sarin-serine adduct 2 with hydroxylamine anion is more efficient than the other nucleophiles reported. The superiority of hydroxylamine anion to reactivate the sarin-inhibited AChE with sarin-serine adducts 3 and 4 compared to formoximate anion was observed in the presence and absence of hydrogen bonding interactions of Gly121 and Gly122. The calculated results show that the rates of reactivation process of adduct 4 with hydroxylamine anion are 261 and 223 times faster than the formoximate anion in the absence and presence of such hydrogen bonding interactions. The DFT calculated results shed light on the importance of the adjacent carbonyl group of Glu202 for the reactivation of sarin-serine adduct, in particular with formoximate anion. The reverse reactivation reaction between hydroxylamine anion and sarin-serine adduct was found to be higher in energy compared to the other nucleophiles, which suggests that this α-nucleophile can be a good antidote agent for the reactivation process.

  8. Binding modes of phosphonic acid derivatives adsorbed on TiO2 surfaces: Assignments of experimental IR and NMR spectra based on DFT/PBC calculations

    NASA Astrophysics Data System (ADS)

    Geldof, D.; Tassi, M.; Carleer, R.; Adriaensens, P.; Roevens, A.; Meynen, V.; Blockhuys, F.

    2017-01-01

    A DFT study on the adsorption of a series of phosphonic acids (PAs) on the TiO2 anatase (101) and (001) surfaces was performed. The adsorption energies and geometries of the most stable binding modes were compared to literature data and the effect of the inclusion of dispersion forces in the energy calculations was gauged. As the (101) surface is the most exposed surface of TiO2 anatase, the calculated chemical shifts and vibrational frequencies of PAs adsorbed on this surface were compared to experimental 31P and 17O NMR and IR data in order to assign the two possible binding modes (mono- and bidentate) to peaks and bands in these spectra; due to the corrugated nature of anatase (101) tridentate binding is not possible on this surface. Analysis of the calculated and experimental 31P chemical shifts indicates that both monodentate and bidentate binding modes are present. For the reactive (001) surface, the results of the calculations indicate that both bi- and tridentate binding modes result in stable systems. Due to the particular sensitivity of 17O chemical shifts to hydrogen bonding and solvent effects, the model used is insufficient to assign these spectra at present. Comparison of calculated and experimental IR spectra leads to the conclusion that IR spectroscopy is not suitable for the characterization of the different binding modes of the adsorption complexes.

  9. Piezoelectric, elastic, Infrared and Raman behavior of ZnO wurtzite under pressure from periodic DFT calculations

    NASA Astrophysics Data System (ADS)

    Marana, Naiara Letícia; Casassa, Silvia Maria; Sambrano, Julio Ricardo

    2017-03-01

    The influence of pressure on elastic, piezoelectric (total and clamped-ion contribution), dielectric constants, Infrared and Raman spectra, and topological properties of ZnO wurtzite structure was carried out via periodic DFT/B3LYP methodology. The computational simulation indicated that, as the pressure increases, the structure becomes more rigid and an enhancement of the direct piezoelectric response along the z-direction was observed. Bader topological analysis and Hirshfeld-I charges showed a slight increase in the ionic character of Zn-O bond. Besides that, changes in the piezoelectric response are mainly due to the approach between Zn and O than to charge transfer phenomena among the two atoms. Pressure induces a sensitive displacement in the Infrared and Raman frequencies and a decrease of the E2 mode. Nevertheless, the increase of pressure does not lead to a change in the semiconductor character, which proves that the ZnO support high pressures and can be applied in different devices.

  10. Identification and Characterization of the Cr_2O3 (0001) Surface by DFT FP-LAPW Calculations

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Gang; Scheffler, Matthias

    2000-03-01

    The physical and chemical properties of Cr_2O3 play an important role in a wide variety of industrial applications (e.g. catalysis and corrosion prevention). Though much has been learned about the Cr-oxide surfaces in recent years, the understanding of how and why this system behaves as it does, is still very shallow. In fact, even with respect to the surface composition and geometry the controversy is significant. Using density-functional theory (DFT) together with the full-potential linearized augmented plane wave (FP-LAPW) method, we investigated the structural, electronic, and magnetic properties of the Cr_2O3 (0001) surface. Our results reveal that the surface structures depend crucially on the environment, i.e. on the partial pressure of oxygen. Under oxygen poor conditions (e.g. at low pressure), the Cr-terminated surface is the most stable one. However, with increasing oxygen pressure, a chromyl (O=Cr) terminated and a O_3-terminated surfaces become energetically favorable. They exhibit pronounced differences in their surface relaxations and surface chemical properties. The differences to Fe_2O3 [1] are significant and explained in terms of the different number of d-electrons. We also studied the adsorption and dissociation of O2 molecules. ^* Present address:Delphi Research and Development Center, Warren, MI 48090-9055, U.S.A. [1] X.G. Wang et al. Phys. Rev. Lett. 81, 1038 (1998).

  11. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali

    2015-05-01

    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  12. 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.

  13. Spectroscopy studies on Schiff base N,N‧-bis(salicylidene)-1,2-phenylenediamine by NMR, infrared, Raman and DFT calculations

    NASA Astrophysics Data System (ADS)

    de Toledo, T. A.; Pizani, P. S.; da Silva, L. E.; Teixeira, A. M. R.; Freire, P. T. C.

    2015-10-01

    N,N‧-bis(salicylidene)-1,2-phenylenediamine, also known as Salophen, is a Schiff base which crystallizes in monoclinic structure and space group P21/c, with four molecules per unit cell. It has been intensely studied in last decades because of its excellent properties with many potential applications. In the present study, the structural and vibrational properties of the Salophen were investigated combining scanning electronic microscopy (SEM), Raman, infrared, nuclear magnetic resonance (NMR) spectroscopy as experimental techniques and theoretical calculation based on density functional theory (DFT). The interpretation of the vibrational modes was carried out by means of potential energy distribution (PED). The theoretical results are in good agreement with experimental ones.

  14. 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).

  15. 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.

  16. Synthesis, structural characterization, and DFT calculations of 3-buthyl-4-(3-methyl-3-mesitylcyclobut-1-yl)-1,3-thiazole-2(3 H)-thione

    NASA Astrophysics Data System (ADS)

    Şen, B.; Barim, E.; Kirilmis, C.; Aygün, M.

    2016-03-01

    The title compound, C21H29NS2, has been synthesized and its crystal structure has been determined from single crystal X-ray diffraction data. Crystals are monoclinic, a = 11.4923(8), b = 13.1842(7), c = 14.6583(8) Å, β = 109.983(6)°, sp. gr. P21/ c, Z = 4. Mesityl and thiazole groups are in cis positions with respect to the cyclobutane ring. The cyclobutane ring is puckered, with a dihedral angle of 26.6(2)° between the two three-atom planes. The crystal structure involves one weak intermolecular C-H···S hydrogen-bond. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G( d, p) basis set in ground state. Geometric parameters (bond lengths, bond angles and torsion angles) and vibrational assignments have been calculated theoretically and compared with the experimental data.

  17. Ligand K-edge X-ray absorption spectroscopy and DFT calculations on [Fe3S4]0,+ clusters: delocalization, redox, and effect of the protein environment.

    PubMed

    Dey, Abhishek; Glaser, Thorsten; Moura, Jose J-G; Holm, Richard H; Hedman, Britt; Hodgson, Keith O; Solomon, Edward I

    2004-12-29

    Ligand K-edge XAS of an [Fe3S4]0 model complex is reported. The pre-edge can be resolved into contributions from the mu(2)S(sulfide), mu(3)S(sulfide), and S(thiolate) ligands. The average ligand-metal bond covalencies obtained from these pre-edges are further distributed between Fe(3+) and Fe(2.5+) components using DFT calculations. The bridging ligand covalency in the [Fe2S2]+ subsite of the [Fe3S4]0 cluster is found to be significantly lower than its value in a reduced [Fe2S2] cluster (38% vs 61%, respectively). This lowered bridging ligand covalency reduces the superexchange coupling parameter J relative to its value in a reduced [Fe2S2]+ site (-146 cm(-1) vs -360 cm(-1), respectively). This decrease in J, along with estimates of the double exchange parameter B and vibronic coupling parameter lambda2/k(-), leads to an S = 2 delocalized ground state in the [Fe3S4]0 cluster. The S K-edge XAS of the protein ferredoxin II (Fd II) from the D. gigas active site shows a decrease in covalency compared to the model complex, in the same oxidation state, which correlates with the number of H-bonding interactions to specific sulfur ligands present in the active site. The changes in ligand-metal bond covalencies upon redox compared with DFT calculations indicate that the redox reaction involves a two-electron change (one-electron ionization plus a spin change of a second electron) with significant electronic relaxation. The presence of the redox inactive Fe(3+) center is found to decrease the barrier of the redox process in the [Fe3S4] cluster due to its strong antiferromagnetic coupling with the redox active Fe2S2 subsite.

  18. 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.

  19. Temperature effects on prevalent structures of hydrated Fe+ complexes: Infrared spectroscopy and DFT calculations of Fe+(H2O)n (n = 3-8)

    NASA Astrophysics Data System (ADS)

    Ohashi, Kazuhiko; Sasaki, Jun; Yamamoto, Gun; Judai, Ken; Nishi, Nobuyuki; Sekiya, Hiroshi

    2014-12-01

    Hydrated Fe+ ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe+(H2O)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+ is observed already at n = 3, indicating the completion of the first hydration shell with two H2O 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+(H2O)2 subunit is solvated with four H2O 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.

  20. FT-IR, FT-Raman spectra, NBO, HOMO-LUMO and thermodynamic functions of 4-chloro-3-nitrobenzaldehyde based on ab initio HF and DFT calculations

    NASA Astrophysics Data System (ADS)

    Karunakaran, V.; Balachandran, V.

    2012-12-01

    FT-IR (4000-400 cm-1) and FT-Raman (3500-100 cm-1) spectral measurements of 4-chloro-3-nitrobenzaldehyde have been done. Ab initio (HF/6-311+G(d,p)) and DFT (B3LYP/6-311+G(d,p)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, infrared intensities and Raman activities. A detailed interpretation of the FT-IR and FT-Raman spectra of 4-chloro-3-nitrobenzaldehyde are reported on the basis of the calculated potential energy distribution. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The thermodynamic functions of the title compound have been performed by HF/6-311+G(d,p) and B3LYP/6-311+G(d,p). The observed and calculated wave numbers are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra. Thermodynamic functions were calculated using vibrational wave numbers for different temperatures.

  1. Probing the mechanism of hypoxia selectivity of copper bis(thiosemicarbazonato) complexes: DFT calculation of redox potentials and absolute acidities in solution.

    PubMed

    Holland, Jason P; Green, Jennifer C; Dilworth, Jonathan R

    2006-02-14

    Density functional theory (DFT) calculations have been performed using the uB3LYP/6-31++G(d,p) model to calculate the solution phase one-electron reduction potentials (E(calc)) and absolute pKa values of a series of copper bis(thiosemicarbazonato) complexes. The effects of solvation in water and dimethylsulfoxide (DMSO) are incorporated as a self-consistent reaction field (SCRF) using the integral equation formalism polarisable continuum model (IEFPCM) and are found to be essential for quantitative agreement with an average error in E(calc) of -0.02 V compared to experiment. The bonding and spin densities are examined through the use of Natural Bond Order analysis and the results used to rationalise the calculated and observed reduction potentials. Calculated estimates of pKa values of several copper(II) species are presented and their implications for the mechanisms of transport and trapping within hypoxic cells are considered. Reduction is found to be a prerequisite for protonation of the complexes which suggests their transport in the blood stream as neutral species, and the mechanistic sequence is identified as a sequential electrochemical-chemical (EC) process. The complex equilibria of protonation, reoxidation and dissociation are discussed and the copper(I) diprotonated, cationic complex of diacetyl bis(4-methyl-3-thiosemicarbazonato)copper(II), Cu(I)ATSMH2(+), is identified as a possible candidate for the initial species trapped in hypoxic cells.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    New ruthenium(II) mononuclear complexes of the type [RuCl2(PPh3)2(η2-triamine)] (2) [RuCl(PPh3)2(η3-triamine)]Cl (5) (triemine = N1-(2-aminoethyl)-1,2-ethanediamine) have been synthesized by reacting [RuCl2(PPh3)3] (1) with one mole equivalent of N1-(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, [RuIICl2(PPh3)2(triamine)]2[PdIIX2](X = Cl, OAc) (3 and 4), bearing bioactive ligand. The progress of the undertaken reactions was monitored by 31P{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.

  4. New mixed ligand palladium(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands: Synthesis, structural characterization, binding interactions with DNA and BSA, in vitro cytotoxicity studies and DFT calculations

    NASA Astrophysics Data System (ADS)

    Tabrizi, Leila; Chiniforoshan, Hossein; Tavakol, Hossein

    2015-04-01

    The complexes [Pd(valp)2(imidazole)2] (1), [Pd(valp)2(pyrazine)2] (2) (valp is sodium valproate) have been synthesized and characterized using IR, 1H NMR, 13C{1H} NMR and UV-Vis spectrometry. The interaction of complexes with CT-DNA has been investigated using spectroscopic tools and viscosity measurement. In each case, the association constant (Kb) was deduced from the absorption spectral study and the number of binding sites (n) and the binding constant (K) were calculated from relevant fluorescence quenching data. As a result, a non-covalent interaction between the metal complex and DNA was suggested, which could be assigned to an intercalative binding. In addition, the interaction of 1 and 2 was ventured with bovine serum albumin (BSA) with the help of absorption and fluorescence spectroscopy measurements. Through these techniques, the apparent association constant (Kapp) and the binding constant (K) could be calculated for each complex. Evaluation of cytotoxic activity of the complexes against four different cancer cell lines proved that the complexes exhibited cytotoxic specificity and significant cancer cell inhibitory rate. Moreover, density functional theory (DFT) calculations were employed to provide more evidence about the observed data. The majority of trans isomers were supported not only by energies, but also by the similarity of its calculated IR frequencies, UV adsorptions and NMR chemical shifts to the experimental values.

  5. DFT calculations of quadrupolar solid-state NMR properties: Some examples in solid-state inorganic chemistry.

    PubMed

    Cuny, Jerome; Messaoudi, Sabri; Alonzo, Veronique; Furet, Eric; Halet, Jean-François; Le Fur, Eric; Ashbrook, Sharon E; Pickard, Chris J; Gautier, Regis; Le Polles, Laurent

    2008-10-01

    This article presents results of first-principles calculations of quadrupolar parameters measured by solid-state nuclear magnetic measurement (NMR) spectroscopy. Different computational methods based on density functional theory were used to calculate the quadrupolar parameters. Through a series of illustrations from different areas of solid state inorganic chemistry, it is shown how quadrupolar solid-state NMR properties can be tackled by a theoretical approach and can yield structural information.

  6. Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of PU and PCL grafted onto PEMA-co-PHEMA with DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Demir, Pınar; Akman, Feride

    2017-04-01

    A newly synthesized polycaprolactone (PCL) and polyurethane (PU) polymers, which grafted onto poly (ethylmethacrylate-co-2-hydroxyethyl methacrylate) (PEMA-co-PHEMA) were characterized both theoretically and experimentally. The FTIR and 1H NMR spectra were recorded for the PCL and PU polymers and the experimental values were compared the theoretical values. The molecular structure evaluation, vibrational frequencies and 1H NMR chemical shift values, which carried out by using gauge including atomic orbital (GIAO) approach, of the PCL and PU polymers were calculated by using density functional method (DFT/B3LYP) with 6-311G (d, p) as a basis set in the ground state. The calculated data such as vibrational frequencies and chemical shift values show good agreement with experimental values. Besides, the thermodynamic properties such as rotational temperatures, rotational constants, zero-point vibrational energy, specific heat capacity, thermal energy, entropy, enthalpy, the electronic properties such as HOMO and LUMO energies, and molecular electrostatic potential (MEP) surfaces for the PCL and PU were calculated and interpreted.

  7. Vibrational spectroscopic analysis of cyanopyrazine-2-carboxamide derivatives and investigation of their reactive properties by DFT calculations and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Beegum, Shargina; Mary, Y. Sheena; Varghese, Hema Tresa; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Zitko, Jan; Dolezal, Martin; Van Alsenoy, C.

    2017-03-01

    Using density functional theory technique in the B3LYP approximation and cc-pVDZ (5D, 7F) basis set, the molecular structural parameters and vibrational wave numbers of two cyanopyrazine-2-carboxamide derivatives have been investigated. On the basis of potential energy distribution detailed vibrational assignments of observed FT-IR and FT-Raman bands have been proposed. Using molecular electrostatic potential map relative reactivities towards electrophilic and nucleophilic attack are predicted. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compounds are greater than that of the standard NLO material urea. Molecular studies reveal that the predicted binding affinities of the best poses were -8.7 kcal/mol for BACPC, -9.0 kcal/mol for CBACPC, and -8.8 kcal/mol for the original inhibitor. Efforts were made in order to investigate local reactivity properties of title compounds as well. In order to do so we have calculated average local ionization energy (ALIE) surfaces, Fukui functions, bond dissociation energies (BDE) (within the framework of DFT calculations) and radial distribution functions (RDF) (within the molecular dynamics simulations). ALIE surfaces and Fukui functions gave us initial information on the site reactivity towards electrophilic and nucleophilic attacks. BDE indicated locations that might be prone to autoxidation mechanism, while RDF indicated which atoms of title molecules are having pronounced interactions with water.

  8. 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

    2015-08-05

    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.

  9. S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity.

    PubMed

    Dey, Abhishek; Jiang, Yonging; Ortiz de Montellano, Paul; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

    2009-06-10

    Experimental covalencies of the Fe-S bond for the resting low-spin and substrate-bound high-spin active site of cytochrome P450 are reported. DFT calculations on the active site indicate that one H-bonding interaction from the protein backbone is needed to reproduce the experimental values. The H-bonding to the thiolate from the backbone decreases the anisotropic pi covalency of the Fe-S bond lowering the barrier of free rotation of the exchangeable axial ligand, which is important for reactivity. The anionic axial thiolate ligand is calculated to lower the Fe(III/II) reduction potential of the active site by more than 1 V compared to a neutral imidazole ligand. About half of this derives from its covalent bonding and half from its electrostatic interaction with the oxidized Fe. This axial thiolate ligand increases the pK(a) of compound 0 (Fe(III)-hydroperoxo) favoring its protonation which promotes O-O bond heterolysis forming compound I. The reactivity of compound I is calculated to be relatively insensitive to the nature of the axial ligand due to opposing reduction potential and proton affinity contributions to the H-atom abstraction energy.

  10. Study of N, N-dimethyl(carboethoxymethyl)-3-phthalimidopropylammonium chloride dihydrate by DFT calculations, NMR and FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Iwona

    2009-06-01

    N, N-dimethyl(carboethoxymethyl)-3-phthalimidopropylammonium chloride dihydrate ( 1) and N, N-dimethyl(carboxymethyl)-3-phthalimidopropylammonium hydrochloride ( 3) have been obtained in reaction of N, N-dimethyl-3-phthalimidopropylamine with ethyl chloroacetate and chloroacetic acid, respectively. N, N-dimethyl(carboethoxymethyl)-3-phthalimido-propylammonium chloride dihydrate ( 1) has been characterized by FTIR and NMR spectroscopy. Moreover, for ( 1) and ( 3) B3LYP calculations have been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been presented. Both FTIR and Raman spectra of ( 1) are consistent with the calculated structures in the gas phase. Correlations between the experimental 1H and 13C NMR chemical shifts ( δexp) of investigated compound in D 2O, and the GIAO/B3LYP/6-31G(d,p) calculated magnetic isotropic shielding tensors ( σcalc), δexp = a + b σcalc, are reported. The assignments of the anharmonic experimental solid state vibrational frequencies of ( 1) based on the calculated B3LYP/6-31G(d,p) harmonic frequencies have been made. Linear correlations between the experimental 1H and 13C chemical shifts and the computed screening constants confirm the optimized geometry.

