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Sample records for addition dft calculations

  1. Wavelet-Based DFT calculations on Massively Parallel Hybrid Architectures

    NASA Astrophysics Data System (ADS)

    Genovese, Luigi

    2011-03-01

    In this contribution, we present an implementation of a full DFT code that can run on massively parallel hybrid CPU-GPU clusters. Our implementation is based on modern GPU architectures which support double-precision floating-point numbers. This DFT code, named BigDFT, is delivered within the GNU-GPL license either in a stand-alone version or integrated in the ABINIT software package. Hybrid BigDFT routines were initially ported with NVidia's CUDA language, and recently more functionalities have been added with new routines writeen within Kronos' OpenCL standard. The formalism of this code is based on Daubechies wavelets, which is a systematic real-space based basis set. As we will see in the presentation, the properties of this basis set are well suited for an extension on a GPU-accelerated environment. In addition to focusing on the implementation of the operators of the BigDFT code, this presentation also relies of the usage of the GPU resources in a complex code with different kinds of operations. A discussion on the interest of present and expected performances of Hybrid architectures computation in the framework of electronic structure calculations is also adressed.

  2. Ab initio DFT calculations of vibrational properties

    NASA Astrophysics Data System (ADS)

    Story, S. M.; Vila, F. D.; Kas, J. J.; Rehr, J. J.

    2014-03-01

    Vibrational properties such as EXAFS and crystallographic Debye-Waller factors, vibrational free energies, phonon self-energies, and phonon contributions to the electron spectral function, are key to understanding many aspects of materials beyond ground state electronic structure. Thus, their simulation using first principles methods is of particular importance. Many of these vibrational properties can be calculated from the dynamical matrix and electron-phonon coupling coefficients obtained from DFT calculations. Here we present a code DMVP that calculates these properties from the output of electronic structure codes such as ABINIT, Gaussian, Quantum Espresso and VASP. Our modular interfacing tool AI2PS allows us to translate the different outputs into a DMVP compatible format and generate vibrational properties in an automated way. Finally, we present some current applications that take advantage of the modular form of AI2PS to extend its capabilities to the calculation of coefficients of thermal expansion and other properties of interest such as infrared spectra. This work was supported by DOE Grant DE-FG02-97ER45623.

  3. 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

  4. Modelling catalyst surfaces using DFT cluster calculations.

    PubMed

    Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

    2009-10-01

    We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO(2), gamma-Al(2)O(3), V(2)O(5)-WO(3)-TiO(2) and Ni/Al(2)O(3). Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies. PMID:20057947

  5. Modelling Catalyst Surfaces Using DFT Cluster Calculations

    PubMed Central

    Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

    2009-01-01

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

  6. The flexibility of Daubechies wavelets for Linear Scaling DFT calculations

    NASA Astrophysics Data System (ADS)

    Genovese, Luigi; Mohr, Stephan; Ratcliff, Laura Elisabeth; Caliste, Damien; Deutsch, Thierry; Goedecker, Stefan

    In recent works, we presented the linear scaling version of the BigDFT code based on Daubechies wavelets, where a minimal set of localized support functions is optimized in situ. Our linear scaling approach is able to generate support functions for systems in various boundary conditions, like isolated, surface and periodic, and it is based on a algorithm which is universally applicable, requiring only moderate amount of computing resources. We will present how the flexibility of this approach is helpful in providing a basis set that is optimally tuned to the chemical environment surrounding each atom. In addition than providing a basis useful to project Kohn-Sham orbitals informations like atomic charges and partial density of states, it can also be reused as-is, i.e. without reoptimization, for charge-constrained DFT calculations within a fragment approach. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Buimaga-Iarinca, L.; Calborean, A.

    2015-12-01

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

  9. 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. 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.

  12. 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)

  13. 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.

  14. Million atom DFT calculations using coarse graining and petascale computing

    NASA Astrophysics Data System (ADS)

    Nicholson, Don; Odbadrakh, Kh.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X. G.; Stocks, G. M.

    2014-03-01

    Researchers performing classical Molecular Dynamics (MD) on defect structures often find it necessary to use millions of atoms in their models. It would be useful to perform density functional calculations on these large configurations in order to observe electron-based properties such as local charge and spin and the Helmann-Feynman forces on the atoms. The great number of atoms usually requires that a subset be ``carved'' from the configuration and terminated in a less that satisfactory manner, e.g. free space or inappropriate periodic boundary conditions. Coarse graining based on the Locally Self-consistent Multiple Scattering method (LSMS) and petascale computing can circumvent this problem by treating the whole system but dividing the atoms into two groups. In Coarse Grained LSMS (CG-LSMS) one group of atoms has its charge and scattering determined prescriptively based on neighboring atoms while the remaining group of atoms have their charge and scattering determined according to DFT as implemented in the LSMS. The method will be demonstrated for a one-million-atom model of a displacement cascade in Fe for which 24,130 atoms are treated with full DFT and the remaining atoms are treated prescriptively. Work supported as part of Center for Defect Physics, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, Basic Energy Sciences, used Oak Ridge Leadership Computing Facility, Oak Ridge National Lab, of DOE Office of Science.

  15. 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. PMID:25958954

  16. 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.

  17. Structural Investigation of Layered Niobates by DFT Calculations

    NASA Astrophysics Data System (ADS)

    Adhikari Subin, Jhashanath

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

  18. Self-consistent calculation of Hubbard U parameters within linear-scaling DFT

    NASA Astrophysics Data System (ADS)

    Moynihan, Glenn; Teobaldi, Gilberto; O'Regan, David D.

    DFT+U has proven to be a computationally efficient method for correcting for the underestimation of electron localization effects, or for the absent derivative discontinuity, inherent in conventional density functionals. Invoking an approximate interpretation of DFT+U as a corrective penalty functional for the spurious curvature of the total-energy with respect to subspace occupancy, the Hubbard U parameter may be calculated, in which case DFT+U may be considered to be fully first-principles approach. We describe our approach for computing the Hubbard U and Hund's J parameters within ONETEP, a linear-scaling DFT code which comprises a complete DFT+U+J implementation including ionic forces and a flexible choice of population analyses. We discuss issues of charge preservation and self-consistency, and we demonstrate the capability of our method by means of numerical tests on the ground-state properties of selected molecules that present challenges for approximate DFT.

  19. 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.

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

    PubMed

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

    2015-11-01

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

  1. DFT calculations of EPR parameters of transition metal complexes: Implications for catalysis

    SciTech Connect

    Saladino, Alexander C.; Larsen, Sarah C.

    2005-07-15

    Transition metal and ligand hyperfine coupling constants for paramagnetic vanadium and copper model complexes have been calculated using DFT methods that are available in commercial software packages. Variations in EPR parameters with ligand identity and ligand orientation are two of the trends that have been investigated with DFT calculations. For example, the systematic variation of the vanadium hyperfine coupling constant with orientation for an imidazole ligand in a VO2+ complex has been observed experimentally and has also been reproduced by DFT calculations. Similarly, changes in the vanadium hyperfine coupling constant with ligand binding have been calculated using model complexes and DFT methods. DFT methods were also used to calculate ligand hyperfine coupling constants in transition metal systems. The variation of the proton hyperfine coupling constant with water ligand orientation was investigated for [VO(H2O)5]2+ and the results were used to interpret high resolution EPR data of VO2+-exchanged zeolites. Nitrogen hyperfine and quadrupole coupling constants for VO2+ model complexes were calculated and compared with experimental data. The computational results were used to enhance the interpretation of the EPR data for vanadium-exchanged zeolites which are promising catalytic materials. The implications of the DFT calculations of EPR parameters with respect to catalysis will be discussed

  2. Molecular structure, spectroscopic properties and DFT calculations of 2-(methylthio)nicotinic acid

    NASA Astrophysics Data System (ADS)

    Gökce, Halil; Bahçeli, Semiha

    2013-10-01

    The analyses of possible conformations, molecular structures, vibrational and electronic properties of 2-(methylthio)nicotinic acid molecule, C7H7NO2S, with the synonym 2-(methylsulfanyl)nicotinic acid have been first presented theoretically. At the same time, FT-IR and micro-Raman spectra of 2-(methylthio)nicotinic acid were recorded in the regions 400-4000 cm-1 and 100-4000 cm-1, respectively. In our calculations, the DFTB3LYP method with 6-311G(d, p) basis set was used to have the structural and spectroscopic data about the mentioned molecule in the ground state and the results obtained were compared with experimental values. Furthermore, gauge invariant atomic orbital (GIAO) 1H and 13C NMR chemical shifts in different solvents, UV-vis TD-DFT calculations, the highest occupied molecular orbitals (HOMO-2, HOMO-1, HOMO), lowest unoccupied molecular orbital (LUMO), molecular electrostatic potantial (MEP) surface, atomic charges and thermodynamic properties of molecule have been theoretically verified and simulated at the mentioned level. The energetic behavior of title molecule in different solvent media was investigated by using DFT/B3LYP method with 6-311G(d, p) basis set in terms of integral equation formalism polarizable continuum model (IEFPCM). In addition, the calculated infrared intensities, Raman activities, reduce masses and force constants of the compound under study have been also reported.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Beni, Alireza Salimi; Zarandi, Maryam

    2016-02-01

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

  6. 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.

  7. 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. PMID:25412189

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

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

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

  10. 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.

  11. 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.

  12. 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. PMID:25880048

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

    PubMed

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

    2016-02-01

    Enantiomerization of allylic trifluoromethyl sulfoxides occurs spontaneously at room temperature through the corresponding allylic trifluoromethanesulfenates via a [2,3]-sigmatropic rearrangement. Dynamic enantioselective high-performance liquid chromatography (HPLC) analysis revealed the stereodynamics of these sulfoxides ranging from chromatographic resolution to peak coalescence at temperatures between 5 and 53 °C. The rate constant of enantiomerization and activation parameters were determined and compared with Density Functional Theory (DFT) calculations. PMID:26689286

  14. 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. PMID:26508426

  15. 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.

  16. Modelling defects in Ni–Al with EAM and DFT calculations

    NASA Astrophysics Data System (ADS)

    Bianchini, F.; Kermode, J. R.; De Vita, A.

    2016-05-01

    We present detailed comparisons between the results of embedded atom model (EAM) and density functional theory (DFT) calculations on defected Ni alloy systems. We find that the EAM interatomic potentials reproduce low-temperature structural properties in both the γ and {γ\\prime} phases, and yield accurate atomic forces in bulk-like configurations even at temperatures as high as  ∼1200 K. However, they fail to describe more complex chemical bonding, in configurations including defects such as vacancies or dislocations, for which we observe significant deviations between the EAM and DFT forces, suggesting that derived properties such as (free) energy barriers to vacancy migration and dislocation glide may also be inaccurate. Testing against full DFT calculations further reveals that these deviations have a local character, and are typically severe only up to the first or second neighbours of the defect. This suggests that a QM/MM approach can be used to accurately reproduce QM observables, fully exploiting the EAM potential efficiency in the MM zone. This approach could be easily extended to ternary systems for which developing a reliable and fully transferable EAM parameterisation would be extremely challenging e.g. Ni alloy model systems with a W or Re-containing QM zone.

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

    NASA Astrophysics Data System (ADS)

    Patterson, C. H.

    2014-08-01

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

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

    PubMed

    Jónsson, Erlendur; Johansson, Patrik

    2012-08-14

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

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

    NASA Astrophysics Data System (ADS)

    Yang, Yue; Gao, Hongwei

    2012-01-01

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

  20. Microwave assisted synthesis, X-ray crystallography and DFT calculations of selected aromatic thiosemicarbazones

    NASA Astrophysics Data System (ADS)

    Serda, Maciej; Małecki, Jan G.; Mrozek-Wilczkiewicz, Anna; Musioł, Robert; Polański, Jarosław

    2013-04-01

    Series of four benzaldehyde thiosemicarbazones has been synthesized under microwave irradiation and characterized structurally by means of infrared and NMR spectroscopies and mass spectrometry. Their crystal structures were determined by single crystal X-ray analysis followed by DFT calculations. Partial charges on the molecular surface and dipole moments of the structures were calculated. Crystal structures are stabilized by intramolecular hydrogen bonding and stacking interactions. Studied compounds are interesting as antiproliferative and antifungal agents acting through interactions with iron. Thus presented results may be useful in design new more active or specific structures.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  2. 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

    2015-12-01

    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. PMID:26151435

  3. 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.

  4. 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.

  5. 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. PMID:26352329

  6. Raman spectroscopy and DFT calculations of As(III) complexation with a cysteine-rich biomaterial.

    PubMed

    Teixeira, Mônica C; Ciminelli, Virgínia S T; Dantas, Maria Sylvia Silva; Diniz, Sirlaine F; Duarte, Hélio A

    2007-11-01

    Arsenite adsorption onto a protein-rich biomass and, more specifically, the chemical groups involved in the uptake were investigated using Raman spectroscopy and DFT calculations. The study was based on spectroscopic analyses of raw and arsenic-loaded biomass as well as standard samples of amino acids and arsenic salts. The predominant secondary structure of the protein was identified as the beta-sheet type, with some contribution from alpha-helix structures. The participation of sulphydryl groups from cystine/cysteine molecules during the adsorption of arsenite was demonstrated. Only the gauche-gauche-gauche (g-g-g) conformation type of the disulfide bonds was involved in arsenic complexation. The formation of a pyramidal trigonal As(HCys)(3) complex was modeled according to the density functional theory (DFT). The agreement of the DFT harmonic frequencies with the RAMAN spectra of the As(HCys)(3) complex demonstrated the relevant features of the cysteine-rich biomaterial regarding arsenic uptake as well as of the mechanism involved in the As(III)/biomass interaction at a molecular level. The results also illustrate that Raman spectroscopy can be successfully applied to investigate the mechanism of metal adsorption onto amorphous biomaterials. PMID:17707392

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  8. 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.

  9. Maximizing the solar energy storage of the four substituted norbornadiene-quadricyclane system: DFT calculations

    NASA Astrophysics Data System (ADS)

    Vessally, Esmail; Aryana, Soma

    2016-01-01

    The purpose of this research is to study the solar energy storage in norbornadiene ( 1)/quadricyclane ( 2) system by four direct attachments of substituents at two carbon atoms on both sides of the double bonds C2=C3 and C5=C6 in 1 X and 2 X; calculating the relative energies at B3LYP/6-311++G** level of theory. The solar energy storage of four electron donating substituents, (push-push effect), X (X =-NH2,-OH) and four electron withdrawing substituents, (pull-pull effect) X (X =-CO2H,-CONH2,-NO2 and CN) were examined. The solar absorption bands were calculated for 1 X. The DFT calculations reveal that the bands were shifted to the visible spectrum region when the electron withdrawing substituents were used rather than the electron donating substituents.

  10. 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.

  11. A big data approach to the ultra-fast prediction of DFT-calculated bond energies

    PubMed Central

    2013-01-01

    Background The rapid access to intrinsic physicochemical properties of molecules is highly desired for large scale chemical data mining explorations such as mass spectrum prediction in metabolomics, toxicity risk assessment and drug discovery. Large volumes of data are being produced by quantum chemistry calculations, which provide increasing accurate estimations of several properties, e.g. by Density Functional Theory (DFT), but are still too computationally expensive for those large scale uses. This work explores the possibility of using large amounts of data generated by DFT methods for thousands of molecular structures, extracting relevant molecular properties and applying machine learning (ML) algorithms to learn from the data. Once trained, these ML models can be applied to new structures to produce ultra-fast predictions. An approach is presented for homolytic bond dissociation energy (BDE). Results Machine learning models were trained with a data set of >12,000 BDEs calculated by B3LYP/6-311++G(d,p)//DFTB. Descriptors were designed to encode atom types and connectivity in the 2D topological environment of the bonds. The best model, an Associative Neural Network (ASNN) based on 85 bond descriptors, was able to predict the BDE of 887 bonds in an independent test set (covering a range of 17.67–202.30 kcal/mol) with RMSD of 5.29 kcal/mol, mean absolute deviation of 3.35 kcal/mol, and R2 = 0.953. The predictions were compared with semi-empirical PM6 calculations, and were found to be superior for all types of bonds in the data set, except for O-H, N-H, and N-N bonds. The B3LYP/6-311++G(d,p)//DFTB calculations can approach the higher-level calculations B3LYP/6-311++G(3df,2p)//B3LYP/6-31G(d,p) with an RMSD of 3.04 kcal/mol, which is less than the RMSD of ASNN (against both DFT methods). An experimental web service for on-line prediction of BDEs is available at http://joao.airesdesousa.com/bde. Conclusion Knowledge could be automatically extracted by

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

    NASA Astrophysics Data System (ADS)

    Zarandi, Maryam; Salimi Beni, Alireza

    2016-09-01

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

  13. Electronic structure and optical properties of Cs2HgI4: Experimental study and band-structure DFT calculations

    NASA Astrophysics Data System (ADS)

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Shkumat, P. N.; Myronchuk, G. L.; Khvyshchun, M.; Fedorchuk, A. O.; Parasyuk, O. V.; Khyzhun, O. Y.

    2015-04-01

    High-quality single crystal of cesium mercury tetraiodide, Cs2HgI4, has been synthesized by the vertical Bridgman-Stockbarger method and its crystal structure has been refined. In addition, electronic structure and optical properties of Cs2HgI4 have been studied. For the crystal under study, X-ray photoelectron core-level and valence-band spectra for pristine and Ar+-ion irradiated surfaces have been measured. The present X-ray photoelectron spectroscopy (XPS) results indicate that the Cs2HgI4 single crystal surface is very sensitive with respect to Ar+ ion-irradiation. In particular, Ar+ bombardment of the single crystal surface alters the elemental stoichiometry of the Cs2HgI4 surface. To elucidate peculiarities of the energy distribution of the electronic states within the valence-band and conduction-band regions of the Cs2HgI4 compound, we have performed first-principles band-structure calculations based on density functional theory (DFT) as incorporated in the WIEN2k package. Total and partial densities of states for Cs2HgI4 have been calculated. The DFT calculations reveal that the I p states make the major contributions in the upper portion of the valence band, while the Hg d, Cs p and I s states are the dominant contributors in its lower portion. Temperature dependence of the light absorption coefficient and specific electrical conductivity has been explored for Cs2HgI4 in the temperature range of 77-300 K. Main optical characteristics of the Cs2HgI4 compound have been elucidated by the first-principles calculations.

  14. 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. PMID:18496791

  15. A three-dimensional domain decomposition method for large-scale DFT electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Duy, Truong Vinh Truong; Ozaki, Taisuke

    2014-03-01

    With tens of petaflops supercomputers already in operation and exaflops machines expected to appear within the next 10 years, efficient parallel computational methods are required to take advantage of such extreme-scale machines. In this paper, we present a three-dimensional domain decomposition scheme for enabling large-scale electronic structure calculations based on density functional theory (DFT) on massively parallel computers. It is composed of two methods: (i) the atom decomposition method and (ii) the grid decomposition method. In the former method, we develop a modified recursive bisection method based on the moment of inertia tensor to reorder the atoms along a principal axis so that atoms that are close in real space are also close on the axis to ensure data locality. The atoms are then divided into sub-domains depending on their projections onto the principal axis in a balanced way among the processes. In the latter method, we define four data structures for the partitioning of grid points that are carefully constructed to make data locality consistent with that of the clustered atoms for minimizing data communications between the processes. We also propose a decomposition method for solving the Poisson equation using the three-dimensional FFT in Hartree potential calculation, which is shown to be better in terms of communication efficiency than a previously proposed parallelization method based on a two-dimensional decomposition. For evaluation, we perform benchmark calculations with our open-source DFT code, OpenMX, paying particular attention to the O(N) Krylov subspace method. The results show that our scheme exhibits good strong and weak scaling properties, with the parallel efficiency at 131,072 cores being 67.7% compared to the baseline of 16,384 cores with 131,072 atoms of the diamond structure on the K computer.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  17. 1H-1,2,4-diazaphospholes: Synthesis, structural characterization, and DFT calculation

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Wen; Ding, Ling-Yan; Wang, Bing-Qiang; He, Yao-Yun; Guo, Yue; Jia, Xue-Feng; Zheng, Wenjun

    2014-01-01

    A few 1H-1,2,4-diazaphospholes H[3,5-R2dp] (R = methyl (5a), p-tolyl (5b), 1-naphthyl (5c), 2-furanyl (5d), 2-thienyl (5e), and isopropyl (5f)) were prepared and structurally characterized by a substantial experimental modification of the synthetic protocol. The molecules of all compounds are linked into oligomers via the bridges of NH⋯N hydrogen bonds in solid state. The tetrameric feature of 5a, and 5d-f represents a new motif of hydrogen-bonded 1H-1,2,4-diazaphospholes in solid state. The DFT calculation at the B3LYP/6-311++G** level suggested the possible proton disorder with intermolecular solid state proton transfer (ISSPT) between 1H-1,2,4-diazaphosphole rings.

  18. Uncovering Intramolecular π-Type Hydrogen Bonds in Solution by NMR Spectroscopy and DFT Calculations.

    PubMed

    Mastrorilli, Piero; Gallo, Vito; Todisco, Stefano; Latronico, Mario; Saielli, Giacomo

    2016-06-01

    Reaction between the phosphinito bridged diplatinum species [(PHCy2 )Pt(μ-PCy2 ){κ(2) P,O-μ-P(O)Cy2 }Pt(PHCy2 )](Pt-Pt) (1), and (trimethylsilyl)acetylene at 273 K affords the σ-acetylide complex [(PHCy2 )(η(1) -Me3 SiC≡C)Pt(μ-PCy2 )Pt(PHCy2 ){κP-P(OH)Cy2 }](Pt-Pt) (2) featuring an intramolecular π-type hydrogen bond. Scalar and dipolar couplings involving the POH proton were detected by 2D NMR experiments. Relativistic DFT calculations of the geometry, relative energy, and NMR properties of model systems of 2 confirmed the structural assignment and allowed the energy of the π-type hydrogen bond to be estimated (ca. 22 kJ mol(-1) ). PMID:27097847

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

    PubMed

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

    2014-07-01

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

  20. 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.

  1. 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.

  2. 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.

  3. Theoretical and practical aspects of chemical functionalization of carbon nanofibers (CNFs): DFT calculations and adsorption study.

    PubMed

    Rokhina, Ekaterina V; Lahtinen, Manu; Makarova, Katerina; Jegatheesan, Veeriah; Virkutyte, Jurate

    2012-06-01

    The nitric acid-functionalized commercial carbon nanofibers (CNFs) were comprehensively studied by instrumental (XRD, BET, SEM, TGA) and theoretical (DFT calculations) methods. The detailed surface study revealed the variation in the characteristics of functionalized CNFs, such as a decreased (up to 34%) surface area and impacted structural, electronic and chemical properties. The effects of functional groups were studied by comparison with pristine nanofibers. The results showed that the C-C bond lengths of the modified CNFs varied significantly. Chemical functionalization altered the frontier orbitals of the pristine material, and therefore altered the nature of their interactions with other substances. Moreover, the pristine and modified CNFs were tested for the removal of phenol from aqueous solutions. It was observed that surface modification tuned the adsorption capacity of carbon nanofibers (up to 0.35 mmol g(-1)), whereas original fibers did not demonstrate any adsorption capacity of phenol. PMID:22209137

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  7. 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. PMID:24607466

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2011-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  11. 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. PMID:25682215

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  14. DFT Ab initio Calculation of Vibrational Frequencies in AsSe glass

    NASA Astrophysics Data System (ADS)

    Shrivastava, Keshav; Kassim, Hasan; Nazrul Rosli, Ahmad

    2008-03-01

    By using DFT double zeta wave functions, we calculated the structure, bond length (picometer, pm), frequencies(intensities)[degeneracy] for various clusters of arsenic selenide. Our results are as follows. (i) AsSe(diatomic) bond length 216pm, 244.0(1/cm). (ii) As2Se(linear) bond length 228.5 pm, frequencies 27.6(1.9) and 387.6(4.3). (iii) As2Se(triangular) As-Se 243.4 pm, As-As 223.3 pm, frequencies 237.3(2.4) and 332.4(0.05)(1/cm). (iv) As3Se (triangular) bond length 238.4 pm, frequencies 107.5 and 296(weak)(1/cm). (v) As4Se (square) bond length 250.2 pm, 58.5(0.04), 241.3(5.9)(1/cm). (vi) AsSe3 (triangular), bond length 231.2 pm, 75.9(0.003), 103.5(1.26)[2], 350.9(33.2)[2]. From this study we identify that linear As-Se-As for which the calculated frequency is 27.6(1/cm) is in agreement with the data of Nemanich, Phys. Rev. B 16, 1655(1977), J. C. Phillips et al Phys. Rev B 21, 5724(1980). We have successfully calculated several vibrational frequencies accurately which agree with the Raman data. *V. R. Devi et al J. Non-Cryst. Solids 351, 489(2005);353,111(2007)

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

    PubMed

    Sojka, Zbigniew; Pietrzyk, Piotr

    2006-03-13

    Density functional theory (DFT) calculations of EPR parameters and their structure sensitivity for selected surface paramagnetic species involved in oxidative dehydrogenation of methanol over silica grafted molybdenum catalyst were investigated. Two surface complexes, Mo(4c)/SiO2 and {O(-)-Mo(4c)}/SiO2, as well as *CH2OH radical trapped on the SiO2 matrix were taken as the examples. The spin-restricted zeroth order regular approximation (ZORA) implemented in the Amsterdam Density Functional suite was used to calculate the electronic g tensor for those species. The predicted values were in satisfactory agreement with experimental EPR results. Five different coordination modes of the *CH2OH radical on the silica surface were considered and the isotropic 13C, 17O, and 1H hyperfine coupling constants (HFCC) of the resultant surface complexes were calculated. Structure sensitivity of the HFCC values was discussed in terms of the angular deformations caused by hydrogen bonding with the silica surface. PMID:16488660

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

    NASA Astrophysics Data System (ADS)

    Sojka, Zbigniew; Pietrzyk, Piotr

    2006-03-01

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

  17. 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.

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

    PubMed

    Muthu, S; Elamuruguporchelvi, E; Varghese, Anitha

    2015-03-01

    The solid phase FTIR and FT-Raman spectra of 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate (25N2LCPA) have been recorded 450-4000cm(-1) and 100-4000cm(-1) respectively. The normal coordinate analysis was carried out to confirm the precision of the assignments. DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies and IR intensities. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31+G(d,p) basis set. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The Vibrational frequencies are calculated in the above method and are compared with experimental frequencies which yield good agreement between observed and calculated frequencies. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In addition, Frontiers molecular orbital and molecular electrostatic potential were computed by using Density Functional Theory (DFT) B3LYP/6-31+G(d,p) basis set. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. PMID:25544190

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  20. 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. PMID:24892542

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  3. Synthesis, crystal structure and ab initio/DFT calculations of a derivative of dithiophosphonates

    NASA Astrophysics Data System (ADS)

    Karakus, M.; Solak, S.; Hökelek, T.; Dal, H.; Bayrakdar, A.; Özdemir Kart, S.; Karabacak, M.; Kart, H. H.

    2014-03-01

    The compound 2 has been synthesized from the reaction of 2,4-Bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide and (R)-1-[3,5-Bis(trifloromethyl)phenyl]ethanol in toluene. The obtained crude dithiophosphonic acid 1 has been treated with the excess of N(C2H5)3 to give rise to 2, [(+HN(C2H5)3][(O-CH3CH-C6H3(CF3)2)(CH3OC6H4)PS2-]. The compound 2 has been characterized by using the spectroscopic methods such as IR, 1H, 13C, 31P NMR and structural analysing method such as X-ray crystallography. It crystallizes in the orthorhombic system, whose space group is P212121. It consists of a dithiophosphonate bridged methoxyphenyl and bis(triflorophenylethyl) groups and a triethylammonium moiety linked by Nsbnd H⋯S and Csbnd H⋯F hydrogen bonds. In the crystal structure, the C17H14F6O2PS2 molecule is elongated along the b-axis and stacked along the a-axis. The triethylammonium, N(CH2CH3)3, molecule fill in the cavities between the C17H14F6O2PS2 molecule. Moreover, ab initio methods based on Hartree-Fock (HF) and Density Functional Theory (DFT) calculations with the basis set of 6-31G(d) are also carried out to determine the molecular structural properties and to calculate FT-IR and NMR spectrum of the compound 2. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.

  4. Relativistic DFT Calculation of (119)Sn Chemical Shifts and Coupling Constants in Tin Compounds.

    PubMed

    Bagno, Alessandro; Casella, Girolamo; Saielli, Giacomo

    2006-01-01

    The nuclear shielding and spin-spin coupling constants of (119)Sn in stannane, tetramethylstannane, methyltin halides Me4-nSnXn (X = Cl, Br, I; n = 1-3), tin halides, and some stannyl cations have been investigated computationally by DFT methods and Slater all-electron basis sets, including relativistic effects by means of the zeroth order regular approximation (ZORA) method up to spin-orbit coupling. Calculated (119)Sn chemical shifts generally correlate well with experimental values, except when several heavy halogen atoms, especially iodine, are bound to tin. In such cases, calculated chemical shifts are almost constant at the scalar (spin-free) ZORA level; only at the spin-orbit level is a good correlation, which holds for all compounds examined, attained. A remarkable "heavy-atom effect", analogous to that observed for analogous alkyl halides, is evident. The chemical shift of the putative stannyl cation (SnH3(+)) has also been examined, and it is concluded that the spectrum of the species obtained in superacids is inconsistent with a simple SnH3(+) structure; strong coordination to even weak nucleophiles such as FSO3H leads to a very satisfactory agreement. On the contrary, the calculated (119)Sn chemical shift of the trimesitylstannyl cation is in very good agreement with the experimental value. Coupling constants between (119)Sn and halogen nuclei are also well-modeled in general (taking into account the large uncertainties in the experimental values); relativistic spin-orbit effects are again quite evident. Couplings to (13)C and (1)H also fall, on the average, on the same correlation line, but individual values show a significant deviation from the expected unit slope. PMID:26626377

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

    SciTech Connect

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

    2009-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  7. 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.

  8. Exchange constants and spin waves of MnV2 O 4 from first principles DFT calculations

    NASA Astrophysics Data System (ADS)

    Nanguneri, Ravindra; Savrasov, Sergey

    2011-03-01

    We present results of DFT calculations of exchange constants of the magnetic spinel Mn V2 O4 . The starting point is the one-particle eigenfunctions of the Kohn-Sham auxiliary Hamiltonian as a function of the self-consistent, converged charge density. Using linear response and perturbation theory, the exchange constants between the magnetic ions Mn and V are calculated in both the collinear and non-collinear, orbital-ordered phases of the spinel. The collinear exchanges have exchange constants proportional to the unit matrix, which means they are isotropic. On the other hand, the non-collinear exchanges have unequal diagonal elements and in addition have off-diagonal elements, revealing anisotropic magnetic interactions. The anisotropy is traced to the orbital-order and non-collinear spin structure of the low-temperature ground-state. We find that the interactions between the V atoms can sometimes be anti-ferromagnetic. The V atoms are located at the vertices of a corner-sharing tetrahedral lattice, commonly known as a pyrochlore lattice. AFM interactions on such a lattice are geometrically frustrated because all pair-wise bond energies cannot be simultaneously minimized with a classical spin configuration. It has been experimentally found that as the temperature is lowered, Mn V2 O4 undergoes a transition from a paramagnet with a cubic symmetry structure phase to a ferrimagnetic with cubic symmetry phase at 56 K.

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

    PubMed

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

    2016-01-01

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

  10. DFT+U calculation of the Cr K pre-edge structures in ZnCr2O4

    NASA Astrophysics Data System (ADS)

    Rozsályi, E.; Verger, L.; Cabaret, D.; Juhin, A.

    2016-05-01

    Zinc chromite ZnCr2O4 has been investigated by X-ray absorption near edge structure (XANES) spectroscopy at the Cr K-edge, with the objective of better understanding the origin of the electronic excitations giving rise to the pre-edge features. In particular, the origin of a third feature visible only in Cr-rich compounds of the ZnAl2O4-ZnCr2O4 solid solution is studied. Standard density functional theory (DFT) XANES calculations were first performed, then a Hubbard U parameter was included in an attempt to improve the relative peak positions by increasing the localization of the Cr 3d states. The origin of the pre-edge features in ZnCr2O4 has been analyzed using DFT+U calculations, local projected densities of states and the assignment of the spectral features for the dilute ZnAl2O4:Cr3+ compound. We show that DFT+U does not overcome the limitations of standard DFT in modeling the relative peak positions, and that approaches including advanced description of the electron-hole interaction are needed.

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

    PubMed

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

    2015-10-01

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

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

    SciTech Connect

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

    2010-12-15

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

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

    NASA Astrophysics Data System (ADS)

    Gökce, H.; Bahçeli, S.

    2014-07-01

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

  14. Study of electronic effects in a catalytic diode: DFT calculations and MEIRAS experiments

    NASA Astrophysics Data System (ADS)

    Deshlahra, Prashant

    The role of electron transfer between metal catalyst and its oxide support in modifying the binding of the molecules adsorbed on the catalyst surface is investigated using Pt/TiO2 catalytic diode as a novel model catalyst system. The effect of electron transfer is interpreted and demonstrated as that of creating an electric field at the metal-support interface. The effect of such electric fields is studied by using Density Functional Theory (DFT) calculations to simulate adsorption of different molecules under a uniform external electric field. Experimentally, the charge transfer at metal support junction and the resulting electric field is controlled by applying an external bias voltage to the catalytic diode. The effect of controlling the charge transfer on CO molecules used as probe adsorbates is studied using a multilayer enhanced reflection adsorption spectroscopy (MEIRAS) technique developed in this work. DFT calculations show that the sensitivity of adsorption energy of a molecule on a metal surface to the external electric field depends on its dipole moment and polarizability. The dipole moment varies significantly from one molecule to another, and changes with the surface adsorbate coverage due to the electrostatic interaction from neighboring adsorbates on the surface. Vibrational frequency of molecules shifting linearly with external electric field is shown to be a key experimental observable useful in the study of these effects. MEIRAS is a new form of the Fourier Transform Infrared (FTIR) spectroscopy performed in reflection mode, in which, the multilayer structure of the sample and its interaction with the incident infrared causes a large enhancement in the sensitivity. The mechanism of sensitivity enhancement is elucidated through experimental measurement of wavelength dependent reflectance of multilayer structures and theoretical optical analysis of infrared reflection on such structures. An experimental setup is developed for MEIRAS measurements

  15. 47 CFR 36.605 - Calculation of safety net additive.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 2 2011-10-01 2011-10-01 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...

  16. 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...

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

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 2 2012-10-01 2012-10-01 false Calculation of safety net additive. 36.605... § 36.605 Calculation of safety net additive. (a) “Safety net additive support.” Beginning January 1... costs, shall be eligible to receive safety net additive pursuant to paragraph (c) of this section....

  18. 47 CFR 36.605 - Calculation of safety net additive.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 2 2013-10-01 2013-10-01 false Calculation of safety net additive. 36.605... § 36.605 Calculation of safety net additive. (a) “Safety net additive support.” Beginning January 1... costs, shall be eligible to receive safety net additive pursuant to paragraph (c) of this section....

  19. 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.

  20. trans-Dichloro-bis-(arylazoimidazole)palladium(II): synthesis, structure, photoisomerization, and DFT calculation.

    PubMed

    Pratihar, P; Mondal, T K; Patra, A K; Sinha, C

    2009-04-01

    Reaction between PdCl(2) and 1-alkyl-2-(arylazo)imidazole (RaaiR') or 1-alkyl-2-(naphthyl-alpha/beta-azo)imidazole (alpha/beta-NaiR') under reflux in ethanol has isolated complexes of compositions Pd(RaaiR')(2)Cl(2) (5, 6) and Pd(alpha/beta-NaiR')(2)Cl(2) (7, 8). The X-ray structure determination of one of the molecules, Pd(alpha-NaiBz)(2)Cl(2) (7c), has reported a trans-PdCl(2) configuration, and alpha-NaiBz acts as monodentate N(imidazole) donor ligand. The spectral (IR, UV-vis, (1)H NMR) data support the structure. UV light irradiation (light source: Perkin-Elmer LS 55 spectrofluorimeter, Xenon discharge lamp, lambda = 360-396 nm) in a MeCN solution of the complexes shows E-to-Z isomerization of the coordinated azoimidazole unit. The reverse transformation, Z-to-E, is very slow with visible light irradiation. Quantum yields (phi(E-->Z)) of E-to-Z isomerization are calculated, and phi is lower than that of the free ligand but comparable with those of Cd(II) and Hg(II) complexes of the same ligand. The Z-to-E isomerization is a thermally induced process. The activation energy (E(a)) of Z-to-E isomerization is calculated by controlled-temperature experimentation. cis-Pd(azoimidazole)Cl(2) complexes (azomidazole acts as N(imidazole) and N(azo) chelating ligand) do not respond upon light irradiation, which supports the idea that the presence of noncoordinated azo-N to make free azo (-N=N-) function is important to reveal photochromic activity. DFT calculation of Pd(alpha-NaiBz)(2)Cl(2) (7c) has suggested that the HOMO of the molecule is constituted of Pd (32%) and Cl (66%), and hence photo excitation may use the energy of Pd and Cl instead of that of the photofunctional -N=N-Ar motif; thus, the rate of photoisomerization and quantum yield decrease versus the free ligand values. PMID:19253980

  1. 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. PMID:25844936

  2. 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...

