Lill, Sten O Nilsson
2010-09-01
An evaluation of a dispersion-corrected density functional theory method (B3LYP-DCP) [I.D. Mackie, G.A. DiLabio, Interactions in large, polyaromatic hydrocarbon dimers: application of density functional theory with dispersion corrections, J. Phys. Chem. A 112 (2008) 10968-10976] for three systems of biochemical interest is presented. Firstly, structures and energies of isomers of the tripeptide Phe-Gly-Phe have been compared with CCSD(T)/CBS//RI-MP2/cc-pVTZ literature values. In the system aromatic interactions compete with XH-pi (X=C, N) interactions and hydrogen bonds which makes it a reliable model for proteins. The resulting mean absolute deviation between B3LYP-DCP and CCSD(T)/CBS relative energies is found to be 0.50 kcal mol(-1). Secondly, a phenylalanine derivative featuring a CH-pi interaction has been investigated. A comparison between the optimized geometry and X-ray crystal data shows that B3LYP-DCP accurately predicts the interaction between the two aromatic rings. Thirdly, the dipeptide Ac-Phe-Phe-NH(2) which contains an edge-to-face interaction between two aromatic rings has been studied. The study demonstrates the general applicability of the B3LYP-DCP method on systems which features interactions typically present in biochemical compounds.
Legler, C R; Brown, N R; Dunbar, R A; Harness, M D; Nguyen, K; Oyewole, O; Collier, W B
2015-06-15
The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.
Indian Academy of Sciences (India)
M Talebian; E Talebian; A Abdi
2012-05-01
We obtained an approximation of the force ﬁeld of -quartz crystal using a new idea of applying density functional theory [J Purton, R Jones, C R A Catlow and M Leslie, Phys. Chem. Minerals 19, 392 (1993)]. Our calculations were based on B3LYP Hamiltonian [A N Lazarev and A P Mirgorodsky, Phys. Chem. Minerals 18, 231 (1991)] in 6−311+G(2d) basis set for H16Si7O6 cluster and included a unit cell of the lattice. The advantage of our method is the increase in the speed of calculations and the better adaption of simulation results with the experimental data.
De la Pierre, M; Orlando, R; Maschio, L; Doll, K; Ugliengo, P; Dovesi, R
2011-07-15
The performance of six different density functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in describing the infrared spectrum of forsterite, a crystalline periodic system with orthorhombic unit cell (28 atoms in the primitive cell, Pbmn space group), is investigated by using the periodic ab initio CRYSTAL09 code and an all-electron Gaussian-type basis set. The transverse optical (TO) branches of the 35 IR active modes are evaluated at the equilibrium geometry together with the oscillator strengths and the high-frequency dielectric tensor ϵ(∞) . These quantities are essential to compute the dielectric function ϵ(ν), and then the reflectance spectrum R(ν), which is compared with experiment. It turns out that hybrid functionals perform better than LDA and GGA, in general; that B3LYP overperforms WC1LYP and, in turn, PBE0; that PBESOL is better than PBE; that LDA is the worst performing functional among the six under study.
Maschio, L.; Ferrabone, M.; Meyer, A.; Garza, J.; Dovesi, R.
2011-01-01
The performance of five different density functionals (LDA, PBE, PBESOL, B3LYP and PBE0) in describing the infrared spectrum of a crystalline periodic system with a large unit cell (spessartine, 80 atoms in the primitive cell) is studied by using the periodic ab initio CRYSTAL09 code and an all electron basis set. The transverse (TO) and longitudinal (LO) optical branches of the 17 IR active modes are evaluated together with the oscillator strengths and the high frequency dielectric tensor ɛ∞ . These ingredients permit to compute the dielectric function ɛ (ν) , and then the reflectance spectrum R (ν) , which is compared with experiment.
Tounsi, Amal; Hamdi, Besma; Zouari, Ridha; Ben Salah, Abdelhamid
2016-10-01
A new organic-inorganic material [C6H10(NH3)2]CoCl4·H2O was reported. The title compound was synthesized at room temperature by slow evaporation and then characterized by a single X-ray diffraction, spectroscopic measurements, thermal analysis and dielectric technique. It crystallizes in the non-centrosymmetric space group Pna21 with the following unit cell parameters: a=12.5328(1) Å, b=9.0908(1) Å, c=11.7440(1) and α=β=γ=90°. The structure can be described by the alternation of two different cationic-anionic layers. It consists of isolated H2O, isolated [CoCl4]2- tetrahedral anions and diammoniumcyclohexane [C6H10(NH3)2]2+ cations, which are connected via N-H…Cl, N-H…O and O-H…N hydrogen bonds. The Hirshfeld surface analysis was conducted to investigate intermolecular interactions and associated 2D fingerprint plots, revealing the relative contribution of these interactions in the crystal structure quantitatively. Theoretical calculations were performed using DFT/B3LYP/LanL2DZ method for studying the molecular structure and vibrational spectra and especially to examine the non-linear optical behavior of the compound. Solid state 13C NMR spectrum shows three signals correspond to three different carbon environments. Thermal analysis discloses a phase transition at the temperature 315 K and the evaporation of water molecule at 327 K. A detailed dielectric study was reported and shows a good agreement with thermal measurements.
Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole
2010-07-15
The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.
B3LYP, BLYP and PBE DFT band structures of the nucleotide base stacks
Szekeres, Zs; Bogár, F.; Ladik, J.
DFT crystal orbital (band structure) calculations have been performed for the nucleotide base stacks of cytosine, thymine, adenine, and guanine arranged in DNA B geometry. The band structures obtained with PBE, BLYP, and B3LYP functionals are presented and compared to other related experimental and theoretical results. The influence of the quality of the basis set on the fundamental gap values was also investigated using Clementi's double ζ, 6-31G and 6-31G* basis sets.
Abkari, A.; Chaabane, I.; Guidara, K.
2016-07-01
The organic-inorganic salt, bis(4-acetylanilinium) tetrachlorocuprate(II), was synthesized and characterized by means of FT-IR (4000-400 cm-1) and Raman (3500-50 cm-1) in solid phase. The structure of [C8H10NO]2CuCl4 compound which was optimized by density functional theory (DFT) using B3LYP method showed that the calculated values obtained by B3LYP with LanL2DZ and 6311G+(d,p) basis sets are in better agreement with the experimental data. The computed vibrational frequencies were scaled by different scale factors to yield a good agreement with the experimental vibrational frequencies. The latter have been discussed on the basis of quantum chemical DFT calculations using the B3LYP/6311G+(d,p) and B3LYP/LanL2DZ method approach in gas phase. Besides, the effects due to the substitutions and the intermolecular interactions were investigated. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was also discussed. The geometries and normal modes of the vibrations obtained from B3LYP/6311G+(d,p) calculation are found to be in good agreement with the experimentally observed data. The complete vibrational assignments and analysis of the observed fundamental bands of molecule were carried out.
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.
Theoretical insight into hydrogen adsorption onto graphene: a first-principles B3LYP-D3 study.
Darvish Ganji, M; Hosseini-Khah, S M; Amini-Tabar, Z
2015-01-28
This work investigates hydrogen adsorption onto various graphene flakes such as coronene and coronene-like as suitable models of graphene within the framework of the DFT-B3LYP method. The non-local van der Waals (vdW) density functional (B3LYP-D3) method is used for both structural geometry optimization and total energy estimations. Calculations were carried out for a hydrogen molecule above a coronene surface with both conventional and vdW corrected DFT to investigate how these approaches perform in the case of hydrogen adsorption on a graphene surface. Our first-principles results within the B3LYP-D3/def2-TZVPP model show that hydrogen physisorbs on a coronene surface with an adsorption energy of -5.013 (kJ mol(-1)) which is in good agreement with the experimental value. The influence of the basis set and graphene flake size were also evaluated and the results indicate that these slightly affect the adsorption properties. We found also that it is crucial to use non-local dispersion interactions to get accurate results for hydrogen adsorption on a graphene surface. Furthermore, the co-adsorption of H2 molecules onto the graphene surface was investigated. The results obtained at the B3LYP-D3/def2-TZVP level show that H2 molecules can be physisorbed on both sides of the graphene layer with adsorption properties similar to those for a single surface. Finally, we showed that H2 molecules might be bound to the graphene surface via a bilayer adsorption scheme with weak adsorption energy. Charge population and electron density analysis confirm the weak binding nature of the system under consideration.
Study of cyclic quaternary ammonium bromides by B3LYP calculations, NMR and FTIR spectroscopies.
Brycki, Bogumił; Szulc, Adrianna; Kowalczyk, Iwona
2010-08-16
N,N-dioctyl-azepanium, -piperidinium and -pyrrolidinium bromides 1-3, have been obtained and characterized by FTIR and NMR spectroscopy. DFT calculations have also been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been presented. Both FTIR and Raman spectra of 1-3 are consistent with the calculated structures in the gas phase. The screening constants for 13C and 1H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental 1H and 13C chemical shifts and the computed screening constants confirm the optimized geometry.
Study of Cyclic Quaternary Ammonium Bromides by B3LYP Calculations, NMR and FTIR Spectroscopies
Directory of Open Access Journals (Sweden)
Iwona Kowalczyk
2010-08-01
Full Text Available N,N-dioctyl-azepanium, -piperidinium and -pyrrolidinium bromides 1-3, have been obtained and characterized by FTIR and NMR spectroscopy. DFT calculations have also been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p approach have been presented. Both FTIR and Raman spectra of 1-3 are consistent with the calculated structures in the gas phase. The screening constants for 13C and 1H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p approach and analyzed. Linear correlations between the experimental 1H and 13C chemical shifts and the computed screening constants confirm the optimized geometry.
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.
DiLabio, Gino A; Torres, Edmanuel
2013-01-01
We recently showed that dispersion-correcting potentials (DCPs), atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys. Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the application of B3LYP-DCP for the {\\beta}-scission of the cumyloxyl radical led a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We show in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C-C covalent-bonding region. In this work, we present a new C-DCP with a form that was expected to influence the electron density farther from the nucleus. Tests of the new C-DCP, with previously published H-, N- and O-DCPs, with B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular i...
Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth
2010-06-01
The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (ɛ∞) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of ɛ∞ and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.
Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth
2010-06-28
The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (epsilon(infinity)) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of epsilon(infinity) and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.
Mohamed, Tarek A.; Hassan, Ali M.; Soliman, Usama A.; Zoghaib, Wajdi M.; Husband, John; Abdelall, Mahmoud M.
2011-01-01
The Raman and infrared spectra of solid 5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbothioamide (AMPC, C 6H 7N 5S 2) were measured in the spectral range of 3700-100 cm -1 and 4000-200 cm -1 with a resolution of 4 and 0.5 cm -1, respectively. Aided by normal coordinate analysis and potential energy distributions, a confident vibrational assignment of all fundamentals is proposed herein. As a result of internal rotation around C sbnd N and/or C sbnd S bonds, 32 rotational isomers are suggested for AMPC (C s symmetry). RHF and DFT/B3LYP quantum mechanical calculations including polarization and diffusion functions up to 6-311++G(d,p) basis sets, predict that after complete relaxation of the 32 possible isomers, four structures lie within 1500 cm -1 of the lowest energy conformer. However, vibrational analysis reveals the lowest energy conformer to be the only structure giving all real frequencies. Thus, the only stable conformer of AMPC is shown to have a fully planar skeleton with the NH 2 groups trans to one another. The recorded IR and Raman spectral measurements favor the calculated structural parameters which are further supported by spectral simulation. Additional support is given by 1H and 13C NMR spectra recorded with the sample dissolved in DMSO-d 6 and by predicted chemical shifts at the B3LYP/6-311+G(2d,p) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). Finally, CH 3, CH 3S, and NH 2 torsional barriers to internal rotation have been investigated using the optimized structural parameters from the B3LYP method with the 6-31G(d) basis set. The results are discussed herein and compared with similar molecules whenever appropriate.
Hole trapping at Al impurities in silica: A challenge for density functional theories
DEFF Research Database (Denmark)
Lægsgaard, Jesper; Stokbro, Kurt
2001-01-01
The atomic geometry and electronic structure around a neutral substitutional Al impurity in silica is investigated using either the unrestricted Hartree-Fock (UHF) approximation, or Beckes three-parameter hybrid functional (B3LYP). It is found that the B3LYP functional fails to describe the struc...
Wang, Ting; Brudvig, Gary; Batista, Victor S
2010-01-29
The capabilities and limitations of the Becke-3-Lee-Yang-Parr (B3LYP) density functional theory (DFT) for modeling proton coupled electron transfer (PCET) in the mixed-valence oxomanganese complex 1 [(bpy)(2)Mn(III)(mu-O)(2)Mn(IV)(bpy)(2)](3+) (bpy = 2,2'-bipyridyl) are analyzed. Complex 1 serves as a prototypical synthetic model for studies of redox processes analogous to those responsible for water oxidation in the oxygen-evolving complex (OEC) of photosystem II (PSII). DFT B3LYP free energy calculations of redox potentials and pKa's are obtained according to the thermodynamic cycle formalism applied in conjunction with a continuum solvation model. We find that the pKa's of the oxo-ligands depend strongly on the oxidation states of the complex, changing by approximately 10 pH units (i.e., from pH~2 to pH~12) upon III,IV-->III,III reduction of complex 1. These computational results are consistent with the experimental pKa's determined by solution magnetic susceptibility and near-IR spectroscopy as well as with the pH dependence of the redox potential reported by cyclic voltammogram measurements, suggesting that the III,IV-->III,III reduction of complex 1 is coupled to protonation of the di-mu-oxo bridge as follows: [(bpy)(2)Mn(III)(mu-O)(2) Mn(IV)(bpy)(2)](3+)+H(+)+e(-)-->[(bpy)(2)Mn(III)(mu-O)(mu-OH)Mn(III)(bpy)(2)](3+). It is thus natural to expect that analogous redox processes might strongly modulate the pKa's of oxo and hydroxo/water ligands in the OEC of PSII, leading to deprotonation of the OEC upon oxidation state transitions.
Bahgat, Khaled; EL-Emary, Talaat
2013-02-01
FT Raman and IR spectra of the crystallized biologically active molecule, 5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (5-APHC, C11H11N3O) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of 5-APHC have been investigated with the help of B3LYP density functional theory (DFT) method with 6-31G(d) and 6-311+G(d,p) as basis set. The calculated molecular geometry has been compared with the experimental data. 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 (SQM) technique. The optimized geometry shows the co-planarity of the aldehyde group with pyrazole ring. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G(d,p) basis set. The red shifting of NH2 stretching wavenumber indicates the formation of N-H⋯O hydrogen bonding. 1H and 13C NMR spectra were recorded and 1H and 13C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-Vis spectrum of the compound was recorded in the region 200-400 nm and the electronic properties HOMO and LUMO energies were calculated by time-dependent TD-DFT approach. Mulliken charges of the 5-APHC molecule was also calculated and interpreted.
Zeffiro, Alberto; Lazzaroni, Simone; Merli, Daniele; Profumo, Antonella; Buttafava, Armando; Serpone, Nick; Dondi, Daniele
2016-06-01
Despite its importance in the prebiotic and biochemical fields, a complete theoretical study of the formation of hexamethylenetetramine (HMT) starting from its precursors ammonia and formaldehyde has not received due considerations in the literature with regard to the thermodynamic feasibility of many of the mechanistically proposed intermediates in its formation. Most of the studies in this area have been mostly concerned with the initial steps of the reaction between formaldehyde and ammonia, while poor attention is dedicated to successive steps. In this article, different results from published literature were critically considered and the most probable hypothesis regarding the mechanism of HMT formation is discussed on the basis of B3LYP calculations of free energies.
Zeffiro, Alberto; Lazzaroni, Simone; Merli, Daniele; Profumo, Antonella; Buttafava, Armando; Serpone, Nick; Dondi, Daniele
2016-06-01
Despite its importance in the prebiotic and biochemical fields, a complete theoretical study of the formation of hexamethylenetetramine (HMT) starting from its precursors ammonia and formaldehyde has not received due considerations in the literature with regard to the thermodynamic feasibility of many of the mechanistically proposed intermediates in its formation. Most of the studies in this area have been mostly concerned with the initial steps of the reaction between formaldehyde and ammonia, while poor attention is dedicated to successive steps. In this article, different results from published literature were critically considered and the most probable hypothesis regarding the mechanism of HMT formation is discussed on the basis of B3LYP calculations of free energies.
Ganji, M. Darvish; Tajbakhsh, M.; Kariminasab, M.; Alinezhad, H.
2016-07-01
The efficiency of polymer solar cells can be essentially enhanced by improving the performance of electron acceptor materials especially by increasing its lowest unoccupied molecular orbital (LUMO) level. To this aim, the electronic properties of an extremely π-extended system, graphene flake and functionalized graphene flake with phenyl-C-butyric methyl ester (PCBM) group, were investigated and compared with those of C60 ones. Several properties of phenyl-C61-butyric methyl ester ([C60]PCBM) derivatives have been calculated and compared against the experimental and other theoretical results. All geometrical and electronic structures calculations were carried out by using the density functional theory (DFT) method at the B3LYP level of theory. The results show that the phenyl ring of [C60]PCBM was substituted with the methoxy groups to increase the LUMO level of the respective system which is in agreement with other studies. We found that graphene flake functionalized by methoxy-PCBM group offer significant increase in the value of the LUMO energy level in comparison with C60 counterpart. Furthermore, the electrophilicity of this compound is lower than that of the other counterparts, which results in higher open circuit voltage (Voc) value in the photovoltaic device. These findings could provide fundamental insights in improving the Voc value as well as raising the LUMO levels of electron acceptor materials and may also serve as an alternative strategy to increase open circuit voltage in polymer solar cells.
The disaccharide, alpha/beta-maltose, has been studied using constant energy ab initio molecular dynamics at the B3LYP/6-31+G* COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles is dependent upon the starting hydroxyl conformation. Tha...
Several mono- and disaccharides have been studied by performing constant energy molecular dynamics at the B3LYP/6-31+G* + COSMO (solvation) level of theory, alpha-maltose is of particular interest as the variation in glycosidic dihedral angles is dependent upon the starting hydroxyl conformation. T...
DEFF Research Database (Denmark)
Jalkanen, Karl J.; Frimand, Kenneth
2002-01-01
-binding method for equilibrium structures, VA and VCD spectra of ethylene oxide and propylene oxide in the gas-phase. Comparison to conventional methods AM1, PM3, MP2, RHF and DFT/B3LYP is carried out. We report results over a wider range of frequencies than previous work. In particular, we find indications...
THz spectroscopic investigation of chlorotoluron by solid-state density functional theory
Wang, Qiang; Wang, H. L.
2012-05-01
The terahertz time-domain spectrum (THz-TDS) of chlorotoluron has been simulated and assigned with solid-state density functional theory (DFT) in the range of 0.5-2.2 THz. The calculations based on the hybrid density functionals B3LYP and PW91 are performed to analyze the origins of observed spectral features in chlorotoluron THz spectra of solid-state forms using the software package CRYSTAL09. The computed THz spectrum of the B3LYP provides better agreements with observed THz spectral characters. Moreover, all the experimental THz absorption peaks are assigned utilizing the B3LYP method.
Xin, Dongyue; Sader, C Avery; Chaudhary, Om; Jones, Paul-James; Wagner, Klaus; Tautermann, Christofer S; Yang, Zheng; Busacca, Carl A; Saraceno, Reginaldo A; Fandrick, Keith R; Gonnella, Nina C; Horspool, Keith; Hansen, Gordon; Senanayake, Chris H
2017-05-19
An accurate and efficient procedure was developed for performing (13)C NMR chemical shift calculations employing density functional theory with the gauge invariant atomic orbitals (DFT-GIAO). Benchmarking analysis was carried out, incorporating several density functionals and basis sets commonly used for prediction of (13)C NMR chemical shifts, from which the B3LYP/cc-pVDZ level of theory was found to provide accurate results at low computational cost. Statistical analyses from a large data set of (13)C NMR chemical shifts in DMSO are presented with TMS as the calculated reference and with empirical scaling parameters obtained from a linear regression analysis. Systematic errors were observed locally for key functional groups and carbon types, and correction factors were determined. The application of this process and associated correction factors enabled assignment of the correct structures of therapeutically relevant compounds in cases where experimental data yielded inconclusive or ambiguous results. Overall, the use of B3LYP/cc-pVDZ with linear scaling and correction terms affords a powerful and efficient tool for structure elucidation.
Mazurek, A. P.; Sadlej-Sosnowska, N.
2000-11-01
A comparison of the ab initio quantum chemical methods: Hartree-Fock (HF) and hybrid density functional theory (DFT)/B3LYP for the treatment of tautomeric equilibria both in the gas phase and in the solution is made. The solvent effects were investigated in terms of the self-consistent reaction field (SCRF). Ionization potentials (IP), calculated by DFT/B3LYP, are also compared with those calculated previously within the HF frame.
Energy Technology Data Exchange (ETDEWEB)
Blanco, Raquel; Orts, Jose Manuel [Departamento de Quimica Fisica e Instituto Universitario de Electroquimica, Universidad de Alicante, Apartado 99, E-03080 Alicante (Spain)
2008-11-01
A density functional theory (DFT) study of the adsorption of a water molecule on Pt(1 1 1), Pt(1 0 0) and Pt(1 1 0) surfaces has been carried out using cluster models, at the B3LYP/LANL2DZ,6-311++G(d,p) level. The water molecule binds preferentially at the top site on Pt(1 1 1) and Pt(1 0 0) with adsorption energy around -27 kJ mol{sup -1}, and is oriented with the molecular plane nearly parallel to the metal surface and the H atoms pointing away from it. On Pt(1 1 0) a hollow site is preferred, with adsorption energy of -32 kJ mol{sup -1}. Potential energy barriers for the rotation around an axis normal to the surface have been estimated to be below 1 kJ mol{sup -1} for Pt(1 1 1) and Pt(1 0 0) when water is adsorbed on top. Upon application of an external electric field (inducing positive charge density on the metal) adsorbed water is additionally stabilized on the three surfaces, especially at the top adsorption site, and adsorption on Pt(1 1 1) and Pt(1 0 0) becomes more favoured than on Pt(1 1 0). Good agreement has been found between harmonic vibrational frequencies calculated at the B3LYP/LANL2DZ,6-311++G(d,p) level and experimental frequencies for adsorbed water monomers on Pt(h k l) surfaces. (author)
Lutnaes, Ola B; Ruden, Torgeir A; Helgaker, Trygve
2004-10-01
Density functional theory, in particular, with the Becke-3-parameter-Lee-Yang-Parr (B3LYP) hybrid functional, has been shown to be a promising method for the calculation of indirect nuclear spin-spin coupling constants. However, no systematic investigation has so far been undertaken to evaluate the capability of B3LYP to calculate these coupling constants accurately, taking properly into account the vibrational contributions. In this work, vibrationally corrected indirect spin-spin coupling constants were calculated using the B3LYP functional for 10 rigid unsubstituted and substituted hydrocarbons: ethyne, ethene, allene, cyclopropene, cyclopropane, cyclobutene, pyrrole, furan, thiophene and benzene. The resulting spin-spin constants were compared with the available experimental values. The basis sets in these calculations give indirect nuclear spin-spin coupling constants of ethyne that are almost converged to the basis-set limit, making the intrinsic error of the computational method and the error in equilibrium geometry the main sources of error. On average, the B3LYP functional overestimates the indirect nuclear spin-spin coupling constants in hydrocarbons by 10%.
Spin-orbit Coupling and Intersystem Crossing in 4H-Pyran-4-thione: CASSCF//TD-B3LYP Study
Institute of Scientific and Technical Information of China (English)
L(U), Ling-Ling; LIU, Xin-Wen; YUAN, Kun; WANG, Yong-Cheng; WANG, Han-Qing
2007-01-01
The intersystem crossing channels of gaseous 4H-pyran-4-thione were investigated using the CASSCF//TD-B3LYP methods and group theory. Using the effective one-electron spin-orbit Hamiltonian, the strengths of spin-orbit coupling were estimated, which plays an essential role in the spin transitions between different spin states. Calculated results show that phosphorescence and non-radiative decay via intersystem crossing to the S0 state are concurrent processes occurring at the T1 state. A rapid depletion of the S1 state via intersystem crossing to the T1 state can be mediated by the T2 state, if spin relaxation is fast within the triplet levels. Our calculated results are in close agreement with experimental observations.
Diaconu, C V; Doll, J D; Freeman, D L; Diaconu, Cristian V.; Cho, Art E.; Freeman, David L.
2004-01-01
In the present work we investigate the adequacy of broken-symmetry (BS) unrestricted (U) density functional theory (DFT) for constructing the potential energy curve of nickel dimer and nickel hydride, as model for larger bare and hydrogenated nickel cluster calculations. We use three hybrid functionals: B3LYP, Becke98, and FSLYP (50% Hartree-Fock and 50% Slater exchange and LYP correlation functional) with two basis sets: all-electron (AE) Wachters+f basis set and Stuttgart RSC effective core potential (ECP) and basis set. We find that, overall, B3LYP functional with Wachters+f AE basis set performs best, with only 1.3% root-mean-square (RMS) deviation from experiment, followed by Becke98/AE and B3LYP/ECP, with RMS deviation from experimental value of 2.5% and 2.7%, respectively. We also find that for Ni dimer, the spin-projection for the broken-symmetry unrestricted singlet states changes the ordering of the states, but the splittings are less than 10 meV. All our calculations predict a (delta)(delta)-hole g...
Ahmad, Faheem; Parveen, Mehtab; Alam, Mahboob; Azaz, Shaista; Malla, Ali Mohammed; Alam, Mohammad Jane; Lee, Dong-Ung; Ahmad, Shabbir
2016-07-01
The present study reports the synthesis of 7-Hydroximinocholest-5-en-3-ol acetate (syn. 3β-acetoxycholest-5-en-7-one oxime; in general, steroidal oxime). The identity of steroidal molecule was confirmed by NMR, FT-IR, MS, CHN microanalysis and X-ray crystallography. DFT calculations on the titled molecule have been performed. The molecular structure and spectra interpreted by Gaussian hybrid computational analysis theory (B3LYP) are found to be in good correlation with the experimental data obtained from the various spectrophotometric techniques. The vibrational bands appearing in the FTIR are assigned with great accuracy using harmonic frequencies along with intensities and animated modes. Molecular properties like HOMO-LUMO analysis, chemical reactivity descriptors, MEP mapping, dipole moment and natural atomic charges have been presented at the same level of theory. Moreover, the Hirshfeld analysis was carried out to ascertain the secondary interactions and associated 2D fingerprint plots. The percentages of various interactions are pictorialized by fingerprint plots of Hirshfeld surface. Steroidal oxime exhibited promising inhibitory activity against acetylcholinesterase (AChE) as compared to the reference drug, tacrine. Molecular docking was performed to introduce steroidal molecules into the X-ray crystal structures of acetylcholinesterase at the active site to find out the probable binding mode. The results of molecular docking admitted that steroidal oxime may exhibit enzyme inhibitor activity.
Zehe, Michael J.; Jaffe, Richard L.
2010-01-01
High-level ab initio calculations have been performed on the exo and endo isomers of gas-phase tetrahydrodicyclopentadiene (THDCPD), a principal component of the jet fuel JP10, using the Gaussian Gx and Gx(MPx) composite methods, as well as the CBS-QB3 method, and using a variety of isodesmic and homodesmotic reaction schemes. The impetus for this work is to help resolve large discrepancies existing between literature measurements of the formation enthalpy Delta (sub f)H deg (298) for exo-THDCPD. We find that use of the isodesmic bond separation reaction C10H16 + 14CH4 yields 12C2H6 yields results for the exo isomer (JP10) in between the two experimentally accepted values, for the composite methods G3(MP2), G3(MP2)//B3LYP, and CBS-QB3. Application of this same isodesmic bond separation scheme to gas-phase adamantane yields a value for Delta (sub f)H deg (298) within 5 kJ/mol of experiment. Isodesmic bond separation calculations for the endo isomer give a heat of formation in excellent agreement with the experimental measurement. Combining our calculated values for the gas-phase heat of formation with recent measurements of the heat of vaporization yields recommended values for Delta (sub f)H deg (298)liq of -126.4 and -114.7 kJ/mol for the exo and endo isomers, respectively.
Quiroga, Diego; Becerra, Lili Dahiana; Sadat-Bernal, John; Vargas, Nathalia; Coy-Barrera, Ericsson
2016-10-11
An efficient methodology to obtain novel antifungal analogs of brassinin 1 is described. Starting from l-tryptophan 2, N,N'-dialkylthiourea 4, 4-[(1H-indol-3-yl)methylene]-2-sulfanylidene-1,3-thiazolidin-5-one 5 and alkyl (2S)-3-(1H-indol-3-yl)-2-{[(alkylsulfanyl)carbonothioyl]amino}propanoate 6 type compounds were obtained as main products in different ratios depending on the reaction conditions via a tandem dithiocarbamate formation and Michael addition reaction. In order to understand the dependence of the reaction conditions on the mechanism pathway, a DFT/B3LYP study was performed. The results suggested the existence of competitive mechanistic routes which involve the presence of an ionic dithiocarbamate intermediate 9. Antifungal activities of all products were then evaluated against Fusarium oxysporum through mycelial growth inhibition using a microscale amended-medium assay. IC50 values were thus determined for each compound. These results showed that 6-related compounds can be considered as promissory antifungal agents.
Navarro-Ruiz, Javier; Ugliengo, Piero; Rimola, Albert; Sodupe, Mariona
2014-08-07
B3LYP periodic simulations have been carried out to study some physicochemical properties of the bulk structures and the corresponding nonpolar (010) surfaces of Mg-pure and Fe-containing olivine systems; i.e., Mg2SiO4 (Fo) and Mg1.5Fe0.5SiO4 (Fo75). A detailed structural analysis of the (010) Fo and Fo75 surface models shows the presence of coordinatively unsaturated metal cations (Mg(2+) and Fe(2+), respectively) with shorter metal-O distances compared to the bulk ones. Energetic analysis devoted to the Fe(2+) electronic spin configuration and to the ion position in the surfaces reveals that Fe(2+) in its quintet state and placed at the outermost positions of the slab constitutes the most stable Fe-containing surface, which is related to the higher stability of high spin states when Fe(2+) is coordinatively unsaturated. Comparison of the simulated IR and the corresponding reflectance spectra indicates that Fe(2+) substitution induces an overall bathochromic shift of the spectra due to the larger mass of Fe compared to Mg cation. In contrast, the IR spectra of the surfaces are shifted to upper values and exhibit more bands compared to the corresponding bulk systems due to the shorter metal-O distances given in the coordinatively unsaturated metals and to symmetry reduction which brings nonequivalent motions between the outermost and the internal modes, respectively.
Preparation of TiO2/SnO2 thin films by sol-gel method and periodic B3LYP simulations.
Floriano, Emerson A; Scalvi, Luis V A; Saeki, Margarida J; Sambrano, Julio R
2014-08-07
Titanium dioxide (TiO2) thin films are grown by the sol-gel dip-coating technique, in conjunction with SnO2 in the form of a heterostructure. It was found that the crystalline structure of the most internal layer (TiO2) depends on the thermal annealing temperature and the substrate type. Films deposited on glass substrate submitted to thermal annealing until 550 °C present anatase structure, whereas films deposited on quartz substrate transform to rutile structure at much higher temperatures, close to 1000 °C, unlike powder samples where the phase transition takes place at about 780 °C. When structured as rutile, the oxide semiconductors TiO2/SnO2 have very close lattice parameters, making the heterostructure assembling easier. The SnO2 and TiO2 have their electronic properties evaluated by first-principles calculations by means of DFT/B3LYP. Taking into account the calculated band structure diagram of these materials, the TiO2/SnO2 heterostructure is qualitatively investigated and proposed to increase the detection efficiency as gas sensors. This efficiency can be further improved by doping the SnO2 layer with Sb atoms. This assembly may be also useful in photoelectrocatalysis processes.
Directory of Open Access Journals (Sweden)
Diego Quiroga
2016-10-01
Full Text Available An efficient methodology to obtain novel antifungal analogs of brassinin 1 is described. Starting from l-tryptophan 2, N,N′-dialkylthiourea 4, 4-[(1H-indol-3-ylmethylene]-2-sulfanylidene-1,3-thiazolidin-5-one 5 and alkyl (2S-3-(1H-indol-3-yl-2-{[(alkylsulfanylcarbonothioyl]amino}propanoate 6 type compounds were obtained as main products in different ratios depending on the reaction conditions via a tandem dithiocarbamate formation and Michael addition reaction. In order to understand the dependence of the reaction conditions on the mechanism pathway, a DFT/B3LYP study was performed. The results suggested the existence of competitive mechanistic routes which involve the presence of an ionic dithiocarbamate intermediate 9. Antifungal activities of all products were then evaluated against Fusarium oxysporum through mycelial growth inhibition using a microscale amended-medium assay. IC50 values were thus determined for each compound. These results showed that 6-related compounds can be considered as promissory antifungal agents.
Tulub, Alexander A
2006-05-14
A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.
Sert, Yusuf; Miroslaw, Barbara; Çırak, Çağrı; Doğan, Hatice; Szulczyk, Daniel; Struga, Marta
2014-07-15
In this study, the experimental and theoretical vibrational spectral analysis of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone have been carried out. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) have been recorded for the solid state samples. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and angles) have been calculated for gas phase using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set. The diversity in molecular geometry of fluorophenyl substituted thiosemicarbazones has been discussed based on the X-ray crystal structure reports and theoretical calculation results from the literature. The assignments of the vibrational frequencies have been done on the basis of potential energy distribution (PED) analysis by using VEDA4 software. A good correlation was found between the computed and experimental geometric and vibrational data. In addition, the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energy levels and other related molecular energy values of the compound have been determined using the same level of theoretical calculations.
Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta
2014-08-28
Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.
Using Density Functional Theory (DFT) for the Calculation of Atomization Energies
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.