  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.

  13. Characterization of flavonoid 3-Methoxyquercetin performed by FT-IR and FT-Raman spectroscopies and DFT calculations

    NASA Astrophysics Data System (ADS)

    de Toledo, T. A.; da Silva, L. E.; Botelho, T. C.; Ramos, R. J.; de Souza, P. T., Jr.; Teixeira, A. M. R.; Freire, P. T. C.; Bento, R. R. F.

    2012-12-01

    In the present study, the natural product 3-Methoxyquercetin, a flavonoid with potential antiviral activity, was characterized through infrared and Raman spectroscopies combined with Density Functional Theory calculation. The flavonoid was extracted from Strychnos pseudoquina St. Hil (Loganiaceae) by chromatographic techniques. The optimized molecular structure and calculated vibrational spectra were performed by B3LYP/6-31G (d,p) basis set. The optimized structure was compared with X-ray diffraction data of other flavonoids compounds, and the theoretical data are in good agreement with experimental ones. Fourier transform-Raman and -infrared spectra, as well as the assignment of the normal modes are also presented.

  14. 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.

  15. Spectroscopic behavior of loratadine and desloratadine in different aqueous media conditions studied by means of TD-DFT calculations.

    PubMed

    Brasca, Romina; Romero, Marcelo A; Goicoechea, Héctor C; Kelterer, Anne-Marie; Fabian, Walter M F

    2013-11-01

    In this study, we explained the influence of the stepwise protonation of two antihistaminic drugs on their experimental absorption spectra. We demonstrated the capability of the TD-CAM-B3LYP method, combined with a polarizable continuum model, to produce good performance for the calculated spectra. The lowest energy transitions and the molecular orbital plots were analyzed in detail. The calculated UV spectra are proposed as potential alternatives to initialize the well-known MCR-ALS algorithm, especially when the spectra of the pure analytes are not available. Moreover, it can be a useful strategy for planning an experimental methodology oriented to multiway analysis when the drug species exhibit acid-base properties.

  16. Spectroscopic behavior of loratadine and desloratadine in different aqueous media conditions studied by means of TD-DFT calculations

    NASA Astrophysics Data System (ADS)

    Brasca, Romina; Romero, Marcelo A.; Goicoechea, Héctor C.; Kelterer, Anne-Marie; Fabian, Walter M. F.

    2013-11-01

    In this study, we explained the influence of the stepwise protonation of two antihistaminic drugs on their experimental absorption spectra. We demonstrated the capability of the TD-CAM-B3LYP method, combined with a polarizable continuum model, to produce good performance for the calculated spectra. The lowest energy transitions and the molecular orbital plots were analyzed in detail. The calculated UV spectra are proposed as potential alternatives to initialize the well-known MCR-ALS algorithm, especially when the spectra of the pure analytes are not available. Moreover, it can be a useful strategy for planning an experimental methodology oriented to multiway analysis when the drug species exhibit acid-base properties.

  17. 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.

  18. 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.

  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. Experimental FTIR, FT-IR (gas phase), FT-Raman and NMR spectra, hyperpolarizability studies and DFT calculations of 3,5-dimethylpyrazole.

    PubMed

    Sundaraganesan, N; Kavitha, E; Sebastian, S; Cornard, J P; Martel, M

    2009-10-15

    In the present study, structural properties of 3,5-dimethylpyrazole (3,5-DMP) have been studied extensively utilizing density functional theory (DFT) employing B3LYP exchange correlation. The Fourier transform infrared (solid phase and gas phase) and Fourier transform Raman spectra of 3,5-DMP were recorded. The Vibrational frequencies of 3,5-DMP in the ground state have been calculated by using density functional method (B3LYP) with 6-31G(d,p), 6-311G(d,p) and 6-311++G(d,p) as basis sets. Comparison of the observed fundamental vibrational frequencies of 3,5-DMP with calculated results show that 6-311++G(d,p) superior to other basis sets for molecular vibrational problems. Non linear optical NLO behavior of the examined molecule was investigated by the determination of the electric dipole moment mu, the polarizability alpha and the hyperpolarizability beta using the B3LYP/cc-pvdz method. The isotropic chemical shifts computed by (13)C and (1)H NMR analysis also show good agreement with experimental observations. The theoretically predicted FTIR and FT-Raman spectra of the title molecule have been constructed.

  1. Preparation and characterizations of SnO2 nanopowder and spectroscopic (FT-IR, FT-Raman, UV-Visible and NMR) analysis using HF and DFT calculations.

    PubMed

    Ayeshamariam, A; Ramalingam, S; Bououdina, M; Jayachandran, M

    2014-01-24

    In this work, pure and singe phase SnO2 Nano powder is successfully prepared by simple sol-gel combustion route. The photo luminescence and XRD measurements are made and compared the geometrical parameters with calculated values. The FT-IR and FT-Raman spectra are recorded and the fundamental frequencies are assigned. The optimized parameters and the frequencies are calculated using HF and DFT (LSDA, B3LYP and B3PW91) theory in bulk phase of SnO2 and are compared with its Nano phase. The vibrational frequency pattern in nano phase gets realigned and the frequencies are shifted up to higher region of spectra when compared with bulk phase. The NMR and UV-Visible spectra are simulated and analyzed. Transmittance studies showed that the HOMO-LUMO band gap (Kubo gap) is reduced from 3.47 eV to 3.04 eV while it is heated up to 800°C. The Photoluminescence spectra of SnO2 powder showed a peak shift towards lower energy side with the change of Kubo gap from 3.73 eV to 3.229 eV for as-prepared and heated up to 800°C.

  2. Molecular structure of 4-hidroxy-3-(3-methyl-2-butenyl) acetophenone, a plant antifungal, by X-ray diffraction, DFT calculation, and NMR and FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Piro, Oscar Enrique; Echeverría, Gustavo Alberto; Lizarraga, Emilio; Romano, Elida; Catalán, César Atilio Nazareno; Brandán, Silvia Antonia

    2013-01-01

    The molecular structure of two mixed and closely related conformers of the title compound, C13H16O2, found in the solid with unequal occupancies has been determined by X-ray diffraction methods. The substance crystallizes in the monoclinic Pca21 space group with a = 17.279(2), b = 5.1716(7), c = 12.549(2) Å, and Z = 4 molecules per unit cell. The structure was solved from 1314 reflections with I > 2σ(I) and refined to an agreement R1-factor of 0.049. The minor conformer (34.7%) is nearly mirror-related to and extensively overlapped with the major one. The skeleton of the 4-hydroxyacetophenone molecular fragment and the prenyl group, sbnd (CH2)sbnd (CH)dbnd C(CH3)2, pendant arm attached to it are both planar and perpendicular to each other. A strong intermolecular Osbnd H⋯O bond links neighboring molecules in the lattice to produce a polymeric structure. The conformational structures of the compound in the gas phase have been calculated by the DFT method and the geometrical results have been compared with the X-ray data. These data allow a complete assignment of vibration modes in the solid state FTIR and Raman spectra. The calculated 1H and 13C chemicals shifts are in good agreement with the corresponding experimental NMR spectra of the compound in solution.

  3. Synthesis, crystal structure, spectroscopic properties, DFT calculation and biological activity of 4-chloro-N-(2-(2-nitrophenyl)acetoxy)-N-phenylbenzamide

    NASA Astrophysics Data System (ADS)

    He, Dian; Yang, Zhu-Qing; Hou, Meng; Teng, Chong; Wang, Xiao-Hong

    2014-11-01

    4-Chloro-N-(2-(2-nitrophenyl)acetoxy)-N-phenylbenzamide was synthesized and characterized by 1H NMR, 13C NMR, MS, IR and X-ray diffraction methods. The structure-property relationship and the antitumor activity based on electrochemical measurements, density functional theory calculations (DFT) and methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay were investigated. The crystal structure adopts monoclinic space group P21/n with the unit cell parameters of a = 12.4385(10) Å, b = 6.5036(5) Å, c = 24.7944(19) Å, β = 103.045(9)°, V = 1954.0(3) Å3, Z = 4, and stabilized by π-π conjugation and hydrogen bonding interactions. The observed results of the compound have been compared with theoretical results and it is found that the experimental data show good agreement with calculated values. And the compound had slightly better inhibition than suberoylanilide hydroxamic acid (SAHA) in NCI-H460 cell line as well as the nearly same as SAHA in MCF-7, HCT-116, PC-3, and A549 cell lines.

  4. A hexaaza macrocyclic ligand containing acetohydrazide pendants for Ln(III) complexation in aqueous solution. Solid-state and solution structures and DFT calculations.

    PubMed

    Núñez, Cristina; Bastida, Rufina; Macías, Alejandro; Mato-Iglesias, Marta; Platas-Iglesias, Carlos; Valencia, Laura

    2008-08-07

    Lanthanide complexes of a hexaaza macrocyclic ligand containing acetohydrazide pendants (L) have been synthesised (Ln = La-Er, except Pm), and structural studies have been carried out both in the solid state and in aqueous solution. Attempts to isolate the complexes of the heaviest Ln(iii) ions (Ln = Tm-Lu) were unsuccessful. The crystal structures of the ligand and its lanthanum complex have been determined by single-crystal X-ray crystallography. The X-ray crystal structure of [La(L)](3+) shows the metal ion being ten-coordinate, with the acetohydrazide pendants situated alternatively above and below the plane of the macrocycle. The two five membered chelate rings formed by the ethylenediamine moieties adopt (deltadelta) [or (lambdalambda)] conformations. The [Ln(L)](3+) complexes have been characterised by means of density-functional theory (DFT) calculations (B3LYP model). The structures obtained from these theoretical calculations are in very good agreement with the experimental solution structures, as obtained from paramagnetic NMR measurements on the Ce(iii), Pr(III), Nd(III) and Eu(III) complexes. The complexes adopt in aqueous solution a D(2) structure with the ligand adopting a (deltadelta) [or (lambdalambda)] conformation.

  5. Spectroscopic characterization, X-ray structure, antimicrobial activity and DFT calculations of novel dipicolinate copper(II) complex with 2,6-pyridinedimethanol.

    PubMed

    Tamer, Omer; Sarıboğa, Bahtiyar; Uçar, Ibrahim; Büyükgüngör, Orhan

    2011-12-15

    Novel dipicolinate complex of copper(II) ion, [Cu(dmp)(dpc)]·0.8H(2)O [dmp: 2,6-pyridinedimethanol; dpc: dipicolinate or pyridine-2,6-dicarboxylate], has been prepared and fully characterized by single crystal X-ray structure determination. The central copper(II) ion is bonded to dpc and dmp ligands through pyridine nitrogen atom together with two oxygen atom, forming the distorted octahedral geometry. The complex molecules, connected via O-H···O hydrogen bonds, form a supramolecular structure. H(2)dpc, [Cu(dpc)(H(2)O)(3)] and [Cu(dmp)(dpc)]·0.8H(2)O were screened for antimicrobial activity against Gram-positive, Gram-negative bacteria and yeast. H(2)dpc and [Cu(dpc)(H(2)O)(3)] exhibited antibacterial and antifungal activity, while [Cu(dmp)(dpc)]·0.8H(2)O exhibited activity only for Gram-positive bacteria. The geometry optimization and EPR parameters were carried out using the following unrestricted hybrid density functionals: LSDA, BPV86, B3LYP, B3PW91, MPW1PW91, PBEPBE and HCTH. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, calculated data show that the predicted geometries can reproduce the structural parameters. The electronic station in the frontier orbitals of the copper complex calculated from the experimental data is compared to the results of time-depended DFT calculations with the polarizable continuum model. Calculated vibrational frequencies are consistent with the experimental IR data.

  6. 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.

  7. 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.

  8. Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT-GIAO calculations

    NASA Astrophysics Data System (ADS)

    Jamróz, Marta K.; Bąk, Joanna; Gliński, Jan A.; Koczorowska, Agnieszka; Wawer, Iwona

    2009-09-01

    Actein is a prominent triterpene glycoside occurring in Actaea racemosa. The triterpene glycosides are believed to be responsible for the estrogenic activity of an extract prepared from this herb. We determined in the crystal structure of actein by X-ray crystallography to be monoclinic P2(1) chiral space group. Refining the disorder, we determined 70% and 30% of contributions of ( S)- and ( R)-actein, respectively. The IR and Raman spectra suggest that actein forms at least four different types of hydrogen bonds. The 13C NMR spectra of actein were recorded both in solution and solid state. The 13C CPMAS spectrum of actein displays multiplet signals, in agreement with the crystallographic data. The NMR shielding constants were calculated for actein using GIAO approach and a variety of basis sets: 6-31G**, 6-311G**, 6-31+G**, cc-pVDZ, cc-pVDZ-su1 and 6-31G**-su1, as well as IGLO approach combined with the IGLO II basis set. The best results (RMSD of 1.6 ppm and maximum error of 3.4 ppm) were obtained with the 6-31G**-su1 basis set. The calculations of the shielding constants are helpful in the interpretation of the 13C CPMAS NMR spectra of actein and actein's analogues.

  9. 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.

  10. 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.

  11. DFT calculation of the chromyl nitrate, CrO2(NO3)2 The molecular force field.

    PubMed

    Brandán, S A; Roldán, M L; Socolsky, C; Ben Altabef, A

    2008-03-01

    We have carried out a structural and vibrational theoretical study for chromyl nitrate. The density functional theory has been used to study its structure and vibrational properties. The geometries were fully optimised at the B3LYP/Lanl2DZ, B3LYP/6-31G* and B3LYP/6-311++G levels of theory and the harmonic vibrational frequencies were evaluated at the same levels. The calculated harmonic vibrational frequencies for chromyl nitrate are consistent with the experimental IR and Raman spectra in the solid and liquid phases. These calculations gave us a precise knowledge of the normal modes of vibration taking into account the type of coordination adopted by nitrate groups of this compound as monodentate and bidentate. We have also made the assignment of all the observed bands in the vibrational spectra for chromyl nitrate. The nature of the Cr-O and Cr<--O bonds in the compound were quantitatively investigated by means of Natural Bond Order (NBO) analysis. The topological properties of electronic charge density are analysed employing Bader's Atoms in Molecules theory (AIM).

  12. Cooperativity of axial and centre chirality in the biaryl disulfoxide/Rh(i)-catalysed asymmetric 1,4-addition of arylboronic aids to 2-cyclohexenone: a DFT study.

    PubMed

    Zha, Gao-Feng; Qin, Hua-Li; Kantchev, Eric Assen B

    2017-03-08

    Atropisomeric biaryl disulfoxides contain two independent chiral elements. Previously, the (M,S,S)-diastereomer showed very high catalytic activity and selectivity in the Rh-catalyzed asymmetric 1,4-addition of arylboronic acids to α,β-enones whereas the (M,R,R) counterpart - none. Herein, DFT computations on the key transmetallation (turnover-determining) and carborhodation (enantioselectivity-determining) steps of the catalytic cycle show that the (M,S,S)-ligand gives rise to lower reaction barriers for these elementary steps. However, the barriers for the (M,R,R)-ligand are not sufficiently high to explain the lack of reactivity. Hence, this phenomenon is most likely due to the failure of catalyst formation from the ligand and the dimeric Rh precatalyst complex. The hitherto unknown (M,S,R)-ligand shows predicted enantioselectivity similar to the (M,S,S)-ligand as a consequence of lower reaction barriers associated with those isomers whose key features resemble the (M,S,S)-ligand.

  13. DFT investigation of the mecahanism and stereochemistry of electrophilic transannular addition reaction of bromine to tricyclo[4.2.2.02,5]deca-3,7-diene.

    PubMed

    Abbasoglu, Rza; Misir, Miraç Nedim

    2012-03-01

    Full geometric optimization of tricyclo[4.2.2.02,5]deca-3,7-diene (TDD) has been done by DFT/B3LYP methods and the structure of the molecule was investigated. Cyclobuten double bond (I) of molecule is syn pyramidalized, and bicyclookten double bond (II) is also exo pyramidalized. The double bond (I) is more pyramidalized than the double bond (II) and it has higher reactivity. The TDD-Br2 system has been investigated by B3LYP/6-311++G(d,p) method and their stable configurations have been determined. The cationic intermediates and products obtained as a result of the addition reaction has been studied using B3LYP/6-311G(d,p) and B3LYP/6-311++G(d,p) methods. Bridged bromonium cation is more stable than U-type cation. Considering that the bridged cation does not isomerize to the less stable U-type cation, it is not possible for the U-type product to be obtained in the reaction. The bridged bromonium cation transformed into the more stable N-type cation and the N-type product was obtained via this cation. The thermodynamic stability of the anti, exo and anti, endo isomers of N-type dibromide molecule were almost identical. N-type product is 11.759 kcal mol more stable than U-type product.

  14. Chemically intuitive indices for charge-transfer excitation based on SAC-CI and TD-DFT calculations.

    PubMed

    Ehara, Masahiro; Fukuda, Ryoichi; Adamo, Carlo; Ciofini, Ilaria

    2013-11-05

    A recently proposed charge-transfer (CT) index and some related quantities aimed to the description of CT excitations in push-pull donor-acceptor model systems were computed in vacuum and in ethanol by the direct symmetry-adapted cluster-configuration interaction (SAC-CI) method including solvent effects by means of the nonequilibrium state-specific approach. The effects of both solvation and electron correlations on these quantities were found to be significant. The present results are also in line with previous time-dependent (TD) density functional theory calculations and they demonstrate that SAC-CI provides a description of the excitation character close to that of TD-PBE0. Indeed, CT indices evaluated by the SAC-CI and TD-PBE0 would be useful in the field of materials chemistry, for the design and development of novel molecular materials.

  15. 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

  16. The far infrared spectrum of naphthalene characterized by high resolution synchrotron FTIR spectroscopy and anharmonic DFT calculations.

    PubMed

    Pirali, O; Goubet, M; Huet, T R; Georges, R; Soulard, P; Asselin, P; Courbe, J; Roy, P; Vervloet, M

    2013-07-07

    Using synchrotron radiation, we performed the rotationally resolved Fourier transform infrared absorption spectroscopy of three bands of naphthalene C10H8, namely ν(46)-0 (centered at 782 cm(-1), 12.7 μm), ν(47)-0 (centered at 474 cm(-1), 21 μm), and ν(48)-0 (centered at 167 cm(-1), 60 μm). The intense CH bending out of plane ν(46)-0 band was recorded under supersonic jet-cooled conditions using a molecular beam (the Jet-AILES apparatus) and the low frequency ν(47)-0 and ν(48)-0 bands were measured at room temperature in a long absorption path cell. The simultaneous rotational analysis of these bands permitted us to refine the ground state (GS) and ν(46) rotational spectroscopic constants and to provide the first sets of constants for the ν(47) and ν(48) modes. The experimental rotational constants were then used as reference data to calibrate theoretical models in order to provide new insights into the accuracy of anharmonic calculations. The B97-1 functional associated with the cc-pVTZ and ANO-RCC basis sets gave a consistent set of results, for rotational constants and fundamental frequencies. The data presented here pave the way for the search of naphthalene through its far-infrared spectrum in different objects of the interstellar medium.