  3. 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. PMID:24845873

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  5. 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.

  6. 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.

  7. 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

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

    PubMed

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

    2016-01-01

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

  9. 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.

  10. Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jabłońska, Agnieszka; Ponikiewski, Łukasz; Ejsmont, Krzysztof; Herman, Aleksander; Dołęga, Anna

    2013-12-01

    The reaction of silicon disulfide with alkylphenols yields tetraphenoxysilane, cyclodisilthiane and silanethiol. The outcome of the reaction depends on the presence of the steric hindrance in the ortho position on the reacting phenol. New products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane or electrostatic dipole-dipole attraction in cyclodisilthiane and silanethiol. The S-H---π interactions in the obtained silanethiol are analyzed with the use of DFT/GGA BLYP-D XC potentials. The energy of intramolecular S-H---π interaction is estimated.

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

    NASA Astrophysics Data System (ADS)

    Sharma, Shatendra; Sharma, Jyotsna; Sharma, Yogita

    2016-05-01

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

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

    PubMed

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

    2016-01-25

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

  13. Analysis of UV and vibrational spectra (FT-IR and FT-Raman) of hexachlorocyclotriphosphazene based on normal coordinate analysis, MP2 and DFT calculations.

    PubMed

    Zoghaib, Wajdi M; Husband, John; Soliman, Usama A; Shaaban, Ibrahim A; Mohamed, Tarek A

    2013-03-15

    The Raman (1400-100 cm(-1)) and infrared (4000-400 cm(-1)) of solid hexachlorocyclotriphosphazene, P(3)N(3)Cl(6) (HCCTP) were recorded. The conformational energies were calculated using MP2 and DFT (B3LYP and B3PW91) methods utilizing a variety of basis sets up to 6-311+G(d). On the basis of D(3h) symmetry, the simulated vibrational spectra of P(3)N(3)Cl(6) from MP2 and DFT methods were in excellent agreement with those obtained experimentally. Additionally, Frontier Molecular Orbitals and electronic transitions were predicted using steady state and time dependent DFT(B3LYP)/PCM calculations respectively, each employing the 6-311+G(d,p) optimized structural parameters. The predicted wavelengths were in excellent agreement with experimental values when CH(2)Cl(2) was used as solvent. The (14)N and (31)P chemical shifts were predicted with B3LYP/6-311+G(2d,p) calculations using the GIAO technique with solvent effect modeled using the PCM method. The computed structural parameters of the planar P(3)N(3)Cl(6) (D(3h)) agree well with experimental values from both X-ray and electron diffraction data with slight distortions observed due to lattice defects in the solid phase. The experimental/computational results favor a slightly distorted D(3h) symmetry for the title compound in the gas and solid phases and in solution (τPNPN and τNPNP ranged from 0.018° to 0.90°). Aided by normal coordinate analysis, and the simulated vibrational spectra utilizing MP2, B3LYP and B3PW91 methods at 6-31G(d) basis set, revised and complete vibrational assignments for all fundamentals are provided herein. PMID:23348197

  14. Analysis of UV and vibrational spectra (FT-IR and FT-Raman) of hexachlorocyclotriphosphazene based on normal coordinate analysis, MP2 and DFT calculations

    NASA Astrophysics Data System (ADS)

    Zoghaib, Wajdi M.; Husband, John; Soliman, Usama A.; Shaaban, Ibrahim A.; Mohamed, Tarek A.

    2013-03-01

    The Raman (1400-100 cm-1) and infrared (4000-400 cm-1) of solid hexachlorocyclotriphosphazene, P3N3Cl6 (HCCTP) were recorded. The conformational energies were calculated using MP2 and DFT (B3LYP and B3PW91) methods utilizing a variety of basis sets up to 6-311+G(d). On the basis of D3h symmetry, the simulated vibrational spectra of P3N3Cl6 from MP2 and DFT methods were in excellent agreement with those obtained experimentally. Additionally, Frontier Molecular Orbitals and electronic transitions were predicted using steady state and time dependent DFT(B3LYP)/PCM calculations respectively, each employing the 6-311+G(d,p) optimized structural parameters. The predicted wavelengths were in excellent agreement with experimental values when CH2Cl2 was used as solvent. The 14N and 31P chemical shifts were predicted with B3LYP/6-311+G(2d,p) calculations using the GIAO technique with solvent effect modeled using the PCM method. The computed structural parameters of the planar P3N3Cl6 (D3h) agree well with experimental values from both X-ray and electron diffraction data with slight distortions observed due to lattice defects in the solid phase. The experimental/computational results favor a slightly distorted D3h symmetry for the title compound in the gas and solid phases and in solution (τPNPN and τNPNP ranged from 0.018° to 0.90°). Aided by normal coordinate analysis, and the simulated vibrational spectra utilizing MP2, B3LYP and B3PW91 methods at 6-31G(d) basis set, revised and complete vibrational assignments for all fundamentals are provided herein.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

    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 (1)H and (13)C 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. PMID:22617215

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  20. 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.

  1. 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).

  2. 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.

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

    PubMed

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

    2015-02-01

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

  4. 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.

  5. Investigation of hydrogen bond in binary mixture (pyridine + propionic acid) by spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chen, Yuan-Zheng; Liu, Tian-Yuan; Qu, Guan-Nan; Sun, Shang; Gao, Shu-Qin; Zhou, Mi; Sun, Chen-Lin; Li, Zuo-Wei

    2011-11-01

    This Letter analyzed the hydrogen bond between pyridine and propionic acid using Raman and infrared spectra as a function of concentrations. The wavenumber shift and line width change were investigated to analyze the effects of hydrogen bond on the ring breathing mode and the triangle mode of pyridine. Density functional theory (DFT) at the B3LYP/6-31++G (d,p) level was performed on the binary solution. The simulated vibrational Raman spectra obtained the experimentally observed spectral features about the blue-shifted of the ring breathing mode. Furthermore, the effect of the hydrogen bond on Fermi Resonance (FR) was discussed.

  6. 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.

  7. DFT and ab initio calculations of the vibrational frequencies and visible spectra of triazenes derived from cyclic amines

    NASA Astrophysics Data System (ADS)

    Dabbagh, Hossein A.; Teimouri, Abbas; Chermahini, Alireza Najafi; Shiasi, Rezvan

    2007-06-01

    We present a detailed analysis of the structural, infrared spectra and visible spectra of the 4-substituted aminoazo-benzenesulfonyl azides. The preparation of 4-sulfonyl azide benzenediazonium chloride with cyclic amines of various ring sizes (pyrrolidine, piperidine, 4-methylpiperidine, N-methylpiperazine, morpholine and hexamethyleneimine) have been investigated theoretically by performing HF and DFT levels of theory using the standard 6-31G* basis set. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FT-IR spectra are assigned modes based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with the calculations.

  8. Interpreting the Paramagnetic NMR Spectra of Potential Ru(III) Metallodrugs: Synergy between Experiment and Relativistic DFT Calculations.

    PubMed

    Novotný, Jan; Sojka, Martin; Komorovsky, Stanislav; Nečas, Marek; Marek, Radek

    2016-07-13

    Ruthenium-based compounds are potential candidates for use as anticancer metallodrugs. The central ruthenium atom can be in the oxidation state +2 (e.g., RAPTA, RAED) or +3 (e.g., NAMI, KP). In this study we focus on paramagnetic NAMI analogs of a general structure [4-R-pyH](+)trans-[Ru(III)Cl4(DMSO)(4-R-py)](-), where 4-R-py stands for a 4-substituted pyridine. As paramagnetic systems are generally considered difficult to characterize in detail by NMR spectroscopy, we performed a systematic structural and methodological NMR study of complexes containing variously substituted pyridines. The effect of the paramagnetic nature of these complexes on the (1)H and (13)C NMR chemical shifts was systematically investigated by temperature-dependent NMR experiments and density-functional theory (DFT) calculations. To understand the electronic factors influencing the orbital (δ(orb), temperature-independent) and paramagnetic (δ(para), temperature-dependent) contributions to the total NMR chemical shifts, a relativistic two-component DFT approach was used. The paramagnetic contributions to the (13)C NMR chemical shifts are correlated with the distribution of spin density in the ligand moiety and the (13)C isotropic hyperfine coupling constants, Aiso((13)C), for the individual carbon atoms. To analyze the mechanism of spin distribution in the ligand, the contributions of molecular spin-orbitals (MSOs) to the hyperfine coupling constants and the spatial distribution of the z-component of the spin density in the MSOs calculated at the relativistic four-component DFT level are discussed and rationalized. The significant effects of the substituent and the solvent on δ(para), particularly the contact contribution, are demonstrated. This work should contribute to further understanding of the link between the electronic structure and the NMR chemical shifts in open-shell systems, including the ruthenium-based metallodrugs investigated in this account. PMID:27312929

  9. Electron, hole and exciton self-trapping in germanium doped silica glass from DFT calculations with self-interactions correction

    SciTech Connect

    Du, Jincheng; Corrales, Louis R.; Tsemekhman, Kiril L.; Bylaska, Eric J.

    2007-02-01

    We performed density functional theory (DFT) calculations of electron, hole and exciton self-trapping in germanium doped silica glass to understand the refractive index change in these glasses induced by UV irradiation. The local structure relaxation and excess electron density distribution upon trapping of the above species were calculated. The results show that both trapped exciton and electron are highly localized on germanium ion and, to some extent, on its oxygen neighbors. Exciton self-trapping is found to lead to the formation of Ge E’ center and non-bridging hole center. Electron trapping changes the GeO4 tetrahedron structure into trigonal bi-pyramid with the majority of the excess electron density located along the equatorial line. Self-trapped hole is localized on bridging oxygen ions that are not coordinated to germanium atoms and leads to elongation of the Si-O bonds and change of the Si-O-Si bond angles. We did comparative study of standard DFT vs. DFT with a hybrid PBE0 exchange and correlation functional. The results show that the two methods give qualitatively similar relaxed structure and charge distribution for the electron and exciton trapping in germanium doped silica glass; however, only using the PBE0 functional reproduces the hole self-trapping. This research is supported by the Divisions of Chemical Science, Office of Basic Energy Sciences, US Department of Energy. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The EMSL is funded by DOE’s Office of Biological and Environmental Research. The pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  10. A novel 3-acetoxy-2-methyl-N-(4-methoxyphenyl)benzamide: Molecular structural describe, antioxidant activity with use X-ray diffractions and DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Cakmak, Sukriye; Dege, Necmi; Kutuk, Halil; Odabasoglu, Mustafa; Kepekci, R. Aysun

    2015-11-01

    In this work, the structure of a novel 3-acetoxy-2-methyl-N-(4-methoxyphenyl) benzamide, was analyzed both experimentally and theoretically using three methods, X-ray single crystal diffraction technique, IR spectroscopy, and quantum chemical computation. The X-ray diffraction analysis indicates that 3-acetoxy-2-methyl-N-(4-methoxyphenyl) benzamide molecula crystallizes in a triclinic system (space group P-1) and the calculated lattice constants are, a = 5.1205 ± 0.0004 Å, b = 9.8598 ± 0.0008 Å, c = 15.3398 ± 0.0013 Å, α = 80.79(7)°, β = 83.142(6)°, γ= 85.411(6)°, and Z = 2. In addition, the molecular geometry and vibrational frequencies of the title compound in ground state have been calculated using density functional theory (DFT) at B3LYP level 6-31G+(d,p) basis set. The geometrical parameters of the title compound obtained from XRD studies are good in agreement with the calculated values. The electronic properties, such as HOMO and LUMO energies and thermodynamic properties were calculated with DFT (using B3LYP/6-31G+(d,p) basis set) approach. To estimate the chemical reactivity of the molecule, the molecular electrostatic potential (MEP) surface map of the title molecule and PES scan were investigated with theoretical calculations at the B3LYP/6-31+G(d,p) and B3LYP/3-21G levels, respectively. Antioxidant properties are determined using DPPH free radical scavenging test.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  12. Understanding cage effects in imidazolium ionic liquids by 129Xe NMR: MD simulations and relativistic DFT calculations.

    PubMed

    Saielli, Giacomo; Bagno, Alessandro; Castiglione, Franca; Simonutti, Roberto; Mauri, Michele; Mele, Andrea

    2014-12-01

    (129)Xe NMR has been recently employed to probe the local structure of ionic liquids (ILs). However, no theoretical investigation has been yet reported addressing the problem of the dependence of the chemical shift of xenon on the cage structure of the IL. Therefore, we present here a study of the chemical shift of (129)Xe in two ionic liquids, [bmim][Cl] and [bmim][PF6], by a combination of classical MD simulations and relativistic DFT calculations of the xenon shielding constant. The bulk structure of the two ILs is investigated by means of the radial distribution functions, paying special attention to the local structure, volume, and charge distribution of the cage surrounding the xenon atom. Relativistic DFT calculations, based on the ZORA formalism, on clusters extracted from the trajectory files of the two systems, yield an average relative chemical shift in good agreement with the experimental data. Our results demonstrate the importance of the cage volume and the average charge surrounding the xenon nucleus in the IL cage as the factors determining the effective shielding. PMID:25394282

  13. 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.

  14. 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).

  15. 1-Pentamethylbenzyl-3-nbuthylbenzimidazolesilver(I)bromide complex: Synthesis, characterization and DFT calculations

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  16. 1-Pentamethylbenzyl-3-(n)buthylbenzimidazolesilver(I)bromide complex: synthesis, characterization and DFT calculations.

    PubMed

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

    2014-01-01

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

  17. Study of structural, electronic and optical properties of tungsten doped bismuth oxychloride by DFT calculations.

    PubMed

    Yang, Wenjuan; Wen, Yanwei; Chen, Rong; Zeng, Dawen; Shan, Bin

    2014-10-21

    First-principle calculations have been carried out to investigate structural stabilities, electronic structures and optical properties of tungsten doped bismuth oxychloride (BiOCl). The structures of substitutional and interstitial tungsten, and in the form of WO6-ligand-doped BiOCl are examined. The substitutional and interstitial tungsten doping leads to discrete midgap states within the forbidden band gap, which has an adverse effect on the photocatalytic properties. On the other hand, the WO6-ligand-doped BiOCl structure induces a continuum of hybridized states in the forbidden gap, which favors transport of electrons and holes and could result in enhancement of visible light activity. In addition, the band gap of WO6-BiOCl decreases by 0.25 eV with valence band maximum (VBM) shifting upwards compared to that of pure BiOCl. By calculating optical absorption spectra of pure BiOCl and WO6-ligand-doped BiOCl structure, it is found that the absorption peak of the WO6-ligand-doped BiOCl structure has a red shift towards visible light compared with that of pure BiOCl, which agrees well with experimental observations. These results reveal the tungsten doped BiOCl system as a promising material in photocatalytic decomposition of organics and water splitting under sunlight irradiation. PMID:25179434

  18. Radical reactions of C 60Ph 5Cl: EPR study and DFT calculations

    NASA Astrophysics Data System (ADS)

    Kalina, O. G.; Tumanskii, B. L.; Chistyakov, A. L.; Stankevich, I. V.; Birkett, P. R.; Taylor, R.

    2003-10-01

    UV-irradiation of a toluene solution of C 60Ph 5Cl leads to the formation of the stable rad C 60Ph 5 cyclopentadienyl-type fullerenyl radical. Under UV-irradiation of a toluene solution of C 60Ph 5Cl containing Hg[P(O)(OPr i) 2] 2 (Pr i=CH(CH 3) 2), three isomers of the adducts of phosphoryl radicals with C 60Ph 5Cl are formed. Density functional (DFT) approach with the B3LYP functional was used for estimating of the enthalpies of the formation and hyperfine coupling constants for all possible adducts of phosphoryl radicals with C 60Ph 5Cl. Biradical particles rad C 60Ph 5[P(O)(OPr i) 2]- rad C 60Ph 5[P(O)(OPr i) 2] with a distance between unpaired electrons of about 10.5 Å, are also obtained.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  20. 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.

  1. 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.

  2. 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.

  3. Structure, bonding and physical properties of tetragonal and orthorhombic SiS{sub 2} from (hybrid) DFT calculations

    SciTech Connect

    Zwijnenburg, Martijn A. Bell, Robert G.; Cora, Furio

    2008-09-15

    The energetics, structure and physical properties of tetragonal and orthorhombic SiS{sub 2} were calculated by periodic density functional theory (DFT) calculations, using both localized orbital and projected augmented wave basis-sets. All methods applied agree upon the relative energies of the different polymorphs but show differences in the predicted geometries, which are minimized upon improving the basis-set quality. The hybrid PBE0 functional was found to give the best match between experimental and calculated structures. When comparing SiS{sub 2} with its much better studied oxide analog silica, we observe that upon substituting sulphur for oxygen, the energy landscape changes dramatically. Other effects of changing S for O are found to be smaller Si-X-Si angles, a broader distribution of X-Si-X angles, a more flexible framework and a significantly reduced band gap. The latter is in line with the experimental observation of photoluminescence in related GaGeS{sub 2} compounds and suggests that SiS{sub 2} might find application in UV light emitting diodes. Finally, a comparison of the maximally localized Wannier functions demonstrates that the Si-S bonds in SiS{sub 2} have a considerably more covalent character than the Si-O bonds in silica. - Graphical abstract: Periodic DFT calculations were employed to study the (physical) properties of tetragonal and orthorhombic SiS{sub 2}. The results obtained were compared with those for SiS{sub 2} better studied oxide analog silica and demonstrate large changes in the materials' energy landscape, nature of bonding, flexibility and band gap, upon substitution of sulphur for oxygen.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    DOE PAGESBeta

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

    2014-11-01

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

  6. 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.

  7. Dispersion of the linear and nonlinear optical susceptibilities of Bismuth subcarbonate Bi2O2CO3: DFT calculations

    NASA Astrophysics Data System (ADS)

    Reshak, A. H.; Auluck, S.

    2014-12-01

    The dispersion of the linear and nonlinear optical susceptibilities of bismuth subcarbonate Bi2O2CO3 are calculated using density functional theory (DFT). We have employed the state-of-art all-electron full potential linearized augmented plane wave (FP-LAPW) method. Calculations are performed within the recently modified Becke-Johnson potential (mBJ) to obtain the self consistency conditions. The calculated linear optical susceptibilities exhibit a considerable anisotropy which is useful for second harmonic generation (SHG) and optical parametric oscillation (OPO). The calculated absorption coefficient show good agreement with the available experimental data. The values of calculated uniaxial anisotropy δɛ = -0.168 and the birefringence Δn(0) = 0.166 indicate considerable anisotropy. The calculated SHG of the dominant component |χ322(2) (ω) | is about d32 = 5.3 pm/V at λ = 1064 nm (1.165 eV) which is in excellent agreement with the available experimental data (d32 = 5.49 pm/V) obtained using pulsed Nd:YAG laser at wavelength λ = 1064 nm (10 ns, 3 mj 10 kHz). To analyze the origin of the high SHG of bismuth subcarbonate Bi2O2CO3 we have correlated the features of |χ322(2) (ω) | spectra with the features of ɛ2(ω) spectra as a function of ω/2 and ω.

  8. 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.

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

    PubMed

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

    2008-11-01

    Oxindole alkaloids, isolated from the bark of Uncaria tomentosa [Willd. ex Schult.] Rubiaceae, are considered to be responsible for the biological activity of this herb. Five pentacyclic and two tetracyclic alkaloids were studied by solid-state NMR and theoretical GIAO DFT methods. The (13)C and (15)N CPMAS NMR spectra were recorded for mitraphylline, isomitraphylline, pteropodine (uncarine C), isopteropodine (uncarine E), speciophylline (uncarine D), rhynchophylline and isorhynchophylline. Theoretical GIAO DFT calculations of shielding constants provide arguments for identification of asymmetric centers and proper assignment of NMR spectra. These alkaloids are 7R/7S and 20R/20S stereoisomeric pairs. Based on the (13)C CP MAS chemical shifts the 7S alkaloids (delta C3 70-71ppm) can be easily and conveniently distinguished from 7R (deltaC3 74.5-74.9ppm), also 20R (deltaC20 41.3-41.7ppm) from the 20S (deltaC20 36.3-38.3ppm). The epiallo-type isomer (3R, 20S) of speciophylline is characterized by a larger (15)N MAS chemical shift of N4 (64.6ppm) than the allo-type (3S, 20S) of isopteropodine (deltaN4 53.3ppm). (15)N MAS chemical shifts of N1-H in pentacyclic alkaloids are within 131.9-140.4ppm. PMID:19019638

  10. Molecular structure of 2-chloromethyl-1H-benzimidazole hydrochloride: Single crystal, spectral, biological studies, and DFT calculations

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    In the present work, structural studies on 2-chloromethyl-1H-benzimidazole hydrochloride have been performed extensively by X-ray crystallography, 1H NMR, FT-IR, UV/vis, and elemental analysis. The title compound crystallizes in a monoclinic space group P21/c with a = 7.1982 (3) Å, b = 9.4513 (5) Å, c = 14.0485 (7) Å and β = 102.440 (3)° forming an infinite chain structure parallel to " b" axis through the intermolecular hydrogen bond. Optimized geometrical structure, harmonic vibrational frequencies, natural bonding orbital (NBO) and frontier molecular orbitals (FMO) were obtained by DFT/B3LYP method combined with 6-31G(d) basis set. TD-DFT calculations help to assign the electronic transitions. The 1H NMR chemical shifts were computed at the B3LYP/6-311 + G(2d,p) level of theory in different solvents by applying GIAO method using the polarizable continuum model (PCM). The title compound was screened for its antibacterial activity referring to Tetracycline as a standard antibacterial agent.

  11. STEPWISE HYDRATION OF CELLOBIOSE BY DFT METHODS: 1. CONFORMATIONAL AND STRUCTURAL CHANGES BROUGHT ABOUT BY THE ADDITION OF ONE TO FOUR WATER MOLECULES.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous density-functional theory (DFT) calculations found that the anti (or "flipped") form of cellobiose (with the H1 and H4' hydrogen atoms on opposite sides of the pseudo-plane formed by the sugar rings) is more stable in vacuo than the syn (or "normal") conformation most often observed in crys...

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

    PubMed

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

    2015-12-01

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

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

    PubMed

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

    2014-03-25

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

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

    PubMed

    Xing, Lidan; Borodin, Oleg

    2012-10-01

    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. PMID:22885926

  15. NIR surface enhanced Raman spectroscopy and bands assignment by DFT calculations of non-natural β-amino acids

    NASA Astrophysics Data System (ADS)

    Iliescu, T.; Maniu, D.; Chis, V.; Irimie, F. D.; Paizs, Cs.; Tosa, M.

    2005-04-01

    FT-Raman and NIR surface-enhanced Raman (SER) spectroscopies have been applied to the vibrational characterization of non-natural β-amino acids, 3-amino-3-(furan-2yl)-propionic acid and 3-amino-3-[(5-benzothiazole-2yl)-furan-2yl]-propionic acid. Semiempirical and density-functional theory (DFT) calculations on both amino acids in their zwitterionic forms have been performed in order to find the optimized structure and to compute the vibrational spectra. The NIR SER spectra in silver hydrosol and Ag-coated filter paper have been recorded, compared and analyzed. Good SER spectra were obtained at the pH values where dipolar ion structures are present proving the chemisorption of β-amino acid molecules on the silver surface via positively charged NH3+ group. The carboxylate anion of both β-amino acids are parallel oriented, whereas the plane of rings is oriented perpendicular to the silver surface.

  16. Equation of state and stability of metal crystals at high pressure by DFT calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2013-06-01

    In this work we present ab initio equation-of-state calculations for crystals of some metals. Density functional theory at finite temperature (VASP code) is used to obatin the properties of electrons; lattice is simulated in quasi-harmonic approximation at non-zero temperature of electrons. Anharmonic effects are taken into account by the thermal expansion of a crystal. All calculations were performed for aluminum, copper and gold. We compare our results with available shock-wave data in crystal phase, including isentropic expansion. The melting curves are calculated by different criteria; the effect of different temperatures of electrons and ions is taken into account. Also we determine thermodynamic and kinetic boundaries of stability of crystals. Our calculations demonstrate that ab initio approaches can be used to theoretically reconstruct thermodynamically complete EOS of metallic crystals. This work was supported by RFBR grant 12-08-31475 mol a.

  17. 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.

  18. Insight into insulator-to-metal transition of sulfur-doped silicon by DFT calculations.

    PubMed

    Zhao, Zong-Yan; Yang, Pei-Zhi

    2014-09-01

    Using density functional theory calculations, the mechanism of insulator-to-metal transition of S-doped Si has been systematically investigated. The calculated crystal structure indicates that the gentle lattice distortion is caused by sulfur doping, and this doping effect is gradually weakened with the increase of sulfur concentration. Two distinct impurity energy levels in the band gap are induced by sulfur doping, and their position and width are linearly varying along with the increase of sulfur concentration. Owing to the overlap and dispersion of these impurity energy levels, the insulator-to-metal transition occurs at the sulfur concentration of 2.095 × 10(20) cm(-3), which is consistent with the experimental measurement. Moreover, the defect states related with sulfur doping show delocalization features and are more outstanding at the higher sulfur concentration. The calculated results suggest that S-hyperdoped Si is a suitable candidate for intermediate band solar cells. PMID:25019287

  19. Antiaromatic character of 16 π electron octaethylporphyrins: magnetically induced ring currents from DFT-GIMIC calculations.

    PubMed

    Fliegl, Heike; Pichierri, Fabio; Sundholm, Dage

    2015-03-19

    The magnetically induced current density susceptibility, also called current density, has been calculated for a recently synthesized octaethylporphyrin (OEP) zinc(II) dication with formally 16 π electrons. Numerical integration of the current density passing selected chemical bonds yields the current pathway around the porphyrinoid ring and the strength of the ring current. The current strengths show that the OEP-Zn(II) dication is strongly antiaromatic, as also concluded experimentally. The calculation of the ring current pathway shows that all 24 π electrons participate in the transport of the ring current because the current splits into inner and outer branches of practically equal strengths at the four pyrrolic rings. The corresponding neutral octaethylporphyrinoid without Zn and inner hydrogens is found to be antiaromatic, sustaining a paratropic ring current along the inner pathway with 16 π electrons. The neutral OEP-Zn(II) molecule with formally 18 π electrons is found to be almost as aromatic as free-base porphyrin. However, also in this case, all 26 π electrons contribute to the ring current, as for free-base porphyrin. A comparison of calculated and measured (1)H NMR chemical shifts is presented. The current strength susceptibility under experimental conditions has been estimated by assuming a linear relation between experimental shielding constants and calculated current strengths. PMID:25141236

  20. 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. PMID:26584368

  1. 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.

  2. DFT calculations of triethyl and trimethyl orthoacetate elimination kinetics in the gas phase.

    PubMed

    Márquez, Edgar; Mora, José R; Cordova, Tania; Chuchani, Gabriel

    2009-03-19

    The reaction paths for the gas-phase molecular elimination of triethyl and trimethyl orthoesters were examined at B3LYP/6-31G(d,p), B3LYP/6-31G++(d,p), B3PW91/6-31G(d,p), B3PW91++G(d,p), MPW1PW91/6-31G(d,p), and MPW1PW91/6-31++G(d,p) levels of theory. The thermal decomposition of ethyl and methyl orthoesters involves similar transition state configurations in a four-membered ring arrangement. Products formed are ethanol and the corresponding unsaturated ketal for ethyl orthoesters, while in methyl orthoesters are methanol and the corresponding unsaturated ketal. Calculated thermodynamic and kinetic parameters from B3LYP calculations were found to be in good agreement with the experimental values. The calculated data imply the polarization of the C3-O4, in the direction C3(delta+)...O4(delta-), is rate determining. The NBO charges, bond indexes, and synchronicity parameters suggest the elimination reactions of ethyl orthoesters occur through a more polar asynchronic mechanism compared to methyl orthoesters. PMID:19222178

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

    NASA Astrophysics Data System (ADS)

    Rad, Ali Shokuhi

    2016-03-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2015-02-01

    In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated. PMID:25440584

  6. 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.

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  10. Iron-Scytonemin Complexes: DFT Calculations on New UV Protectants for Terrestrial Cyanobacteria and Astrobiological Implications

    NASA Astrophysics Data System (ADS)

    Varnali, Tereza; Edwards, Howell G. M.

    2010-09-01

    Cyanobacterial colonies produce the radiation-protectant biomolecule scytonemin as part of their response strategy for survival in environmentally stressed conditions in hot and cold deserts. These colonies frequently use sandstone rocks as host matrices for subsurface colonization, which is accompanied by a zone of depletion of iron and transportation of iron compounds to the mineral surface. It is suggested that an iron-scytonemin complex could feature in this survival strategy and facilitate the movement of iron through the rock. Calculations were as host matrices for subsurface colonization, which is accompanied by a zone of depletion of iron and transportation of iron compounds to the mineral surface. It is suggested that an iron-scytonemin complex could feature in this survival strategy and facilitate the movement of iron through the rock. Calculations were carried out on several hypothetical iron-scytonemin complexes to evaluate the most stable structure energetically and examine the effect of the complexation of the biomolecule upon the electronic absorption characteristics of the radiation-protectant species. The implications for extraterrestrial planetary detection and analytical monitoring of an iron-scytonemin complex are assessed.

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

    SciTech Connect

    Aras, Mehmet; Kılıç, Çetin

    2014-07-28

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

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

    NASA Astrophysics Data System (ADS)

    Aras, Mehmet; Kılıç, ćetin

    2014-07-01

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

  13. Direct comparison between two γ-alumina structural models by DFT calculations

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

    We selected two important γ-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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  16. DFT Calculation of Vibrational Frequencies of FeCoB m-RAM

    NASA Astrophysics Data System (ADS)

    Ling, Lee Li; Jesudason, Christopher; Shrivastava, Keshav N.

    2010-07-01

    The present available random access memory materials are semiconductors. It is proposed to develop magnetoresistance based random access memory (m-RAM) materials. Hence, we consider an alloy of Fe, Co and B which will be strongly magnetic and work well as a memory device. We calculate the vibrational frequencies of clusters of atoms of Fe, Co and B. The larger vibrational frequencies indicate larger force constants. The result show that CoB3Fe to have the largest vibrational frequency of 1293.03 cm-1 whereas BFeCo2 has 509.59 cm-1. We identify the ratio of constituents and the structures which have large force constant. Hence, CoB3Fe is better than BFeCo2. The cluster formation depends on the method of quenching. Hence, method of preparation can be modified to achieve large force constants.

  17. Four-Component Relativistic DFT Calculations of (13)C Chemical Shifts of Halogenated Natural Substances.

    PubMed

    Casella, Girolamo; Bagno, Alessandro; Komorovsky, Stanislav; Repisky, Michal; Saielli, Giacomo

    2015-12-14

    We have calculated the (13)C NMR chemical shifts of a large ensemble of halogenated organic molecules (81 molecules for a total of 250 experimental (13)C NMR data at four different levels of theory), ranging from small rigid organic compounds, used to benchmark the performance of various levels of theory, to natural substances of marine origin with conformational degrees of freedom. Carbon atoms bonded to heavy halogen atoms, particularly bromine and iodine, are known to be rather challenging when it comes to the prediction of their chemical shifts by quantum methods, due to relativistic effects. In this paper, we have applied the state-of-the-art four-component relativistic density functional theory for the prediction of such NMR properties and compared the performance with two-component and nonrelativistic methods. Our results highlight the necessity to include relativistic corrections within a four-component description for the most accurate prediction of the NMR properties of halogenated organic substances. PMID:26541625

  18. DFT calculation of the electronic properties of fluorene-1,3,4-thiadiazole oligomers.

    PubMed

    Sánchez-Bojorge, Nora Aydeé; Rodríguez-Valdez, Luz María; Flores-Holguín, Norma

    2013-09-01

    Thiadiazole derivatives have been widely employed in the areas of pharmaceutical, agricultural, industrial, and polymer chemistry. The electronic and molecular structures of thiadiazoles are of interest because they have an equal number of valence electrons and similar molecular structures to thiophenes, which are currently used in the construction of organic solar cells due to their relatively high hole mobilities and good light-harvesting properties. For this reason, the electronic properties of fluorene-1,3,4-thiadiazole oligomers warrant investigation. In the present work, the structure of fluorene-1,3,4-thiadiazole with one thiadiazole unit in the structure was analyzed. This molecule was then expanded until there were 10 thiadiazole units in the structure. The band gap, HOMO and LUMO distributions, and absorption spectrum were analyzed for each molecule. All calculations were performed by applying the B3LYP/6-31G(d) chemical model in the Gaussian 03W and GaussView software packages. The electronic properties were observed to significantly enhance as the number of monomeric units increased, which also caused the gap energy to decrease from 3.51 eV in the oligomer with just one thiadiazole ring to 2.33 eV in the oligomer with 10 units. The HOMO and LUMO regions were well defined and separated for oligomers with at least 5 monomer units of thiadiazole. PMID:23722558

  19. 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.

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

    SciTech Connect

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

    2004-10-01

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

  1. 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.

  2. 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+). PMID:24797021

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

    PubMed

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

    2016-08-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2012-07-01

    One new and six known triterpene xylosides were isolated from Cimicifuga racemosa (black cohosh, Actaea racemosa). The structure of a new compound, designated as isocimipodocarpaside (1), was established to be (24S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10-seco-9,19-cyclolanost-1(10),7(8),9(11)-trien 3-O-β-d-xylopyranoside, by means of (1)H and (13)C NMR, IR and Raman spectroscopies and Mass Spectrometry. The six known compounds are: 23-epi-26-deoxycimicifugoside (2), 23-epi-26-deoxyactein (3), 25-anhydrocimigenol xyloside (4), 23-O-acetylshengmanol xyloside (5), 25-O-acetylcimigenol xyloside (6) and 3'-O-acetylcimicifugoside H-1 (7). On the basis of NMR data supported by DFT calculations of NMR shielding constants of (2), its structure, previously described as 26-deoxycimicifugoside was corrected and determined as 23-epi-26-deoxycimicifugoside. The (13)C CPMAS NMR spectra of the studied compounds (1)-(7) provided data on their solid-state interactions. The IR and Raman spectra in the CO, CC, and CH stretching vibration regions clearly discriminate different triterpenes found in C. racemosa. PMID:22465763

  7. Structure of [Ru(bpy)n(AP)(6-2n)]2+ homogeneous complexes: DFT calculation vs. EXAFS

    NASA Astrophysics Data System (ADS)

    Salassa, Luca; Gianolio, Diego; Garino, Claudio; Salassa, Giovanni; Borfecchia, Elisa; Ruiu, Tiziana; Nervi, Carlo; Gobetto, Roberto; Bizzarri, Ranieri; Sadler, Peter J.; Lamberti, Carlo

    2009-11-01

    We used EXAFS and DFT calculations to investigate the structure of [Ru(bpy)(AP)4]2+ and [Ru(bpy)2(AP)2]2+ (bpy=2-2'-bipyridyne, AP=4-aminopyridyne) in aqueous solution (10 mM). These derivatives are of potential interest since, upon direct irradiation, they can form reactive aqua-species able to bind to macromolecules. An attempt has been made to determine with EXAFS the structure of the photodissociation product of the [Ru(bpy)2(AP)2]2+ complex, where a water molecule fill the coordination vacancy left by an AP ligand resulting in [Ru(bpy)2(AP)(H2O)]2+. Unfortunately, co-presence in the experimental sample of both original and photodissociated complexes, causes the failure of the analysis. This failure was due to the structural complexity of both systems and to the similarity in their EXAFS signals. This work underlines the potentialities and the limits of EXAFS spectroscopy when dealing with highly diluted samples where the local environment of the adsorbing atom is characterized by structured ligands: the local environment of Ru is correctly reproduced when dealing with homogeneous samples, while the co-presence of two or more different species makes the data analysis highly critical.

  8. Oxygen species on the silver surface oxidized by MW-discharge: Study by photoelectron spectroscopy and DFT model calculations

    NASA Astrophysics Data System (ADS)

    Kibis, Lidiya S.; Avdeev, Vasilii I.; Koscheev, Sergei V.; Boronin, Andrei I.

    2010-07-01

    A polycrystalline silver surface has been studied by synchrotron radiation photoelectron spectroscopy after deep oxidation by microwave discharge in an O 2 atmosphere. Oxidized structures with high oxygen content, AgO x with x > 1, have been found on the silver surface after oxidation at 300-400 K. The line shapes observed in the O1s spectra were decomposed into five components and indicated that complex oxidized species were formed. An analysis of the oxidized structures with binding energies, Еb(O1s), greater than 530 eV pointed to the presence of both Ag-O and O-O bonds. We have carried out a detailed experimental study of the valence band spectra in a wide spectral range (up to 35 eV), which has allowed us to register the multicomponent structure of spectra below Ag4d band. These features were assigned to the formation of Ag-O and O-O bonds composed of molecular (associative) oxygen species. DFT model calculations showed that saturation of the defect oxidized silver surface with oxygen leads to the formation of associative oxygen species, such as superoxides, with electrophilic properties and covalent bonding. The high stability of oxygen-rich silver structures, AgO x, can be explained by the formation of small silver particles during the intensive MW oxidation, which can stabilize such oxygen species.