Institute of Scientific and Technical Information of China (English)
YUAN Qing-Hui; ZHOU Li-Xin
2007-01-01
In the present work, the hydrolysis process of non-classical transplatin(Ⅱ) with two same planar heterocycle amines has been studied using hybrid density functional theory (B3LYP) and IEF-PCM solvation models. Optimizations were performed at the B3LYP level using a combined basis set of (LanL2DZ+6-31+G(d,p)) with single-point energy evaluations using the B3LYP/6-31++G(3df,2pd) approach in vacuo and in aqueous solution. For the obtained structures of reactants, intermediates, transition states, and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (reaction barriers) characteristics were estimated. In comparison with cisplatin, decreased activation energies were obtained. The result implies that the non-classical transplatin with two same planar heterocycle amines increases the equatorial steric effect and lowers reaction barriers, which may assist in designing novel Pt-based anticancer drugs.
Bushnell, Eric A C; Gauld, James W
2013-01-15
The performance of a range density functional theory functionals combined in a quantum mechanical (QM)/molecular mechanical (MM) approach was investigated in their ability to reliably provide geometries, electronic distributions, and relative energies of a multicentered open-shell mechanistic intermediate in the mechanism 8R-Lipoxygenase. With the use of large QM/MM active site chemical models, the smallest average differences in geometries between the catalytically relevant quartet and sextet complexes were obtained with the B3LYP(*) functional. Moreover, in the case of the relative energies between (4) II and (6) II, the use of the B3LYP(*) functional provided a difference of 0.0 kcal mol(-1). However, B3LYP(±) and B3LYP also predicted differences in energies of less than 1 kcal mol(-1). In the case of describing the electronic distribution (i.e., spin density), the B3LYP(*), B3LYP, or M06-L functionals appeared to be the most suitable. Overall, the results obtained suggest that for systems with multiple centers having unpaired electrons, the B3LYP(*) appears most well rounded to provide reliable geometries, electronic structures, and relative energies. Copyright © 2012 Wiley Periodicals, Inc.
Ramalingam, S; Periandy, S
2011-03-01
In the present study, the FT-IR and FT-Raman spectra of 4-chloro-2-methylaniline (4CH2MA) have been recorded in the range of 4000-100 cm(-1). The fundamental modes of vibrational frequencies of 4CH2MA are assigned. All the geometrical parameters have been calculated by HF and DFT (LSDA, B3LYP and B3PW91) methods with 6-31G (d, p) and 6-311G (d, p) basis sets. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for aniline and some substituted aniline. The harmonic and anharmonic vibrational wavenumbers, IR intensities and Raman activities are calculated at the same theory levels used in geometry optimization. The calculated frequencies are scaled and compared with experimental values. The scaled vibrational frequencies at LSDA/B3LYP/6-311G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The impact of substitutions on the benzene structure is investigated. The molecular interactions between the substitutions (Cl, CH(3) and NH(2)) are also analyzed.
Luzon, Javier; Castro, Miguel; Vertelman, Esther J.M.; Gengler, Régis Y.N.; van Koningsbruggen, Petra J.; Molodtsova, Olga; Knupfer, Martin; Rudolf, Petra; Loosdrecht, Paul H.M. van; Broer, Ria
2008-01-01
A periodic density functional theory method using the B3LYP hybrid exchange-correlation potential is applied to the Prussian blue analogue RbMn[Fe(CN)(6)] to evaluate the suitability of the method for studying, and predicting, the photomagnetic behavior of Prussian blue analogues and related materia
Enhanced NLO response in BODIPY-coumarin hybrids: density functional theory approach
Indian Academy of Sciences (India)
YOGESH ERANDE; NAGAIYAN SEKAR
2017-09-01
We have thoroughly investigated the first, second and third polarizability characteristics of four hybrid chromophores by spectroscopic and computational methods. B3LYP, CAMB3LYP and BHandHLYP functionals in combination with 6-311+G(d,p) basis set were used to evaluate the polarizability and hyperpolarizability characteristics of these chromophores. Generalized Mulliken Hush analysis and frontier molecular orbital electronic distribution images of chromophores obtained from Density functional theory computation has established the charge transfer characteristics of these hybrid chromophores. On the basis of charge transfer characteristic, these red absorbing and NIR emissive chromophores possess high nonlinear optical response. Comparison of isolated units with their analogous hybrid chromophores shows that fusion ofcoumarin with BODIPY enhances the nonlinear optical response.
Téllez Soto, Claudio Alberto; Pereira, Liliane; dos Santos, Laurita; Rajasekaran, Ramu; Fávero, Priscila; Martin, Airton Abrahão
2016-12-01
In the confocal Raman spectra of skin dermis, the band area in the spectral region of proline and hydroxyproline varies according to the age and health condition of the volunteers, classified as healthy young women, healthy elderly women, and diabetic elderly women. Another observation refers to the intensity variation and negative Raman shift of the amide I band. To understand these effects, we adopted a model system using the DFT/B3LYP:3-21G procedure, considering the amino acid chain formed by glycine, hydroxyproline, proline, and alanine, which interacts with two and six water molecules. Through these systems, polarizability variations were analyzed to correlate its values with the observed Raman intensities of the three groups of volunteers and to assign the vibrational spectra of the skin dermis. As a way to correlate other experimental trends, we propose a model of chemical reaction of water interchange between the bonding amino acids, in which water molecules are attached with glucose by hydrogen bonds. The theoretical results are in accordance with the observed experimental trends.
Guido, Ciro A; Knecht, Stefan; Kongsted, Jacob; Mennucci, Benedetta
2013-05-14
We analyze potentials and limits of the Time-Dependent Density Functional Theory (TD-DFT) approach for the determination of excited-state geometries of organic molecules in gas-phase and in solution. Three very popular DFT exchange-correlation functionals, two hybrids (B3LYP and PBE0) and one long-range corrected (CAM-B3LYP), are here investigated, and the results are compared to the correlated RI-CC2 wave function approach. Solvent effects are further analyzed by means of a polarizable continuum model. A total of 15 organic chromophores (including both small molecules and larger push-pull systems) are considered as prototypes of n → π* and π → π* singlet excitations. Our analysis allows to point out specific correlations between the accuracy of the various functionals and the type of excitation and/or the type of chemical bonds involved. We find that while the best ground-state geometries are obtained with PBE0 and B3LYP, CAM-B3LYP yields the most accurate description of electronic and geometrical characteristics of excited states, both in gas-phase and in solution.
Chan, Bun; Radom, Leo
2016-08-09
In the present study, we have obtained geometries and frequency scale factors for a number of double-hybrid density functional theory (DH-DFT) procedures. We have evaluated their performance for obtaining thermochemical quantities [zero-point vibrational energies (ZPVE) and thermal corrections for 298 K enthalpies (ΔH298) and 298 K entropies (S298)] to be used within high-level composite protocols (using the W2X procedure as a probe). We find that, in comparison with the previously prescribed protocol for optimization and frequency calculations (B3-LYP/cc-pVTZ+d), the use of contemporary DH-DFT methods such as DuT-D3 and DSD-type procedures leads to a slight overall improved performance compared with B3-LYP. A major strength of this approach, however, lies in the better robustness of the DH-DFT methods in that the largest deviations are notably smaller than those for B3-LYP. In general, the specific choices of the DH-DFT procedure and the associated basis set do not drastically change the performance. Nonetheless, we find that the DSD-PBE-P86/aug'-cc-pVTZ+d combination has a very slight edge over the others that we have examined, and we recommend its general use for geometry optimization and vibrational frequency calculations, in particular within high-level composite methods such as the higher-level members of the WnX series of protocols. The scale factors determined for DSD-PBE-P86/aug'-cc-pVTZ+d are 0.9830 (ZPVE), 0.9876 (ΔH298), and 0.9923 (S298).
Elsässer, Brigitta; Fels, Gregor; Weare, John H
2014-01-22
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.
Energy Technology Data Exchange (ETDEWEB)
Elsasser, Brigitta M.; Fels, Gregor; Weare, John H.
2014-01-22
The mechanism of the backbone cleavage transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report QM/MM free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2? oxygen on the neighboring diester phosphate bond and both reach the same product state (PS) (a O3??O2? cyclic phosphate and a O5? hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition state (TS) general acid (His 119)/base (His 12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2? migrates to the non-bridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN+DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 1011 difference in rate strongly supporting the less accepted triester mechanism.
Bjornsson, Ragnar; Bühl, Michael
2010-06-14
Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C(6)H(6))(CO)(3), MnO(3)F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omegaPBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.
Performance of density functional theory methods to describe intramolecular hydrogen shifts
Indian Academy of Sciences (India)
Nelly González-Rivas; Andrés Cedillo
2005-09-01
The performance of three exchange and correlation density functionals, LDA, BLYP and B3LYP, with four basis sets is tested in three intramolecular hydrogen shift reactions. The best reaction and activation energies come from the hybrid functional B3LYP with triple- basis sets, when they are compared with high-level post-Hartree-Fock results from the literature. For a fixed molecular geometry, the electrophilic Fukui function is computed from a finite difference approximation. Fukui function shows a small dependence with both the exchange and correlation functional and the basis set. Evolution of the Fukui function along the reaction path describes important changes in the basic sites of the corresponding molecules. These results are in agreement with the chemical behavior of those species.
Paranthaman, Selvarengan; Hong, Kiryong; Kim, Joonghan; Kim, Dong Eon; Kim, Tae Kyu
2013-09-26
We report the results of a benchmarking study on hybrid, hybrid-meta, long-range-corrected, meta-generalized gradient approximation (meta-GGA), and GGA density functional theory (DFT) methods for aluminum (Al) clusters. A range of DFT functionals, such as B3LYP, B1B95, PBE0, mPW1PW91, M06, M06-2X, ωB97X, ωB97XD, TPSSh, BLYP, PBE, mPWPW91, M06-L, and TPSS, have been used to optimize the molecular structures and calculate the vibrational frequencies and four energetic parameters for neutral and anionic Al(n) (n = 2-10) clusters. The performances of these functionals are assessed systematically by calculating the vertical ionization energy for neutral Al clusters and the vertical electron detachment energy for anionic Al clusters, along with the cohesive energy and dissociation energy. The results are compared with the available experimental and high-level ab initio calculated results. The calculated results showed that the PBE0 and mPW1PW91 functionals generally provide better results than the other functionals studied. TPSS can be a good choice for the calculations of very large Al clusters. On the other hand, the B3LYP, BLYP, and M06-L functionals are in poor agreement with the available experimental and theoretical results. The calculated results suggest that the hybrid DFT functionals like B3LYP do not always provide better performance than GGA functionals.
Nemykin, Victor N; Hadt, Ryan G
2006-10-01
Influence of molecular geometry, type of exchange-correlation functional, and contraction scheme of basis set applied at the iron nuclei have been tested in the calculation of 57Fe Mössbauer isomer shifts and quadrupole splittings for a wide range of ligand types, as well as oxidation and spin states, in inorganic and organometallic systems. It has been found that uncontraction of the s-part of Wachter's full-electron basis set at the iron nuclei does not appreciably improve the calculated isomer shifts. The observed correlations for all tested sets of geometries are close to each other and predominantly depend on the employed exchange-correlation functional with B3LYP functional being slightly better as compared to BPW91. Both hybrid (B3LYP) and pure (BPW91) exchange-correlation functionals are suitable for the calculation of isomer shifts in organometallic compounds. Surprisingly, it has been found that the hybrid B3LYP exchange-correlation functional completely fails in accurate prediction of quadrupole splittings in ferrocenes, while performance of the pure BPW91 functional for the same systems was excellent. This observation has been explained on the basis of relationship between the amount of Hartree-Fock exchange involved in the applied exchange-correlation functional and the calculated HOMO-LUMO energy gap in ferrocenes. On the basis of this explanation, use of only pure exchange-correlation functionals has been suggested for accurate prediction of Mössbauer spectra parameters in ferrocenes.
Chemistry by Way of Density Functional Theory
Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Partridge, Harry; Langohff, Stephen R.; Arnold, James O. (Technical Monitor)
1996-01-01
In this work we demonstrate that density functional theory (DFT) methods make an important contribution to understanding chemical systems and are an important additional method for the computational chemist. We report calibration calculations obtained with different functionals for the 55 G2 molecules to justify our selection of the B3LYP functional. We show that accurate geometries and vibrational frequencies obtained at the B3LYP level can be combined with traditional methods to simplify the calculation of accurate heats of formation. We illustrate the application of the B3LYP approach to a variety of chemical problems from the vibrational frequencies of polycyclic aromatic hydrocarbons to transition metal systems. We show that the B3LYP method typically performs better than the MP2 method at a significantly lower computational cost. Thus the B3LYP method allows us to extend our studies to much larger systems while maintaining a high degree of accuracy. We show that for transition metal systems, the B3LYP bond energies are typically of sufficient accuracy that they can be used to explain experimental trends and even differentiate between different experimental values. We show that for boron clusters the B3LYP energetics are not as good as for many of the other systems presented, but even in this case the B3LYP approach is able to help understand the experimental trends.
A generalized exchange-correlation functional: the Neural-Networks approach
Zheng, X; Wang, X J; Chen, G H; Zheng, Xiao; Hu, LiHong; Wang, XiuJun; Chen, GuanHua
2003-01-01
A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation functional for density functional theory. It is applied to improve B3LYP functional by taking into account of high-order contributions to the exchange-correlation functional. The improved B3LYP functional is based on a neural network whose structure and synaptic weights are determined from 116 known experimental atomization energies, ionization potentials, proton affinities or total atomic energies which were used by Becke in his pioneer work on the hybrid functionals [J. Chem. Phys. ${\\bf 98}$, 5648 (1993)]. It leads to better agreement between the first-principles calculation results and these 116 experimental data. The new B3LYP functional is further tested by applying it to calculate the ionization potentials of 24 molecules of the G2 test set. The 6-311+G(3{\\it df},2{\\it p}) basis set is employed in the calculation, and the resulting root-mean-square error is reduced to 2.2 kcal$\\cdot$mol$^{-1}$ in comparison to ...
Ramalingam, S; Jayaprakash, A; Mohan, S; Karabacak, M
2011-11-01
FT-IR and FT-Raman (4000-100 cm(-1)) spectral measurements of 3-methyl-1,2-butadiene (3M12B) have been attempted in the present work. Ab-initio HF and DFT (LSDA/B3LYP/B3PW91) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, IR intensities and Raman activities. Complete vibrational assignments on the observed spectra are made with vibrational frequencies obtained by HF and DFT (LSDA/B3LYP/B3PW91) at 6-31G(d,p) and 6-311G(d,p) basis sets. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The potential energy distribution (PED) corresponding to each of the observed frequencies are calculated which confirms the reliability and precision of the assignment and analysis of the vibrational fundamentals modes. The oscillation of vibrational frequencies of butadiene due to the couple of methyl group is also discussed. A study on the electronic properties such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties of the title compound at different temperatures reveal the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H).
Fekete, Attila; Komáromi, István
2016-12-07
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to
Energy Technology Data Exchange (ETDEWEB)
Gerosa, Matteo [Department of Energy, Politecnico di Milano, via Ponzio 34/3, 20133 Milano (Italy); Di Valentin, Cristiana; Pacchioni, Gianfranco [Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milan (Italy); Bottani, Carlo Enrico, E-mail: carlo.bottani@polimi.it [Department of Energy, Politecnico di Milano, via Ponzio 34/3, 20133 Milano (Italy); Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, via Pascoli 70/3, 20133 Milano (Italy); Onida, Giovanni [Dipartimento di Fisica dell’ Universita’ degli Studi di Milano and European Theoretical Spectroscopy Facility (ETSF), Via Celoria 16, 20133 Milan (Italy)
2015-09-21
We investigate the long-standing problem of hole localization at the Al impurity in quartz SiO{sub 2}, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained ab initio, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators.
Ivanov, Petko
2016-03-01
The balances of interactions were studied by computational methods in the translational isomers of a solvent switchable fullerene-stoppered [2]rotaxane (1) manifesting unexpected behavior, namely that due to favorable dispersion interactions the fullerene stopper becomes the second station upon change of the solvent. For comparison, another system, a pH switchable molecular shuttle (2), was also examined as an example of prevailing electrostatic interactions. Tested for 1 were five global hybrid Generalized Gradient Approximation functionals (B3LYP, B3LYP-D3, B3LYP-D3BJ, PBEh1PBE and APFD), one long-range corrected, range-separated functional with D2 empirical dispersion correction, ωB97XD, the Zhao-Truhlar's hybrid meta-GGA functional M06 with double the amount of nonlocal exchange (2X), and a pure functional, B97, with the Grimme's D3BJ dispersion (B97D3). The molecular mechanics method qualitatively correctly reproduced the behavior of the [2]rotaxanes, whereas the DFT models, except for M06-2X to some extent, failed in the case of significant dispersion interactions with participation of the fulleropyrrolidine stopper (rotaxane 1). Unexpectedly, the benzylic amide macrocycle tends to adopt preferentially 'boat'-like conformation in most of the cases. Four hydrogen bonds interconnect the axle with the wheel for the translational isomer with the macroring at the succinamide station (station II), whereas the number of hydrogen bonds vary for the isomer with the macroring at the fulleropyrrolidine stopper (station I) depending of the computational model used. The B3LYP and the PBEh1PBE results show strong preference of station II in the gas phase and in the model solvent DMSO. After including empirical dispersion correction, the translational isomer with the macroring at station I has the lower energy with B3LYP, both in the gas phase and in DMSO. The same result, but with higher preference of station I, was estimated with APFD, ωB97XD and B97D3. Only M06-2X
DFT study on the covalent adsorption of drug carvedilol onto COOH functionalized carbon nanotubes
Directory of Open Access Journals (Sweden)
M. Rahbar
2015-09-01
Full Text Available In this work, using quantum mechanics, the interaction of drug carvedilol with (5, 5 COOH functionalized single wall carbon nanotubes (SWNT have been studied. All of the calculations have been performed using a hybrid density functional method (B3LYP in gas and solution phases. Two possible modes of covalent interaction of carvedilol onto COOH functionalized SWNT were investigated. Quantum molecular descriptors and frontier orbital analysis in the drug-nanotube systems were studied. It was found that bonding of carvedilol to COOH functionalized carbon nanotubes through hydroxyl group is stronger than amino group.
Timón, V; Praveen, C S; Escamilla-Roa, E; Valant, M
2013-07-01
A hybrid density functional based study of a phyllosilicate (PS) is presented here for the first time. Using all-electron electronic structure calculations with the B3LYP hybrid functional, we have investigated the electronic and structural properties of a series of trioctahedral 1M-polytype K-bearing micas starting from phlogopite (the Mg-end member), ending with the annite (the Fe-end member), and passing through the biotite (a solid solution of the end members). Electronic band gap is calculated for all the compositions and nature of the electronic transition is discussed with the aid of band structure and density of states plots. An excellent agreement with the available experimental data has been observed. An insulator to semiconductor transition is explained on the basis of orbital hybridization. A further comparison is made using the pure GGA functional. For the completeness of the study, the dielectric properties of phlogopite are calculated using the coupled perturbed Kohn-Sham scheme, as implemented within the CRYSTAL09 code.
Shi, Haifeng; Lan, Benyue; Zhang, Chengliang; Ye, Enjia; Nie, Yanguang; Bian, Baoan
2016-10-01
The influences of a series of anion doping on the electronic structures of sodium niobate (NaNbO3) have been systematically investigated by density functional theory (DFT) calculations with the hybrid B3LYP functional. As for B(C,P)-doped NaNbO3, the isolated B 2p (C 2p, P 3p) states were formed above the valence band maximum (VBM) of NaNbO3, which were too weak to mix with O 2p states and thus produced band gap narrowing. While the band gap of NaNbO3 was slightly narrowed after F doping. As for S-doped NaNbO3, the S 3p states mixed with O 2p states well and thus reduced the band gap energy. According to the calculation results, we tentatively put forward that S doping would be appropriate for single anion doping NaNbO3, while the B(C,P) elements would be suitable candidates for co-doping NaNbO3.
Kesharwani, Manoj K; Brauer, Brina; Martin, Jan M L
2015-03-05
We have obtained uniform frequency scaling factors λ(harm) (for harmonic frequencies), λ(fund) (for fundamentals), and λ(ZPVE) (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.
DFT STUDY OF THE HYDROLYSIS OF SOME S-TRIAZINES
The acid-catalyzed hydrolysis of atrazine and related 2-chloro-s-triazines to the corresponding 2-hydroxy-s-triazines was investigated using the B3LYP hybrid density functional theory method. Gas-phase calculations were performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of ...
Sproviero, Eduardo M
2017-02-20
We present a theoretical study of the reaction pathway for dioxygen molecular formation catalyzed by the [(terpy)(H2O)Mn(III)(O)2Mn(IV)(OH2) (terpy)](NO3)3 (terpy=2,2':6',2″-terpyridine) complex based on DFT-B3LYP calculations. In the initial state of the reaction, a partial oxido radical (0.44 spins) is formed ligated to Mn. This radical is involved in a nucleophylic attack by bulk water in the OO bond reaction formation step, in which the oxido fractional unpaired electron is delocalized toward the outermost Mn of the μ-oxo bridge, instead of the ligated Mn center. The reaction then follows with a series of proton-coupled electron transfer steps, in which the oxidation state, as well as the bond strength of the OO moiety increase, while the OOMn(1) bond gets weaker until O2 is released. In this model, basic acetate ions from the buffer solution capture protons in the proton-transfer steps. In each step there is reduction of the OOMn(1) binding strength, with concomitant increase of the OO bond strength, which culminates with the release of O2 in the last step. This last step is entropy driven, while formation of hydroperoxide and superoxide moieties is enthalpy driven. According with experiments, the rate-limiting step is the double oxidation of Mn(IV,III) or peroxymonosulfate binding, which occur prior to the OO bond formation step. This supports our findings that the barriers of all intermediate steps are below the experimental barrier of 19-21kcal/mol. The implications of these findings for understanding photosynthetic water-splitting catalysis are also discussed.
Density functional theory study on the molecular structure of loganin
Pandey, Anoop Kumar; Siddiqui, Shamoon Ahmad; Dwivedi, Apoorva; Raj, Kanwal; Misra, Neeraj
2011-01-01
The computational Quantum Chemistry (QC) has been used for different types of problems, for example: structural biology, surface phenomena and liquid phase. In this paper we have employed the density functional method for the study of molecular structure of loganin. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by B3LYP/6-311G (d, p) method and basis set combinations. It was found that the optimized parameters obtained by the DFT/B3LYP met...
Analytic cubic and quartic force fields using density-functional theory
Energy Technology Data Exchange (ETDEWEB)
Ringholm, Magnus; Gao, Bin; Thorvaldsen, Andreas J.; Ruud, Kenneth [Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); Jonsson, Dan [Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); High Performance Computing Group, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); Bast, Radovan [Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-10691 Stockholm, Sweden and PDC Center for High Performance Computing, Royal Institute of Technology, S-10044 Stockholm (Sweden); Ekström, Ulf; Helgaker, Trygve [Center for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo (Norway)
2014-01-21
We present the first analytic implementation of cubic and quartic force constants at the level of Kohn–Sham density-functional theory. The implementation is based on an open-ended formalism for the evaluation of energy derivatives in an atomic-orbital basis. The implementation relies on the availability of open-ended codes for evaluation of one- and two-electron integrals differentiated with respect to nuclear displacements as well as automatic differentiation of the exchange–correlation kernels. We use generalized second-order vibrational perturbation theory to calculate the fundamental frequencies of methane, ethane, benzene, and aniline, comparing B3LYP, BLYP, and Hartree–Fock results. The Hartree–Fock anharmonic corrections agree well with the B3LYP corrections when calculated at the B3LYP geometry and from B3LYP normal coordinates, suggesting that the inclusion of electron correlation is not essential for the reliable calculation of cubic and quartic force constants.
Labat, Frédéric; Baranek, Philippe; Domain, Christophe; Minot, Christian; Adamo, Carlo
2007-04-21
The two polymorphs of TiO2, rutile and anatase, have been investigated at the ab initio level using different Hamiltonians with all-electron Gaussian and projector augmented plane wave basis sets. Their equilibrium lattice parameters, relative stabilities, binding energies, and band structures have been evaluated. The calculations have been performed at the Hartree-Fock, density functional theory (DFT), and hybrid (B3LYP and PBE0) levels. As regards DFT, the local density and generalized gradient (PBE) approximations have been used. Our results show an excellent agreement with the experimental band structures and binding energies for the B3LYP and PBE0 functionals, while the best structural descriptions are obtained at the PBE0 level. However, no matter which Hamiltonian and method are used, anatase is found more stable than rutile, in contrast with recent experimental reports, although the relative stabilities of the two phases are very close to each other. Nevertheless, based on the overall results, the hybrid PBE0 functional appears as a good compromise to obtain an accurate description of both structural and electronic properties of solids.
Energy Technology Data Exchange (ETDEWEB)
Silverstein, Daniel W.; Govind, Niranjan; van Dam, Hubertus J. J.; Jensen, Lasse
2013-12-10
A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The implementation is based on the Lagrangian approach developed by Furche and Ahlrichs. To validate our implementation, we first calculate the Stokes shifts for a range of organic dye molecules using a diverse set of exchange-correlation functionals (traditional density functionals, global hybrids, and range-separated hybrids) followed by simulations of the one-photon absorption and resonance Raman scattering spectrum of the phenoxyl radical, the well-studied dye molecule rhodamine 6G, and a molecular host–guest complex (TTFcCBPQT^{4+}). The study of organic dye molecules illustrates that B3LYP and CAM-B3LYP generally give the best agreement with experimentally determined Stokes shifts unless the excited state is a charge transfer state. Absorption, resonance Raman, and fluorescence simulations for the phenoxyl radical indicate that explicit solvation may be required for accurate characterization. For the host–guest complex and rhodamine 6G, it is demonstrated that absorption spectra can be simulated in good agreement with experimental data for most exchange-correlation functionals. Finally, however, because one-photon absorption spectra generally lack well-resolved vibrational features, resonance Raman simulations are necessary to evaluate the accuracy of the exchange-correlation functional for describing a potential energy surface.
Hybrid density functional theory study of Cu(In1−xGaxSe2 band structure for solar cell application
Directory of Open Access Journals (Sweden)
Xu-Dong Chen
2014-08-01
Full Text Available Cu(In1−xGaxSe2 (CIGS alloy based thin film photovoltaic solar cells have attracted more and more attention due to its large optical absorption coefficient, long term stability, low cost and high efficiency. However, the previous theoretical investigation of this material with first principle calculation cannot fulfill the requirement of experimental development, especially the accurate description of band structure and density of states. In this work, we use first principle calculation based on hybrid density functional theory to investigate the feature of CIGS, with B3LYP applied in the CuIn1−xGaxSe2 stimulation of the band structure and density of states. We report the simulation of the lattice parameter, band gap and chemical composition. The band gaps of CuGaSe2, CuIn0.25Ga0.75Se2, CuIn0.5Ga0.5Se2, CuIn0.75Ga0.25Se2 and CuInSe2 are obtained as 1.568 eV, 1.445 eV, 1.416 eV, 1.275 eV and 1.205 eV according to our calculation, which agree well with the available experimental values. The band structure of CIGS is also in accordance with the current theory.
National Research Council Canada - National Science Library
Fahmi, Amir; Pietsch, Torsten; Mendoza, Cesar; Cheval, Nicolas
2009-01-01
.... This paper describes our group's achievements towards the development of multifunctional nanostructures via self-assembly of hybrid systems based on the block copolymer PS-b-P4VP and inorganic nanoparticles (NPs...
Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A
2008-12-07
This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.
Svozil, Daniel; Jungwirth, Pavel
2006-07-27
In the present study, the performance of six popular density functionals (B3LYP, PBE0, BLYP, BP86, PBE, and SVWN) for the description of the autoionization process in the water octamer was studied. As a benchmark, MP2 energies with complete basis sets limit extrapolation and CCSD(T) correction were used. At this level, the autoionized structure lies 28.5 kcal.mol(-1) above the neutral water octamer. Accounting for zero-point energy lowers this value by 3.0 kcal.mol(-1). The transition state of the proton transfer reaction, lying only 0.7 kcal.mol(-1) above the energy of the ionized system, was identified at the MP2/aug-cc-pVDZ level of theory. Different density functionals describe the reactant and product with varying accuracy, while they all fail to characterize the transition state. We find improved results with hybrid functionals compared to the gradient-corrected ones. In particular, B3LYP describes the reaction energetics within 2.5 kcal.mol(-1) of the benchmark value. Therefore, this functional is suggested to be preferably used both for Carr-Parinello molecular dynamics and for quantum mechanics/molecular mechanics (QM/MM) simulations of autoionization of water.
Hybrid density functional calculations of the defect properties of ZnO:Rh and ZnO:Ir
Energy Technology Data Exchange (ETDEWEB)
Muñoz Ramo, David, E-mail: dm586@cam.ac.uk; Bristowe, Paul D., E-mail: pdb1000@cam.ac.uk
2014-03-31
We report density functional calculations of the atomic and electronic structure of the spinel phases ZnRh{sub 2}O{sub 4} and ZnIr{sub 2}O{sub 4} as well as crystalline ZnO lightly doped (1 at.%) with Rh and Ir ions using the B3LYP hybrid functional. Calculations for the spinels show band gaps (∼ 3 eV) and lattice parameters (∼ 2% difference) in reasonable agreement with experimental data. Incorporation of the transition metals into ZnO induces local distortions in the lattice and the appearance of metal d levels in the low gap region and near the conduction band minimum, with a d–d splitting of about 2 eV, which reduces the effective transparency of the material. Addition of a hole to the simulation cell of both spinels and doped ZnO leads to charge localization in the neighbourhood of Rh/Ir accompanied by local lattice deformations to form a small polaron which may lead to low hole mobility. We calculate polaron diffusion barriers in the spinels and obtain values around 0.02–0.03 eV. These very low barrier energies suggest that at high Rh/Ir concentrations polaron hopping is not going to be detected at room temperature. - Highlights: • Rh/Ir incorporation into ZnO at low doping induces local distortions in the lattice. • Localized levels appear in the gap of ZnO:Rh/ZnO:Ir near band edges. • Hole trapping is found in ZnO:Rh/ZnO:Ir and in the ZnRh{sub 2}O{sub 4}/ZnIr{sub 2}O{sub 4} spinels. • Hole diffusion barriers in the spinels are very small.
Milko, Petr; Iron, Mark A
2014-01-14
The electronic structures of a number of iron, cobalt, vanadium, and titanium complexes with the 2,2'-bipyridine (bpy) ligand were considered using the multireference CASSCF and NEVPT2 methods. Many of these systems have been studied in the past using B3LYP and were then found to contain the bpy ligand as a radical anion. For many of the cases, this is contradicted by our multireference calculations. While there are instances where the ligand is indeed a radical anion, in many cases it remains neutral and is involved in backbonding from the metal center. For those cases where CASSCF is too costly, a number of DFT functionals, including the newer double-hybrid functionals, were evaluated against the CASSCF data. It was found that nonhybrid functionals, especially those containing the kinetic energy density τ, were the best at predicting the electronic nature of the complexes. The τ-HCTH and HCTH functionals were the top performers, correctly predicting eleven out of eleven test cases and with the lowest mean unsigned errors (MUE, 7.6 and 7.8 kcal·mol(-1), respectively); the M06-L, N12, BLYP, PBE, and TPSS functionals also did well, while B3LYP had significant problems.
Energy Technology Data Exchange (ETDEWEB)
Marana, Naiara L. [Modeling and Molecular Simulations Group, São Paulo State University, UNESP, 17033-360 Bauru, SP (Brazil); Albuquerque, Anderson R. [Federal Institute of Education, Science and Technology of Sertão Pernambucano, 56400-000 Floresta, PE (Brazil); La Porta, Felipe A. [Chemistry Department, Federal Technological University of Paraná, 86036-370 Londrina, PR (Brazil); Longo, Elson [São Paulo State University, Chemistry Institute, UNESP, 14801-907 Araraquara, SP (Brazil); Sambrano, Julio R. [Modeling and Molecular Simulations Group, São Paulo State University, UNESP, 17033-360 Bauru, SP (Brazil)
2016-05-15
Periodic density functional theory calculations with the B3LYP hybrid functional and all-electron Gaussian basis set were performed to simulate the structural and electronic properties as well as the strain and formation energies of single-walled ZnO nanotubes (SWZnONTs) and Carbon nanotubes (SWCNTs) with different chiralities as functions of their diameters. For all SWZnONTs, the band gap, strain energy, and formation energy converge to ~4.5 eV, 0.0 eV/atom, and 0.40 eV/atom, respectively. This result suggests that the nanotubes are formed more easily from the surface than from the bulk. For SWCNTs, the strain energy is always positive, while the formation energy is negative for armchair and zigzag nanotubes, therefore suggesting that these types of nanotubes can be preferentially formed from the bulk. The electronic properties of SWCNTs depend on the chirality; all armchair nanotubes are metallic, while zigzag and chiral nanotubes can be metallic or semiconducting, depending on the n and m vectors. - Graphical abstract: DFT/B3LYP were performed to simulate the structural and electronic properties as well as the strain and formation energies of SWZnONTs and SWCNTs with different chiralities as functions of their diameters. - Highlights: • The energies of SWZnONTs converge for chirality with diameters up 20 Å. • SWCNTs electronic properties depend on the chirality. • The properties of SWZnONTs are very similar to those of monolayer surface.
Directory of Open Access Journals (Sweden)
Georges Dive
2004-11-01
Full Text Available Abstract: Vertical ionization energies (IE as a function of the conformation are determined at the quantum chemistry level for eighteen ÃŽÂ±-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT framework using the hybrid method B3LYP and the 6-31G**(5d basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO can change a lot as a function of the nuclear structure.