  17. 1H NMR spectra of alcohols and diols in chloroform: DFT/GIAO calculation of chemical shifts.

    PubMed

    Lomas, John S

    2014-12-01

    Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in chloroform have been computed on the basis of density functional theory, the solvent being included by the integral-equation-formalism polarisable continuum model of Gaussian 09. Relative energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311+G(d,p) level, and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311+G(d,p) geometry and the cc-pVTZ basis set. The 208 computed CH proton NMR shifts for 34 alcohols correlate very well with the experimental values, with a gradient of 1.00 ± 0.01 and intercept close to zero; the overall root mean square difference (RMSD) is 0.08 ppm. Shifts for CH protons of diols in chloroform are well correlated with the theoretical values for (isotropic) benzene, with similar gradient and intercept (1.02 ± 0.01, -0.13 ppm), but the overall RMSD is slightly higher, 0.12 ppm. This approach generally gives slightly better results than the CHARGE model of Abraham et al. The shifts of unsaturated alcohols in benzene have been re-examined with Gaussian 09, but the overall fit for CH protons is not improved, and OH proton shifts are worse. Shifts of vinyl protons in alkenols are systematically overestimated, and the correlation of computed shifts against the experimental data for unsaturated alcohols follows a quadratic equation. Splitting the 20 compounds studied into two sets, and applying empirical scaling based on the quadratic for the first set to the second set, gives an RMSD of 0.10 ppm. A multi-standard approach gives a similar result.

  18. Tracking Co(I) Intermediate in operando in Photocatalytic Hydrogen Evolution by X-ray transient Absorption Spectroscopy and DFT Calculation

    SciTech Connect

    Li, Zhi-Jun; Zhan, Fei; Xiao, Hongyan; Zhang, Xiaoyi; Kong, Qing-Yu; Fan, Xiang-Bing; Liu, Wen-Qiang; Huang, Mao-Yong; Huang, Cheng; Gao, Yu-Ji; Li, Xu-Bing; Meng, Qing-Yuan; Feng, Ke; Chen, Bin; Tung, Chen-Ho; Zhao, Hai-Feng; Tao, Ye; Wu, Li-Zhu

    2016-12-07

    X-ray transient absorption spectroscopy (XTA) and optical transient spectroscopy (OTA) were used to probe the Co(I) intermediate generated in situ from an aqueous photocatalytic hydrogen evolution system, with [RuII(bpy)3]Cl2·6H2O as the photosensitizer, ascorbic acid/ascorbate as the electron donor, and the Co-polypyridyl complex ([CoII(DPABpy) Cl]Cl) as the pre-catalyst. Upon exposure to light, the XTA measured at Co K-edge visualizes the grow and decay of the Co(I) intermediate, and reveals its Co-N bond contraction of 0.09 ± 0.03 Å. Density functional theory (DFT) calculations support the bond contraction and illustrate that the metal-to-ligand π back-bonding greatly stabilizes the penta-coordinated Co(I) intermediate, which provides easy photon access. To the best of our knowledge, this is the first example of capturing the penta-coordinated Co(I) intermediate in operando with bond contraction by XTA, thereby providing new insights for fundamental understanding of structure– function relationship of cobalt-based molecular catalysts.

  19. 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).

  20. 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.

  1. 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.

  2. Synthesis, spectroscopic, thermal and DFT calculations of 2-(3-amino-2-hydrazono-4-oxothiazolidin-5-yl) acetic acid binuclear metal complexes

    NASA Astrophysics Data System (ADS)

    Hassan, Walid M. I.; Badawy, M. A.; Mohamed, Gehad G.; Moustafa, H.; Elramly, Salwa

    2013-07-01

    The binuclear complexes of 2-(3-amino-2-hydrazono-4-oxothiazolidin-5-yl) acetic acid ligand (HL) with Fe(III), Co(II), Ni(II), Cu(II) and Zn(II) ions were prepared and their stoichiometry was determined by elemental analysis. The stereochemistry of the studied series of metal complexes was established by analyzing their infrared, 1H NMR spectra and the magnetic moment measurements. According to the elemental analysis data, the complexes were found to have the formulae [Fe2L(H2O)8]Cl5 and [M2L(H2O)8]Cl3 (M = Co(II), Ni(II), Cu(II) and Zn(II)). The present analyses demonstrate that all metal ions coordinated to the ligand via O(9), O(11), N(16) and N(18) atoms. Thermal decomposition studies of the ligand-metal complexes have been performed to verify the status of water molecules present in these metal complexes and their general decomposition pattern. Density Functional Theory (DFT) calculations at the B3LYP/6-31G* level of theory have been carried out to investigate the equilibrium geometry of the ligand and complexes. Moreover, charge density distribution, extent of distortion from regular geometry, dipole moment and orientation have been performed and discussed.

  3. 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.

  4. Advanced Photoemission Spectroscopy Investigations Correlated with DFT Calculations on the Self-Assembly of 2D Metal Organic Frameworks Nano Thin Films.

    PubMed

    Elzein, Radwan; Chang, Chun-Min; Ponomareva, Inna; Gao, Wen-Yang; Ma, Shengqian; Schlaf, Rudy

    2016-11-16

    Metal-organic frameworks (MOFs) deposited from solution have the potential to form 2-dimensional supramolecular thin films suitable for molecular electronic applications. However, the main challenges lie in achieving selective attachment to the substrate surface, and the integration of organic conductive ligands into the MOF structure to achieve conductivity. The presented results demonstrate that photoemission spectroscopy combined with preparation in a system-attached glovebox can be used to characterize the electronic structure of such systems. The presented results demonstrate that porphyrin-based 2D MOF structures can be produced and that they exhibit similar electronic structure to that of corresponding conventional porphyrin thin films. Porphyrin MOF multilayer thin films were grown on Au substrates prefunctionalized with 4-mercaptopyridine (MP) via incubation in a glovebox, which was connected to an ultrahigh vacuum system outfitted with photoelectron spectroscopy. The thin film growth process was carried out in several sequential steps. In between individual steps the surface was characterized by photoemission spectroscopy to determine the valence bands and evaluate the growth mode of the film. A comprehensive evaluation of X-ray photoemission spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and inverse photoemission spectroscopy (IPES) data was performed and correlated with density functional theory (DFT) calculations of the density of states (DOS) of the films involved to yield the molecular-level insights into the growth and the electronic properties of MOF-based 2D thin films.

  5. Template synthesis of square-planar Ni(II) complexes with new thiophene appended Schiff base ligands: Characterization, X-ray structure and DFT calculation

    NASA Astrophysics Data System (ADS)

    Kundu, Subhankar; Biswas, Sujan; Mondal, Apurba Sau; Roy, Puspendu; Mondal, Tapan Kumar

    2015-11-01

    The square planar nickel(II) complexes have been synthesized by the reaction of nickel(II) chloride hexahydrate and the in situ condensed thiophene appended Schiff base ligands of thiophene-2-ethylamine with 3,5-dimethyl-2-hydroxybenzaldehyde or 3,5-dichloro-2-hydroxybenzaldehyde for [Ni(L1)2] (1) and [Ni(L2)2] (2) respectively. The complexes have been characterized by several spectroscopic techniques, viz. FT-IR, 1H NMR, absorption and emission spectroscopy. The complexes crystallize in monoclinic crystal system with C2/c space group for 1 and triclinic crystal system with P-1 space group for 2. In complex 1 the nickel sits on an inversion centre with symmetry -x, 2-y, -z. Cyclic voltammgrams of the complexes show quasi-reversible NiII/NiIII oxidation couple along with irreversible NiII/NiI reduction. Electronic structure and spectral properties are well interpreted by DFT and TDDFT calculations.

  6. 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.

  7. Synthesis, spectroscopic characterization and DFT calculations of monohydroxyalkylated derivatives of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione

    NASA Astrophysics Data System (ADS)

    Szyszkowska, Agnieszka; Hęclik, Karol; Trzybiński, Damian; Woźniak, Krzysztof; Klasek, Antonin; Zarzyka, Iwona

    2017-01-01

    Synthesis of new derivatives with an imidazo[1,5-c]quinazoline-3,5-dione ring has been presented. Two new alcohols with the imidazo[1,5-c]quinazoline-3,5-dione ring were obtained and characterized by spectral (1H, 13C NMR, IR and UV) and crystallography methods. A reaction chemoselectivity has been observed with a formation of monohydroxyalkyl derivatives of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione substituted at the 2. nitrogen atom. The absence of derivatives substituted at the 6. nitrogen atom was proven experimentally. The synthesis with chemoselectivity over 99% without control of the substituent effect happens very rarely. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione in the region of the 2. and the 6. nitrogen atoms. Quantum-mechanical DFT calculations proved to be very useful to explain the reason of selectivity reaction of 1-phenyl-2H,6H-imidazo[1,5-c]quinazoline-3,5-dione with oxiranes.

  8. Analysis of the [CuL n ]2+ and [CuG n ]2+ ( n = 2-4) complex structures: Comparison with CID experiment and DFT calculation

    NASA Astrophysics Data System (ADS)

    Zhang, Shuqin; Liu, Hai; Cheng, Ping; Ren, Dajun; Gong, Xiangyi

    2016-12-01

    The collision-induced dissociation (CID) of the copper-cytidine complex [CuL n ]2+ (L is cytidine, n = 2-4) shows that the inter-ligand proton transfer (PT) is the dominating process. This is quite different from the CID of copper-guanosine complex [CuG n ]2+ (G is guanosine, n = 2-4), in which the inter-electron transfer (ET) dominates. The possible structures and zero-point energies for the majority of these structures were calculated using density functional theory (DFT) methods, and the Δ G Gibbs energy analysis of the CID processes also demonstrated the difference between the two complex structures. The results show that the steric hindrance effects and the intermolecular hydrogen bonds are the main reasons that cause the coordination between Cu(II) and the ligands of the cytidine and guanosine molecule. Cu(II) coordinates 4 ligands for [CuL n ]2+, forming the primary order sphere and presenting non-covalent bonding of the ligands. A greater steric effect was observed in the purine ring, which could be unstable if the guanosine molecules distributed around the copper ions to form coordination compounds. The [CuG n ]2+ complex tends to form intermolecular hydrogen bonds to enhance its structural stability by amino N and carbonyl O of purine ring.

  9. Synthesis and structural study of precursors of novel methylsilanediols by IR and Raman spectroscopies, single-crystal X-ray diffraction and DFT calculations.

    PubMed

    Rodríguez Ortega, M P G; Docampo, M L; Thomas, L H; Montejo, M; Marchal Ingraín, A; Wilson, C C; López González, J J

    2014-01-24

    On the way towards the development of a synthetic route aimed at obtaining new methylsilanediol derivatives with an aminocarbonyl group in β to silicon (which may have a potential biological interest), we have synthesized, isolated and purified five diphenylic possible precursors, namely chloromethyl(methyl)diphenylsilane, 2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione, N-[(methyl(diphenyl) silanyl)-methyl]-benzamide, N-[(methyl(diphenyl)silyl)-methyl]-acetamide and N-[(methyl(diphenyl)silyl)-methyl]-formamide. The conformational landscape of the five species in this study are explored by means of DFT calculations at the B3LYP/6-311++G(∗∗) level. The theoretical molecular structures predicted are confirmed by the reproduction of their respective IR and Raman spectral profiles, that are completely assigned. Some evidence in the vibrational spectra points to the occurrence of conformational mixtures in the samples. Further, single-crystal X-ray diffraction has allowed the elucidation of the crystalline structure of 2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione.

  10. 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.

  11. 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

  12. 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.

  13. (1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts.

    PubMed

    Lomas, John S

    2016-01-01

    Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.

  14. Synthesis, X-ray structure analysis, thermodynamic and electronic properties of 4-acetamido benzaldehyde using vibrational spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    Theoretical Spectrograms, namely, FT-Raman (3500-50 cm-1) and FT-Infrared (4000-400 cm-1) spectra have been studied for 4-acetamido benzaldehyde (4ABA) and are assigned to different normal modes of the molecule. Vibrational spectral analysis was compared with the experimental and theoretical, FT-IR and FT-Raman spectra. The effect of polarity on the Harmonic vibrational frequencies, intensities, optimized geometrical parameters and several thermodynamic parameters in the ground state have been computed by the B3LYP method using 6-311 + G(d,p) basis set. The results of the optimized molecular structure is presented and compared with the XRD values. The global chemical reactivity relate to some parameters, such as HOMO, LUMO, gap energy (ΔE) and other parameters, including electronegativity (χ) and global hardness (η). The values of the reactivity descriptors indicated that the interaction between 4ABA molecules reduced its reactivity in comparison with the exhibited in gas phase. In addition, the local reactivity has been analyzed through the Fukui function and condensed softness indices.

  15. On the molecular and supramolecular properties of N,N‧-disubstituted iminoisoindolines: Synthesis, spectroscopy, X-ray structure and Hirshfeld surface analyses, and DFT calculations of two (E)-N,N‧-bis(aryl)iminoisoindolines (aryl = 2-tert-butylphenyl or perfluorophenyl)

    NASA Astrophysics Data System (ADS)

    Bitzer, Rodrigo S.; Visentin, Lorenzo C.; Hörner, Manfredo; Nascimento, Marco A. C.; Filgueiras, Carlos A. L.

    2017-02-01

    Supramolecular studies of iminoisoindoline-derived compounds have been prompted by their biological and photophysical properties. In this article, we report the synthesis, spectroscopy, X-ray structural characterization, and DFT study of two N,N‧-(aryl)-disubstituted 1-iminoisoindolines, namely (E)-N,N‧-bis(2-tert-butylphenyl)iminoisoindoline (2-t-BuPhimiso) and (E)-N,N‧-bis(perfluorophenyl)iminoisoindoline (F5Phimiso). Our X-ray structural analyses have shown that the isoindoline N2 atom of 2-t-BuPhimiso is slightly pyramidalized whereas the respective atom of F5Phimiso displays the expected trigonal planar geometry. The supramolecular arrangement of 2-t-BuPhimiso comprises one-dimensional chains along the [101] direction formed by Csbnd H···πarene interactions, in which the isoindoline ring behaves as a hydrogen-bond donor. For 2-t-BuPhimiso, DFT calculations at the B97-D3/6-311G** level have shown that the dimer formed by this Csbnd H···πarene contact displays a binding energy of -12.83 kcal mol-1. Product F5Phimiso assembles in the crystal state through type-I F3 synthons in addition to Csbnd H⋯F, C-Fδ-···πF+, and πarene/F-πarene/F stacking interactions. Accordingly, our DFT-D3 calculations have confirmed that these interactions synergistically play a dominating role in the crystal packing of F5Phimiso. Finally, the relative stability of the (Z) and (E) isomers of each product has been evaluated at the DFT level of theory. Our calculations have shown that the (E) forms are the most stable ones.

  16. 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

    2015-02-05

    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.

  17. 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

  18. Use of delayed addition techniques to accelerate integer and floating-point calculations in configurable hardware

    NASA Astrophysics Data System (ADS)

    Luo, Zhen; Martonosi, Margaret

    1998-10-01

    This paper proposes and evaluates an approach for improving the performance of arithmetic calculations via delayed addition. Our approach employs the idea used in Wallace trees to delay addition until the end of a repeated calculation such as accumulation or dot-product; this effectively removes carry propagation overhead from the calculation's critical path. We present imager and floating- point designs that use this technique. Our pipelined integer multiply-accumulate design is based on a fairly traditional multiplier design, but with delayed addition as well. This design achieves a 37 MHz clock rate on an XC4036XL-2 FPGA. Next, we present a 32-bit floating-point accumulator based on delayed addition. Here delayed addition requires a novel alignment technique that decouples the incoming operands from the accumulated result. A conservative version of this design achieves a 33 MHz clock rate. Finally, we also present a more aggressive 32-bit floating-point accumulator design that achieves a 66 MHz clock rate. These designs demonstrate the utility of delayed addition for accelerating FPGA calculations in both the integer and floating-point domains.

  19. 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

    NASA Astrophysics Data System (ADS)

    Bharty, M. K.; Dani, R. K.; Kushawaha, S. K.; Prakash, Om; Singh, Ranjan K.; Sharma, V. K.; Kharwar, R. N.; Singh, N. K.

    2015-06-01

    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.

  20. Calculation of arrangement of oxygen ions and vacancies in double perovskite GdBaCo2O(5+δ) by first-principles DFT with Monte Carlo simulations.

    PubMed

    Shiiba, Hiromasa; Nakayama, Masanobu; Kasuga, Toshihiro; Grimes, Robin W; Kilner, John A

    2013-07-07

    The configurations of oxygen ions and vacancies at various oxygen stoichiometries and temperatures in double perovskite oxides (GdBaCo2O(5+δ), 0 ≤ δ ≤ 1) have been determined by density functional theory (DFT) combined with Monte Carlo (MC) simulations. The MC simulations confirmed the existence of a superstructure at δ = 0.5, showing alternating linear ordering of oxygen ions and vacancies along the b-axis in the GdO layer. This structure is identical to that reported experimentally. Increasing the temperature up to 1200 K induces a phase transition manifested in the breaking of the oxygen/vacancy arrangement at around δ = 0.5. In the high-temperature phase, vacancies are distributed in the GdO and CoO2 layers, whereas there are no vacancies in the BaO layer. In addition, the characteristic linear arrangement is partly preserved even in the disordered high-temperature phase. Consequently, oxygen ions can migrate between the GdO and CoO2 layers, as reported in previous classical molecular dynamics simulation studies.

  1. Thermodynamic method of calculating the effect of alloying additives on interphase interaction in composite materials

    NASA Technical Reports Server (NTRS)

    Tuchinsky, L. I.

    1986-01-01

    The effect of alloying additives to the matrix of a composite on the high temperature solubility rate of a single component fiber was analyzed thermodynamically. With an example of binary Ni alloys, with Group IV-VI transition metals reinforced with W fibers, agreement between the calculated and experimental data was demonstrated.

  2. 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

  3. 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.

  4. Structural study of (±) ethyl 3-acyloxy-1-azabicyclo[2.2.2]octane-3-carboxylates by 1H, 13C NMR spectroscopy, X-ray crystallography and DFT calculations

    NASA Astrophysics Data System (ADS)

    Arias-Pérez, M. S.; Cosme, A.; Gálvez, E.; Morreale, A.; Sanz-Aparicio, J.; Fonseca, I.

    2006-05-01

    1H, 13C NMR spectroscopy and DFT/B3LYP calculations were applied to investigate the conformational preferences of the ethoxycarbonyl and acyloxy groups of some α-acyloxyesters derived from (±) ethyl 3-hydroxy-1-azabicyclo[2.2.2]octane-3-carboxylate. The crystal structure of (±) ethyl 3-diphenylacetoxy-1-azabicyclo[2.2.2]octane-3-carboxylate was determined by X-ray diffraction. To correlate between calculated conformations and the structure in solution, NMR chemical shifts calculations were also performed using the GIAO approach. It has been found that the lowest energetic conformer computed gives the greatest correspondance with experimental solution and solid state data.