  9. DFT calculations, spectroscopic, thermal analysis and biological activity of Sm(III) and Tb(III) complexes with 2-aminobenzoic and 2-amino-5-chloro-benzoic acids.

    PubMed

    Essawy, Amr A; Afifi, Manal A; Moustafa, H; El-Medani, S M

    2014-10-15

    The complexes of Sm(III) and Tb(III) with 2-aminobenzoic acid (anthranilic acid, AA) and 2-amino-5-chlorobenzoic acid (5-chloroanthranilic acid, AACl) were synthesized and characterized based on elemental analysis, IR and mass spectroscopy. The data are in accordance with 1:3 [Metal]:[Ligand] ratio. On the basis of the IR analysis, it was found that the metals were coordinated to bidentate anthranilic acid via the ionised oxygen of the carboxylate group and to the nitrogen of amino group. While in 5-chloroanthranilic acid, the metals were coordinated oxidatively to the bidentate carboxylate group without bonding to amino group; accordingly, a chlorine-affected coordination and reactivity-diversity was emphasized. Thermal analyses (TGA) and biological activity of the complexes were also investigated. Density Functional Theory (DFT) calculations at the B3LYP/6-311++G (d,p)_ level of theory have been carried out to investigate the equilibrium geometry of the ligand. The optimized geometry parameters of the complexes were evaluated using SDDALL basis set. Moreover, total energy, energy of HOMO and LUMO and Mullikan atomic charges were calculated. In addition, dipole moment and orientation have been performed and discussed. PMID:24835942

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

    PubMed

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

    2016-08-18

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

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

    PubMed

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

    2016-08-01

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

  12. Characterization of novel isobenzofuranones by DFT calculations and 2D NMR analysis.

    PubMed

    Teixeira, Milena G; Alvarenga, Elson S

    2016-08-01

    Phthalides are frequently found in naturally occurring substances and exhibit a broad spectrum of biological activities. In the search for compounds with insecticidal activity, phthalides have been used as versatile building blocks for the syntheses of novel potential agrochemicals. In our work, the Diels-Alder reaction between furan-2(5H)-one and cyclopentadiene was used successfully to obtain (3aR,4S,7R,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4R,7S,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (2) and (3aS,4S,7R,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4R,7S,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (3). The endo adduct (2) was brominated to afford (3aR,4R,5R,7R,7aS,8R)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4S,5S,7S,7aR,8S)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (4) and (3aS,4R,5R,6S,7S,7aR)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4S,5S,6R,7R,7aS)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (5). Following the initial analysis of the NMR spectra and the proposed two novel unforeseen products, we have decided to fully analyze the classical and non-classical assay structures with the aid of computational calculations. Computation to predict the (13) C and (1) H chemical shifts for mean absolute error analyses have been carried out by gauge-including atomic orbital method at M06-2X/6-31+G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for all viable conformers. Characterization of the novel unforeseen compounds (4) and (5) were not possible by employing only the experimental NMR data; however, a more conclusive structural identification was performed by comparing the experimental and theoretical (1) H and (13) C chemical shifts by mean absolute error and DP4 probability analyses. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26811211

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  15. 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.

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

    PubMed

    Demissie, Taye B; Hansen, Jørn H

    2016-08-19

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

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

    PubMed

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

    2015-02-01

    The values of extinction coefficients of CC and CC IR bands of ethyne and ethene interacting with Cu+ and Ag+ in zeolites were determined in quantitative IR experiments and also by quantumchemical DFT calculations with QM/MM method. Both experimental and calculated values were in very good agreement validating the reliability of calculations. The values of extinction coefficients of ethyne and ethene interacting with bare cations and cations embedded in zeolite-like clusters were calculated. The interaction of organic molecules with Cu+ and Ag+ in zeolites ZSM-5 and especially charge transfers between molecule, cation and zeolite framework was also discussed in relation to the values of extinction coefficients. PMID:25307963

  18. Molecular structure and vibrational bands and chemical shift assignments of 4-allyl-5-(2-hydroxyphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione by DFT and ab initio HF calculations

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Dinçer, Muharrem; Çetin, Ahmet; Şekerci, Memet

    2010-09-01

    The title molecule, 4-allyl-5-(2-hydroxyphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione (C 11H 11N 3OS), was synthesized and characterized by IR-NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group is P2 1/ c, a = 9.0907(5) Å, b = 9.1288(7) Å, c = 13.6222(7) Å, α = 90°, β = 98.442 (4), γ = 90° and V = 2683.7(6) Å 3, F(000) = 488, Dx = 1.386 g/cm 3. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) 1H and 13C chemical shift values of the title compound in the ground state have been calculated using the Hartree-Fock (HF) and density functional method (DFT/BLYP and DFT/B3LYP) with 6-31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by HF/6-31G(d) calculations with respect to selected degree of torsional freedom, which was varied from -180° to +180° in steps of 10°. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO), and several thermodynamic properties were performed by the HF and DFT methods.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  20. First principle calculation of physical properties of barium based chalcogenides BaM4S7 (M = Ga, Al); a DFT, DFT-D and hybrid functional HSE06 study

    NASA Astrophysics Data System (ADS)

    Benghia, Ali; Dahame, Tahar; Bentria, Bachir

    2016-04-01

    The electronic structure, elastic and optical properties have been calculated for the novel nonlinear optical (NLO) crystals BaQ4S7 (Q = Ga, Al) using plane wave pseudo-potential density functional theory (DFT) method as implemented in CASTEP and ABINIT codes. In this study we used both hybrid HSE06 and DFT-D functionals with GGA approximation. These NLO compounds, which belong to the mm2 point group, are particularly interesting because of their transparency in the mid-infrared region and wide energy band gap. We present results for electronic structure, elastic tensor coefficients, refractive indices and second order nonlinear optical susceptibilities. The calculated energy band gap and frequency dependent refractive indices as well as the NLO coefficients of BaGa4S7 are in good agreement with the experimental values. With no reported theoretical or experimental energy band gap and optical properties of BaAl4S7, we present for the first time its electronic structure and above mentioned optical coefficients. This compound has higher direct band gap with 3.74 eV, better optical birefringence and second-order NLO coefficients than most NLO compounds. The second-order NLO coefficients for BaAl4S7 have been calculated as d31 = 3.15 pm/V, d31 = 2.20 pm/V, d33 = -6.31 pm/V.

  1. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

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

    PubMed

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

    2010-06-01

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

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

    PubMed

    Aree, Thammarat; Jongrungruangchok, Suchada

    2016-10-20

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

  5. 2-[(1H-Benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester: Crystal structure, DFT calculations and biological activity evaluation

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

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

    PubMed

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

    2016-01-01

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

  7. 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.

  8. Non-redox metal ion promoted oxidative coupling of indoles with olefins by the palladium(ii) acetate catalyst through dioxygen activation: experimental results with DFT calculations.

    PubMed

    Zhang, Sicheng; Chen, Zhuqi; Qin, Shuhao; Lou, Chenlin; Senan, Ahmed M; Liao, Rong-Zhen; Yin, Guochuan

    2016-04-26

    Developing new catalytic technologies through C-H bond activation to synthesize versatile pharmaceuticals has attracted much attention in recent decades. This work introduces a new strategy in catalyst design for Pd(ii)-catalyzed C-H bond activation in which non-redox metal ions serving as Lewis acids play significant roles. In the oxidative coupling of indoles with olefins using dioxygen, it was found that Pd(OAc)2 alone as the catalyst is very sluggish at ambient temperature which provided a low yield of the olefination product, whereas adding non-redox metal ions to Pd(OAc)2 substantially improves its catalytic efficiency. In particular, it provided bis(indolyl)methane derivatives as the dominant product, a category of pharmacological molecules which could not be synthesized by Pd(ii)-catalyzed oxidative coupling previously. Detailed investigations revealed that the reaction proceeds by heterobimetallic Pd(ii)/Sc(iii)-catalyzed oxidative coupling of an indole with an olefin followed by Sc(iii)-catalyzed addition with a second indole molecule. DFT calculations disclosed that the formation of heterobimetallic Pd(ii)/Sc(iii) species substantially decreases the C-H bond activation energy barrier, and shifts the rate determining step from C-H bond activation of indole to the olefination step. This non-redox metal ion promoted Pd(ii)-catalyzed C-H bond activation may offer a new opportunity for catalyst design in organic synthesis, which has not been fully recognized yet. PMID:27075840

  9. FT-IR, FT-Raman, UV spectra and DFT calculations on monomeric and dimeric structure of 2-amino-5-bromobenzoic acid

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Cinar, Mehmet

    2012-02-01

    In this work, the molecular conformation, vibrational and electronic transition analysis of 2-amino-5-bromobenzoic acid (2A5BrBA) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000 cm -1 and 50-4000 cm -1, respectively. There are four conformers, C1, C2, C3 and C4 for this molecule. The geometrical parameters, energies and wavenumbers have been obtained for all four conformers. The computational results diagnose the most stable conformer of 2A5BrBA as the C1 form. 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. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. The UV spectra of investigated compound were recorded in the region of 200-400 nm for ethanol and water solutions. The electronic properties were evaluated with help of time-dependent DFT (TD-DFT) theoretically and results were compared with experimental observations. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. The observed and the calculated geometric parameters, vibrational wavenumbers and electronic transitions were compared with observed data and found to be in good agreement.

  10. Approximate two-electron spin-orbit coupling term for density-functional-theory DFT calculations using the Douglas-Kroll-Hess transformation

    NASA Astrophysics Data System (ADS)

    Boettger, J. C.

    2000-09-01

    A simple approximation is developed for the two-electron spin-orbit coupling terms generated by the Douglas-Kroll-Hess transformation, in the context of density-functional theory (DFT). For the special case of an isolated atom, the two-electron spin-orbit matrix element for each pair of basis functions of type l is replaced with the spin-orbit matrix element for a point charge -Q(l) placed at the origin; where Q(l)=0,2,10,28,... . Application of this screened-nuclear-spin-orbit (SNSO) approximation to linear combination of Gaussian-type orbital (LCGTO) DFT calculations on Ce, Ta, and Pu atoms yields spin-orbit splittings that agree with results from a numerical solution of the Dirac-Kohn-Sham equations to within about 6%. This is a marked improvement over the nuclear-only spin-orbit approximation, which systematically overestimates spin-orbit splittings; in some cases by as much as 100%. Crystalline LCGTO DFT calculations on the fcc phases of the light-actinide metals Th-->Pu, using a multiatom generalization of the SNSO approximation, yield atomic volumes that are in excellent agreement with results from full-potential linear-augmented-plane-wave calculations.

  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. Vibrational spectroscopic studies, NLO, HOMO-LUMO and electronic structure calculations of α,α,α-trichlorotoluene using HF and DFT

    NASA Astrophysics Data System (ADS)

    Govindarajan, M.; Karabacak, M.; Periandy, S.; Xavier, S.

    FT-IR and FT-Raman spectra of α,α,α-trichlorotoluene have been recorded and analyzed. The geometry, fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) B3LYP/6-311++G(d,p) method and a comparative study between HF level and various basis sets combination. The fundamental vibrational wavenumbers as well as their intensities were calculated and a good agreement between observed and scaled calculated wavenumbers has been achieved. The complete vibrational assignments of wavenumbers are made on the basis of potential energy distribution (PED). The effects due to the substitutions of methyl group and halogen were investigated. The absorption energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT). The electric dipole moment, polarizability and the first hyperpolarizability values of the α,α,α-trichlorotoluene have been calculated. 1H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF and B3LYP methods with 6-311++G(d,p) basis set. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken and natural charges of the title molecule were also calculated and interpreted.

  13. Vibrational spectroscopic studies, NLO, HOMO-LUMO and electronic structure calculations of α,α,α-trichlorotoluene using HF and DFT.

    PubMed

    Govindarajan, M; Karabacak, M; Periandy, S; Xavier, S

    2012-08-01

    FT-IR and FT-Raman spectra of α,α,α-trichlorotoluene have been recorded and analyzed. The geometry, fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) B3LYP/6-311++G(d,p) method and a comparative study between HF level and various basis sets combination. The fundamental vibrational wavenumbers as well as their intensities were calculated and a good agreement between observed and scaled calculated wavenumbers has been achieved. The complete vibrational assignments of wavenumbers are made on the basis of potential energy distribution (PED). The effects due to the substitutions of methyl group and halogen were investigated. The absorption energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT). The electric dipole moment, polarizability and the first hyperpolarizability values of the α,α,α-trichlorotoluene have been calculated. (1)H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF and B3LYP methods with 6-311++G(d,p) basis set. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken and natural charges of the title molecule were also calculated and interpreted. PMID:22516115

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  16. 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.

  17. Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

    NASA Astrophysics Data System (ADS)

    Emül, Y.; Erbahar, D.; Açıkgöz, M.

    2014-11-01

    The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

  18. 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...

  19. 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...

  20. 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...

  1. 37 CFR 1.776 - Calculation of patent term extension for a food additive or color additive.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  2. 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...

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  5. Combined EXAFS and DFT Structure Calculations Provide Structural Insights into the 1:1 Multi-Histidine Complexes of CuII, CuI and ZnII with the Tandem Octarepeats of the Mammalian Prion Protein

    PubMed Central

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

    2014-01-01

    The metal coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of copper interaction with PrP just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, and yet the structural details of the various metal coordination modes have not been fully elucidated in some cases. Herein we employ X-ray absorption near edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for CuII, CuI and ZnII with an N-terminal fragment of PrP. The PrP fragment constitutes four tandem repeats representative of the mammalian octarepeat domain, designated OR4, which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations provide additional structural and thermodynamic data, and candidate structures are used to inform EXAFS data analysis. The optimized geometries from DFT calculations are used to identify potential coordination complexes for multi-histidine coordination of CuII, CuI and ZnII in an aqueous medium, modeled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve fitting, using full multiple scattering on candidate structures from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of CuII, CuI and ZnII with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as a square planar [CuII(His)4]2+, digonal [CuI(His)2]+ and tetrahedral [ZnII(His)3(OH2)]2+, respectively. PMID:25042361

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

    PubMed

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

    2015-12-14

    The quantum dynamics of electron transfer in mixed-valence organic compounds is investigated using a reaction path model calibrated by constrained density functional theory (cDFT). Constrained DFT is used to define diabatic states relevant for describing the electron transfer, to obtain equilibrium structures for each of these states and to estimate the electronic coupling between them. The harmonic analysis at the diabatic minima yields normal modes forming the dissipative bath coupled to the electronic states. In order to decrease the system-bath coupling, an effective one dimensional vibronic Hamiltonian is constructed by partitioning the modes into a linear reaction path which connects both equilibrium positions and a set of secondary vibrational modes, coupled to this reaction coordinate. Using this vibronic model Hamiltonian, dissipative quantum dynamics is carried out using Redfield theory, based on a spectral density which is determined from the cDFT results. In a first benchmark case, the model is applied to a series of mixed-valence organic compounds formed by two 1,4-dimethoxy-3-methylphenylene fragments linked by an increasing number of phenylene bridges. This allows us to examine the coherent electron transfer in extreme situations leading to a ground adiabatic state with or without a barrier and therefore to the trapping of the charge or to an easy delocalization. PMID:26041466

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

    NASA Astrophysics Data System (ADS)

    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 13C 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.

  8. 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. PMID:23845985

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  11. FT-IR, FT-Raman and UV spectral investigation: computed frequency estimation analysis and electronic structure calculations on chlorobenzene using HF and DFT.

    PubMed

    Govindarajan, M; Karabacak, M; Udayakumar, V; Periandy, S

    2012-03-01

    In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 100-4000 cm(-1) and 400-4000 cm(-1) respectively, for the title molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartree Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The effects due to the substitution of halogen bond were investigated. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), and thermodynamic properties were performed. The thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between heat capacity (C), entropy (S), and enthalpy changes (H) and temperatures. PMID:22197345

  12. FT-IR, FT-Raman and UV spectral investigation: Computed frequency estimation analysis and electronic structure calculations on chlorobenzene using HF and DFT

    NASA Astrophysics Data System (ADS)

    Govindarajan, M.; Karabacak, M.; Udayakumar, V.; Periandy, S.

    2012-03-01

    In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 100-4000 cm-1 and 400-4000 cm-1 respectively, for the title molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartree Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The effects due to the substitution of halogen bond were investigated. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), and thermodynamic properties were performed. The thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between heat capacity (C), entropy (S), and enthalpy changes (H) and temperatures.

  13. Experimental and CIS, TD-DFT, ab initio calculations of visible spectra and the vibrational frequencies of sulfonyl azide-azoic dyes

    NASA Astrophysics Data System (ADS)

    Teimouri, Abbas; Chermahini, Alireza Najafi; Taban, Keivan; Dabbagh, Hossein A.

    2009-03-01

    The detailed experimental and computational analysis [Hartree-Fock (HF), Time-Dependent Density-Functional Theory (TD-DFT) and Second-Order Møller-Plesset Perturbation Theory (PM2) levels of theory at standard 6-31G* basis set] of structure, infrared spectra and visible spectra of azo dyes are investigated. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FT-IR spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with the calculated values. The geometry optimization yields a planar conformation for phenyl rings with azo moiety. The energy and oscillator strength calculated by Configuration Interaction Singles (CIS) complements the Time-Dependent Density-Functional Theory (TD-DFT) results and the experimental findings. Unfortunately, PM2 method could not predict vibrational frequencies and visible spectra of the azo dyes under conditions of this investigation.

  14. 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.

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

    PubMed

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

    2016-06-01

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

  16. Atomistic structures and phase transition of In2Se3 nanowires studied by DFT calculations and synchrotron radiation X-ray diffraction

    NASA Astrophysics Data System (ADS)

    Yu, Xiaohui; Hou, Tingjun; Sun, Xuhui; Li, Youyong

    2013-05-01

    In2Se3 has potential application in photovoltaic cell, solid-state batteries, phase change memories, and in the manufacture of detectors of ionizing radiation. Here we study the crystal structures and phase transition of In2Se3 by using DFT calculations. Crystal structures of In2Se3 include layered structures and vacancy-ordered-in-screw-form structures. Combining with SR-XRD techniques, our studies show that thermal annealing will merge the layer structures of In2Se3 and improves conductivity of In2Se3. Our results provide structural information for different phases and phase transition mechanism of In2Se3.

  17. 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

  18. 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. PMID:24910110

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

    PubMed

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

    2016-08-23

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

  20. A non-Karplus effect: evidence from phosphorus heterocycles and DFT calculations of the dependence of vicinal phosphorus-hydrogen NMR coupling constants on lone-pair conformation.

    PubMed

    Hersh, William H; Lam, Sherrell T; Moskovic, Daniel J; Panagiotakis, Antonios J

    2012-06-01

    In contrast to literature reports of a Karplus-type curve that correlates (3)J(PH) with phosphorus-hydrogen dihedral angle, a recently reported glycine-derived 1,3,2-oxazaphospholidine (7c) has two hydrogen atoms on the ring with identical PNCH dihedral angles but measured coupling constants of ∼6 and 1.5 Hz. DFT calculations were in accord with these values and suggested that the smaller coupling constant is negative. Experimental evidence of the opposite signs of these coupling constants was obtained by analysis of the ABX NMR spectrum of the new glycine-derived N-p-toluenesulfonyl phosphorus heterocycle 6c. DFT calculations on 6c and on Me(2)NPCl(2) and t-BuPCl(2) were also in accord with NMR data and allowed confirmation of unusual features including a lone pair effect on (3)J(PH), the negative coupling constant, temperature-dependent chemical shifts due to rotation about the sulfonamide S-N bond, and vicinal phosphorus-hydrogen coupling constants over 40 Hz. Calculation of phosphorus-hydrogen coupling constants both as a function of PYCH dihedral angle θ (Y = O, N, C) and lone pair-PYC dihedral angle ω shows similar θ,ω surfaces for (3)J(PH) with a range of (3)J(PH) from -4.4 to +51 Hz and demonstrates the large non-Karplus effect of lone-pair conformation on vicinal phosphorus-hydrogen coupling constants. PMID:22612503

  1. Infrared spectrum, DFT: pBP86/DN** and NCA vibrational calculations of 2-methylthiosemicarbazide copper(II) nitrate [Cu(2MeTSC) 2(NO 3) 2

    NASA Astrophysics Data System (ADS)

    Ramos, Joanna Maria; Viana, Robson M.; Téllez S, Claudio A.; Pereira, Wagnyr C.; Izolani, Antônio O.; da Silva, Maria Isabel P.

    2006-10-01

    To elucidate tentative assignments of metal-ligand modes of thiosemicarbazide complexes, a structural study and a assignment of the normal vibrations of 2-methylthiosemicarbazide copper(II) nitrate, [Cu(2MeTSC) 2(NO 3) 2] have been done through the ab initio DFT: pBP86/DN** procedure, and through the normal coordinate analysis (NCA). In the vibrational calculations, the elongated Cu sbnd ONO 2 bonds of the nitrate groups were considered in the C dbnd S and C dbnd N tautomers of the complex. DFT calculations had revealed that the infrared spectra can be well interpreted through the C dbnd N tautomer, failing in the prediction of the -NO 2 group wavenumbers. A little difference stabilization energy for the tautomers were found: for the C dbnd N tautomer was E = -3487,36376 a.u., and for the C dbnd S tautomer, E = -3473,93598 a.u. The observed combination bands at 1763.0 and at 1754.0 cm -1 are an indicative that the -NO 3- groups acts as monodentate ligands. Calculations had confirmed the experimental assignment of the infrared spectrum.

  2. A Non–Karplus Effect: Evidence from Phosphorus Heterocycles and DFT Calculations of the Dependence of Vicinal Phosphorus-Hydrogen NMR Coupling Constants on Lone-Pair Conformation

    PubMed Central

    Lam, Sherrell T.; Moskovic, Daniel J.; Panagiotakis, Antonios J.

    2012-01-01

    In contrast to literature reports of a Karplus-type curve that correlates 3JPH with phosphorus-hydrogen dihedral angle, a recently-reported glycine-derived 1,3,2-oxazaphospholidine (7c) has two hydrogen atoms on the ring with identical PNCH dihedral angles but measured coupling constants of ~6 Hz and 1.5 Hz. DFT calculations were in accord with these values, and suggested that the smaller coupling constant is negative. Experimental evidence of the opposite signs of these coupling constants was obtained by analysis of the ABX NMR spectrum of the new glycine-derived N-p-toluenesulfonyl phosphorus heterocycle 6c. DFT calculations on 6c and on Me2NPCl2 and t-BuPCl2 were also in accord with NMR data, and allowed confirmation of unusual features including a lone pair effect on 3JPH, the negative coupling constant, temperature-dependent chemical shifts due to rotation about the sulfonamide S-N bond, and vicinal phosphorus-hydrogen coupling constants over 40 Hz. Calculation of phosphorus-hydrogen coupling constants both as a function of PYCH dihedral angle θ(Y = O, N, C) and lone pair-PYC dihedral angle ω showed similar θ,ω surfaces for 3JPH with a range of 3JPH from −4.4 Hz to +51 Hz, and demonstrates the large non–Karplus effect of lone-pair conformation on vicinal phosphorus-hydrogen coupling constants. PMID:22612503

  3. 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.

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

    PubMed

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

    2014-09-15

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

  5. 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.

  6. 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.

  7. 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

    2015-01-01

    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. PMID:26528963

  8. DFT +DMFT calculation of band gaps for the transition metal monoxides NiO, CoO, FeO and MnO

    NASA Astrophysics Data System (ADS)

    Zhang, Long; Staar, Peter; Kozhevnikov, Anton; Schulthess, Thomas; Cheng, Hai-Ping

    We report calculated spectral functions of the four late transition metal monoxides MnO, FeO, CoO and NiO in the paramagnetic phase. We used density functional theory (DFT) in combination with dynamic mean field theory (DMFT), which gives much better description of band gaps. Both projected Wannier orbitals and the on-site screened Coulomb interactions are obtained from DFT ground states to ensure consistency. Because of the p-d hybridization in these materials, we calculated Coulomb interactions for the dp model as well as the d-dp model using the cRPA method. With the standard fully localized limit double counting correction, we found that the d-dp model gives results in better agreement with experiments. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences (BES), under Contract No. DE-FG02-02ER45995. Supported by the US Department of Energy (DOE), Office of Basic Energy Sciences (BES), under Contract No. DE-FG02-02ER45995.

  9. 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. PMID:23097264

  10. Conformational flexibility and absolute stereochemistry of (3R)-3-hydroxy-4-aryl-β-lactams investigated by chiroptical properties and TD-DFT calculations.

    PubMed

    Tedesco, Daniele; Zanasi, Riccardo; Guerrini, Andrea; Bertucci, Carlo

    2012-09-01

    The effect of conformational flexibility on the chiroptical properties of a series of synthetic (3R)-3-hydroxy-4-aryl-β-lactams of known stereochemistry (1-6) was investigated by means of electronic circular dichroism (ECD) measurements and time-dependent density functional theory (TD-DFT) calculations. The application of the β-lactam sector rules allowed a correct stereochemical characterization of these compounds, with the exception of a thienyl-substituted derivative (cis-). TD-DFT calculations yielded accurate predictions of experimental ECD spectra and [α](D) values, allowing us to assign the correct absolute configuration to all the investigated compounds. A detailed analysis of the β-lactam ring equilibrium geometry on optimized conformers identified regular patterns for the arrangement of atoms around the amide chromophore, confirming the validity of the β-lactam sector rules. However, relevant variations in theoretical chiroptical properties were found for compounds bearing a heterocyclic substituent at C4 or a phenyl substituent at C3, whose conformers deviate from these regular geometric patterns. This behavior explains the failure of the β-lactam sector rules in cis-. This study showed the importance of conformational flexibility for the determination of chiroptical properties and highlighted the strengths and weaknesses of the different methods for the stereochemical characterization of chiral molecules in solution. PMID:22544665

  11. 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.

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

    PubMed

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

    2015-02-25

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

  13. Spectroscopy studies, crystal structure and DFT calculations of 4-4{E-[(2-Fluorophenyl)imino]methyl}-2-methoxyphenol

    NASA Astrophysics Data System (ADS)

    Alaşalvar, Can; Soylu, Mustafa Serkan; Hayvali, Zeliha; Ünver, Hüseyin

    2015-01-01

    The title compound 4{E-[(2-fluorophenyl)imino]methyl}-2-methoxyphenol has been synthesized and characterized by using FTIR, 1H and 13C NMR spectroscopic, and X-ray crystallographic techniques experimentally and using B3LYP/6-31 G ( d, p) method theoretically. The structure of the compound is stabilized by four intermolecular non-classical hydrogen bonds and an intramolecular interaction. As a result of all intermolecular interaction, non-classical hydrogen bonds that give rise to 2D network structures on the (100) plane. The crystal packing shows a tubular channel running parallel to the c axis. The solvent accessible void occupies a volume of 77.9 Å3. The molecular geometry, vibration frequencies, and gauge including atomic orbital (GIAO) 1H and 13C chemical shift values of the title compound in the ground state have been calculated using the density functional (B3LYP) with the 6-31 G ( d, p) basis set. The calculated results show that the optimized geometry parameters, the theoretical vibration frequencies, and chemical shift values show good agreement with experimental values. In addition, HOMO-LUMO energy gap, molecular electrostatic potential map, thermodynamic properties for the compound were performed at B3LYP/6-31 G ( d, p) level of theory.

  14. 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. PMID:24890025

  15. Study of structure-activity relationship of enantiomeric, protonated and deprotonated forms of warfarin via vibrational spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mishra, Alok; Srivastava, Sunil Kumar; Swati, D.

    2013-09-01

    The structure-activity relationship of the anticoagulant drug warfarin were studied by studying two enantiomeric forms (S-form and R-form) of warfarin and its protonated as well as deprotonated structures in aqueous media using density functional theory (DFT). Theoretically computed Raman and IR spectra of all the computed structures were compared and their specific vibrational spectroscopic signatures were discussed. The percentage contributions of individual normal modes of warfarin, which provides direct evidence of the different molecular activity due to change in relative atomic position of atoms in molecule, were investigated through potential energy distribution (PED). The optimized energy and molecular electrostatic potential (MEP) maps show that the S-form of the drug molecules warfarin is energetically more stable than R-form and provides higher docking opportunity for the molecular binding with the receptors in the bio-systems.

  16. 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.

  17. 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. PMID:25031082

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

    PubMed

    Lattach, Youssef; Archirel, Pierre; Remita, Samy

    2012-02-01

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

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

    SciTech Connect

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

    2009-06-09

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

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

    PubMed

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

    2013-11-01

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

  1. 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.

  2. A new Schiff base, (E)-4-((4-chlorophenylimino) methyl)-2-methoxyphenol: Crystal structure, thermal behavior, solid-state fluorescence, DFT calculations and FT NMR spectral analysis

    NASA Astrophysics Data System (ADS)

    Nagapandiselvi, P.; Baby, C.; Gopalakrishnan, R.

    2014-01-01

    A new Schiff base, (E)-4-((4-chlorophenylimino) methyl)-2-methoxyphenol (4CMP), was synthesized and grown as single crystal by slow evaporation solution growth technique. The crystal structure of the compound, elucidated from single crystal X-ray diffraction analysis, was in good agreement with the calculated structure using Density functional theory (DFT) with B3LYP/6-311G(d,p) basis set of Gaussian 03 program. The physicochemical characterization of the title compound was further performed by modern spectroscopic techniques like FT-IR, FT-Raman, FT-NMR (both 1D and 2D), UV-Vis-NIR, and fluorescence analysis. UV-Vis-NIR spectrum showed the transparent nature of 4CMP crystal in the region 500-1200 nm. Solid state fluorescence of the crystal indicate that the title compound can serve as a photoactive material. Thermogravimetric analysis revealed that the grown crystal is thermally stable up to a temperature of 225 °C. From DSC, the phase transition of the compound was found to be at 131 °C. The dependence of both dielectric constant and dielectric loss with frequency was measured. Microscopic nonlinear optical properties like dipole moment (μ) and first order hyperpolarizability (β) were also measured using DFT.

  3. Metal coordination study at Ag and Cd sites in crown thioether complexes through DFT calculations and hyperfine parameters.

    PubMed

    do Nascimento, Rafael R; Lima, Filipe C D A; Gonçalves, Marcos B; Errico, Leonardo A; Rentería, Mario; Petrilli, Helena M

    2015-04-01

    Structural and electronic properties of [C12H24S6X], [C13H26S6OX], and [C14H28S6OX] (X: Ag(+), Cd(2+)) crown thioether complexes were investigated within the framework of the density functional theory (DFT) using the projector augmented wave (PAW) method. The theoretical results were compared with time-differential perturbed γ-γ angular correlations (TDPAC) experiments reported in the literature using the (111)Ag→(111)Cd probe. In the case of X=Ag(+), a refinement of the structure was performed and the predicted equilibrium structures compared with available X-ray diffraction experimental data. Structural distortions induced by replacing Ag(+) with Cd(2+) were investigated as well as the electric-field gradient (EFG) tensor at the Cd(2+) sites. Our results suggest that the EFG at Cd(2+) sites corresponds to the Ag(+) coordination sphere structure, i.e., before the structural relaxations of the molecule with X=Cd(2+) are completed. The results are discussed in terms of the characteristics of the TDPAC (111)Ag→(111)Cd probe and the time window of the measurement, and provide an interesting tool with which to probe molecular relaxations. PMID:25814377

  4. 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).

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

    PubMed

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

    2016-06-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

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

  10. Ti3GaC2 and Ti3InC2: First bulk synthesis, DFT stability calculations and structural systematics

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    A simple methodology for identifying possible higher order Mn+1AXn phases (n≥2) from the chemical characteristics of known phases was developed. The method was used to identify two potential M3AC2 phases Ti3GaC2 and Ti3InC2. 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 Ti3InC2 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.

  11. Base-catalyzed intramolecular hydroamination of cyclohexa-2,5-dienes: insights into the mechanism through DFT calculations and application to the total synthesis of epi-elwesine.

    PubMed

    Rousseau, Géraldine; Lebeuf, Raphaël; Schenk, Kurt; Castet, Frédéric; Robert, Frédéric; Landais, Yannick

    2014-11-01

    The base-catalyzed intramolecular hydroamination of 1-ethylaminocyclohexa-2,5-dienes is described. The transformation proceeds through isomerization of the cyclohexa-1,4-dienyl fragment into the corresponding conjugated 1,3-diene prior to the hydroamination step. Attaching a chiral glycinol ether auxiliary on the amino group allows the protonation to occur with complete diastereocontrol. The resulting lithium amide then adds onto the 1,3-dienyl moiety, affording the desired fused pyrrolidine ring along with the corresponding lithium allylic anion. Protonation of the latter then proceeds with high regiocontrol to favor the resulting allylic amines. In contrast, when the reaction was performed on primary amines, fused pyrrolidines bearing a homoallylic amino group were obtained. The stereochemical course of the process and determination of the reaction pathways were established based on calculations performed at the DFT level. Finally, application of the methodology to the enantioselective synthesis of (+)-epi-elwesine, a crinane alkaloid, is described. PMID:25223607

  12. A novel iron complex containing an N,O-type bidentate oxazoline ligand: Synthesis, X-ray studies, DFT calculations and catalytic activity

    NASA Astrophysics Data System (ADS)

    Amini, Mojtaba; Arab, Ali; Derakhshandeh, Parviz Gohari; Bagherzadeh, Mojtaba; Ellern, Arkady; Woo, L. Keith

    2014-12-01

    A five-coordinated Fe(III) complex with the distorted trigonal bipyramidal configuration was synthesized by reactions of FeCl3ṡ6H2O and 2-(2";-hydroxyphenyl)oxazoline (Hphox) as a bidentate Osbnd N donor oxazoline ligand. Complex [Fe(phox)2Cl] was fully characterized, including by single-crystal X-ray structure analysis. DFT calculations were accompanied with experimental results in order to obtain a deeper insight into the electronic structure and vibrational normal modes of complex. Oxidation of sulfides to sulfoxides in one-step was conducted by this complex as catalyst using urea hydrogen peroxide (UHP) in mixture of CH2Cl2/CH3OH (1:1) under air at room temperature. The results show that using this system in oxidation of sulfides, sulfoxides are obtained as the main products, together with variable amounts of sulfones (⩽13%), depending on the nature of the substrate.

  13. 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).

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

    PubMed

    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 L(2-)=(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. PMID:25725448

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    PubMed

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

    2016-03-14

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

  17. Nonheme iron-mediated amination of C(sp3)-H bonds. Quinquepyridine-supported iron-imide/nitrene intermediates by experimental studies and DFT calculations.

    PubMed

    Liu, Yungen; Guan, Xiangguo; Wong, Ella Lai-Ming; Liu, Peng; Huang, Jie-Sheng; Che, Chi-Ming

    2013-05-15

    The 7-coordinate complex [Fe(qpy)(MeCN)2](ClO4)2 (1, qpy = 2,2':6',2″:6″,2''':6''',2''''-quinquepyridine) is a highly active nonheme iron catalyst for intra- and intermolecular amination of C(sp(3))-H bonds. This complex effectively catalyzes the amination of limiting amounts of not only benzylic and allylic C(sp(3))-H bonds of hydrocarbons but also the C(sp(3))-H bonds of cyclic alkanes and cycloalkane/linear alkane moieties in sulfamate esters, such as those derived from menthane and steroids cholane and androstane, using PhI═NR or "PhI(OAc)2 + H2NR" [R = Ts (p-toluenesulfonyl), Ns (p-nitrobenzenesulfonyl)] as nitrogen source, with the amination products isolated in up to 93% yield. Iron imide/nitrene intermediates [Fe(qpy)(NR)(X)](n+) (CX, X = NR, solvent, or anion) are proposed in these amination reactions on the basis of experimental studies including ESI-MS analysis, crossover experiments, Hammett plots, and correlation with C-H bond dissociation energies and with support by DFT calculations. Species consistent with the formulations of [Fe(qpy)(NTs)2](2+) (CNTs) and [Fe(qpy)(NTs)](2+) (C) were detected by high-resolution ESI-MS analysis of the reaction mixture of 1 with PhI═NTs (4 equiv). DFT calculations revealed that the reaction barriers for H-atom abstraction of cyclohexane by the ground state of 7-coordinate CNTs and ground state of C are 15.3 and 14.2 kcal/mol, respectively, in line with the observed high activity of 1 in catalyzing the C-H amination of alkanes under mild conditions. PMID:23634746

  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. Optimization of the surface stability of the LiMn2O4 spinel by employing DFT calculations

    NASA Astrophysics Data System (ADS)

    Karim, Altaf; Persson, Kristin

    2012-02-01

    One of the most important materials for the lithium batteries electrodes is LiMn2O4. We used GGA+U method to calculate the bulk and surface properties of LiMn2O4. Our calculations show that the both correct AFM and electron localization (GGA+U) are necessary to obtain the semiconducting, Jahn-Teller distorted electronic ground state of LiMn2O4. Further we calculated energies of different surfaces such as (100), (110), and (111) to study their stability. Our calculations show that (111) surface has the lowest energy which makes it more stable than other surfaces and it also confirms the experimental results, whereas (101) and (001) similar energies. Absolute surface energies change with +U value, but the ratios between the energies are very similar. Based on these calculations we constructed the equilibrium (Wulff) shape of LiMn2O4 particle, which is similar to the cubo-octahedral shape with predominant 1 1 1 facets as it was found in experiments. Our density of states calculations show that the bulk and (100) are semiconducting, whereas (110) and (111) surfaces exhibit metallic behavior. We also calculated the LiMn2O4 bulk and surface potentials as a function of lithium concentration.