Anitha, K; Balachandran, V
2015-07-05
Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the N-(2-cyanoethyl)-N-butylaniline. The geometry, structural properties, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of DFT (B3LYP) and LC-DFT (CAM-B3LYP) method. Molecular electrostatic potential (MEP) have been performed. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. Global reactivity and local reactivity descriptors of the title molecule have been calculated. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicated the electron transport in the molecule and thereby NLO activity. The effect of solvent on second-order NLO properties has been studied using polarized continuum model (PCM) in the tetrahydrofuran (THF) solution. The solvent leads to a slight enhancement of the NLO responses for the studied complexes relevant to their NLO responses in gas phase. The electronic absorption spectra were investigated by the TDDFT methods. The frequency-dependent first hyperpolarizabilities of the N-(2-cyanoethyl)-N-butylaniline were also evaluated. The (1)H and (13)C NMR chemical shifts have been calculated by gauge-indepedent atomic orbital (GIAO) method with B3LYP/6-311++G(d, p) approach. Copyright © 2015 Elsevier B.V. All rights reserved.
Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib
2015-04-15
Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.
Körzdörfer, Thomas
2014-11-18
Density functional theory (DFT) and its time-dependent extension (TD-DFT) are powerful tools enabling the theoretical prediction of the ground- and excited-state properties of organic electronic materials with reasonable accuracy at affordable computational costs. Due to their excellent accuracy-to-numerical-costs ratio, semilocal and global hybrid functionals such as B3LYP have become the workhorse for geometry optimizations and the prediction of vibrational spectra in modern theoretical organic chemistry. Despite the overwhelming success of these out-of-the-box functionals for such applications, the computational treatment of electronic and structural properties that are of particular interest in organic electronic materials sometimes reveals severe and qualitative failures of such functionals. Important examples include the overestimation of conjugation, torsional barriers, and electronic coupling as well as the underestimation of bond-length alternations or excited-state energies in low-band-gap polymers.In this Account, we highlight how these failures can be traced back to the delocalization error inherent to semilocal and global hybrid functionals, which leads to the spurious delocalization of electron densities and an overestimation of conjugation. The delocalization error for systems and functionals of interest can be quantified by allowing for fractional occupation of the highest occupied molecular orbital. It can be minimized by using long-range corrected hybrid functionals and a nonempirical tuning procedure for the range-separation parameter.We then review the benefits and drawbacks of using tuned long-range corrected hybrid functionals for the description of the ground and excited states of π-conjugated systems. In particular, we show that this approach provides for robust and efficient means of characterizing the electronic couplings in organic mixed-valence systems, for the calculation of accurate torsional barriers at the polymer limit, and for the
Energy Technology Data Exchange (ETDEWEB)
Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it [Dipartimento di Scienze Biologiche e Geologico-Ambientali, Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Università di Bologna “Alma Mater Studiorum” Piazza di Porta San Donato 1, 40126 Bologna (Italy); Tosoni, Sergio [Departament de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/ Martí i Franquès 1, E-08028 Barcelona (Spain)
2013-11-28
The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.
LANL2DZ basis sets recontracted in the framework of density functional theory.
Chiodo, S; Russo, N; Sicilia, E
2006-09-14
In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.
Electrostatic potential of several small molecules from density functional theory
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A number of density functional theory (DFT) methods were used to calculate the electrostatic potential for the series of molecules N2, F2, NH3, H2O, CHF3, CHCl3, C6H6, TiF4, CO(NH2)2 and C4H5N3O compared with QCISD (quadratic configuration interaction method including single and double substitutions) results. Comparisons were made between the DFT computed results and the QCISD ab initio ones and MP2 ab initio ones, compared with the root-mean-square deviation and electrostatic potential difference contours figures. It was found that the hybrid DFT method B3LYP, yields electrostatic potential in good agreement with the QCISD results. It is suggest this is a useful approach, especially for large molecules that are difficult to study by ab initio methods.
Daramola, Damilola A; Muthuvel, Madhivanan; Botte, Gerardine G
2010-07-29
Geometry and vibration properties for monoclinic zirconium oxide were studied using Gaussian basis sets and LDA, GGA, and B3LYP functionals. Bond angles, bond lengths, lattice parameters, and Raman frequencies were calculated and compared to experimental values. Bond angles and lengths were found to agree within experimental standard deviations. The B3LYP gave the best performance of all three functionals with a percent error of 1.35% for the lattice parameters while the average difference between experimental and calculated Raman frequency values was -3 cm(-1). The B3LYP functional was then used to assign the atomic vibrations causing each frequency mode using isotopic substitution of (93.40)Zr for (91.22)Zr and (18.00)O for (16.00)O. This resulted in seven modes assigned to the Zr atom, ten modes to the O atom, and one mode being a mixture of both.
Sternheimer shieldings and EFG polarizabilities: a density-functional theory study
Rizzo, Antonio; Ruud, Kenneth; Helgaker, Trygve; Sałek, Paweł; Ågren, Hans; Vahtras, Olav
2003-04-01
The electric field gradient (EFG) at the nucleus, the generalized Sternheimer shielding constants, and the EFG hyperpolarizabilities of a set of reference molecules are computed using analytic density-functional (up to quadratic) response theory. At the three-parameter Becke-Lee-Yang-Parr (B3LYP) level, density functional theory (DFT) underestimates correlation effects compared with other approaches such as coupled-cluster and multiconfigurational self-consistent field. For the prediction of EFG properties of hydrogen nuclei and electron-rich atoms such as halides, DFT/B3LYP provides results even less reliable than Hartree-Fock theory.
Density Functional Investigations into the Adsorption of Methanol on Isomorphously Substituted ZSM-5
Institute of Scientific and Technical Information of China (English)
Shuping Yuan; Jianguo Wang; Yongwang Li; Haijun Jiao
2003-01-01
The adsorption of methanol in the acid sites of zeolites has attracted a great deal of attention because of its relevance to the industrial methanol to gasoline conversion process. In this work, the B3LYP hybrid density functional method was used to investigate the adsorption behavior of methanol on Bronsted acid sites in B, Al, Ga and Fe isomorphously substituted ZSM-5 zeolites. The optimized structures reveal a physisorbed methanol interacting with the zeolite framework through two hydrogen bonds. The order of the computed adsorption energy correlates with the acid strength of the isomorphously substituted ZSM-5:B-ZSM-5《Fe-ZSM-5＜Ga-ZSM-5＜Al-ZSM-5. The adsorption difference between methanol and ammonia is compared.
Edwin, Bismi; Hubert Joe, I
2012-11-01
Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the anti-neuro-degenerative drug Orphenadrine hydrochloride. The geometry, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of B3LYP method. The calculated molecular geometry has been compared with the experimental data. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of Mulliken atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicates electron transport in the molecule and thereby bioactivity. Effective docking of the drug molecule with NMDA receptor subunit 3A also enhances its bioactive nature. Copyright © 2012 Elsevier B.V. All rights reserved.
Da Silva, Júlio C S; Rocha, Willian R
2011-12-01
In this study, we investigated the C-H bond activation of methane catalyzed by the complex [PtCl(4)](2-), using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary steps that compose the catalytic cycle of the Shilov reaction. Our B3LYP/SBKJC/cc-pVDZ/EFP results show that the methane activation may proceed through two pathways: (i) electrophilic addition or (ii) direct oxidative addition of the C-H bond of the alkane. The electrophilic addition pathway proceeds in two steps with formation of a σ-methane complex, with a Gibbs free energy barrier of 24.6 kcal mol(-1), followed by the cleavage of the C-H bond, with an energy barrier of 4.3 kcal mol(-1) . The activation Gibbs free energy, calculated for the methane uptake step was 24.6 kcal mol(-1), which is in good agreement with experimental value of 23.1 kcal mol(-1) obtained for a related system. The results shows that the activation of the C-H bond promoted by the [PtCl(4)](2-) catalyst in aqueous solution occurs through a direct oxidative addition of the C-H bond, in a single step, with an activation free energy of 25.2 kcal mol(-1), as the electrophilic addition pathway leads to the formation of a σ-methane intermediate that rapidly undergoes decomposition. The inclusion of long-range solvent effects with polarizable continuum model does not change the activation energies computed at the B3LYP/SBKJC/cc-pVDZ/EFP level of theory significantly, indicating that the large EFP water cluster used, obtained from Monte Carlo simulations and analysis of the center-of-mass radial pair distribution function, captures the most important solvent effects.
Liakos, Dimitrios G; Neese, Frank
2015-09-08
The recently developed domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) delivers results that are closely approaching those of the parent canonical coupled cluster method at a small fraction of the computational cost. A recent extended benchmark study established that, depending on the three main truncation thresholds, it is possible to approach the canonical CCSD(T) results within 1 kJ (default setting, TightPNO), 1 kcal/mol (default setting, NormalPNO), and 2-3 kcal (default setting, LoosePNO). Although thresholds for calculations with TightPNO are 2-4 times slower than those based on NormalPNO thresholds, they are still many orders of magnitude faster than canonical CCSD(T) calculations, even for small and medium sized molecules where there is little locality. The computational effort for the coupled cluster step scales nearly linearly with system size. Since, in many instances, the coupled cluster step in DLPNO-CCSD(T) is cheaper or at least not much more expensive than the preceding Hartree-Fock calculation, it is useful to compare the method against modern density functional theory (DFT), which requires an effort comparable to that of Hartree-Fock theory (at least if Hartree-Fock exchange is part of the functional definition). Double hybrid density functionals (DHDF's) even require a MP2-like step. The purpose of this article is to evaluate the cost vs accuracy ratio of DLPNO-CCSD(T) against modern DFT (including the PBE, B3LYP, M06-2X, B2PLYP, and B2GP-PLYP functionals and, where applicable, their van der Waals corrected counterparts). To eliminate any possible bias in favor of DLPNO-CCSD(T), we have chosen established benchmark sets that were specifically proposed for evaluating DFT functionals. It is demonstrated that DLPNO-CCSD(T) with any of the three default thresholds is more accurate than any of the DFT functionals. Furthermore, using the aug-cc-pVTZ basis set and
Di Valentin, Cristiana; Pacchioni, Gianfranco
2014-11-18
, for a more accurate description of the oxide band gap and of the electron localization of the impurity states associated with dopants or defects, we resorted to the use of hybrid functionals (B3LYP), where a portion of exact exchange in the exchange-correlation functional partly corrects for the self-interaction error inherent in DFT. In many cases, the self-interaction correction is very important, and these results can lead to a completely different physical picture than that obtained using local or semilocal functionals. We analyzed the electronic transitions in terms of their transition energy levels, which provided a more accurate comparison with experimental spectroscopic data than Kohn-Sham eigenvalues. The effects of N-doping were similar among the three oxides that we considered. The nature of the impurity state is always localized at the dopant site, which may limit their application in photocatalytic processes. Photocatalytic systems require highly delocalized photoexcited carriers within the material to effectively trigger redox processes at the surface. The nature of the electronic states associated with the oxygen deficiency differed widely in the three investigated oxides. In ZnO1-x and WO3-x the electronic states resemble the typical F-centers in insulating oxides or halides, with the excess electron density localized at the vacancy site. However, TiO2 acts as a reducible oxide, and the removal of neutral oxygen atoms reduced Ti(4+) to Ti(3+).
DEFF Research Database (Denmark)
Frimand, Kenneth; Bohr, Henrik; Jalkanen, Karl J.;
2000-01-01
at the density functional theory level using the B3LYP functional with the 6-31G* basis set. The Hessians and atomic polar tensors and atomic axial tensors were all calculated at the B3LYP/6-31G* level of theory. An important result is the method of treating solvent effects by both adding explicit water....... The calculated VA and VCD spectra of this conformer are in better agreement with experimentally measured VA and VCD spectra previously reported. (C) 2000 Elsevier Science B.V. All rights reserved....
Directory of Open Access Journals (Sweden)
Bahjat A. Saeed
2010-01-01
Full Text Available Problem statement: QSAR techniques increase the probability of success and reduce time and coast in drug discovery process. The study presented QSAR investigation on 32 bioactive aziridinylbenzoquinones that have activity against lymphoid leukemia. Approach: Molecular descriptors, molecular weight, total energy, hardness, chemical potential, electrophilicity index, HOMO and LUMO energies were calculated. Initial geometry optimizations were carried out with the AM1 Hamiltonian. The lowest energy conformations were subjected to single point calculations by the DFT method by employing Beck's Three-Parameter hybrid functional (B3LYP and pvDZ basis set. Several models for the prediction of biological activity have been drawn up by using the multiple regression technique. Results: A model with hapta parametric linear equation with R2 value of 0.886 was presented. Conclusion: The biological activity of the studied compounds can be modeled with quantum chemical molecular descriptors.
A multiconfigurational hybrid density-functional theory
Sharkas, Kamal; Jensen, Hans Jørgen Aa; Toulouse, Julien; 10.1063/1.4733672
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension of the usual hybrid approximations by essentially adding a fraction \\lambda of exact static correlation in addition to the fraction \\lambda of exact exchange. Test calculations on the cycloaddition reactions of ozone with ethylene or acetylene and the dissociation of diatomic molecules with the Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) density functionals show that a good value of \\lambda is 0.25, as in the usual hybrid approximations. The results suggest that the proposed multiconfigurational hybrid approximations can improve over usual density-functional calculations for situations with strong static correlation effects.
Directory of Open Access Journals (Sweden)
Sérgio Ricardo de Lázaro
2005-02-01
Full Text Available Calculations based on density functional theory at the B3LYP hybrid functional level applied to periodic models have been performed to characterize the structural and electronic properties of PbTiO3. Two different slab terminations (PbO and TiO2 have been considered to obtain and discuss the results of band structure, density of states, charge distribution on bulk and surface relaxation. It is observed that the relaxation processes are most prominent for the Ti and Pb surface atoms. The electron density maps confirm the partial covalent character of the Ti-O bonds. The calculated optical band gap and other results are in agreement with experimental data.
Electroactive functional hybrid layered nanocomposites
Energy Technology Data Exchange (ETDEWEB)
Destri, Giovanni Li; Torrisi, Vanna; Marletta, Giovanni [Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN) - University of Catania and CSGI - Catania (Italy)
2012-07-11
Two methodologies to build new nanostructured hybrid layered nanocomposites are presented. The first one involves the preparation of hybrid metal/polymer nanolayers (NLs) by combining two monolayer preparation techniques: Horizontal Precipitation Langmuir Blodgett method (HP-ML), for copolymer monolayers and sputter deposition technique, for Au NLs deposition. The second methodology is aimed to prepare regular arrays of nanopores, with diameter ranging between 40-100 nm, in ultra-thin films of electroactive polymers, to obtain embedded regular arrays of nanopores filled by a further electroactive organic component. The produced hybrid MLs have been characterized by means of X-ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM) and Grazing Incidence X-ray Diffraction (GI-XRD). In the first case, current-voltage (I-V) measurements demonstrate that the multilayers exhibit a bipolar conduction behaviour (electrons and holes carriers), with a peculiar transition in the nature of the majority carriers (from holes to electrons) above a threshold number of bilayers. In the second case, it is found that the degree of pore filling, as well as the polymer crystallinity can be easily modulated, prompting the tuning of the photoresponse of the nanocomposites.
Exchange-correlation interaction and AO-hybridization of alkali-metal atomic clusters.
Liu, Xuan; Ito, Haruhiko; Torikai, Eiko
2013-09-19
The structure of alkali-metal atomic clusters is optimized with B3P86 hybrid functional for the highest spin state as well as with B3LYP hybrid functional for the lowest spin state. A dramatic change from plane to solid occurs in the highest spin state when the number of constituent atoms is four. The binding, exchange, and correlation energies are evaluated for both the highest and lowest spin states. Next, we explore the dependence of the exchange and correlation energies on the binding energy. The exchange energy contributes to the formation of the highest spin clusters, whereas the correlation energy contributes to the formation of the lowest spin clusters. The highest spin clusters are most stable when the exchange energy is a minimum. Then, to see why the ferromagnetic bond among spin-aligned identical atoms arises against Pauli exclusion principle, we estimate the mixing ratio of p orbitals in molecular orbitals. The s-p hybridization increases the binding energy in absolute value due to the extensive overlap of molecular orbitals and leads to generation of the highest spin clusters.
Density functional theory/B3LYP has been employed to optimize the conformations of selected 4-arylflavan-3-ols and their phenolic methyl ether 3-O-acetates. The electronic circular dichroism spectra of the major conformers have been calculated using time-dependent density functional theory to valida...
A multiconfigurational hybrid density-functional theory
DEFF Research Database (Denmark)
Sharkas, Kamal; Savin, Andreas; Jensen, Hans Jørgen Aagaard
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension ...
A multiconfigurational hybrid density-functional theory
DEFF Research Database (Denmark)
Sharkas, Kamal; Savin, Andreas; Jensen, Hans Jørgen Aagaard
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension ...
El-Nahas, Ahmed M.; Simmie, John M.; Mangood, Ahmed H.; Hirao, Kimihiko; Song, Jong-Won; Watson, Mark A.; Taketsugu, Tetsuya; Koga, Nobuaki
2015-07-01
The enthalpies of formation for some selected oxygenates have been calculated by the atomisation energy approach using B3LYP, BHandHLYP, MPW3LYP, MPW1K, MPWB1K, BB1K, MPW1B95, BMK, and long-range corrected (LC-ωPBE, LC-BOP, LCgau-BOP, LC-BOP12, LCgau-B97) density functionals, as well as the composite CBS-QB3 method. Compared with experiment, BMK, LC-ωPBE, LCgau-BOP, LC-BOP12, LCgau-B97, MPW195, MPW3LYP functionals and CBS-QB3 give root mean square errors (RMSE) in enthalpies of formation no greater than 4 kcal/mol, whilst MPW1K and BHandHLYP show much worse performance (RMSE of 20-40 kcal/mol). The B3LYP, MPWB1K, and BB1K results fall between the two extremes. Energy barriers for the dominant paths in the unimolecular decomposition of simple esters (HCO2CH3, C2H5CO2C2H5), C1-C3 acids, and 1-butanol are reproduced well by CBS-QB3, BMK, BB1K, LCgau-B97, and PW1B95 (RMSE = 1-2 kcal/mol), while other LC methods (LC-ωPBE, LC-BOP, LCgau-BOP, and LC-BOP12) show a deviation of up to 4 kcal/mol. For the ionisation potentials, calculated from Koopman's theorem, all of the investigated LC-methods give good results compared with other density functional theory functionals with a maximum deviation of 0.4 eV, except for LCgau-B97, which has an RMSE of 0.7 eV.
Jensen, Lasse; Govind, Niranjan
2009-09-10
In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.
SCAN-based hybrid and double-hybrid density functionals from models without fitted parameters
Hui, Kerwin; Chai, Jeng-Da
2015-01-01
By incorporating the nonempirical SCAN semilocal density functional [Sun, Ruzsinszky, and Perdew, Phys. Rev. Lett. 115, 036402 (2015)] in the underlying expression of four existing hybrid and double-hybrid models, we propose one hybrid (SCAN0) and three double-hybrid (SCAN0-DH, SCAN-QIDH, and SCAN0-2) density functionals, which are free from any fitted parameters. The SCAN-based double-hybrid functionals consistently outperform their parent SCAN semilocal functional for self-interaction probl...
DEFF Research Database (Denmark)
List, Nanna Holmgaard; Olsen, Jógvan Magnus Haugaard; Rocha-Rinza, Tomás
2012-01-01
are found to give the overall best performance. The Coulomb-attenuated CAM-B3LYP functional systematically overestimates the excitation energies of the charged states; however, its error has the attractive feature of being size-independent and almost identical for the considered anionic and cationic systems...
Ruíz, Alberto; Morera-Boado, Cercis; Almagro, Luis; Coro, Julieta; Maroto, Enrique E; Herranz, María Ángeles; Filippone, Salvatore; Molero, Dolores; Martínez-Álvarez, Roberto; Garcia de la Vega, José M; Suárez, Margarita; Martín, Nazario
2014-04-18
New [60]fullerene-steroid conjugates (4-6) have been synthesized by 1,3-dipolar cycloaddition and Bingel-Hirsch cyclopropanation reactions from suitably functionalized epiandrosterone and [60]fullerene. Since a new stereocenter is created in the formation of the Prato monoaduct, two different diastereomers were isolated by HPLC (4, 5) whose absolute configurations were assigned according to the highly reliable "sector rule" on fullerenes. A further reaction of the malonate-containing diastereomer 5 with a second C60 molecule has afforded dumbbell fullerene 6 in which the two fullerene units are covalently connected through an epiandrosterone moiety. The new compounds have been spectroscopically characterized and their redox potentials, determined by cyclic voltametry, reveal three reversible reduction waves for hybrids 4 and 5, whereas these signals are split in dumbbell 6. Theoretical calculations at semiempirical (AM1) and single point B3LYP/6-31G(d) levels have predicted the most stable conformations for the hybrid compounds (4-6), showing the importance of the chlorine atom on the D ring of the steroid. Furthermore, TDDFT calculations have allowed assignments of the experimentally determined circular dichroism (CD) of the [60]fullerene-steroid hybrids based on the sign and position of the Cotton effects, despite the exceptionally large systems under study.
Hybrid CIS-DFT method to study electric field effects on electronic excited states of ethylene
Institute of Scientific and Technical Information of China (English)
Ma Mei-Zhong; Zhu Zheng-He; Chen Xiao-Jun; Xu Guo-Liang; Zhang Yong-Bin; Mao Hua-Ping; Shen Xiao-Hong
2005-01-01
The present work is devoted to the study of the effects of external dipole electric field on the molecular structure of ethylene using a hybrid method which combines the single-excitation configuration interactions (CIS) with density functional theory (DFT), i.e. CIS-DFT(B3LYP). It is found that the effects of electric dipole field on the molecular geometry (D2h, D2d and C2v), dipole moment, transition dipole moment, polarizability and, particularly, excitation energy of ethylene are remarkable. The advantages of the hybrid CIS-DFT method are that it can determine the symmetry of molecule and the correct order of excitation as well as the Molecular Orbital (MO) electron configuration;thereby the electronic excitation states of ethylene are easily derived, and most of them are in agreement with those obtained in experiments or references. It may be the first time the effects of external electric field on ethylene molecule have been considered. Compared with other ab initio methods, the CIS-DFT method is relatively accurate and low cost in computation. We expect that it can be used to study other closed-shell molecules.
On the hybrid glassy carbon electrode/OligoThiophene/Ag(NP) interface.
Tassinari, Francesco; Tancini, Erik; Innocenti, Massimo; Schenetti, Luisa; Fontanesi, Claudio
2012-11-06
GC/OligoThiophene/Ag(NP) hybrid interfaces are synthesized and characterized: GC is the glassy carbon surface; OligoThiophene stands for both an ultrathin bithiophene grafted film and a 4-Br-Bithiophene grafted polymer; Ag(NP) stands for silver nanoparticles. The hybrid interface preparation involves different steps: first, the electrode surface is functionalized through a combination of electrochemically assisted grafting (under reduction regime) and polymerization (under oxidation regime); then, silver nanoparticles are chemisorbed by dipping. In particular, an ultrathin film of grafted bithiophene can be obtained by applying one cyclic voltammetry reduction cycle (GC/BT surface), while subsequent cyclic voltammetry cycling under oxidation regime yields an immobilized 4Br-Bithiophene polymer (GC/4BrBT surface). AFM and TEM images were recorded to investigate the morphology and chemical composition of the Ag(NP). Fe(II)/Fe(III) cyclic voltammetry, Zn underpotential deposition (UPD), XPS, LA-ICP-MS, and Raman techniques were exploited to characterize both the GC/OligoThiophene and GC/OligoThiophene/Ag(NP) interfaces. Theoretical calculation, at the B3LYP/6-311G** level of the theory, enabled rationalization of the electroreduction mechanism and the Raman results.
National Research Council Canada - National Science Library
Lee, Richmond; Tan, Davin; Liu, Chaoli; Li, Huaifeng; Guo, Hao; Shyue, Jing-Jong; Huang, Kuo-Wei
2017-01-01
Mechanistic insights into the selective C–H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using...
Ben Gzaiel, M.; Oueslati, A.; Chaabane, I.; Gargouri, M.
2016-10-01
The molecular structure and vibrational spectra of bis-tetrapropyl-ammonium hexachloro-dizincate in the ground state have been investigated by density functional method (DFT) using the B3LYP method with the LanL2DZ and LanL2MB basis set. Infrared and Raman spectroscopes of the [N(C3H7)4]2Zn2Cl6 compound have been measured at room temperature in the frequencies range (3500-400 cm-1) and (3500-100 cm-1), respectively. The optimized geometric shows that the calculated values obtained by B3LYP/LanL2DZ basis are in much better agreement with the experimental data than those obtained by B3LYP/LanL2MB. Actually the theoretical vibrational spectra (B3LYP/LanL2DZ) of the title compound have been interpreted by means of potential energy distribution (PED) which is in good agreement with the experimental data. The comparison of the infrared spectrum of the tetrapropyl-ammonium chloride ligand with those of the bis-tetrapropyl-ammonium hexachloro-dizincate compound confirms an increase of the wavenumber in the [N(C3H7)4]2Zn2Cl6 compound. This can be explained by an increase of the electrostatic interactions of the [N(C3H7)4]Cl ligand.
SCAN-based hybrid and double-hybrid density functionals from parameter-free models
Hui, Kerwin
2015-01-01
By incorporating the nonempirical SCAN semilocal density functional [Sun, Ruzsinszky, and Perdew, Phys. Rev. Lett. 115, 036402 (2015)] in the underlying expression, we propose one hybrid (SCAN0) and three double-hybrid (SCAN0-DH, SCAN-QIDH, and SCAN0-2) density functionals, which are free of any empirical parameter. The SCAN-based hybrid and double-hybrid functionals consistently outperform their parent SCAN semilocal functional for a wide range of applications. The SCAN-based semilocal, hybrid, and double-hybrid functionals generally perform better than the corresponding PBE-based functionals. In addition, the SCAN0-2 and SCAN-QIDH double-hybrid functionals significantly reduce the qualitative failures of the SCAN semilocal functional, such as the self-interaction error and noncovalent interaction error, extending the applicability of the SCAN-based functionals to a very diverse range of systems.
Density functional theory studies of etoricoxib
Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.
2016-05-01
Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.
Hartley, Madeline K; Vine, Seanna; Walsh, Elizabeth; Avrantinis, Sara; Daub, G William; Cave, Robert J
2016-03-03
We investigate several representative density functional theory approaches for the calculation of relative activation energies and free energies of a set of model pericyclic reactions, some of which have been studied experimentally. In particular, we use a standard hybrid functional (B3LYP), the same hybrid functional augmented with a basis set superposition error and dispersion correction, a meta-hybrid functional developed to treat transition states and weak interactions (M06-2X), and the recently implemented random phase approximation (RPA) based on Kohn-Sham orbitals from conventional density functional theory by Furche and co-workers. We apply these methods to calculate relative activation energies and estimated free energies for the amide acetal Claisen rearrangement. We focus on relative activation energies to assess the effects of steric and weak interactions in the various methods and compare with experiment where possible. We also discuss the advantages of using this set of reactions as a test bed for the comparison of treatments of weak interactions. We conclude that all methods yield similar trends in relative reactivity, but the RPA yields results in best agreement with the experimental values.
Hybrid functional study of α-uranium
Kaur, Gurpreet; Chinnappan, Ravi; Panigrahi, B. K.
2016-05-01
We have used the hybrid density functionals to study the structural and electronic properties of alpha-U. The fraction of exact Hartree Folk exchange used is varied from 0.0 to 0.6. The equilibrium volume is found to be underestimated and bulk modulus overestimated with HSE as compared to both calculated by PBE and the experimental values. Electronic bands below the Fermi level are found to shift to lower energy with respect to PBE electronic bands which itself gives the bands shifted to lower energies as compared to UPS experiments.
Thicoipe, Sandrine; Carbonniere, Philippe; Pouchan, Claude
2013-08-15
This study presents structural properties of microhydrated nucleic acid bases (NABs) - uracil (U), thymine (T), guanine (G), adenine (A), and cytosine (C) - investigated by theoretical computations at the B3LYP level of theory. To obtain the different representations of these microhydrated species, we applied the GSAM procedure: the most stable conformers labeled X,nH2O (X = U, T, G, A and n = 1...5) for which the Boltzmann population is higher than 2% at 298K are calculated at the B3LYP and B3LYP-D levels of theory. At the B3LYP level, our calculated geometries are compared with those obtained in the literature. New physically relevant isomers are found with the GSAM algorithm, especially for the tetra- and pentahydrated species. The use of DFT-D functional does not strongly modify the relative energies of the isomers for the monohydrated species. When the number of water molecules increases, the results become extremely sensitive to the consideration of dispersion contributions.
Noël, Yves; De La Pierre, Marco; Zicovich-Wilson, Claudio M; Orlando, Roberto; Dovesi, Roberto
2014-07-14
The properties of the (n,n) icosahedral family of carbon fullerenes up to n = 10 (6000 atoms) have been investigated through ab initio quantum-mechanical simulation by using a Gaussian type basis set of double zeta quality with polarization functions (84,000 atomic orbitals for the largest case), the hybrid B3LYP functional and the CRYSTAL14 code featuring generalization of symmetry treatment. The geometry of giant fullerenes shows hybrid features, between a polyhedron and a sphere; as n increases, it approaches the former. Hexagon rings at face centres take a planar, graphene-like configuration; the 12 pentagon rings at vertices impose, however, a severe structural constraint to which hexagon rings at the edges must adapt smoothly, adopting a bent (rather than sharp) transversal profile and an inward longitudinal curvature. The HOMO and LUMO electronic levels, as well as the band gap, are well described using power laws. The gap is predicted to become zero for n ≥ 34 (69,360 atoms). The atomic excess energy with respect to the ideal graphene sheet goes to zero following the log(Nat)/Nat law, which is well described through the continuum elastic theory applied to graphene; the limits for the adopted model are briefly outlined. Compared to larger fullerenes of the series, C60 shows unique features with respect to all the considered properties; C240 presents minor structural and energetic peculiarities, too.
Hybrid distortion function for JPEG steganography
Wang, Zichi; Zhang, Xinpeng; Yin, Zhaoxia
2016-09-01
A hybrid distortion function for JPEG steganography exploiting block fluctuation and quantization steps is proposed. To resist multidomain steganalysis, both spatial domain and discrete cosine transformation (DCT) domain are involved in the proposed distortion function. In spatial domain, a distortion value is allotted for each 8×8 block according to block fluctuation. In DCT domain, quantization steps are employed to allot distortion values for DCT coefficients in a block. The two elements, block distortion and quantization steps, are combined together to measure the embedding risk. By employing the syndrome trellis coding to embed secret data, the embedding changes are constrained in complex regions, where modifications are hard to be detected. When compared to current state-of-the-art steganographic methods for JPEG images, the proposed method presents less detectable artifacts.
Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus.
Ellison, Christopher K; Burton, Ronald S
2006-07-01
Electron transport system (ETS) function in mitochondria is essential for the aerobic production of energy. Because ETS function requires extensive interactions between mitochondrial and nuclear gene products, coadaptation between mitochondrial and nuclear genomes may evolve within populations. Hybridization between allopatric populations may then expose functional incompatibilities between genomes that have not coevolved. The intertidal copepod Tigriopus californicus has high levels of nucleotide divergence among populations at mitochondrial loci and suffers F2 hybrid breakdown in interpopulation hybrids. We hypothesize that hybridization results in incompatibilities among subunits in ETS enzyme complexes and that these incompatibilities result in diminished mitochondrial function and fitness. To test this hypothesis, we measured fitness, mitochondrial function, and ETS enzyme activity in inbred recombinant hybrid lines of Tigriopus californicus. We found that (1) both fitness and mitochondrial function are reduced in hybrid lines, (2) only those ETS enzymes with both nuclear and mitochondrial subunits show a loss of activity in hybrid lines, and (3) positive relationships exist between ETS enzyme activity and mitochondrial function and between mitochondrial function and fitness. We also present evidence that hybrid lines harboring mitochondrial DNA (mtDNA) and mitochondrial RNA polymerase (mtRPOL) from the same parental source population have higher fitness than those with mtDNA and mtRPOL from different populations, suggesting that mitochondrial gene regulation may play a role in disruption of mitochondrial performance and fitness of hybrids. These results suggest that disruption of coadaptation between nuclear and mitochondrial genes contributes to the phenomenon of hybrid breakdown.
Double-hybrid density-functional theory made rigorous
Sharkas, Kamal; Savin, Andreas
2010-01-01
We provide a rigorous derivation of a class of double-hybrid approximations, combining Hartree-Fock exchange and second-order Moller-Plesset correlation with a semilocal exchange-correlation density functional. These double-hybrid approximations contain only one empirical parameter and use a density-scaled correlation energy functional. Neglecting density scaling leads to an one-parameter version of the standard double-hybrid approximations. We assess the performance of these double-hybrid schemes on representative test sets of atomization energies and reaction barrier heights, and we compare to other hybrid approximations, including range-separated hybrids. Our best one-parameter double-hybrid approximation, called 1DH-BLYP, roughly reproduces the two parameters of the standard B2-PLYP or B2GP-PLYP double-hybrid approximations, which shows that these methods are not only empirically close to an optimum for general chemical applications but are also theoretically supported.
He, C C; Kimutai, B; Bao, X; Hamlow, L; Zhu, Y; Strobehn, S F; Gao, J; Berden, G; Oomens, J; Chow, C S; Rodgers, M T
2015-11-01
To gain a better understanding of the binding mechanism and assist in the optimization of chemical probing and drug design applications, experimental and theoretical studies of a series of amino acid-linked cisplatin derivatives are being pursued. Glyplatin (glycine-linked cisplatin) was chosen for its structural simplicity and to enable backbone effects to be separated from side-chain effects on the structure and reactivity of ornithine- and lysine-linked cisplatin (Ornplatin and Lysplatin, respectively). Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on Glyplatin to characterize its structure and guide the selection of the most effective hybrid theoretical approach for determining its structure and IR spectrum. The simplicity of the Glyplatin system allows a wide variety of density functionals, treatments of the Pt center including the use of all-electron basis sets vs valence basis sets combined with an effective core potential (ECP), and basis sets for all other atoms to be evaluated at a reasonable computational cost. The results for Glyplatin provide the foundation for calculations of more complex amino acid-linked cisplatin derivatives such as Ornplatin and Lysplatin. Present results suggest that the B3LYP/mDZP/def2-TZVP hybrid method can be effectively employed for structural and IR characterization of more complex amino acid-linked cisplatin complexes and their nucleic acid derivatives.