  5. Kinetic and DFT studies on the mechanism of C-S bond formation by alkyne addition to the [Mo3S4(H2O)9]4+ cluster.

    PubMed

    Pino-Chamorro, Jose Ángel; Algarra, Andrés G; Fernández-Trujillo, M Jesús; Hernández-Molina, Rita; Basallote, Manuel G

    2013-12-16

    Reaction of [Mo3(μ3-S)(μ-S)3] clusters with alkynes usually leads to formation of two C-S bonds between the alkyne and two of the bridging sulfides. The resulting compounds contain a bridging alkenedithiolate ligand, and the metal centers appear to play a passive role despite reactions at those sites being well illustrated for this kind of cluster. A detailed study including kinetic measurements and DFT calculations has been carried out to understand the mechanism of reaction of the [Mo3(μ3-S)(μ-S)3(H2O)9](4+) (1) cluster with two different alkynes, 2-butyne-1,4-diol and acetylenedicarboxylic acid. Stopped-flow experiments indicate that the reaction involves the appearance in a single kinetic step of a band at 855 or 875 nm, depending on the alkyne used, a position typical of clusters with two C-S bonds. The effects of the concentrations of the reagents, the acidity, and the reaction medium on the rate of reaction have been analyzed. DFT and TD-DFT calculations provide information on the nature of the product formed, its electronic spectrum and the energy profile for the reaction. The structure of the transition state indicates that the alkyne approaches the cluster in a lateral way and both C-S bonds are formed simultaneously.

  6. DFT study with inclusion of the Grimme potential on anatase TiO2: structure, electronic, and vibrational analyses.

    PubMed

    Albuquerque, Anderson R; Garzim, Marcos L; Santos, Iêda M G dos; Longo, Valeria; Longo, Elson; Sambrano, Julio R

    2012-11-29

    Periodic DFT/B3LYP calculations for TiO(2) anatase bulk were carried out including semiempirical dispersive interactions (DFT-D2) to pure Khon-Sham DFT energy. From this standard methodology, van der Waals (vdW) radii were optimized to 1.4214 Å for titanium and 1.3420 Å for oxygen centers in order to achieve a better structural description. The results from this approach (here named DFT/B3LYP-D*) showed a better description for lattice constants, vibrational IR and Raman, energy band gaps, and bulk modulus than default DFT/B3LYP and DFT/B3LYP-D. The dispersion correction showed more reliable results and was necessary to achieve a good agreement with reported single crystal results, without new formalism or additional computational cost.

  7. Synthesis, DFT calculations, electronic structure, electronic absorption spectra, natural bond orbital (NBO) and nonlinear optical (NLO) analysis of the novel 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6] naphthyridine-6(5H),8-dione (MBCND)

    NASA Astrophysics Data System (ADS)

    Halim, Shimaa Abdel; Ibrahim, Magdy A.

    2017-02-01

    New derivative of heteroannulated chromone identified as 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6]naphthyridine-6(5H),8-dione (5, MBCND) was easily and efficiently synthesized from DBU catalyzed condensation reaction of 2-aminochromone-3-carboxaldehyde (1) with 4-hydroxy-1-methylquinolin-2(1H)-one (2). The same product 5 was isolated from condensation reaction of aldeyde 1 with 3-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-3-oxopropanoic acid (3) or ethyl 4-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-2,4-dioxobutanoate (4). Structure of compound (5, MBCND) was deduced based on their elemental analyses and spectral data (IR, 1H NMR and mass spectra). 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 novel compound (5, MBCND). Moreover, total energy, energy of HOMO and LUMO and Mullikan atomic charges were calculated. In addition, the dipole moment, theoretical study of the electronic structure, nonlinear optical properties (NLO), and natural bonding orbital (NBO) analysis and orientation have been performed and discussed. Also the electronic absorption spectra were measured in polar (methanol) as well as non polar (dioxane) solvents and the assignment of the observed bands has been discussed by TD-DFT calculations. The correspondences between calculated and experimental transitions energies are satisfactory.

  8. 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

  9. Synthesis, crystal structure and DFT studies of a Zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n. The additional stabilizing role of S⋯π chalcogen bond

    NASA Astrophysics Data System (ADS)

    Alotaibi, Mshari A.; Alharthi, Abdulrahman I.; Zierkiewicz, Wiktor; Akhtar, Muhammad; Tahir, Muhammad Nawaz; Mazhar, Muhammad; Isab, Anvarhusein A.; Ahmad, Saeed

    2017-04-01

    A zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n (1) has been prepared and characterized by elemental analysis, IR, 1H &13C NMR spectroscopy, and its crystal structure was determined by X-ray crystallography. The crystal structure of 1 consists of two types of molecules, a discrete monomer and a polymeric one. In the monomeric unit, the zinc atom is bound to one terminal Dap molecule and to two N-bound thiocyanate ions, while in the polymeric unit, Dap acts as a bridging ligand forming a linear chain. The Zn(II) ions in both assume a slightly distorted tetrahedral geometry. The structures of two systems: the [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]3 complex as a model of 1 and [Zn(Dap)(NCS)2]4 as a simple polymeric structure were optimized with the B3LYP-D3 method. The DFT results support that the experimentally determined structure (1) is more stable in comparison to a simple polymeric structure, [Zn(Dap)(NCS)2]n (2). The interaction energies (ΔE) for NCS anions obtained by B3LYP-D3 method are about -145 kcal mol-1, while the calculated ΔE values for neutral organic ligands are about twice smaller. The X-ray structure of 1 shows that the complex is stabilized mainly by hydrogen bonds. We also found that weak chalcogen bonds play an additional role in stabilization of compound 1. Some of the intermolecular S⋯N distances are smaller than the sum of the van der Waals radii of the corresponding atoms. To the best of our knowledge, this is the first study that shows the structure where the trivalent sulfur is involved in formation of a S⋯π chalcogen bond. The NBO and NCI analyses confirm the existence of this kind of interactions.

  10. Synthesis, molecular structure and vibrational analysis of D-D-A based carbazole decorated phenothiazine-3-carbaldehyde: Experimental (FT-IR, UV and NMR) and density functional theory (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Karuppasamy, Ayyanar; Gokula Krishnan, Kannan; Pillai Velayutham Pillai, Muthiah; Ramalingan, Chennan

    2017-01-01

    A novel molecule, 10-(9-hexyl-9H-carbazol-3yl)-10H-phenothiazine-3-carbaldehyde (CZPTZA) has been synthesized and characterized through FT-IR, UV-Vis, NMR spectroscopic studies and molecular orbital calculations. Optimized geometrical structure, harmonic vibrational frequencies and NMR are computed with B3LYP method using 6-311++G (d,p) basis set. The geometrical parameters of the title compound obtained from Single Crystal XRD studies have been found in accord with the calculated (DFT) values. The experimentally observed vibrational frequencies are compared with the calculated ones, which were found to be in good agreement with each other. UV-Vis spectra of the title compound have also been recorded and the electronic properties, viz. excitation energies, calculated energies, oscillator strengths, frontier orbital energies and band gap energies are computed with TD-DFT/CAM-B3LYP method using 6-311++G (d,p) as the basis set. The 1H and 13C NMR chemical shifts of the molecule have been calculated by the Gauge Independent Atomic Orbital (GIAO) method and compared with the experimental outcome. Also, the values of dipole moment, polarizabilities and first order hyperpolarizabilities have been computed.

  11. Observations and model calculations of an additional layer in the topside ionosphere above Fortaleza, Brazil

    NASA Astrophysics Data System (ADS)

    Jenkins, B.; Bailey, G. J.; Abdu, M. A.; Batista, I. S.; Balan, N.

    1997-06-01

    Calculations using the Sheffield University plasmasphere ionosphere model have shown that under certain conditions an additional layer can form in the low latitude topside ionosphere. This layer (the F3 layer) has subsequently been observed in ionograms recorded at Fortaleza in Brazil. It has not been observed in ionograms recorded at the neighbouring station São Luis. Model calculations have shown that the F3 layer is most likely to form in summer at Fortaleza due to a combination of the neutral wind and the E×B drift acting to raise the plasma. At the location of São Luis, almost on the geomagnetic equator, the neutral wind has a smaller vertical component so the F3 layer does not form.

  12. A complete vibrational study on a potential environmental toxicant agent, the 3,3',4,4'-tetrachloroazobenzene combining the FTIR, FTRaman, UV-Visible and NMR spectroscopies with DFT calculations.

    PubMed

    Castillo, María V; Pergomet, Jorgelina L; Carnavale, Gustavo A; Davies, Lilian; Zinczuk, Juan; Brandán, Silvia A

    2015-01-05

    In this study 3,3',4,4'-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet-visible spectroscopies. The density functional theory (DFT) together with the 6-31G(*) and 6-311++G(**) basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet-visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated (1)H and (13)C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The npp(*) transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader's Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands.

  13. 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

    ... UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT... shall be extended by the time as calculated in days in the manner indicated by this section. The patent...) The number of days in the period beginning on the date a major health or environmental effects test...

  14. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

    SciTech Connect

    Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

    2016-09-09

    In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

  15. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

    DOE PAGES

    Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; ...

    2016-09-09

    In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

  16. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

    PubMed

    Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

    2016-10-11

    In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

  17. Halide ligated iron porphines: a DFT+U and UB3LYP study.

    PubMed

    Panchmatia, Pooja M; Ali, Md Ehesan; Sanyal, Biplab; Oppeneer, Peter M

    2010-12-30

    We apply the density functional theory + U (DFT+U) and unrestricted hybrid functional DFT-UB3LYP methods to study the electronic structure and magnetic properties of two prototypical iron porphines: iron(III) porphine chloride (FePCl) and difluoro iron(III-IV) porphine. Plain DFT within the generalized gradient approximation (GGA) implementation fails in describing the correct high-spin ground state of these porphine molecules, whereas DFT+U and UB3LYP provide an improved description. For a range of U values (4-8 eV), we compare the results of the DFT+U approach to those obtained previously with the hybrid functional (B3LYP) and with the CASPT2 approach. The DFT+U and UB3LYP methods successfully predict the molecular high spin (S = 5/2) ground state of FePCl, and also provide the nontrivial S = 3 high spin ground state for FePF(2). For the latter six-coordinated Fe porphine, our DFT+U calculations show that the S = 2, S = 5/2, and S = 3 states are energetically very close together (differences of 30 meV). Nonetheless, S = 3 is obtained as the ground state of the whole molecule, in accordance with the spin expected from the electron count. Our DFT+U calculations show furthermore that the Fe 3d occupancy is similar for FePF(2) and FePCl, i.e., DFT+U does not support Fe(IV) for FePF(2), but rather an Fe(III) porphyrin π-cation radical species, with an Fe high spin S(Fe) = 5/2, and an additional S = 1/2 stemming from spin density distributed over the porphine ring. This observation is also supported by our UB3LYP calculations.

  18. The molecular pathway to ZIF-7 microrods revealed by in situ time-resolved small- and wide-angle X-ray scattering, quick-scanning extended X-ray absorption spectroscopy, and DFT calculations.

    PubMed

    Goesten, Maarten; Stavitski, Eli; Pidko, Evgeny A; Gücüyener, Canan; Boshuizen, Bart; Ehrlich, Steven N; Hensen, Emiel J M; Kapteijn, Freek; Gascon, Jorge

    2013-06-10

    We present an in situ small- and wide-angle X-ray scattering (SAXS/WAXS) and quick-scanning extended X-ray absorption fine-structure (QEXAFS) spectroscopy study on the crystallization of the metal-organic framework ZIF-7. In combination with DFT calculations, the self-assembly and growth of ZIF-7 microrods together with the chemical function of the crystal growth modulator (diethylamine) are revealed at all relevant length scales, from the atomic to the full crystal size.

  19. 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.

  20. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T)

    NASA Astrophysics Data System (ADS)

    Caldararu, Octav; Olsson, Martin A.; Riplinger, Christoph; Neese, Frank; Ryde, Ulf

    2017-01-01

    We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO-CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by 50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11-16 kJ/mol. DLPNO-CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates

  1. Indirect "no-bond" ³¹P···³¹P spin-spin couplings in P,P-[3]ferrocenophanes: insights from solid-state NMR spectroscopy and DFT calculations.

    PubMed

    Wiegand, Thomas; Eckert, Hellmut; Ren, Jinjun; Brunklaus, Gunther; Fröhlich, Roland; Daniliuc, Constantin G; Lübbe, Gerrit; Bussmann, Kathrin; Kehr, Gerald; Erker, Gerhard; Grimme, Stefan

    2014-03-27

    No-bond (31)P-(31)P indirect dipolar couplings, which arise from the transmission of nuclear spin polarization through interaction of proximal nonbonded electron pairs have been investigated in the solid state for a series of closely related substituted P,P-[3]ferrocenophanes and model systems. Through variation and combination of ligands (phenyl, cyclohexyl, isopropyl) at the two phosphorus sites, the P···P distances in these compounds can be varied from 3.49 to 4.06 Å. Thus, the distance dependence of the indirect no-bond coupling constant J(nb) can be studied in a series of closely related compounds. One- and two-dimensional solid-state NMR experiments serve to establish the character of these couplings and to measure the isotropic coupling constants J(iso), which were found to range between 12 and 250 Hz. To develop an understanding of the magnitude of J(nb) in terms of molecular structure, their dependences on intramolecular internuclear distances and relative orbital orientations is discussed by DFT-calculations on suitable models. In agreement with the literature the dependence of J(nb) on the P···P distance is found to be exponential; however, the steepness of this curve is highly dependent on the internuclear equilibrium distance. For a quantitative description, the off-diagonal elements of the expectation value of the Kohn-Sham-Fock operator in the LMO basis for the LMOs of the two phosphorus lone-pairs is proposed. This parameter correlates linearly with the calculated J(nb) values and possesses the same distance-dependence. In addition, the simulations indicate a distinct dependence of J(nb) on the dihedral angle defined by the two C-P bonds providing ligation to the molecular backbone. For disordered materials or those featuring multiple sites, conformers, and/or polymorphism, a new double-quantum NMR method termed DQ-DRENAR can be used to conveniently measure internuclear (31)P-(31)P distances. If conducted on compounds with known P

  2. Syntheses, crystal structures, spectral study and DFT calculation of three new copper(II) complexes derived from pyridoxal hydrochloride, N,N-dimethylethylenediamine and N,N-diethylethylenediamine

    NASA Astrophysics Data System (ADS)

    Mandal, Senjuti; Naskar, Barnali; Modak, Ritwik; Sikdar, Yeasin; Chatterjee, Sudipta; Biswas, Sujan; Mondal, Tapan Kumar; Modak, Debadrita; Goswami, Sanchita

    2015-05-01

    Two pyridoxal containing Schiff bases obtained by condensation of pyridoxal hydrochloride with N,N-dimethylethylenediamine (HL1) and N,N-diethylethylenediamine (HL2) are used for the syntheses of three new copper (II) complexes [Cu(HL1)(H2O)Cl]Cl (1), [Cu(L1)Cl] (2) and [Cu(L2)Cl] (3). The single crystal X-ray structures of all the three copper(II) complexes are determined. Redox potentials for the mononuclear complexes are measured by cyclic voltammetry experiments. The DFT and TDDFT results have been used to interpret the experimental properties.

  3. 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.

  4. 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.

  5. X-ray and DFT-calculated structures of a vanadyl Schiff base complex: (methanol-κO)[2-methoxy-6-({2-[(2-oxido-3-methoxybenzylidene)amino]benzyl}iminomethyl)phenolato-κ4O1,N,N,O1']oxidovanadium(IV) monohydrate.

    PubMed

    Kurzak, Krzysztof; Ejsmont, Krzysztof; Koprek, Katarzyna

    2012-06-01

    The central V(V) atom in the title mononuclear oxovanadium complex, [VO(C(23)H(20)N(2)O(4))(CH(3)OH)]·H(2)O, has a distorted octahedral coordination. Two N atoms and two O atoms of the Schiff base define the base of the bipyramid and two O atoms are in the apical positions, one from vanadyl and the second from methanol. Density functional theory (DFT) calculations were performed for the title complex and its ligand to compare their geometry in the solid and gas phases. Additional analyses were made of the changes in the geometry of the ligand during complex formation. The HOMA (harmonic oscillator model of aromaticity) descriptor of π-electron delocalization was calculated to estimate the aromaticity of the benzene rings in the title complex and its ligand.

  6. New Fe(III) complex with 8-(4-chlorophenyl)-3-butyl-3H-imidazo[4‧,5‧:3,4]benzo[1,2-c]isoxazol-5-amine (5-AIBI) ligand: Synthesis, spectroscopic characterization and DFT calculations

    NASA Astrophysics Data System (ADS)

    Agheli, Zahra; Pordel, Mehdi; Beyramabadi, S. Ali

    2017-02-01

    The new heterocyclic ligand 8-(4-chlorophenyl)-3-butyl-3H-imidazo[4‧,5‧:3,4]benzo [1,2-c]isoxazol-5-amine (5-AIBI) was synthesized from the reduction of 3-butyl-8-(4-chlorophenyl)-5-nitro-3H-imidazo[4‧,5‧:3,4]benzo[1,2-c]isoxazole in high yield. The coordination ability of the ligand with some cations was examined by spectrophotometric method at rt condition. Results showed that only the absorption spectra of the Fe3+-5-AIBI complex show a high redshift of the absorption maximum in the aqueous ethanol solution. The effect of pH on the absorption spectrum of the green iron-5-AIBI complex was also investigated. In addition, density functional theory (DFT) calculations are performed to provide the optimized geometries, structural parameters, calculated chemical shifts and vibrational frequencies of the investigated Fe(III) complex.

  7. Additivity rule for the calculation of electron scattering from polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Jiang, Yuhai; Sun, Jinfeng; Wan, Lingde

    2000-12-01

    Total cross sections (TCSs) for electron scattering by polyatomic molecules C2F4, C2F6, C3F6, C3F8, C6F6, and C6H6 are calculated in the incident electron energy range 30-3000 eV employing the 100% additivity rule and energy-dependent geometric additivity rule (EGAR) approaches. The EGAR, proposed by Jiang et al. [J. Phys. B 30, 5025 (1997); Phys. Lett. A 237, 53 (1997)], relates to molecular properties and the energy of incident electrons. Two approaches for the TCS of C2F6, C3F8, C6F6, and C6H6 molecules are compared and the EGAR yields better accord with available experimental measurements in the whole energy region. The new results for C2F4 and C3F6 are also presented although no experimental data are available for comparison. The atoms are presented by spherical complex optical potential, which is composed of static, exchange, polarization, and absorption terms.

  8. 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.

  9. 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.

  10. 19F NMR-, ESR-, and vis-NIR-spectroelectrochemical study of the unconventional reduction behaviour of a perfluoroalkylated fullerene: dimerization of the C70(CF3)10 – radical anion† †Electronic supplementary information (ESI) available: Additional electrochemical and spectroscopic results, mass spectrometry study, and DFT-optimized Cartesian coordinates. See DOI: 10.1039/c5an01129a Click here for additional data file.

    PubMed Central

    Machata, Peter; Clikeman, Tyler T.; Rosenkranz, Marco

    2015-01-01

    The most abundant isomer of C70(CF3)10 (70-10-1) is a rare example of a perfluoroalkylated fullerene exhibiting electrochemically irreversible reduction. We show that electrochemical reversibility at the first reduction step is achieved at scan rates higher than 500 V s–1. Applying ESR-, vis-NIR-, and 19F NMR-spectroelectrochemistry, as well as mass spectrometry and DFT calculations, we show that the (70-10-1)– radical monoanion is in equilibrium with a singly-bonded diamagnetic dimeric dianion. This study is the first example of 19F NMR spectroelectrochemistry, which promises to be an important method for the elucidation of redox mechanisms of fluoroorganic compounds. Additionally, we demonstrate the importance of combining different spectroelectrochemical methods and quantitative analysis of the transferred charge and spin numbers in the determination of the redox mechanism. PMID:26359514

  11. 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.