  20. 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.

  1. Unravelling the structure of protic ionic liquids with theoretical and experimental methods: ethyl-, propyl- and butylammonium nitrate explored by Raman spectroscopy and DFT calculations.

    PubMed

    Bodo, E; Mangialardo, S; Ramondo, F; Ceccacci, F; Postorino, P

    2012-11-29

    We present an analysis of gas-phase structures of small clusters of n-alkylammonium nitrates (ethyl, propyl, and butyl) together with vibrational Raman spectroscopy of their respective liquid phases. The assignment and interpretation of the resonant frequencies have been performed by comparison with high-quality ab initio (DFT) computations. The theoretical spectra are in excellent agreement with the measured ones and allow the interpretation and assignment of almost all the spectral features. A careful analysis of the vibrational frequencies and of the electronic structure of the compounds has provided additional information on various structural features and on the rather complex hydrogen bonding network that exists in such compounds. A geometric structure of the short-range local arrangement in the bulk phases is also proposed. PMID:22973943

  2. A structural and vibrational study on the first condensed borosulfate K5[B(SO4)4] by using the FTIR-Raman spectra and DFT calculations

    NASA Astrophysics Data System (ADS)

    Höppe, Henning Alfred; Kazmierczak, Karolina; Romano, Elida; Brandán, Silvia Antonia

    2013-04-01

    The first borosulfate, K5[B(SO4)4] (recently synthesized by Henning A. Höppe, Karolina Kazmierczak, Michael Daub, Katharina Förg, Franziska Fuchs, Harald Hillebrecht, 2012) was characterized by infrared and Raman spectroscopies. Density functional theory (DFT) calculations were used to study the structure and vibrational properties of the compound. Employing the B3P86 and B3LYP levels of theory, the molecular structures of the compound were theoretically determined in gas phase and the harmonic vibrational frequencies were evaluated at the same levels. The calculated harmonic vibrational frequencies for the borosulfate compound are consistent with the experimental IR and Raman spectra. These calculations gave us a precise knowledge of the normal modes of vibration taking into account the type of coordination adopted by sulfate groups of this compound as ligands with C3v and C2v symmetries. A complete assignment of all the observed bands in the IR and Raman spectra for K5[B(SO4)4] was performed. Here, the infrared and Raman spectra of K5[B(SO4)4] were interpreted, discussed and completely assigned. The nature of the Ksbnd O, Ksbnd S, Bsbnd O, and Ssbnd O bonds and the topological properties of the compound were investigated and analyzed by means of Natural Bond Order (NBO) and Bader's Atoms in Molecules theory (AIM), respectively.

  3. Assessment of theoretical prediction of the NMR shielding tensor of 195PtClxBr(6-x)(2-) complexes by DFT calculations: experimental and computational results.

    PubMed

    Fowe, Emmanuel Penka; Belser, Peter; Daul, Claude; Chermette, Henry

    2005-04-21

    In the present work, the ZORA spin-orbit Hamiltonian, in conjunction with the gauge including orbital (GIAO) method based on DFT theory has been used to calculate 195Pt chemical shift of 195PtClxBr(6-x)(2-) complexes. Excellent agreement with experiments has been obtained for calculations bearing on optimized geometries and all electrons triple zeta + polarization (TZP) STO basis sets: the relative error with respect to experiment amounts to <1.5%. It is found that the Pt chemical shift is dominated by the paramagnetic and the spin orbit contribution, whereas the diamagnetic term remains negligible. The influence of the quality of the basis sets has been studied and found to be small, provided a basis set like TZP is used. Several calculations have been performed in order to establish the sensitivity of the chemical shift to a variation in the bond lengths. A strong dependence has been found, with an increase of the chemical shift amounting to 150 ppm pm(-1) for a distance decrease. Large sensitivity to the solvation, leading to changes in the structure, is then expected. Different tests using conductor-like screening models have been performed in order to establish the sensitivity of the chemical shift to solvation. It has been observed that the changes in the geometry are more important than charge transfers. Finally, the sensitivity of the system to the exchange-correlation functional is found rather weak, at least among the GGA functionals. PMID:19787932

  4. FT-IR, FT-Raman, ab initio, HF and DFT studies, NBO, HOMO-LUMO and electronic structure calculations on 4-chloro-3-nitrotoluene

    NASA Astrophysics Data System (ADS)

    Govindarajan, M.; Karabacak, M.; Suvitha, A.; Periandy, S.

    2012-04-01

    In this work, the vibrational spectral analysis was carried out by using Raman and infrared spectroscopy in the range 100-4000 cm-1 and 50-4000 cm-1, respectively, for 4-chloro-3-nitrotoluene (C7H6NO2Cl) molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartree Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The calculated HOMO and LUMO energies shows that charge transfer within the molecule. The effects due to the substitutions of methyl group, nitro group and halogen were investigated. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed.

  5. FT-IR, FT-Raman, ab initio, HF and DFT studies, NBO, HOMO-LUMO and electronic structure calculations on 4-chloro-3-nitrotoluene.

    PubMed

    Govindarajan, M; Karabacak, M; Suvitha, A; Periandy, S

    2012-04-01

    In this work, the vibrational spectral analysis was carried out by using Raman and infrared spectroscopy in the range 100-4000 cm(-1) and 50-4000 cm(-1), respectively, for 4-chloro-3-nitrotoluene (C7H6NO2Cl) molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartree Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The calculated HOMO and LUMO energies shows that charge transfer within the molecule. The effects due to the substitutions of methyl group, nitro group and halogen were investigated. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. PMID:22261102

  6. DFT calculation of 1J(119Sn,13C) and 2J(119Sn,1H) coupling constants in di- and trimethyltin(IV) compounds.

    PubMed

    Casella, Girolamo; Ferrante, Francesco; Saielli, Giacomo

    2008-06-01

    We have tested several computational protocols, at the nonrelativistic DFT level of theory, for the calculation of 1J(119Sn, 13C) and 2J(119Sn, 1H) spin-spin coupling constants in di- and trimethyltin(IV) derivatives with various ligands. Quite a good agreement with experimental data has been found with several hybrid functionals and a double-zeta basis set for a set of molecules comprising tetra-, penta-, and hexa-coordinated tin(IV). Then, some of the protocols have been applied to the calculation of the 2J(119Sn, 1H) of the aquodimethyltin(IV) ion and dimethyltin(IV) complex with D-ribonic acid and to the calculation of 1J(119Sn, 13C) and 2J(119Sn, 1H) of the dimethyltin(IV)-glycylglycine and glycylhistidine complexes in water solutions. Solvent effects have been considered in these cases by including explicit water molecules and/or the solvent reaction field, resulting in a good agreement with experimental data. The proposed protocols constitute a helpful tool for the structural determination of di- and triorganotin(IV) derivatives. PMID:18459719

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  9. Molecular structure, spectroscopic characterization of (S)-2-Oxopyrrolidin-1-yl Butanamide and ab initio, DFT based quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Ramya, T.; Gunasekaran, S.; Ramkumaar, G. R.

    2015-10-01

    The experimental and theoretical spectra of (S)-2-Oxopyrrolidin-1-yl Butanamide (S2OPB) were studied. FT-IR and FT-Raman spectra of S2OPB in the solid phase were recorded and analyzed in the range 4000-450 and 5000-50 cm-1 respectively. The structural and spectroscopic analyses of S2OPB were calculated using ab initio Hartree Fock (HF) and density functional theory calculations (B3PW91, B3LYP) with 6-31G(d,p) basis set. A complete vibrational interpretation has been made on the basis of the calculated Potential Energy Distribution (PED). The HF, B3LYP and B3PW91 methods based NMR calculation has been used to assign the 1H NMR and 13C NMR chemical shift of S2OPB. Comparative study on UV-Vis spectral analysis between the experimental and theoretical (B3PW91, B3LYP) methods and the global chemical parameters and local descriptor of reactivity through the Fukui function were performed. Finally the thermodynamic properties of S2OPB were calculated at different temperatures and the corresponding relations between the properties and temperature were also studied.

  10. Molecular structure, spectroscopic characterization of (S)-2-Oxopyrrolidin-1-yl Butanamide and ab initio, DFT based quantum chemical calculations.

    PubMed

    Ramya, T; Gunasekaran, S; Ramkumaar, G R

    2015-10-01

    The experimental and theoretical spectra of (S)-2-Oxopyrrolidin-1-yl Butanamide (S2OPB) were studied. FT-IR and FT-Raman spectra of S2OPB in the solid phase were recorded and analyzed in the range 4000-450 and 5000-50 cm(-1) respectively. The structural and spectroscopic analyses of S2OPB were calculated using ab initio Hartree Fock (HF) and density functional theory calculations (B3PW91, B3LYP) with 6-31G(d,p) basis set. A complete vibrational interpretation has been made on the basis of the calculated Potential Energy Distribution (PED). The HF, B3LYP and B3PW91 methods based NMR calculation has been used to assign the (1)H NMR and (13)C NMR chemical shift of S2OPB. Comparative study on UV-Vis spectral analysis between the experimental and theoretical (B3PW91, B3LYP) methods and the global chemical parameters and local descriptor of reactivity through the Fukui function were performed. Finally the thermodynamic properties of S2OPB were calculated at different temperatures and the corresponding relations between the properties and temperature were also studied. PMID:25956325

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

    PubMed

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

    2014-08-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    4-Phenyl-1-(3-phenylallylidene)thiosemicarbazide (HL) and its metal complex of NiL2 have been synthesized. For them, elemental analysis, IR and X-ray single crystal diffraction have been carried out. In complex NiL2, the central Ni2+ ion coordinates with two deprotonated ligands of L- and adopts a distorted square planar configuration with the Ni2+ ion being located at the inversion center. The thermal analyses result shows that complex NiL2 undergoes two decomposition processes. For the title compounds, DFT calculations of the structures and natural population analysis (NPA) have been performed at B3LYP/LANL2DZ level of theory. The predicted geometric parameters are compared with the experimental values and they are supported each other. By using TD-DFT method, electron spectra of ligand HL and complex NiL2 have been predicted, which suggest the B3LYP/LANL2DZ method can approximately simulate the electron spectra for the system presented here. The NPA results indicate that, for ligand HL, the electronic absorption spectra are mainly assigned to n-π∗ and π-π∗ electron transitions, while for the complex NiL2, the electronic transitions are mainly derived from the contribution of an intra-ligand (IL) transition, a metal-to-ligand charge transfer (MLCT) transition and a d-d transition. Based on vibrational analysis, thermodynamic properties for ligand HL and complex NiL2 at different temperatures have been obtained.

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

  15. 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.

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

    PubMed

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

    2009-11-01

    The stoichiometries and stability constants of a series of Al(3+)-N-phosponomethyl glycine (PMG/H(3)L) complexes have been determined in acidic aqueous solution using a combination of precise potentiometric titration data, quantitative (27)Al and (31)P NMR spectra, ATR-FTIR spectrum and ESI-MS measurements (0.6M NaCl, 25 degrees C). Besides the mononuclear AlH(2)L(2+), Al(H(2)L)(HL), Al(HL)(2)(-) and Al(HL)L(2-), dimeric Al(2)(HL)L(+) and trinuclear Al(3)H(5)L(4)(2+) complexes have been postulated. (1)H and (31)P NMR data show that different isomers co-exist in solution and the isomerization reactions are slow on the (31)P NMR time scale. The geometries of monomeric and dimeric complexes likely double hydroxo bridged and double phosphonate bridged isomers have been optimized using DFT ab initio calculations starting from rational structural proposals. Energy calculations using the PCM solvation method also support the co-existence of isomers in solutions. PMID:19766319

  17. Vibrational spectroscopic (FTIR and FT-Raman), first-order hyperpolarizablity, HOMO, LUMO, NBO, Mulliken charge analyses of 2-ethylimidazole based on Hartree-Fock and DFT calculations.

    PubMed

    Arivazhagan, M; Manivel, S; Jeyavijayan, S; Meenakshi, R

    2015-01-01

    The FTIR and FT-Raman spectra of 2-ethylimidazole (2EIDZ) have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimized molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of 2EIDZ is also reported based on total energy distribution (TED). The values of the total dipole moment (μ) and the first-order hyperpolarizability (β) of the compound were computed. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. Besides, HOMO and LUMO analysis, Mulliken's charge analysis and several thermodynamic properties have been calculated. PMID:25048284

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

    PubMed

    Costanzo, Francesca

    2016-03-14

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

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

    NASA Astrophysics Data System (ADS)

    Leniak, Arkadiusz; Jaźwiński, Jarosław

    2015-03-01

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

  20. A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes.

    PubMed

    Vícha, Jan; Patzschke, Michael; Marek, Radek

    2013-05-28

    A methodology for optimizing the geometry and calculating the NMR shielding constants is calibrated for octahedral complexes of Pt(IV) and Ir(III) with modified nucleic acid bases. The performance of seven different functionals (BLYP, B3LYP, BHLYP, BP86, TPSS, PBE, and PBE0) in optimizing the geometry of transition-metal complexes is evaluated using supramolecular clusters derived from X-ray data. The effects of the size of the basis set (ranging from SVP to QZVPP) and the dispersion correction (D3) on the interatomic distances are analyzed. When structural deviations and computational demands are employed as criteria for evaluating the optimizations of these clusters, the PBE0/def2-TZVPP/D3 approach provides excellent results. In the next step, the PBE0/def2-TZVPP approach is used with the continuum-like screening model (COSMO) to optimize the geometry of single molecules for the subsequent calculation of the NMR shielding constants in solution. The two-component zeroth-order regular approximation (SO-ZORA) is used to calculate the NMR shielding constants (PBE0/TZP/COSMO). The amount of exact exchange in the PBE0 functional is validated for the nuclear magnetic shieldings of atoms in the vicinity of heavy transition metals. For the PBE0/TZP/COSMO setup, an exact exchange of 40% is found to accurately reproduce the experimental NMR shielding constants for both types of complexes. Finally, the effect of the amount of exact exchange on the NMR shielding calculations (which is capable of compensating for the structural deficiencies) is analyzed for various molecular geometries (SCS-MP2, BHLYP, and PBE0) and the influence of a trans-substituent on the NMR chemical shift of nitrogen is discussed. The observed dependencies for an iridium complex cannot be rationalized by visualizing the Fermi-contact (FC) induced spin density and probably originate from changes in the d-d transitions that modulate the spin-orbit (SO) part of the SO/FC term. PMID:23598437

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

    PubMed

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

    2016-08-01

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

  2. 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.

  3. 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.

  4. As(III) immobilization on gibbsite: Investigation of the complexation mechanism by combining EXAFS analyses and DFT calculations

    NASA Astrophysics Data System (ADS)

    Duarte, Graziele; Ciminelli, Virginia S. T.; Dantas, Maria S. S.; Duarte, Helio A.; Vasconcelos, Igor F.; Oliveira, Augusto F.; Osseo-Asare, Kwadwo

    2012-04-01

    The complexation of aqueous As(III) species on gibbsite was investigated as a function of pH. Theoretical calculations and X-ray absorption fine structure spectroscopy (XAFS) were combined to elucidate the structure of arsenite surface complexes on synthetic gibbsite. Several adsorption sites were evaluated using the self-consistent charge corrected density-functional based tight-binding (SCC-DFTB) method. The formation of bidentate-binuclear, bidentate-mononuclear, monodentate-mononuclear, and monodentate-binuclear complexes by means of both acid-base and non-dissociative mechanisms was studied in detail. The SCC-DFTB calculations showed the bidentate-binuclear/acid-base complex as the most thermodynamically stable geometry for As(III) bonding to gibbsite surface, estimating As-O and As-Al distances of 1.75 and 3.24 Å, respectively. EXAFS results also demonstrated As(III) complexation to three oxygen atoms in the first shell, at a distance of 1.77 Å, and to aluminum in the second shell at a distance of 3.21 Å, characteristic of bidentate-binuclear configuration, at pH 5.0, 7.0 and 9.0. Another As-Al interaction, attributed to the monodentate-binuclear complex due to its distance of 3.49 Å, was shown from EXAFS results to provide a minor contribution to As(III) sorption on gibbsite. Therefore, results from theoretical calculations and experimental measurements confirmed the occurrence of inner-sphere complexation during the As(III) adsorption on gibbsite, in a pH range of 5-9. Hence, the higher As(III) mobility in the environment, when compared to As(V), was suggested to be related to the protonation of the As(III) adsorbed complexes. This protonation would restore the neutral H3AsO3 molecule, which could be then released from the mineral surface. These results might be useful to predict and control arsenic mobility in aqueous environments, particularly where Al oxy-hydroxides are often found.

  5. 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

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

    NASA Astrophysics Data System (ADS)

    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

    2015-10-01

    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.

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

    PubMed

    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 (13)C 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

  8. Vibrational spectra and DFT calculations of the vibrational modes of Schiff base C18H17N3O2

    NASA Astrophysics Data System (ADS)

    Antunes, J. A.; Silva, L. E.; Bento, R. R. F.; Teixeira, A. M. R.; Freire, P. T. C.; Faria, J. L. B.; Ramos, R. J.; Silva, C. B.; Lima, J. A.

    2012-04-01

    The Schiff base 4-{[(1E)-(2-Hydroxyphenyl)methylidene]amino}-1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one (C18H17N3O2) is a synthetic compound with a variety of scientific and technological applications, such as clinic, analytic and pharmacologic. In this work FT-Raman spectrum and FT-infrared spectrum of C18H17N3O2 were investigated at 300 K. Vibrational wavenumber and wave vector have been predicted using Density Functional Theory (B3LYP) calculations with the 6-31 G(d,p) basis set. The description of the normal modes was performed by means of the potential energy distribution. A comparison with experiment allowed us to assign most of the normal modes of the crystal.

  9. meso-Tetrahydropyranylperoxides: molecular structures in solution, in the crystal, and by DFT calculations and their isomerization to the racemate.

    PubMed

    Balaban, Teodor Silviu; Eichhöfer, Andreas; Ghiviriga, Ion; Hugo, Holger; Wenzel, Wolfgang

    2003-06-27

    The crystalline peroxide 3a is the main product (out of 10 theoretically possible) from the aerial peroxidation of all-cis-2,4,6-trimethyltetrahydropyran (2a). It has a similar structure both in solution and in the crystal as shown by nuclear Overhauser effects and X-ray analysis, respectively. Theoretical calculations at a density functional theory level (B3LYP/6-31G) provide insight into the stabilities of the different stereoisomers of this peroxide, accounting for the facile, acid-catalyzed isomerization from the meso form to the racemate. Peroxide 3b, which is the 2-tert-butyl analogue of 3a, out of 22 theoretically possible isomers, crystallizes in a similar meso form. As a result of crystal packing effects and the intrinsically (axial) chiral peroxy "chromophore" that deviates slightly from the antiperiplanar conformation, both enantiomorphic forms of 3b are encountered in the lattice. PMID:12816495

  10. DFT calculations of the electric field gradient at the tin nucleus as a support of structural interpretation by 119Sn Mössbauer spectroscopy.

    PubMed

    Barone, Giampaolo; Silvestri, Arturo; Ruisi, Giuseppe; La Manna, Gianfranco

    2005-10-21

    DFT calculations, using an all-electron basis set and with full geometry optimization, were performed on 34 Sn(II) and Sn(IV) compounds of known structure and (119)Sn Mössbauer parameters, to obtain the theoretical values of the electric field gradient components, V(xx), V(yy), and V(zz), at the tin nucleus. These were used to determine the quantity V = V(zz)[1+ 1/3((V(xx) - V(yy))/((V(zz))(2)](1/2), for each investigated compound, which is related to the quadrupole splitting (DeltaE) parameter according to DeltaE = 1/2eQV, where e is the electronic charge and Q is the quadrupole moment of the tin nucleus. The linear fitting of the correlation plot of the experimental DeltaE, versus the corresponding calculated V values, produced a slope that is equal to 0.93 +/- 0.03 and a correlation coefficient R = 0.982. The value of Q obtained, 15.2 +/- 4.4 fm(2), is in agreement with that previously experimentally determined or calculated by analogous procedures. The calculation method is able to establish the sign of the electric field gradient component V(zz), in agreement with the sign of DeltaE determined experimentally by Mössbauer-Zeeman spectroscopy. The calculated structural parameters are in good agreement with the corresponding experimental data, determined by X-ray crystallography in the solid state, with average structural deviations of about 3 % for bond lengths and angles in the tin environment. Calculated values of DeltaE were obtained from the calibration fitting constant and from the values of V. By comparing experimental and calculated DeltaE parameters, the structure assignment of configurational isomers was successful in two test cases, in agreement with the experimental X-ray crystallographic structures. These results indicate that the method can be used as a tool to support the routine structure interpretation of tin compounds by (119)Sn Mössbauer spectroscopy. PMID:16052634

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  12. Overlooked difference between hydrogen bonds of equal strength formed between catechol and an oxygen or nitrogen base. Experiments and DFT calculations.

    PubMed

    Foti, Mario C; DiLabio, Gino A; Ingold, K U

    2003-11-26

    The IR spectrum of catechol in CCl(4) shows two fairly sharp O-H stretching bands of roughly equal absorbance at 3615.0 and 3569.6 cm(-1) due, respectively, to the "free" OH and the intramolecularly H-bonded OH groups. Intermolecular H-bond formation between the "free" OH and a hydrogen bond acceptor (HBA) decreases its stretching frequency by several hundred wavenumbers and simultaneously decreases the frequency of the intramolecularly H-bonded OH by a few tens of wavenumbers. The magnitude of these frequency shifts, Deltaupsilon(inter) and Deltaupsilon(intra), respectively, are very well reproduced by DFT calculations. As would be expected, the magnitudes of Deltaupsilon(inter) and Deltaupsilon(intra) increase as the HB accepting ability of the HBA increases as quantified, on a relative scale, by the HBA's values (Abraham et al. J. Chem. Soc. Perkin Trans. 2 1990, 521). However, plots of experimental, or calculated, frequency shifts versus reveal that Deltaupsilon(inter) and Deltaupsilon(intra) are ca. 40% larger for a nitrogen atom HBA than for an oxygen atom HBA having equal HBA activity. We hypothesize that for HBAs of equal strength, i.e., of equal, the H-bond in (O-H- - -O)(inter) is shorter and, hence, intrinsically stronger than the H-bond in the (O-H- - -N)(inter). However, we further hypothesize that there is more charge separation in the H-bond to N because N is a better proton acceptor than O. Hence, it is the greater Coulombic attraction in (O-H- - -N)(inter) which strengthens this H-bond and compensates for its greater length. Theoretical calculations lend support to these hypotheses. PMID:14624616

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

    PubMed

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

    2016-05-14

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

  14. Tuning of Aggregation Enhanced Emission and Solid State Emission from 1,8-Naphthalimide Derivatives: Nanoaggregates, Spectra, and DFT Calculations.

    PubMed

    Srivastava, Ashish Kumar; Singh, Avinash; Mishra, Lallan

    2016-07-01

    Four new 1,8-naphthalimide based compounds, 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoic acid (LH), 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoic acid methyl ester (LMe), 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoyl chloride (LCl), and 4-(1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-ylmethyl)-benzoic acid hydrazide (LN) are synthesized and characterized using spectral data and X-ray crystallography. They form nanoaggregates in aqueous-DMF solution and exhibited aggregation enhanced emission. The nanoaggregates are characterized using their scanning electron and atomic force microscopy images. The emission intensity follows the order as LH > LMe > LCl > LN. Their photophysical properties are recorded both in solution and in the solid-state and are correlated with the nature of benzoic acid derivatives owing to the combinatorial effect of π-π stacking and intermolecular and intramolecular interactions. The density functional theory calculations empower the understanding of their molecular and cumulative electronic behaviors. Antiparallel dimeric interactions in the solid-state extend a herringbone arrangement to LH and 2D channel and stair-like arrangement for LCl and LN, respectively. PMID:27294534

  15. A DFT study on the NHC catalysed Michael addition of enols to α,β-unsaturated acyl-azoliums. A base catalysed C-C bond-formation step.

    PubMed

    Domingo, Luis R; Sáez, José A; Arnó, Manuel

    2014-02-14

    The NHC catalysed nucleophilic additions of enols to α,β-unsaturated acyl-azolium intermediates have been investigated using DFT methods at the MPWB1K/6-31G** computational level. In the direct and the conjugate additions, formation of a hydrogen bond (HB) with the carboxyl oxygen is not sufficient to favour the C-C bond formation as a consequence of the low nucleophilic character of enols. Interestingly, when enols form a HB with the chloride counterion, the activation energies associated with the conjugate addition decrease as a consequence of the increased nucleophilic character of enols and the increased electrophilic character of the 'acyl-azolium + Cl' ion pair. Analysis of the DFT reactivity indices allows establishing a base catalysed C-C bond-formation step promoted by the chloride counterion. PMID:24343422

  16. Tuning electronic and magnetic properties of blue phosphorene by doping Al, Si, As and Sb atom: A DFT calculation

    NASA Astrophysics Data System (ADS)

    Sun, Minglei; Hao, Yitong; Ren, Qingqiang; Zhao, Yiming; Du, Yanhui; Tang, Wencheng

    2016-09-01

    Using density functional theory computations, we systematically investigated the structural, electronic and magnetic properties of Al, Si, As and Sb doped blue phosphorene. The electronic properties of blue phosphorene can be effectively turned by substitutional doping. Especially, Al and Sb lead to an indirect-to-direct-gap transition. The interaction between the impurity and P atoms should be responsible for the transition. In addition, blue phosphorene can exhibit dilute magnetic semiconductor property with doping of Si impurity. The magnetic moment in Si-substituted blue phosphorene predominantly originates from the hybridization of Si-s pz and P-pz orbitals. These results provide many useful applications of blue phosphorene in electronics, optoelectronics and spintronics.

  17. Magnetic and binding properties of metal-divacancy complexes at MgO (0 0 1) surface: DFT calculations

    NASA Astrophysics Data System (ADS)

    Shalabi, A. S.; Abdel Halim, W. S.; Ghonaim, M. S.

    2011-02-01

    We have analyzed the magnetic and binding properties of Ni, Cr, Mo, and Pt metals deposited on the defect free and defect containing surfaces of MgO by means of density functional theory calculations and embedded cluster model. Clusters of moderate sizes with no border anions, to avoid artificial polarization effects, were embedded in the simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. Spin quenching occurs for Cr and Mo complexes at the defect free (terrace) surface, and Cr, Mo, and Pt complexes at the defect containing “pit” divacancy surface. The binding energies of the metals are significantly enhanced on the cationic vacancy end of the divacancy. The adsorption energies of the low spin states of spin quenched complexes are always greater than those of the high spin states. The metal-support interactions stabilize the low spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. The encountered variations in magnetic properties of free metals and of metal complexes are correlated with the energy gaps of the frontier orbitals. Spin contamination affect the adsorbate-substrate distances, Mulliken charges, Mulliken spin densities, natural charge, natural orbital population, and provide rationalization for the reported magnetic and binding properties. The electrostatic potential energy curves provide clearer understanding of the nature of magnetic and binding interactions. The magnetic and binding properties of a single metal atom adsorbed on a particular surface result from a competition between Hund's rule for the adsorbed metal, and the formation of a chemical bond at the interface.

  18. 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. PMID:25199903

  19. Effect of the components' interface on the synthesis of methanol over Cu/ZnO from CO2/H2: a microkinetic analysis based on DFT + U calculations.

    PubMed

    Tang, Qian-Lin; Zou, Wen-Tian; Huang, Run-Kun; Wang, Qi; Duan, Xiao-Xuan

    2015-03-21

    The elucidation of chemical reactions occurring on composite systems (e.g., copper (Cu)/zincite (ZnO)) from first principles is a challenging task because of their very large sizes and complicated equilibrium geometries. By combining the density functional theory plus U (DFT + U) method with microkinetic modeling, the present study has investigated the role of the phase boundary in CO2 hydrogenation to methanol over Cu/ZnO. The absence of hydrogenation locations created by the interface between the two catalyst components was revealed based on the calculated turnover frequency under realistic conditions, in which the importance of interfacial copper to provide spillover hydrogen for remote Cu(111) sites was stressed. Coupled with the fact that methanol production on the binary catalyst was recently believed to predominantly involve the bulk metallic surface, the spillover of interface hydrogen atoms onto Cu(111) facets facilitates the production process. The cooperative influence of the two different kinds of copper sites can be rationalized applying the Brönsted-Evans-Polanyi (BEP) relationship and allows us to find that the catalytic activity of ZnO-supported Cu catalysts is of volcano type with decrease in the particle size. Our results here may have useful implications in the future design of new Cu/ZnO-based materials for CO2 transformation to methanol. PMID:25697118

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

    PubMed

    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, (1)H 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. PMID:23624211

  1. 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).

  2. 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

  3. Water displacement by cyanogold complexes in binuclear nickel(II) compounds based on bridging oxalate. Synthesis, structural diversity, magnetic properties, and DFT calculations.

    PubMed

    Vitoria, Pablo; Muga, Iñaki; Gutiérrez-Zorrilla, Juan M; Luque, Antonio; Román, Pascual; Lezama, Luis; Zúniga, F Javier; Beitia, Javier I

    2003-02-24

    Several cyanogold complexes react with the binuclear nickel complex [(Ni(dien)(H(2)O))(2)(mu-ox)](PF(6))(2).2H(2)O to give the compounds [(Ni(dien)(H(2)O))(2)(mu-ox)]Br(2) (1), [(Ni(dien)(Au(CN)(2)))(2)(mu-ox)] (2), and [(Ni(dien))(2)(mu-ox)(mu-Au(CN)(4))](PF(6)) (3) (dien, diethilenetriamine; ox, oxalate). In the case of compounds 2 and 3, water displacement by the corresponding cyanogold complex takes place, whereas compound 1 is formed by a substitution of the anion. The crystal structures of compounds 1 and 2 present a 2D arrangement where the layers are connected by van der Waals forces (1) or N-H.Ntbd1;C hydrogen bonds (2), where each binuclear complex is hydrogen bonded to its neighbors, whereas compound 3 presents a novel structure where the tetracyanoaurate acts as a bridging ligand to give a polymeric compound. Magnetic studies of these compounds reveal an antiferromagnetic behavior. Finally, density functional theory (DFT) calculations have been performed on isolated models of compounds 2 and 3 in order to gain some insight about the different behavior of the [Au(CN)(2)](-) and [Au(CN)(4)](-) groups as ligands and proton acceptors in hydrogen bonds. PMID:12588126

  4. 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.

  5. Study of morphology effects on magnetic interactions and band gap variations for 3d late transition metal bi-doped ZnO nanostructures by hybrid DFT calculations

    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.

  6. Tip enhanced Raman spectroscopy, DFT and PED calculations of 4″-trimethylsilylethylsulfanyl-4,4‧-di(phenyleneethynylene)benzene thiol adsorbed on silver

    NASA Astrophysics Data System (ADS)

    Fletcher, Melissa C.; Alexson, Dimitri M.; Moore, Martin M.; Prokes, S. M.; Glembocki, Orest; Vivoni, Alberto; McCoy, Rhonda; Mishra, Soni; Tandon, Poonam; Hosten, Charles M.

    2015-11-01

    Monolayers of α,ω-dithiol oligo(phenyleneethynlene) molecules are critical to the field of molecular electronics because of their abilities to form bonds with many metallic surfaces and rectify current. In this study Fourier Transformation-Raman, surface-enhanced Raman scattering (SERS) spectroscopy and Tip-enhanced Raman Spectroscopy (TERS) were used to characterize a selectively oriented self-assembled monolayer of 4″-trimethylsilylethylsulfanyl-4,4‧-bis-(phenyleneethynylene)benzenethiol (OPE‧) on silver coated nanospheres. Selective orientation was achieved by synthesizing 4″-trimethylsilylethylsulfanyl-4,4‧-bis-(phenyleneethynylene)benzene disulfide, which undergoes oxidative dissociation and covalently bonds to the metal surface. The Ag coated nanosphere surfaces were characterized by scanning electron microscopy (SEM), which showed a large area of surface charging. The SERS and TERS spectra show similar results; however, a greater enhancement was achieved with the TERS relative to the SERS spectra. Assignments of vibrational bands were based on DFT calculations performed at the B3LYP level with good agreement between theoretical and experimental values. An average percent difference of 2.5 cm-1 was obtained for the non-CH stretching frequencies and a scaling factor was not applied to theoretically generated frequencies. A red shift of the ν(C-S) peak at 1087 cm-1 was observed when OPE‧ was adsorbed on a Ag surface. Vibrations specific to the trimethylsilylethyl (TMSE) group were visible in the TERS spectra, and disappear upon deprotection.

  7. Ammonia-Containing Species Formed in Cu-Chabazite As Per In Situ EPR, Solid-State NMR, and DFT Calculations.

    PubMed

    Moreno-González, Marta; Hueso, Beatriz; Boronat, Mercedes; Blasco, Teresa; Corma, Avelino

    2015-03-19

    Nowadays, the most attractive technology for the elimination of nitric oxides from the exhaust gas of diesel vehicles is the selective catalytic reduction with ammonia (NH3-SCR-NOx) using Cu zeolite with the chabazite structure as the catalyst. Isolated copper species are the active sites, but the reaction intermediates and the overall reaction mechanism are still under debate. Here, we study the interaction of ammonia with zeolite Cu-SSZ-13 (CHA topology) with a uniform distribution of Cu(2+) sites prepared in one pot and a conventional Cu-ZSM-5 (MFI topology) for comparison. In situ EPR and solid-state NMR spectroscopies combined with DFT calculations have allowed the identification of NH4(+), [Cu(NH3)5](2+), [Cu(Of)2(NH3)2](2+), [Cu(Of)3NH3](2+), [Cu(NH3)2](+), and [CuOf(NH3)](+) (Of being framework oxygen) under different conditions. The results demonstrate that ammonia is able to reduce Cu(2+) to Cu(+) and provide new information on the species formed in Cu-SSZ-13, which have important implications for the elucidation of the SCR reaction mechanism. PMID:26262861

  8. Insights into metal-ligand and metal-metal interaction in coinage metal triangles. Insights of d10-d10, d10-d8 and d8-d8 contacts from [Au3In(CH3Ndbnd COCH3)3] (n = 2, 4, 6) via relativistic DFT calculations

    NASA Astrophysics Data System (ADS)

    Guajardo Maturana, R.; Muñoz-Castro, A.

    2016-05-01

    The successive addition of one, two and three equivalents of iodide to [Au3(CH3Ndbnd COCH3)3], gives rise to the [Au3In(CH3Ndbnd COCH3)3] (n = 2, 4, 6) oxidized systems. Such structures have been studied by using scalar relativistic DFT calculations and TD-DFT. Our results demonstrate a stronger ligand-to-metal charge donation, which increases in covalency. The long metal-metal contacts observed through the series result from the similarly population of bonding, non-bonding and slightly anti-bonding combinations of the 6s-Au atomic shells in the [Au3]n+ core, leading to distances in the range of the sum of their van der Waals radii for all the systems.

  9. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations.

    PubMed

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-01

    The vibrational and reorientational motions of NH3 ligands and ClO4(-) anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385cm(-1), associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR≈10(-12)-10(-13)s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5kJmol(-1), in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TC(c)=137.6K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6](2+) cation and ClO4(-) anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models. PMID:25459713

  10. Vibrations and reorientations of NH3 molecules in [Mn(NH3)6](ClO4)2 studied by infrared spectroscopy and theoretical (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward

    2015-02-01

    The vibrational and reorientational motions of NH3 ligands and ClO4- anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385 cm-1, associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR ≈ 10-12-10-13 s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5 kJ mol-1, in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TCc = 137.6 K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311 + G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6]2+ cation and ClO4- anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models.

  11. Synthesis, spectral characterization, thermal behaviour, antibacterial activity and DFT calculation on N'-[bis(methylsulfanyl) methylene]-2-hydroxybenzohydrazide and N'-(4-methoxy benzoyl)-hydrazinecarbodithioic acid ethyl ester.