Calculations of Optical Rotation from Density Functional Theory
Institute of Scientific and Technical Information of China (English)
António Canal Neto; Francisco Elias Jorge
2007-01-01
Density function theory calculations of frequency-dependent optical rotations [α]ω for three rigid chiral molecules are reported. Calculations have been carried out at the sodium D line frequency, using the ADZP basis set and a wide variety of functionals. Gauge-invariant atomic orbitals are used to guarantee origin-independent values of [α]D. In addition, study of geometry dependence of [α]D. Is reported. Using the geometries optimized at the B3LYP/ADZP level, the mean absolute deviation of B3LYP/ADZP and experimental [α]D values yields 60.1°/(dm g/cm3). According to our knowledge, this value has not been achieved until now with any other model.
Theory Study on Structures and Vibrational Frequencies of Pyruvic acid
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
Density functional theory BLYP (using Becke's and Lee-Yang-Parr's correlation functionals ), ab initio Hartree-Fock (HF) and hybrid DFT/HF B3LYP calculations were carried out to study the structure and vibrational spectra of pyruvic acid. The scaled B3LYP/6-31G* frequencies correspond well with available experimental assignment of the functional vibrational modes and the mean absolut devation is only 12.3cm-1.
Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman
2008-04-24
We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results
The accuracy of geometries for iron porphyrin complexes from density functional theory
DEFF Research Database (Denmark)
Rydberg, Patrik Åke Anders; Olsen, Lars
2009-01-01
Iron porphyrin complexes are cofactors in many important proteins such as cytochromes P450, hemoglobin, heme peroxidases, etc. Many computational studies on these systems have been done over the past decade. In this study, the performance of some of the most commonly used density functional theory...... functionals is evaluated with regard to how they reproduce experimental structures. Seven different functionals (BP86, PBE, PBE0, TPSS, TPSSH, B3LYP, and B97-D) are used to study eight different iron porphyrin complexes. The results show that the TPSSH, PBE0, and TPSS functionals give the best results...... (absolute bond distance deviations of 0.015-0.016 A), but the geometries are well-reproduced by all functionals except B3LYP. We also test four different basis sets of double-zeta quality, and we find that a combination of double-zeta basis set of Schafer et al. on the iron atom and the 6-31G* basis set...
Ramalingam, S.; Karabacak, M.; Periandy, S.; Puviarasan, N.; Tanuja, D.
2012-10-01
In the present analysis, FT-IR/FT-Raman spectra of the cyclohexanone oxime (CHO, C6H11NO) are recorded. The observed vibrational frequencies are assigned and the computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-311++G(d,p) basis set and the corresponding results are tabulated. In order to yield good coherence with observed values, the calculated frequencies are scaled by appropriate scale factors. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The alternation of structure of cyclohexanone due to the substitution of NOH is investigated. The vibrational sequence pattern of the molecule related to the substitutions is analyzed. Comparison of the observed fundamental vibrational frequencies of CHO and calculated results by density functional (B3LYP and B3PW91) and HF methods indicates that B3LYP is superior to the scaled HF and B3PW91 approach for molecular vibrational problems. Moreover, 13C NMR and 1H NMR chemical shifts are calculated by using the gauge independent atomic orbital (GIAO) method with HF/B3LYP/B3PW91 methods and the same basis set. A study on the electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, are performed by HF and DFT methods. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. NLO properties and Mulliken charges of the CHO was also calculated and interpreted. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures are calculated in gas phase.
Gao, Aifang; Du, Hongli; Li, Aiguo; Pei, Huiyi
2013-06-01
The equilibrium geometries and electron affinities of the R-SS/R-SS(-)(R=CH₃, C₂H₅, n-C₃H7, i-C₃H₇, n-C₄H₉, t-C₄H₉, n-C₅H₁₁) species have been studied using the higher level of the Gaussian-3(G3) theory and 21 carefully calibrated pure and hybrid density functionals (five generalized gradient approximation (GGA) methods, seven hybrid GGAs, three meta GGA methods, and six hybrid meta GGAs) in conjunction with diffuse function augmented double-ζ plus polarization (DZP++) basis sets. The geometries are fully optimized with each method and discussed. The reliable adiabatic electron affinity has been presented by means of the high level of G3 technique. With the DZP++ DFT method, three measures of neutral/anion energy differences reported in this work are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The adiabatic electron affinities, obtained at the BP86, M05-2X, B3LYP, M06, B98, M06-2X, mPW1PW91, HCTH, B97-1, M05, PBE1PBE, and VSXC methods, are in agreement with the G3 results. These methods perform better for EA prediction and are considered to be reliable.
Kóňa, Juraj; Fabian, Walter M F
2011-08-09
The first reaction step of the redox cycle of bovine erythrocyte glutathione peroxidase from class 1 (GPX1) was investigated using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations using the ONIOM methodology. The reduction of hydrogen peroxide by the active-site selenocysteine in selenolate form assisted by the Arg177 residue was modeled based on a proposal from previous molecular dynamics simulations and pKa calculations (J. Chem. TheoryComput. 2010, 6, 1670-1681). The redox reaction is predicted as a concerted SN2 nucleophilic substitution with a concomitant proton transfer from Arg177 onto leaving hydroxide ion upon reduction of hydrogen peroxide. The height of the reaction barrier was predicted in range of 6-11 kcal mol(-1), consistent with an experimental rate constant of ca. 10(7) M(-1) s(-1). The proposed GPX1-Se(-)-Arg177H(+) mechanism for GPX1 is compared with the GPX3-SeH-Gln83 one proposed for human glutathione peroxidase from class 3 (GPX3) and with the solvent-assisted proton exchange mechanism proposed for GPX-like organic selenols. The structural and energetic parameters predicted by various density functional theory methods (B3LYP, MPW1PW91, MPW1K, BB1K, M05-2X, M06-2X, and M06) are also discussed.
DFT studies of CNT-functionalized uracil-acetate hybrids
Mirzaei, Mahmoud; Gulseren, Oguz
2015-09-01
Calculations based on density functional theory (DFT) have been performed to investigate the stabilities and properties of hybrid structures consisting of a molecular carbon nanotube (CNT) and uracil acetate (UA) counterparts. The investigated models have been relaxed to minimum energy structures and then various physical properties and nuclear magnetic resonance (NMR) properties have been evaluated. The results indicated the effects of functionalized CNT on the properties of hybrids through comparing the results of hybrids and individual structures. The oxygen atoms of uracil counterparts have been seen as the detection points of properties for the CNT-UA hybrids.
Density Functionals with Broad Applicability in Chemistry
Energy Technology Data Exchange (ETDEWEB)
Zhao, Yan; Truhlar, Donald G.
2008-02-01
The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by mediumrange correlation energy, such as van der Waals attraction, aromatic-aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid) functionals, Hartree-Fock exchange. We have developed four new functionals that overcome the above-mentioned difficulties: (a) M06, a hybrid meta functional, is a functional with good accuracy “across-theboard” for transition metals, main group thermochemistry, medium-range correlation energy, and barrier heights; (b) M06- 2X, another hybrid meta functional, is not good for transition metals but has excellent performance for main group chemistry, predicts accurate valence and Rydberg electronic excitation energies, and is an excellent functional for aromatic-aromatic stacking interactions; (c) M06-L is not as accurate as M06 for barrier heights but is the most accurate
Local hybrid functionals: an assessment for thermochemical kinetics.
Kaupp, Martin; Bahmann, Hilke; Arbuznikov, Alexei V
2007-11-21
Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b(tau(W)(r)tau(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.
Institute of Scientific and Technical Information of China (English)
HE Xiang; WANG Fan
2006-01-01
@@ Thioaldehydes and thioketones are candidates of new photoluminescence materials. The time-dependent density functional theory is applied to calculate the absorption and emission wavelengths of ten thiocarbonyl compounds using both B3LYP and PBE0 functionals. The theoretical results are in agreement with the measurable ones.Furthermore, it is found that the maximum absorption and emission wavelengths are linearly correlated to the C-S bond lengths.
Coumarin Dyes for Dye-Sensitized Solar Cells - A Long-Range-Corrected Density Functional Study
Wong, Bryan M; 10.1063/1.3025924
2010-01-01
The excited-state properties in a series of coumarin solar cell dyes are investigated with a long-range-corrected (LC) functional which asymptotically incorporates Hartree-Fock exchange. Using time-dependent density functional theory (TDDFT), we calculate excitation energies, oscillator strengths, and excited-state dipole moments in each of the dyes as a function of the range-separation paramenter, mu. To investigate the acceptable range of mu and assess the quality of the LC-TDDFT formalism, an extensive comparison is made between LC-BLYP excitation energies and approximate coupled cluster singles and doubles (CC2) calculations. When using a properly-optimized value of mu, we find that the LC technique provides a consistent picture of charge-transfer excitations as a function of molecular size. In contrast, we find that the widely-used B3LYP hybrid functional severely overestimates excited-state dipole moments and underestimates vertical excitations energies, especially for larger dye molecules. The results ...
Density functional theory investigations of radical scavenging activity of 3′-Methyl-quercetin
Directory of Open Access Journals (Sweden)
Abdullah G. Al-Sehemi
2016-09-01
Full Text Available The possible eight rotamers of 3′-Methyl-quercetin have been optimized by using density functional theory (DFT at B3LYP/6-31G∗ level of theory. The molecular structure and molecular properties of the most stable rotamers have been investigated at the same level of theory. We have computed the descriptors; electronegativity (χ, hardness (η, electrophilicity (ω, softness (S and electrophilicity index (ωi by DFT approach. We have shed light on the structure–property relationship. The absorption spectrum has been computed by time dependent density functional theory (TD-DFT at TD-B3LYP/6-31G∗ level of theory. Radical scavenging activity has been explained on the basis of bond dissociation enthalpy (BDE and the adiabatic ionization potential (IP. Two mechanisms have been explained for the radical scavenging processes, i.e., hydrogen atom transfer and one-electron transfer.
Density functional theory study on the ionic liquid pyridinium hydrogen sulfate
Tankov, Ivaylo; Yankova, Rumyana; Genieva, Svetlana; Mitkova, Magdalena; Stratiev, Dicho
2017-07-01
The geometry, electronic structure and chemical reactivity of a pyridinium-based ionic liquid, pyridinium hydrogen sulfate ([H-Pyr]+[HSO4]-), have been discussed on the basis of quantum chemical density functional theory calculations using B3LYP/6-311+G(d,p) and B3LYP/6-311++G(2d,2p) approaches. The calculations indicated that [H-Pyr]+[HSO4]- exists in the form of an ion pair. A large electropositive potential was found on the pyridinium ring, while the regions of a negative electrostatic potential is linked with the lone pair of electronegative oxygen atoms in hydrogen sulfate anion ([HSO4]-). Electron transfer both within the anion, and between the anion and cation of an ion pair were described using natural bond orbital theory. The energy values of -7.1375 and -2.8801 eV were related to HOMO and LUMO orbitals, respectively.
Directory of Open Access Journals (Sweden)
Giorgio Molteni
2017-01-01
Full Text Available Conventional frontier molecular orbital theory is not able to satisfactorily explain the regioselectivity outcome of the nitrilimine–alkene cycloaddition. We considered that conceptual density functional theory (DFT could be an effective theoretical framework to rationalize the regioselectivity of the title reaction. Several nitrilimine–alkene cycloadditions were analyzed, for which we could find regioselectivity data in the literature. We computed DFT reactivity indices at the B3LYP/6-311G(2d,p//B3LYP/6-31G(d,p and employed the grand potential stabilization criterion to calculate the preferred regioisomer. Experimental and calculated regioselectivity agree in the vast majority of cases. It was concluded that predominance of a single regioisomer can be obtained by maximizing (i the chemical potential difference between nitrilimine and alkene and (ii the local softness difference between the reactive atomic sites within each reactant. Such maximization can be achieved by carefully selecting the substituents on both reactants.
Regli, Laura; Bordiga, Silvia; Busco, Claudia; Prestipino, Carmelo; Ugliengo, Piero; Zecchina, Adriano; Lamberti, Carlo
2007-10-10
Insertion of B atoms into an Al-free zeolitic framework with CHA topology results in the formation of B-SSZ-13 zeotype with Si/B = 11. B K-edge NEXAFS testifies that B forms [B(OSi)4] units in a Td-like geometry (sp3-hybridized B atoms). According to B K-edge NEXAFS and IR, template burning results in the formation of [B(OSi)3] units in a D3h-like geometry (sp2-hybridized B atoms) with a break of a B-O-Si bond and the formation of a Si-OH group. The activated material contains B(III) Lewis acid centers able to specifically coordinate bases like NH3. Such [B(OSi)3] units are reactive toward ammonia, resulting in the formation of B-NH2 surface functionality inside the pores of B-SSZ-13 already under mild conditions, i.e., 35 mbar of NH3 at 373 K for 30 min and without crystallinity degradation. A minor fraction of Si-NH2 cannot be excluded owing to the presence of two IR doublets at 3500 and 3430 cm-1 and at 1600 and 1550 cm-1. Ab initio B3LYP/6-31+G(d,p) calculations on a cluster model, supported by a single-point MP2 on B3LYP/6-31+G(D,P) optimized structures, found the break by NH3 of a B-O-Si bond of the [B(OSi)3] unit with formation of [SiOH] and [H2N-B(OSi)2] species to be energetically favored. Comparison between experimental and computed frequency shifts shows them to be in semiquantitative agreement. The high stability of the B-NH2 surface functionality is probed by N K-edge NEXAFS spectra collected under UHV conditions. These findings can open a new route in the preparation of shape selective solid basic catalysts.
Laury, Marie L; Carlson, Matthew J; Wilson, Angela K
2012-11-15
Calculated harmonic vibrational frequencies systematically deviate from experimental vibrational frequencies. The observed deviation can be corrected by applying a scale factor. Scale factors for: (i) harmonic vibrational frequencies [categorized into low (1000 cm(-1))], (ii) vibrational contributions to enthalpy and entropy, and (iii) zero-point vibrational energies (ZPVEs) have been determined for widely used density functionals in combination with polarization consistent basis sets (pc-n, n = 0,1,2,3,4). The density functionals include pure functionals (BP86, BPW91, BLYP, HCTH93, PBEPBE), hybrid functionals with Hartree-Fock exchange (B3LYP, B3P86, B3PW91, PBE1PBE, mPW1K, BH&HLYP), hybrid meta functionals with the kinetic energy density gradient (M05, M06, M05-2X, M06-2X), a double hybrid functional with Møller-Plesset correlation (B2GP-PLYP), and a dispersion corrected functional (B97-D). The experimental frequencies for calibration were from 41 organic molecules and the ZPVEs for comparison were from 24 small molecules (diatomics, triatomics). For this family of basis sets, the scale factors for each property are more dependent on the functional selection than on basis set level, and thus allow for a suggested scale factor for each density functional when employing polarization consistent basis sets (pc-n, n = 1,2,3,4). A separate scale factor is recommended when the un-polarized basis set, pc-0, is used in combination with the density functionals.
Neese, Frank
2007-10-28
The zero-field splitting (ZFS) (expressed in terms of the D tensor) is the leading spin-Hamiltonian parameter for systems with a ground state spin S>12. To first order in perturbation theory, the ZFS arises from the direct spin-spin dipole-dipole interaction. To second order, contributions arise from spin-orbit coupling (SOC). The latter contributions are difficult to treat since the SOC mixes states of different multiplicities. This is an aspect of dominant importance for the correct prediction of the D tensor. In this work, the theory of the D tensor is discussed from the point of view of analytic derivative theory. Starting from a general earlier perturbation treatment [F. Neese and E. I. Soloman, Inorg. Chem. 37, 6568 (1998)], straightforward response equations are derived that are readily transferred to the self-consistent field (SCF) Hartree-Fock (HF) or density functional theory (DFT) framework. The main additional effort in such calculations arises from the solution of nine sets of nonstandard coupled-perturbed SCF equations. These equations have been implemented together with the spin-orbit mean-field representation of the SOC operator and a mean-field treatment of the direct spin-spin interaction into the ORCA electronic structure program. A series of test calculations on diatomic molecules with accurately known zero-field splittings shows that the new approach corrects most of the shortcomings of previous DFT based methods and, on average, leads to predictions within 10% of the experimental values. The slope of the correlation line is essentially unity for the B3LYP and BLYP functionals compared to approximately 0.5 in previous treatments.
Haghdani, Shokouh; Åstrand, Per-Olof; Koch, Henrik
2016-02-01
We have calculated the electronic optical rotation of seven molecules using coupled cluster singles-doubles (CCSD) and the second-order approximation (CC2) employing the aug-cc-pVXZ (X = D, T, or Q) basis sets. We have also compared to time-dependent density functional theory (TDDFT) by utilizing two functionals B3LYP and CAM-B3LYP and the same basis sets. Using relative and absolute error schemes, our calculations demonstrate that the CAM-B3LYP functional predicts optical rotation with the minimum deviations compared to CCSD at λ = 355 and 589.3 nm. Furthermore, our results illustrate that the aug-cc-pVDZ basis set provides the optical rotation in good agreement with the larger basis sets for molecules not possessing small-angle optical rotation at λ = 589.3 nm. We have also performed several two-point inverse power extrapolations for the basis set convergence, i.e., OR(∞) + AX(-n), using the CC2 model at λ = 355 and 589.3 nm. Our results reveal that a two-point inverse power extrapolation with the aug-cc-pVTZ and aug-cc-pVQZ basis sets at n = 5 provides optical rotation deviations similar to those of aug-cc-pV5Z with respect to the basis limit.
Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît
2014-05-13
The linear [χ((1))] and second-order nonlinear [χ((2))] optical susceptibilities of the 2-methyl-4-nitroaniline (MNA) crystal are calculated within the local field theory, which consists of first computing the molecular properties, accounting for the dressing effects of the surroundings, and then taking into account the local field effects. Several aspects of these calculations are tackled with the aim of monitoring the convergence of the χ((1)) and χ((2)) predictions with respect to experiment by accounting for the effects of (i) the dressing field within successive approximations, of (ii) the first-order ZPVA corrections, and of (iii) the geometry. With respect to the reference CCSD-based results, besides double hybrid functionals, the most reliable exchange-correlation functionals are LC-BLYP for the static χ((1)) and CAM-B3LYP (and M05-2X, to a lesser extent) for the dynamic χ((1)) but they strongly underestimate χ((2)). Double hybrids perform better for χ((2)) but not necessarily for χ((1)), and, moreover, their performances are much similar to MP2, which is known to slightly overestimate β, with respect to high-level coupled-clusters calculations and, therefore, χ((2)). Other XC functionals with less HF exchange perform poorly with overestimations/underestimations of χ((1))/χ((2)), whereas the HF method leads to underestimations of both. The first-order ZPVA corrections, estimated at the B3LYP level, are usually small but not negligible. Indeed, after ZPVA corrections, the molecular polarizabilities and first hyperpolarizabilities increase by 2% and 5%, respectively, whereas their impact is magnified on the macroscopic responses with enhancements of χ((1)) by up to 5% and of χ((2)) by as much as 10%-12% at λ = 1064 nm. The geometry plays also a key role in view of predicting accurate susceptibilities, particularly for push-pull π-conjugated compounds such as MNA. So, the geometry optimized using periodic boundary conditions is characterized
Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.
2016-10-01
The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.
Comparative Studies of 1,4-Bis[ 2-(4-Pyridyl) ethenyl ]-benzene Using Density Functional Theory
Institute of Scientific and Technical Information of China (English)
CHENG Jian-bo; L(U) Jia-ping; GONG Bao-an; LI Wen-zuo
2007-01-01
The optimized molecular structure and harmonic vibrational frequencies of a 1,4-bis [ 2-( 4-pyridyl ) ethenyl ] -benzene(BPENB) molecule were calculated via five popular density functional theory(DFT) methods. On the basis of the comparison between calculated and experimental results, it is concluded that the B3PW91 and B3LYP methods are superior to the others in optimizing structures, and the BPW91 method reproduces the observed fundamental frequencies most satisfactorily.
Ensling, David; Thissen, Andreas; Laubach, Stefan; Schmidt, Peter C.; Jaegermann, Wolfram
2010-11-01
The electronic properties of LiCoO2 have been studied by theoretical band-structure calculations (using density functional theory) and experimental methods (photoemission). Synchrotron-induced photoelectron spectroscopy, resonant photoemission spectroscopy (ResPES), and soft x-ray absorption (XAS) have been applied to investigate the electronic structure of both occupied and unoccupied states. High-quality PES spectra were obtained from stoichiometric and highly crystalline LiCoO2 thin films deposited “in situ” by rf magnetron sputtering. An experimental approach of separating oxygen- and cobalt-derived (final) states by ResPES in the valence-band region is presented. The procedure takes advantage of an antiresonant behavior of cobalt-derived states at the 3p-3d excitation threshold. Information about the unoccupied density of states has been obtained by OK XAS. The structure of the CoL absorption edge is compared to semiempirical charge-transfer multiplet calculations. The experimental results are furthermore compared with band-structure calculations considering three different exchange potentials [generalized gradient approximation (GGA), using a nonlocal Hubbard U (GGA+U) and using a hybrid functional (Becke, three-parameter, Lee-Yang-Parr [B3LYP])]. For these different approaches total density of states and partial valence-band density of states have been investigated. The best qualitative agreement with experimental results has been obtained by using a GGA+U functional with U=2.9eV .
Generalization of Dielectric-Dependent Hybrid Functionals to Finite Systems
Brawand, Nicholas P.; Vörös, Márton; Govoni, Marco; Galli, Giulia
2016-10-01
The accurate prediction of electronic and optical properties of molecules and solids is a persistent challenge for methods based on density functional theory. We propose a generalization of dielectric-dependent hybrid functionals to finite systems where the definition of the mixing fraction of exact and semilocal exchange is physically motivated, nonempirical, and system dependent. The proposed functional yields ionization potentials, and fundamental and optical gaps of many, diverse molecular systems in excellent agreement with experiments, including organic and inorganic molecules and semiconducting nanocrystals. We further demonstrate that this hybrid functional gives the correct alignment between energy levels of the exemplary TTF-TCNQ donor-acceptor system.
Energy Technology Data Exchange (ETDEWEB)
Carrasquilla, Rafael J; Neira, Oscar L, E-mail: rjcarrasquilla@yahoo.com [Grupo de Espectroscopia Optica y Laser, Universidad Popular del Cesar, Valledupar (Colombia)
2011-01-01
Time dependent density functional (TD-DFT) calculations were performed on 1,3-benzoxazole and substituted benzoxazoles using the B3LYP functional and the 6-31+G(d) basis sets. The geometry of the S{sub 0} and S{sub 1} singlet ground and excited states were optimized in gas phase, toluene and methanol using B3LYP/6-31+G(d) y CIS/6-31+G(d) methods, respectively, and the vertical {pi} {yields} {pi}{sup *} absorption largest wavelength transitions were determined. Several global molecular descriptors were considered such as the hardness, chemical potential, electronegativity and the dipole moment for each molecule and was determined the influence that has, about the values of these descriptors, the alteration of the main molecular chain of an initial structure (1,3 not substituted Benzoxazole). Generally, the predicted spectra are in agreement with the experimental data.
A Hybrid Algorithm for Optimizing Multi- Modal Functions
Institute of Scientific and Technical Information of China (English)
Li Qinghua; Yang Shida; Ruan Youlin
2006-01-01
A new genetic algorithm is presented based on the musical performance. The novelty of this algorithm is that a new genetic algorithm, mimicking the musical process of searching for a perfect state of harmony, which increases the robustness of it greatly and gives a new meaning of it in the meantime, has been developed. Combining the advantages of the new genetic algorithm, simplex algorithm and tabu search, a hybrid algorithm is proposed. In order to verify the effectiveness of the hybrid algorithm, it is applied to solving some typical numerical function optimization problems which are poorly solved by traditional genetic algorithms. The experimental results show that the hybrid algorithm is fast and reliable.
Preparation and characterization of functional silica hybrid magnetic nanoparticles
Digigow, Reinaldo G.; Dechézelles, Jean-François; Dietsch, Hervé; Geissbühler, Isabelle; Vanhecke, Dimitri; Geers, Christoph; Hirt, Ann M.; Rothen-Rutishauser, Barbara; Petri-Fink, Alke
2014-08-01
We report on the synthesis and characterization of functional silica hybrid magnetic nanoparticles (SHMNPs). The co-condensation of 3-aminopropyltriethoxysilane (APTES) and tetraethyl orthosilicate (TEOS) in presence of superparamagnetic iron oxide nanoparticles (SPIONs) leads to hybrid magnetic silica particles that are surface-functionalized with primary amino groups. In this work, a comprehensive synthetic study is carried out and completed by a detailed characterization of hybrid particles' size and morphology, surface properties, and magnetic responses using different techniques. Depending on the mass ratio of SPIONs and the two silanes (TEOS and APTES), we were able to adjust the number of surface amino groups and tune the magnetic properties of the superparamagnetic hybrid particles.
Weber, Valéry; Tymczak, Christopher J; Challacombe, Matt
2006-06-14
The application of theoretical methods based on density-functional theory is known to provide atomic and cell parameters in very good agreement with experimental values. Recently, construction of the exact Hartree-Fock exchange gradients with respect to atomic positions and cell parameters within the Gamma-point approximation has been introduced. In this article, the formalism is extended to the evaluation of analytical Gamma-point density-functional atomic and cell gradients. The infinite Coulomb summation is solved with an effective periodic summation of multipole tensors. While the evaluation of Coulomb and exchange-correlation gradients with respect to atomic positions are similar to those in the gas phase limit, the gradients with respect to cell parameters needs to be treated with some care. The derivative of the periodic multipole interaction tensor needs to be carefully handled in both direct and reciprocal space and the exchange-correlation energy derivative leads to a surface term that has its origin in derivatives of the integration limits that depend on the cell. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm to optimize one-dimensional and three-dimensional periodic systems at the density-functional theory and hybrid Hartree-Fock/density-functional theory levels. We also report the full relaxation of forsterite supercells at the B3LYP level of theory.
Hybride magnetic nanostructure based on amino acids functionalized polypyrrole
Nan, Alexandrina; Bunge, Alexander; Turcu, Rodica
2015-12-01
Conducting polypyrrole is especially promising for many commercial applications because of its unique optical, electric, thermal and mechanical properties. We report the synthesis and characterization of novel pyrrole functionalized monomers and core-shell hybrid nanostructures, consisting of a conjugated polymer layer (amino acids functionalized pyrrole copolymers) and a magnetic nanoparticle core. For functionalization of the pyrrole monomer we used several amino acids: tryptophan, leucine, phenylalanine, serine and tyrosine. These amino acids were linked via different types of hydrophobic linkers to the nitrogen atom of the pyrrole monomer. The magnetic core-shell hybrid nanostructures are characterized by various methods such as FTIR spectroscopy, transmission electron microscopy (TEM) and magnetic measurements.
Hybride magnetic nanostructure based on amino acids functionalized polypyrrole
Energy Technology Data Exchange (ETDEWEB)
Nan, Alexandrina, E-mail: alexandrina.nan@itim-cj.ro; Bunge, Alexander; Turcu, Rodica [National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca (Romania)
2015-12-23
Conducting polypyrrole is especially promising for many commercial applications because of its unique optical, electric, thermal and mechanical properties. We report the synthesis and characterization of novel pyrrole functionalized monomers and core-shell hybrid nanostructures, consisting of a conjugated polymer layer (amino acids functionalized pyrrole copolymers) and a magnetic nanoparticle core. For functionalization of the pyrrole monomer we used several amino acids: tryptophan, leucine, phenylalanine, serine and tyrosine. These amino acids were linked via different types of hydrophobic linkers to the nitrogen atom of the pyrrole monomer. The magnetic core-shell hybrid nanostructures are characterized by various methods such as FTIR spectroscopy, transmission electron microscopy (TEM) and magnetic measurements.
Application of Hybrid Functions for Solving Duffing-Harmonic Oscillator
Directory of Open Access Journals (Sweden)
Mohammad Heydari
2014-01-01
Full Text Available A numerical method for finding the solution of Duffing-harmonic oscillator is proposed. The approach is based on hybrid functions approximation. The properties of hybrid functions that consist of block-pulse and Chebyshev cardinal functions are discussed. The associated operational matrices of integration and product are then utilized to reduce the solution of a strongly nonlinear oscillator to the solution of a system of algebraic equations. The method is easy to implement and computationally very attractive. The results are compared with the exact solution and results from several recently published methods, and the comparisons showed proper accuracy of this method.
Ulian, Gianfranco; Valdrè, Giovanni
2015-02-01
The knowledge of the P, T behavior of talc is very important in mineralogical-petrological and geophysical research fields because talc can be considered a hydrous phase that can recycle water into the Earth's mantle and also an important mineral in both industrial and technological applications. However, very few works have been presented to fully characterize the thermodynamic properties of this mineral, especially at atomic scale. In a previous work, we modeled the structural and mechanical properties of talc using the B3LYP-D* hybrid density functional, which included a correction for the dispersive forces and all-electron Gaussian-type orbital basis sets. The results were in good agreement with single-crystal X-ray and neutron diffraction experimental data. Here, we extend the investigation to the thermochemical and thermophysical properties of talc using the same density functional approach and the quasi-harmonic approximation, providing the thermal equation of state, the heat capacity and the entropy of the mineral at different P, T conditions.
Energy Technology Data Exchange (ETDEWEB)
Dimakis, N; Mion, T [Department of Physics and Geology, University of Texas-Pan American, Edinburg, TX 78539 (United States); Bunker, G, E-mail: dimakis@utpa.ed [Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616 (United States)
2009-11-15
We present an accurate and efficient technique for calculating thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) applicable to crystalline materials. Using Density Functional Theory on a 3x3x3 supercell pattern of MnO structure, under the nonlocal hybrid B3LYP functional paired with Gaussian local basis sets, we obtain the normal mode eigenfrequencies and eigenvectors; these parameters are in turn used to calculate single and multiple scattering XAFS DWFs. The DWFs obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters, when experimental spectra are fitted with a hypothetical structure. The size of the supercell size limits the R-space range that these parameters could be used. Therefore corresponding DWFs for paths outside of this range are calculated using the correlated Debye model. Our method is compared with prior cluster calculations and with corresponding values obtained from fitting experimental XAFS spectra on manganosite with simulated spectra.
Institute of Scientific and Technical Information of China (English)
Zheng Guo Huang; Li Zhou; En Cui Yang
2008-01-01
Density functional theoretical calculations have been made on the electronic structure of (CH)n(BCO)6-n(n=0-6) at B3LYP/6-311 + G(d) level.The nuclear-independent chemical shifts (NICS) values calculated using the gauge-including atomic orbitals (GIAO) method were used to assess on the aromaticities of these molecules.The results shows that (CH)n(BCO)6-n(n=0-6)species are aromatic.
Hansen, Jared A; Ehara, Masahiro; Piecuch, Piotr
2013-10-10
The left-eigenstate completely renormalized coupled-cluster (CC) method with singles, doubles, and noniterative triples [CR-CC(2,3)] and a few representative density functional theory (DFT) approaches have been applied to methanol oxidation to formic acid on a Au8(-) cluster, which is a model for aerobic oxidations on gold nanoparticles. It is demonstrated that CR-CC(2,3) supports the previous exothermic reaction mechanism, placing the initial rate-determining transition state, which corresponds to hydrogen transfer from the methoxy species to the molecular oxygen, at about 20 kcal/mol above the reactants, less than 40 kcal/mol above the O2 and CH3O(-) species coadsorbed on Au8(-), and considerably above the remaining two transition states along the reaction pathway. The DFT calculations using the previously exploited M06 hybrid functional show reasonable agreement with CR-CC(2,3), but B3LYP offers additional improvements in the description of the relevant activation energies. Pure functionals, including M06-L, BP86, and TPSS, do not work well, significantly underestimating the activation barriers, but dispersion corrections, as in B97-D, bring the results closer to the M06 accuracy level.
甲基苯丙胺光谱性质的密度泛函分析与指认%Density Functional Analysis and Spectral Identification of Methamphetamine
Institute of Scientific and Technical Information of China (English)
陈凯浩; 钟爱国
2014-01-01
采用密度泛函理论的DFT/B3LYP/6-311+G(d,p)方法和基组,对甲基苯丙胺的UV-Vis光谱，IR光谱,1HNMR光谱和荧光光谱进行了理论模拟和指认。自然电荷计算表明，胺基N和H原子很可能是其发挥药理活性的亲电和亲核反应中心。%Using density functional theory DFT/B3LYP/6-311+G (d, p) method and basis set, UV-Vis spectroscopy, IR spectroscopy, 1HNMR spectrum and fluorescence spectroscopy of methamphetamine were studied by the theoretical simulation and identification. Natural charge calculation shows that N and H atoms of amine may be electrophilic and nucleophilic reaction center to play the pharmacological activity.
Institute of Scientific and Technical Information of China (English)
LIU Hongfei; JIA Tiekun; MIN Xinmin
2014-01-01
Density functional theory calculations were carried out to explore the potential energy surface (PES) associated with the gas-phase reaction of NiL2(L=SO3CH3) with acetone. The geometries and energies of the reactants, intermediates, products and transition states of the triplet ground potential energy surfaces of [Ni, O, C2, H4] were obtained at the B3LYP/6-311++G(d,p) levels in C,H,O atoms and B3LYP/Lanl2dz in Ni atom. It was found through our calculations that the decabonylation of acetaldehyde contains four steps including encounter complexation, C-C activation, aldehyde H-shift and nonreactive dissociation. The results revealed that C-C activation induced by NiL2(L=SO3CH3) led to the decarbonylation of acetaldehyde.
Spin projection with double hybrid density functional theory.