  12. 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.

  13. Crystal structure and DFT calculations of 5-(4-Chlorophenyl)-1-(6-methoxypyridazin-3-yl)-1H-pyrazole-3-carboxylic acid.

    PubMed

    Alaşalvar, Can; Soylu, Mustafa Serkan; Ünver, Hüseyin; Ocak İskeleli, Nazan; Yildiz, Mustafa; Çiftçi, Murat; Banoğlu, Erden

    2014-11-11

    The title compound, 5-(4-Chlorophenyl)-1-(6-methoxypyridazin-3-yl)-1H-pyrazole-3-carboxylic acid, has been characterized by using elemental analysis, MS, FT-IR, 1H NMR and 13C NMR spectroscopic, and crystallographic techniques. The title compound crystallizes in the triclinic space group P-1 with a=9.612(1), b=9.894(1), c=17.380(1)Å, α=90.213(5)°, β=104.99(1)°, γ=111.072(5)°, V=1481.3(2)Å3 and Dx=1.483 g cm(-3) respectively. The structure of the compound has also been examined by using quantum chemical methods. The molecular geometry and vibrational frequencies of monomeric and dimeric form of the title compound in the ground state have been calculated by using the B3LYP/6-31G(d,p) level of the theory. The calculated results show that the optimized geometry and the theoretical vibration frequencies of the dimeric form are good agreement with experimental data. In addition, HOMO-LUMO energy gap, molecular electrostatic potential map, thermodynamic properties of the title compound were performed at B3LYP/6-31G(d,p) level of theory.

  14. Crystal structure and DFT calculations of 5-(4-Chlorophenyl)-1-(6-methoxypyridazin-3-yl)-1H-pyrazole-3-carboxylic acid

    NASA Astrophysics Data System (ADS)

    Alaşalvar, Can; Soylu, Mustafa Serkan; Ünver, Hüseyin; Ocak İskeleli, Nazan; Yildiz, Mustafa; Çiftçi, Murat; Banoğlu, Erden

    2014-11-01

    The title compound, 5-(4-Chlorophenyl)-1-(6-methoxypyridazin-3-yl)-1H-pyrazole-3-carboxylic acid, has been characterized by using elemental analysis, MS, FT-IR, 1H NMR and 13C NMR spectroscopic, and crystallographic techniques. The title compound crystallizes in the triclinic space group P-1 with a = 9.612(1), b = 9.894(1), c = 17.380(1) Å, α = 90.213(5)°, β = 104.99(1)°, γ = 111.072(5)°, V = 1481.3(2) Å3 and Dx = 1.483 g cm-3 respectively. The structure of the compound has also been examined by using quantum chemical methods. The molecular geometry and vibrational frequencies of monomeric and dimeric form of the title compound in the ground state have been calculated by using the B3LYP/6-31G(d,p) level of the theory. The calculated results show that the optimized geometry and the theoretical vibration frequencies of the dimeric form are good agreement with experimental data. In addition, HOMO-LUMO energy gap, molecular electrostatic potential map, thermodynamic properties of the title compound were performed at B3LYP/6-31G(d,p) level of theory.

  15. Molecular interactions investigated with DFT calculations of QTAIM and NBO analyses: An application to dimeric structures of rice α-amylase/subtilisin inhibitor

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    Characterization of the dimer interactions at the dimeric interface of the crystal structure of rice α-amylase/subtilisin inhibitor (RASI) were performed using the quantum theory of atoms in molecules (QTAIM) and natural bonding orbital (NBO) analyses at the density-functional theory (DFT) level. The results revealed that Gly27 and Arg151 of chain A are the main residues involved in hydrogen bonds, dipole-dipole, and charge-dipole interactions with Gly64, Ala66, Ala67 and Arg81 of chain B at the dimeric interface. Calcium ion of chain A plays the significant role in the stability of the dimeric structure through a strong charge-charge interaction with Ala66.

  16. Spin- and phase transition in the spin crossover complex [Fe(ptz) 6](BF 4) 2 studied by nuclear inelastic scattering of synchrotron radiation and by DFT calculations

    NASA Astrophysics Data System (ADS)

    Böttger, Lars H.; Chumakov, Aleksandr I.; Matthias Grunert, C.; Gütlich, Philipp; Kusz, Joachim; Paulsen, Hauke; Ponkratz, Ulrich; Rusanov, Ventzislav; Trautwein, Alfred X.; Wolny, Juliusz A.

    2006-09-01

    Nuclear inelastic scattering (NIS) spectra of [Fe(ptz) 6](BF 4) 2 (ptz = 1- n-propyl-tetrazole) have been measured for five phases differing in spin state and crystallographic structure. Different spectral patterns have been found for the low-spin and high-spin phases and are described in terms of normal coordinate analysis of the complex molecule. For both low-spin and high-spin phases the conversion from ordered to disordered phase results in splitting of the observed NIS bands. Packing becomes visible in the NIS spectra via coupling of the Fe-N stretching vibrations with those of the terminal n-propyl groups. The DFT-based normal coordinate analysis also reveals the character of Raman markers.

  17. 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.

  18. 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.

  19. Investigation of ground state charge transfer complex between paracetamol and p-chloranil through DFT and UV-visible studies

    NASA Astrophysics Data System (ADS)

    Shukla, Madhulata; Srivastava, Nitin; Saha, Satyen

    2012-08-01

    The present report deals with the theoretical investigation on ground state structure and charge transfer (CT) transitions in paracetamol (PA)/p-chloranil (CA) complex using Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) method. It is found that Cdbnd O bond length of p-chloranil increases on complexation with paracetamol along with considerable amount of charge transfer from PA to CA. TD-DFT calculations have been performed to analyse the observed UV-visible spectrum of PA-CA charge transferred complex. Interestingly, in addition to expected CT transition, a weak symmetry relieved π-π* transition in the chloranil is also observed.

  20. Development and implementation of a DFT/MIA method

    NASA Astrophysics Data System (ADS)

    Rousseau, Bart

    2001-11-01

    In the last half of the century that has passed since the advent of the quantum chemical era the computational quantum chemistry methods have matured into valuable tools for researchers in industry and academia alike. However, for these methods to be competitive with e.g. the high-throughput experimental techniques used in the pharmaceutical industry, they must not only be accurate but at the same time must be computationally inexpensive. Most of the contemporary computational methods succeed only in fulfilling one of these criteria. Therefore the goal of this Ph.D. project was to combine the MIA approach, which allows efficient SCF calculations on large systems, and the DFT method, that takes electron correlation into account at a moderate computational cost. The new DFT method thus obtained, the DFT/MIA method, allows for efficient correlated calculations on large systems. The MIA method, an efficient combination of the Multiplicative Integral Approximation and the direct SCF procedure, is implemented in the ab-initio quantum chemical program package BRABO. In the MIA approximation the product of two basis functions is expanded in terms of an auxiliary basis set. This reduces the N4 four-center two-electron integrals to a sum of N3 three-center two-electron integrals. In addition this allows for a very fast build- up of the Fock matrix. The MIA approach has already proven its effectiveness in calculations on systems that belong to the largest that have been calculated at this level of theory, such as the calculation on the 46- peptide crambin. In addition this method was implemented using the `Parallel Virtual Machine' method, allowing parallel execution on a heterogeneous cluster of workstations. The MIA approach is applied to both the calculation of the electron density and the calculation of the exchange-correlation contribution to the Fock matrix. For both these quantities a recursive procedure is used. Test calculations on water clusters ranging in size from

  1. Co(II), Ni(II), Cu(II) and Zn(II) complexes of tridentate ONO donor Schiff base ligand: Synthesis, characterization, thermal, non-isothermal kinetics and DFT calculations

    NASA Astrophysics Data System (ADS)

    Kusmariya, Brajendra S.; Mishra, A. P.

    2017-02-01

    We report here four mononuclear Co(II), Ni(II), Cu(II) and Zn(II) coordination compounds of general formula [M(L)2] {L = dcp; M = CoII, CuII & ZnII} and [M(L)(H2O)]·H2O {L = dcp; M = NiII} derived from tridentate 2,4-dichloro-6-{[(3-chloro-2-hydroxy-5-nitrophenyl)imino]methyl}phenol (dcp) ligand. These compounds were synthesized and characterized by elemental analysis, FT-IR, uv-vis, 1H NMR, molar conductance, magnetic moment, thermal, PXRD and SEM-EDX. The Powder X-ray Diffraction patterns and SEM analyses showed the crystalline nature of synthesized compounds. The peak broadening was explained in terms of crystallite size and the lattice strain using Scherrer and Williamson-Hall method. Thermogravimetric analysis was performed to determine the thermal stability of synthesized compounds under nitrogen atmosphere up to 820 K at 10 Kmin-1 heating rate. The kinetic and thermodynamic parameters of thermal decomposition were calculated using Coats-Redfern (C-R), Piloyan-Novikova (P-N) and Horowitz-Metzger (H-M) methods assuming first order degradation. The calculated optical band gap values of complexes were found to be in semiconducting range. To support the experimental findings, and derive some fruitful information viz. frequency calculations, HOMO-LUMO, energy gap (ΔE), molecular electrostatic potential (MEP), spin density, absorption spectra etc.; theoretical calculations by means of DFT and TD-DFT at B3LYP level were incorporated.

  2. Vibrational spectra, NBO analysis, first order hyperpolarizabilities, thermodynamic functions and NMR chemical shielding anisotropy (CSA) parameters of 5-nitro-2-furoic acid by ab initio HF and DFT calculations.

    PubMed

    Balachandran, V; Rajeswari, S; Lalitha, S

    2013-09-01

    In this work, FT-IR and FT-Raman spectra are recorded on the solid phase of 5-nitro-2-furoic acid (abbreviated as NFA) in the regions 4000-400 cm(-1) and 3500-100 cm(-1) respectively. The geometrical parameters, vibrational assignments, HOMO-LUMO energies and NBO calculations are obtained for the monomer and dimer of NFA from HF and DFT (B3LYP) with 6-311++G (d, p) basis set calculations. Second order perturbation energies and electron density (ED) transfer from filled lone pairs of Lewis base to unfilled Lewis acid sites of NFA are discussed on the basis of NBO analysis. Intermolecular hydrogen bonds exist through COOH groups; give the evidence for the formation of dimer entities in the title molecule. The theoretically calculated harmonic frequencies are scaled by common scale factor. The observed and the calculated frequencies are found to be in good agreement. The thermodynamic functions were obtained for the range of temperature 100-1000 K. The polarizability, first hyperpolarizability, anisotropy polarizability invariant has been computed using quantum chemical calculations. The chemical parameters were calculated from the HOMO and LUMO values. The NMR chemical shielding anisotropy (CSA) parameters were also computed for the title molecule.

  3. Calculation of the optical spectra of the copper(I) complex with triphenylphosphine, iodine, and 3-pyridine-2-yl-5-phenyl-1 H-1,2,4-triazole by the DFT method

    NASA Astrophysics Data System (ADS)

    Minaeva, V. A.; Minaev, B. F.; Baryshnikov, G. V.

    2017-02-01

    The IR and UV spectra of the [CuIL(PPh3)] complex (PPh3 = triphenylphosphine, L = 3-pyridine- 2-yl-5-phenyl-1 H-1,2,4-triazole) have been analyzed in detail within the density functional theory (DFT) and its time-dependent version TD DFT. The standard functional B3LYP and sets of basis orbitals 6-311G(d,p) and Lanl2DZ are used for the atoms of the elements of periods I and II and for the iodine atom, respectively. The calculated IR spectra of the complex and free ligands coincide with the observed IR bands, due to which one can completely interpret all normal modes and confirm X-ray diffraction (XRD) data. Particular attention is paid to the structure of excited triplet ( T 1) state in order to explain the role of copper and iodine ions in the formation of photo- and electroluminescence spectra. It is shown that the equilibrium T 1 state undergoes structural relaxation after the vertical excitation and significantly changes its electronic nature and the charge transfer structure.

  4. 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.

  5. Raman and infrared spectroscopy, DFT calculations, and vibrational assignment of the anticancer agent picoplatin: performance of long-range corrected/hybrid functionals for a platinum(II) complex.

    PubMed

    Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta

    2014-08-28

    Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.

  6. The synergetic effect of V and Fe-co-doping in TiO2 studied from the DFT + U first-principle calculation

    NASA Astrophysics Data System (ADS)

    Liu, Baoshun; Zhao, Xiujian

    2017-03-01

    Based on the density functional theory (DFT + U), a detailed study on the energetic, electronic, and optical properties of Fe-, V-, and Fe & V-co-doping anatase and rutile TiO2 was performed The synergetic effect of Fe & V bimetal co-doping on the optical absorption was discussed on electronic level. Two kinds of co-dopants were considered, which included edge-shared and corner-shared co-doping. It was shown that Fe and V atoms prefer to replace Ti atom in the O-rich contions than in the Ti-rich conditions. Co-doping in anatase reduces the formation energies in both cases, while the formation energies for rutile cannot be decreased. The Bader charge analysis indicates the +3 of Fe atom and +4 of V atom, and the obvious electron exchange between Fe and V atom in co-doping cases can be identified, which indicates the presence of synergetic effect induced by co-doping. The cooperation of Fe & V co-dopants was also supported by the result of projected density of states and spin charge density differences, as the hybridization of Fe3d with V3d orbitals was seen within the TiO2 forbidden band. Different from single-dopant systems, the V3d-Fe3d co-interaction leads to the formation of some spin mid-gap states, which have an obvious effect on the optical absorptions.

  7. Raman spectroscopy studies of temperature induced phase transitions in [N(CH3)3H]CdCl3 and DFT (B3LYP) calculations

    NASA Astrophysics Data System (ADS)

    Kchaou, H.; Karoui, K.; Bulou, A.; Ben Rhaiem, A.

    2017-04-01

    [N(CH3)3H]CdCl3 between 295 and 433 K possesses four phases. Three phase transition at T1=416 K, T2=373 K and T3=330 K (on heating) and T1=410 K, T2=386 K and T3=322 K (on cooling) was determined by differential scanning calorimetry. Thermal hysteresis of these transitions ∆T1=6 K, ∆T2=13 K and ∆T3=8 K, indicating a first order character. The X-ray diffraction study at room temperature revealed an orthorhombic system with Pbnm space group. The vibrational characteristics have been measured at room temperature by infrared spectroscopy (400-3800 cm-1) and by polarized Raman spectroscopy (10-3800 cm-1) on microcrystals orientated with respect to the organic and inorganic sublattice. The structure of this compound was optimized by density functional theory (DFT) using B3LYP with LanL2DZ and LanL2MB basis sets. The temperature dependence of the Raman line shifts ν and the half-width ∆ν detect the phase transitions (T1, T2 and T3).

  8. 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.

  9. 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.

  10. Structure, photophysics, electrochemistry, DFT calculation, and in-vitro antioxidant activity of coumarin Schiff base complexes of Group 6 metal carbonyls.

    PubMed

    Datta, Papia; Mukhopadhyay, Ambika Prasad; Manna, Prasenjit; Tiekink, Edward R T; Sil, Parames Chandra; Sinha, Chittaranjan

    2011-04-01

    N-[(2-Pyridyl)methyliden]-6-coumarin (L) is synthesized by the condensation of 6-aminocoumarin and pyridine-2-carboxaldehyde. Group-6 tetracarbonyl complexes, [M(CO)(4)(L)] (M=Cr, Mo, and W) are synthesized and characterized by mass spectrometry and NMR, FT-IR and UV-visible spectroscopy. X-ray crystal structure of [Cr(CO)(4)(L)] shows N(pyridine), N(imine) chelation to chromium(0). A supramolecular chain is formed by C-H⋯O and π⋯π interactions. The ligand and the complexes are fluorescent. Cyclic voltammetry of the complexes exhibit quasireversible M(I)/M(0) redox couple. The complexes exhibit potential antioxidant property both in cell free and in-vitro studies and highest activity is observed to [W(CO)(4)(L)]. Density functional theory (DFT) computation has been performed to correlate with the electronic configuration, composition of wave functions with the UV-visible spectra and redox properties.

  11. 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.

  12. Charged vacancy diffusion in chromium oxide crystal: DFT and DFT+U predictions

    NASA Astrophysics Data System (ADS)

    Gray, Corinne; Lei, Yinkai; Wang, Guofeng

    2016-12-01

    In this work, we computationally studied the lattice diffusion through the ion-vacancy exchange mechanism in α-Cr2O3 crystal using the first-principles density functional theory (DFT) and DFT+U calculation methods. For both O and Cr vacancies, we have identified four elementary diffusion paths in α-Cr2O3 crystal. Our DFT+U calculations predict that the O vacancy with charge +2 ( VO2 + ) is stable when Fermi energy is near to valence band maximum, whereas the Cr vacancy with charge -3 ( VCr 3 - ) is stable when Fermi energy is close to conduction band minimum. Moreover, the DFT+U calculations predict that the migration energy for VO2 + diffusion varies from 1.18 to 2.98 eV, whereas that for VCr 3 - diffusion varies from 2.02 to 2.59 eV, close to experimental data. Both DFT and DFT+U results indicate that the migration energy of neutral vacancies ( VO0 and VCr 0 ) is higher than that of the charged vacancies ( VO2 + and VCr 3 - ) along any diffusive path. Importantly, it is found that the DFT+U method describes α-Cr2O3 crystal better in terms of the magnetism, band gap, charge state of vacancies, and migration energies for charged vacancy diffusion as compared to the DFT method.

  13. Calculations of the enthalpies of combustion of organic compounds by the additive scheme

    NASA Astrophysics Data System (ADS)

    Sagadeev, E. V.; Barabanov, V. P.

    2006-11-01

    The enthalpies of combustion of more than 200 organic compounds were analyzed. Group contributions to Δc H o were calculated and used to estimate the enthalpies of combustion of a wide range of organic substances of various classes.

  14. A DFT study of the role of water in the rhodium-catalyzed hydrogenation of acetone.

    PubMed

    Polo, Victor; Schrock, Richard R; Oro, Luis A

    2016-11-24

    The positive effect of the addition of water to acetone hydrogenation by [RhH2(PR3)2S2](+) catalysts has been studied by DFT calculations. The studied energetic profiles reveal that the more favourable mechanistic path involves a hydride migration to the ketone followed by a reductive elimination that is assisted by two water molecules.

  15. Isomeric ruthenium terpyridine complexes [Ru(trpy)(L)Cl]n+ containing the unsymmetrically bidentate acceptor L=3-amino-6-(3,5-dimethylpyrazol-1-yl)-1,2,4,5-tetrazine. Synthesis, structures, electrochemistry, spectroscopy and DFT calculations.

    PubMed

    Patra, Srikanta; Sarkar, Biprajit; Ghumaan, Sandeep; Patil, Mahendra P; Mobin, Shaikh M; Sunoj, Raghavan B; Kaim, Wolfgang; Lahiri, Goutam Kumar

    2005-04-07

    The isomeric title complexes were obtained in almost equimolar ratio from the reaction of Ru(trpy)Cl3 and L. Crystal structure analyses of the perchlorate hemihydrates, electrochemical and spectroscopic (NMR, UV/VIS, EPR) studies, supported by DFT calculations, reveal distinct differences between the isomeric redox series [1]n+(tetrazine-Nt trans to Cl) and [2]n+(pyrazolyl-Np trans to Cl; n= 0, 1, 2). The latter system with the pi acceptors trpy and tetrazine in the equatorial plane and the pyrazolyl and chloride donors in the axial positions exhibits facilitated oxidation, lower energy MLCT transitions, more balanced chelate coordination, and a higher g anisotropy in the oxidised (RuIII) state. According to partially resolved EPR spectra of one-electron reduced neutral compounds and they have the unpaired electron predominantly in the tetrazine ring of L.