    PubMed

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

    2015-06-15

    Two new compounds N'-[bis(methylsulfanyl) methylene]-2-hydroxybenzohydrazide {Hbmshb (1)} and N'-(4-methoxy benzoyl)-hydrazinecarbodithioic acid ethyl ester {H2mbhce (2)} have been synthesized and characterized with the aid of elemental analyses, IR, NMR and single crystal X-ray diffraction data. Compounds 1 and 2 crystallize in orthorhombic and monoclinic systems with space group Pna21 and P21/n, respectively. Inter and intra molecular hydrogen bonding link two molecules and provide linear chain structure. In addition to this, compound 2 is stabilized by CH⋯π and NH⋯π interactions. Molecular geometry from X-ray analysis, geometry optimization, charge distribution, bond analysis, frontier molecular orbital (FMO) analysis and non-linear optical (NLO) effects have been performed using the density functional theory (DFT) with the B3LYP functional. The bioefficacy of compounds has been examined against the growth of bacteria to evaluate their anti-microbial potential. Compounds 1 and 2 are thermally stable and show NLO behaviour better than the urea crystal. PMID:25767993

  12. Molecular structure and hydrogen bonding in liquid cyclohexanol and cyclohexanol/water mixtures studied by FT-NIR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Czarnecki, Mirosław Antoni; Muszyński, Andrzej S.; Troczyńska, Helena

    2010-06-01

    The molecular structure and hydrogen bonding in liquid cyclohexanol and cyclohexanol/water mixtures has been examined by Fourier-transform near-infrared (FT-NIR) spectroscopy. FT-NIR spectra of pure cyclohexanol and binary mixtures with water at selected water mole fractions ( XO) from 30 to 80 °C and the spectra of the mixtures from XO = 0-0.4 at 30 °C were measured. Besides, FT-IR and FT-NIR spectra of cyclohexanol in CCl 4 and cyclohexane solutions were recorded. The experimental spectra were analyzed by two-dimensional (2D) correlation approach and chemometrics methods. Interpretation of the spectra was guided by DFT calculations. It has been shown that small to moderate water content has a negligible effect on the structure of liquid cyclohexanol at constant temperature. Water molecules predominantly act as double donors to different species of cyclohexanol and this hydrogen bonding is stronger than that in bulk water. At lower water content appears a noticeable amount of singly bonded water molecules, however, population of this species in cyclohexanol is significantly smaller as compared with that in butyl alcohols. This results from much higher viscosity of cyclohexanol that stabilizes the cyclohexanol-water interactions. Increasing water content leads to creation of small clusters of water, where the water-water interaction is much weaker than that in bulk water. The temperature-induced breaking of smaller associates of cyclohexanol occurs easier in the presence of water, while an opposite effect was observed for the higher associates. The hydrophobic interactions in the cyclohexanol/water mixtures are of minor importance.

  13. Antioxidant potential of curcumin-related compounds studied by chemiluminescence kinetics, chain-breaking efficiencies, scavenging activity (ORAC) and DFT calculations.

    PubMed

    Slavova-Kazakova, Adriana K; Angelova, Silvia E; Veprintsev, Timur L; Denev, Petko; Fabbri, Davide; Dettori, Maria Antonietta; Kratchanova, Maria; Naumov, Vladimir V; Trofimov, Aleksei V; Vasil'ev, Rostislav F; Delogu, Giovanna; Kancheva, Vessela D

    2015-01-01

    This study compares the ability to scavenge different peroxyl radicals and to act as chain-breaking antioxidants of monomers related to curcumin (1): dehydrozingerone (2), zingerone (3), (2Z,5E)-ethyl 2-hydroxy-6-(4-hydroxy-3-methoxyphenyl)-4-oxohexa-2,5-dienoate (4), ferulic acid (5) and their corresponding C 2-symmetric dimers 6-9. Four models were applied: model 1 - chemiluminescence (CL) of a hydrocarbon substrate used for determination of the rate constants (k A) of the reactions of the antioxidants with peroxyl radicals; model 2 - lipid autoxidation (lipidAO) used for assessing the chain-breaking antioxidant efficiency and reactivity; model 3 - oxygen radical absorbance capacity (ORAC), which yields the activity against peroxyl radicals generated by an azoinitiator; model 4 - density functional theory (DFT) calculations at UB3LYP/6-31+G(d,p) level, applied to explain the structure-activity relationship. Dimers showed 2-2.5-fold higher values of k A than their monomers. Model 2 gives information about the effects of the side chains and revealed much higher antioxidant activity for monomers and dimers with α,β-unsaturated side chains. Curcumin and 6 in fact are dimers of the same monomer 2. We conclude that the type of linkage between the two "halves" by which the molecule is made up does not exert influence on the antioxidant efficiency and reactivity of these two dimers. The dimers and the monomers demonstrated higher activity than Trolox (10) in aqueous medium (model 3). A comparison of the studied compounds with DL-α-tocopherol (11), Trolox and curcumin is made. All dimers are characterized through lower bond dissociation enthalpies (BDEs) than their monomers (model 4), which qualitatively supports the experimental results. PMID:26425195

  14. 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

  15. DFT Calculations of Comparative Energetics and ENDOR/Mössbauer Properties for Two Protonation States of the Iron Dimer Cluster of Ribonucleotide Reductase Intermediate X

    PubMed Central

    Han, Wen-Ge; Noodleman, Louis

    2009-01-01

    Two models (I and II) for the active site structure of class-I ribonucleotide reductase (RNR) intermediate X in subunit R2 have been studied in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) calculations. Only one of the bridging groups between the two iron centers is different between Model-I and Model-II. Model-I contains two μ-oxo bridges, while Model-II has one bridging oxo and one bridging hydroxo. These are large active site models including up to the fourth coordination shell H-bonding residues. Mössbauer and ENDOR hyperfine property calculations show that Model-I is more likely to represent the active site structure of RNR-X. However, energetically our pKa calculations at first highly favored the bridging oxo and hydroxo (in Model-II) structure of the diiron center rather than having the di-oxo bridge (in Model-I). Since the Arg236 and the nearby Lys42, which are very close to the diiron center, are on the protein surface of RNR-R2, it is highly feasible that one or two anion groups in solution would interact with the positively charged side chains of Arg236 and Lys42. The anion group(s) can be a reductant, phosphate, sulfate, nitrate, and other negatively charged groups existing in biological environment or in the buffer of the experiment. Since sulfate ions certainly exist in the buffer of the ENDOR experiment, we have examined the effect of the sulfate (SO42-, surrounded by explicit water molecules) H-bonding to the side chain of Arg236. We find that when sulfate interacts with Arg236, the carboxylate group of Asp237 tends to be protonated, and once Asp237 is protonated, the Fe(III)Fe(IV) center in X favors the di-oxo bridge (Model-I). This would explain that the ENDOR observed RNR-X active site structure is likely to be represented by Model-I rather than Model-II. PMID

  16. Molecular and electron-spin structures of a ring-shaped mixed-valence polyoxovanadate (IV, V) studied by (11)B and (23)Na solid-state NMR spectroscopy and DFT calculations.

    PubMed

    Iijima, Takahiro; Yamase, Toshihiro; Nishimura, Katsuyuki

    2016-01-01

    (11)B and (23)Na solid-state nuclear magnetic resonance (NMR) spectra of ring-shaped paramagnetic crystals of H15[V7(IV)V5(V)B32O84Na4]·13H2O containing seven d(1) electrons from V(IV) were studied. Magic-angle-spinning (MAS) and multiple-quantum MAS NMR experiments were performed at moderate (9.4T) and ultrahigh magnetic fields (21.6T). The NMR parameters for quadrupole and isotropic chemical shift interactions were estimated by simulation of the NMR spectra and from relativistic density functional theory (DFT) calculations. Four Na ions incorporated into the framework were found to occupy four distinct sites with different populations. The DFT calculation showed that d(1) electrons with effectively one up-spin caused by strong antiferromagnetic interactions were delocalized over the 12V ions. PMID:27018827

  17. FT-IR and FT-Raman, UV spectroscopic investigation of 1-bromo-3-fluorobenzene using DFT (B3LYP, B3PW91 and MPW91PW91) calculations.

    PubMed

    Mahadevan, D; Periandy, S; Karabacak, M; Ramalingam, S

    2011-11-01

    The FT-IR and FT-Raman spectra of 1-bromo-3-fluorobenzene (C(6)H(4)FBr) molecule have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1). The molecular geometry and vibrational frequencies in the ground state are calculated using the DFT (B3LYP, B3PW91 and MPW91PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The isotropic DFT (B3LYP, B3PW91 and MPW1PW91) analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by B3LYP methods. The complete data of this molecule provide the information for future development of substituted benzene. The influence of bromine and fluorine atom on the geometry of benzene and its normal modes of vibrations has also been discussed. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, was performed by time dependent DFT (TD-DFT) approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds were discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated in gas phase, revealing the correlations between standard heat capacities (C) standard entropies (S), standard enthalpy changes (H) and temperatures. PMID:21840753

  18. Implementation of DFT +DMFT in local-orbital pseudopotential code

    NASA Astrophysics Data System (ADS)

    Oh, Hyungju; Lee, Choong-Ki; Choi, Hyoung Joon

    2014-03-01

    Density functional theory (DFT) has been remarkably successful at describing ground-state properties of many solids from first principles. This is also the state-of-the-art method for band structure calculations, with the additional assumption that Kohn-Sham eigenvalues can be interpreted as single-particle excitations. However, DFT has limitations for strongly correlated materials. Dynamical mean-field theory (DMFT) is one of various approaches that have been developed for overcoming the shortcomings of DFT. DMFT goes beyond DFT by allowing the interaction potential of the correlated orbitals to be energy (frequency) dependent. This frequency dependent potential, or self-energy, is computed for the correlated orbitals using many-body techniques within an accurate impurity solver. We have implemented DMFT to the SIESTA code based on pseudo-atomic orbital basis set. For an impurity solver, we use exact diagonalization. We calculate electronic states of LaFeAsO using our DFT +DMFT code and confirm the band-narrowing, corresponding to an enhancement of the effective masses of quasiparticles. This work was supported by the NRF of Korea (Grant No. 2011-0018306). Computational resources have been provided by KISTI Supercomputing Center (Project No. KSC-2013-C3-008).

  19. 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.

  20. 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

  1. 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

    2015-01-01

    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. PMID:25106816

  2. Graph model for calculating the properties of saturated monoalcohols based on the additivity of energy terms

    NASA Astrophysics Data System (ADS)

    Grebeshkov, V. V.; Smolyakov, V. M.

    2012-05-01

    A 16-constant additive scheme was derived for calculating the physicochemical properties of saturated monoalcohols CH4O-C9H20O and decomposing the triangular numbers of the Pascal triangle based on the similarity of subgraphs in the molecular graphs (MGs) of the homologous series of these alcohols. It was shown, using this scheme for calculation of properties of saturated monoalcohols as an example, that each coefficient of the scheme (in other words, the number of methods to impose a chain of a definite length i 1, i 2, … on a molecular graph) is the result of the decomposition of the triangular numbers of the Pascal triangle. A linear dependence was found within the adopted classification of structural elements. Sixteen parameters of the schemes were recorded as linear combinations of 17 parameters. The enthalpies of vaporization L {298/K 0} of the saturated monoalcohols CH4O-C9H20O, for which there were no experimental data, were calculated. It was shown that the parameters are not chosen randomly when using the given procedure for constructing an additive scheme by decomposing the triangular numbers of the Pascal triangle.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Evaluation of additive element to improve PZT piezoelectricity by using first-principles calculation

    NASA Astrophysics Data System (ADS)

    Yasoda, Yutaka; Uetsuji, Yasutomo; Tsuchiya, Kazuyoshi

    2015-12-01

    Recently, piezoelectric material has a very important potential for functional material which configure Bio-MEMS (Biological Micro Electro Mechanical Systems) actuator and sensor. Specifically, in implementation of piezoelectric material for Bio-MEMS, thin film fabrication by sputtering method is made from the viewpoint of miniaturization. Furthermore, in piezoelectric material, perovskite type material composed of ABO3 has a high piezoelectricity. Then, PZT (Lead Zirconate Titanate) as the perovskite type piezoelectric material is widely used since it is easy to produce and has high piezoelectricity. PZT has zirconium or titanium in the B site of ABO3 structure. PZT has the features such as physical properties to greatly change by change in the B site composition ratio of zirconium and titanium. Thus, the B site greatly influences physical properties and therefore function improvement by additive element is tried widely. However, experimental method to lack in economy and quantitativeness is mainstream. Therefore, application of the result is difficult and new evaluation method of B site additive element for sputtering fabrication is necessary. Accordingly, in this research, search of an additive element at low cost and quantitative from the viewpoint of energy by first-principles calculation. First of all, the additive elements which capable of substituting for a B site of PZT were searched. Next, change of piezoelectricity was evaluated by change of crystal structure in a PZT system was introduced an additive element that substitution of the B site was possible. As a result, additive elements for the PZT B site capable of improving piezoelectricity were determined.

  8. Performance on paced serial addition tasks indicates an associative network for calculation.

    PubMed

    Hiscock, M; Caroselli, J S; Kimball, L E; Panwar, N

    2001-06-01

    Although paced serial addition (PSA) tasks are considered to be tests of general information-processing capacity, recent work suggests that performance on such tasks is influenced by arithmetic-specific variables. We designed two visual PSA experiments to determine whether the performance of normal adults would support predictions derived from the cognitive psychology of calculation. Experiment 1 showed that mixing familiar (Arabic numeral) and less familiar (Roman numeral) stimulus formats reduced scores below the averaged scores for pure Arabic and Roman lists. The Roman-Arabic order of addends was more difficult than the Arabic-Roman order. Experiment 2, which involved only Arabic numerals as addends, showed that performance could be impaired by constraining the trial-to-trial variability of sums. The results of both experiments confirm the importance of arithmetic-specific variables in PSA and provide support for an associative network model of calculation. In addition, the findings implicate interference from extraneous addends and responses as the performance-limiting factor. PMID:11404809

  9. 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.

  10. Free energy calculation of water addition coupled to reduction of aqueous RuO4-

    NASA Astrophysics Data System (ADS)

    Tateyama, Yoshitaka; Blumberger, Jochen; Ohno, Takahisa; Sprik, Michiel

    2007-05-01

    Free energy calculations were carried out for water addition coupled reduction of aqueous ruthenate, RuO4-+H2O +e-→[RuO3(OH)2]2-, using Car-Parrinello molecular dynamics simulations. The full reaction is divided into the reduction of the tetrahedral monoanion, RuO4-+e-→RuO42-, followed by water addition, RuO42-+H2O →[RuO3(OH)2]2-. The free energy of reduction is computed from the fluctuations of the vertical energy gap using the MnO4-+e -→MnO42- reaction as reference. The free energy for water addition is estimated using constrained molecular dynamics methods. While the description of this complex reaction, in principle, involves multiple reaction coordinates, we found that reversible transformation of the reactant into the product can be achieved by control of a single reaction coordinate consisting of a suitable linear combination of atomic distances. The free energy difference of the full reaction is computed to be -0.62eV relative to the normal hydrogen electrode. This is in good agreement with the experimental value of -0.59eV, lending further support to the hypothesis that, contrary to the ruthenate monoanion, the dianion is not tetrahedral but forms a trigonal-bipyramidal dihydroxo complex in aqueous solution. We construct an approximate two-dimensional free energy surface using the coupling parameter for reduction and the mechanical constraint for water addition as variables. Analyzing this surface we find that in the most favorable reaction pathway the reduction reaction precedes water addition. The latter takes place via the protonated complex [RuO3(OH)]- and subsequent transport of the created hydroxide ion to the fifth coordination site of Ru.

  11. 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.

  12. Hydrogen and halogen bonding patterns and π-π aromatic interactions of some 6,7-disubstituted 1,3-benzothiazoles studied by X-ray diffraction and DFT calculations

    NASA Astrophysics Data System (ADS)

    Čičak, Helena; Đaković, Marijana; Mihalić, Zlatko; Pavlović, Gordana; Racané, Livio; Tralić-Kulenović, Vesna

    2010-06-01

    The structures of five 6,7-disubstituted 1,3-benzothiazole (1,3-benzothiazole = bta) derivatives: 6-chloro-7-nitro-bta ( 3), 6-iodo-7-nitro-bta ( 5), 6-amino-7-iodo-bta ( 6), 6-acetylamino-7-iodo-bta ( 7) and 6-amino-7-bromo-bta ( 8) are reported and investigated by X-ray crystallography and DFT calculations. The crystal structures of 3 and 5- 8 are characterized by: (i) relatively weak C sbnd H⋯O/N/Br and N sbnd H⋯O/N/S hydrogen bonds, (ii) C sbnd Cl⋯O and C sbnd I⋯O/N halogen bonds and Br⋯Br interactions and (iii) π-π interactions. DFT optimized structures of 3, 5, 6 and 8 are in a good agreement with the corresponding X-ray molecular data. Calculated structure of 7 deviates from the experimental geometry because of more favourable intermolecular hydrogen bonding in crystal phase compared to the weak intramolecular hydrogen bond in the gas phase. The molecular electrostatic potential maps were used for predicting possible hydrogen and halogen bonding sites in structures of 3, 5, 6 and 8, and AIM analysis in order to characterize the nature and strength of intermolecular interactions in all of the examined crystal structures. Experimental results agree well with AIM analysis suggesting that the detected hydrogen and halogen bonds are weak and mostly of electrostatic origin.

  13. 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.

  14. Glaucoma Surgery Calculator: Limited Additive Effect of Phacoemulsification on Intraocular Pressure in Ab Interno Trabeculectomy

    PubMed Central

    Schuman, Joel S.; Brown, Eric N.

    2016-01-01

    Purpose To compare intraocular pressure (IOP) reduction and to develop a predictive surgery calculator based on the results between trabectome-mediated ab interno trabeculectomy in pseudophakic patients versus phacoemulsification combined with trabectome-mediated ab interno trabeculectomy in phakic patients. Methods This observational surgical cohort study analyzed pseudophakic patients who received trabectome-mediated ab interno trabeculectomy (AIT) or phacoemulsification combined with AIT (phaco-AIT). Follow up for less than 12 months or neovascular glaucoma led to exclusion. Missing data was imputed by generating 5 similar but non-identical datasets. Groups were matched using Coarsened Exact Matching based on age, gender, type of glaucoma, race, preoperative number of glaucoma medications and baseline intraocular pressure (IOP). Linear regression was used to examine the outcome measures consisting of IOP and medications. Results Of 949 cases, 587 were included consisting of 235 AIT and 352 phaco-AIT. Baseline IOP between groups was statistically significant (p≤0.01) in linear regression models and was minimized after Coarsened Exact Matching. An increment of 1 mmHg in baseline IOP was associated with a 0.73±0.03 mmHg IOP reduction. Phaco-AIT had an IOP reduction that was only 0.73±0.32 mmHg greater than that of AIT. The resulting calculator to determine IOP reduction consisted of the formula -13.54+0.73 × (phacoemulsification yes:1, no:0) + 0.73 × (baseline IOP) + 0.59 × (secondary open angle glaucoma yes:1, no:0) + 0.03 × (age) + 0.09 × (medications). Conclusions This predictive calculator for minimally invasive glaucoma surgery can assist clinical decision making. Only a small additional IOP reduction was observed when phacoemulsification was added to AIT. Patients with a higher baseline IOP had a greater IOP reduction. PMID:27077914

  15. Tailoring the electronic and optical properties of rutile TiO2 by (Nb + Sb, C) codoping from DFT + U calculations

    NASA Astrophysics Data System (ADS)

    Fang, Yu; Cheng, Daojian; Niu, Mang; Yi, Yongjun; Wu, Wei

    2013-04-01

    The electronic structures and optical properties of the rutile TiO2 doped by C, (2Sb, C), (2Nb, C), (Nb + Sb, C) have been investigated by density functional theory plus U calculations. It is found that (2Sb, C), (2Nb, C), (Nb + Sb, C) codoping results in band gap narrowing, due to the appearance of the mid-bandgap states from C 2p and the introduction of Sb 5s and Nb 4d states. In addition, the rutile TiO2 codoped by (Nb + Sb, C) and (2Nb, C) is much more effective for the enhancement of visible light absorption than that for C monodoping and (2Sb, C) codoping.

  16. 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.

  17. 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.

  18. 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.

  19. Magnetic property, DFT calculation, and biological activity of bis[(μ(2)-chloro)chloro(1,10-phenanthroline)copper(II)] complex.

    PubMed

    Mroueh, Mohammad; Daher, Costantine; Hariri, Essa; Demirdjian, Sally; Isber, Samih; Choi, Eun Sang; Mirtamizdoust, Babak; Hammud, Hassan H

    2015-04-25

    The dinuclear complex bis[(μ(2)-chloro)chloro(1,10-phenanthroline)copper(II)] (1) was synthesized, and characterized by X-ray, FTIR and thermal analysis. The fitting of magnetic susceptibility and magnetization curve of (1) indicates the occurrence of weak antiferromagnetic exchange interaction between copper(II) ions. The electronic structure has been also determined by density functional theory (DFT) method. Complex (1) displayed potent anticancer activity against B16 (Melanoma), MDA-MB-32 (Breast Adenocarcinoma), A549 (Lung Adenocarcinoma), HT-29 (Colon Adenocarcinoma) and SF (Astrocytoma) cell lines with an average IC50 value of 0.726 μg/ml compared to 4.88 μg/ml for cisplatin. Complex (1) has a better therapeutic index and toxicological profile than cisplatin, and has demonstrated a potential chemotherapeutic property. PMID:25753321

  20. Montecrinanes A-C: Triterpenes with an Unprecedented Rearranged Tetracyclic Skeleton from Celastrus vulcanicola. Insights into Triterpenoid Biosynthesis Based on DFT Calculations.

    PubMed

    Purino, Martín; Ardiles, Alejandro E; Callies, Oliver; Jiménez, Ignacio A; Bazzocchi, Isabel L

    2016-05-23

    Three new triterpenoids with an unprecedented 6/6/6/6-fused tetracyclic carbon skeleton, montecrinanes A-C (1-3), were isolated from the root bark of Celastrus vulcanicola, along with known D:B-friedobaccharanes (4-6), and lupane-type triterpenes (7-12). The stereostructures of the new metabolites were elucidated based on spectroscopic (1D and 2D NMR) and spectrometric (HR-EIMS and HR-ESIMS) techniques. Their absolute configurations were determined by both NMR spectroscopy, with (R)-(-)-α-methoxyphenylacetic acid as a chiral derivatizing agent, and biogenetic considerations. Biogenetic pathways for montecrinane and D:B-friedobaccharane skeletons were proposed and studied by DFT methods. The theoretical results support the energetic feasibility of the putative biogenetic pathways, in which the 1,2-methyl shift from the secondary baccharenyl cation represents a novel and key reaction step for a new montecrinane skeleton. PMID:27106132

  1. Study on the adsorption properties of O3, SO2, and SO3 on B-doped graphene using DFT calculations

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    We investigated the structure, adsorption, electronic states, and charge transfer of O3, SO2 and SO3 molecules on the surface of a B-doped graphene using density functional theory (DFT). We found weak physisorption of SO2 (-10.9 kJ/mole, using B3LYP-D) and SO3 (-15.7 kJ/mole, using B3LYP-D) on the surface of B-doped graphene while there is strong chemisorption for O3 (-96.3 kJ/mole, using B3LYP-D) on this surface. Our results suggest the potential of B-doped graphene as a selective sensor/adsorbent for O3 molecule. We noticed some change in hybridizing of boron from sp2 to sp3 upon adsorption of O3 which cases transformation of the adsorbent from 2D to 3D.

  2. Synthesis, structure, DFT calculations, electrochemistry, fluorescence, DNA binding and molecular docking aspects of a novel oxime based ligand and its palladium(II) complex.

    PubMed

    Bandyopadhyay, Nirmalya; Pradhan, Ankur Bikash; Das, Suman; Lu, Liping; Zhu, Miaoli; Chowdhury, Shubhamoy; Naskar, Jnan Prakash

    2016-07-01

    A novel oxime based ligand, phenyl-(pyridine-2-yl-hydrazono)-acetaldehyde oxime (LH), and its palladium(II) complex (1) have been synthesised and spectroscopically characterised. The ligand crystallizes in the monoclinic space group (P21/c). The X-ray crystal structure of the ligand shows that it forms a hydrogen bonded helical network. The ligand has been characterised by C, H and N microanalyses, (1)H and (13)C NMR, ESI-MS, FT-IR and UV-Vis spectral measurements. Geometry optimizations at the level of DFT show that the Pd(II) centre is nested in a square-planar 'N3Cl' coordination chromophore. The diamagnetic palladium complex has been characterised by C, H and N microanalyses, FAB-MS, FT-IR, UV-Vis spectra and molar electrical conductivity measurements. The observed electronic spectrum of 1 correlates with our theoretical findings as evaluated through TD-DFT. 1 displays quasi-reversible Pd(II)/Pd(III) and Pd(III)/Pd(IV) redox couples in its CV in acetonitrile. 1 is nine-fold more emissive with respect to the binding ligand. Biophysical studies have been carried out to show the DNA binding aspects of both the ligand and complex. The binding constants for the ligand and complex were found to be 3.93×10(4) and 1.38×10(3)M(-1) respectively. To have an insight into the mode of binding of LH and 1 with CT DNA a hydrodynamic study was also undertaken. The mode of binding has also been substantiated through molecular docking. A promising groove binding efficacy has been revealed for the ligand. PMID:27179300

  3. The effect of Cu(2+) chelation on the direct photolysis of oxytetracycline: A study assisted by spectroscopy analysis and DFT calculation.

    PubMed

    Jin, Xin; Qiu, Shanshan; Wu, Ke; Jia, Mingyun; Wang, Fang; Gu, Chenggang; Zhang, Aiqian; Jiang, Xin

    2016-07-01

    The extensive usage of OTC and Cu(2+) in livestock and poultry industry caused high residues in natural environment. Co-contamination of OTC and Cu(2+) was a considerable environmental problem in surface waters. In this study, Cu(2+) mediated direct photolysis of OTC was studied. Cu(2+) chelating with OTC was found to greatly inhibit OTC photodegradation. To reveal the chelation mechanism of OTC-Cu complexes, multiple methods including UV-Vis absorption spectra, Infrared (IR) spectra, mass spectroscopy, and density functional theoretical (DFT) modeling were performed. Four OTC-Cu complexes were proposed. Cu(2+) preferably bond to O11O12 site with the binding constants logK = 8.19 and 7.86 for CuHL+ and CuL±, respectively. The second chelating site was suggested to be O2O3 with the binding constants of logK = 4.41 and 4.62 for Cu2HL3+ and Cu2L2+, respectively. The suppressed quantum yield of OTC by Cu2+ chelation was accused for their intra-/inter-molecular electron transfer, by which the energy in activated states was distributed. The occurrence of electron transfer between BCD ring and A ring also from BCD ring to Cu was evidenced by the TD-DFT result only for the OTC-Cu complexes. Besides, the cyclic voltammetry measurement also suggested one OTC-Cu(II)/OTC-Cu(I) redox couple. These results suggested that the persistence of OTC in environmental surface waters will probably be underestimated for neglecting the chelating effect of Cu2+. The photolysis quantum yield of OTC-Cu complexes, as well as the specific molar absorption constants, the equilibrium binding constants of Cu2+ with OTC could contribute to more accurate kinetic models of OTC. PMID:27155101

  4. Dicarboxylate assisted synthesis of the monoclinic heterometallic tetrathiocyanato bridged copper(II) and mercury(II) coordination polymer {l_brace}Cu[Hg(SCN){sub 4}]{r_brace}{sub n}: Synthesis, structural, vibration, luminescence, EPR studies and DFT calculations

    SciTech Connect

    Khandar, Ali Akbar; Klein, Axel; Bakhtiari, Akbar; Mahjoub, Ali Reza; Pohl, Roland W.H.

    2011-02-15

    The synthesis of the monoclinic polymorph of {l_brace}Cu[Hg(SCN){sub 4}]{r_brace}{sub n} is reported. The compound, as determined by X-ray diffraction of a twinned crystal, consists of mercury and copper atoms linked by {mu}{sub 1,3}-SCN bridges. The crystal packing shows a highly porous infinite 3D structure. Diagnostic resonances for the SCN{sup -} 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 {pi}{sup *} 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 d{sub x}{sup 2}{sub -y}{sup 2} orbital. -- Graphical abstract: Synthesis and X-ray structure determination of the monoclinic {l_brace}Cu[Hg(SCN){sub 4}]{r_brace}{sub n} is reported. The IR, far-IR, Raman, photoluminescence as well as EPR spectra of the compound is discussed. Also, the emission and semiconducting behavior of the compound is illustrated through the density functional theory calculation of electronic band structure along with density of states. Display Omitted Research highlights: > The monoclinic {l_brace}Cu[Hg(SCN){sub 4}]{r_brace}{sub n} has been prepared. > The structure of the compound is determined by XRD of a twinned crystal. > The IR, far-IR, Raman, EPR and emission spectra of the compound is investigated. > As shown by DFT calculations, the emission bands of the compound are mainly LLCT. > Small MLCT from the copper to the thiocyanate groups contributes to these bands.

  5. Understanding the Adsorption of PFOA on MIL-101(Cr)-Based Anionic-Exchange Metal-Organic Frameworks: Comparing DFT Calculations with Aqueous Sorption Experiments.

    PubMed

    Liu, Kai; Zhang, Siyu; Hu, Xiyue; Zhang, Kunyang; Roy, Ajay; Yu, Gang

    2015-07-21

    To examine the effects of different functionalization methods on adsorption behavior, anionic-exchange MIL-101(Cr) metal-organic frameworks (MOFs) were synthesized using preassembled modification (PAM) and postsynthetic modification (PSM) methods. Perfluorooctanoic acid (PFOA) adsorption results indicated that the maximum PFOA adsorption capacity was 1.19 and 1.89 mmol g(-1) for anionic-exchange MIL-101(Cr) prepared by PAM and PSM, respectively. The sorption equilibrium was rapidly reached within 60 min. Our results indicated that PSM is a better modification technique for introducing functional groups onto MOFs for adsorptive removal because PAM places functional groups onto the aperture of the nanopore, which hinders the entrance of organic contaminants. Our experimental results and the results of complementary density functional theory calculations revealed that in addition to the anion-exchange mechanism, the major PFOA adsorption mechanism is a combination of Lewis acid/base complexation between PFOA and Cr(III) and electrostatic interaction between PFOA and the protonated carboxyl groups of the bdc (terephthalic acid) linker. PMID:26066631

  6. Synthesis, characterization of (3E)-1-(6-chloro-2-methyl-4-phenyl quinolin-3-Yl)-3-aryl prop-2-en-1-ones through IR, NMR, single crystal X-ray diffraction and insights into their electronic structure using DFT calculations

    NASA Astrophysics Data System (ADS)

    Sarveswari, S.; Srikanth, A.; Arul Murugan, N.; Vijayakumar, V.; Jasinski, Jerry P.; Beauchesne, Hanna C.; Jarvis, Ethan E.

    2015-02-01

    3E-1-(6-Chloro-2-methyl-4-phenylquinolin-3-yl)-3-arylprop-2-en-1-ones were synthesized and characterized by FTIR, 1H NMR, 13C NMR, HSQC, DEPT-135. In addition the compound 3E-1-(6-chloro-2-methyl-4-phenylquinolin-3-yl)-3-(2,5-dimethoxyphenyl)prop-2-en-1-one was subjected to the single crystal X-ray diffraction studies. Density functional theory calculations were carried out for this chalcone and its derivatives to investigate into their electronic structure, chemical reactivity, linear and non-linear optical properties. The structure predicted from DFT for chalcone is in good agreement with the structure from XRD measurement.

  7. Synthesis, crystal structures HOMO-LUMO analysis and DFT calculation of new complexes of p-substituted dibenzyltin chlorides and 1,10-phenanthroline.

    PubMed

    Chandrasekar, S; Balachandran, V; Evans, Helen-Stoeckli; Latha, A

    2015-05-15

    In the present work, the complex formation of p-substituted dibenzyltin dichlorides with 1,10-phenanthroline. The reaction of (p-MeBz)2SnCl2 with 1,10-phenanthroline results (p-MeBz)2SnCl2-1,10-phenanthroline complex, (2a). Likewise (p-ClBz)2SnCl2 with 1,10-phenanthroline results (p-ClBz)2SnCl2-1,10-phenanthroline complex, (2b), in the similar reaction conditions. The IR, (1)H NMR, (13)C NMR, (119)Sn NMR spectral analyses indicate that the formation of hexacoordinated tin(IV) complexes in 1:1 ratio. The crystal structures of complexes 2a and 2b show that the tin atom is in regular octahedral geometry with the benzyl groups in the equidirectional positions. A comparison was made with the structural data of other R2SnX2-1,10-phenathroline derivatives. Fourier transforms infrared and Raman spectral studies were performed for analyzing and assigning the vibrations and to identify the functional groups. Optimized geometrical parameters, harmonic vibrational frequencies, frontier molecular orbitals were obtained by DFT/B3LYP method combined with LanL2DZ basis set. PMID:25725209

  8. Comparative spectroscopic and DFT calculations of binary and ternary complexes derived from 4-allyl-1-(2-hydroxybenzoyl) thiosemicarbazide (L¹) and 2,2'-dipyridyl.

    PubMed

    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 (L(1)) with MX2 (M=Co(2+), Cu(2+) and Zn(2+) ions; X=Cl(-) in case of Co(2+) and Cu(2+) ions and Cl(-) and Ac(-) in case of Zn(2+) ion) in EtOH were synthesized and characterized. The results suggested that the binary and ternary complexes have the general formulae, [Cu(L(1)-2H)(EtOH)], [Co(L(1)-2H)(H₂O)₂]⋅H₂O and [Zn(L(1)-2H) (H₂O)1/2]⋅½EtOH, [Cu₂(dipy)(L(1)-2H)(OH)₂(H₂O)], [Co(dipy)(L(1)-2H)]⋅4H₂O and [Zn(dipy)(L(1)-2H)]. The binary and ternary complexes were characterized by elemental analyses, molar conductivities, spectral (IR, UV-vis; (1)H 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 (1)H NMR spectra. All the geometries of the ligands and the complexes are confirmed using DFT method from DMOL(3). The biological activity for the L(1) and two metal complexes were tested against DNA. PMID:25036455

  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. 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.

  11. 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.

  12. 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. PMID:26492162

  13. 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.

  14. 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.

  15. FT-IR and FT-Raman spectral investigation, computed IR intensity and Raman activity analysis and frequency estimation analysis on 4-chloro-2-bromoacetophenone using HF and DFT calculations

    NASA Astrophysics Data System (ADS)

    Ramalingam, S.; Anbusrinivasan, P.; Periandy, S.

    2011-02-01

    In this work, the experimental and theoretical spectra of 4-chloro-2-bromoacetophenone (4C2BAP) are studied. FT-IR and FT-Raman spectra of title molecule have been recorded in the region 4000-100 cm -1. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock and density functional method (B3LYP) with the 6-31G (d, p) and 6-311G (d, p) basis sets. The vibrational frequencies are calculated and scaled values are compared with the experimental FT-IR and FT-Raman spectra. The DFT (B3LYP/6-311G (d, p)) calculations are more reliable than the ab initio HF/6-311G (d, p) calculations for the vibrational study of 4C2BAP. The optimized geometric parameters (bond lengths and bond angles) are compared with experimental values of the molecule. The alteration of vibrational bands of the carbonyl and acetyl groups due to the presence of halogens (Cl and Br) in the base molecule is also investigated from their characteristic region of linked spectrum.

  16. FT-IR and FT-Raman spectral investigation, computed IR intensity and Raman activity analysis and frequency estimation analysis on 4-chloro-2-bromoacetophenone using HF and DFT calculations.

    PubMed

    Ramalingam, S; Anbusrinivasan, P; Periandy, S

    2011-02-01

    In this work, the experimental and theoretical spectra of 4-chloro-2-bromoacetophenone (4C2BAP) are studied. FT-IR and FT-Raman spectra of title molecule have been recorded in the region 4000-100 cm(-1). The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock and density functional method (B3LYP) with the 6-31G (d, p) and 6-311G (d, p) basis sets. The vibrational frequencies are calculated and scaled values are compared with the experimental FT-IR and FT-Raman spectra. The DFT (B3LYP/6-311G (d, p)) calculations are more reliable than the ab initio HF/6-311G (d, p) calculations for the vibrational study of 4C2BAP. The optimized geometric parameters (bond lengths and bond angles) are compared with experimental values of the molecule. The alteration of vibrational bands of the carbonyl and acetyl groups due to the presence of halogens (Cl and Br) in the base molecule is also investigated from their characteristic region of linked spectrum. PMID:21216662

  17. GGA+U-DFT+U modeling structural, electronic and magnetic properties investigation on the ferromagnetic and anti-ferromagnetic BaFeO3 characteristics: Insights from First-principle calculation

    NASA Astrophysics Data System (ADS)

    Noura, Hamdad

    2014-12-01

    Based on first-principles calculation the change of magnetic configurations and electronic structure of perovskite oxide BaFeO3 is investigated by introducing a new potential energy function which has been determined via the density functional theory basis with U-Hubbard Hamiltonian (DFT+U). The exchange and correlation potential is employed using GGA+U approach by combining available experimental measurements and the data from the current theoretical calculations. The implementation of the U-Hubbard term in this calculation allows more comprehension on the BaFeO3 behavior and has ameliorated the obtained results. The spin effect is given for the considerable oxide by investing the cubic phase. Possible different magnetic configurations (ferromagnetic FM and anti-ferromagnetic AFM) for the BaFeO3 oxide. The implementation of the new approach GGA+U shows the Coulomb interaction inside the d-states exactly which can play an important role in the orbital systems of both elements the ferrite (Fe) and barium (Ba). By the band structure and the densities of states analysis. BaFeO3 is a strong candidate for spintronic applications.