Thompson, Lee M; Hratchian, Hrant P
2014-07-21
A spin projected double-hybrid density functional theory is presented that accounts for different scaling of opposite and same spin terms in the second order correction. This method is applied to three dissociation reactions which in the unprojected formalism exhibit significant spin contamination with higher spin states. This gives rise to a distorted potential surface and can lead to poor geometries and energies. The projected method presented is shown to improve the description of the potential over unprojected double hybrid density functional theory. Comparison is made with the reference states of the two double hybrid functionals considered here (B2PLYP and mPW2PLYP) in which the projected potential surface is degraded by an imbalance in the description of dynamic and static correlation.
Wang, Ying; Qian, Hu-Jun; Morokuma, Keiji; Irle, Stephan
2012-07-05
Ab initio coupled cluster and density functional theory studies of atomic hydrogen addition to the central region of pyrene and coronene as molecular models for graphene hydrogenation were performed. Fully relaxed potential energy curves (PECs) were computed at the spin-unrestricted B3LYP/cc-pVDZ level of theory for the atomic hydrogen attack of a center carbon atom (site A), the midpoint of a neighboring carbon bond (site B), and the center of a central hexagon (site C). Using the B3LYP/cc-pVDZ PEC geometries, we evaluated energies at the PBE density functional, as well as ab initio restricted open-shell ROMP2, ROCCSD, and ROCCSD(T) levels of theory, employing cc-pVDZ and cc-pVTZ basis sets, and performed a G2MS extrapolation to the ROCCSD(T)/cc-pVTZ level of theory. In agreement with earlier studies, we find that only site A attack leads to chemisorption. The G2MS entrance channel barrier heights, binding energies, and PEC profiles are found to agree well with a recent ab initio multireference wave function theory study (Bonfanti et al. J. Chem. Phys.2011, 135, 164701), indicating that single-reference open-shell methods including B3LYP are sufficient for the theoretical treatment of the interaction of graphene with a single hydrogen atom.
Balachandran, V.; Parimala, K.
This study is a comparative analysis of FT-IR and FT-Raman spectra of vanillin (3-methoxy-4-hydroxybenzaldehyde) and isovanillin (3-hydroxy-4-methoxybenzaldehyde). The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for both molecules using the B3LYP density functional theory (DFT) with the standard 6-311++G∗∗ basis set. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. The calculated harmonic vibrational frequencies are compared with experimental FT-IR and FT-Raman spectra. The geometrical parameters and total energies of vanillin and isovanillin were obtained for all the eight conformers (a-h) from DFT/B3LYP method with 6-311++G∗∗ basis set. The computational results identified the most stable conformer of vanillin and isovanillin as in the "a" form. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecules have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules.
Institute of Scientific and Technical Information of China (English)
2008-01-01
Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1-4) and HSO3Cl-NH3-(H2O)n (n = 0-3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density func- tional (B3LYP) method and the second order M?ller-Plesset approximation (MP2) method with the 6-311++G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.
Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin
2016-05-01
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin
2016-05-21
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Crenshaw, Jasmine Davenport
2011-12-01
formation are calculated for organic molecules using B3LYP, BMK, and B98 hybrid functionals. G3 and CBS-QB3 are used as standards in conjunction, due to their accurate thermochemistry parameters, with experimental values. The BMK functional proves to perform best with the selected organic molecules.
Donzello, Maria Pia; Ercolani, Claudio; Cai, Xiaohui; Kadish, Karl M; Ricciardi, Giampaolo; Rosa, Angela
2009-10-19
Following previous cyclic voltammetric studies of tetrakis(thiadiazole)porphyrazines [TTDPzM] where M = Zn(II), Mg(II)(H(2)O), Cu(II), or 2H(I) in nonaqueous media, a thin-layer spectroelectrochemical investigation was carried out in pyridine to characterize each stepwise one-electron reduction of the electrogenerated [TTDPzM](n-) complexes where n = 1-4. A similar UV-visible spectrum was observed for each form of the anion, independent of the central metal ion and detailed theoretical calculations by density functional theory (DFT) and time-dependent DFT (TDDFT) methods were applied to interpret the spectral features of [TTDPzZn](n-) (n = 1-4) which was selected as representative for describing the ground and excited-state electronic structures of the entire [TTDPzM](n-) series. The use of two exchange-correlation functionals, the pure, asymptotically correct statistical average of orbital potentials (SAOP) and the hybrid B3LYP functionals, proved to be essential for attaining a correct assignment of the key spectral features. The nature and intensity of the main spectral features are highlighted and interpreted on the basis of the ground-state electronic structure of the complexes.
Directory of Open Access Journals (Sweden)
Toh Pek–Lan
2015-01-01
Full Text Available We have employed first principle Density Functional Theory (DFT investigations to study the physical and electronic properties of 4–Azidomethyl–6–isopropyl–2H–chromen–2–one, C13H13N3O2. Complete geometry optimization calculations were carried out to find local energy minimum of the molecular system using the B3LYP approach with a variety of basis sets. The optimized geometries were then used to determine the HOMO–LUMO gaps, Mulliken atomic charges, and others. Our calculation results show that the computed geometrical properties of C13H13N3O2 cluster model are in good agreement with the corresponding measured experimental value. The calculated energies obtained are close to each other using the B3LYP density functional method combined with a variety of basis sets. Furthermore, using B3LYP/6–31G** method, the oxygen–attached carbon, C2 atom has the highest positively charge, with the corresponding value of +0.59. For both oxygen atoms (O1 and O2, the calculated charge values obtained are about –0.52 and –0.46, respectively.
Density-based mixing parameter for hybrid functionals
Marques, Miguel A. L.; Vidal, Julien; Oliveira, Micael J. T.; Reining, Lucia; Botti, Silvana
2011-01-01
A very popular ab initio scheme to calculate electronic properties in solids is the use of hybrid functionals in density functional theory (DFT) that mixes a portion of the Fock exchange with DFT functionals. In spite of its success, a major problem still remains, related to the use of one single mixing parameter for all materials. Guided by physical arguments that connect the mixing parameter to the dielectric properties of the solid, and ultimately to its band gap, we propose a method to calculate this parameter from the electronic density alone. This approach is able to cut significantly the error of traditional hybrid functionals for large and small gap materials, while retaining a good description of the structural properties. Moreover, its implementation is simple and leads to a negligible increase of the computational time.
Nori-Shargh, Davood; Mousavi, Seiedeh Negar; Kayi, Hakan
2014-05-01
Complete basis set CBS-4, hybrid-density functional theory (hybrid-DFT: B3LYP/6-311+G**) based methods and natural bond orbital (NBO) interpretations have been used to examine the contributions of the hyperconjugative, electrostatic, and steric effects on the conformational behaviors of trans-2,3-dihalo-1,4-diselenane [halo = F (1), Cl (2), Br (3)] and trans-2,5-dihalo-1,4-diselenane [halo = F (4), Cl (5), Br (6)]. Both levels of theory showed that the axial conformation stability, compared to its corresponding equatorial conformation, decreases from compounds 1 → 3 and 4 → 6. Based on the results obtained from the NBO analysis, there are significant anomeric effects for compounds 1-6. The anomeric effect associated with the electron delocalization is in favor of the axial conformation and increases from compounds 1 → 3 and 4 → 6. On the other hand, dipole moment differences between the axial and equatorial conformations [Δ(μ(eq)-μ(ax)] decrease from compounds 1 → 3. Although Δ(μ(eq)-μ(ax)) parameter decreases from compound 1 to compound 3, the dipole moment values of the axial conformations are smaller than those of their corresponding equatorial conformations. Therefore, the anomeric effect associated with the electron delocalizations (for halogen-C-Se segments) and the electrostatic model associated with the dipole-dipole interactions fail to account for the increase of the equatorial conformations stability on going from compound 1 to compound 3. Since there is no dipole moment for the axial and equatorial conformations of compounds 4-6, consequently, the conformational preferences in compounds 1-6 is in general dictated by the steric hindrance factor associated with the 1,3-syn-axial repulsions. Importantly, the CBS-4 results show that the entropy difference (∆S) between the equatorial axial conformations increases from compounds 1 → 3 and 4 → 6. This fact can be explained by the anomeric effect associated
Hybrid bounds for Dirichlet's L-function
Huxley, M. N.; Watt, N.
2000-11-01
This is a paper about upper bounds for Dirichlet's L-function, L(s, [chi]), on its critical line (s + s¯ = 1). It is to be assumed throughout that, unless otherwise stated, the Dirichlet character, [chi], is periodic modulo a prime, r, and is not the principal character mod r. Our main theorem below shows that, if [epsilon] > 0, thenformula here(where A is an absolute constant), for 0 < [alpha] = (log r)/(log t) [less-than-or-eq, slant] 2/753 [minus sign] [epsilon]. Somewhat weaker bounds are obtained for other cases where 0 < [alpha] [less-than-or-eq, slant] 11/180 [minus sign] [epsilon]. Note that in [13] it was shown that, for 0 < [alpha] [less-than-or-eq, slant] 2/57,formula hereOur main theorem is a corollary of the new bounds we prove for certain exponential sums, S, with a Dirichlet character factor:formula herewhere M2 [less-than-or-eq, slant] 2M and f(x) is a real function whose derivatives satisfy certain conditions restricting their size.
Application and future challenges of functional nanocarbon hybrids.
Shearer, Cameron J; Cherevan, Alexey; Eder, Dominik
2014-04-16
Hybridizing nanocarbons, such as carbon nanotubes (CNTs) or graphene, with an active material is a powerful strategy towards designing next-generation functional materials for environmental and sustainable energy applications. While research on nanocomposites, created by dispersing the nanocarbon into polymer or ceramic matrices, began almost immediately after the popularization of CNTs and graphene in 1991 and 2004, respectively, nanocarbon hybrids are a relatively recent addition to the family of composite materials. In contrast to nanocomposites, which typically combine the intrinsic properties of both compounds, nanocarbon hybrids additionally provide access to both a large surface area required for gas/liquid-solid interactions and an extended interface, through which charge and energy transfer processes create synergistic effects that result in unique properties and superior performance. This progress report looks at the history of research on nanocarbons (fullerenes, CNTs and graphene) and their composites and hybrids, presents the origin of synergistic effects, reviews the most intriguing results on nanocarbon hybrid performance in heterogeneous catalysis, electrocatalysis, photocatalysis, batteries, supercapacitors, photovoltaics and sensors, and discusses remaining challenges and future research directions.
Ab initio molecular dynamics using hybrid density functionals
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Hybrid functional studies of defects and hole polarons in oxides
Varley, Joel
Transparent conducting oxides (TCOs) are ubiquitous, appearing in windows, flat-panel displays, solar cells, solid-state lighting, and transistors that all exploit TCOs' combination of high electrical conductivity and optical transparency. Thanks to this large and growing list of applications, there has been a surge of interest in the science of these materials, focusing on the fundamental properties and doping opportunities in traditional TCOs as well as the exploration of promising new candidate materials. Hybrid density functional theory has proven instrumental in elucidating the physics of TCOs. One example is the study of dopants and defects that determine the conductivity. Accurate formation energies and charge-state transition levels can now be obtained thanks to the accurate electronic structure provided by a hybrid functional. This allows us to address the origins of unintentional conductivity: for SnO2, In2O3, and Ga2O3, we demonstrate that this is not due to native defects such as oxygen vacancies, but must be attributed to unintentional incorporation of impurities. We can also provide guidelines for achieving higher doping levels, suggesting several impurities as candidate donors with high solubility. Limitations on doping due to the formation or incorporation of compensating centers are addressed as well. Hybrid functional calculations also overcome the shortcomings associated with traditional local or semi-local functionals, which do not properly describe charge localization. Hybrid functionals accurately describe polaron formation, i.e., the self-trapping of holes when p - type doping of the oxide materials is attempted. Consequences of polaron formation for optical characterization of the material will be discussed. This work was performed in collaboration with Anderson Janotti and Chris G. Van de Walle, and was in part under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Denis, Pablo A
2005-09-01
We have investigated the SX (X = first- or second-row atom), SO2, and SO3 molecules employing the correlation-consistent (cc), the recently developed polarization-consistent (pc), and three Pople-type basis sets, in conjunction with the B3LYP functional. The results confirmed that the aug-pc basis sets represent a great contribution in terms of cost-benefits. In the case of the B3LYP functional, when employing the aug-pc-3 and aug-pc-4 basis sets, it is possible to obtain results that are of aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z quality, respectively, at a much lower cost. The estimations obtained employing smaller members of the family are of nearly double-ζ quality and do not provide reliable results. There is no basis set of quadruple-ζ quality among the polarized-consistent basis sets, although in terms of composition, the aug-pc-3 basis set is a QZ basis set. A precise estimation of the Kohn-Sham complete basis set (CBS) limit with the aug-pc-X basis sets is too difficult for the B3LYP functional because the ∞(aug-pc-4, aug-pc-3, aug-pc-2) extrapolation gives the same results as those of the aug-pc-4 basis set. This is in contrast with the results observed for ab initio methodologies for which the largest basis sets provided the best estimation of the CBS limit. In our opinion, the closest results to the B3LYP/CBS limit are expected to be those obtained with a two-point extrapolation employing the aug-cc-pV(X+d)Z (X = 5, 6) basis sets. The results obtained with this extrapolation are very close to those predicted by the ∞(aug-pc-3, aug-pc-2, aug-pc-1) extrapolation, and that provides a cheaper but more inaccurate alternative to estimate the CBS limit. Minor problems were found for the aug-pc-X basis sets and the B3LYP functional for molecules in which sulfur is bound to a very electronegative element, such as SO, SF, SO2, and SO3. For these molecules, the cc basis sets were demonstrated to be more useful. The importance of tight d functions was observed
From molecular chemistry to hybrid nanomaterials. Design and functionalization.
Mehdi, Ahmad; Reye, Catherine; Corriu, Robert
2011-02-01
This tutorial review reports upon the organisation and functionalization of two families of hybrid organic-inorganic materials. We attempted to show in both cases the best ways permitting the organisation of materials in terms of properties at the nanometric scale. The first family concerns mesoporous hybrid organic-inorganic materials prepared in the presence of a structure-directing agent. We describe the functionalization of the channel pores of ordered mesoporous silica, that of the silica framework, as well as the functionalization of both of them simultaneously. This family is currently one of the best supports for exploring polyfunctional materials, which can provide a route to interactive materials. The second family concerns lamellar hybrid organic-inorganic materials which is a new class of nanostructured materials. These materials were first obtained by self-assembly, as a result of van der Waals interactions of bridged organosilica precursors containing long alkylene chains during the sol-gel process, without any structure directing agent. This methodology has been extended to functional materials. It is also shown that such materials can be obtained from monosilylated precursors.
Indian Academy of Sciences (India)
Andrea Alparone
2014-05-01
Structural, energetic, spectroscopic, linear and nonlinear optical (NLO) properties of the environmental mutagens 1- and 3-nitro-6-azabenzo[]pyrene -oxides were characterized by means of Hartree-Fock as well as B3LYP and CAM-B3LYP density functional theory computations. The NLO investigations were performed for the second harmonic generation (SHG) and electro-optical Pockels effect (EOPE) at the incident wavelength of 1064 nm. The results show that, the predicted structures, vibrational spectra, nucleus independent chemical shifts, ionization energy, electron affinity as well as electronic polarizabilities are little influenced by the position of the nitro substituent. Differently, the dipole moment () and the first-order hyperpolarizabilities () are significantly dependent on the isomerization. The rather different mutagenic activity of the investigated isomers could be related to their diverse polarity. At the CAM-B3LYP level, when passing from the 1- to the 3-nitro-6-azabenzo[a]pyrene -oxide isomer, the datum increases by about 5 D (a factor of three), whereas the static and dynamic values decrease by ca. 50%. Dipole moment measurement and SHG and EOPE NLO techniques are potentially useful to distinguish these important environmental mutagens.
Dispersion corrections to density functionals for water aromatic interactions.
Zimmerli, Urs; Parrinello, Michele; Koumoutsakos, Petros
2004-02-08
We investigate recently published methods for extending density functional theory to the description of long-range dispersive interactions. In all schemes an empirical correction consisting of a C6r(-6) term is introduced that is damped at short range. The coefficient C6 is calculated either from average molecular or atomic polarizabilities. We calculate geometry-dependent interaction energy profiles for the water benzene cluster and compare the results with second-order Møller-Plesset calculations. Our results indicate that the use of the B3LYP functional in combination with an appropriate mixing rule and damping function is recommended for the interaction of water with aromatics.
The novel generating algorithm and properties of hybrid-P-ary generalized bridge functions
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
In this paper, we develop novel non-sine functions, named hybrid-P-ary generalized bridge functions, based on the copy and shift methods. The generating algorithm of hybrid-P-ary generalized bridge functions is introduced based on the hybrid-P-ary generalized Walsh function's copy algorithm. The main property, product property, is also discussed. This function may be viewed as the generalization of the theory of bridge functions. And a lot of non-sine orthogonal functions are the special subset of these novel functions. The hybrid-P-ary generalized bridge functions can be used to search many unknown non-sine functions by defining different parameters.
Directory of Open Access Journals (Sweden)
Đurović Igor B.
2015-01-01
Full Text Available Aromatic hydroxy acids, the compounds of large industrial importance, can be prepared in the Kolbe-Schmitt reaction, i.e. a carboxylation reaction of alkali metal phenoxides (MOPh and naphthoxides (MONaph. On the basis of the experimental results two contradictory reaction mechanisms have been proposed: the one of direct carboxylation, and the other involving initial formation of the MOPh-CO2 or MONaph-CO2 complex. Previous theoretical investigations of the carboxylation reaction of sodium 2-naphthoxide, performed by means of the B3LYP method, confirmed the initial formation of the NaONaph-CO2 complex, and showed that the carbon of the CO2 moiety performs an electrophilic attack at C1 of the ring, leading to the formation of sodium 2-hydroxy-1-naphthoate (E1. Surprisingly, transition states for possible electrophilic attacks at C3 and C6 were not revealed, and the formation of other two products (E3 and E6 was explained by a number of consecutive rearrangements. In addition, this mechanism includes a reaction step with rather high activation energy. Since more sophisticated functionals are today available, the aim of this work is to reinvestigate the mechanism of the Kolbe-Schmitt reaction of NaONaph in all three positions (1, 3, and 6. Our investigations with the M062X method demonstrated that CO2 and NaONaph can spontaneously build two complexes: B (the one previously reported and C. While B cannot be further transformed to yield the reaction products, the CO2 moiety in C takes perfect position for electrophilic attacks at all three sites of the ring. These attacks are realized via the transition states TS1, which lead to the formation of the new C-C bonds, and corresponding intermediates D. In the next, bimolecular reaction step two D intermediates exchange the protons adjacent to the CO2 groups. These intermolecular reaction steps require significantly lower activation energies in comparison to the intramolecular proton shift from C to O
Epoxy Resin Composite Based on Functional Hybrid Fillers
Directory of Open Access Journals (Sweden)
Mariusz Oleksy
2014-08-01
Full Text Available A study was carried out involving the filling of epoxy resin (EP with bentonites and silica modified with polyhedral oligomeric silsesquioxane (POSS. The method of homogenization and the type of filler affect the functional and canceling properties of the composites was determined. The filler content ranged from 1.5% to 4.5% by mass. The basic mechanical properties of the hybrid composites were found to improve, and, in particular, there was an increase in tensile strength by 44%, and in Charpy impact strength by 93%. The developed hybrid composites had characteristics typical of polymer nanocomposites modified by clays, with a fine plate morphology of brittle fractures observed by SEM, absence of a plate separation peak in Wide Angles X-ray Scattering (WAXS curves, and an exfoliated structure observed by TEM.
Epoxy Resin Composite Based on Functional Hybrid Fillers
Oleksy, Mariusz; Szwarc-Rzepka, Karolina; Heneczkowski, Maciej; Oliwa, Rafał; Jesionowski, Teofil
2014-01-01
A study was carried out involving the filling of epoxy resin (EP) with bentonites and silica modified with polyhedral oligomeric silsesquioxane (POSS). The method of homogenization and the type of filler affect the functional and canceling properties of the composites was determined. The filler content ranged from 1.5% to 4.5% by mass. The basic mechanical properties of the hybrid composites were found to improve, and, in particular, there was an increase in tensile strength by 44%, and in Charpy impact strength by 93%. The developed hybrid composites had characteristics typical of polymer nanocomposites modified by clays, with a fine plate morphology of brittle fractures observed by SEM, absence of a plate separation peak in Wide Angles X-ray Scattering (WAXS) curves, and an exfoliated structure observed by TEM. PMID:28788177
Chemical reactivity of quinmerac herbicide through the Fukui function.
Mendoza-Huizar, Luis Humberto
2014-01-01
In the present work we have calculated DFT reactivity descriptors for quinmerac (7-chloro-3-methylquinoline-8-carboxylic acid) at the MP2/6-311++G(d,p)//B3LYP/6-311++G(2d,2p) level of theory to analyze its reactivity. Reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, condensed Fukui function and total energies were calculated to predict changes in its reactivity. The Fukui function values predict that electrophilic and free radical attacks on quinmerac might cause aromatic substitutions, while nucleophilic attacks would cause cleavage of the C=N bond.
Ochoa-Calle, A J; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ramírez-Solís, A
2015-03-10
The experimentally characterized ε and ζ phases of solid oxygen are studied by periodic Hartree-Fock (HF) and Density Functional Theory calculations at pressures from 10 to 160 GPa using different types of exchange-correlation functionals with Gaussian atomic basis sets. Full geometry optimizations of the monoclinic C2/m (O2)4 unit cell were done to study the evolution of the structural and electronic properties with pressure. Vibrational calculations were performed at each pressure. While periodic HF does not predict the ε-ζ phase transition in the considered range, Local Density approximation and Generalized Gradient approximation methods predict too low transition pressures. The performance of hybrid functional methods is dependent on the amount of non-local HF exchange. PBE0, M06, B3PW91, and B3LYP approaches correctly predict the structural and electronic changes associated with the phase transition. GGA and hybrid functionals predict a pressure range where both phases coexist, but only the latter type of methods yield results in agreement with experiment. Using the optimized (O2)4 unit cell at each pressure we show, through CASSCF(8,8) calculations, that the greater accuracy of the optimized geometrical parameters with increasing pressure is due to a decreasing multireference character of the unit cell wave function. The mechanism of the transition from the non-conducting to the conducting ζ phase is explained through the Electron Pair Localization Function, which clearly reveals chemical bonding between O2 molecules in the ab crystal planes belonging to different unit cells due to much shorter intercell O2-O2 distances.
DEFF Research Database (Denmark)
Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.;
2008-01-01
Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...... moments are computed using the same geometries (MP2/6-31G*) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio...
Clustomesogens: Liquid Crystalline Hybrid Nanomaterials Containing Functional Metal Nanoclusters.
Molard, Yann
2016-08-16
Inorganic phosphorescent octahedral metal nanoclusters fill the gap between metal complexes and nanoparticles. They are finite groups of metal atoms linked by metal-metal bonds, with an exact composition and structure at the nanometer scale. As their phosphorescence internal quantum efficiency can approach 100%, they represent a very attractive class of molecular building blocks to design hybrid nanomaterials dedicated to light energy conversion, optoelectronic, display, lighting, or theragnostic applications. They are obtained as AnM6X(i)8X(a)6 ternary salt powders (A = alkali cation, M = Mo, Re, W, X(i): halogen inner ligand, X(a) = halogen apical ligand) by high temperature solid state synthesis (750-1200 °C). However, their ceramic-like behavior has largely restricted their use as functional components in the past. Since these last two decades, several groups, including ours, started to tackle the challenge of integrating them in easy-to-process materials. Within this context, we have extensively explored the nanocluster ternary salt specificities to develop a new class of self-organized hybrid organic-inorganic nanomaterials known as clustomesogens. These materials, combine the specific properties of nanoclusters (magnetic, electronic, luminescence) with the anisotropy-related properties of liquid crystals (LCs). This Account covers the research and development of clustomesogens starting from the design concepts and synthesis to their introduction in functional devices. We developed three strategies to build such hybrid super- or supramolecules. In the covalent approach, we capitalized on the apical ligand-metal bond iono-covalent character to graft tailor-made organic LC promoters on the {M6X(i)8}(n+) nanocluster cores. The supramolecular approach relies on the host-guest complexation of the ternary cluster salt alkali cations with functional crown ether macrocycles. We showed that the hybrid LC behavior depends on the macrocycles structural features
Nonempirical range-separated hybrid functionals for solids and molecules.
Energy Technology Data Exchange (ETDEWEB)
Skone, Jonathan H.; Govoni, Marco; Galli, Giulia
2016-06-03
Dielectric-dependent hybrid (DDH) functionals were recently shown to yield accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than that of GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. Here we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using system dependent, non-empirical parameters. We show that RS DDHs yield accurate electronic properties of inorganic and organic solids, including energy gaps and absolute ionization potentials. Furthermore we show that these functionals may be generalized to finite systems.
Nonempirical Range-separated Hybrid Functionals for Solids and Molecules
Skone, Jonathan H; Galli, Giulia
2016-01-01
Dielectric-dependent hybrid (DDH) functionals were recently shown to yield accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than that of GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. Here we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using system dependent, non-empirical parameters. We show that RS DDHs yield accurate electronic properties of inorganic and organic solids, including energy gaps and absolute ionization potentials. Furthermore we show that these functionals may be generalized to finite systems.
Nonempirical range-separated hybrid functionals for solids and molecules
Skone, Jonathan H.; Govoni, Marco; Galli, Giulia
2016-06-01
Dielectric-dependent hybrid (DDH) functionals were recently shown to yield accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than that of GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. Here we introduce a range-separated (RS) version of DDH functionals where short- and long-range components are matched using system-dependent, nonempirical parameters. We show that RS-DDHs yield accurate electronic properties of inorganic and organic solids, including energy gaps and absolute ionization potentials. Furthermore we show that these functionals may be generalized to finite systems.
Kolev, Stefan K; St Petkov, Petko; Rangelov, Miroslav A; Vayssilov, Georgi N
2011-12-08
Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.
Hydrogels from biopolymer hybrid for biomedical, food, and functional food applications
Hybrid hydrogels from biopolymers have been applied for various indications across a wide range of biomedical, pharmaceutical, and functional food industries. In particular, hybrid hydrogels synthesized from two biopolymers have attracted increasing attention. The inclusion of a second biopolymer st...
Band Anticrossing in Dilute Germanium Carbides Using Hybrid Functionals
Stephenson, Chad A; Qi, Meng; Penninger, Michael; Schneider, William; Wistey, Mark A
2014-01-01
Dilute germanium carbides (Ge1-xCx) offer a direct bandgap for compact silicon photonics, but widely varying results have been reported. This work uses ab initio simulations with HSE06 hybrid functionals and spin-orbit coupling to study the band structure behavior in the absence of defects. Contrary to Vegard's law, the conduction band minimum at k=0 is consistently found to decrease with increasing C content, while L and X valleys remain nearly unchanged. A vanishing bandgap was observed for all alloys with x>0.017. Conduction bands deviate from a constant-potential band anticrossing model except near the center of the Brillouin zone.
Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning.
Ribière, Céline; Beugnot, Réjane; Parisot, Nicolas; Gasc, Cyrielle; Defois, Clémence; Denonfoux, Jérémie; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre
2016-01-01
Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.
Grimme, Stefan; Steinmetz, Marc
2013-10-14
A benchmark set of 25 rotational constants measured in the gas phase for nine molecules (termed ROT25) was compiled from available experimental data. The medium-sized molecules with 18-35 atoms cover common (bio)organic structure motifs including hydrogen bonding and flexible side chains. They were each considered in a single conformation. The experimental B0 values were back-corrected to reference equilibrium rotational constants (Be) by computation of the vibrational corrections ΔBvib. Various density functional theory (DFT) methods and Hartree-Fock with and without dispersion corrections as well as MP2 type methods and semi-empirical quantum chemical approaches are investigated. The ROT25 benchmark tests their ability to describe covalent bond lengths, longer inter-atomic distances, and the relative orientation of functional groups (intramolecular non-covalent interactions). In general, dispersion corrections to DFT and HF increase Be values (shrink molecular size) significantly by about 0.5-1.5% thereby in general improving agreement with the reference data. Regarding DFT methods, the overall accuracy of the optimized structures roughly follows the 'Jacobs ladder' classification scheme, i.e., it decreases in the series double-hybrid > (meta)hybrid > (meta)GGA > LDA. With B2PLYP-D3, SCS-MP2, B3LYP-D3/NL, or PW6B95-D3 methods and extended QZVP (def2-TZVP) AO basis sets, Be values, accurate to about 0.3-0.6 (0.5-1)% on average, can be computed routinely. The accuracy of B2PLYP-D3/QZVP with a mean deviation of only 3 MHz and a standard deviation of 0.24% is exceptional and we recommend this method when highly accurate structures are required or for problematic conformer assignments. The correlation effects for three inter-atomic distance regimes (covalent, medium-range, long) and the performance of minimal basis set (semi-empirical) methods are discussed.
Hybrid density functional theory band structure engineering in hematite.
Pozun, Zachary D; Henkelman, Graeme
2011-06-14
We present a hybrid density functional theory (DFT) study of doping effects in α-Fe(2)O(3), hematite. Standard DFT underestimates the band gap by roughly 75% and incorrectly identifies hematite as a Mott-Hubbard insulator. Hybrid DFT accurately predicts the proper structural, magnetic, and electronic properties of hematite and, unlike the DFT+U method, does not contain d-electron specific empirical parameters. We find that using a screened functional that smoothly transitions from 12% exact exchange at short ranges to standard DFT at long range accurately reproduces the experimental band gap and other material properties. We then show that the antiferromagnetic symmetry in the pure α-Fe(2)O(3) crystal is broken by all dopants and that the ligand field theory correctly predicts local magnetic moments on the dopants. We characterize the resulting band gaps for hematite doped by transition metals and the p-block post-transition metals. The specific case of Pd doping is investigated in order to correlate calculated doping energies and optical properties with experimentally observed photocatalytic behavior.
Fonseca, Matheus C.; Nascimento, Clebio S.; Borges, Keyller B.
2016-02-01
The purpose of this Letter was to study for the first time the interaction process of tramadol (TRM) with distinct functional monomers (FM) in the formation of molecular imprinted polymer (MIP), using density functional theory (DFT) calculations at B3LYP/6-31G(d,p). As result we were able to establish that the best MIP synthesis conditions are obtained with acrylic acid as FM in 1:3 molar ratio and with chloroform as solvent. This condition presented the lowest stabilization energy for the pre-polymerization complexes. Besides, the intermolecular hydrogen bonds found between the template molecule and functional monomers play a primary role to the complex stability.
Water cluster anions studied by the long-range corrected density functional theory.
Yagi, Kiyoshi; Okano, Yuko; Sato, Takeshi; Kawashima, Yukio; Tsuneda, Takao; Hirao, Kimihiko
2008-10-09
Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).
Potential Function and Thermodynamic Property of UO
Institute of Scientific and Technical Information of China (English)
Xiu-lin Zeng; Si-yu Xu; Xue-hai Ju
2013-01-01
Potential energy scan for uranium oxide (UO) was performed by ab initio configuration interaction (CI) method and density functional theory methods at the PBE1 and the B3LYP levels in combination with the (ECP80MWB_AVQZ+2f) basis set for uranium and 6-311+G* for oxygen.The dissociation energies of UO,after being corrected for the zero-point vibrational energy,are 2.38,3.76,and 3.31 eV at the CI,PBE1,and B3LYP levels,respectively.The calculated energy was fitted to potential functions of Morse,Lennard-Jones,and Rydberg.Only the Morse function is eligible for the potential.The anharmonicity constant is 0.00425.The anharmonic frequency is 540.95 cm-1 deduced from the PBE1 results.Thermodynamic properties of entropy and heat capacity at 298.2-1500 K were calculated using DFT-UPBE1 results and Morse parameters.The relationship between entropy and temperature was established.
Study of Magnesium Diboride Clusters Using Hybrid Density Functional Theory
Directory of Open Access Journals (Sweden)
D. Rodríguez
2007-12-01
Full Text Available Using hybrid density functional theory and a relatively large basis set, the lowest energy equilibrium structure, vibrational spectrum, and natural orbital analysis were obtained for magnesium diboride clusters [(MgB2x for x=1,2, and 3]. For comparison, boron clusters [BxÃ‚Â forÃ‚Â x=2,4,Ã‚Â andÃ‚Â 6] were also considered. The MgB2 and (MgB22 showed equilibrium structures with the boron atoms in arrangements similar to what was obtained for pure boron atoms, whereas, for (MgB23 a different arrangement of boron was obtained. From the population analysis, large electron density in the boron atoms forming the clusters was observed.
Multilayer crack-free hybrid coatings for functional devices
Islam, Shumaila; Bidin, Noriah; Riaz, Saira; Naseem, Shahzad; Marsin Sanagi, Mohd.; Imran, M.
2016-04-01
Porous acid catalyzed TiO2 single, SiO2-TiO2 hybrid, and TiO2/SiO2-TiO2/SiO2 multilayer coatings are synthesized and characterized for optical and electro-optical applications. The reflection value is reasonably reduced from the surface of the glass by integrating sol-gel based spin-coated single and multilayer thin films. Structurally, the films show uniform, crack-free, and porous nanofilms with good surface roughness of below 10 nm, which has potential for optical applications. Wide range tunability of refractive index (2.83 to 1.59) with more than 78% optical transparency is observed. The multilayered reflection profile is observed around 0.18%, so these coatings are desirable for optochemical functional devices.
A Hybrid Imperative and Functional Molecular Mechanics Application
Directory of Open Access Journals (Sweden)
Thomas Deboni
1996-01-01
Full Text Available Molecular mechanics applications model the interactions among large ensembles of discrete particles. They are used where probabilistic methods are inadequate, such as drug chemistry. This methodology is difficult to parallelize with good performance, due to its poor locality, uneven partitions, and dynamic behavior. Imperative programs have been written that attempt this on shared and distributed memory machines. Given such a program, the computational kernel can be rewritten in Sisal, a functional programming language, and integrated with the rest of the imperative program under the Sisal Foreign Language Interface. This allows minimal effort and maximal return from parallelization work, and leaves the work appropriate to imperative implementation in its original form. We describe such an effort, focusing on the parts of the application that are appropriate for Sisal implementation, the specifics of mixed-language programming, and the complex performance behavior of the resulting hybrid code.