  16. 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.

  17. Spectroscopic studies, DFT calculations, and cytotoxic activity of novel silver(I) complexes of hydroxy ortho-substituted-nitro-2H-chromen-2-one ligands and a phenanthroline adduct.

    PubMed

    Mujahid, Muhammad; Kia, Agnieszka Foltyn-Arfa; Duff, Brian; Egan, Denise A; Devereux, Michael; McClean, Siobhán; Walsh, Maureen; Trendafilova, Natasha; Georgieva, Ivelina; Creaven, Bernadette S

    2015-12-01

    Silver(I) complexes of coumarin-based ligands and one of their phenanthroline (phen) adducts have been prepared and characterized using microanalytical data, molar conductivity, IR, (1)H and (13)C NMR, UV-Vis, and atomic absorption (AAS) spectroscopies. The binding modes of the coumarin-based ligands and the most probable structure of their Ag(I) complexes were predicted by means of molecular modeling and calculations of their IR, NMR, and absorption spectra using density functional theory (DFT). The cytotoxicity of the compounds studied against human-derived hepatic carcinoma cells (Hep-G2) and a renal cancer cell line (A498) showed that the complexes were more cytotoxic than the clinically used chemotherapeutic, mitoxantrone. The compounds showed little interaction with DNA and also did not show nuclease activity but manifested excellent superoxide dismutase activity which may indicate that their mechanism of action is quite different to many metal-based therapeutics.

  18. 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

    2008-12-05

    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

  19. 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

    2016-08-03

    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.

  20. 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.

  1. 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.

  2. Study on the adsorption properties of O{sub 3}, SO{sub 2}, and SO{sub 3} on B-doped graphene using DFT calculations

    SciTech Connect

    Rad, Ali Shokuhi; Shabestari, Sahand Sadeghi; Mohseni, Soheil; Aghouzi, Samaneh Alijantabar

    2016-05-15

    We investigated the structure, adsorption, electronic states, and charge transfer of O{sub 3}, SO{sub 2} and SO{sub 3} molecules on the surface of a B-doped graphene using density functional theory (DFT). We found weak physisorption of SO{sub 2} (−10.9 kJ/mole, using B3LYP-D) and SO{sub 3} (−15.7 kJ/mole, using B3LYP-D) on the surface of B-doped graphene while there is strong chemisorption for O{sub 3} (−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 O{sub 3} molecule. We noticed some change in hybridizing of boron from sp{sup 2} to sp{sup 3} upon adsorption of O{sub 3} which cases transformation of the adsorbent from 2D to 3D. - Graphical abstract: The electronic property of B-doped graphene is responsible to highly adsorption of O{sub 3} molecules while the adsorption of SO{sub 2} and SO{sub 3} molecules on this surface exhibits only a weak interaction. - Highlights: • B-doped graphene clearly is n-type semiconductor. • High negatively charge of C-atoms neighboring the boron dopant. • Chemisorption of O{sub 3} and physisorption of SO{sub 2} and SO{sub 3} on the surface of B-doped graphene.

  3. Additional Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media

    EPA Pesticide Factsheets

    EFED compiled examples where the PestDF (version 0.8.4), the tool used most commonly by USEPA to conduct kinetic analysis following the NAFTA guidance, results required additional interpretation. Here are some of these examples.

  4. Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    War, Javeed Ahmad; Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Srivastava, Santosh Kumar; Van Alsenoy, C.

    2017-02-01

    IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm-1 in the IR spectrum, 1014 cm-1 in the Raman spectrum and at 1014 cm-1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

  5. 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.

  6. 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.

    PubMed

    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.

  7. Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-dihydro-1,3,4-thiadiazol-2-ylidene)-4-methylbenzenesulfonamide using DFT-D calculations and (13)C solid-state NMR.

    PubMed

    Li, Xiaozhou; Bond, Andrew D; Johansson, Kristoffer E; Van de Streek, Jacco

    2014-08-01

    The crystal structure of the title compound, C11H13N3O2S2, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated (13)C solid-state NMR spectra [Hangan et al. (2010). Acta Cryst. B66, 615-621]. The molecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thiadiazol-2-yl)-p-toluenesulfonamide], rather than the correct imine tautomer. The protonation site on the molecule's 1,3,4-thiadiazole ring is indicated by the intermolecular 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 intermolecular interactions. 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 quantitative 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 (13)C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured (13)C SS-NMR spectrum.

  8. Spectroscopic characterization of 4-[2-(5-Ethylpyridin-2-yl)ethoxy]benzaldehyde oxime and investigation of its reactive properties by DFT calculations and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Sagar, B. K.; Girisha, M.; Yathirajan, H. S.; Van Alsenoy, C.

    2017-01-01

    The molecular structure, vibrational wave numbers, NLO, NBO, MEP and HOMO, LUMO analysis of 4-[2-(5-Ethylpyridin-2-yl)ethoxy]benzaldehyde oxime were reported. The theoretically predicted geometrical parameters are in agreement with the XRD data. Using NBO analysis the change in the electron density in the anti-bonding orbital and stabilization energies have been calculated to give clear evidence of stabilization in the hyper-conjugation of hydrogen bonded interactions. The calculated first hyperpolarizability is 46.761 times that of the standard NLO material urea. From molecular electrostatic potential plot, phenyl ring, pyridine ring and oxygen atoms are the most electronegative regions and the hydrogen atom in the OH group is the most electropositive region. ALIE surfaces and Fukui functions have been calculated in order to obtain information related to the local reactivity properties of the title molecule. Intra-molecular non-covalent interactions have also been searched for. In order to investigate autoxidation and degradation properties we have calculated bond dissociation energies for all single acyclic bonds. To determine which atoms have the most pronounced interactions with water molecules we have conducted molecular dynamics simulations and calculated radial distribution functions. Molecular docking studies suggest that the title compound can be a lead compound for developing new anti-cancerous drug.

  9. [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.

  10. DFT Investigation of the Mechanism and Stereochemistry of Electrophilic Transannular Addition Reaction of Chlorine to Bisbenzotetracyclo[6.2.2.23,6 .02,7]tetradeca-4,9,11,13-tetraene.

    PubMed

    Abbasoglu, Rza

    2010-12-01

    The mechanism and stereochemistry of electrophilic addition of chlorine to bisbenzotetracyclo[6.2.2.23,6.02,7]tetradeca-4,9,11,13-tetraene (BBTT) molecule were investigated by DFT methods. The geometry and the electronic structure of BBTT molecule was studied by DFT/B3LYP method using the 6-311G(d) and 6-311++G(d,p) basis sets. The double bonds of BBTT molecule are endo-pyramidalized. The structure and stability of the cationic intermediates and products of the addition reaction were investigated by B3LYP/6-311G(d) and B3LYP/6-311+G(2d,p) methods. The solvent effect was evaluated using SCI-PCM method. The bridged chloronium cation is isomerized into the more stable nonclassical delocalized N- and U-type cations, and the difference between the stability of these cations is small. For the determination of the direction of addition reaction and the stereochemistry of the products, the stability of nonclassical delocalized N- and U-type ions and the structure of their cationic centres play a vital role for the determination of the direction of addition reaction and the stereochemistry of the products. Since the cationic centre of the N-type ion is in interaction with the benzene ring from the exo face, the nucleophilic attack of the chloride anion to this centre occurs from the endo face, and the exo,endo-isomer of the N-type product is obtained. The attack of chloride anion towards the cationic centre of U-type ion from the endo face is sterically hindered by the hydrogen atom, therefore the attack occurs from the exo face, which interacts with the benzene ring and the more stable exo,exo-isomer of U-type product is formed. Although, the U-type cation was 3.485 kcal mol-1 more stable than the N-type cation, the U-type product was 1.886 kcal mol-1 [SCI-PCM-B3LYP/6-311++G(2d,p)// B3LYP/6-311G(d)] less stable than the N-type product.

  11. The substitution reactions RH + O 2 → RO 2 + H: transition state theory calculations based on the ab initio and DFT potential energy surface

    NASA Astrophysics Data System (ADS)

    Bogdanchikov, G. A.; Baklanov, A. V.; Parker, D. H.

    2004-02-01

    The new class of substitution reactions with oxygen molecule as an agent has been studied by combination of quantum chemistry calculation and transition state theory (TST). The 'inversion substitution' processes RH + O 2 → RO 2 + H (R=CH 3 and SiH 3) have been investigated. The energy for the stationary points (reagents, products and transition states) on the reaction coordinate has been calculated by G2M(CC,MP2) method and rate constants have been calculated within TST approach. The results show that in methane case the reaction considered (CH 4 + O 2 → CH 3O 2 + H) does not compete with generally accepted mechanism (CH 4 + O 2 → CH 3 + HO 2), but it does at elevated temperature in silane case.

  12. Studies on the synthesis, spectroscopic analysis, molecular docking and DFT calculations on 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazol 3-oxide

    NASA Astrophysics Data System (ADS)

    Benzon, K. B.; Sheena, Mary Y.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Pradhan, Kiran; Nanda, Ashis Kumar; Van Alsenoy, C.

    2017-02-01

    In this work we have investigated in details the spectroscopic and reactive properties of newly synthesized imidazole derivative, namely the 1-hydroxy-2-(4-hydroxyphenyl)-4,5-dimethyl-imidazole 3-oxide (HHPDI). FT-IR and NMR spectra were measured and compared with theoretically obtained data provided by calculations of potential energy distribution and chemical shifts, respectively. Insight into the global reactivity properties has been obtained by analysis of frontier molecular orbitals, while local reactivity properties have been investigated by analysis of charge distribution, ionization energies and Fukui functions. NBO analysis was also employed to understand the stability of molecule, while hyperpolarizability has been calculated in order to assess the nonlinear optical properties of title molecule. Sensitivity towards autoxidation and hydrolysis mechanisms has been investigated by calculations of bond dissociation energies and radial distribution functions, respectively. Molecular docking study was also performed, in order to determine the pharmaceutical potential of the investigated molecule.

  13. 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.

  14. 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

    2015-02-05

    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.

  15. 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.

  16. Conditional probability calculations for the nonlinear Schrödinger equation with additive noise.

    PubMed

    Terekhov, I S; Vergeles, S S; Turitsyn, S K

    2014-12-05

    The method for the computation of the conditional probability density function for the nonlinear Schrödinger equation with additive noise is developed. We present in a constructive form the conditional probability density function in the limit of small noise and analytically derive it in a weakly nonlinear case. The general theory results are illustrated using fiber-optic communications as a particular, albeit practically very important, example.

  17. Abstraction and addition kinetics of C2H radicals with CH4, C2H6, C3H8, C2H4, and C3H6: CVT/SCT/ISPE and hybrid meta-DFT methods.

    PubMed

    Dash, Manas Ranjan; Rajakumar, B

    2015-02-07

    Rate coefficients for the reactions of C2H radicals with methane (k1), ethane (k2), propane (k3), ethylene (k4), and propylene (k5) were computed using canonical variational transition state theory (CVT) coupled with hybrid-meta density functional theory (DFT) over a wide range of temperatures from 150 to 5000 K. The quantum chemical tunneling effect was corrected by the small curvature tunneling (SCT) method. The dynamic calculations are performed using the variational transition state theory (VTST) with the interpolated single-point energies (ISPE) method at the CCSD(T)/cc-pVTZ//M06-2X/6-31+G(d,p) level of theory. Intrinsic reaction coordinate (IRC) calculations were performed to verify that the transition states are connected to the reactants and products. The rate coefficients obtained over the studied temperature range yield the following Arrhenius expressions (cm(3) molecule(-1) s(-1)): k1 = 4.69 × 10(-19)T(2.44) exp[331/T], k2 = 4.29 × 10(-17)T(2.11) exp[432/T], k3 = 4.81 × 10(-17)T(1.98) exp[697/T], k4 = 7.54 × 10(-21)T(2.96) exp[1942/T], and k5 = 8.04 × 10(-23)T(3.44) exp[3011/T] cm(3) molecule(-1) s(-1). Branching ratio calculation for the reactions of C2H radicals with ethylene and propylene shows that the abstraction reactions are not important at lower temperatures. However, as the temperature increases, abstraction reactions become more important.

  18. Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets

    NASA Astrophysics Data System (ADS)

    Schröder, Heiner; Hühnert, Jens; Schwabe, Tobias

    2017-01-01

    We present an evaluation of our newly developed density functional theory (DFT)-D3 dispersion correction D3(CSO) in comparison to its predecessor D3(BJ) for geometry optimizations. Therefore, various benchmark sets covering bond lengths, rotational constants, and center of mass distances of supramolecular complexes have been chosen. Overall both corrections give accurate structures and show no systematic differences. Additionally, we present an optimized algorithm for the computation of the DFT-D3 gradient, which reduces the formal scaling of the gradient calculation from O (N3) to O (N2) .

  19. Tailoring the electronic structure of anatase TiO2(001) surface through W and N codoping: a DFT calculation

    NASA Astrophysics Data System (ADS)

    Li, Zongbao; Wang, Xia; Xing, Xiaobo; Wang, Ying

    2017-02-01

    Using density functional theory, we calculated the geometries, band structures and densities of states of W-doped, N-doped, and W/N-codoped anatase TiO4 (001) and (101) surfaces, as well as while the formation energies, based on the overall reaction energy diagram. The calculated results reveal that, on the two surfaces, the absorption of W atoms are more stable than that of N atoms while a larger energy barrier blocks the transfer of W atoms from the surfaces to the body. For TiO2(001), the W-doping and the N/W-codoping lead to a visible lattice distortion while the recombination of photo-generated electron-holes pairs is reduced. A comprehensive analysis of the electronic structures show that the band-gap narrows and a new W-N bond appears, which obviously enhance the photocatalytic activity.

  20. 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.

  1. Vibrational spectroscopic and DFT calculation studies of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    The vibrational spectra of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile were recorded using fourier transform-infrared and fourier transform-Raman spectrometer. The optimized structural parameters, vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals, thermodynamic properties, temperature dependence of thermodynamic parameters, first order hyperpolarizability and natural bond orbital calculations of the molecule were performed using the Gaussian 09 program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program. The calculated first order hyperpolarizability of ABOBPC molecule was obtained as 6.908 × 10-30 issue, which was 10.5 times greater than urea. The nonlinear optical activity of the molecule was also confirmed by the frontier molecular orbitals and natural bond orbital analysis. The frontier molecular orbitals analysis shows that the lower energy gap of the molecule, which leads to the higher value of first order hyperpolarizability. The natural bond orbital analysis indicates that the nonlinear optical activity of the molecule arises due to the π → π∗ transitions. The Mulliken atomic charge distribution confirms the presence of intramolecular charge transfer within the molecule. The reactive site of the molecule was predicted from the molecular electrostatic potential contour map. The values of thermo dynamic parameters were increasing with increasing temperature.

  2. Vibrational spectroscopic and DFT calculation studies of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile.

    PubMed

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

    2015-03-05

    The vibrational spectra of 2-amino-7-bromo-5-oxo-[1]benzopyrano [2,3-b]pyridine-3 carbonitrile were recorded using fourier transform-infrared and fourier transform-Raman spectrometer. The optimized structural parameters, vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals, thermodynamic properties, temperature dependence of thermodynamic parameters, first order hyperpolarizability and natural bond orbital calculations of the molecule were performed using the Gaussian 09 program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program. The calculated first order hyperpolarizability of ABOBPC molecule was obtained as 6.908×10(-30) issue, which was 10.5 times greater than urea. The nonlinear optical activity of the molecule was also confirmed by the frontier molecular orbitals and natural bond orbital analysis. The frontier molecular orbitals analysis shows that the lower energy gap of the molecule, which leads to the higher value of first order hyperpolarizability. The natural bond orbital analysis indicates that the nonlinear optical activity of the molecule arises due to the π→π(∗) transitions. The Mulliken atomic charge distribution confirms the presence of intramolecular charge transfer within the molecule. The reactive site of the molecule was predicted from the molecular electrostatic potential contour map. The values of thermo dynamic parameters were increasing with increasing temperature.

  3. Vibrational spectrum of the spin crossover complex [Fe(phen)(2)(NCS)(2)] studied by IR and Raman spectroscopy, nuclear inelastic scattering and DFT calculations.

    PubMed

    Ronayne, Kate L; Paulsen, Hauke; Höfer, Andreas; Dennis, Andrew C; Wolny, Juliusz A; Chumakov, Aleksandr I; Schünemann, Volker; Winkler, Heiner; Spiering, Hartmut; Bousseksou, Azzedine; Gütlich, Philipp; Trautwein, Alfred X; McGarvey, John J

    2006-10-28

    The vibrational modes of the low-spin and high-spin isomers of the spin crossover complex [Fe(phen)(2)(NCS)(2)] (phen = 1,10-phenanthroline) have been measured by IR and Raman spectroscopy and by nuclear inelastic scattering. The vibrational frequencies and normal modes and the IR and Raman intensities have been calculated by density functional methods. The vibrational entropy difference between the two isomers, DeltaS(vib), which is--together with the electronic entropy difference DeltaS(el)--the driving force for the spin-transition, has been determined from the measured and from the calculated frequencies. The calculated difference (DeltaS(vib) = 57-70 J mol(-1) K(-1), depending on the method) is in qualitative agreement with experimental values (20-36 J mol(-1) K(-1)). Only the low energy vibrational modes (20% of the 147 modes of the free molecule) contribute to the entropy difference and about three quarters of the vibrational entropy difference are due to the 15 modes of the central FeN(6) octahedron.

  4. Vibrational investigation on FT-IR and FT-Raman spectra, IR intensity, Raman activity, peak resemblance, ideal estimation, standard deviation of computed frequencies analyses and electronic structure on 3-methyl-1,2-butadiene using HF and DFT (LSDA/B3LYP/B3PW91) calculations

    NASA Astrophysics Data System (ADS)

    Ramalingam, S.; Jayaprakash, A.; Mohan, S.; Karabacak, M.

    2011-11-01

    FT-IR and FT-Raman (4000-100 cm -1) spectral measurements of 3-methyl-1,2-butadiene (3M12B) have been attempted in the present work. Ab-initio HF and DFT (LSDA/B3LYP/B3PW91) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, IR intensities and Raman activities. Complete vibrational assignments on the observed spectra are made with vibrational frequencies obtained by HF and DFT (LSDA/B3LYP/B3PW91) at 6-31G(d,p) and 6-311G(d,p) basis sets. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The potential energy distribution (PED) corresponding to each of the observed frequencies are calculated which confirms the reliability and precision of the assignment and analysis of the vibrational fundamentals modes. The oscillation of vibrational frequencies of butadiene due to the couple of methyl group is also discussed. A study on the electronic properties such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties of the title compound at different temperatures reveal the correlations between standard heat capacities ( C) standard entropies ( S), and standard enthalpy changes ( H).

  5. 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.

  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

    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.