  18. 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.

  19. Revised vibrational band assignments for the experimental IR and Raman spectra of 2,3,4-trifluorobenzonitrile based on ab initio, DFT and normal coordinate calculations

    NASA Astrophysics Data System (ADS)

    Hiremath, C. S.; Kalkoti, G. B.; Aralakkanavar, M. K.

    2009-09-01

    In the present study, a systematic vibrational spectroscopic investigation for the experimental IR and Raman spectra of 2,3,4-trifluorobenzonitrile (TFB), aided by electronic structure calculations has been carried out. The electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) - have been performed with 6-31G* basis set. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. The results of the calculations have been used to simulate IR and Raman spectra for TFB that showed excellent agreement with the observed spectra. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed. A complete assignment of the observed spectra has been proposed.

  20. The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods

    NASA Astrophysics Data System (ADS)

    Pohl, Gabor; Plumley, Joshua A.; Dannenberg, J. J.

    2013-06-01

    We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.

  1. Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene.

    PubMed

    Bayrakdar, A; Kart, H H; Elcin, S; Deligoz, H; Karabacak, M

    2015-02-01

    In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and (1)H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000-400 cm(-1). (1)H NMR spectrum is recorded for 0.1-0.2 M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for (1)H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO-LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement. PMID:25448961

  2. Simulation of a tetramer form of 5-chlorouracil: The vibrational spectra and molecular structure in the isolated and in the solid state by using DFT calculations

    NASA Astrophysics Data System (ADS)

    Ortiz, S.; Alcolea Palafox, M.; Rastogi, V. K.; Akitsu, T.; Hubert Joe, I.; Kumar, Satendra

    2013-06-01

    A Raman and FT-IR study of the biomolecule 5-chlorouracil in the solid state was carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify the assignments of the experimentally observed bands in the spectra. Calculations in the monomer form and comparisons with the experimental data in Ar matrix were also carried out. The error in the calculated frequencies was analyzed and reduced by using scaling equations and scaling factors deduced from the uracil molecule. The calculations with the B3LYP method and with the 6-31G(d,p) and 6-311+G(2d,p) basis set, appear in general to be useful, when combining with a scaling equation procedure or with the specific scale factors, for interpretation of the general features of the IR and Raman spectra. The scaled values were used in the reassignment of the IR and Raman experimental bands. Comparison of the results with those determined in uracil and 5-halogenated derivatives were performed. The substitution at 5-position of the uracil ring by a chlorine atom has a little effect on the geometric parameters.

  3. 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.

  4. Molecular structure-optical property relationships of 1,3-bis (4-methoxyphenyl) prop-2-en-1-one: A DFT and TD-DFT investigation

    NASA Astrophysics Data System (ADS)

    Ghomrasni, S.; Aribi, I.; Ayachi, S.; Haj Said, A.; Alimi, K.

    2015-08-01

    Some fundamental properties of the 1,3-bis (4-methoxyphenyl) prop-2-en-1-one, as functional monomer, are measured as well as calculated. The combined results are used for modeling and predicting monomer structure-property relationships. Thus, theoretical calculations based on Density Functional Theory (DFT) and its Time-Dependent counterpart (TD-DFT) are performed to evaluate the vibrational frequencies [IR and Raman], magnetic shielding for nuclear magnetic resonance [1H and 13C NMR], electronic and optical properties of the studied material, respectively. The DFT/TD-DFT at B3LYP with 6-31G(d,p), 6-31G(d) and 3-21G(d) were employed to choose appropriate basis set that provides a more accurate molecular-property description. The simulated spectra are found to agree well, in shape, position, and relative intensity of peaks, with the available experimental measurements. In addition, frontier molecular orbitals, Mullikan charge and electron spin density distributions are carried out. Our results highlight the use of predictive calculations to provide an in-depth understanding evidence of the electrochemically-initiated monomer reactivity.

  5. 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.

  6. 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.

  7. 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

    2015-03-01

    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. PMID:25498822

  8. (2-Aminopyrimidine-κN(1))aqua(pyridine-2,6-dicarboxylato-κ(3)O(2),N,O(6))copper(II): X-ray and DFT calculated structure.

    PubMed

    Yousefi, Zakieh; Eshtiagh-Hosseini, Hossein; Salimi, Alireza; Soleimannejad, Janet

    2015-05-01

    In the title compound, [Cu(C7H3N2O4)(C4H5N2)(H2O)], (I), pyridine-2,6-dicarboxylate (pydc(2-)), 2-aminopyrimidine and aqua ligands coordinate the Cu(II) centre through two N atoms, two carboxylate O atoms and one water O atom, respectively, to give a nominally distorted square-pyramidal coordination geometry, a common arrangement for copper complexes containing the pydc(2-) ligand. Because of the presence of Cu...Xbridged contacts (X = N or O) between adjacent molecules in the crystal structures of (I) and three analogous previously reported compounds, and the corresponding uncertainty about the effective coordination number of the Cu(II) centre, density functional theory (DFT) calculations were used to elucidate the degree of covalency in these contacts. The calculated Wiberg and Mayer bond-order indices reveal that the Cu...O contact can be considered as a coordination bond, whereas the amine group forming a Cu...N contact is not an effective participant in the coordination environment. PMID:25940895

  9. 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.

  10. Inelastic and elastic neutron scattering studies of the vibrational and reorientational dynamics, crystal structure and solid-solid phase transition in [Mn(OS(CH₃)₂)₆](ClO₄)₂ supported by theoretical (DFT) calculations.

    PubMed

    Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna

    2015-06-15

    The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made. PMID:25795611

  11. 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.

  12. [CALCULATION OF RADIATION LOADS ON THE ANTHROPOMORPHIC PHANTOM ONBOARD THE SPACE STATION IN THE CASE OF ADDITIONAL SHIELDING].

    PubMed

    Kartashov, D A; Shurshakov, V A

    2015-01-01

    The paper presents the results of calculating doses from space ionizing radiation for a modeled orbital station cabin outfitted with an additional shield aimed to reduce radiation loads on cosmonaut. The shield is a layer with the mass thickness of -6 g/cm2 (mean density = 0.62 g/cm3) that covers the outer cabin wall and consists of wet tissues and towels used by cosmonauts for hygienic purposes. A tissue-equivalent anthropomorphic phantom imitates human body. Doses were calculated for the standard orbit of the International space station (ISS) with consideration of the longitudinal and transverse phantom orientation relative to the wall with or without the additional shield. Calculation of dose distribution in the human body improves prediction of radiation loads. The additional shield reduces radiation exposure of human critical organs by -20% depending on their depth and body spatial orientation in the ISS compartment. PMID:26554132

  13. Structural, Electronic, and Optical Properties of BiOX1-xYx (X, Y = F, Cl, Br, and I) Solid Solutions from DFT Calculations.

    PubMed

    Zhao, Zong-Yan; Liu, Qing-Lu; Dai, Wen-Wu

    2016-01-01

    Six BiOX1-xYx (X, Y = F, Cl, Br, and I) solid solutions have been systematically investigated by density functional theory calculations. BiOCl1-xBrx, BiOBr1-xIx, and BiOCl1-xIx solid solutions have very small bowing parameters; as such, some of their properties increase almost linearly with increasing x. For BiOF1-xYx solid solutions, the bowing parameters are very large and it is extremely difficult to fit the related calculated data by a single equation. Consequently, BiOX1-xYx (X, Y = Cl, Br, and I) solid solutions are highly miscible, while BiOF1-xYx (Y = Cl, Br, and I) solid solutions are partially miscible. In other words, BiOF1-xYx solid solutions have miscibility gaps or high miscibility temperature, resulting in phase separation and F/Y inhomogeneity. Comparison and analysis of the calculated results and the related physical-chemical properties with different halogen compositions indicates that the parameters of BiOX1-xYx solid solutions are determined by the differences of the physical-chemical properties of the two halogen compositions. In this way, the large deviation of some BiOX1-xYx solid solutions from Vegard's law observed in experiments can be explained. Moreover, the composition ratio of BiOX1-xYx solid solutions can be measured or monitored using optical measurements. PMID:27549344

  14. 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

  15. Raman spectrum, conformational stability, barriers to internal rotations and DFT calculations of 1,1,1-trifluoro-propane-2-thione with double-internal-symmetric rotor.

    PubMed

    Mohamed, Tarek A; Farag, Rabei S

    2005-12-01

    The Raman spectrum (3500-100 cm-1) of 1,1,1-trifluoro-propane-2-thione (TFPT), CF3C(S)CH3 of the solid phase has been recorded. The internal rotation of CH3 and/or CF3 moieties around CC bonds in TFPT allow five hypothetical conformers (Cs and C1 point groups). Aided by quantum chemical (QC) calculations, the Cc conformer is the only stable form (CF3 and CH3 groups are eclipsing the CS bond) which contains a planar FCC(S)CH backbone and possess intramolecular hydrogen sulfur interactions. However, other conformations (with the orientation of sulfur atom being trans to either hydrogen or fluorine atom) are either transition states or not fully converged geometry with "gauche" orientation. Moreover, the calculation were carried out at the level of Becke three Lee-Yan-Parr (B3LYP) parameters up to 6-311++G(d,p) basis sets. The torsional barriers are adequately described by a three-fold potential, V3 which have been determined utilizing the optimized structural parameters from the B3LYP/6-31G(d) basis set along with potential surface scan. Barriers of 1.28 kcal/mol (448 cm-1) and 1.94 kcal/mol (678 cm-1) were calculated for CH3 and CF3 symmetric rotors, respectively. Complete vibrational assignments have been reported for the stable Cc isomer which is supported by normal coordinate analysis and potential energy distributions (PEDs) for all fundamentals. Moreover, equilibrium geometries, vibrational frequencies are compared to the corresponding experimental values of acetone, 1,1,1-trifluoroacetone (TFA), hexafluoroacetone (HFA) and other molecules having the CF3 moiety whenever appropriate. PMID:16303627

  16. 1-Vinyl-5-amino-1 H-tetrazole: X-ray molecular and crystal structures and quantum-chemical DFT calculations

    NASA Astrophysics Data System (ADS)

    Lyakhov, Alexander S.; Matulis, Vadim E.; Gaponik, Pavel N.; Voitekhovich, Sergei V.; Ivashkevich, Oleg A.

    2008-03-01

    The crystal and molecular structures of 1-vinyl-5-amino-1 H-tetrazole (VAT) were determined by single crystal X-ray diffraction. The amino group lies in the plane of the tetrazole ring and valence angles around the N atom are close to 120°, the exocyclic C sbnd N amino bond being substantially shorter in comparison with "normal" C sbnd N bond. Natural bond orbital analysis was performed, using density functional theory B3LYP method, to explain the structural peculiarities of crystalline VAT. By using MO calculations, relative stability of all possible tautomeric forms of protonated VAT molecule was investigated.

  17. 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.

  18. 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.

  19. Crystal structure, DFT and HF calculations and radical scavenging activities of (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol

    NASA Astrophysics Data System (ADS)

    Alaşalvar, Can; Soylu, Mustafa Serkan; Güder, Aytaç; Albayrak, Çiğdem; Apaydın, Gökhan; Dilek, Nefise

    In this study, (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol has been synthesized and characterized by using X-ray technique and FT-IR experimentally and using B3LYP/6-31G(d,p) and HF/6-31G(d,p) methods theoretically. The intermolecular and intramolecular interactions of the title compound have been determined according to X-ray results. The molecular geometry, vibrational frequencies of the title compound in the ground state have been calculated using the density functional B3LYP and HF method with the 6-31G(d,p) basis set and calculated bond parameters and vibrational frequencies values show good agreement with experimental values. Theoretical and experimental results show that tautomeric form of the structure is phenol-imine form. Besides HOMO-LUMO energy gap, molecular electrostatic potential map were performed at B3LYP/6-31G(d,p) level. It is worthy note of that, the free radical scavenging activities of the title compound were assessed using DPPHrad , DMPDrad +, and ABTSrad + assays. The obtained results show that the title compound has effective DPPHrad (SC50 2.61 ± 0.09 μg/mL), DMPDrad + (SC50 2.82 ± 0.14 μg/mL), and ABTSrad + (SC50 4.91 ± 0.18 μg/mL) radical scavenging activities when compared with standard antioxidants (BHA, rutin, and trolox).

  20. Determination of a solvent hydrogen-bond acidity scale by means of the solvatochromism of pyridinium-N-phenolate betaine dye 30 and PCM-TD-DFT calculations.

    PubMed

    Cerón-Carrasco, José P; Jacquemin, Denis; Laurence, Christian; Planchat, Aurélien; Reichardt, Christian; Sraïdi, Khadija

    2014-05-01

    Empirical parameters of solvents describing their hydrogen-bond (HB) acidity (e.g., the Kamlet-Taft α parameter) are often difficult to determine for new solvents because they are not directly related to a single definition process. Here, we propose a simple method based on one probe, the betaine dye 30, and one reference process, the solvatochromism of this dye, measured by its first electronic transition energy, ET(30). These ET(30) values are calculated within the time-dependent density functional theory framework, using a polarizable continuum solvent model (PCM). The part of ET(30) values that is not included in the PCM calculation is taken as the HB component of the measured ET(30) values, allowing us to deduce a solvent HB acidity parameter α1. The validity of this simple model is assessed by good linear correlations between α1 and a variety of solute properties mainly depending on the solvent's HB acidity. The quality of fit observed with α1 is at least comparable with that obtained by previous solvent HB acidity scales. The simplicity of our method is illustrated by the determination of α1 and of its companion, the electrostatic solvent parameter ES, for some new green solvents derived from glycerol. PMID:24702635

  1. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation.

    PubMed

    Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-28

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals. PMID:27475350

  2. 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.

  3. A comparison of experimental and DFT calculations of ¹⁹⁵Pt NMR shielding trends for [PtX(n)Y(6-n)](2-) (X, Y = Cl, Br, F and I) anions.

    PubMed

    Burger, Marga R; Kramer, J; Chermette, H; Koch, Klaus R

    2010-12-01

    A comparison between experimental and calculated gas-phase as well as the conductor-like screening model DFT (195)Pt chemical shifts of a series of octahedral [PtX(6-n)Y(n)](2-) complexes for X = Cl, Br, F, I was carried out to assess the accuracy of computed NMR shielding and to gain insight into the dominant σ(dia), σ(para) and σ(SO) shielding contributions. The discrepancies between the experimental and the DFT-calculated (195)Pt chemical shifts vary for these complexes as a function of the coordinated halide ions, the largest being obtained for the fluorido-chlorido and fluorido-bromido complexes, while negligible discrepancies are found for the [PtCl(6-n)Br(n)](2-) series; the discrepancies are somewhat larger where a significant deviation from the ideal octahedral symmetry such as for the geometric cis/trans or fac/mer isomers of [PtF(6-n)Cl(n)](2-) and [PtF(6-n)Br(n)](2-) may be expected. The discrepancies generally increase in the order [PtCl(6-n)Br(n)](2-) < [PtBr(6-n)I(n)](2-) < [PtCl(6-n)I(n)](2-) < [PtF(6-n)Br(n)](2-) ≈ [PtF(6-n)Cl(n)](2-), and show a striking correlation with the increase in electronegativity difference Δχ between the two halide ligands (X(-) and Y(-)) bound to Pt(IV) for these anions: 0.09 < 0.52 < 0.63 < 1.36 ≈ 1.27, respectively. The computed (195)Pt sensitivity to Pt-X bond displacement, ∂(δ(195)Pt)/∂(ΔPt-X), of these complexes is very large and depends on the halide ion, decreasing from 24 800, 18 300, 15 700 to 12 000 ppm/Å for [PtF(6)](2-), [PtCl(6)](2-), [PtBr(6)](2-) and [PtI(6)](2-), respectively. PMID:21104761

  4. Modeling Ti/Ge Distribution in LiTi2-xGex(PO4)3 NASICON Series by (31)P MAS NMR and First-Principles DFT Calculations.

    PubMed

    Diez-Gómez, Virginia; Arbi, Kamel; Sanz, Jesús

    2016-08-01

    Ti/Ge distribution in rhombohedral LiTi2-xGex(PO4)3 NASICON series has been analyzed by (31)P magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and first-principles density functional theory (DFT) calculations. Nuclear magnetic resonance is an excellent probe to follow Ti/Ge disorder, as it is sensitive to the atomic scale environment without long-range periodicity requirements. In the samples considered here, PO4 units are surrounded by four Ti/Ge octahedra, and then, five different components ascribed to P(OTi)4, P(OTi)3(OGe), P(OTi)2(OGe)2, P(OTi)(OGe)3, and P(OGe)4 environments are expected in (31)P MAS NMR spectra of R3̅c NASICON samples. However, (31)P MAS NMR spectra of analyzed series display a higher number of signals, suggesting that, although the overall symmetry remains R3̅c, partial substitution causes a local decrement in symmetry. With the aid of first-principles DFT calculations, 10 detected (31)P NMR signals have been assigned to different Ti4-nGen arrangements in the R3 subgroup symmetry. In this assignment, the influence of octahedra of the same or different R2(PO4)3 structural units has been considered. The influence of bond distances, angles and atom charges on (31)P NMR chemical shieldings has been discussed. Simulation of the LiTi2-xGex(PO4)3 series suggests that detection of 10 P environments is mainly due to the existence of two oxygen types, O1 and O2, whose charges are differently affected by Ge and Ti occupation of octahedra. From the quantitative analysis of detected components, a random Ti/Ge distribution has been deduced in next nearest neighbor (NNN) sites that surround tetrahedral PO4 units. This random distribution was supported by XRD data displaying Vegard's law. PMID:27373306

  5. Improved DFT Potential Energy Surfaces via Improved Densities.

    PubMed

    Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron

    2015-10-01

    Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases. PMID:26722874

  6. Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

    NASA Astrophysics Data System (ADS)

    Tarcan, Erdoğan; Altındağ, Özgü; Avcı, Davut; Atalay, Yusuf

    2008-11-01

    The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C 3H 7N 6+·C 8H 5O 4-) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000-100 cm -1 region where the theoretical evaluation and assignment of all observed bands were made.

  7. Validation of Relativistic DFT Approaches to the Calculation of NMR Chemical Shifts in Square-Planar Pt(2+) and Au(3+) Complexes.

    PubMed

    Pawlak, Tomasz; Munzarová, Markéta L; Pazderski, Leszek; Marek, Radek

    2011-12-13

    Recently implemented hybrid density functional methods of calculating nuclear magnetic shielding using the two-component zeroth-order regular approximation approach (J. Phys. Chem. A2009, 113, 11495) have been employed for a series of compounds containing heavy transition-metal atoms. These include Pt(2+), Pd(2+), and Au(3+) organometallics and metal complexes with azines, some of which exhibit interesting biological and catalytic activities. In this study we investigate the effects of geometry, exchange-correlation functional, solvent, and scalar relativistic and spin-orbit corrections on the nuclear magnetic shielding-mainly for (13)C and (15)N atoms connected to a heavy-atom center. Our calculations demonstrate that the B3LYP method using effective core potentials and a cc-pwCVTZ-PP/6-31G** basis set augmented with the polarizable continuum model of the dimethylsulfoxide solvent provides geometries for the complexes in question which are compatible with the experimental NMR results in terms of both the trends and the absolute values of the (13)C shifts. The important role of the exact exchange admixture parameter for hybrid functionals based on B3LYP and PBE0 is investigated systematically for selected Pt(2+) and Au(3+) complexes. The (13)C and (15)N NMR chemical shifts are found to be best reproduced by using a B3LYP or PBE0 approach with 30% and 40-50% exact exchange admixtures for the Pt(2+) and Au(3+) complexes, respectively. The spin-orbit contributions to the (15)N NMR chemical shifts reflect metal-ligand bonding that is much more ionic for the Au(3+) than for the Pt(2+) complex. Finally, an optimized density functional method is applied to a series of transition-metal complexes to estimate the scope and the limitations of the current approach. PMID:26598337

  8. Crystal structure, DFT and HF calculations and radical scavenging activities of (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol.

    PubMed

    Alaşalvar, Can; Soylu, Mustafa Serkan; Güder, Aytaç; Albayrak, Çiğdem; Apaydın, Gökhan; Dilek, Nefise

    2014-05-01

    In this study, (E)-4,6-dibromo-3-methoxy-2-[(3-methoxyphenylimino)methyl]phenol has been synthesized and characterized by using X-ray technique and FT-IR experimentally and using B3LYP/6-31G(d,p) and HF/6-31G(d,p) methods theoretically. The intermolecular and intramolecular interactions of the title compound have been determined according to X-ray results. The molecular geometry, vibrational frequencies of the title compound in the ground state have been calculated using the density functional B3LYP and HF method with the 6-31G(d,p) basis set and calculated bond parameters and vibrational frequencies values show good agreement with experimental values. Theoretical and experimental results show that tautomeric form of the structure is phenol-imine form. Besides HOMO-LUMO energy gap, molecular electrostatic potential map were performed at B3LYP/6-31G(d,p) level. It is worthy note of that, the free radical scavenging activities of the title compound were assessed using DPPH˙, DMPD˙(+), and ABTS˙(+) assays. The obtained results show that the title compound has effective DPPH˙ (SC50 2.61±0.09 μg/mL), DMPD˙(+) (SC50 2.82±0.14 μg/mL), and ABTS˙(+) (SC50 4.91±0.18 μg/mL) radical scavenging activities when compared with standard antioxidants (BHA, rutin, and trolox). PMID:24566110

  9. 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.

  10. Interface morphology and DFT computation of L-valinium fumarate

    NASA Astrophysics Data System (ADS)

    Liu, Xiaojing; Xu, Xijin; Zhang, Changwen

    2015-02-01

    Based on crystal surface observation from AFM, the growth mechanism of L-valinium fumarate (LVF) crystal is in agreement with continuous growth mode. It is suggested that the microcrystals and pits may lead to the formation of inclusion macrodefects during growth. In addition, quantum chemical computations based on density functional theory (DFT) have been performed on LVF. The optimized molecular geometry, natural bond orbital analysis, Mulliken's net charges and frontier molecular orbital analysis have been calculated. The linear polarizability and first hyperpolarizability have also been computed.

  11. Structural, magnetic, and redox diversity of first-row transition metal complexes of a pyridine-based macrocycle: well-marked trends supported by theoretical DFT calculations.

    PubMed

    Drahoš, Bohuslav; Herchel, Radovan; Trávníček, Zdeněk

    2015-04-01

    A series of first-row transition metal complexes with 15-membered pyridine-based macrocycle (3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1(18),14,16-triene = L) was prepared ([M(II)(L)Cl2], where M = Mn, Co, Ni, Zn (1, 3, 4, 6); [Fe(III)(L)Cl2]Cl (2), [Cu(II)(L)Cl]Cl (5)) and thoroughly characterized. Depending on the complexated metal atom, the coordination number varies from 7 (Mn, Fe, Co), through 5 + 2 for Ni and 4 + 1 for Cu, to 5 for Zn accompanied by changes in the coordination geometry from the pentagonal bipyramid (1-4) to the square pyramid (5 and 6). Along the series, the metal-oxygen distances were prolonged in such manner that their bonding character was investigated, apart from X-ray structural analysis, also by ab initio calculations (Mayer's bond order, electron localization function), which confirmed that, in 4 and 5, two and one oxygen donor atoms are semicoordinated, respectively, and one and two oxygen atoms are uncoordinated in 5, and 6, respectively. On the basis of the temperature variable magnetic susceptibility measurements, 1 and 2 behave as expected for 3d(5) high-spin configuration with negligible zero-field splitting (ZFS). On the other hand, a large axial ZFS (D(Co) ≈ 40 cm(-1), D(Ni) ≈ -6.0 cm(-1)) was found for 3 and 4, and rhombic ZFS (E/D ≈ 0.15) for 4. Antiferromagnetic exchange coupling was observed for 4 and 5 (J(Ni) = -0.48 cm(-1), and J(Cu) = -2.43 cm(-1), respectively). The obtained results correlate well with ab initio calculations of ZFS parameters as well as J-values, which indicate that the antiferromagnetic exchange is mediated by hydrogen bonds. The complexes were also investigated by cyclic voltammetry in water or acetonitrile. A quasi-reversible couple Mn(II)/Mn(III) at 1.13/0.97 V, an almost reversible couple Fe(II)/Fe(III) at 0.51/0.25 V, and a one-step/multistep reduction/oxidation of Cu(II) complex 5 at -0.33 V/0.06-0.61 V were detected. PMID:25761063

  12. A highly oxidizing and isolable oxoruthenium(V) complex [Ru(V)(N4O)(O)]2+: electronic structure, redox properties, and oxidation reactions investigated by DFT calculations.

    PubMed

    Guan, Xiangguo; Chan, Sharon Lai-Fung; Che, Chi-Ming

    2013-09-01

    The electronic structure and redox properties of the highly oxidizing, isolable Ru(V)=O complex [Ru(V)(N4O)(O)](2+), its oxidation reactions with saturated alkanes (cyclohexane and methane) and inorganic substrates (hydrochloric acid and water), and its intermolecular coupling reaction have been examined by DFT calculations. The oxidation reactions with cyclohexane and methane proceed through hydrogen atom transfer in a transition state with a calculated free energy barrier of 10.8 and 23.8 kcal mol(-1), respectively. The overall free energy activation barrier (ΔG(≠)=25.5 kcal mol(-1)) of oxidation of hydrochloric acid can be decomposed into two parts: the formation of [Ru(III)(N4O)(HOCl)](2+) (ΔG=15.0 kcal mol(-1)) and the substitution of HOCl by a water molecule (ΔG(≠)=10.5 kcal mol(-1)). For water oxidation, nucleophilic attack on Ru(V)=O by water, leading to O-O bond formation, has a free energy barrier of 24.0 kcal mol(-1), the major component of which comes from the cleavage of the H-OH bond of water. Intermolecular self-coupling of two molecules of [Ru(V)(N4O)(O)](2+) leads to the [(N4O)Ru(IV)-O2-Ru(III)(N4O)](4+) complex with a calculated free energy barrier of 12.0 kcal mol(-1). PMID:23788366

  13. Effects of Fe2+ and Zn2+ substitution on the structure and high-pressure stability of MgAl2O4 spinel from DFT calculations

    NASA Astrophysics Data System (ADS)

    Dutta, Rajkrishna; Mandal, Nibir

    2012-09-01

    Using density functional theory we show the effects of transition (Fe2+) and non-transition (Zn2+) divalent cationic substitutions on the following structural parameters: lattice parameters, bond lengths and polyhedral volumes under varying hydrostatic pressures. Fe2+ and Zn2+ substitutions lead to contrasting modifications of tetrahedral Mg-O bond lengths. Fe2+ (50%)increase the tetrahedral Mg-O bond lengths by 0.21%, whereas Zn2+ (50%) reduce it by 0.06%.We present the equations of state of Mg spinel with 50% Fe and Zn substitutions as a function of pressure. This study presents the decomposition pressure (PT) of spinel to periclase (MgO) and corundum (α-Al2O3) as a function of Fe and Zn concentrations (x). For pure spinel, PT=12.1 GPa. Fe2+substitution lowers PT linearly with its concentration as PT=-12.56x+12.02. But, Zn2+ increases PT non-linearly along a quadratic relation: PT=42.057x2+14.171x+12.174. We calculated the C44 elastic constant to explain the contrasting effects of Fe and Zn on the decomposition pressure of spinel phase.

  14. 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.

  15. H2 adsorption and dissociation on PdO(101) films supported on rutile TiO2 (110) facet: elucidating the support effect by DFT calculations.

    PubMed

    Sun, Xiongfei; Peng, Xing; Xu, Xianglan; Jin, Hua; Wang, Hongming; Wang, Xiang

    2016-09-01

    To explore metal oxide-support interactions and their effect, H2 adsorption and dissociation on PdO(101)/TiO2(110) films with different film thicknesses, in comparison with that on pure PdO(101) surface without TiO2(110) support, were studied by density functional theory calculation. A monolayer PdO(101) film supported on TiO2 facet shows different properties to a pure PdO(101) surface. On the monolayer PdO(101)/TiO2(110) film, TiO2 support leads to stronger molecular adsorption of H2 on coordinatively unsaturated Pd top sites than that on a pure PdO surface. H2 dissociation with the formation of OH was preferred thermodynamically but slightly unfavorable kinetically on the monolayer PdO film due to the TiO2 support effect. Graphical abstract On the monolayer PdO(101)/TiO2(110) film, the TiO2 support effect leads to stronger H2 molecular adsorption on coordinatively unsaturated Pd top sites than on pure PdO surface. H2 dissociation with the formation of OH is preferred thermodynamically but slightly unfavorable kinetically on the film due to the TiO2 support effect. PMID:27491853

  16. Unusual 2:3:2 complex of DABCO mono-betaine with HCl and H 2O 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.

    2009-12-01

    DABCO mono-betaine (1,4-diazabicyclo[2.2.2]octane-1-acetate) forms a complex with HCl and water in the ratio 2:3:2. The crystals are triclinic, space group P1¯. Two non-equivalent molecules of protonated DABCO mono-betaines form a homoconjugated cation through the short and asymmetric O·H·O hydrogen bond of 2.470(3) Å. Two chloride anions are involved in the N-H···Cl hydrogen bonds of 3.049(2) and 3.023(3) Å. The third chloride anion is solvated by the water molecules. The molecules of bis(1,4-diazoniumbicyclo[2.2.2]octane-1-acetate) trihydrochloride dihydrate are linked into comb-like chains by the hydrogen bond formed between water molecules of the neighboring complexes; the O(W)-H···O(W) distance is 2.920(5) Å. FTIR spectrum shows several broad bands attributed to the νO-H, νN-H and νO·H·O vibrations. The structure of three bis(1,4-diazoniumbicyclo[2.2.2]octane-1-acetate) hydrochlorides are optimized at the B3LYP/6-31G(d,p) level of theory and a theoretical IR spectrum is calculated. The values of p Ka of DABCO, DABCO mono- and di-betaines are determined by the potentiometric titration of their hydrohalides.

  17. Tailoring the electronic and optical properties of anatase TiO2 by (S, Nb) co-doping from a DFT plus U calculation

    NASA Astrophysics Data System (ADS)

    Ren, Dahua; Li, Huiran; Cheng, Xinlu

    2015-12-01

    The geometrical structure, defect formation, electronic and optical properties of S-doped, Nb-doped, and (S, Nb)-codoped anatase TiO2 were successfully calculated by the first-principles plane-wave ultrasoft pseudopotential method based on the density functional theory with plus U method. Firstly, the geometrical structure demonstrates that the (S, Nb) co-doping can effectively induce lattice distortion and reduce the recombination of electron-hole pairs. Note that the (S, Nb)-codoped system further reduces the band gap compared with pure and mono-doped TiO2 due to the mixture of S 2p and Nb 4d states appears in the gap, which results in an obvious red-shift in the optical absorption spectra and improves the photocatalytic activity. Moreover, the (S, Nb) co-doping should be grown under Ti-rich conditions while S or Nb mono-doping is expected to be easier under O-rich conditions. The above results would be beneficial to further developing for titanium dioxide photocatalyst.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    A complete structural and vibrational analysis of the 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid (TPBA), was carried out by ab initio calculations, at the density functional theory (DFT) method. Molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) 13C NMR and 1H NMR chemical shift values of (TPBA), in the ground state have been calculated by using ab initio density functional theory (DFT/B3LYP) method with 6-311G(d,p) as basis set for the first time. Comparison of the observed fundamental vibrational modes of (TPBA) and calculated results by DFT/B3LYP method indicates that B3LYP level of theory giving yield good results for quantum chemical studies. Vibrational wavenumbers obtained by the DFT/B3LYP method are in good agreement with the experimental data. The study was complemented with a natural bond orbital (NBO) analysis, to evaluate the significance of hyperconjugative interactions and electrostatic effects on such molecular structure. By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals analysis and thermodynamic properties of TPBA were investigated using theoretical calculations.

  19. O2 adsorption on MO2 (M=Ru, Ir, Sn) films supported on rutile TiO2(110) by DFT calculations: Probing the nature of metal oxide-support interaction.

    PubMed

    Xu, Xianglan; Sun, Xiongfei; Sun, Baozhen; Peng, Honggen; Liu, Wenming; Wang, Xiang

    2016-07-01

    To explore metal oxide-support interaction and its effect on O2 adsorption, periodic DFT calculations were used to explore the most preferred O2 molecular and dissociative adsorption on stoichiometric (MO2) and defective (MO2-x) (M=Ru, Ir, Sn) films supported on rutile TiO2(110), and compared with that on pure surfaces without TiO2(110) support. For defective RuO2-x films, it is revealed that the TiO2(110) support and the film thickness have an evident impact on the O2 adsorbed species. On the contrary, the two factors show little influence for defective IrO2-x and SnO2-x films. The analyses for Bader charge and density of states indicate that the reducibility change of the unsaturated surface Ru atoms, which are adjacent to the bridge oxygen vacancies, is responsible for this O2 adsorption alteration. These results provide insights into the oxide-oxide interaction, and its effect on the properties of supported oxide catalysts. PMID:27060230

  20. Evaluation of the Performance of the B3LYP, PBE0, and M06 DFT Functionals, and DBLOC-Corrected Versions, in the Calculation of Redox Potentials and Spin Splittings for Transition Metal Containing Systems.

    PubMed

    Coskun, Dilek; Jerome, Steven V; Friesner, Richard A

    2016-03-01

    We have evaluated the performance of the M06 and PBE0 functionals in their ability to calculate spin splittings and redox potentials for octahedral complexes containing a first transition metal series atom. The mean unsigned errors (MUEs) for these two functionals are similar to those obtained for B3LYP using the same data sets. We then apply our localized orbital correction approach for transition metals, DBLOC, in an effort to improve the results obtained with both functionals. The PBE0-DBLOC results are remarkably close in both MUE and parameter values to those obtained for the B3LYP-DBLOC method. The M06-DBLOC results are less accurate, but the parameter values and trends are still qualitatively very similar. These results demonstrate that DBLOC corrected methods are substantially more accurate for these systems than any of the uncorrected functionals we have tested and that the deviations between hybrid DFT methods and experiment for transition metal containing systems exhibit striking physically based regularities which are very similar for the three functionals that we have examined, despite significant differences in the details of each model. PMID:26808695

  1. 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.

  2. 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.

  3. Fabrication of two supramolecular self-assemblies of Mn(II)-dicarboxylates with trans-4,4‧-azobispyridine: Analysis of H-bonding interactions with Hirshfeld surfaces and DFT calculations

    NASA Astrophysics Data System (ADS)

    Dey, Rajdip; Bhattacharya, Biswajit; Mondal, Pallab; Mondal, Rajarshi; Ghoshal, Debajyoti

    2014-06-01

    Reactions with an aliphatic dicarboxylate (oxalate) as well as an aromatic dicarboxylate (terepthalate) in combination with an N,N‧ donor ligand (trans-4,4‧-azobispyridine) results two new coordination polymer of divalent manganese, namely {[Mn(azbpy)(H2O)4]·(bdc)·(H2O)2}n, (1) and {[Mn(ox)(H2O)2]·(azbpy)·(H2O)2}n,(2). Both the coordination polymers have one dimensional structure and extended to two-dimension by means of H-bonding. Interestingly, in solid state structure, the hydrogen bonding interaction recognizes the dicarboxylate (bdc) in case of 1 and N donor ligands (azbpy) in 2. The variation in the use of dicarboxylates, creates here a huge variation in the co-ordination modes of the metal ion as well as in the supramolecular structure within the crystal of 1 and 2. The contribution of various types of non-covalent forces are quantitatively explained in the light of Hrishfield surface analysis, which justifies the role of hydrogen bonding in the recognition of the above organic linkers. A DFT calculation of NBO also gives a quantitative understanding of the formation of the solid state structure by H-bonding. A thermogravimetric analysis, solid state fluorescence spectra and EPR spectroscopic study of the complexes have also performed which also nicely corroborated their crystal structures.

  4. 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.

  5. 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.

  6. 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. PMID:27423117

  7. Structure and absorption of Co(III) azo complex dyes based on pyrrolinone esters: DFT and TD DFT study

    NASA Astrophysics Data System (ADS)

    Luňák, Stanislav; Aysha, Tarek; Lyčka, Antonín; Machalický, Oldřich; Hrdina, Radim

    2014-07-01

    The relation between structure and absorption of three symmetrical 2:1 octahedral Co(III) azo complexes was studied. Quantum chemical calculations based on density functional theory (DFT) relate well with E-azo configuration of ligands with coordinated nitrogen atoms coming solely from phenolic residues. DFT calculations estimate the mer stereoisomer as remarkably preferred with respect to any fac arrangement. Time dependent DFT calculations using B3LYP and CAM-B3LYP functionals were successfully used to interpret the absorption spectra in a visible range.