Ben Ahmed, A; Feki, H; Abid, Y
2014-12-10
A new organic-inorganic hybrid material, [((CH3)2NH2)(+)]6·[(BiBr6)(3-)]2, has been synthesized and characterized by X-ray diffraction, FT-IR, Raman spectroscopy and UV-Visible absorption. The studied compound crystallizes in the triclinic system, space group P1¯ with the following parameters: a=8.4749(6)(Å), b=17.1392(12)(Å), c=17.1392(12)(Å), α=117.339(0)°, β=99.487(0)°, γ=99.487(0)° and Z=2. The crystal lattice is composed of a two discrete (BiBr6)(3-) anions surrounded by six ((CH3)2NH2)(+) cations. Complex hydrogen bonding interactions between (BiBr6)(3-) and organic cations from a three-dimensional network. Theoretical calculations were performed using density functional theory (DFT) for studying the molecular structure, vibrational spectra and optical properties of the investigated molecule in the ground state. The full geometry optimization of designed system is performed using DFT method at B3LYP/LanL2DZ level of theory using the Gaussian03. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from FT-IR and Raman spectra are assigned based on the results of the theoretical calculations. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental UV-Visible spectrum. The results show good consistent with the experiment and confirm the contribution of metal orbital to the HOMO-LUMO boundary. Copyright © 2014 Elsevier B.V. All rights reserved.
DEFF Research Database (Denmark)
Bast, Radovan; Jensen, Hans Jørgen Aagaard; Saue, Trond
2009-01-01
We report an implementation of adiabatic time-dependent density functional theory based on the 4-component relativistic Dirac-Coulomb Hamiltonian and a closed-shell reference. The implementation includes noncollinear spin magnetization and full derivatives of functionals, including hybrid...... and time reversal symmetry on trial vectors to obtain even better reductions in terms of memory and run time, and without invoking approximations. Further reductions are obtained by exploiting point group symmetries for D2h and subgroups in a symmetry scheme where symmetry reductions translate...... into reduction of algebra from quaternion to complex or real. For hybrid GGAs with noncollinear spin magnetization we derive a new computationally advantageous equation for the full second variational derivatives of such exchange-correlation functionals. We apply our implementation to calculations on the ns2...
Dziedzic, J; Hill, Q; Skylaris, C-K
2013-12-07
We present a method for the calculation of four-centre two-electron repulsion integrals in terms of localised non-orthogonal generalised Wannier functions (NGWFs). Our method has been implemented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations with hybrid exchange-correlation functionals. As the NGWFs are optimised in situ in terms of a systematically improvable basis set which is equivalent to plane waves, it is possible to achieve large basis set accuracy in routine calculations. The spatial localisation of the NGWFs allows us to exploit the exponential decay of the density matrix in systems with a band gap in order to compute the exchange energy with a computational effort that increases linearly with the number of atoms. We describe the implementation of this approach in the ONETEP program for linear-scaling first principles quantum mechanical calculations. We present extensive numerical validation of all the steps in our method. Furthermore, we find excellent agreement in energies and structures for a wide variety of molecules when comparing with other codes. We use our method to perform calculations with the B3LYP exchange-correlation functional for models of myoglobin systems bound with O2 and CO ligands and confirm that the same qualitative behaviour is obtained as when the same myoglobin models are studied with the DFT+U approach which is also available in ONETEP. Finally, we confirm the linear-scaling capability of our method by performing calculations on polyethylene and polyacetylene chains of increasing length.
Khanniche, Sarah; Louis, Florent; Cantrel, Laurent; Černušák, Ivan
2016-03-17
To get an insight into the possible reactivity between iodine oxides and CO, a first step was to study the thermochemical properties and kinetic parameters of the reaction between IO and CO using theoretical chemistry tools. All stationary points involved were optimized using the Becke's three-parameter hybrid exchange functional coupled with the Lee-Yang-Parr nonlocal correlation functional (B3LYP) and the Møller-Plesset second-order perturbation theory (MP2). Single-point energy calculations were performed using the coupled cluster theory with the iterative inclusion of singles and doubles and the perturbative estimation for triple excitations (CCSD(T)) and the aug-cc-pVnZ (n = T, Q, and 5) basis sets on geometries previously optimized at the aug-cc-pVTZ level. The energetics was then recalculated using the one-component DK-CCSD(T) approach with the relativistic ANO basis sets. The spin-orbit coupling for the iodine containing species was calculated a posteriori using the restricted active space state interaction method in conjunction with the multiconfigurational perturbation theory (CASPT2/RASSI) employing the complete active space (CASSCF) wave function as the reference. The CCSD(T) energies were also corrected for BSSE for molecular complexes and refined with the extrapolation to CBS limit while the DK-CCSD(T) values were refined with the extrapolation to FCI. The exploration of the potential energy surface revealed a two-steps mechanism with a trans and a cis pathway. The rate constants for the direct and complex mechanism were computed as a function of temperature (250-2500 K) using the canonical transition state theory. The three-parameter Arrhenius expressions obtained for the direct and indirect mechanism at the DK-CCSD(T)-cf level of theory is 1.49 × 10(-17) × T(1.77) exp(-47.4 (kJ mol(-1))/RT).
Fábri, Csaba; Szidarovszky, Tamás; Magyarfalvi, Gábor; Tarczay, György
2011-05-12
Scaling factors for Pulay's scaled quantum mechanical (SQM) scheme have been determined for four different widely used DFT functionals (PBE, B3LYP, B3PW91, and M06-2X) and for two basis sets (6-31++G** and aug-cc-pVTZ) by fitting computed results to 347 fundamental experimental vibrational frequencies of 33 molecules. Measurements in the gas phase and in solid argon matrices were used independently in the fitting procedure in order to provide a simple method of estimating matrix shifts. The accuracy of the new scaling factors is demonstrated on test molecules including hydrogen-bonded systems and molecules containing chlorine and sulfur atoms.
Ulian, Gianfranco; Valdrè, Giovanni
2015-07-01
Pyrophyllite has a significant role in both geophysics as a hydrous phase, which can recycle water into the Earth's mantle, and many industrial applications, such as petroleum and civil engineering. However, very few works have been proposed to fully characterize the thermodynamic properties of this mineral, especially at atomic scale. In the present work, we report structural, vibrational, thermochemical and thermophysical properties of pyrophyllite, calculated at the density functional theory level with the hybrid B3LYP functional, all-electron Gaussian-type orbitals and taking into account a correction to include dispersive forces. V( P, T) data at 300 K fit with isothermal third-order Birch-Murnaghan equations of state and yield K T 0 = 46.57 GPa, K' = 10.51 and V 0 = 213.67 Å3, where K T 0 is the thermal bulk modulus at 0 GPa, K' is the first derivative and V 0 is the volume at zero pressure, in very good agreement with recent experimental results obtained by in situ single-crystal synchrotron XRD. The compressional behaviour is highly anisotropic, with axial compressibility in ratio β( a):β( b):β( c) = 1.218:1.000:4.188. Pyrophyllite bulk modulus, thermal expansion coefficients and heat capacity at different P- T conditions are provided. The results of this kind of analysis can be useful in both geophysical and technological applications of the mineral and expand the high-temperature and high-pressure knowledge of this phase at physical conditions that are still difficult to obtain by experimental means. The simulated vibrational spectrum can also be used as a guideline by other authors in their experimental investigation of pyrophyllite.
Directory of Open Access Journals (Sweden)
Cong Zhang
2015-01-01
Full Text Available Although both battery and super-capacitor are important power sources for hybrid electric vehicles, there is no accurate configuration theory to match the above two kinds of power sources which have significantly different characteristics on energy and power storage for the goal of making good use of their individual features without size wasting. In this paper, a new performance is presented that is used for analysis and optimal design method of battery and super-capacitor for hybrid energy storage system of a parallel hybrid electrical vehicle. In order to achieve optimal design with less consumption, the power-energy function is applied to establish direct mathematical relationship between demand power and the performance. During matching process, firstly, three typical operating conditions are chosen as the basis of design; secondly, the energy and power capacity evaluation methods for the parameters of battery and super-capacitor in hybrid energy storage system are proposed; thirdly, the mass, volume, and cost of the system are optimized simultaneously by using power-energy function. As a result, there are significant advantages on mass, volume, and cost for the hybrid energy storage system with the matching method. Simulation results fit well with the results of analysis, which confirms that the optimized design can meet the demand of hybrid electric vehicle well.
Oshima, Masamitsu; Inoue, Kaoru; Nakajima, Kei; Tachikawa, Tetsuhiko; Yamazaki, Hiromichi; Isobe, Tomohide; Sugawara, Ayaka; Ogawa, Miho; Tanaka, Chie; Saito, Masahiro; Kasugai, Shohei; Takano-Yamamoto, Teruko; Inoue, Takashi; Tezuka, Katsunari; Kuboki, Takuo; Yamaguchi, Akira; Tsuji, Takashi
2014-01-01
Bio-hybrid artificial organs are an attractive concept to restore organ function through precise biological cooperation with surrounding tissues in vivo. However, in bio-hybrid artificial organs, an artificial organ with fibrous connective tissues, including muscles, tendons and ligaments, has not been developed. Here, we have enveloped with embryonic dental follicle tissue around a HA-coated dental implant, and transplanted into the lower first molar region of a murine tooth-loss model. We successfully developed a novel fibrous connected tooth implant using a HA-coated dental implant and dental follicle stem cells as a bio-hybrid organ. This bio-hybrid implant restored physiological functions, including bone remodelling, regeneration of severe bone-defect and responsiveness to noxious stimuli, through regeneration with periodontal tissues, such as periodontal ligament and cementum. Thus, this study represents the potential for a next-generation bio-hybrid implant for tooth loss as a future bio-hybrid artificial organ replacement therapy.
An improved theoretical approach to the empirical corrections of density functional theory
Lii, Jenn-Huei; Hu, Ching-Han
2012-02-01
An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization-dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond ( 1,2-) and angle ( 1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported Δ H f values of the training set containing alkane, alcohol and ether molecules. The Δ H f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in Δ H f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.
Kumar, N V Suresh; Priyakumar, U Deva; Singh, Harjinder; Roy, Saumya; Chakraborty, Tushar Kanti
2012-07-01
Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.
Shukla, Manoj K.; Leszczynski, Jerzy
2010-11-01
A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson-Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson-Crick adenine-thymine and guanine-cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.
DEFF Research Database (Denmark)
Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek
2016-01-01
Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for non-relativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton and xenon dimers and free atoms. Relativistic...
Mesbeh, Radhia; Hamdi, Besma; Zouari, Ridha
2016-12-01
Single crystals of a hybrid organic/inorganic material with the formula [C9H6NOBr2]2CuBr4·2H2O were studied by X-ray diffraction. The compound crystallizes in the monoclinic system, space group C2/c with the following unit cell parameters: a = 7.8201 (12) Ǻ, b = 18.203 (3) Ǻ, c = 19.486 (3) Ǻ, β = 98.330 (5)°, Z = 4, V = 2744.6 (7) Ǻ3. Crystal structure was solved with a final R = 5.66% for 3483 independent reflections. The atomic arrangement shows an alternation of organic and inorganic layers. Between layers, the cohesion is performed via Osbnd H⋯Br, Csbnd H⋯Br, Nsbnd H⋯Br, Nsbnd H⋯O and Osbnd H⋯O hydrogen bending. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) measurements have been carried out on [C9H6NOBr2]2CuBr4·2H2O crystal in the temperature range between 50 and 500 °C. The assignment of the observed bands in the solid state FTIR and Raman spectra of the compound was assisted by the theoretically predicted frequencies and compared with data previously reported for similar compounds. The theoretical geometrical parameters in the ground state have been investigated by density functional theory (DFT) with the B3LYP/LanL2DZ level of theory. The optical properties were investigated by optical absorption and show two bands at 279, 300 nm. The percentages of hydrogen bonding interactions are analyzed by Fingerprint plots of Hirshfeld surface.
Density functional theory predictions of isotropic hyperfine coupling constants.
Hermosilla, L; Calle, P; García de la Vega, J M; Sieiro, C
2005-02-17
The reliability of density functional theory (DFT) in the determination of the isotropic hyperfine coupling constants (hfccs) of the ground electronic states of organic and inorganic radicals is examined. Predictions using several DFT methods and 6-31G, TZVP, EPR-III and cc-pVQZ basis sets are made and compared to experimental values. The set of 75 radicals here studied was selected using a wide range of criteria. The systems studied are neutral, cationic, anionic; doublet, triplet, quartet; localized, and conjugated radicals, containing 1H, 9Be, 11B, 13C, 14N, 17O, 19F, 23Na, 25Mg, 27Al, 29Si, 31P, 33S, and 35Cl nuclei. The considered radicals provide 241 theoretical hfcc values, which are compared with 174 available experimental ones. The geometries of the studied systems are obtained by theoretical optimization using the same functional and basis set with which the hfccs were calculated. Regression analysis is used as a basic and appropriate methodology for this kind of comparative study. From this analysis, we conclude that DFT predictions of the hfccs are reliable for B3LYP/TZVP and B3LYP/EPR-III combinations. Both functional/basis set scheme are the more useful theoretical tools for predicting hfccs if compared to other much more expensive methods.
Energy Technology Data Exchange (ETDEWEB)
Merawa, Mohammadou [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, FR ' IPREM' 2606, BP 27540 IFR-rue Jules Ferry 64075 Pau-Cedex (France); Noel, Yves [Laboratoire de Petrologie et Modelisation des Materiaux et des Processus, Universite P and M Curie Paris 6, 4 place Jussieu 75252 Paris Cedex 05 (France); Civalleri, Bartolomeo [Dipartimento di Chimica IFM, University of Torino, Via Giuria 7, I-10125 Torino (Italy); Brown, Ross [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, FR ' IPREM' 2606, BP 27540 IFR-rue Jules Ferry 64075 Pau-Cedex (France); Dovesi, Roberto [Dipartimento di Chimica IFM, University of Torino, Via Giuria 7, I-10125 Torino (Italy)
2005-01-26
The structural, elastic, vibrational and electronic properties of barium fluorochloride (BaFCl) have been investigated for the first time at the ab initio level, by using the periodic CRYSTAL program. Both Hartree-Fock (HF) and density functional theory (DFT) Hamiltonians have been used, with the latter in its local density (LV), gradient-corrected (PP), and hybrid (B3LYP) versions. All properties, and in particular the phonon frequencies and the elastic constants, are strongly Hamiltonian dependent. The structural features are in reasonable agreement with experiment, the percentage deviation being smaller than 5% in all cases. The B3LYP elastic constants are in good agreement with experiment, whereas LV systematically overestimates them. PP and B3LYP provide the best results for the vibrational frequencies, the mean percentage absolute difference with respect to experiment being 2.9 and 4.3%, for Raman and 4.8 and 6.3%, for infrared mode frequencies, respectively.
Pathak, Arup Kumar; Samanta, Alok Kumar; Maity, Dilip Kumar
2011-04-07
We report conformationally averaged VDEs (VDE(w)(n)) for different sizes of NO(3)(-)·nH(2)O clusters calculated by using uncorrelated HF, correlated hybrid density functional (B3LYP, BHHLYP) and correlated ab intio (MP2 and CCSD(T)) theory. It is observed that the VDE(w)(n) at the B3LYP/6-311++G(d,p), B3LYP/Aug-cc-Pvtz and CCSD(T)/6-311++G(d,p) levels is very close to the experimentally measured VDE. It is shown that the use of calculated results of the conformationally averaged VDE for small-sized solvated negatively-charged clusters and a microscopic theory-based general expression for the same provides a route to obtain the VDE for a wide range of cluster sizes, including bulk.
Density Functional Investigation of Methanethiol and Dimethyl Sulfide Adsorption on Zeolite
Institute of Scientific and Technical Information of China (English)
Renqing Lü; Guangmin Qiu; Chenguang Liu
2006-01-01
The density functional theory and cluster model methods have been employed to investigate the interactions between methanethiol, dimethyl sulfide and zeolites. The molecular complexes formed by adsorption of methanethiol or dimethyl sulfide on silanol H3SiOSi(OH)2OSiH3 with five coordination forms or four coordination forms, and complexes formed by interactions of Br(o)nsted acid sites of bridging hydroxyl H3Si(OH)Al(OH)2OSiH3 with methanethiol or dimethyl sulfide have been investigated. Full optimization and frequency analysis of all cluster models have been carried out using the B3LYP hybrid method at 6-31+G (d,p) basis set level for hydrogen, silicon, aluminum, oxygen,carbon, and sulfur atoms. The structures and energy changes of different coordination forms between methanethiol and H3Si(OH)Al(OH)2OSiH3, dimethyl sulfide and H3Si(OH)Al(OH)2OSiH3, methanethiol and H3SiOSi(OH)2OSiH3, dimethyl sulfide and H3SiOSi(OH)2OSiH3 complexes have been comparatively studied. The calculated results showed the nature of interactions that led to the formation of all complexes was van der Waals force confirmed by an insignificant change of geometric structures and properties. The conclusions that methanethiol and dimethyl sulfide molecules were adsorbed on bridging hydroxyl group prior to silanol group were obtained on the basis of adsorption heat, the most stable adsorption models of a 6 ring structure for interaction between bridging hydroxyl and methanethiol, and a 7 ring structure for interaction between bridging hydroxyl and dimethyl sulfide.
Arakaki, Atsushi; Shimizu, Katsuhiko; Oda, Mayumi; Sakamoto, Takeshi; Nishimura, Tatsuya; Kato, Takashi
2015-01-28
Organisms produce various organic/inorganic hybrid materials, which are called biominerals. They form through the self-organization of organic molecules and inorganic elements under ambient conditions. Biominerals often have highly organized and hierarchical structures from nanometer to macroscopic length scales, resulting in their remarkable physical and chemical properties that cannot be obtained by simple accumulation of their organic and inorganic constituents. These observations motivate us to create novel functional materials exhibiting properties superior to conventional materials--both synthetic and natural. Herein, we introduce recent progress in understanding biomineralization processes at the molecular level and the development of organic/inorganic hybrid materials by these processes. We specifically outline fundamental molecular studies on silica, iron oxide, and calcium carbonate biomineralization and describe material synthesis based on these mechanisms. These approaches allow us to design a variety of advanced hybrid materials with desired morphologies, sizes, compositions, and structures through environmentally friendly synthetic routes using functions of organic molecules.
Density Functional Study on the Mechanism of Collision Reaction among Protons,N2 and Water Vapor
Institute of Scientific and Technical Information of China (English)
SUN,Hao(孙昊); PAN,Xiu-Mei(潘秀梅); ZHAO,Min(赵岷); LIU,Peng-Jun(刘朋军); SU,Zhong-Min(苏忠民); WANG,Rong-Shun(王荣顺)
2004-01-01
The mechanism of collision reaction among protons, N2 and water vapor was theoretically studied using Density Functional Theory. The geometries of reactants, transition states, intermediates and products were optimized at the B3LYP/6-311 + G** level by the BERNY gradient analysis method. Transition states and intermediates have been identified by vibrational frequency analysis. The relationship among reactants, intermediates, transition states and products was affirmed by IRC calculation. The variations of energy and geometry along the IRC-determined reaction paths were described. The possible reaction pathways were represented and the optimal one was decided from the viewpoint of energy.
Dutton, Andrew S; Fukuto, Jon M; Houk, K N
2004-02-09
The mechanism of decomposition of dialkylamino diazeniumdiolate salts, R(2)N[NONO](-)M(+), to form nitric oxide, NO, was explored using theoretical methods. B3LYP/6-311+G(d) density functional theory calculations gave the optimized geometries, and energetics were further evaluated with the high accuracy CBS-QB3 method, when feasible. Relative pK(a) values were estimated using the PCM model for aqueous solvation. The terminal oxygen is the most basic site, followed closely by the internal oxygen. Protonation of these sites does not lead to decomposition. However, protonation of the weakly basic amino nitrogen leads to very rapid decomposition and NO generation.
Directory of Open Access Journals (Sweden)
Ramzan Ullah
2013-01-01
Full Text Available We present terahertz time domain spectra of acrylamide in the frequency range from 0.2 to 2 THz with nearly constant refractive index having an average value of 1.33 and an absorption coefficient. Raman (95–3000 cm−1 and FTIR (450–4000 cm−1 spectra also show good agreement with density functional theory (DFT B3LYP 6-311G++ (3df 3pd calculations except C-H and N-H stretching frequencies even after scaling with scale factor of 0.9679. We use MOLVIB to rescale such frequencies to match experimental values.
Demircioğlu, Zeynep; Kaştaş, Çiğdem Albayrak; Büyükgüngör, Orhan
2015-03-15
A new o-hydroxy Schiff base, (E)-2-[(2-hydroxy-6-methoxybenzylidene)amino]benzonitrile was isolated and investigated by experimental and theoretical methodologies. The solid state molecular structure was determined by X-ray diffraction method. The vibrational spectral analysis was carried out by using FT-IR spectroscopy in the range of 4000-400cm(-)(1). Theoretical calculations were performed by density functional theory (DFT) method using 6-31G(d,p) basis set. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The UV-vis spectrum of the compound was recorded in the region 200-800 nm in several solvents and electronic properties such as excitation energies, and wavelengths were calculated by TD-DFT/B3LYP method. The most prominent transitions were corresponds to π→π∗. Hybrid density functional theory (DFT) was used to investigate the enol-imine and keto-amine tautomers of titled compound. The titled compound showed the preference of enol form, as supported by X-ray and spectroscopic analysis results. The geometric and molecular properties were compaired for both enol-imine and keto-amine forms. Additionally, geometry optimizations in solvent media were performed with the same level of theory by the integral equation formalism polarizable continuum (IEF-PCM). Stability of the molecule arises from hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed using natural bond orbital (NBO) analysis. Mulliken population method and natural population analysis (NPA) have been studied. Also, condensed Fukui function and relative nucleophilicity indices calculated from charges obtained with orbital charge calculation methods (NPA). Molecular electrostatic potential (MEP) and non linear optical (NLO) properties are also examined.
DEFF Research Database (Denmark)
Barsberg, S.; Berg, Rolf W.
2006-01-01
. study of FA in weakly interacting environments. It is the first study of FA vibrational properties based on d. functional theory (DFT/B3LYP), and a recently proposed hybrid approach to the calcn. of fundamental frequencies, which also includes an anharmonic contribution. FA occupies five different...
Oxidative addition of aryl chlorides to monoligated palladium(0): A DFT-SCRF study
DEFF Research Database (Denmark)
Ahlquist, Mårten Sten Gösta; Norrby, Per-Ola
2007-01-01
Oxidative addition of aryl chlorides to palladium has been investigated by hybrid density functional theory methods (B3LYP), including a continuum model describing the solvent implicitly. A series of para-substituted aryl chlorides were studied to see the influence of electronic effects on the re...
Weymuth, Thomas; Chen, Peter; Reiher, Markus
2014-01-01
We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition metal complexes for the assessment of approximate exchange--correlation functionals. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3, B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison to experimental gas-phase data measured with well-known precision. The comparison of all calculated data reveals a large, system-dependent scattering of results with nonnegligible consequences for computational chemistry studies on transition metal compounds. Considering further the comparison with experiment, the non-empirical functionals PBE and TPSS turn out to be among the best functionals for our reference data set. The deviation can be lowered further by including Hartree--Fock exchange. Accordingly, PBE0 and TPSSh are the two most accurate functionals for our test set, but also these functionals exhibit deviations from experiment by up to 50 kJ/mol for individual reactions. A...
Sharma, Divya; Paterson, Martin J
2014-11-01
DFT and MP2 calculations are performed to obtain optimized ground state geometries and binding energies of the cage and the prism conformers of water W6 clusters and Bz-W6 clusters using the aug-cc-pVDZ basis set. The cage conformer of Bz-W6 system is found to be more stable than prism conformer for all range of DFT functionals and MP2. Time dependent-DFT is then used to study UV spectroscopy of Bz, water W6 clusters and Bz-W6 clusters at both the MP2 and wB97XD optimized ground state geometries using the B3LYP, CAM-B3LYP and M06-2X functionals with 6-31++G(d,p) and aug-cc-pVTZ basis sets. Our results predict minor differences in the UV spectroscopy of cage and prism conformers W6 and Bz-W6 clusters that may be observable with high-resolution spectroscopy. The M06-2X and CAM-B3LYP functionals perform consistently with each other. Benzene-mediated excitations of the water W6 cluster towards longer wavelengths above 170 nm are noticed in both the cage and prism geometries of Bz-W6. Benzene is found to be influenced after interacting with the cage and prism W6 geometries, and is seen to undergo a red shift in the main π→π* electronic transition, in which the degeneracy is slightly broken. Charge transfer (CT) states and diffuse Rydberg-type states are also found to play an important role in the spectroscopy of such systems.
Jacobian Elliptic Function Method and Solitary Wave Solutions for Hybrid Lattice Equation
Institute of Scientific and Technical Information of China (English)
WANG Rui-Min; DAI Chao-Qing; ZHANG Jie-Fang
2006-01-01
In this paper, we have successfully extended the Jacobian elliptic function expansion approach to nonlinear differential-difference equations. The Hybrid lattice equation is chosen to illustrate this approach. As a consequence,twelve families of Jacobian elliptic function solutions with different parameters of the Hybrid lattice equation are obtained.When the modulus m → 1 or 0, doubly-periodic solutions degenerate to solitonic solutions and trigonometric function solutions, respectively.
Tuned range separated hybrid functionals for solvated low bandgap oligomers
Energy Technology Data Exchange (ETDEWEB)
Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan [Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth (Germany)
2015-07-21
The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is to use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.
One- and many-electron self-interaction error in local and global hybrid functionals
Schmidt, Tobias; Kümmel, Stephan
2016-04-01
Electronic self-interaction poses a fundamental challenge in density-functional theory. It greatly limits, e.g., the physical interpretation of eigenvalues as electron removal energies. We here investigate whether local hybrid functionals that are designed to be free from one-electron self-interaction lead to occupied Kohn-Sham eigenvalues and orbitals that approximate photoemission observables well. We compare the local hybrid results to the ones from global hybrid functionals that only partially counteract the self-interaction, and to the results that are obtained with a Perdew-Zunger-type self-interaction correction. Furthermore, we check whether being nominally free from one-electron self-interaction translates into a reduced many-electron self-interaction error. Our findings show that this is not the case for the local hybrid functionals that we studied: In practice they are similar to global hybrids in many respects, despite being formally superior. This finding indicates that there is a conceptual difference between the Perdew-Zunger way and the local hybrid way of translating the one-electron condition to a many-electron system. We also point out and solve some difficulties that occur when using local hybrid functionals in combination with pseudopotentials.
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*B. Semire
2012-12-01
Full Text Available Theoretical calculations using Density Functional Theory (DFT were performed on 2,5-bis[4-N,N-diethylaminostyryl]thiophene and its furan and pyrrole derivatives The energy band gaps calculated at B3LYP/6-31G(d level for thiophene derivatives are lower than that of furan and pyrrole analogues. The absorption λmax calculated using DFT was shifted to longer wavelength by replacement of R = CH3 by C2H5 for all studied molecules. The geometries and electronic properties of the compounds were also studied.
Liu, Xing; Wang, Xuefeng; Wang, Qiang; Andrews, Lester
2012-07-02
Infrared spectra of the matrix isolated OMS, OM(η(2)-SO), and OM(η(2)-SO)(η(2)-SO(2)) (M = Ti, Zr, Hf) molecules were observed following laser-ablated metal atom reactions with SO(2) during condensation in solid argon and neon. The assignments for the major vibrational modes were confirmed by appropriate S(18)O(2) and (34)SO(2) isotopic shifts, and density functional vibrational frequency calculations (B3LYP and BPW91). Bonding in the initial OM(η(2)-SO) reaction products and in the OM(η(2)-SO)(η(2)-SO(2)) adduct molecules with unusual chiral structures is discussed.
APPLICATION OF PENALTY FUNCTION METHOD IN ISOPARAMETRIC HYBRID FINITE ELEMENT ANALYSIS
Institute of Scientific and Technical Information of China (English)
CHEN Dao-zheng; JIAO Zhao-ping
2005-01-01
By the aid of the penalty function method, the equilibrium restriction conditions were introduced to the isoparametric hybrid finite element analysis, and the concrete application course of the penalty function method in three-dimensional isoparametric hybrid finite element was discussed. The separated penalty parameters method and the optimal hybrid element model with penalty balance were also presented.The penalty balance method can effectively refrain the parasitical stress on the premise of no additional degrees of freedom. The numeric experiment shows that the presented element not only is effective in improving greatly the numeric calculation precision of distorted grids but also has the universality.
Directory of Open Access Journals (Sweden)
Özgür Alver
2013-01-01
Full Text Available FT-IR and Raman spectra of methacrylamidoantipyrine (MAAP have been reported in the region of 4000–10 cm−1 and 4000–100 cm−1, respectively. The optimized geometric parameters, conformational analysis, normal mode frequencies, and corresponding vibrational assignments of MAAP (C15H17N3O2 have been examined by means of density functional theory (DFT method using the Becke-3-Lee-Yang-Parr (B3LYP exchange-correlation functional and the 6-31G++(d,p basis sets. Vibrational assignments have been made on the basis of potential energy distribution (PED and the thermodynamics functions, and the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO of MAAP have been predicted. Calculations are carried out with the possible seven (amide-1–5 and imide-1-2 conformational isomers of MAAP. Comparison between the experimental and theoretical results indicates that the B3LYP method provides satisfactory evidence for the prediction of vibrational wavenumbers, and the amide-1 conformational isomer is supposed to be the most stable form of MAAP.
López-Vallejo, Fabian; Fragoso-Serrano, Mabel; Suárez-Ortiz, Gloria Alejandra; Hernández-Rojas, Adriana C; Cerda-García-Rojas, Carlos M; Pereda-Miranda, Rogelio
2011-08-05
A protocol for stereochemical analysis, based on the systematic comparison between theoretical and experimental vicinal (1)H-(1)H NMR coupling constants, was developed and applied to a series of flexible compounds (1-8) derived from the 6-heptenyl-5,6-dihydro-2H-pyran-2-one framework. The method included a broad conformational search, followed by geometry optimization at the DFT B3LYP/DGDZVP level, calculation of the vibrational frequencies, thermochemical parameters, magnetic shielding tensors, and the total NMR spin-spin coupling constants. Three scaling factors, depending on the carbon atom hybridizations, were found for the (1)H-C-C-(1)H vicinal coupling constants: f((sp3)-(sp3)) = 0.910, f((sp3)-(sp2)) = 0.929, and f((sp2)-(sp2))= 0.977. A remarkable correlation between the theoretical (J(pre)) and experimental (1)H-(1)H NMR (J(exp)) coupling constants for spicigerolide (1), a cytotoxic natural product, and some of its synthetic stereoisomers (2-4) demonstrated the predictive value of this approach for the stereochemical assignment of highly flexible compounds containing multiple chiral centers. The stereochemistry of two natural 6-heptenyl-5,6-dihydro-2H-pyran-2-ones (14 and 15) containing diverse functional groups in the heptenyl side chain was also analyzed by application of this combined theoretical and experimental approach, confirming its reliability. Additionally, a geometrical analysis for the conformations of 1-8 revealed that weak hydrogen bonds substantially guide the conformational behavior of the tetraacyloxy-6-heptenyl-2H-pyran-2-ones.
Hybrid function method for solving Fredholm and Volterra integral equations of the second kind
Hsiao, Chun-Hui
2009-08-01
Numerical solutions of Fredholm and Volterra integral equations of the second kind via hybrid functions, are proposed in this paper. Based upon some useful properties of hybrid functions, integration of the cross product, a special product matrix and a related coefficient matrix with optimal order, are applied to solve these integral equations. The main characteristic of this technique is to convert an integral equation into an algebraic; hence, the solution procedures are either reduced or simplified accordingly. The advantages of hybrid functions are that the values of n and m are adjustable as well as being able to yield more accurate numerical solutions than the piecewise constant orthogonal function, for the solutions of integral equations. We propose that the available optimal values of n and m can minimize the relative errors of the numerical solutions. The high accuracy and the wide applicability of the hybrid function approach will be demonstrated with numerical examples. The hybrid function method is superior to other piecewise constant orthogonal functions [W.F. Blyth, R.L. May, P. Widyaningsih, Volterra integral equations solved in Fredholm form using Walsh functions, Anziam J. 45 (E) (2004) C269-C282; M.H. Reihani, Z. Abadi, Rationalized Haar functions method for solving Fredholm and Volterra integral equations, J. Comp. Appl. Math. 200 (2007) 12-20] for these problems.
Skin-inspired hydrogel-elastomer hybrids with robust interfaces and functional microstructures
Yuk, Hyunwoo; Zhang, Teng; Parada, German Alberto; Liu, Xinyue; Zhao, Xuanhe
2016-06-01
Inspired by mammalian skins, soft hybrids integrating the merits of elastomers and hydrogels have potential applications in diverse areas including stretchable and bio-integrated electronics, microfluidics, tissue engineering, soft robotics and biomedical devices. However, existing hydrogel-elastomer hybrids have limitations such as weak interfacial bonding, low robustness and difficulties in patterning microstructures. Here, we report a simple yet versatile method to assemble hydrogels and elastomers into hybrids with extremely robust interfaces (interfacial toughness over 1,000 Jm-2) and functional microstructures such as microfluidic channels and electrical circuits. The proposed method is generally applicable to various types of tough hydrogels and diverse commonly used elastomers including polydimethylsiloxane Sylgard 184, polyurethane, latex, VHB and Ecoflex. We further demonstrate applications enabled by the robust and microstructured hydrogel-elastomer hybrids including anti-dehydration hydrogel-elastomer hybrids, stretchable and reactive hydrogel-elastomer microfluidics, and stretchable hydrogel circuit boards patterned on elastomer.
