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.
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.
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
Modelling catalyst surfaces using DFT cluster calculations.
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
Modelling Catalyst Surfaces Using DFT Cluster Calculations
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
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
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.
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.
Predicting the properties of the lead alloys from DFT calculations
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.
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.
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.
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)
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.
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.
Accurate and efficient linear scaling DFT calculations with universal applicability.
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
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.
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
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.
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.
Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.
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
DFT calculations of EPR parameters of transition metal complexes: Implications for catalysis
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
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.
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
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.
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.
Hexakis(4-phormylphenoxy)cyclotriphosphazene: X-ray and DFT-calculated structures
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.
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
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
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.
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.
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.
Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations.
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
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
Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.
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
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.
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.
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.
Modern battery electrolytes: ion-ion interactions in Li+/Na+ conductors from DFT calculations.
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
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.
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.
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.
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
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.
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.
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
Raman spectroscopy and DFT calculations of As(III) complexation with a cysteine-rich biomaterial.
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
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
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.
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.
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.
A big data approach to the ultra-fast prediction of DFT-calculated bond energies
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
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.
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.
A first-principles DFT study of UN bulk and (001) surface: comparative LCAO and PW calculations.
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
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.
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.
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.
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
MCD spectroscopy and TD-DFT calculations of low symmetry subnaphthalocyanine analogs.
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
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.
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.
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.
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
NO Chemisorption on Cu/SSZ-13: a Comparative Study from Infrared Spectroscopy and DFT Calculations
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.
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.
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.
FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate.
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
A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations.
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
A DFT study of addition reaction between fragment ion (CH₂) units and fullerene (C₆₀) molecule.
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
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.
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
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.
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.
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)
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
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.
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.
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
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)...
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
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.
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.
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.
Relativistic DFT Calculation of (119)Sn Chemical Shifts and Coupling Constants in Tin Compounds.
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
Performance of DFT Methods in the Calculation of Optical Spectra of TCF-Chromophores
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.
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.
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.
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.
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
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.
Interaction evaluation of silver and dithizone complexes using DFT calculations and NMR analysis.
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
(E)-2-[(2-Bromophenylimino)methyl]-5-methoxyphenol: X-ray and DFT-calculated structures
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.
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.
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
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...
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...
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....
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....
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.
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
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
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...
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
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.
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.
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.
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
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
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.
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.
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.
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
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
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.
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.
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
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.
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.
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.
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.
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).
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.
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
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.
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.
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.
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.
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
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.
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.
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.
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
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.
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).
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.
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
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
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.
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.
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.
Optical properties of alkali halide crystals from all-electron hybrid TD-DFT calculations
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.
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.
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.
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.
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
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 PbFeBO_{4} 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.
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.
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.
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
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.
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...
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
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
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
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.
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.
Infrared and Raman spectra, DFT-calculations and spectral assignments of germacyclohexane
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.
Insight into insulator-to-metal transition of sulfur-doped silicon by DFT calculations.
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
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
Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST.
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
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.
DFT calculations of triethyl and trimethyl orthoacetate elimination kinetics in the gas phase.
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
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.
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
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
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.
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.
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 νCN, dramatic increases in the corresponding integrated intensities (136-fold, total value), strong enhancement of the νCN 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 CPh and CCN 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) 2SO⋯HC(CN) 2C 6H 5 hydrogen bonds has been found experimentally.
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.
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.
Combined hybrid functional and DFT+U calculations for metal chalcogenides
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.
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.
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.
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.
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%.
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.
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
DFT calculation of the electronic properties of fluorene-1,3,4-thiadiazole oligomers.
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
Direct comparison between two {gamma}-alumina structural models by DFT calculations
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.
Growth of Silicon Nanoclusters: Elucidation by gas-phase experiments and DFT calculations
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.
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.
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
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
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.
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.
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
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.
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.
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
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
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
Characterization of novel isobenzofuranones by DFT calculations and 2D NMR analysis.
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
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.
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.
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.
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
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
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.
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.
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.
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).
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.
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
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
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.
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
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.
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
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.
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.
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.
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.
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
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
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.
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.
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.
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...
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...
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...
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...
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...
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.
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.
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
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
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.
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
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.
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.
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
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.
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.
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.
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
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.
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
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
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
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
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.
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
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.
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
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.
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.
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
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.
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
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