  8. 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.

  9. Calculating the properties of C2H2-C9H16 alkynes, based on the additivity of energy contributions

    NASA Astrophysics Data System (ADS)

    Smolyakov, V. M.; Grebeshkov, V. V.

    2015-05-01

    A ten-constant additive model is obtained for calculating the physicochemical properties of a number of C n H2 n-2 alkynes, based on the group additivity method (with allowance for the initial atomic environment), two topological indices that allow for the second atomic environment, and pairwise non-valence interactions (in implicit form) between three atoms, four atoms, and so forth along the chain of a molecule. Two linear dependences are revealed. The obtained formula is used for numerical calculations of the normal heats of vaporization L NBT and normal boiling temperatures T b of C2H2-C9H16 alkynes, neither of which had been studied experimentally.

  10. A Boron-Fluorinated Tris(pyrazolyl)borate Ligand ((F) Tp*) and Its Mono- and Dinuclear Copper Complexes [Cu((F) Tp*)2 ] and [Cu2 ((F) Tp*)2 ]: Synthesis, Structures, and DFT Calculations.

    PubMed

    Augenstein, Timo; Dorner, Franziska; Reiter, Kevin; Wagner, Hanna E; Garnier, Delphine; Klopper, Wim; Breher, Frank

    2016-06-01

    Reaction of [Si(3,5-Me2 pz)4 ] (1) with [Cu(MeCN)4 ][BF4 ] (2) gave the mono- and dinuclear copper complexes [Cu2 ((F) Tp*)2 ] (3) and [Cu((F) Tp*)2 ] (4). Both complexes contain the so-far unprecedented boron-fluorinated (F) Tp* ligand ([FB(3,5-Me2 pz)3 ](-) with pz=pyrazolyl) originating from 1, acting as a pyrazolyl transfer reagent, and the [BF4 ](-) counter anion of 2, serving as the source of the {BF} entity. The solid-state structures as well as the NMR and EPR spectroscopic characteristics of the complexes were elaborated. Pulsed gradient spin echo (PGSE) experiments revealed that 3 retains (almost entirely) its dimeric structure in benzene, whereas dimer cleavage and formation of acetonitrile adducts, presumably [Cu((F) Tp*)(MeCN)], is observed in acetonitrile. The short Cu⋅⋅⋅Cu distance of 269.16 pm in the solid-state is predicted by DFT calculations to be dictated by dispersion interactions between all atoms in the complex (the Cu-Cu dispersion contribution itself is only very small). As revealed by cyclic voltammetry studies, 3 shows an irreversible (almost quasi-reversible at higher scan rates) oxidation process centred at E(pa) =-0.23 V (E(0) 1/2 =-0.27 V) (vs. Fc/Fc(+) ). Oxidation reactions on a preparative scale with one equivalent of the ferrocenium salt [Fc][BF4 ] (very slow reaction) or air (fast reaction) furnished blue crystals of the mononuclear copper(II) complex [Cu((F) Tp*)2 ] (4). As expected for a Jahn-Teller-active system, the coordination sphere around copper(II) is strongly distorted towards a stretched octahedron, in accordance with EPR spectroscopic findings. PMID:27106294

  11. L-edge X-ray absorption spectroscopy and DFT calculations on Cu2O2 species: direct electrophilic aromatic attack by side-on peroxo bridged dicopper(II) complexes.

    PubMed

    Qayyum, Munzarin F; Sarangi, Ritimukta; Fujisawa, Kiyoshi; Stack, T Daniel P; Karlin, Kenneth D; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

    2013-11-20

    The hydroxylation of aromatic substrates catalyzed by coupled binuclear copper enzymes has been observed with side-on-peroxo-dicopper(II) (P) and bis-μ-oxo-dicopper(III) (O) model complexes. The substrate-bound-O intermediate in [Cu(II)2(DBED)2(O)2](2+) (DBED = N,N'-di-tert-butyl-ethylenediamine) was shown to perform aromatic hydroxylation. For the [Cu(II)2(NO2-XYL)(O2)](2+) complex, only a P species was spectroscopically observed. However, it was not clear whether this O-O bond cleaves to proceed through an O-type structure along the reaction coordinate for hydroxylation of the aromatic xylyl linker. Accurate evaluation of these reaction coordinates requires reasonable quantitative descriptions of the electronic structures of the P and O species. We have performed Cu L-edge XAS on two well-characterized P and O species to experimentally quantify the Cu 3d character in their ground state wave functions. The lower per-hole Cu character (40 ± 6%) corresponding to higher covalency in the O species compared to the P species (52 ± 4%) reflects a stronger bonding interaction of the bis-μ-oxo core with the Cu(III) centers. DFT calculations show that 10-20% Hartree-Fock (HF) mixing for P and ~38% for O species are required to reproduce the Cu-O bonding; for the P species this HF mixing is also required for an antiferromagnetically coupled description of the two Cu(II) centers. B3LYP (with 20% HF) was, therefore, used to calculate the hydroxylation reaction coordinate of P in [Cu(II)2(NO2-XYL)(O2)](2+). These experimentally calibrated calculations indicate that the electrophilic attack on the aromatic ring does not involve formation of a Cu(III)2(O(2-))2 species. Rather, there is direct electron donation from the aromatic ring into the peroxo σ* orbital of the Cu(II)2(O2(2-)) species, leading to concerted C-O bond formation with O-O bond cleavage. Thus, species P is capable of direct hydroxylation of aromatic substrates without the intermediacy of an O-type species

  12. The solvatochromic, spectral, and geometrical properties of nifenazone: a DFT/TD-DFT and experimental study.

    PubMed

    Bani-Yaseen, Abdulilah Dawoud; Al-Balawi, Mona

    2014-08-01

    The solvatochromic, spectral, and geometrical properties of nifenazone (NIF), a pyrazole-nicotinamide drug, were experimentally and computationally investigated in several neat solvents and in hydro-organic binary systems such as water-acetonitrile and water-dioxane systems. The bathochromic spectral shift observed in NIF absorption spectra when reducing the polarity of the solvent was correlated with the orientation polarizability (Δf). Unlike aprotic solvents, a satisfactory correlation between λ(max) and Δf was determined (linear correlation of regression coefficient, R, equal to 0.93) for polar protic solvents. In addition, the medium-dependent spectral properties were correlated with the Kamlet-Taft solvatochromic parameters (α, β, and π*) by applying a multiple linear regression analysis (MLRA). The results obtained from this analysis were then employed to establish MLRA relationships for NIF in order to estimate the spectral shift in different solvents, which in turn exhibited excellent correlation (R > 0.99) with the experimental values of ν(max). Density functional theory (DFT) and time-dependent DFT theory calculations coupled with the integral equation formalism-polarizable continuum model (IEF-PCM) were performed to investigate the solvent-dependent spectral and geometrical properties of NIF. The calculations showed good and poor agreements with the experimental results using the CAM-B3LYP and B3LYP functionals, respectively. Experimental and theoretical results confirmed that the chemical properties of NIF are strongly dependent on the polarity of the chosen medium and its hydrogen bonding capability. This in turn supports the hypothesis of the delocalization of the electron density within the pyrazole ring of NIF. PMID:24954054

  13. Time-resolved study on the reactions of organic selenides with hydroxyl and oxide radicals, hydrated electrons, and H-atoms in aqueous solution, and DFT calculations of transients in comparison with sulfur analogues.

    PubMed

    Tobien, Thomas; Bonifacić, Marija; Naumov, Sergej; Asmus, Klaus-Dieter

    2010-07-01

    A complementary experimental and quantum chemical study has been undertaken on the reactivity, formation and properties of transients generated in the reaction of selected organic selenides with hydroxyl radicals, oxide radical ions, hydrated electrons and hydrogen atoms in aqueous solution. A detailed study of the OH and O (-) reactions with Me(2)Se revealed the formation of the respective adduct-radicals as precursors of (Me(2)Se thereforeSeMe(2))(+) radical cations. In case of the neutral adduct radical Me(2)Se (OH) the conversion into the three-electron bonded dimer species proceeds, in part, via the molecular (Me(2)Se thereforeOH(2))(+) radical cation. Absolute rate constants have been determined for all the underlying processes. The respective reactions with hydrated electrons and hydrogen atoms indicate that selenides exhibit a higher reactivity towards redox-active species than sulfides. A most interesting finding is that the reaction of Me(2)Se with H atoms is faster (k = 4.1 x 10(9) M(-1) s(-1)) than the reduction by hydrated electrons (k = 2.1 x 10(8) M(-1) s(-1)), precluding an electron transfer as mechanistic background. The rationale is rather an effective dissociative attack of the hydrogen atom on the selenium. Both, the e(aq)(-)- and H -induced reductions of Me(2)Se and Me(2)S lead, under cleavage of CH(3) radicals, to the direct formation of selenol and thiol, respectively. Complementary quantum chemical studies, performed with Density Functional Theory (DFT) BHandHLYP methods, confirm this mechanism. They also reveal a generally higher thermodynamic stability of the Se-centered radicals relative to the S-centered ones, e.g., for the molecular radical anions (Me(2)Se) (-) (DeltaH-27 kJ mol(-1)) and (Me(2)S) (-) (DeltaH-16 kJ mol(-1)). Despite of these stabilization energies the calculations indicate an instantaneous Se/S-CH(3) bond lengthening in the respective molecular radical anions. The same applies for the reaction of Me(2)S and Me(2)Se with

  14. Iodine adsorption on Ni(111): STM and DFT study

    NASA Astrophysics Data System (ADS)

    Komarov, N. S.; Pavlova, T. V.; Andryushechkin, B. V.

    2016-09-01

    Iodine adsorption on the Ni(111) surface has been studied in ultra-high vacuum conditions with scanning tunneling microscopy (STM), Auger electron spectroscopy (AES), low-energy electron diffraction (LEED) and density functional theory (DFT) calculations. At the first stage of adsorption, iodine was found to form a simple commensurate (√{ 3 } ×√{ 3 }) R 30∘ structure at the coverage of 0.33 ML. According to DFT calculations, all iodine atoms in the (√{ 3 } ×√{ 3 }) R 30∘ structure occupy fcc hollow sites. Increase of the coverage in the range of (0.333 ML <θ < 0.364 ML) results in the uniaxial compression of the iodine lattice and the formation of the high-order commensurate structure (11 ×√{ 3 } R 30∘). The mechanism of compression involves the formation and the development of the striped super-heavy domain wall network. Further iodine dosing gives rise to nucleation and growth of flat 2D islands of surface nickel iodide. Atomic resolution STM images of iodide islands, in addition to atomic modulation, exhibit clear visible moiré-like superstructures with a period about 26 Å. The origin of the moiré-patterns was explained by the incommensurability of lattices of the surface nickel iodide and underlying Ni(111).

  15. 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

    2014-05-01

    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. PMID:24599509

  16. 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.

  17. 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.

  18. 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.

  19. Electrochemical oxidation stability of anions for modern battery electrolytes: a CBS and DFT study.

    PubMed

    Jónsson, Erlendur; Johansson, Patrik

    2015-02-01

    The electrochemical stability vs. oxidation is a crucial property of anions in order to be suitable as components in lithium-ion batteries. Here the applicability of a number of computational approaches and methods to assess this property, employing a wide selection of DFT functionals, has been studied using the CCSD(T)/CBS method as the reference. In all, the vertical anion oxidation potential, ΔEv, is a fair way to calculate the stability vs. oxidation, however, a functional of at least hybrid quality is recommended. In addition, the chemical hardness, η, is identified as a novel approach to calculate the stability vs. oxidation. PMID:25557392

  20. Using DFT Methods to Study Activators in Optical Materials

    DOE PAGESBeta

    Du, Mao-Hua

    2015-08-17

    Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for new materials.more » DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn4+ activated red phosphors, scintillators activated by Ce3+, Eu2+, Tl+, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.« less

  1. Using DFT Methods to Study Activators in Optical Materials

    SciTech Connect

    Du, Mao-Hua

    2015-08-17

    Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for new materials. DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn4+ activated red phosphors, scintillators activated by Ce3+, Eu2+, Tl+, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.

  2. Understanding density functional theory (DFT) and completing it in practice

    SciTech Connect

    Bagayoko, Diola

    2014-12-15

    We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.

  3. Adaptive DFT-based Interferometer Fringe Tracking

    NASA Technical Reports Server (NTRS)

    Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

    2004-01-01

    An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) observatory at Mt. Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on off-line data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 2.0 milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse.

  4. Semiempirical and DFT Investigations of the Dissociation of Alkyl Halides

    ERIC Educational Resources Information Center

    Waas, Jack R.

    2006-01-01

    Enthalpy changes corresponding to the gas phase heats of dissociation of 12 organic halides were calculated using two semiempirical methods, the Hartree-Fock method, and two DFT methods. These calculated values were compared to experimental values where possible. All five methods agreed generally with the expected empirically known trends in the…

  5. Development of noncollinear-spin DFT +U method with spin-orbit interaction

    NASA Astrophysics Data System (ADS)

    Ko, Eunjung; Lee, Hyungjun; Oh, Hyungju; Park, Se Young; Choi, Hyoung Joon

    2014-03-01

    We developed a DFT +U +SOI method by incorporating spin-orbit interaction (SOI) into a noncollinear-spin generalization of the density functional theory (DFT) plus Coulomb interaction among d electrons, parameterized by U and J. The Coulomb interaction, which is based on the rotationally invariant form, is generalized for noncollinear-spin configuration, and the fully localized limit is adopted for the double-counting term. The spin-orbit interaction is treated in the l-dependent fully separable nonlocal form using additional Kleinman-Bylander projectors generated by relativistic calculations of atoms. We implemented our DFT +U +SOI method into the SIESTA code and performed test calculations for the 4 d or 5 d transition metal oxides, the all-in-all-out noncollinear magnetic insulator Cd2Os2O7, the canted antiferromagnetic order insulator Sr2IrO4, and the paramagnetic insulator Ca2RuO4. This work was supported by NRF of Korea (Grant No. 2011-0018306) and KISTI supercomputing center (Project No. KSC-2012-C3-046).

  6. Syntheses, spectral characterization, single crystal X-ray diffraction and DFT computational studies of novel thiazole derivatives

    NASA Astrophysics Data System (ADS)

    Anbazhagan, R.; Sankaran, K. R.

    2013-10-01

    A novel thiazole (E)-1-((E)-2-methyl-3-phenylallylidene)-2-(4-phenylthiazole-2-yl)hydrazine 2 and its derivatives 3-8 were synthesized by cyclo condensation of (1E)-1-((E)-2-methyl-3-phenylallylidene)thiosemicarbazide 1 with substituted 2-bromoacetophenones. The synthesized thiazole derivatives were characterized by FT-IR, 1H NMR and 13C NMR analyses. For compound 8 single crystals X-ray diffraction analysis and density functional theory (DFT) calculation were carried out. The compound 8 crystallizes in the monoclinic space group P21/c with a = 7.4601 (3) Å, b = 5.7259 (2) Å, c = 41.0823 (13) Å, α = 90°, β = 91.715 (2)° and γ = 90°. The molecular geometrical parameters, frontier molecular orbital energies (HOMO, LUMO), their energy gap (ΔE), molecular electrostatic potential (MEP) and natural bond orbital (NBO) analysis of the compounds 2 and8 have been calculated by using DFT/B3LYP with 6-311G (d, p) level. In addition, IR frequencies, 1H and 13C NMR chemical shifts of compound 8 were also calculated by using DFT calculations at the same level basis set. The calculated geometrical parameters, IR frequencies, 1H and 13C NMR chemical shifts of the compound 8 were in good agreement with the observed single crystal-XRD data, IR, 1H and 13C NMR spectral values.

  7. DFT investigations of structural and electronic properties of gallium arsenide (GaAs)

    NASA Astrophysics Data System (ADS)

    Anua, N. Najwa; Ahmed, R.; Saeed, M. A.; Shaari, A.; Haq, Bakhtiar Ul

    2012-09-01

    First principles calculations for structural and electronic properties of GaAs have been reported using a full potential linearized augmented plane wave (FP-LAPW) scheme of calculations developed within density functional theory (DFT). We use in this study local density approximation (LDA), Perdew-Burke-Ernzerhof parameterized generalized gradient approximation (PBE-GGA), Wu-Cohen parameterized GGA (WC-GGA) executed in WIEN2k code. In addition, to calculate band structure with high accuracy we used modified Becke-Johnson exchange potential (MBJ) + LDA approach. Our calculated lattice constant with GGA-WC is in good agreement to experimental value than LDA and PBE-GGA. Whereas our calculations for the band structure show that MBJ+ LDA approach gives much better results for band gap value as compared to other exchange correlation approaches.

  8. Oxidative addition of carbon-carbon bonds to gold.

    PubMed

    Joost, Maximilian; Estévez, Laura; Miqueu, Karinne; Amgoune, Abderrahmane; Bourissou, Didier

    2015-04-20

    The oxidative addition of strained CC bonds (biphenylene, benzocyclobutenone) to DPCb (diphosphino-carborane) gold(I) complexes is reported. The resulting cationic organogold(III) complexes have been isolated and fully characterized. Experimental conditions can be adjusted to obtain selectively acyl gold(III) complexes resulting from oxidative addition of either the C(aryl)C(O) or C(alkyl)C(O) bond of benzocyclobutenone. DFT calculations provide mechanistic insight into this unprecedented transformation. PMID:25727203

  9. Molecular structure and charge transfer contributions to nonlinear optical property of 2-Methyl-4-nitroaniline: A DFT study

    NASA Astrophysics Data System (ADS)

    Jasmine, G. Femina; Amalanathan, M.; Roy, S. Dawn Dharma

    2016-05-01

    The Charge transfer contributions to the second-order nonlinear optical properties of 2-Methyl-4-nitroaniline have been performed by means of DFT computation. The vibrational contribution studies of 2-Methyl-4-nitroaniline have also been performed using FTIR, FT-Raman analysis. More support on the experimental findings were added from the quantum chemical studies performed with DFT (B3LYP) method using 6-311++G(d,p)basis sets. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. The HOMO and LUMO analysis reveals the possibility of charge transfer within the molecule. The first order hyperpolarizability (α0) and related properties (β,α0 and Δα) of 2-Methyl-4-nitroaniline were calculated. In addition, molecular electrostatic potential (MEP), charge analysis also were investigated using theoretical calculations.

  10. Vibrational spectroscopic studies, NMR, HOMO-LUMO, NLO and NBO analysis of 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole with use X-ray diffractions and DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Tinmaz, Feyza; Dege, Necmi; Ilhan, Ilhan Ozer

    2016-03-01

    The crystal and molecular structure of the title compound, 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole, was reported and confirmed by single crystal X-ray diffraction and spectroscopic data. The structure, geometry optimization, vibrational frequencies and nuclear magnetic resonance were also investigated. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (ED) in the σ∗ and π∗ antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. Satisfactory theoretical aspects were made for the stable conformer of the molecule using density functional theory DFT-B3LYP methods with the 6-311G++(d,p) basis set.

  11. A new constraint DFT technique for self-consistent determination of U values

    NASA Astrophysics Data System (ADS)

    Hamada, Tomoyuki; Ohno, Takahisa

    A new constraint density functional (DFT) technique workable in combination with the projector augmented wave (PAW) and pseudoptential (PP) methods was developed. This technique calculates the effective on-site-interaction parameter, Ueff , of correlated electrons of materials, self-consistently, by using the DFT +U method. The Ueff determined by this technique has a clear physical meaning in that it determines the electronic structures of strongly correlated electronic systems (SCESs) andvice versa. The technique was used to determine the Ueff of correlated electrons of hexagonal neodymium sesquioxide (h-Nd2O3) and orthorhombic iron oxide (o-FeO) in the antiferromagnetic states, and it was shown to be effective for this purpose. The newly developed constraint DFT technique enables first principles DFT +U PAW and PP calculations of SCESs free from any empirical parameters, which are more reliable than the DFT +U PAW and PP calculations of them using empirical Ueffs. Hatoyama, Saitama, 350-0395, Japan.

  12. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    NASA Astrophysics Data System (ADS)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  13. DFT modeling of Spectral and Redox Properties of Di-and Tetranuclear Ruthenium Transition Metal Complexes with Bridging Ligands

    SciTech Connect

    Zalis, S.; Winter, R. S.; Linseis, M.; Kaim, A.; Sarkar, B.; Kratochvilova, I.

    2009-08-13

    The electronic structures of di-and tetranuclear transition metal complexes with bridging ligands (tetracyanoethene, tetracyano-p-quinodimethane, divinylphenylene and tetrakis(4-styryl)ethene) were calculated by density functional (DFT) method. DFT method was used for calculations of IR frequencies in different oxidation states and EPR parameters of radical ions. The observed electronic transitions of closed shell systems were assigned by TD DFT. The different aspects of bridge mediated metal-metal interaction are discussed.

  14. Simultaneous presence of (Si{sub 3}O{sub 10}){sup 8−} and (Si{sub 2}O{sub 7}){sup 6−} groups in new synthetic mixed sorosilicates: BaY{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}) and isotypic compounds, studied by single-crystal X-ray diffraction, Raman spectroscopy and DFT calculations

    SciTech Connect

    Wierzbicka-Wieczorek, Maria; Többens, Daniel M.; Kolitsch, Uwe; Tillmanns, Ekkehart

    2013-11-15

    Three new, isotypic silicate compounds, BaY{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}), SrYb{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}) and SrSc{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}), were synthesized using high-temperature flux growth techniques, and their crystal structures were solved from single-crystal X-ray intensity data: monoclinic, P2{sub 1}/m, with a=5.532(1)/5.469(1)/5.278(1), b=19.734(4)/19.447(4)/19.221(4), c=6.868(1)/6.785(1)/6.562(1) Å, β=106.53(3)/106.20(3)/106.50(3)°, V=718.8(2)/693.0(2)/638.3(2) Å{sup 3}, R(F)=0.0225/0.0204/0.0270, respectively. The topology of the novel structure type contains isolated horseshoe-shaped Si{sub 3}O{sub 10} groups (Si–Si–Si=93.15–95.98°), Si{sub 2}O{sub 7} groups (Si–O{sub bridge}–Si=180°, symmetry-restricted) and edge-sharing M(1)O{sub 6} and M(2)O{sub 6} octahedra. Single-crystal Raman spectra of the title compounds were measured and compared with Raman spectroscopic data of chemically and topologically related disilicates and trisilicates, including BaY{sub 2}(Si{sub 3}O{sub 10}) and SrY{sub 2}(Si{sub 3}O{sub 10}). The band assignments are supported by additional theoretical calculation of Raman vibrations by DFT methods. - Graphical abstract: View of BaY{sub 4}(Si{sub 2}O{sub 7})(Si{sub 3}O{sub 10}) along [100], showing zigzag chains and the tri- and disilicate groups. The unit cell is outlined. Display Omitted - Highlights: • We report a novel interesting crystal structure type for mixed sorosilicates containing Y, Yb, and Sc. • Synthesis of such mixed sorosilicates is possible by a high-temperature flux-growth technique. • Calculation of Raman vibrations by advanced DFT methods allows a considerably improved interpretation of measured Raman spectra.

  15. One component metal sintering additive for {beta}-SiC based on thermodynamic calculation and experimental observations

    SciTech Connect

    Noviyanto, Alfian; Yoon, Dang-Hyok

    2011-08-15

    Graphical abstract: . Standard Gibbs formation free energies vs. temperature for various metal carbides. The heavy line represents the standard Gibbs free energy for {beta}-SiC. The hatched area denotes the typical liquid phase hot pressing temperature of {beta}-SiC (1973-2123 K). Highlights: {yields} Various metal elements were examined as a sintering additive for {beta}-SiC. {yields} Al and Mg enhanced the density significantly without decomposing {beta}-SiC, as predicted by thermodynamic simulation. {yields} Cr, Fe, Ta, Ti, V and W additives formed metal carbide and/or silicide compounds by decomposing {beta}-SiC. {yields} This approach would be useful for selecting effective sintering additive for high temperature ceramics. -- Abstract: Various types of metals were examined as sintering additives for {beta}-SiC by considering the standard Gibbs formation free energy and vapor pressure under hot pressing conditions (1973-2123 K), particularly for applications in nuclear reactors. Metallic elements having the low long-term activation under neutron irradiation condition, such as Cr, Fe, Ta, Ti, V and W, as well as widely used elements, Al, Mg and B, were considered. The conclusions drawn from thermodynamic considerations were compared with the experimental observations. Al and Mg were found to be effective sintering additives, whereas the others were not due to the formation of metal carbides or silicides from the decomposition of SiC under hot pressing conditions.

  16. Nitrogen Fixation by a Molybdenum Catalyst Mimicking the Function of the Nitrogenase Enzyme:  A Critical Evaluation of DFT and Solvent Effects.

    PubMed

    Magistrato, Alessandra; Robertazzi, Arturo; Carloni, Paolo

    2007-09-01

    Compounds mimicking the enzyme nitrogenase represent promising alternative routes to the current Haber-Bosch industrial synthesis of ammonia from molecular hydrogen and nitrogen. In this work, we investigated the full catalytic cycle of one of such compounds, Mo(HIPTN3N) (with HIPT = hexaisopropylterphenyl), by means of DFT calculations. Our results suggest these large ligands to exert mainly a steric influence on the structural properties of the catalyst. In addition, we provided a structural and electronic characterization of the putative reaction intermediates along with a picture of the electronic mechanism of molecular nitrogen N-N bond breaking. A large discrepancy was observed between calculated and experimental reaction free energies, suggesting that in the present case the predictability of DFT reaction energies is limited. Investigation of explicit solvation of specific catalytic intermediates as well as of the protonation and reducing agents reveal the crucial role played by the solvent molecules (benzene and heptane) particularly for protonation steps. Furthermore, the analysis of several DFT functionals indicates that these have to be carefully chosen in order to reproduce the energetic profile of reduction steps. This study shows how DFT calculations may be a powerful tool to describe structural and electronic properties of the intermediates of the catalytic cycle, yet, due to the complexity of the system, reaction energies cannot be easily reproduced without a careful choice of the solvation model and the exchange-correlation functional. PMID:26627617

  17. Synthesis, crystal structure, spectral analysis and DFT computational studies on a novel isoindoline derivative

    NASA Astrophysics Data System (ADS)

    Evecen, Meryem; Duru, Gülcan; Tanak, Hasan; Ağar, Ayşen Alaman

    2016-08-01

    The isoindoline compound, 2-(3-chloro-4-(4-chlorophenoxy)phenyl)isoindoline-1,3-dione, has been synthesized and characterized by FT-IR, UV-Vis and X-ray single-crystal determination. The compound crystallizes in the monoclinic space group P21/c with a = 20.441 (3) Å, b = 4.0258 (4) Å, c = 23.836 (2) Å, β = 121.918 (7)° and Z = 4. The molecular structure and vibrational frequencies in the ground state were calculated using the density functional theory method (B3LYP) with 6-311++G(d,p) basis set. The results obtained from the optimization and vibrational analyses are agree with the experimental results. Using the TD-DFT method, electronic absorption spectra have been calculated, and they are compatible with the experimental ones. The electric dipole moment (μ), polarizability (α) and the first hyperpolarizability (β) values of the compound were calculated theoretically. The first hyperpolarizability of the molecule shows that the compound can be a good candidate of nonlinear optical material. In addition, DFT calculations of the compound, atomic charges, molecular electrostatic potential and thermodynamic properties were also performed at B3LYP/6-311++G(d,p) level of theory.

  18. Mechanical Properties Evaluation of Zr Addition in L12-Al3(Sc1- x Zr x ) Using First-Principles Calculation

    NASA Astrophysics Data System (ADS)

    Qian, Yi; Xue, Jilai; Wang, Zengjie; Yang, Zhenhai; Qian, Ping

    2016-05-01

    L12-Al3(Sc1- x Zr x ) can be used as a grain refiner and recrystallization inhibitor in forming and heat-treatment of wrought aluminum alloy. In this work, the mechanical properties of L12-Al3(Sc1- x Zr x ) (0 < x< 0.5) have been systematically evaluated using first principles calculations. The optimized structural parameters obtained through the virtual crystal approximation were in good agreement with available experimental and calculated data. The computed bulk modulus of L12-Al3(Sc1- x Zr x ) increased while the shear modulus and Young's modulus decreased with increasing Zr addition. The ductility of L12-Al3(Sc1- x Zr x ) estimated by Pugh empirical criterion and Cauchy pressure were improved with Zr addition. The calculated ideal strength of L12-Al3(Sc1- x Zr x ) along the [001], [110] and { 111} [1bar{1}0] directions increased linearly with Zr additions. The addition of Zr gave great improvements in the ideal strength along the [110] direction and the ductility in the [001] direction, respectively. The calculated electronic density of states and the charge density distribution revealed that the valence electron increased with Zr addition and hence strengthened the p-d covalent bonding and d-d bonding, resulting in the improvements in ideal strength and ductility. The evaluation data would be useful in materials design and process optimization for Al alloys in forming and heat treatment.

  19. Spectroscopic investigation, photophysical parameters and DFT calculations of 4,4'-(1E,1'E)-2,2'-(pyrazine-2,5-diyl)bis(ethene-2,1-diyl)bis(N,N-dimethylaniline) (PENDA) in different solvents.

    PubMed

    Asiri, Abdullah M; Alamry, Khalid A; Pannipara, Mehboobali; Al-Sehemi, Abdullah G; El-Daly, Samy A

    2015-10-01

    A comprehensive investigation on the photophysics of a π-conjugated potential push-pull chromophore system 4,4'-(1E,1'E)-2,2'-(Pyrazine-2,5-diyl)bis(ethene-2,1-diyl)bis(N,N-dimethylaniline) (PENDA) has been carried out spectroscopically. The optical absorption and emission properties of this molecule have been studied in different solvents. The molecule PENDA shows strong solvatochromic emission upon changing the solvent polarity from nonpolar to polar; indicating that emission state is of intramolecular charge transfer (ICT) character. The solvent effect on the spectral properties such as singlet absorption, molar absorptivity, oscillator strength, dipole moment and fluorescence quantum yield of PENDA have been studied in detail. Lippert-Mataga and Reichardt correlations were used to estimate the difference between the excited and ground state dipole moments (Δμ). Ground and electronic excited states geometric optimizations were performed using density functional theory (DFT) and time-dependent density functional theory (TDDFT), respectively, with the Gaussian 09 package. A solution of (8×10(-5) M) PENDA in THF, dioxane, CH3CN and CHCl3 gives laser emission when pumped by a nitrogen laser pulse (λex=337.1 nm) of 800 ps duration and 1.48 mJ pulse energy. PENDA dye displays fluorescence quenching by colloidal silver nanoparticles (Ag NPs) in ethanol. The fluorescence data reveal that dynamic quenching and energy transfer play a major role in the fluorescence quenching mechanism. PMID:25988818

  20. Experimental and DFT studies of the conversion of ethanol and acetic acid on PtSn-based catalysts.

    PubMed

    Alcala, Rafael; Shabaker, John W; Huber, George W; Sanchez-Castillo, Marco A; Dumesic, James A

    2005-02-17

    Reaction kinetics studies were conducted for the conversions of ethanol and acetic acid over silica-supported Pt and Pt/Sn catalysts at temperatures from 500 to 600 K. Addition of Sn to Pt catalysts inhibits the decomposition of ethanol to CO, CH4, and C2H6, such that PtSn-based catalysts are active for dehydrogenation of ethanol to acetaldehyde. Furthermore, PtSn-based catalysts are selective for the conversion of acetic acid to ethanol, acetaldehyde, and ethyl acetate, whereas Pt catalysts lead mainly to decomposition products such as CH4 and CO. These results are interpreted using density functional theory (DFT) calculations for various adsorbed species and transition states on Pt(111) and Pt3Sn(111) surfaces. The Pt3Sn alloy slab was selected for DFT studies because results from in situ (119)Sn Mössbauer spectroscopy and CO adsorption microcalorimetry of silica-supported Pt/Sn catalysts indicate that Pt-Sn alloy is the major phase present. Accordingly, results from DFT calculations show that transition-state energies for C-O and C-C bond cleavage in ethanol-derived species increase by 25-60 kJ/mol on Pt3Sn(111) compared to Pt(111), whereas energies of transition states for dehydrogenation reactions increase by only 5-10 kJ/mol. Results from DFT calculations show that transition-state energies for CH3CO-OH bond cleavage increase by only 12 kJ/mol on Pt3Sn(111) compared to Pt(111). The suppression of C-C bond cleavage in ethanol and acetic acid upon addition of Sn to Pt is also confirmed by microcalorimetric and infrared spectroscopic measurements at 300 K of the interactions of ethanol and acetic acid with Pt and PtSn on a silica support that had been silylated to remove silanol groups. PMID:16851198

  1. FAST TRACK COMMUNICATION A DFT + DMFT approach for nanosystems

    NASA Astrophysics Data System (ADS)

    Turkowski, Volodymyr; Kabir, Alamgir; Nayyar, Neha; Rahman, Talat S.

    2010-11-01

    We propose a combined density-functional-theory-dynamical-mean-field-theory (DFT + DMFT) approach for reliable inclusion of electron-electron correlation effects in nanosystems. Compared with the widely used DFT + U approach, this method has several advantages, the most important of which is that it takes into account dynamical correlation effects. The formalism is illustrated through different calculations of the magnetic properties of a set of small iron clusters (number of atoms 2 <= N <= 5). It is shown that the inclusion of dynamical effects leads to a reduction in the cluster magnetization (as compared to results from DFT + U) and that, even for such small clusters, the magnetization values agree well with experimental estimations. These results justify confidence in the ability of the method to accurately describe the magnetic properties of clusters of interest to nanoscience.

  2. Comparative studies between 4-allyl-, 4-phenyl- and 4-ethyl-1-(2-hydroxybenzoyl) thiosemicarbazides and the synthesis, characterization and DFT calculations of binary and ternary complexes derived from 4-ethyl (L(1)) and 2,2'-dipyridyl.

    PubMed

    Azhari, Shaker J; Mlahi, Mosaad R; Mostafa, Mohsen M

    2015-11-01

    The metal complexes of 4-ethyl-1-(2-hydroxybenzoyl) thiosemicarbazide (L(1)) with MCl2 (M=Co(2+), Cu(2+) and Zn(2+)) and Zn(Ac)2 in EtOH were synthesized and characterized using spectral (IR, (1)H-NMR, mass, UV-Visible), magnetic moment and thermal measurements. Binary and ternary complexes with the general formulae, [Cu(L(1)-H)2]·EtOH, [Co(L(1)-H)2], [Zn3(L(1)-H)(L(1))(Ac)5], [Cu2(L(2))2(L(1)-2H)2(H2O)2]·4H2O, [Co(L(2))(L(1)-2H)]·3H2O and [Zn2(L(2))(OH)(L(1)-3H)(H2O)]·1/2EtOH where L(2) is 2,2'-dipyridyl, have been suggested and characterized. The bond lengths, bond angles, chemical reactivates, energy components, binding energies and dipole moments for the isolated complexes were evaluated by DFT method from DMOL(3). Also, the MEP for L(1) is illustrated. The existence of the OH group in the Zn(2+) ternary complexes is confirmed by IR, mass and (1)H-NMR spectra. Biological activity for the L(1) and some its complexes was tested against DNA. Comparative studies between the ligation behavior and reactivity of our previous work derived from 4-phenyl- and 4-allyl-1-(2-hydroxybenzoyl) thiosemicarbazides have been investigated. PMID:26123512

  3. Liquid-liquid extraction of metal ions, DFT and TD-DFT analysis of some 1,2,4-triazole Schiff Bases with high selectivity for Pb(II) and Fe(II)

    NASA Astrophysics Data System (ADS)

    Khoutoul, Mohamed; Lamsayah, Morad; Al-blewi, Fawzia F.; Rezki, Nadjet; Aouad, Mohamed Reda; Mouslim, Messali; Touzani, Rachid

    2016-06-01

    Liquid-liquid extraction of metal ions using some 1,2,4-triazole Schiff base derivatives as new extractants was studied. Fe2+, Zn2+, Cu2+, Co2+, Cd2+ and Pb2+ were extracted from the aqueous phase into the organic phase and the extractability for each metal ion was determined by atomic absorption. Interestingly, a competitive extraction was also investigated and then examined at different pH in order to explore the effect of the different substituent groups on metal extraction. Accordingly, high selectivity towards Fe2+ (90.1%) and Pb2+ (94.3%) provided respectively by the presence of electron withdrawing group and electron donor group was attained. In addition, geometry optimizations of the ground and excited-states of the ligands in order to get better insight into the geometry and the electronic structure were carried out by means of DFT and TD-DFT calculations.