Skin-inspired hydrogel–elastomer hybrids with robust interfaces and functional microstructures
Yuk, Hyunwoo; Zhang, Teng; Parada, German Alberto; Liu, Xinyue; Zhao, Xuanhe
2016-01-01
Inspired by mammalian skins, soft hybrids integrating the merits of elastomers and hydrogels have potential applications in diverse areas including stretchable and bio-integrated electronics, microfluidics, tissue engineering, soft robotics and biomedical devices. However, existing hydrogel–elastomer hybrids have limitations such as weak interfacial bonding, low robustness and difficulties in patterning microstructures. Here, we report a simple yet versatile method to assemble hydrogels and elastomers into hybrids with extremely robust interfaces (interfacial toughness over 1,000 Jm−2) and functional microstructures such as microfluidic channels and electrical circuits. The proposed method is generally applicable to various types of tough hydrogels and diverse commonly used elastomers including polydimethylsiloxane Sylgard 184, polyurethane, latex, VHB and Ecoflex. We further demonstrate applications enabled by the robust and microstructured hydrogel–elastomer hybrids including anti-dehydration hydrogel–elastomer hybrids, stretchable and reactive hydrogel–elastomer microfluidics, and stretchable hydrogel circuit boards patterned on elastomer. PMID:27345380
Biomolecule-nanoparticle hybrids as functional units for nanobiotechnology.
Baron, Ronan; Willner, Bilha; Willner, Itamar
2007-01-28
Biomolecule-metal or semiconductor nanoparticle (NP) hybrid systems combine the recognition and catalytic properties of biomolecules with the unique electronic and optical properties of NPs. This enables the application of the hybrid systems in developing new electronic and optical biosensors, to synthesize nanowires and nanocircuits, and to fabricate new devices. Metal NPs are employed as nano-connectors that activate redox enzymes, and they act as electrical or optical labels for biorecognition events. Similarly, semiconductor NPs act as optical probes for biorecognition processes. Double-stranded DNA or protein chains that are modified with metallic nanoclusters act as templates for the synthesis of metallic nanowires. The nanowires are used as building blocks to assemble nano-devices such as a transistor or a nanotransporter.
Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R
2015-02-25
A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.
Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jurečka, Petr; Sponer, Jiří
2013-05-21
The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-ζ basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as
Functional evaluation of ES-somatic cell hybrids in vitro and in vivo.
Sumer, Huseyin; Kim, Kitai; Liu, Jun; Ng, Kitwa; Daley, George Q; Verma, Paul J
2014-06-01
Embryonic stem cells (ESCs) have previously been reported to reprogram somatic cells following fusion. The resulting ES-somatic cell hybrids have been shown to adopt the transcriptional profile of ESCs, suggesting that the pluripotent program is dominant. ES-somatic cell hybrids have most characteristics of pluripotent cells in vitro; however, it remains unclear whether the somatic genome is an active partner in the hybrid cells or simply retained predominately as silent cargo. Furthermore, the functional properties of ES-somatic cell hybrids in vivo have been limited to studies on their contribution to teratomas and developing embryos/chimeras. The extent of their pluripotency remains largely unclear. Here we determined that the somatic genome is actively transcribed by generating ES-somatic cell hybrids using Rag2-deficient ESCs fused to autologous wild-type somatic cells. Rag2 expression was detected during in vitro differentiation, suggesting that the somatic genome follows the correct temporal cues during differentiation. Furthermore, ES-somatic cell hybrids maintain their tetraploid state following 4 weeks of differentiation in vivo and are immune tolerated when transferred into matched individuals. The ES-somatic cell hybrids can efficiently differentiate into hematopoietic precursors in both myeloid and lymphoid lineages in vitro, suggesting that the somatic genome is actively transcribed following cell fusion based reprogramming. However, the ES-somatic cell hybrids showed an altered hematopoietic potential following in vitro differentiation and were unable to show hematopoietic engraftment in a mouse model.
Saravanan, S; Balachandran, V
2015-03-05
The experimental and theoretical study on the structures and vibrations of 4-hexylacetophenone (abbreviated as 4HAP) are presented. The FT-IR and FT-Raman spectra of the title compound have been recorded in the region 4000-400cm(-1) and 3500-100cm(-1) respectively. The molecular structures, vibrational wavenumbers, infrared intensities and Raman activities were calculated using DFT (B3LYP and LSDA) method with 6-311++G(d,p) basis set. The most stable conformer of 4HAP is identified from the computational results. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMEF). The linear polarizability (α) and the first hyperpolarizability (βtot) values of the investigated molecule have been computed using B3LYP and LSDA with 6-311++G(d,p) basis set. Stability of the molecule arising from hyper conjugative interaction and charge transfer delocalization has been analyzed using natural bond orbital (NBO) analysis. The molecule orbital contributions are studied by density of energy states (DOSs). UV-Vis spectrum and effects of solvents have been discussed effects of solvents have been discussed and the electronic properties such as HOMO and LUMO energies were determined by time-dependent TD-DFT approach. Fukui function and Mulliken analysis on atomic charges of the title compound have been calculated. Finally, electrophilic and nucleophilic descriptors of the title molecule have been calculated.
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Daniel A Barbash
2004-06-01
Full Text Available Interspecific hybrid lethality and sterility are a consequence of divergent evolution between species and serve to maintain the discrete identities of species. The evolution of hybrid incompatibilities has been described in widely accepted models by Dobzhansky and Muller where lineage-specific functional divergence is the essential characteristic of hybrid incompatibility genes. Experimentally tractable models are required to identify and test candidate hybrid incompatibility genes. Several Drosophila melanogaster genes involved in hybrid incompatibility have been identified but none has yet been shown to have functionally diverged in accordance with the Dobzhansky-Muller model. By introducing transgenic copies of the X-linked Hybrid male rescue (Hmr gene into D. melanogaster from its sibling species D. simulans and D. mauritiana, we demonstrate that Hmr has functionally diverged to cause F1 hybrid incompatibility between these species. Consistent with the Dobzhansky-Muller model, we find that Hmr has diverged extensively in the D. melanogaster lineage, but we also find extensive divergence in the sibling-species lineage. Together, these findings implicate over 13% of the amino acids encoded by Hmr as candidates for causing hybrid incompatibility. The exceptional level of divergence at Hmr cannot be explained by neutral processes because we use phylogenetic methods and population genetic analyses to show that the elevated amino-acid divergence in both lineages is due to positive selection in the distant past-at least one million generations ago. Our findings suggest that multiple substitutions driven by natural selection may be a general phenomenon required to generate hybrid incompatibility alleles.
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Hideharu Mori
2012-01-01
Full Text Available This paper presents a short overview of recent advances in the design and synthesis of organic-inorganic hybrids using silsesquioxane-based nanoparticles having nanometer size, relatively narrow size distribution, high functionalities, and various characteristic features, mainly focusing on our recent researches related to the subject. A highlight of this paper is the water-soluble silsesquioxane-based nanoparticles, including hydroxyl-functionalized and cationic silsesquioxanes, which were synthesized via the one-step condensation of the bulky triethoxysilane precursors. The design and synthesis of R-SiO1.5/SiO2 and R-SiO1.5/TiO2 hybrids by hydrolytic cocondensation of a triethoxysilane precursor and metal alkoxides are briefly introduced. This paper also deals with recent results in stimuli-responsive hybrids based on the water-soluble silsesquioxane nanoparticles and fluorinated and amphiphilic silsesquioxane hybrids.
A New Hybrid MGBPSO-GSA Variant for Improving Function Optimization Solution in Search Space
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Narinder Singh
2017-03-01
Full Text Available In this article, a newly hybrid nature-inspired approach (MGBPSO-GSA is developed with a combination of Mean Gbest Particle Swarm Optimization (MGBPSO and Gravitational Search Algorithm (GSA. The basic inspiration is to integrate the ability of exploitation in MGBPSO with the ability of exploration in GSA to synthesize the strength of both approaches. As a result, the presented approach has the automatic balance capability between local and global searching abilities. The performance of the hybrid approach is tested on a variety of classical functions, ie, unimodal, multimodal, and fixed-dimension multimodal functions. Furthermore, Iris data set, Heart data set, and economic dispatch problems are used to compare the hybrid approach with several metaheuristics. Experimental statistical solutions prove empirically that the new hybrid approach outperforms significantly a number of metaheuristics in terms of solution stability, solution quality, capability of local and global optimum, and convergence speed.
Reis, H; Rasulev, B; Papadopoulos, M G; Leszczynski, J
2015-01-01
Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives.
Institute of Scientific and Technical Information of China (English)
Shao Ju-Xiang; Cheng Xin-Lu; Ynag Xiang-Dong; He Bi
2006-01-01
By using the density functional theory (B3LYP) and four highly accurate complete basis set (CBS-Q, CBS-QB3, CBS-Lq, and CBS-4M) ab initio methods, the X(C, N, O)-NO2 bond dissociation energies (BDEs) for ChsNO2, C2H3NO2) C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2 (CH3)2NNO2 are computed. By comparing the computed BDEs and experimental results, it is found that the B3LYP method is unable to predict satisfactorily the results of bond dissociation energy (BDE); however, all four CBS models are generally able to give reliable predication of the X(C, N, O)-NO2 BDEs for these nitro compounds. Moreover, the CBS-4M calculation is the least computationally demanding among the four CBS methods considered. Therefore, we recommend CBS-4M method as a reliable method of computing the BDEs for this nitro compound system.
Rahman, Adhip; Ali, Mohammad Tuhin; Shawan, Mohammad Mahfuz Ali Khan; Sarwar, Mohammed Golam; Khan, Mohammad A K; Halim, Mohammad A
2016-01-01
A series of halogen-directed donepezil drugs has been designed to inhibit acetyl cholinesterase (AChE). Density Functional theory (DFT) has been employed to optimize the chair as well as boat conformers of the parent drug and modified ligands at B3LYP/MidiX and B3LYP/6-311G + (d,p) level of theories. Charge distribution, dipole moment, enthalpy, free energy and molecular orbitals of these ligands are also investigated to understand how the halogen-directed modifications impact the ligand structure and govern the non-bonding interactions with the receptors. Molecular docking calculation has been performed to understand the similarities and differences between the binding modes of unmodified and halogenated chair-formed ligands. Molecular docking indicated donepezil and modified ligands had non-covalent interactions with hydrophobic gorges and anionic subsites of AChE. The -CF3-directed ligand possessed the most negative binding affinity. Non-covalent interactions within the ligand-receptor systems were found to be mostly hydrophobic and π- stacking type. F, Cl and -CF3 containing ligands emerge as effective and selective AChE inhibitors, which can strongly interact with the two active sites of AChE. In addition, we have also investigated selected pharmacokinetic parameters of the parent and modified ligands.
Institute of Scientific and Technical Information of China (English)
刘红飞
2015-01-01
There was a large number of O-H�X(X=N、O、S) hydrogen in thick oil which resulted the poor flowability, high vis-cosity and large intermolecular force. Using a transition metal compound as a catalyst to weaken the hydrogen bond was the primary method of reducing the intermolecular forces. CrCl3 attacking the O-H�X(X=N、O、S) hydrogen to weaken hydrogen was cal-culated with GAUSSIAN 03 package. The density functional method in its hybrid B3LYP functional was used in the calculations. The results showed that the hydrogen bond length was increased, the charge of N, O and S atom transfer, the system front energy gap drop. The hydrogen bonds were effectively weaken by CrCl3.%稠油分子间大量O-H�X(X=N、O、S)氢键，造成其分子间作用力、黏度较大，使用过渡金属化合物作为催化剂削弱氢键是降低分子间作用力的主要方法。采用密度泛函理论B3LYP方法，使用Gaussian 03程序，CrCl3作为催化剂，对稠油间CrCl3-O-H�X(X=N、O、S)氢键的攻击削弱情况进行了计算。结果表明，CrCl3不仅增加了氢键的键长，N、O、S的电荷发生了转移，同时还使得系统的前线能隙下降，有效地削弱了氢键。
Heart visualization based on hybrid transfer function using size and gradient.
Xia, Yong; Liu, Yixuan; Wang, Kuanquan
2014-01-01
Having the ability to visualize the heart clearly and precisely would be beneficial for pathology research, presurgical planning, and clinical approaches. Multi-dimensional transfer functions were employed to improve the overall performance of images. To provide a satisfactory visualization quality on the shape and boundaries of the heart, a new hybrid transfer function combining structure size with gradient was designed to highlight the area of the heart. Initially, a histogram of gradient and histogram of size was computed and then classification was performed for providing the spatial information. Finally, several hybrid strategies were presented for the design of the transfer function, including opacity and color. By experimental evaluation, the proposed hybrid transfer function visualized the cardiac outline and internal structure more clearly and easily.
Hydrogels from Biopolymer Hybrid for Biomedical, Food, and Functional Food Applications
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Robert C. Spiro
2012-04-01
Full Text Available Hybrid hydrogels from biopolymers have been applied for various indications across a wide range of biomedical, pharmaceutical, and functional food industries. In particular, hybrid hydrogels synthesized from two biopolymers have attracted increasing attention. The inclusion of a second biopolymer strengthens the stability of resultant hydrogels and enriches its functionalities by bringing in new functional groups or optimizing the micro-environmental conditions for certain biological and biochemical processes. This article presents approaches that have been used by our groups to synthesize biopolymer hybrid hydrogels for effective uses for immunotherapy, tissue regeneration, food and functional food applications. The research has achieved some challenging results, such as stabilizing physical structure, increasing mucoadhesiveness, and the creation of an artificial extracellular matrix to aid in guiding tissue differentiation.
Fornaro, Teresa; Carnimeo, Ivan; Biczysko, Malgorzata
2015-05-28
Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra- and intermolecular interactions that may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size or is placed in a complex environment, such as condensed phases. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes, with increasing complexity toward condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely polycrystalline uracil. First we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) whereas the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes. The good agreement between the
Coccia, Emanuele; Guidoni, Leonardo
2014-01-01
In this letter we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) {\\AA}, larger than the values obtained by DFT (PBE, B3LYP and CAM-B3LYP) and shorter than that calculated at the Hartree-Fock (HF) level. TDDFT and EOM-CCSD calculations on a reduced peridinin model confirm the HOMO-LUMO major contribution of the Bu+-like (S2) bright excited state. Many Body Green's Function Theory (MBGFT) calculations of the vertical excitation energy of the Bu+-like state for the VMC structure (VMC/MBGFT) provide excitation energy of 2.62 eV, in agreement with experimental results in n-hexane (2.72 eV). The dependence of the excitation energy on the bond length alternation in the MBGFT and TDDFT calculations with different functionals is discussed.
Ovchinnikov, Vasily A; Sundholm, Dage
2014-04-21
The 0-0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations. Excitation energies have also been calculated at the linear-response time-dependent density functional theory (TDDFT) level using the B3LYP functional. Large basis sets have been employed for ensuring that the obtained excitation energies are close to the basis-set limit. Zero-point vibrational energy corrections have been calculated at the B3LYP and CC2 levels for the ground and excited states rendering direct comparisons with high-precision spectroscopy measurements feasible. The obtained excitation energies for the 0-0 transitions of the first excited states of guanine tautomers are in good agreement with experimental values confirming the experimental assignment of the energetic order of the tautomers of the DNA bases. For the experimentally detected guanine tautomers, the first excited state corresponds to a π→π* transition, whereas for the tautomers of adenine, thymine, and the lowest tautomer of cytosine the transition to the first excited state has n →π* character. The calculations suggest that the 0-0 transitions of adenine, thymine, and cytosine are not observed in the absorption spectrum due to the weak oscillator strength of the formally symmetry-forbidden transitions, while 0-0 transitions of thymine have been detected in fluorescence excitation spectra.
Saravanan, S. P.; Sankar, A.; Parimala, K.
2017-01-01
The complete structural and vibrational analysis of the 2,5-Difluoronitrobenzene (DNB) was carried out by Hartree-Fock (HF) and density functional theory (DFT) method (B3LYP) with 6-311++G (d,p) basis set. The fundamental vibrations are assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. Using the time-dependent density functional theory (TD-DFT) method, electronic absorption spectra of the title compound have been predicted and a good agreement with the experimental ones is determined. 13C and 1H NMR spectra were recorded and chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The hyperconjugative interaction energy (E(2)) and electron densities of donor (i) and acceptor (j) bonds were calculated using natural bond orbital (NBO) analysis. In addition, molecular electrostatic potential (MEP) and atomic charges were calculated using B3LYP/6-311++G (d,p) level of theory. Moreover, thermodynamic properties (heat capacities, entropy, enthalpy and Gibb's free energy) of the title compound at different temperatures were calculated.
Pandey, Manju; Muthu, S.; Nanje Gowda, N. M.
2017-02-01
Theoretical analysis of the molecular structure, spectroscopic (FT-IR, FT-Raman, 1H, 13C NMR, UV-Vis) studies, and thermodynamic characteristics of 5-Methoxy-1H-benzo[d]imidazole-2(3H)-thione (5MBIT) molecule were done by DFT/B3LYP using 6-311++G(d, p) basis set. Theoretical parameters were compared with experimental data. The dipole moment (μ), polarizability (Δα) and first order hyperpolarizability (β) of the molecule were calculated. Thermodynamic properties, HOMO and LUMO energies were determined. Global reactivity parameters and Fukui function of the 5MBIT molecule were predicted.
Chai, Jeng-Da
2016-01-01
We propose hybrid schemes incorporating exact exchange into thermally-assisted-occupation density functional theory (TAO-DFT) [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)] for an improved description of nonlocal exchange effects. With a few simple modifications, global and range-separated hybrid functionals in Kohn-Sham density functional theory (KS-DFT) can be combined seamlessly with TAO-DFT. In comparison with global hybrid functionals in KS-DFT, the resulting global hybrid functionals in TAO-DFT yield promising performance for systems with strong static correlation effects (e.g., the H2 dissociation and electronic properties of linear acenes), while maintaining similar performance for systems without strong static correlation effects. Besides, a reasonably accurate description of noncovalent interactions can be efficiently achieved through the inclusion of dispersion corrections in hybrid TAO-DFT. Relative to TAO-DFAs (i.e., TAO-DFT with the conventional density functional approximations), global hybrid...
A Comparative Study of Several Hybrid Particle Swarm Algorithms for Function Optimization
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Yanhua Zhong
2012-11-01
Full Text Available Currently, the researchers have made a lot of hybrid particle swarm algorithm in order to solve the shortcomings that the Particle Swarm Algorithms is easy to converge to local extremum, these algorithms declare that there has been better than the standard particle swarm. This study selects three kinds of representative hybrid particle swarm optimizations (differential evolution particle swarm optimization, GA particle swarm optimization, quantum particle swarm optimization and the standard particle swarm optimization to test with three objective functions. We compare evolutionary algorithm performance by a fixed number of iterations of the convergence speed and accuracy and the number of iterations under the fixed convergence precision; analyzing these types of hybrid particle swarm optimization results and practical performance. Test results show hybrid particle algorithm performance has improved significantly.
A Comparative Study of Several Hybrid Particle Swarm Algorithms for Function Optimization
Directory of Open Access Journals (Sweden)
Yanhua Zhong
2013-01-01
Full Text Available Currently, the researchers have made a lot of hybrid particle swarm algorithm in order to solve the shortcomings that the Particle Swarm Algorithms is easy to converge to local extremum, these algorithms declare that there has been better than the standard particle swarm. This study selects three kinds of representative hybrid particle swarm optimizations (differential evolution particle swarm optimization, GA particle swarm optimization, quantum particle swarm optimization and the standard particle swarm optimization to test with three objective functions. We compare evolutionary algorithm performance by a fixed number of iterations of the convergence speed and accuracy and the number of iterations under the fixed convergence precision, analyzing these types of hybrid particle swarm optimization results and practical performance. Test results show hybrid particle algorithm performance has improved significantly.
Kashinski, D O; Chase, G M; Nelson, R G; Di Nallo, O E; Scales, A N; VanderLey, D L; Byrd, E F C
2017-03-23
We propose new approximate global multiplicative scaling factors for the DFT calculation of ground state harmonic vibrational frequencies using functionals from the TPSS, M06, and M11 functional families with standard correlation consistent cc-pVxZ and aug-cc-pVxZ (x = D, T, and Q), 6-311G split valence family, Sadlej and Sapporo polarized triple-ζ basis sets. Results for B3LYP, CAM-B3LYP, B3PW91, PBE, and PBE0 functionals with these basis sets are also reported. A total of 99 harmonic frequencies were calculated for 26 gas-phase organic and nonorganic molecules typically found in detonated solid propellant residue. Our proposed approximate multiplicative scaling factors are determined using a least-squares approach comparing the computed harmonic frequencies to experimental counterparts well established in the scientific literature. A comparison of our work to previously published global scaling factors is made to verify method reliability and the applicability of our molecular test set.
Toward a Representation of Hybrid Functional Petri Nets by MP Systems
Castellini, Alberto; Franco, Giuditta; Manca, Vincenzo
In this work we analyse and compare Hybrid Functional Petri Nets [10], an extension of Petri Nets [12] for biopathways simulation, and Metabolic P Systems [8,9]. An introduction to both of them is given, together with highlights about respective similarities and differences for biopathways modelling. The case study of glycolytic pathway with the lac operon gene regulatory mechanism was modeled by traditional Petri Nets in [6] and recently by Hybrid Functional Petri Nets in [10,4]. This model is here mapped into an MP system having the same dynamics.
Hybridization State Detection of DNA-Functionalized Gold Nanoparticles Using Hyperspectral Imaging
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Richard C. Murdock
2017-01-01
Full Text Available Hyperspectral imaging has the unique ability of capturing spectral data for multiple wavelengths at each pixel in an image. This gives the ability to distinguish, with certainty, different nanomaterials and/or distinguish nanomaterials from biological materials. In this study, 4 nm and 13 nm gold nanoparticles (Au NPs were synthesized, functionalized with complimentary oligonucleotides, and hybridized to form large networks of NPs. Scattering spectra were collected from each sample (unfunctionalized, functionalized, and hybridized and evaluated. The spectra showed unique peaks for each size of Au NP sample and also exhibited narrowing and intensifying of the spectra as the NPs were functionalized and then subsequently hybridized. These spectra are different from normal aggregation effects where the LSPR and reflected spectrum broaden and are red-shifted. Rather, this appears to be dependent on the ability to control the interparticle distance through oligonucleotide length, which is also investigated through the incorporation of a poly-A spacer. Also, hybridized Au NPs were exposed to cells with no adverse effects and retained their unique spectral signatures. With the ability to distinguish between hybridization states at nearly individual NP levels, this could provide a new method of tracking the intracellular actions of nanomaterials as well as extracellular biosensing applications.
Hybrid input function estimation using a single-input-multiple-output (SIMO) approach
Su, Yi; Shoghi, Kooresh I.
2009-02-01
A hybrid blood input function (BIF) model that incorporates region of interests (ROIs) based peak estimation and a two exponential tail model was proposed to describe the blood input function. The hybrid BIF model was applied to the single-input-multiple-output (SIMO) optimization based approach for BIF estimation using time activity curves (TACs) obtained from ROIs defined at left ventricle (LV) blood pool and myocardium regions of dynamic PET images. The proposed BIF estimation method was applied with 0, 1 and 2 blood samples as constraints for BIF estimation using simulated small animal PET data. Relative percentage difference of the area-under-curve (AUC) measurement between the estimated BIF and the true BIF was calculated to evaluate the BIF estimation accuracy. SIMO based BIF estimation using Feng's input function model was also applied for comparison. The hybrid method provided improved BIF estimation in terms of both mean accuracy and variability compared to Feng's model based BIF estimation in our simulation study. When two blood samples were used as constraints, the percentage BIF estimation error was 0.82 +/- 4.32% for the hybrid approach and 4.63 +/- 10.67% for the Feng's model based approach. Using hybrid BIF, improved kinetic parameter estimation was also obtained.
Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-
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Wei Li
2009-07-01
Full Text Available The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A' electronic state for neutral molecule and 4A' state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad, the vertical electron affinity (EAvert, and the vertical detachment energy (VDE. The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om (m = 1-4 and De- (BrO4F- → BrO4-mF- + Om and BrO4F- → BrO4-mF + Om- are predicted. The adiabatic electron affinities (EAad were predicted to be 4.52 eV for F-Br…O2…O2 (3A'← 4A' (B3LYP method.
Alpaslan, Gökhan; Macit, Mustafa
2014-03-01
The Schiff base compound (E)-1-((3-methoxyphenylimino)methyl)naphthalen-2-ol was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 3-methoxyaniline. The structural properties of the compound has been characterized by using FT-IR, UV-vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the phenol-imine tautomeric form. The molecular geometry, vibrational frequencies of the compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the 6-311++G(d,p) basis set, and compared with the experimental data. The obtained results show that the optimized molecular geometry is well reproduce the crystal structure. The theoretical vibrational frequencies are in good agreement with the experimental values. The calculations of electronic absorption spectra of tautomeric forms of the compound were performed by using TD-DFT calculations both in the gas phase and ethanol solvent. To investigate the tautomeric stability, optimization calculations at the B3LYP/6-311++G(d,p) level were performed for the phenol-imine and keto-amine forms of the compound. According to calculated results, the OH form is more stable than NH form. In addition, molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO), thermodynamic and, non-linear optical (NLO) properties of the compound were investigated using same theoretical calculations.
Jone Pradeepa, S; Sundaraganesan, N
2014-05-05
In this present investigation, the collective experimental and theoretical study on molecular structure, vibrational analysis and NBO analysis has been reported for 2-aminofluorene. FT-IR spectrum was recorded in the range 4000-400 cm(-1). FT-Raman spectrum was recorded in the range 4000-50 cm(-1). The molecular geometry, vibrational spectra, and natural bond orbital analysis (NBO) were calculated for 2-aminofluorene using Density Functional Theory (DFT) based on B3LYP/6-31G(d,p) model chemistry. (13)C and (1)H NMR chemical shifts of 2-aminofluorene were calculated using GIAO method. The computed vibrational and NMR spectra were compared with the experimental results. The total energy distribution (TED) was derived to deepen the understanding of different modes of vibrations contributed by respective wavenumber. The experimental UV-Vis spectra was recorded in the region of 400-200 nm and correlated with simulated spectra by suitably solvated B3LYP/6-31G(d,p) model. The HOMO-LUMO energies were measured with time dependent DFT approach. The nonlinearity of the title compound was confirmed by hyperpolarizabilty examination. Using theoretical calculation Molecular Electrostatic Potential (MEP) was investigated.
Organic/inorganic hybrid nanomaterials with vitamin B12 functions
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Yoshio Hisaeda, Takahiro Masuko, Erika Hanashima and Takashi Hayashi
2006-01-01
Full Text Available A hybrid nanomaterial was prepared by human serum albumin (HSA and vitamin B12 derivatives. The incorporation of hydrophobic vitamin B12 derivatives, which have ester groups in place of the peripheral amide moieties of the natural cobalamin, into HSA is primarily controlled by the hydrophobicity of the peripheral ester groups. Microenvironmental property around the hydrophobic vitamin B12 in HSA was examined by fluorescence and fluorescence polarization measurements. The hydrophobic vitamin B12 itself in HSA is in a microenvironment equivalent in medium polarity to dichloromethane. The molecular motion of hydrophobic vitamin B12 in HSA was markedly suppressed under such microenvironmental conditions. Carbon-skeleton rearrangement reaction of an alkyl radical derived from an alkyl ligand bound to the hydrophobic vitamin B12 was markedly favored in HSA aqueous solution, relative to the reactions in methanol and benzene. The 1,2-migration of the electron-withdrawing group arises from both the suppression of molecular motion and desolvation effects on the alkylated hydrophobic vitamin B12 in HSA.
Mesoporous silica nanotubes hybrid membranes for functional nanofiltration
Energy Technology Data Exchange (ETDEWEB)
El-Safty, Sherif A; Shahat, Ahmed; Mekawy, Moataz; Nguyen, Hoa; Warkocki, Wojciech; Ohnuma, Masato, E-mail: sherif.elsafty@nims.go.jp, E-mail: sherif@aoni.waseda.jp [National Institute for Materials Science, Exploratory Materials Research Laboratory for Energy and Environment, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047 (Japan)
2010-09-17
The development of nanofiltration systems would greatly assist in the production of well-defined particles and biomolecules with unique properties. We report a direct, simple synthesis of hexagonal silica nanotubes (NTs), which vertically aligned inside anodic alumina membranes (AAM) by means of a direct templating method of microemulsion phases with cationic surfactants. The direct approach was used as soft templates for predicting ordered assemblies of surfactant/silica composites through strong interactions within AAM pockets. Thus, densely packed NTs were successfully formed in the entirety of the AAM channels. These silica NTs were coated with layers of organic moieties to create a powerful technique for the ultrafine filtration. The resulting modified-silica NTs were chemically robust and showed affinity toward the transport of small molecular particles. The rigid silica NTs inside AAM channels had a pore diameter of {<=} 4 nm and were used as ultrafine filtration systems for noble metal nanoparticles (NM NPs) and semiconductor nanocrystals (SC NCs) fabricated with a wide range of sizes (1.0-50 nm) and spherical/pyramidal morphologies. Moreover, the silica NTs hybrid membranes were also found to be suitable for separation of biomolecules such as cytochrome c (CytC). Importantly, this nanofilter design retains high nanofiltration efficiency of NM NPs, SC NCs and biomolecules after a number of reuse cycles. Such retention is crucial in industrial applications.
A hybrid method for the parallel computation of Green's functions
DEFF Research Database (Denmark)
Petersen, Dan Erik; Li, Song; Stokbro, Kurt;
2009-01-01
Quantum transport models for nanodevices using the non-equilibrium Green's function method require the repeated calculation of the block tridiagonal part of the Green's and lesser Green's function matrices. This problem is related to the calculation of the inverse of a sparse matrix. Because...
Hybrid density functional theory LCAO calculations on phonons in Ba (Ti,Zr,Hf) O3
Evaestov, Robert A
2010-01-01
Phonon frequencies at {\\Gamma},X,M,R-points of Brilloin zone in cubic phase of Ba(Ti,Zr,Hf)O3 were first time calculated by frozen phonon method using density functional theory (DFT) with hybrid exchange correlation functional PBE0. The calculations use linear combination of atomic orbitals (LCAO) basis functions as implemented in CRYSTAL09 computer code. The Powell algorithm was applied for basis set optimization. In agreement with the experimental observations the structural instability via...
Yan, Bing; Qian, Kai
2009-01-01
A series of novel photoactive hybrid materials with organic parts covalently linked to inorganic parts via the acylamino group have been assembled by sol-gel process. The organic parts as molecular bridge derive from alpha-hydroxypyridine (HP) functionalized by 3-(triethoxysilyl)-propyl isocyanate (TESPIC). Finally homogeneous, molecular-based hybrid materials with different microstructure (uniform spherical or clubbed) are obtained, in which no phase separation is observed. This may be ascribed as the different coordination behavior of metal ions (Eu3+ (Tb3+) or Zn2+). Red emission of Eu-HP-Si, green emission of Tb-HP-Si and violet-blue luminescence of Zn-HP-Si hybrids can be achieved within these molecular-based hybrid materials. Besides, both Eu(Tb) and Zn are introduced into the same hybrid systems (Eu(Zn)-HP-Si or Tb(Zn)-HP-Si) through the covalent Si-O bond, whose sphere particle size can be modified. Especially the photoluminescence behavior can be enhanced, suggesting that intramolecular energy transfer takes place between inert Zn2+ and Eu3+ (Tb3+) in the covalently bonded hybrid systems.
Falcaro, Paolo; Costacurta, Stefano; Malfatti, Luca; Buso, Dario; Patelli, Alessandro; Schiavuta, Piero; Piccinini, Massimo; Grenci, Gianluca; Marmiroli, Benedetta; Amenitsch, Heinz; Innocenzi, Plinio
2011-02-01
A phenyl-based hybrid organic - inorganic coating has been synthesized and processed by hard X-ray lithography. The overall lithography process is performed in a two-step process only (X-rays exposure and chemical etching). The patterns present high aspect ratio, sharp edges, and high homogeneity. The coating has been doped with a variety of polycyclic aromatic hydrocarbon functional molecules, such as anthracene, pentacene, and fullerene. For the first time, hard X-rays have been combined with thick hybrid functional coatings, using the sol-gel thick film directly as resist. A new technique based on a new material combined with hard X-rays is now available to fabricate optical devices. The effect due to the high-energy photon exposure has been investigated using FT-IR and Raman spectroscopy, laser scanner, optical profilometer, and confocal and electron microscope. High-quality thick hybrid fullerene-doped microstructures have been fabricated.
Rahman, Taj Ur; Uddin, Ghias; Nisa, Riffat Un; Ludwig, Ralf; Liaqat, Wajiha; Mahmood, Tariq; Mohammad, Ghulam; Choudhary, M Iqbal; Ayub, Khurshid
2015-09-05
A new isoflavone 7-hydroxy 3'-methoxyisoflavone (1) is isolated from the seeds of Indigofera heterantha. The structure of this new compound was established using spectroscopic techniques such as ID, 2D NMR, and mass spectrometry. Density functional theory calculations are carried out for the first time for geometric, electronic and spectroscopic properties of 1 (isoflavone). DFT calculations have been performed at B3LYP/6-311G(d,p) level of theory for obtaining geometric and spectroscopic properties of compound 1. The simulated vibrational spectrum of compound 1 at B3LYP/6-311G(d,p) shows nice correlation with the experimental IR spectrum after a scaling factor of 0.973. (1)H and (13)C NMR chemical shifts were calculated using Cramer's re-parameterized function WP04 at 6-311G(d,p) basis set, and show nice correlation with the experimental data. Four conformers were considered for NMR chemical shift calculations. Electronic properties such as band gap, Ionization potential and electron affinities were also simulated for the first time; however, no comparison could be made with the experiment.