  7. Solvent polarity and hydrogen-bonding effects on the nitrogen NMR shieldings of N-nitrosamines and DFT calculations of the shieldings of C-, N-, and O-nitroso systems

    NASA Astrophysics Data System (ADS)

    Witanowski, Michal; Biedrzycka, Zenobia; Sicinska, Wanda; Grabowski, Zbigniew

    2003-10-01

    High-precision nitrogen NMR shieldings, bulk susceptibility corrected, are reported for dimethyl- N-nitrosamine ( I) and diethyl- N-nitrosamine ( II) in a variety of solvents which represent a wide range of solvent properties from the point of view of polarity as well as hydrogen bond donor and acceptor strength. The observed range of solvent-induced nitrogen shielding variations of ( I) and ( II) is significant for the amino-type nitrogens, up to about 16 ppm, and originates essentially from the deshielding effect of the increasing polarity of solvent. On the other side, the nitroso nitrogen shieldings reveal an even stronger response to solvent effects, within about 20 ppm, but in this case the increasing polarity and hydrogen bond donor strength of solvent produce enhanced shielding. DFT quantum-mechanical calculations using the GIAO/B3PW91/6-311++G** approach and geometry optimizations employing the same basis set and hybrid density functionals show an excellent correlation with the experimental data on C-, N-, and O-nitroso moieties and reproduce not only major changes but also most of the subtle variations in the experimental nitrogen shieldings of the nitroso systems as a whole. A combination of the calculations involving the corresponding N and O-protonated species and the trends observed in the solvent-induced nitrogen shielding variations shows clearly that the prime acceptor site for hydrogen bonding is the nitroso oxygen atom.

  8. 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…

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Reinvestigation of the crystal structure, vibrational spectroscopic studies and DFT calculations of 5-bromo-7-azaindole with dual N-HṡṡṡN hydrogen bonds in dimers

    NASA Astrophysics Data System (ADS)

    Morzyk-Ociepa, Barbara; Dysz, Karolina; Turowska-Tyrk, Ilona; Michalska, Danuta

    2015-12-01

    5-Bromo-7-azaindole (5Br7AI) may act as the carrier ligand for platinum(II), in new anticancer agent, cis-[PtCl2(5Br7AI)2]. The crystal and molecular structure of the title molecule has been reinvestigated by a single crystal X-ray diffraction. The FT-IR and FT-Raman spectra of (5Br7AI) and its N-deuterated derivative have been recorded. The molecular structures of monomer and dimer, natural charges on atoms and theoretical vibrational spectra have been studied by density functional B3LYP method using 6-311++G(d,p) basis set. The results have shown that in the crystal, a pair of 5Br7AI molecules forms a centrosymmetric dimer linked by the moderately strong, dual and nearly linear N-HṡṡṡN hydrogen bonds between the pyrrole and pyridine rings. The optimized geometry of the (5Br7AI)2 dimer and the calculated spectra show very good agreement with the experiment. Detailed vibrational assignments for all the species have been made on the basis of the calculated potential energy distributions (PEDs). It is concluded that a complicated spectral features of the NH (ND) stretching absorption bands are due to multiple Fermi resonances, and they are characteristic for the doubly hydrogen bonded N-HṡṡṡN dimers of 7-azaindole and its halogeno derivatives.

  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.

    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.

  15. 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.

  16. 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.

  17. X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: a case of dual N-H⋯N hydrogen bonds in dimers.

    PubMed

    Morzyk-Ociepa, Barbara; Dysz, Karolina; Turowska-Tyrk, Ilona; Michalska, Danuta

    2015-02-05

    3-Chloro-7-azaindole (3Cl7AI) is the carrier ligand in a new anticancer platinum(II) agent cis-[PtCl2(3Cl7AI)2]. In this work 3Cl7AI has been studied by a single crystal X-ray diffraction, infrared and Raman spectroscopy and density functional calculations. The compound crystallizes in the monoclinic system, space group P21/n, with a=12.3438(3), b=3.85964(11), c=14.4698(4)Å, β=100.739(2)°, V=677.31(3)Å(3) and Z=4. In the crystal, a pair of 3Cl7AI molecules forms a centrosymmetric dimer linked by the moderately strong dual N-H⋯N hydrogen bonds. The nitrogen atom in the pyrrole ring acts as the proton donor, while the nitrogen atom in the pyridine ring is the proton acceptor. The FT-IR and FT-Raman spectra (3500-60 cm(-1)) have been recorded. The theoretical studies on the molecular structures and vibrational spectra of the monomeric and dimeric forms of 3Cl7AI and its N-deuterated derivative were performed using the B3LYP method with 6-311++G(d,p) basis set. The theoretically predicted Raman spectrum for the dimer shows very good agreement with experiment. Detailed vibrational assignments for the two isotopomers have been made on the basis of the calculated potential energy distributions (PEDs). The dual N-H⋯N hydrogen bonds in 3Cl7AI dimer are characterized by a very broad and complicated structure of the absorption band between 3300 and 2500 cm(-1), which is caused by multiple Fermi resonances between the N-H stretching vibration and various combinations bands.

  18. 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.

  19. Why the standard B3LYP/6-31G* model chemistry should not be used in DFT calculations of molecular thermochemistry: understanding and correcting the problem.

    PubMed

    Kruse, Holger; Goerigk, Lars; Grimme, Stefan

    2012-12-07

    We analyze the error compensations that are responsible for the relatively good performance of the popular B3LYP/6-31G* model chemistry for molecular thermochemistry. We present the B3LYP-gCP-D3/6-31G* scheme, which corrects for missing London dispersion and basis set superposition error (BSSE) in a physically sound manner. Benchmark results for the general main group thermochemistry, kinetics, and noncovalent interactions set (GMTKN30) are presented. A detailed look is cast on organic reactions of several arenes with C(60), Diels-Alder reactions, and barriers to [4 + 3] cycloadditions. We demonstrate the practical advantages of the new B3LYP-gCP-D3/6-31G* scheme and show its higher robustness over standard B3LYP/6-31G*. B3LYP-gCP-D3/6-31G* is meant to fully substitute standard B3LYP/6-31G* calculations in the same black-box sense at essentially no increase in computational cost. The energy corrections are made available by a Web service ( http://www.thch.uni-bonn.de/tc/gcpd3 ) and by freely available software.

  20. 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.

  1. Evaluation of Hollow Golden Icosahedrons: Bonding and Spherical Aromatic Properties of [Au11 E](3-) Superatoms (E=Se and Te) from Relativistic DFT calculations, Persistent Structures?

    PubMed

    Muñoz-Castro, Alvaro

    2017-01-04

    Two novel clusters were proposed according to the superatom model involving a favorable inclusion of Se and Te into a Au12 cage leading to [Au11 E](3-) clusters. Such structures retain a hollow gold-based icosahedron with spherical aromatic character, according to the 18-valence electron rule. Interestingly, it is shown that despite the favorable electronic structure and aromatic behavior, the titled structure is further found to be a local minimum in the potential surface, which exhibits a planar isomer as a plausible candidate for the lowest-energy structure. The proposed strategy employed to vary the electron count of the cage is useful for the further design of novel spherical aromatic superatoms and ligand-protected clusters, for which the main variation is generated directly in the surface of the cluster, in addition to the extensive formation of endohedral clusters with different heteroatoms.

  2. 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.

  3. A new trinuclear zinc(II) complex and a heptacoordinated mononuclear cadmium(II) complex with a pyrimidine derived Schiff base ligand: Syntheses, crystal structures, photoluminescence and DFT calculations

    NASA Astrophysics Data System (ADS)

    Das, Kinsuk; Jana, Atanu; Konar, Saugata; Chatterjee, Sudipta; Mondal, Tapan Kumar; Barik, Anil Kumar; Kar, Susanta Kumar

    2013-09-01

    The new N6 donor hexadentate Schiff base 2,4-bis [2-(pyridine-2-ylmethylidene) hydrazinyl] pyrimidine (L), its trinuclear Zn(II) complex, [Zn3(L)2Cl6] (1) and mononuclear heptacoordinate Cd(II) complex [Cd(L)(H2O)2](ClO4)2 (2) have been synthesised and characterised by crystallographically and spectroscopically. Complex 1 is featured by the triangular arrangement of three zinc atoms where the neighbouring Zn atoms are linked via half portion (N3 chromophore) of the same ligand molecule. In 1, the ligand molecules behave as hexadentate ones (employing both pyrimidine nitrogen atoms as active donor centres) to create the octahedral environment around Zn(II). The central and terminal Zn(II) atom has N6 and N3Cl3 chromophores respectively. In 2 the same ligand (L) behaves as pentadentate one (ignoring one pyrimidine nitrogen in the coordination process) to produce a pentagonal bipyramidal geometry with two apical water molecules. The geometries of both complexes were optimised in the singlet state by DFT method. The TDDFT calculations have been done on the optimised geometries to understand the electronic structure and spectral transition in the complexes. Complex 1 exhibits intraligand 1(π → π*) fluorescence in aqueous methanol solvent at room temperature.

  4. Crystal structure, solvothermal synthesis, thermogravimetric studies and DFT calculations of a five-coordinate cobalt(II) compound based on the N,N-bis-(2-hy-droxy-eth-yl)glycine anion.

    PubMed

    Zhou, Yanling; Liu, Xianrong; Wang, Qijun; Wang, Lisheng; Song, Baoling

    2016-10-01

    The reaction of CoCl2·6H2O, N,N-bis-(2-hy-droxy-eth-yl)glycine and tri-ethyl-amine (Et3N) in ethanol solution under solvothermal conditions produced crystals of [N,N-bis-(2-hy-droxy-eth-yl)glycinato]chloridocobalt(II), [Co(C6H12NO4)Cl]. The Co(II) 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 mol-ecules, forming a two-dimensional network parallel to (001). The mol-ecular 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.

  5. Sulfur K-Edge XAS and DFT Calculations on [Fe4S4]2+Clusters: Effects of H-bonding and Structural Distortion on Covalency and SpinTopology

    SciTech Connect

    Dey, A.; Roche, C.L.; Walters, M.A.; Hodgson, K.O.; B., Hedman; Solomon, E.I.; /Stanford U., Chem. Dept. /SLAC, SSRL

    2006-09-28

    Sulfur K-edge X-ray absorption spectroscopy of a hydrogen-bonded elongated [Fe{sub 4}S{sub 4}]{sup 2+} cube is reported. The data show that this synthetic cube is less covalent than a normal compressed cube with no hydrogen bonding. DFT calculations reveal that the observed difference in electronic structure has significant contributions from both the cluster distortion and from hydrogen bonding. The elongated and compressed Fe{sub 4}S{sub 4} structures are found to have different spin topologies (i.e., orientation of the delocalized Fe{sub 2}S{sub 2} subclusters which are antiferromagnetically coupled to each other). It is suggested that the H-bonding interaction with the counterion does not contribute to the cluster elongation. A magneto-structural correlation is developed for the Fe{sub 4}S{sub 4} cube that is used to identify the redoxactive Fe{sub 2}S{sub 2} subclusters in active sites of HiPIP and ferredoxin proteins involving these clusters.

  6. Relativistic four-component DFT calculations of 1H NMR chemical shifts in transition-metal hydride complexes: unusual high-field shifts beyond the Buckingham-Stephens model.

    PubMed

    Hrobárik, Peter; Hrobáriková, Veronika; Meier, Florian; Repiský, Michal; Komorovský, Stanislav; Kaupp, Martin

    2011-06-09

    State-of-the-art relativistic four-component DFT-GIAO-based calculations of (1)H NMR chemical shifts of a series of 3d, 4d, and 5d transition-metal hydrides have revealed significant spin-orbit-induced heavy atom effects on the hydride shifts, in particular for several 4d and 5d complexes. The spin-orbit (SO) effects provide substantial, in some cases even the dominant, contributions to the well-known characteristic high-field hydride shifts of complexes with a partially filled d-shell, and thereby augment the Buckingham-Stephens model of off-center paramagnetic ring currents. In contrast, complexes with a 4d(10) and 5d(10) configuration exhibit large deshielding SO effects on their hydride (1)H NMR shifts. The differences between the two classes of complexes are attributed to the dominance of π-type d-orbitals for the true transition-metal systems compared to σ-type orbitals for the d(10) systems.

  7. NMR spectroscopic characterization and DFT calculations of zirconium(IV)-3,3'-Br2-BINOLate and related complexes used in an enantioselective Friedel-Crafts alkylation of indoles with α,β-unsaturated ketones.

    PubMed

    Blay, Gonzalo; Cano, Joan; Cardona, Luz; Fernández, Isabel; Muñoz, M Carmen; Pedro, José R; Vila, Carlos

    2012-12-07

    Experimental and theoretical studies on the structure of several complexes based on (R)-3,3'-Br(2)-BINOL ligand and group (IV) metals used as catalysts in an enantioselective Friedel-Crafts alkylation of indoles with α,β-unsaturated ketones have been carried out. NMR spectroscopic studies of these catalysts have been performed, which suggested that at room temperature the catalysts would form a monomeric structure in the case of Ti(IV) and a dimeric structure in the cases of Zr(IV) and Hf(IV). Density functional theory (DFT) calculations clearly corroborate the conclusions of these experimental spectroscopic studies. The dimeric structure with a doubly bridged motif [Zr(IV)(2)(μ-(R)-3,3'-Br(2)-BINOL)(2)] where each binaphthol ligand acts as bridge between the metal centers (Novak's model) is more stable than the dimeric structure with a doubly bridged motif [Zr(IV)(2)(μ-O(t)Bu)(2)] where the tert-butoxide groups act as bridging ligands (Kobayashi's model). The scope of the Friedel-Crafts alkylation with regard to the indole structure has been studied. Finally a plausible mechanism for the Friedel-Crafts reaction and a stereomodel for the mode of action of the catalyst that explain the observed stereochemistry of the reaction products have been proposed.

  8. New bisphosphomide ligands, 1,3-phenylenebis((diphenylphosphino)methanone) and (2-bromo-1,3-phenylene)bis((diphenylphosphino)methanone): synthesis, coordination behavior, DFT calculations and catalytic studies.

    PubMed

    Kumar, Pawan; Siddiqui, Mujahuddin M; Reddi, Yerrnaidu; Mague, Joel T; Sunoj, Raghavan B; Balakrishna, Maravanji S

    2013-08-28

    )}AuCl] (19), in good yield. The structures of complexes 5, 7-10, 12 and 14a were confirmed by single-crystal X-ray diffraction studies. DFT calculations were performed in order to gain additional insights into the structure and bonding of the pincer complexes. An additional analysis of the orbital interactions in the case of palladium complex 9 is also included. The in situ generated rhodium complex of bisphosphomide 1 showed moderate to good selectivity in the hydroformylation of hex-1-ene and styrene derivatives.

  9. 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.

  10. Conventional and microwave-assisted synthesis, characterization, DFT calculations, in vitro DNA binding and cleavage studies of potential chemotherapeutic diorganotin(IV) mandelates.

    PubMed

    Mridula; Nath, Mala

    2016-09-01

    Diorganotin(IV) complexes of the general formulae {[R2Sn(L)]2O}(R=Me (1), n-Bu (2), and n-Oct (3); L=anion of mandelic acid) and {[R2Sn(L)]2Cl2}(R=Ph (4)) have been synthesized by conventional thermal method (1a-3a), except 4a and by microwave-assisted reactions (1b-4b). The elemental analysis, IR, NMR ((1)H, (13)C and (119)Sn) and ESI-MS/DART-mass spectral studies revealed that dimeric 1:1 complexes with SnOSn bridges (1-3) are formed possessing distorted trigonal bipyramidal geometry around the Sn atoms, except 4b which exhibits octahedral geometry with SnClSn bridges. The proposed geometries have been validated by density functional theory calculations. Thermal behavior of 1b-4b, studied by using thermogravimetry (TG), differential thermal analysis (DTA) and derivative thermogravimetric (DTG) techniques, indicated that all except 4b are stable up to 200°C. In vitro interaction studies of 1b-4b with CT-DNA were performed by UV-Vis, fluorescence titrations and results suggest that the complexes are binding to DNA via an intercalative mode. The binding affinity and quenching ability were quantified in terms of intrinsic binding constant (Kb) (3.74×10(4)M(-1), 2b; >3.67×10(4)M(-1), 4b; >3.03×10(4)M(-1), 3b; >0.72×10(4)M(-1), 1b) and Stern-Volmer quenching constant (Ksv) (2.16×10(5), 2b; >1.73×10(5), 4b; >1.66×10(5)3b; >1.51×10(5), 1b) which showed high binding affinity of 2b with CT-DNA. The cleavage studies of 1b-4b with pBR322 plasmid DNA was ascertained by agarose gel electrophoresis. They exhibited effective cleavage of supercoiled plasmid DNA into its nicked form (1b, 3b, 4b) and even into its linear form in presence of 2b.

  11. 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.

  12. The Application of DFT to Systems Containing Metal Atoms

    NASA Technical Reports Server (NTRS)

    Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

    1996-01-01

    The application of density functional theory (DFT) to a series of metal containing systems will be described. The focus will be on the calculation of accurate bond energies, especially metal-ligand successive bond energies. The DFT results will be compared with experiment and other levels of theory. If time permits, metal clusters will also be discussed.

  13. Effects of organic solvent and crystal water on γ-chymotrypsin in acetonitrile media: observations from molecular dynamics simulation and DFT calculation.

    PubMed

    Zhu, Lijuan; Yang, Wei; Meng, Yan Yan; Xiao, Xiuchan; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

    2012-03-15

    The use of enzymes in nonaqueous solvent has been one of the most exciting facets of enzymology in recent times; however, the mechanism of how organic solvent and essential water influence on structure and function of enzyme has been not satisfactorily explained in experiments, which limit its further application. Herein, we used molecular dynamics (MD) simulation to study γ-chymotrypsin in two types of media (viz., acetonitrile media with inclusion of 151 crystal water molecules and aqueous solution). On the basis of the MD result, the truncated active site modes containing two specific solvent molecules are furthered studied at the B3LYP/6-31+G(d,p) level of theory within the framework of PCM model. The results show that the acetontrile solvent gives rise to an extent deviation of enzyme structure from the native one, a drop in the flexibility and the total SASA of enzyme. The QM study further reveals that the structure variation of the active pocket caused by acetonitrile would lead to a weakened strength in the catalytic H-bond network, a drop in the pK(a) value of His57, and an increase in the proton transfer barriers from the Ser195 to the His57 residue, which may contribute to the drop in the enzymatic activity in acetontrile media. In addition, the crystal waters play an importance role in retaining the catalytic H-bond network and weakening the acetonitrile-induced variations above, which may be associated with the fact that the enzyme could retain catalytic activity in microhydration acetonitrile media.

  14. Synthesis and spectroscopic characterization on 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid: A DFT approach.

    PubMed

    Kurt, M; Sas, E Babur; Can, M; Okur, S; Icli, S; Demic, S; Karabacak, M; Jayavarthanan, T; Sundaraganesan, N

    2016-01-05

    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) (13)C NMR and (1)H 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.

  15. 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.

  16. Photo release of nitrous oxide from the hyponitrite ion studied by infrared spectroscopy. Evidence for the generation of a cobalt-N2O complex. Experimental and DFT calculations.