  4. Does DFT-SAPT method provide spectroscopic accuracy?

    SciTech Connect

    Shirkov, Leonid; Makarewicz, Jan

    2015-02-14

    Ground state potential energy curves for homonuclear and heteronuclear dimers consisting of noble gas atoms from He to Kr were calculated within the symmetry adapted perturbation theory based on the density functional theory (DFT-SAPT). These potentials together with spectroscopic data derived from them were compared to previous high-precision coupled cluster with singles and doubles including the connected triples theory calculations (or better if available) as well as to experimental data used as the benchmark. The impact of midbond functions on DFT-SAPT results was tested to study the convergence of the interaction energies. It was shown that, for most of the complexes, DFT-SAPT potential calculated at the complete basis set (CBS) limit is lower than the corresponding benchmark potential in the region near its minimum and hence, spectroscopic accuracy cannot be achieved. The influence of the residual term δ(HF) on the interaction energy was also studied. As a result, we have found that this term improves the agreement with the benchmark in the repulsive region for the dimers considered, but leads to even larger overestimation of potential depth D{sub e}. Although the standard hybrid exchange-correlation (xc) functionals with asymptotic correction within the second order DFT-SAPT do not provide the spectroscopic accuracy at the CBS limit, it is possible to adjust empirically basis sets yielding highly accurate results.

  5. Molecular structure, vibrational spectral assignments (FT-IR and FT-Raman), UV-Vis, NMR, NBO, HOMO-LUMO and NLO properties of 3t-pentyl-2r,6c-diphenylpiperidin-4-one picrate based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Savithiri, S.; Arockia doss, M.; Rajarajan, G.; Thanikachalam, V.

    2016-02-01

    The FT-IR and FT-Raman spectra were recorded for title compound 3t-pentyl-2r,6c-diphenylpiperidin-4-one picrate (3-PDPPP) and the data were compared with the theoretical values. The stability of the molecule due to hyper-conjugative interaction and charge delocalization was studied by NBO analysis. The UV-Vis spectral data calculated by using the DFT method were correlated with the experimental values. The calculated HOMO and LUMO energies revealed that charge transfer occurs within the molecule and Mulliken charges were also obtained. Molecular electrostatic potential (MEP) analyses were performed to predict the reactive sites of the molecule. The calculated first hyperpolarizabilty is high suggesting an extended π-electron delocalization over the picryl ring and piperidone moiety which is also responsible for the nonlinear optical property of the molecule. The 1H and 13C NMR chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with the experimental results. The thermodynamic properties of the compound at different temperatures have been determined and correlations between heat capacity, entropy, enthalpy and temperature have been done.

  6. A comparative ab initio and DFT study of polyaniline leucoemeraldine base and its oligomers.

    PubMed

    Mishra, Abhishek Kumar; Tandon, Poonam

    2009-11-01

    Ab initio Hartree-Fock (HF) and density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the polyaniline leucoemeraldine base (PANI-LB). Vibrational spectra of PANI-LB have been analyzed using the DFT oligomer approach, and complete assignments are being reported. Lower region spectral assignments of the PANI-LB which were not being reported earlier are being done in the present work. DFT calculations with the 6-31G** basis set produce very good results of not only vibrational modes but also of energy band gap. PMID:19827802

  7. DFT studies on vibrational spectra, HOMO-LUMO, NBO and thermodynamic function analysis of cyanuric fluoride

    NASA Astrophysics Data System (ADS)

    Prabhaharan, M.; Prabakaran, A. R.; Gunasekaran, S.; Srinivasan, S.

    2015-02-01

    In this work, the theoretical vibrational spectral characteristics of cyanuric fluoride (C3N3F3) have been investigated and compared with existing experimental results. The density functional theoretical (DFT) computations were performed at the B3LYP level with the basis sets 6-31G(d,p) and 6-311++G(d,p) levels to derive the optimized geometry, vibrational wavenumbers with IR intensities of cyanuric fluoride. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), HOMO-LUMO energy gap and Mapped molecular Electrostatic Potential (MEP) surfaces were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Effective stabilization energy E(2) connected with the interactions of the π and the lone pair of electrons was determined by the NBO analysis. Mulliken population analysis on atomic charges is also calculated. The thermodynamic properties of the cyanuric fluoride at different temperatures have also been calculated for the range of temperature 50-1000 K.

  8. Adaptive DFT-Based Interferometer Fringe Tracking

    NASA Astrophysics Data System (ADS)

    Wilson, Edward; Pedretti, Ettore; Bregman, Jesse; Mah, Robert W.; Traub, Wesley A.

    An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) Observatory at Mount Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier-transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on offline data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately 2.0 milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse. One example of such an application might be to the field of thin-film measurement by ellipsometry, using a broadband light source and a Fourier-transform spectrometer to detect the resulting fringe patterns.

  9. Design Techniques for Uniform-DFT, Linear Phase Filter Banks

    NASA Technical Reports Server (NTRS)

    Sun, Honglin; DeLeon, Phillip

    1999-01-01

    Uniform-DFT filter banks are an important class of filter banks and their theory is well known. One notable characteristic is their very efficient implementation when using polyphase filters and the FFT. Separately, linear phase filter banks, i.e. filter banks in which the analysis filters have a linear phase are also an important class of filter banks and desired in many applications. Unfortunately, it has been proved that one cannot design critically-sampled, uniform-DFT, linear phase filter banks and achieve perfect reconstruction. In this paper, we present a least-squares solution to this problem and in addition prove that oversampled, uniform-DFT, linear phase filter banks (which are also useful in many applications) can be constructed for perfect reconstruction. Design examples are included illustrate the methods.

  10. IR, Raman, SERS and DFT study of amoxicillin

    NASA Astrophysics Data System (ADS)

    Bebu, Andreea; Szabó, László; Leopold, Nicolae; Berindean, Cătălin; David, Leontin

    2011-05-01

    In this work a joint experimental and theoretical study on amoxicillin is reported. The molecular vibrations of amoxicillin were investigated by FTIR, FT-Raman and SERS spectroscopies. In parallel, quantum chemical calculations based on density functional theory (DFT) were used to determine the geometrical, energetic and vibrational characteristics of the molecule with particular emphasis put on the interaction and adsorption geometry of the molecule to the silver colloidal surface. The SERS spectrum of amoxicillin was recorded using a 532 nm laser line and hydroxylamine reduced silver colloid as SERS substrate. FTIR, FT-Raman and SERS spectra of amoxicillin were assigned based on DFT calculations with the hybrid B3LYP exchange-correlation functional, coupled with the standard 6-31G(d) basis set. The calculated molecular electrostatic potential (MEP) was used in conjunction with SERS data to predict the adsorption geometry of the molecule on the silver surface.

  11. IR, Raman, SERS and DFT study of paroxetine

    NASA Astrophysics Data System (ADS)

    Cozar, I. B.; Szabó, L.; Mare, D.; Leopold, N.; David, L.; Chiş, V.

    2011-05-01

    Structural investigations by different vibrational spectroscopic methods (FTIR, Raman and SERS), as well as density functional theory (DFT) calculations were performed on paroxetine (IUPAC name: (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine. After the identification of the lowest energy conformer of the investigated molecule, the FTIR, FT-Raman and SERS spectra were assigned on the basis of DFT calculations at B3LYP/6-31G(d) level of theory. The very good correlation found between experimental and theoretical data is a clear evidence for a reliable assignment of the vibrational bands. The molecular electrostatic potential was calculated and used for the prediction of preferred adsorption sites of the paroxetine molecule on the silver nanoparticles surface. Based on SERS spectra analysis it is shown that the molecule is adsorbed on the silver surface through the benzodioxol ring, in a tilted orientation.

  12. Understanding Density Functional Theory (DFT) and Completing it in Practice

    NASA Astrophysics Data System (ADS)

    Bagayoko, Diola

    2015-03-01

    A brief review of the seminal article by Hohenberg and Kohn leads to two conditions that have to be met by electronic structure calculations in order for their results to represent the physics content of DFT. One of these conditions is often the verifiable attainment of the absolute minima of the occupied energies. Using the second Hohenberg Kohn theorem, we show that results of calculations that do not meet this condition, when it applies, do not necessarily represent DFT findings. We illustrate this fact with over 100 calculated band gaps that are much smaller than corresponding, measured ones; in contrast, we list calculations that strictly adhered to the aforementioned conditions and whose results are in excellent agreement with experiment. We describe two crucial steps in the latter calculations that add to or complete DFT in practice. Some implications of our findings for academia, industry, and program package developers will be discussed. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  13. Self-interaction error in DFT-based modelling of ionic liquids.

    PubMed

    Lage-Estebanez, Isabel; Ruzanov, Anton; García de la Vega, José M; Fedorov, Maxim V; Ivaništšev, Vladislav B

    2016-01-21

    The modern computer simulations of potential green solvents of the future, involving the room temperature ionic liquids, heavily rely on density functional theory (DFT). In order to verify the appropriateness of the common DFT methods, we have investigated the effect of the self-interaction error (SIE) on the results of DFT calculations for 24 ionic pairs and 48 ionic associates. The magnitude of the SIE is up to 40 kJ mol(-1) depending on the anion choice. Most strongly the SIE influences the calculation results of ionic associates that contain halide anions. For these associates, the range-separated density functionals suppress the SIE; for other cases, the revPBE density functional with dispersion correction and triple-ζ Slater-type basis is suitable for computationally inexpensive and reasonably accurate DFT calculations. PMID:26690957

  14. Characterization, photophysical and DFT calculation study on 2-(2,4-difluorophenyl)-1-(4-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline ligand

    NASA Astrophysics Data System (ADS)

    Jayabharathi, Jayaraman; Thanikachalam, Venugopal; Venkatesh Perumal, Marimuthu

    The synthesized imidazole derivative 2-(2,4-difluorophenyl)-1-(4-methoxyphenyl)-1H-imidazo[4,5-f][1,10] phenanthroline (dfpmpip) has been characterized using IR, mass, 1H, 13C NMR and elemental analysis. The photophysical properties of dfpmpip have been studied using UV-visible and fluorescence spectroscopy in different solvents. The solvent effect on the absorption and fluorescence bands has been analyzed by a multi-component linear regression. Theoretically calculated bond lengths, bond angles and dihedral angles are found to be slightly higher than that of X-ray Diffraction (XRD) values of its parent compound. The charge distribution has been calculated from the atomic charges by non-linear optical (NLO) and natural bond orbital (NBO) analysis. Since the synthesized imidazole derivative has the largest μgβ0 value, the reported imidazole can be used as potential NLO material. The energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels and the molecular electrostatic potential (MEP) energy surface studies evidenced the existence of intramolecular charge transfer (ICT) within the molecule. Theoretical calculations regarding the chemical potential (μ), hardness (η) and electrophilicity index (ω) have also been calculated.

  15. Partial vs. integer electron transfer in molecular assemblies: On the importance of multideterminant theoretical description and the necessity to find a solution within DFT

    SciTech Connect

    Geskin, Victor; Cornil, Jérôme; Stadler, Robert

    2015-01-22

    Nonequilibrium Green's function techniques (NEGF) combined with density functional theory (DFT) calculations have become a standard tool for the description of electron transport through single molecule nanojunctions in the coherent tunneling (CT) regime. However, the applicability of these methods for transport in the Coulomb blockade (CB) regime is questionable. For a molecular assembly model, with multideterminant calculations as a benchmark, we show how a closed-shell ansatz, the usual ingredient of mean-field methods, fails to properly describe the step like electron-transfer characteristic in weakly coupled systems. Detailed analysis of this misbehavior allows us to propose a practical scheme to extract the addition energies in the CB regime for single-molecule junctions from NEGF DFT within the local-density approximation (closed shell). We show also that electrostatic screening effects are taken into account within this simple approach.

  16. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    C. F. Melius; M. D. Allendorf

    1999-04-01

    In the 1980's, the authors developed a bond-additivity correction procedure for quantum chemical calculations called BAC-MP4, which has proven reliable in calculating the thermochemical properties of molecular species, including radicals as well as stable closed-shell species. New Bond Additivity Correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid DFT/MP2 method, BAC-Hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method due to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-Hybrid and BAC-MP4. The BAC-Hybrid method should scale well for large molecules. The BAC-Hybrid method uses the differences between the DFT and MP2 as an indicator of the method's accuracy, while the BAC-G2 method uses its internal methods (G1 and G2MP2) to provide an indicator of its accuracy. Indications of the average error as well as worst cases are provided for each of the BAC methods.

  17. First-principles DFT +GW study of oxygen vacancies in rutile TiO2

    NASA Astrophysics Data System (ADS)

    Malashevich, Andrei; Jain, Manish; Louie, Steven G.

    2014-02-01

    We perform first-principles calculations of the quasiparticle defect states, charge transition levels, and formation energies of oxygen vacancies in rutile titanium dioxide. The calculations are done within the recently developed combined DFT +GW formalism, including the necessary electrostatic corrections for the supercells with charged defects. We find the oxygen vacancy to be a negative U defect, where U is the defect electron addition energy. For Fermi level values below ˜2.8 eV (relative to the valence-band maximum), we find the +2 charge state of the vacancy to be the most stable, while above 2.8 eV we find that the neutral charge state is the most stable.

  18. Alkenes as Chelating Groups in Diastereoselective Additions of Organometallics to Ketones

    PubMed Central

    2015-01-01

    Alkenes have been discovered to be chelating groups to Zn(II), enforcing highly stereoselective additions of organozincs to β,γ-unsaturated ketones. 1H NMR studies and DFT calculations provide support for this surprising chelation mode. The results expand the range of coordinating groups for chelation-controlled carbonyl additions from heteroatom Lewis bases to simple C–C double bonds, broadening the 60 year old paradigm. PMID:25328269

  19. Physicochemical studies of chemosensor imidazole derivatives: DFT based ESIPT process

    NASA Astrophysics Data System (ADS)

    Jayabharathi, Jayaraman; Thanikachalam, Venugopal; Jayamoorthy, Karunamoorthy

    2012-04-01

    A series of substituted imidazoles have been synthesized in very good yield under a solvent free condition using molecular iodine as the catalyst. An excited state intramolecular proton transfer (ESIPT) process in hydroxy imidazole has been studied using emission spectroscopy. DFT calculations on energy, dipole moment, charge distribution of the rotamers in the ground and excited states of the imidazole derivatives have been performed and discussed. DFT analysis about HOMO, HOMO-1, LUMO and LUMO+1 has been carried out and discussed. The energy barrier for the interconversion of two rotamers is too high in the excited state than the ground state that is shown by PES calculation. The molecular electrostatic potential surface (MEP) has also been employed to show the higher electron density at N(3) nitrogen. Fluorescence enhancement has been found in the presence of transition metal ions and this may result from the suppression of radiationless transitions from the n-π* state in the chemosensors.

  20. Copper(II) and nickel(II) complexes of tetradentate Schiff base ligand: UV-Vis and FT-IR spectra and DFT calculation of electronic, vibrational and nonlinear optical properties

    NASA Astrophysics Data System (ADS)

    Zarei, Seyed Amir; Khaledian, Donya; Akhtari, Keivan; Hassanzadeh, Keyumars

    2015-11-01

    The experimental fourier transform infrared (FT-IR) and ultraviolet-visible (UV-Vis) spectra of copper(II) and nickel(II) complexes of the deprotonated tetradentate Schiff base ligand N,N‧-bis(2-hydroxybenzylidene)-2,2-dimethyl-1,3-propanediamine (H2L) are compared with their corresponding theoretical ones. The applied theoretical method is based on the density functional theory and time-dependent density functional theory at the UPBE0/PBE0 levels using Def2-TZVP basis set. The computational optimised geometric parameters of the complexes are in good agreement with their corresponding experimental data. The FT-IR and UV-Vis spectra of the complexes were reproduced on the basis of their optimised structures. The vibrational assignments of some fundamental modes of the complexes are performed. The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies are calculated. The analyses of the calculated electronic absorption spectra of the complexes are carried out to elucidate the electronic transitions assignments and their characters. Second-order nonlinear optical property of the complexes is evaluated by the above-mentioned theoretical method that implies much greater values for the complexes in comparison with the corresponding value of urea.

  1. The mechanism of the reduction of [AnO2]2+ (An = U, Np, Pu) in aqueous solution, and by Fe(II) containing proteins and mineral surfaces, probed by DFT calculations.

    PubMed

    Sundararajan, Mahesh; Assary, Rajeev S; Hillier, Ian H; Vaughan, David J

    2011-11-14

    The fate of actinyl species in the environment is closely linked to oxidation state, since the reduction of An(VI) to An(IV) greatly decreases their mobility due to the precipitation of the relatively insoluble An(IV) species. Here we study the mechanism of the reduction of [AnO(2)](2+) (An = U, Np, Pu) both in aqueous solution and by Fe(II) containing proteins and mineral surfaces, using density functional theory calculations. We find a disproportionation mechanism involving a An(V)-An(V) cation-cation complex, and we have investigated how these complexes are formed in the different environments. We find that the behaviour of U and Pu complexes are similar, but the reduction of Np(V) to Np(IV) would seems to be more difficult, in line with the experimental finding that Np(V) is generally more stable than U(V) or Pu(V). Although the models we have used are somewhat idealised, our calculations suggest that there are strong similarities between the biotic and abiotic reduction pathways. PMID:21837318

  2. Absorption intensity changes and frequency shifts of fundamental and first overtone bands for OH stretching vibration of methanol upon methanol-pyridine complex formation in CCl4: analysis by NIR/IR spectroscopy and DFT calculations.

    PubMed

    Futami, Yoshisuke; Ozaki, Yasushi; Ozaki, Yukihiro

    2016-02-21

    Infrared (IR) and near infrared (NIR) spectra were measured for methanol and the methanol-pyridine complex in carbon tetrachloride. Upon the formation of the methanol-pyridine complex, the frequencies of both the fundamental and first overtone bands of the OH stretching vibration shifted to lower frequencies, and the absorption intensity of the fundamental increased significantly, while that of the first overtone decreased markedly. By using quantum chemical calculations, we estimated the absorption intensities and frequencies of the fundamental and first overtone bands for the OH stretching vibration based on the one-dimensional Schrödinger equation. The calculated results well reproduced the experimental results. The molecular vibration potentials and dipole moment functions of the OH stretching vibration modes were compared between methanol and the methanol-pyridine complex in terms of absorption intensity changes and frequency shifts. The large change in the dipole moment function was found to be the main cause for the variations in absorption intensity for the fundamental and first overtone bands. PMID:26862859

  3. Molecular structure and vibrational and chemical shift assignments of 3-(2-Hydroxyphenyl)-4-phenyl-1 H-1,2,4-triazole-5-(4 H)-thione by DFT and ab initio HF calculations

    NASA Astrophysics Data System (ADS)

    Avcı, Davut; Atalay, Yusuf; Şekerci, Mehmet; Dinçer, Muharrem

    2009-07-01

    The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) 1H and 13C chemical shift values and several thermodynamic parameters of 3-(2-Hydroxyphenyl)-4-phenyl-1 H-1,2,4-triazole-5-(4 H)-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density functional methods (BLYP and B3LYP) with 6-31G(d) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The molecule contains one O-H···N and one C-H···π (phenyl) intramolecular interactions. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Data of the title compound display significant structure-correlation and provide the basis for future design of efficient materials having the derivatives of 1,2,4-triazole. Also, calculated 1H chemical shift values compared with the experimental ones.

  4. A comparative study of 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under high pressures using Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Zeng, Yangyang; Song, Yunfei; Yu, Guoyang; Zheng, Xianxu; Guo, Wencan; Zhao, Jun; Yang, Yanqiang

    2016-09-01

    High pressure Raman experiment was performed to compare RDX and HMX crystals. Ab initio calculations using B3LYP Density Functional Theory method with Sadlej's medium-sized polarized basis set (SadlejpVTZ) were carried out for Caae RDX and 1,5-diaxial-3,7-diequatorial chair HMX molecules. Our calculations and measured Raman vibrational spectra reveal both molecules have similarities on bonding and vibrational properties at ambient pressure. However, high pressure responses for both molecules aren't the same. For RDX, at pressure near 4 GPa, a number of changes become apparent in the Raman spectra, such as modes splitting, intensity modification, and discontinuity of pressure-dependence of frequency shifts, which are consistent with previous experiment and believed to associate with α-γ phase transition. For HMX, only slight conformational deformation involving NO2 group was observed, and was considered as an onset of β-ε phase transition. It is proposed that the markedly different behavior under high pressure for these two molecules results from different molecular packing in unit cell.

  5. A DFT Approach to the Mechanistic Study of Hydrozone Hydrolysis.

    PubMed

    Yildiz, Ibrahim

    2016-05-26

    Hydrazone chemistry is widely utilized in biomedical field as a means of bioconjugation protocol, especially in drug delivery field due to pH labile nature of this linkage. In the light of kinetics studies, the generally accepted mechanism for the hydrolysis of hydrazones involves two main steps, namely, nucleophilic addition of water molecule to the hydrazone molecule to form carbinolamine intermediate and subsequent decomposition of this intermediate into the hydrazine and aldehyde/ketone moieties. Hydrolysis of hydrazones is catalyzed in the acidic environments and is thought to proceed through several proton transfer steps. To the best of our knowledge, in the literature no detailed theoretical study has been reported related to the mechanism of hydrolysis. In this study, we evaluated the proposed mechanism with DFT calculations with M06-2X functional at the 6-311+g(d,p) level including conductor-like polarizable continuum model solvation model. We also analyzed possible proton transfer pathways and assessed energetics of each step. PMID:27136330

  6. DFT studies and vibrational spectra of isoquinoline and 8-hydroxyquinoline

    NASA Astrophysics Data System (ADS)

    Krishnakumar, V.; Ramasamy, R.

    2005-02-01

    The geometry, frequency and intensity of the vibrational bands of isoquinoline (IQ) and 8-hydroxyquinoline (8-HQ) were obtained by the density functional theory (DFT) calculations with the B3LYP functional and 6-31 G* basis set. The vibrational spectral data obtained from the solid phase mid and far FT-IR and FT-Raman spectra of IQ and 8-HQ are assigned based on the results of the normal coordinate calculations. The observed and the calculated spectra are found to be in good agreement.

  7. Influence of xc functional on thermal-elastic properties of metal oxides: A DFT-based Debye-Gr"uneisen model approach

    NASA Astrophysics Data System (ADS)

    Lee, Taehun; Soon, Aloysius

    2012-02-01

    For high-temperature applications, the chemical stability, as well as the mechanical integrity of the oxide material used is of utmost importance. Solving these problems demands a thorough and fundamental understanding of their thermal-elastic properties. In this work, we report density-functional theory (DFT) calculations to investigate the influence of the xc functional on specific thermal-elastic properties of some common oxides CeO2, Cu2O, and MgO. Namely, we consider the local-density approximation (LDA), the generalized gradient approximation due to Perdew, Burke, and Ernzerhof (GGA-PBE), as well as a recently popularized hybrid functional due to Heyd-Scuseria-Ernzehof (HSE06). In addition, we will also report DFT+U results where we introduce a Hubbard U term to the Cu 3d and the Ce 4f states. Upon obtaining the DFT total energies, we then couple this to a volume-dependent Debye-Gr"uneisen model [1] to determine the thermodynamic quantities of these oxides at arbitrary pressures and temperatures. We find an explicit description of the strong correlation (e.g. via the DFT+U approach and using HSE06) is necessary to have a good agreement with experimental values. [1] A. Otero-de-la-Roza, D. Abbasi-P'erez et al. Com. Phys. Com. 182 (2011) 2232

  8. Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis.

    PubMed

    Afonin, Andrei V; Ushakov, Igor A; Pavlov, Dmitry V; Ivanov, Andrei V; Mikhaleva, Al'bina I

    2010-09-01

    The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer. PMID:20623827

  9. 3D QSAR Pharmacophore Modeling, in Silico Screening, and Density Functional Theory (DFT) Approaches for Identification of Human Chymase Inhibitors

    PubMed Central

    Arooj, Mahreen; Thangapandian, Sundarapandian; John, Shalini; Hwang, Swan; Park, Jong Keun; Lee, Keun Woo

    2011-01-01

    Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (r = 0.942) pharmacophore model (Hypo1) with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating “Hypo1”, it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high GOLD fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC50) data thus successfully validating “Hypo1” by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors. PMID:22272131

  10. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3Thermus thermophilus

    PubMed Central

    2016-01-01

    The Fea33+···CuB2+ dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO’s were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea32+···CuB+ DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779–5783) revealed multiple 57Fea32+ and 57Fea33+ components. Moreover, one of the 57Fea33+ components observed at 4.2 K transformed from a proposed “low-spin” state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin 57Fea33+ component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the 57Fea33+ components, and how the coordination and spin states of the Fea33+/2+ and Cu2+/1+ sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB+ site, and they may become potential proton loading sites during the catalytic cycle

  11. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus.

    PubMed

    Han Du, Wen-Ge; Noodleman, Louis

    2015-08-01

    The Fea3(3+)···CuB(2+) dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO's were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea3(2+)···CuB(+) DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779-5783) revealed multiple (57)Fea3(2+) and (57)Fea3(3+) components. Moreover, one of the (57)Fea3(3+) components observed at 4.2 K transformed from a proposed "low-spin" state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin (57)Fea3(3+) component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the (57)Fea3(3+) components, and how the coordination and spin states of the Fea3(3+/2+) and Cu(2+/1+) sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB(+) site, and they may become potential proton loading sites

  12. The construction of graph models for calculations of the properties of substitution isomers of basis structures on the basis of additivity of energy contributions

    NASA Astrophysics Data System (ADS)

    Nilov, D. Yu.; Smolyakov, V. M.

    2012-05-01

    A method for the construction of additive models for calculations of the properties of substitution isomers of basis structures is described for the example of a series of X-substituted methylsilanes CH3 - k X k -SiH3 - l X l (where X = CH3, F, Cl, …, k, l = 0, 1, 2, 3). The method is based on similarity of subgraphs in graphs of several molecules and the arrangement of polygonal numbers (triangular, tetrahedral) of the Pascal triangle. Parameters taking into account multiple nonvalence interactions (-C-Si<, >C-Si<, …) through two atoms along the molecular chain of an X-substituted methylsilane (X = CH3) were for the first time explicitly included in the calculation scheme. Taking these interactions into account allows us to completely differentiate all the structural isomers of certain molecules and obtain numerical parameter values for predicting properties P under consideration in various approximations. Numerical calculations of Δf H {g,298/K o} were performed for 16 alkylsilanes (as X-substituted methylsilanes), including 7 compounds not studied experimentally.

  13. O sbnd H⋯O and O sbnd H⋯N hydrogen bonds in the complex of DABCO mono-betaine with p-hydroxybenzoic acid studied by X-ray diffraction, DFT calculations and spectroscopic methods

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

    DABCO mono-betaine (1,4-diazabicyclo[2.2.2]octane-1-acetate) forms a complex with p-hydroxybenzoic acid (HBA) at the 1:1 ratio. The crystals are monoclinic, space group P2 1/ m. The HBA and DABCO mono-betaine molecules are linked into infinite chains through the COOH⋯OOC and O sbnd H⋯N hydrogen bonds of 2.604(1) and 2.771(2) Å, respectively. The DABCO mono-betaine is located on a mirror plane and the HBA molecule lies on this plane. In the structure of the 1:1 complex optimized by the B3LYP/6-31G(d,p) approach, the DABCO ring has a planar conformation, while in the chains formed by two complexes, the DABCO moieties assume the propeller conformations. The FTIR spectrum shows several bands attributed to the O sbnd H, O sbnd H⋯O, O sbnd H⋯N, C dbnd O and COO stretching vibrations. 1H and 13C chemical shifts assignments were confirmed by the magnetic isotropic shielding constants, calculated by the GIAO/B3LYP/6-31G(d,p) approach.

  14. Novel and unusual triterpene from Black Cohosh. Determination of structure of 9,10- seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jamróz, Marta K.; Jamróz, Michał H.; Dobrowolski, Jan Cz.; Gliński, Jan A.; Davey, Matthew H.; Wawer, Iwona

    2011-01-01

    A new triterpene xyloside, designated cimipodocarpaside was isolated from a Black Cohosh ( Actea racemosa L.) extract and its structure was elucidated by means of 1H, 13C NMR, IR and Raman spectroscopy supported by B3LYP/6-31G** calculations. The vibrational spectra were interpreted using the PED analysis of 273 fundamentals. Its structure comprises four condensed rings A-D which are 6, 7, 6, and 5-membered, respectively. An oxiirane ring is located in the side chain and a xylose moiety is attached to the A-ring. Comparison of the experimental 13C NMR data with the theoretical chemical shifts of 24 S- and 24 R-cimipodocarpaside isomers revealed that the isolated compound has the 24 S-configuration. Combined spectroscopic and computational studies enabled the determination of the structure of cimipodocarpaside as (24 S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10- seco-9,19-cyclolanost-7(8),9(11),10(19)-trien-3-O-β- D-xylopyranoside. Triterpenes with 7-membered ring were thus far isolated from only Actea podocarpa DC. plants. This is the first report on the isolation of such a compound from Black Cohosh.

  15. Novel and unusual triterpene from Black Cohosh. Determination of structure of 9,10-seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations.

    PubMed

    Jamróz, Marta K; Jamróz, Michał H; Dobrowolski, Jan Cz; Gliński, Jan A; Davey, Matthew H; Wawer, Iwona

    2011-01-01

    A new triterpene xyloside, designated cimipodocarpaside was isolated from a Black Cohosh (Actea racemosa L.) extract and its structure was elucidated by means of 1H, 13C NMR, IR and Raman spectroscopy supported by B3LYP/6-31G** calculations. The vibrational spectra were interpreted using the PED analysis of 273 fundamentals. Its structure comprises four condensed rings A-D which are 6, 7, 6, and 5-membered, respectively. An oxiirane ring is located in the side chain and a xylose moiety is attached to the A-ring. Comparison of the experimental 13C NMR data with the theoretical chemical shifts of 24S- and 24R-cimipodocarpaside isomers revealed that the isolated compound has the 24S-configuration. Combined spectroscopic and computational studies enabled the determination of the structure of cimipodocarpaside as (24S)-3β-hydroxy-24,25-oxiirane-16,23-dione-9,10-seco-9,19-cyclolanost-7(8),9(11),10(19)-trien-3-O-β-D-xylopyranoside. Triterpenes with 7-membered ring were thus far isolated from only Actea podocarpa DC. plants. This is the first report on the isolation of such a compound from Black Cohosh. PMID:20934376

  16. Density versus spin-density functional in DFT+U and DFT+DMFT

    NASA Astrophysics Data System (ADS)

    Park, Hyowon; Millis, Andrew; Marianetti, Chris

    2015-03-01

    The construction of multi-variable effective action theories such as DFT+U and DFT+DMFT requires the choice of a local subspace of correlated orbitals and an additional variable being either the charge density or spin density. This talk examines the differences between using charge-only and spin-dependent exchange-correlation functionals with the aim of providing guidance for constructing more sophisticated beyond-density functional theories. The widely used spin-dependent approximations to the exchange-correlation functional are found to lead to a large and in some cases unphysical effective exchange coupling within the correlated subspace. Additionally, the differences between Wannier and Projector based definitions of the correlated orbitals are examined, and only small differences are found provided that the orbitals are orthonormal and strongly localized. These results are documented in the context of the rare earth nickelates. This work is supported under the Grant DOE-ER-046169 and under the FAME grant, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

  17. Introducing constricted variational density functional theory in its relaxed self-consistent formulation (RSCF-CV-DFT) as an alternative to adiabatic time dependent density functional theory for studies of charge transfer transitions

    SciTech Connect

    Krykunov, Mykhaylo; Seth, Mike; Ziegler, Tom

    2014-05-14

    We have applied the relaxed and self-consistent extension of constricted variational density functional theory (RSCF-CV-DFT) for the calculation of the lowest charge transfer transitions in the molecular complex X-TCNE between X = benzene and TCNE = tetracyanoethylene. Use was made of functionals with a fixed fraction (α) of Hartree-Fock exchange ranging from α = 0 to α = 0.5 as well as functionals with a long range correction (LC) that introduces Hartree-Fock exchange for longer inter-electronic distances. A detailed comparison and analysis is given for each functional between the performance of RSCF-CV-DFT and adiabatic time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation. It is shown that in this particular case, all functionals afford the same reasonable agreement with experiment for RSCF-CV-DFT whereas only the LC-functionals afford a fair agreement with experiment using TDDFT. We have in addition calculated the CT transition energy for X-TCNE with X = toluene, o-xylene, and naphthalene employing the same functionals as for X = benzene. It is shown that the calculated charge transfer excitation energies are in as good agreement with experiment as those obtained from highly optimized LC-functionals using adiabatic TDDFT. We finally discuss the relation between the optimization of length separation parameters and orbital relaxation in the RSCF-CV-DFT scheme.

  18. Adsorption and spin state properties of Cr, Ni, Mo, and Pt deposited on Li⁺ and Na⁺ monovalent cation impurities of MgO (001) surface: DFT calculations.

    PubMed

    Shalabi, Ahmad S; Assem, Mervat M; Soliman, Kamal A

    2011-12-01

    We have analyzed, by means of density functional theory calculations and the embedded cluster model, the adsorption and spin-state properties of Cr, Ni, Mo, and Pt deposited on a MgO crystal. We considered deposition at the Mg(2+) site of a defect-free surface and at Li(+) and Na(+) sites of impurity-containing surfaces. To avoid artificial polarization effects, clusters of moderate sizes with no border anions were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The interaction between a transition metal atom and a surface results from a competition between Hund's rule for the adsorbed atom and the formation of a chemical bond at the interface. We found that the adsorption energies of the metal atoms are significantly enhanced by the cation impurities, and the adsorption energies of the low-spin states of spin-quenched complexes are always more favorable than those of the high-spin states. Spin polarization effects tend to preserve the spin states of the adsorbed atoms relative to those of the isolated atoms. The metal-support interactions stabilize the low-spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. Spin quenching occurs for Cr and Mo complexes at the Mg(2+) site of the pure surface and at Li(+) and Na(+) sites of the impurity-containing surfaces. Variations of the spin-state properties of free metals and of the adsorption and spin-state properties of metal complexes are correlated with the energies of the frontier orbitals. The electrostatic potential energy curves provide further understanding of the nature of the examined properties. PMID:21369929

  19. X-ray and DFT calculated structures of 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-phenylthiosemicarbazone and 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-(4-chlorophenyl)thiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Sahin, Z. S.; Septioglu, E.; Calis, U.; Isik, S.

    2014-12-01

    Crystal and molecular structures of two new compounds 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-phenylthiosemicarbazone, C22H19N5S, ( I) and 2-(1 H-imidazol-1-yl)-1-(2-naphthyl)ethan-1-one N-(4-chlorophenyl)thiosemicarbazone, C22H18ClN5S, ( II) have been determined by single-crystal X-ray diffraction. Molecular geometries from X-ray experiment of I and II have been compared with those calculated using the Density Functional Theory (DFT) with B3LYP/6-31G( d, p) basis set. Both compounds crystallize in the monoclinic space group P21/ c with Z = 4: a = 13.2880(5), 14.2648(3) Å, b = 9.4122(2), 9.3892(3) Å, c = 15.6341(6), 15.6268(4) Å, β = 101.779(3)°, 104.926(2)°, for I and II, respectively. An extensive two-dimensional network of N-H⋯N hydrogen bonds and π-ring interactions are responsible for crystal stabilization in both structures.

  20. Trans/cis isomerization of [RuCl2{H2Cdbnd C(CH2PPh2)2)}(diamine)] complexes: Synthesis, spectral, crystal structure and DFT calculations and catalytic activity in the hydrogenation of α,β-unsaturated ketones

    NASA Astrophysics Data System (ADS)

    Warad, Ismail; Al-Noaimi, Mousa; Abdel-Rahman, Obadah S.; Awwadi, Firas F.; Hammouti, Belkheir; Hadda, Taibi B.

    2014-01-01

    Three complexes of the general formula trans/cis-[Ru(II)(dppme)(Nsbnd N)Cl2] {dppme is H2Cdbnd C(CH2PPh2)2 and Nsbnd N is 1,2-diaminocyclohexane (trans/cis-(1)) and 1-methyl-1,2-diaminopropane (trans-(2)} were obtained by reacting trans-[RuCl2(dppme)2] with an excess amount of corresponding diamine in CH2Cl2 as a solvent. The complexes were characterized by an elemental analysis, IR, 1H, 13C and 31P{1H} NMR, FAB-MS and UV-visible. The trans-(1) (kinetic product) readily isomerizes to the cis-(1) (thermodynamic product) and this process was followed by using 31P{1H} NMR, cyclic voltammetry and UV-vis spectroscopy. The electrochemical studies on complex (1) reveal that the Ru(III)/Ru(II) couples are sensitive to the isomer (trans/cis) formed. The cis-(1) was confirmed by X-ray structure and 31P{1H} NMR. Transfer-hydrogenation reactions for reduction of trans-4-phenyl-3-butene-2-one were conducted using complexes trans/cis-(1) and trans-(2). The electronic spectra of cis/trans-(1) in dichloromethane were calculated with the use of time-dependent DFT methods.