    PubMed

    Chacón Villalba, M Elizabeth; Franca, Carlos A; Güida, Jorge A

    2017-04-05

    The solid state photolysis of sodium, silver and thallium hyponitrite (M2N2O2, M=Na, Ag, Tl) salts and a binuclear complex of cobalt bridged by hyponitrite ([Co(NH3)5-N(O)-NO-Co(NH3)5](4+)) were studied by irradiation with visible and UV light in the electronic absorption region. The UV-visible spectra for free hyponitrite ion and binuclear complex of cobalt were interpreted in terms of Density Functional Theory calculations in order to explain photolysis behavior. The photolysis of each compound depends selectively on the irradiation wavelength. Irradiation with 340-460nm light and with the 488nm laser line generates photolysis only in silver and thallium hyponitrite salts, while 253.7nm light photolyzed all the studied compounds. Infrared spectroscopy was used to follow the photolysis process and to identify the generated products. Remarkably, gaseous N2O was detected after photolysis in the infrared spectra of sodium, silver, and thallium hyponitrite KBr pellets. The spectra for [Co(NH3)5-N(O)-NO-Co(NH3)5](4+) suggest that one cobalt ion remains bonded to N2O from which the generation of a [(NH3)5CoNNO](+3) complex is inferred. Density Functional Theory (DFT) based calculations confirm the stability of this last complex and provide the theoretical data which are used in the interpretation of the electronic spectra of the hyponitrite ion and the cobalt binuclear complex and thus in the elucidation of their photolysis behavior. Carbonate ion is also detected after photolysis in all studied compounds, presumably due to the reaction of atmospheric CO2 with the microcrystal surface reaction products. Kinetic measurements for the photolysis of the binuclear complex suggest a first order law for the intensity decay of the hyponitrite IR bands and for the intensity increase in the N2O generation. Predicted and experimental data are in very good agreement.

  17. Photo release of nitrous oxide from the hyponitrite ion studied by infrared spectroscopy. Evidence for the generation of a cobalt-N2O complex. Experimental and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chacón Villalba, M. Elizabeth; Franca, Carlos A.; Güida, Jorge A.

    2017-04-01

    The solid state photolysis of sodium, silver and thallium hyponitrite (M2N2O2, M = Na, Ag, Tl) salts and a binuclear complex of cobalt bridged by hyponitrite ([Co(NH3)5-N(O)-NO-Co(NH3)5]4 +) were studied by irradiation with visible and UV light in the electronic absorption region. The UV-visible spectra for free hyponitrite ion and binuclear complex of cobalt were interpreted in terms of Density Functional Theory calculations in order to explain photolysis behavior. The photolysis of each compound depends selectively on the irradiation wavelength. Irradiation with 340-460 nm light and with the 488 nm laser line generates photolysis only in silver and thallium hyponitrite salts, while 253.7 nm light photolyzed all the studied compounds. Infrared spectroscopy was used to follow the photolysis process and to identify the generated products. Remarkably, gaseous N2O was detected after photolysis in the infrared spectra of sodium, silver, and thallium hyponitrite KBr pellets. The spectra for [Co(NH3)5-N(O)-NO-Co(NH3)5]4 + suggest that one cobalt ion remains bonded to N2O from which the generation of a [(NH3)5CoNNO]+ 3 complex is inferred. Density Functional Theory (DFT) based calculations confirm the stability of this last complex and provide the theoretical data which are used in the interpretation of the electronic spectra of the hyponitrite ion and the cobalt binuclear complex and thus in the elucidation of their photolysis behavior. Carbonate ion is also detected after photolysis in all studied compounds, presumably due to the reaction of atmospheric CO2 with the microcrystal surface reaction products. Kinetic measurements for the photolysis of the binuclear complex suggest a first order law for the intensity decay of the hyponitrite IR bands and for the intensity increase in the N2O generation. Predicted and experimental data are in very good agreement.

  18. 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.

    PubMed

    İskeleli, Nazan Ocak; Alpaslan, Yelda Bingöl; Direkel, Şahin; Ertürk, Aliye Gediz; Süleymanoğlu, Nevin; Ustabaş, Reşat

    2015-03-15

    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 (13)C NMR, (1)H NMR, 2D NMR ((1)H-(1)H COSY and (13)C 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 3.92eV 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.

  19. Unprecedented π···π interaction between an aromatic ring and a pseudo-aromatic ring formed through intramolecular H-bonding in a bidentate Schiff base ligand: crystal structure and DFT calculations.

    PubMed

    Dutta, Arpan; Jana, Atish Dipankar; Gangopadhyay, Sumana; Das, Kalyan Kumar; Marek, Jaromir; Marek, Radek; Brus, Jiri; Ali, Mahammad

    2011-09-21

    A combination of a single crystal X-ray diffraction study and density functional theory calculations has been applied to a bidentate Schiff base compound to elucidate different cooperative non-covalent interactions involved in the stabilization of the keto form over the enol one in the solid state. The single crystal X-ray structure reveals a remarkable supramolecular assembly of the keto form through a cyclic hydrogen bonded dimeric motif. The most interesting feature in the supramolecular assembly is the formation of a 'dimer of dimer' motif by π···π, CH···π and N···O/O···O interactions in which the π···π interaction involving the aromatic phenyl ring and the intramolecularly hydrogen bonded pseudo-aromatic ring of the keto form lying just above or below the phenyl ring of the other dimer seems to be unprecedented. The optimized geometry of the hydrogen bonded dimeric motif of the keto form of the organic molecule has been obtained by DFT calculations and agrees very well with that found within the crystalline state. The X-ray crystallographic geometry of the 'dimer of dimer' has also been computed, which shows that in the HOMO, the π electrons are localized in the phenyl rings away from each other, while in the LUMO, there is a strong π-π interaction between the phenyl ring of one dimer with the pseudo-aromatic ring of another dimer with an energy estimated to be 7.95 kJ mol(-1). Therefore, on HOMO → LUMO excitation there is localization of π electrons in the central part of the complex moiety which plays a stabilizing role of the dimer of dimer motif in the solid state.

  20. A structural study of [CpM(CO)3H] (M = Cr, Mo and W) by single-crystal X-ray diffraction and DFT calculations: sterically crowded yet surprisingly flexible molecules.

    PubMed

    Burchell, Richard P L; Sirsch, Peter; Decken, Andreas; McGrady, G Sean

    2009-08-14

    The single-crystal X-ray structures of the complexes [CpCr(CO)3H] 1, [CpMo(CO)3H] 2 and [CpW(CO)3H] 3 are reported. The results indicate that 1 adopts a structure close to a distorted three-legged piano stool geometry, whereas a conventional four-legged piano stool arrangement is observed for 2 and 3. Further insight into the equilibrium geometries and potential energy surfaces of all three complexes was obtained by DFT calculations. These show that in the gas phase complex 1 also prefers a geometry close to a four-legged piano stool in line with its heavier congeners, and implying strong packing forces at work for 1 in the solid state. Comparison with their isolelectronic group 7 tricarbonyl counterparts [CpM(CO)3] (M = Mn 4 and Re 5) illustrates that 1, 2 and 3 are sterically crowded complexes. However, a surprisingly soft bending potential is evident for the M-H moiety, whose order (1 approximately = 2 < 3) correlates with the M-H bond strength rather than with the degree of congestion at the metal centre, indicating electronic rather than steric control of the potential. The calculations also reveal cooperative motions of the hydride and carbonyl ligands in the M(CO)3H unit, which allow the M-H moiety to move freely, in spite of the closeness of the four basal ligands, helping to explain the surprising flexibility of the crowded coordination sphere observed for this family of high CN complexes.

  1. 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

    2014-05-07

    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.

  2. Calculation of multicenter electric field gradient integrals over Slater-type orbitals using unsymmetrical one-range addition theorems.

    PubMed

    Guseinov, Israfil I; Görgün, Nurşen Seçkin

    2011-06-01

    The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range addition theorems introduced by one of the authors, the sets of series expansion relations for multicenter electric field gradient integrals over Slater-type orbitals in terms of multicenter charge density expansion coefficients and two-center basic integrals are presented. The convergence of the series is tested by calculating concrete cases for different values of quantum numbers, parameters and locations of orbitals.

  3. Calculation of ionization energy, electron affinity, and hydride affinity trends in pincer-ligated d(8)-Ir((tBu4)PXCXP) complexes: implications for the thermodynamics of oxidative H2 addition.

    PubMed

    Baroudi, Abdulkader; El-Hellani, Ahmad; Bengali, Ashfaq A; Goldman, Alan S; Hasanayn, Faraj

    2014-12-01

    DFT methods are used to calculate the ionization energy (IE) and electron affinity (EA) trends in a series of pincer ligated d(8)-Ir((tBu4)PXCXP) complexes (1-X), where C is a 2,6-disubstituted phenyl ring with X = O, NH, CH2, BH, S, PH, SiH2, and GeH2. Both C2v and C2 geometries are considered. Two distinct σ-type ((2)A1 or (2)A) and π-type ((2)B1 or (2)B) electronic states are calculated for each of the free radical cation and anion. The results exhibit complex trends, but can be satisfactorily accounted for by invoking a combination of electronegativity and specific π-orbital effects. The calculations are also used to study the effects of varying X on the thermodynamics of oxidative H2 addition to 1-X. Two closed shell singlet states differentiated in the C2 point group by the d(6)-electon configuration are investigated for the five-coordinate Ir(III) dihydride product. One electronic state has a d(6)-(a)(2)(b)(2)(b)(2) configuration and a square pyramidal geometry, the other a d(6)-(a)(2)(b)(2)(a)(2) configuration with a distorted-Y trigonal bipyramidal geometry. No simple correlations are found between the computed reaction energies of H2 addition and either the IEs or EAs. To better understand the origin of the computed trends, the thermodynamics of H2 addition are analyzed using a cycle of hydride and proton addition steps. The analysis highlights the importance of the electron and hydride affinities, which are not commonly used in rationalizing trends of oxidative addition reactions. Thus, different complexes such as 1-O and 1-CH2 can have very similar reaction energies for H2 addition arising from opposing hydride and proton affinity effects. Additional calculations on methane C-H bond addition to 1-X afford reaction and activation energy trends that correlate with the reaction energies of H2 addition leading to the Y-product.

  4. Synthesis, characterization, DFT calculations and biological studies of Mn(II), Fe(II), Co(II) and Cd(II) complexes based on a tetradentate ONNO donor Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Abdel-Rahman, Laila H.; Ismail, Nabawia M.; Ismael, Mohamed; Abu-Dief, Ahmed M.; Ahmed, Ebtehal Abdel-Hameed

    2017-04-01

    This study highlights synthesis and characterization of a tetradentate ONNO Schiff base ligand namely (1, 1‧- (pyridine-2, 3-dimethyliminomethyl) naphthalene-2, 2‧-diol) and hereafter denotes as "HNDAP″ and selected metal complexes including Mn(II), Fe(II), Co(II) and Cd(II) as a central metal. HNDAP was synthesized from 1:2 M ratio condensation of 2, 3-diaminopyridine and 2- hydroxy-1-naphthaldhyde, respectively. The stoichiometric ratios of the prepared complexes were estimated using complementary techniques such as; elemental analyses (-C, H, N), FT-IR, magnetic measurements and molar conductivity. Furthermore, their physicochemical studies were carried out using thermal TGA, DTA and kinetic-thermodynamic studies along with DFT calculations. The results of elemental analyses showed that these complexes are present in a 1:1 metal-to- ligand molar ratio. Moreover, the magnetic susceptibilities values at room temperature revealed that Mn(II), Fe(II) and Co(II) complexes are paramagnetic in nature and have an octahedral (Oh) geometry. In contrast, Cd(II) is diamagnetic and stabilizes in square planar sites. The molar conductivity measurements indicated that all complexes are nonelectrolytes in dimethyl formamide. Spectral data suggested that the ligand is as tetradentate and coordinated with Co(II) ion through two phenolic OH and two azomethine nitrogen. However, for Mn(II), Fe(II) and Cd(II) complexes, the coordination occurred through two phenolic oxygen and two azomethine nitrogen with deprotonation of OH groups. The proposed chemical structures have been validated by quantum mechanics calculations. Antimicrobial activities of both the HNDAP Schiff base ligand and its metal complexes were tested against strains of Gram (-ve) E. coli and Gram (+ve) B. subtilis and S. aureus bacteria and C. albicans, A. flavus and T. rubrum fungi. All the prepared compounds showed good results of inhibition against the selected pathogenic microorganisms. The investigated

  5. Unveiling the non-covalent interactions of molecular homodimers by dispersion-corrected DFT calculations and collision-induced broadening of ro-vibrational transitions: application to (CH2F2)2 and (SO2)2.

    PubMed

    Tasinato, Nicola; Grimme, Stefan

    2015-02-28

    Thermodynamic and spectroscopic properties of molecular complexes featuring non-covalent interactions, such as van der Waals forces and hydrogen bonds, are of fundamental interest in many fields, ranging from chemistry and biology to nanotechnology. In the present work the homodimers of difluoromethane (CH2F2) and sulfur dioxide (SO2) are investigated theoretically using dispersion-corrected density functional theory (DFT-D3) and experimentally by tunable diode laser (TDL) infrared (IR) spectroscopy. The dissociation energies of (CH2F2)2 and (SO2)2 are determined experimentally from the broadening of the ro-vibrational transitions of the corresponding monomers collisionally perturbed by a range of damping gases. The resulting dissociation energies are 2.79 ± 0.32 and 2.62 ± 0.16 kcal mol(-1) for the CH2F2 and SO2 dimers, respectively. Six to nine different stationary points on the PES of the two complexes are investigated theoretically at the DFT-D3 level, retrieving the corresponding dissociation energies, structures and rotational constants. Computations are carried out by employing six different density functionals (BLYP, TPSS, B3LYP, PBE0, TPSSh, and PW6B95) in conjunction with def2-TZVP and in a few cases def2-QZVP basis sets. DFT-D3 dissociation energies are benchmarked against reference values from CCSD(T)/CBS computations, and furthermore compared to experimental ones. A very good agreement between theory and experiment is attained, showing that DFT-D3 provides a significant improvement over standard DFT. This work shows that dissociation energies of homodimers can be consistently derived from collisional broadening cross sections and that interaction energies at various DFT-D3 levels (nearly) reach the accuracy of highly correlated wavefunction methods.

  6. Investigation of coordination properties of isolated adenine to copper metal: a systematic spectroscopic and DFT study.

    PubMed

    Prakash, Om; Singh, Sachin Kumar; Singh, Bachcha; Singh, Ranjan K

    2013-08-01

    The coordination properties of copper with adenine have been studied by the analyzing the changes in Fourier Transform Infra-red (FTIR) and Raman spectra of adenine and adenine-copper complex. The geometry of adenine and adenine copper complex were optimized and theoretical Infra-red and Raman spectra of the optimized structures were calculated using Density Functional Theory (DFT). During synthesis of adenine-copper complex specific procedure was adopted to attach the Cu atom with particular N-atom of adenine (N9). The results of Raman and DFT confirmed the attachment. The Raman bands at 625, 330 and 230 cm(-1) of adenine-copper complex contain significant contribution of the vibrational motions of Cu metal coordinated to N9 and Cl atoms. The DFT calculations give additional vibrational modes containing the Cu, N9 and N9* atoms, which are not observed in FTIR and Raman spectra. The Raman, IR and DFT study confirm that Cu metal has good binding affinity to the isolated adenine base.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Crystal structures and DFT calculations of new chlorido-dimethylsulfoxide-M(III) (M = Ir, Ru, Rh) complexes with the N-pyrazolyl pyrimidine donor ligand: kinetic vs. thermodynamic isomers.

    PubMed

    Cánaves, María M; Cabra, María I; Bauzá, Antonio; Cañellas, Pablo; Sánchez, Kika; Orvay, Francisca; García-Raso, Angel; Fiol, Juan J; Terrón, Angel; Barceló-Oliver, Miquel; Ballester, Pablo; Mata, Ignasi; Molins, Elies; Hussain, Firasat; Frontera, Antonio

    2014-05-07

    New chlorido-dimethylsulfoxide-iridium(III), ruthenium(III) and rhodium(III) complexes with the 2-(1H-pyrazol-1-yl)-pyrimidine (pyrapyr) ligand (OC-6-N1)-[Rh(III)Cl3(DMSO-κS)(pyrapyr)] (1a, N = 3 and 1b, N = 4); (OC-6-N1)-[Ru(III)Cl3(DMSO-κS)(pyrapyr)] (2a, N = 3 and 2b, N = 4) and (OC-6-N1)-[Ir(III)Cl3(DMSO-κS)(pyrapyr)] (3a, N = 3 and 3b, N = 4) have been synthesized and characterized by spectroscopic techniques and by single crystal X-ray diffraction studies (1a, 1b, 2a, 2b, a disordered crystal 3a/3b and a cocrystal 3a·3b). In all cases, the metal centers show octahedral geometry coordinated to three chloride ligands and one S coordinated dimethylsulfoxide (DMSO-κS). The coordination sphere of the metal is completed by the pyrapyr molecule. Two different coordination modes are observed: (i) the DMSO-κS is opposite to the pyrimidinic N atom (IUPAC nomenclature is OC-6-31 denoted herein as trans); (ii) DMSO-κS is opposite to the pyrazolic N atom (IUPAC nomenclature is OC-6-41 denoted as cis). For Rh(III) the kinetic product (cis) yields the thermodynamic (trans) upon heating a solution of the kinetic product and both isomers have been X-ray characterized. Conversely for Ru(III), both kinetic and thermodynamic complexes have been obtained by using different procedures. Both isomers have been characterized by X-ray crystallography and the kinetic product does not yield the thermodynamic upon heating a solution of the former. Furthermore, the Ir(III) behaves differently, since both isomers are energetically equivalent and both isomers co-crystallize in the solid state. The kinetic/thermodynamic mechanism that yields the different isomers has been studied by using theoretical DFT calculations for each metal. Finally, two Ru(II) complexes (OC-6-N1)-[Ru(II)Cl2(DMSO-κS)2(pyrapyr)] (1a, N = 3 and 4b, N = 4) are also described and X-ray characterized. They were obtained as minor products during the synthesis of 2a.

  12. Selective activation of C-F and C-H bonds with iron complexes, the relevant mechanism study by DFT calculations and study on the chemical properties of hydrido iron complex.

    PubMed

    Xu, Xiaofeng; Jia, Jiong; Sun, Hongjian; Liu, Yuxia; Xu, Wengang; Shi, Yujie; Zhang, Dongju; Li, Xiaoyan

    2013-03-14

    The reactions of (2,6-difluorophenyl)phenylmethanone (2,6-F(2)C(6)H(3)-C(=O)-C(6)H(5)) (1) and (2,6-difluorophenyl)phenylmethanimine (2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(5)) (3) with Fe(PMe(3))(4) afforded different selective C-F/C-H bond activation products. The reaction of 1 with Fe(PMe(3))(4) gave rise to bis-chelate iron(II) complex [C(6)H(5)-C(=O)-3-FC(6)H(3))Fe(PMe(3))](2) (2) via C-F bond activation. The reaction of 3 with Fe(PMe(3))(4) delivered chelate hydrido iron(II) complex 2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(4))Fe(H)(PMe(3))(3) (4) through C-H bond activation. The DFT calculations show the detailed elementary steps of the mechanism of formation of hydrido complex 4 and indicate 4 is the kinetically preferred product. Complex 4 reacted with HCl, CH(3)Br and CH(3)I delivered the chelate iron halides (2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(4))Fe(PMe(3))(3)X (X = Cl (5); Br (6); I (7)). A ligand (PMe(3)) replacement by CO of 4 was observed giving (2,6-F(2)C(6)H(3)-C(=NH)-C(6)H(4))Fe(H)(CO)(PMe(3))(2) (8). The chelate ligand exchange occurred through the reaction of 4 with salicylaldehydes. The reaction of 4 with Me(3)SiC[triple bond, length as m-dash]CH afforded (2,6-F(2)C(6)H(3)-C([double bond, length as m-dash]N)-C(6)H(5))Fe(C≡C-SiMe(3))(PMe(3))(3) (11). A reaction mechanism from 4 to 11 was discussed with the support of IR monitoring. The molecular structures of complexes 2, 4, 6, 7, 10 and 11 were determined by X-ray diffraction.

  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. 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-cat