Hydroxyapatite-Functionalized Graphene: A New Hybrid Nanomaterial
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C. Rodríguez-González
2014-01-01
Full Text Available Graphene oxide sheets (GO were functionalized with hydroxyapatite nanoparticles (nHAp through a simple and effective hydrothermal treatment and a novel physicochemical process. Microstructure and crystallinity were investigated by Fourier transform infrared spectroscopy (FT-IR, Raman spectroscopy, X-ray diffraction (XRD, ultraviolet-visible (UV-Vis absorption spectroscopy, and thermogravimetric analysis (TGA. Transmission electron microscopy (TEM and scanning electron microscopy (SEM were performed to characterize the morphology of the functionalized material. The resulting novel materials combine the biocompatibility of the nHAp with the strength and physical properties of the graphene.
A hybrid fuzzy MCDM approach to maintenance Quality Function Deployment
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Davy George Valavi
2015-01-01
Full Text Available Maintenance Quality Function Deployment (MQFD is a model, which enhances the synergic power of Quality Function Deployment (QFD and Total Productive Maintenance (TPM. One of the crucial and important steps during the implementation of MQFD is the determination of the importance or weightages of the critical factors (CF and sub factors (SF. The CFs and SFs have to be compared precisely for the successful implementation of MQFD. The crisp pair-wise comparison in the conventional Analytical Hierarchy Process (AHP may be insufficient to determine the degree of weightage of CFs and SFs where vagueness and uncetainties are associated. In this paper, a modification of AHP based MQFD by incorporating fuzzy operations is proposed, which can improve the accuracy of determination of the weightages. A case study showing the applicability of this method is illustrated in this paper.
Functionally Graded Multifunctional Hybrid Composites for Extreme Environments
2010-02-01
1AXn Phases (n = 1, 2 and 3) 211 312 413 Barsoum and El-Raghy, American Scientist 2001 Barsoum and El-Raghy, Met. Mat. Trans., 1999 Jeitschko and...layer Ti2AlC Ti2AlC block after hammer blows Ti3SiC2 1. Barsoum and El-Raghy, American Scientist , 2001 2. www.3one2.com AFOSR-MURI Functionally
Use of discrete Wigner functions in the study of a hybrid dissipative system
Reboiro, M.; Civitarese, O.; Ramirez, R.; Tielas, D.
2017-09-01
The persistence of coherence in a hybrid dissipative system, which is composed of superconducting flux-qubits (SFQs) and an electron ensemble, is analyzed. Both the interactions between the electrons and the SFQs are taken into account. The time evolution of the hybrid system is discussed in terms of the discrete Wigner function of each subsystem and in terms of the entropic uncertainty relations. The inclusion of a linewidth, both for the electrons and the SFQs, influences the coherence of each subsystem and the pattern of spin squeezing of the corresponding steady state.
Fessler, J A
1995-01-01
This paper describes rapidly converging algorithms for computing attenuation maps from Poisson transmission measurements using penalized-likelihood objective functions. We demonstrate that an under-relaxed cyclic coordinate-ascent algorithm converges faster than the convex algorithm of Lange (see ibid., vol.4, no.10, p.1430-1438, 1995), which in turn converges faster than the expectation-maximization (EM) algorithm for transmission tomography. To further reduce computation, one could replace the log-likelihood objective with a quadratic approximation. However, we show with simulations and analysis that the quadratic objective function leads to biased estimates for low-count measurements. Therefore we introduce hybrid Poisson/polynomial objective functions that use the exact Poisson log-likelihood for detector measurements with low counts, but use computationally efficient quadratic or cubic approximations for the high-count detector measurements. We demonstrate that the hybrid objective functions reduce computation time without increasing estimation bias.
Directory of Open Access Journals (Sweden)
Imanelakehal
2016-05-01
Full Text Available Complex of cerium (III with (E-N-benzylidene-4-methoxyaniline is synthesized through a one-pot three-componentreaction from aromatical dehyde, aromatic amine and the CeCl3· 7 H2O, as an efficient catalyst. This cerium(IIIcom- plexis characterized by IR, 1H, and 13 CNMR-spectros copy and mass-spectraldata. Molecular structure, Mullikan charges, thermodynamic parameters; vibrational frequencies and intensities were calculated by Density Functional theory methods (B3LYP,B3PW91,mPW1PW91 and PBEPBE using the SDD basis set. The comparison between the calculated and experimental data inorder to attain the best quality and to predict the structure, the best perfor-mance in the vibration spectra perfected of the title compound,we have found that the harmonic vibration computed are in a good agreement with the observed in IRspectrum, for closest match we calculated optimal scaling factors can recommend for the IR spectral future predictions for unknown compounds of this class. In order to better comparison, we also root meansqu are values of the experimental and calculated IR bands are 16.64,16.64,17.45,17.66 and the mean absolute percentage error values are1.33,1.39,1.40, and 1.5forB3LYP, B3PW91,mPW1PW91, and PBEPBE methods respectively
Zheng, Xiaoyan; Wang, Xueye; Shen, Keqi; Miao, Yuan; Ouyang, Dan
2011-10-01
Theoretical studies of an unsymmetrical calix[4]-crown-5-N-azacrown-5 (1) in a fixed 1,3-alternate conformation and the complexes 1·K(+)(a), 1·K(+)(b), 1·K(+)(c) and 1·K(+)K(+) were performed using density functional theory (DFT) at the B3LYP/6-31G level. The fully optimized geometric structures of the free macroligand and its 1:1 and 1:2 complexes, as obtained from DFT calculations, were used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal-ligand and cation-π interactions were investigated. NBO analysis indicated that the stabilization interaction energies (E (2)) for O…K(+) and N…K(+) are larger than the other intermolecular interactions in each complex. The significant increase in electron density in the RY or LP orbitals of K(+) results in strong host-guest interactions. In addition, the intermolecular interaction thermal energies (ΔE, ΔH, ΔG) were calculated by frequency analysis at the B3LYP/6-31G level. For all structures, the most pronounced changes in the geometric parameters upon interaction are observed in the calix[4]arene molecule. The results indicate that both the intermolecular electrostatic interactions and the cation-π interactions between the metal ion and π orbitals of the two pairs that face the inverted benzene rings play a significant role.
Range-separated double-hybrid density-functional theory applied to periodic systems
Sansone, Giuseppe; Civalleri, Bartolomeo; Usvyat, Denis; Toulouse, Julien; Sharkas, Kamal; Maschio, Lorenzo
2015-01-01
International audience; Quantum chemistry methods exploiting density-functional approximations for short-range electron-electron interactions and second-order M{{\\o}}ller-Plesset (MP2) perturbation theory for long-range electron-electron interactions have been implemented for periodic systems using Gaussian-type basis functions and the local correlation framework. The performance of these range-separated double hybrids has been benchmarked on a significant set of systems including rare-gas, m...
A Numerical Method for Lane-Emden Equations Using Hybrid Functions and the Collocation Method
Directory of Open Access Journals (Sweden)
Changqing Yang
2012-01-01
Full Text Available A numerical method to solve Lane-Emden equations as singular initial value problems is presented in this work. This method is based on the replacement of unknown functions through a truncated series of hybrid of block-pulse functions and Chebyshev polynomials. The collocation method transforms the differential equation into a system of algebraic equations. It also has application in a wide area of differential equations. Corresponding numerical examples are presented to demonstrate the accuracy of the proposed method.
Garavand, Ali; Dadkhah Tehrani, Abbas
2016-11-05
Organic-inorganic functional hybrid materials play a major role in the development of advanced functional materials and recently have gained growing interest of the worldwide community. In this context, new hybrid organic-inorganic gel consisting of cellulose nanowhisker xanthate (CNWX) and S-H functionalized polypseudorotaxane (PPR) as organic parts of gel and gold nanorods (GNRs) as inorganic cross-linking agent were prepared. Firstly, thiolated α-cyclodextrin (α-CD-SH) was threaded onto poly-(ethylene glycol) bis (mercaptoethanoate ester) (PEG-SH) to give polypseudorotaxane (PPR) and then it reacted with GNRs in the presence of CNWX to give the new hybrid gel material. The new synthesized gel and its components characterized by spectroscopic measurement methods such as FT-IR, UV-vis and NMR spectroscopy. Interestingly, hybrid gel showed new polygonal plate like morphology with 45-60nm thickness and 400-600nm width. The obtained gel may have potential application in many fields especially in biomedical applications.
Thermochemical Storage of Middle Temperature Wasted Heat by Functionalized C/Mg(OH2 Hybrid Materials
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Emanuela Mastronardo
2017-01-01
Full Text Available For the thermochemical performance implementation of Mg(OH2 as a heat storage medium, several hybrid materials have been investigated. For this study, high-performance hybrid materials have been developed by exploiting the authors’ previous findings. Expanded graphite (EG/carbon nanotubes (CNTs-Mg(OH2 hybrid materials have been prepared through Mg(OH2 deposition-precipitation over functionalized, i.e., oxidized, or un-functionalized EG or CNTs. The heat storage performances of the carbon-based hybrid materials have been investigated through a laboratory-scale experimental simulation of the heat storage/release cycles, carried out by a thermogravimetric apparatus. This study offers a critical evaluation of the thermochemical performances of developed materials through their comparison in terms of heat storage and output capacities per mass and volume unit. It was demonstrated that both EG and CNTs improves the thermochemical performances of the storage medium in terms of reaction rate and conversion with respect to pure Mg(OH2. With functionalized EG/CNTs-Mg(OH2, (i the potential heat storage and output capacities per mass unit of Mg(OH2 have been completely exploited; and (ii higher heat storage and output capacities per volume unit were obtained. That means, for technological applications, as smaller volume at equal stored/released heat.
Energy Technology Data Exchange (ETDEWEB)
Lee, Sang Uck [Univ. of Ulsan, Ulsan (Korea, Republic of)
2013-08-15
The accurate prediction of vertical excitation energies is very important for the development of new materials in the dye and pigment industry. A time-dependent density functional theory (TD-DFT) approach coupled with 22 different exchange-correlation functionals was used for the prediction of vertical excitation energies in the halogenated copper phthalocyanine molecules in order to find the most appropriate functional and to determine the accuracy of the prediction of the absorption wavelength and observed spectral shifts. Among the tested functional, B3LYP functional provides much more accurate vertical excitation energies and UV-vis spectra. Our results clearly provide a benchmark calibration of the TD-DFT method for phthalocyanine based dyes and pigments used in industry.
Hybrid model decomposition of speech and noise in a radial basis function neural model framework
DEFF Research Database (Denmark)
Sørensen, Helge Bjarup Dissing; Hartmann, Uwe
1994-01-01
applied is based on a combination of the hidden Markov model (HMM) decomposition method, for speech recognition in noise, developed by Varga and Moore (1990) from DRA and the hybrid (HMM/RBF) recognizer containing hidden Markov models and radial basis function (RBF) neural networks, developed by Singer...... and Lippmann (1992) from MIT Lincoln Lab. The present authors modified the hybrid recognizer to fit into the decomposition method to achieve high performance speech recognition in noisy environments. The approach has been denoted the hybrid model decomposition method and it provides an optimal method...... for decomposition of speech and noise by using a set of speech pattern models and a noise model(s), each realized as an HMM/RBF pattern model...
Combined hybrid functional and DFT+U calculations for metal chalcogenides
Energy Technology Data Exchange (ETDEWEB)
Aras, Mehmet; Kılıç, Çetin, E-mail: cetin-kilic@gyte.edu.tr [Department of Physics, Gebze Institute of Technology, Gebze, Kocaeli 41400 (Turkey)
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.
Li, Haiqing; Song, Sing I; Song, Ga Young; Kim, Il
2014-02-01
Carbon nanostructures (CNSs) such as carbon nanotubes, graphene sheets, and nanodiamonds provide an important type of substrate for constructing a variety of hybrid nanomaterials. However, their intrinsic chemistry-inert surfaces make it indispensable to pre-functionalize them prior to immobilizing additional components onto their surfaces. Currently developed strategies for functionalizing CNSs include covalent and non-covalent approaches. Conventional covalent treatments often damage the structure integrity of carbon surfaces and adversely affect their physical properties. In contrast, the non-covalent approach offers a non-destructive way to modify CNSs with desired functional surfaces, while reserving their intrinsic properties. Thus far, a number of surface modifiers including aromatic compounds, small-molecular surfactants, amphiphilic polymers, and biomacromolecules have been developed to non-covalently functionalize CNS surfaces. Mediated by these surface modifiers, various functional components such as organic species and inorganic nanoparticles were further decorated onto their surfaces, resulting in versatile carbon-based hybrid nanomaterials with broad applications in chemical engineering and biomedical areas. In this review, the recent advances in the generation of such hybrid nanostructures based on non-covalently functionalized CNSs will be reviewed.
Institute of Scientific and Technical Information of China (English)
Qiu-shuang Gao; Guo-feng Tian; Sheng-li Qi; Zhan-peng Wu; De-zhen Wu
2013-01-01
Ladder-like polysilsesquioxanes (LPSQs) with different amino contents have been synthesized by controlling of the dosage of Pd/C catalyst.The concentration and activity of amino groups were investigated by Fourier transform infrared spectroscopy.Polyimide (PI)/LPSQ hybrid films have been prepared by incorporating of the obtained LPSQs with different amino contents into PI matrix,respectively.The interfacial interactions between PI matrix and LPSQ were studied with scanning electron microscopy and X-ray photoelectron spectroscopy,meanwhile the thermal and mechanical properties of the hybrid films were studied using dynamic mechanical analysis and tensile tests.The results indicate that the functionality of LPSQ has great effects on the interfacial interactions and the properties of hybrid films.With the increase of amino content,both the interracial interactions and the cross-linking density of hybrids enhanced,which results in the decline of surface silicon concentration,increase of Young's modulus and drop of elongation at break.Excessive amino content makes the hybrid films brittle and leads to incomplete imidization.
Band Anticrossing in Dilute Germanium Carbides Using Hybrid Density Functionals
Stephenson, Chad A.; O'brien, William A.; Qi, Meng; Penninger, Michael; Schneider, William F.; Wistey, Mark A.
2016-04-01
Dilute germanium carbides (Ge1- x C x ) offer a direct bandgap for compact silicon photonics, but widely varying properties have been reported. This work reports improved band structure calculations for Ge1- x C x using ab initio simulations that employ the HSE06 exchange-correlation density functional. Contrary to Vegard's law, the conduction band minimum at Γ is consistently found to decrease with increasing C content, while L and X valleys change much more slowly. The calculated Ge bandgap is within 11% of experimental values. A decrease in energy at the Γ conduction band valley of (170 meV ± 50)/%C is predicted, leading to a direct bandgap for x > 0.008. These results indicate a promising material for Group IV lasers.
Importance of local exact exchange potential in hybrid functionals for accurate excited states
Kim, Jaewook; Hwang, Sang-Yeon; Ryu, Seongok; Choi, Sunghwan; Kim, Woo Youn
2016-01-01
Density functional theory has been an essential analysis tool for both theoretical and experimental chemists since accurate hybrid functionals were developed. Here we propose a local hybrid method derived from the optimized effective potential (OEP) method and compare its distinct features with conventional nonlocal ones from the Hartree-Fock (HF) exchange operator. Both are formally exact for ground states and thus show similar accuracy for atomization energies and reaction barrier heights. For excited states, the local version yields virtual orbitals with N-electron character, while those of the nonlocal version have mixed characters between N- and (N+1)-electron orbitals. As a result, the orbital energy gaps from the former well approximate excitation energies with a small mean absolute error (MAE = 0.40 eV) for the Caricato benchmark set. The correction from time-dependent density functional theory with a simple local density approximation kernel further improves its accuracy by incorporating multi-config...
Neese, Frank; Schwabe, Tobias; Grimme, Stefan
2007-03-28
A recently proposed new family of density functionals [S. Grimme, J. Chem. Phys. 124, 34108 (2006)] adds a fraction of nonlocal correlation as a new ingredient to density functional theory (DFT). This fractional correlation energy is calculated at the level of second-order many-body perturbation theory (PT2) and replaces some of the semilocal DFT correlation of standard hybrid DFT methods. The new "double hybrid" functionals (termed, e.g., B2-PLYP) contain only two empirical parameters that have been adjusted in thermochemical calculations on parts of the G2/3 benchmark set. The methods have provided the lowest errors ever obtained by any DFT method for the full G3 set of molecules. In this work, the applicability of the new functionals is extended to the exploration of potential energy surfaces with analytic gradients. The theory of the analytic gradient largely follows the standard theory of PT2 gradients with some additional subtleties due to the presence of the exchange-correlation terms in the self-consistent field operator. An implementation is reported for closed-shell as well as spin-unrestricted reference determinants. Furthermore, the implementation includes external point charge fields and also accommodates continuum solvation models at the level of the conductor like screening model. The density fitting resolution of the identity (RI) approximation can be applied to the evaluation of the PT2 part with large gains in computational efficiency. For systems with approximately 500-600 basis functions the evaluation of the double hybrid gradient is approximately four times more expensive than the calculation of the standard hybrid DFT gradient. Extensive test calculations are provided for main group elements and transition metal containing species. The results reveal that the B2-PLYP functional provides excellent molecular geometries that are superior compared to those from standard DFT and MP2.
Kataoka, Sho; Banerjee, Subhabrata; Kawai, Akiko; Kamimura, Yoshihiro; Choi, Jun-Chul; Kodaira, Tetsuya; Sato, Kazuhiko; Endo, Akira
2015-04-01
Layered organic-inorganic hybrid perovskites that consist of metal halides and organic interlayers are a class of low-dimensional materials. Here, we report the fabrication of layered hybrid perovskites using metal halides and silsesquioxane with a cage-like structure. We used a silsesquioxane as an interlayer to produce a rigid structure and improve the functionality of perovskite layers. Propylammonium-functionalized silsesquioxane and metal halide salts (CuCl2, PdCl2, PbCl2, and MnCl2) were self-assembled to form rigid layered perovskite structures with high crystallinity. The rigid silsesquioxane structure produces micropores between the perovskite layers that can potentially be filled with different molecules to tune the dielectric constants of the interlayers. The obtained silsesquioxane-metal halide hybrid perovskites exhibit some characteristic properties of layered perovskites including magnetic ordering (CuCl4(2-) and MnCl4(2-)) and excitonic absorption/emission (PbCl4(2-)). Our results indicate that inserting silsesquioxane interlayers into hybrid perovskites retains and enhances the low-dimensional properties of the materials.
Cembran, Alessandro; Song, Lingchun; Mo, Yirong; Gao, Jiali
2009-10-13
A multistate density functional theory in the framework of the valence bond model is described. The method is based on a block-localized density functional theory (BLDFT) for the construction of valence-bond-like diabatic electronic states and is suitable for the study of electron transfer reactions and for the representation of reactive potential energy surfaces. The method is equivalent to a valence bond theory with the treatment of the localized configurations by using density functional theory (VBDFT). In VBDFT, the electron densities and energies of the valence bond states are determined by BLDFT. A functional estimate of the off-diagonal matrix elements of the VB Hamiltonian is proposed, making use of the overlap integral between Kohn-Sham determinants and the exchange-correlation functional for the ground state substituted with the transition (exchange) density. In addition, we describe an approximate approach, in which the off-diagonal matrix element is computed by wave function theory using block-localized Kohn-Sham orbitals. The key feature is that the electron density of the adiabatic ground state is not directly computed nor used to obtain the ground-state energy; the energy is determined by diagonalization of the multistate valence bond Hamiltonian. This represents a departure from the standard single-determinant Kohn-Sham density functional theory. The multistate VBDFT method is illustrated by the bond dissociation of H2+ and a set of three nucleophilic substitution reactions in the DBH24 database. In the dissociation of H2+, the VBDFT method yields the correct asymptotic behavior as the two protons stretch to infinity, whereas approximate functionals fail badly. For the S(N)2 nucleophilic substitution reactions, the hybrid functional B3LYP severely underestimates the barrier heights, while the approximate two-state VBDFT method overcomes the self-interaction error, and overestimates the barrier heights. Inclusion of the ionic state in a three
Premnath, P; Tan, B; Venkatakrishnan, K
2015-12-01
We introduce a hybrid nanostructured biomaterial that is a combination of rare phases of immiscible gold and silicon oxide, functionalized via ultrafast laser synthesis. For the first time, we show cancer controlling properties of rare phases of gold silicides, which include Au7Si, Au5Si, Au0.7Si2.3 and Au8Si2. Conventionally, pure forms of gold and silicon/silicon oxide are extensively employed in targeted therapy and drug delivery systems due to their unique properties. While silicon and silicon oxide nanoparticles have shown biocompatibility, gold nanoparticles show conflicting results based on their size and material properties. Several studies have shown that gold and silicon combinations produce cell controlling properties, however, these studies were not able to produce a homogenous combination of gold and silicon, owing to its immiscibility. A homogenous combination of gold and silicon may potentially enable properties that have not previously been reported. We describe rare phased gold-silicon oxide nanostructured hybrid biomaterials and its unique cancer controlling properties, owing to material properties, concentration, size and density. The gold-silicon oxide nanostructured hybrid is composed of individual gold-silicon oxide nanoparticles in various concentrations of gold and silicon, some nanoparticles possess a gold-core and silicon-shell like structure. The individual nanoparticles are bonded together forming a three dimensional nanostructured hybrid. The interaction of the nanostructured hybrids with cervical cancer cells showed a 96% reduction in 24h. This engineered nanostructured hybrid biomaterial presents significant potential due to the combination of immiscible gold and silicon oxide in varying phases and can potentially satiate the current vacuum in cancer therapy.
Kweon, Kyoung E.; Hwang, Gyeong S.
2012-10-01
The structure and property prediction of metal oxides can significantly be improved by incorporating exact Hartree-Fock (HF) exchange into density functional theory (DFT), which is the so-called hybrid DFT. We explored the impact of HF exchange inclusion on the predicted structural, bonding, and electronic properties of bismuth vanadate (BiVO4), with particular attention to the difference between its monoclinic and tetragonal scheelite phases. The applied exchange-correlation (xc) functionals include the gradient corrected Perdew-Burke-Ernzerhof (PBE) and the PBE-HF hybrid functionals with HF exchange amounts of 10%, 25%, and 50%. We find that the PBE-HF25% yields a monoclinic structure in very close agreement with the experimentally determined structure, while the PBE-HF50% tends to overestimate the monoclinic distortion and the PBE/PBE-HF10% can hardly identify a distinct monoclinic configuration at ambient conditions. Electronic structure analysis reveals that the increasing monoclinic distortion with the amount of HF exchange is related to the enhancement of hybridization between Bi 6s-O 2p antibonding states and unoccupied Bi 6p states. The bonding mechanisms and band structures of the monoclinic and tetragonal phases of BiVO4 were also investigated, and we discuss how the predictions are sensitive to the xc functional choice.
Directory of Open Access Journals (Sweden)
Mohsen Alipour
2014-01-01
Full Text Available We introduce a new combination of Bernstein polynomials (BPs and Block-Pulse functions (BPFs on the interval [0, 1]. These functions are suitable for finding an approximate solution of the second kind integral equation. We call this method Hybrid Bernstein Block-Pulse Functions Method (HBBPFM. This method is very simple such that an integral equation is reduced to a system of linear equations. On the other hand, convergence analysis for this method is discussed. The method is computationally very simple and attractive so that numerical examples illustrate the efficiency and accuracy of this method.
Modeling on the size dependent properties of InP quantum dots: a hybrid functional study
Cho, Eunseog; Jang, Hyosook; Lee, Junho; Jang, Eunjoo
2013-05-01
Theoretical calculations based on density functional theory were performed to provide better understanding of the size dependent electronic properties of InP quantum dots (QDs). Using a hybrid functional approach, we suggest a reliable analytical equation to describe the change of energy band gap as a function of size. Synthesizing colloidal InP QDs with 2-4 nm diameter and measuring their optical properties was also carried out. It was found that the theoretical band gaps showed a linear dependence on the inverse size of QDs and gave energy band gaps almost identical to the experimental values.
VV and VO2 defects in silicon studied with hybrid density functional theory
Christopoulos, Stavros Richard G
2014-12-07
The formation of VO (A-center), VV and VO2 defects in irradiated Czochralski-grown silicon (Si) is of technological importance. Recent theoretical studies have examined the formation and charge states of the A-center in detail. Here we use density functional theory employing hybrid functionals to analyze the formation of VV and VO2 defects. The formation energy as a function of the Fermi energy is calculated for all possible charge states. For the VV and VO2 defects double negatively charged and neutral states dominate, respectively.
Shahidha, R; Muthu, S; Elamurugu Porchelvi, E; Govindarajan, M
2014-11-11
Vibrational spectral analysis of 5-methyl-N-[4-(trifluoromethyl) phenyl]-isoxazole-4-carboxamide is (5MN4TPI4C) molecule was carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, harmonic vibrational wavenumbers, various bonding features have been computed using density functional B3LYP method with 6-311G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFFM). Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The non-linear optical (NLO) behavior of 5MN4TPI4C has been studied by determination of the electric dipole moment (μ) and hyperpolarizability (β) by using B3LYP/6-311G(d,p) method. The molecular orbital compositions and their contributions to the chemical bonding are studied by Total density of energy states (TDOS), sum of α and β electron (αβDOS) density of states. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are calculated.
Energy Technology Data Exchange (ETDEWEB)
Gudmundsdóttir, Hildur [Science Institute and Faculty of Physical Sciences VR-III, University of Iceland, 107 Reykjavík (Iceland); Zhang, Yao; Weber, Peter M. [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Jónsson, Hannes [Science Institute and Faculty of Physical Sciences VR-III, University of Iceland, 107 Reykjavík (Iceland); Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States)
2014-12-21
Theoretical calculations of Rydberg excited states of molecular clusters consisting of N,N-dimethylisopropylamine molecules using a Perdew-Zunger self-interaction corrected energy functional are presented and compared with results of resonant multiphoton ionization measurements. The binding energy of the Rydberg electron in the monomer is calculated to be 2.79 eV and 2.27 eV in the 3s and 3p state, respectively, which compares well with measured values of 2.88 eV and 2.21 eV. Three different stable configurations of the dimer in the ground state were found using an energy functional that includes van der Waals interaction. The lowest ground state energy conformation has the two N-atoms widely separated, by 6.2 Å, while the Rydberg state energy is lowest for a configuration where the N-atoms of the two molecules come close together, separated by 3.7 Å. This conformational change is found to lower the Rydberg electron binding energy by 0.2 eV. The self-interaction corrected functional gives a highly localized hole on one of the two molecules, unlike results obtained using the PBE functional or the hybrid B3LYP functional which give a delocalized hole. For the trimer, the self-interaction corrected calculation gives a Rydberg electron binding energy lowered further by 0.13 eV as compared with the dimer. The calculated results compare well with trends observed in experimental measurements. The reduction of the Rydberg electron binding energy with cluster size can be ascribed to an effective delocalization of the positive charge of the hole by the induced and permanent dipole moments of the neighboring molecules. A further decrease observed to occur on a time scale of tens of ps can be ascribed to a structural rearrangement of the clusters in the Rydberg state where molecules rotate to orient their dipoles in response to the formation of the localized hole.
Ultrathin gold nanowire-functionalized carbon nanotubes for hybrid molecular sensing.
Cui, Huizhong; Hong, Chenglin; Ying, Andrew; Yang, Xinmai; Ren, Shenqiang
2013-09-24
Carbon nanotubes (CNTs) have shown great potential as sensing component in the electrochemical field effect transistor and optical sensors, because of their extraordinary one-dimensional electronic structure, thermal conductivity, and tunable and stable near-infrared emission. However, the insolubility of CNTs due to strong van der Waals interactions limits their use in the field of nanotechnology. In this study, we demonstrate that noncovalent ultrathin gold nanowires functionalized multiwalled carbon nanotube (GNW-CNT) hybrid sensing agents show highly efficient and selective immune molecular sensing in electrochemical and near-infrared photoacoustic imaging methods. A detection limit of 0.01 ng/mL for the alpha-fetoprotein (AFP) antigen with high selectivity is shown. The extraordinary optical absorption, thermal, and electric conductivity of hybrid GNW-CNTs presented in this study could be an effective tactic to integrate imaging, sensing, and treatment functionalities.
Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan
2016-06-21
We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results.
Ge, Xiaochuan; Rocca, Dario; Gebauer, Ralph; Baroni, Stefano
2014-01-01
We present a new release of the turboTDDFT code featuring an implementation of hybrid functionals, a recently introduced pseudo-Hermitian variant of the Liouville-Lanczos approach to time-dependent density-functional perturbation theory, and a newly developed Davidson-like algorithm to compute selected interior eigenvalues/vectors of the Liouvillian super-operator. Our implementation is thoroughly validated against benchmark calculations performed on the cyanin (C$_{21}$O$_{11}$H$_{21}$) molecule using the Gaussian09 and turboTDDFT 1.0 codes.
A Dynamic Multistage Hybrid Swarm Intelligence Optimization Algorithm for Function Optimization
Directory of Open Access Journals (Sweden)
Daqing Wu
2012-01-01
Full Text Available A novel dynamic multistage hybrid swarm intelligence optimization algorithm is introduced, which is abbreviated as DM-PSO-ABC. The DM-PSO-ABC combined the exploration capabilities of the dynamic multiswarm particle swarm optimizer (PSO and the stochastic exploitation of the cooperative artificial bee colony algorithm (CABC for solving the function optimization. In the proposed hybrid algorithm, the whole process is divided into three stages. In the first stage, a dynamic multiswarm PSO is constructed to maintain the population diversity. In the second stage, the parallel, positive feedback of CABC was implemented in each small swarm. In the third stage, we make use of the particle swarm optimization global model, which has a faster convergence speed to enhance the global convergence in solving the whole problem. To verify the effectiveness and efficiency of the proposed hybrid algorithm, various scale benchmark problems are tested to demonstrate the potential of the proposed multistage hybrid swarm intelligence optimization algorithm. The results show that DM-PSO-ABC is better in the search precision, and convergence property and has strong ability to escape from the local suboptima when compared with several other peer algorithms.
Liu, Rui; Hu, Jinyang; Zhu, Senqiang; Lu, Jiapeng; Zhu, Hongjun
2017-09-12
Recently, graphene-based materials have become well-known nonlinear optical materials for the potential application of laser protection. Two new graphene oxide-platinum complex (GO-Pt) hybrid materials (GO-Pt-1, GO-Pt-2) have been fabricated through covalent modification and electrostatic adsorption of different Pt complexes with GO. The structural and photophysical properties of the resultant hybrid materials were studied. The nonlinear optical properties and optical power limiting (OPL) performance of Pt complexes, GO, and GO-Pt hybrid materials were investigated by using Z-scan measurements at 532 nm. At the same transmittance, the results illustrate that functionalization of GO makes GO-Pt hybrid materials possess better nonlinear optical properties and OPL performance than individual Pt complexes and GO due to a combination of nonlinear scattering, nonlinear absorption, and photoinduced electron and energy transfer between GO and Pt complex moieties. Furthermore, the nonlinear optics and OPL performance of GO-Pt-2 are better than those of GO-Pt-1, due to not only the excellent optical limiting of Pt-2 and more molecules per area of GO but also the way of combination of Pt-2 and GO.
Long-Range Corrected Hybrid Density Functionals with Improved Dispersion Corrections
Lin, You-Sheng; Mao, Shan-Ping; Chai, Jeng-Da
2012-01-01
By incorporating the improved empirical atom-atom dispersion corrections from DFT-D3 [Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys. 2010, 132, 154104], two long-range corrected (LC) hybrid density functionals are proposed. Our resulting LC hybrid functionals, omegaM06-D3 and omegaB97X-D3, are shown to be accurate for a very wide range of applications, such as thermochemistry, kinetics, noncovalent interactions, frontier orbital energies, fundamental gaps, and long-range charge-transfer excitations, when compared with common global and LC hybrid functionals. Relative to omegaB97X-D [Chai, J.-D.; Head-Gordon, M. Phys. Chem. Chem. Phys. 2008, 10, 6615], omegaB97X-D3 (reoptimization of omegaB97X-D with improved dispersion corrections) is shown to be superior for non-bonded interactions, and similar in performance for bonded interactions, while omegaM06-D3 is shown to be superior for general applications.
Institute of Scientific and Technical Information of China (English)
李浩宏; 陈之荣; 黄长沧; 肖光参; 李俊篯; 张文选
2005-01-01
A one dimensional coordination polymer, [(C7H18N)(Ag2I3)]n((C7H18N)+=Methyltriethylammonium) has been successfully synthesized and characterized by X-ray single-crystal diffraction method. Structure analysis shows that the compound consists of organic cations(Methyltriethylammonium) and inorganic anion chains (Ag2I3)n-.The inorganic moiety consists of AgI4 tetrahedron, which shares the same edges with adjacent AgI4 tetrahedrons to the crystal. Anion chains are surrounded by Methyltriethylammonium cations. Anion chains and cations are in combination with each other by static attracting forces in the crystal to form so-called organic-inorganic hybrid structure. According to the crystal structure data, quantum chemistry calculation with DFT on B3LYP level was used to reveal the electronic structure of title compound. CCDC: 254288.
Institute of Scientific and Technical Information of China (English)
LIU Jun-Bo; SUN Jia-Ni; TANG Shan-Shan; CHEN Kai-Yin; JIN Rui-Fa
2012-01-01
As a widely used herbicide, the threat of atrazine to both environment and health of people has become the focus. Therefore, the research and analysis of atrazine are getting more important. In this work, the MIT was used to detect atrazine theoretically. Atrazine was taken as a template molecule. MAA, MMA and TFMAA were taken as the functional monomers, respectively. The geometry optimization, the nature of hydrogen bonds, the NBO charge, and the binding energies of the imprinted molecule with the functional monomers were investigated at the B3LYP/6-31g(d,p) level. Results indicated that atrazine had the strongest interaction with TFMAA. When the ratio of atrazine and TFMAA was 1:6, the amount of H-bond formed from atrazine and TFMAA was the largest. Moreover, TFMAA owned the largest binding energy with atrazine while MMA owned the smallest. The study is helpful to interpret experiment phenomena of molecular imprinting and select better functional monomers.
DFT studies of COOH tip-functionalized zigzag and armchair single wall carbon nanotubes.
Chełmecka, Elżbieta; Pasterny, Karol; Kupka, Teobald; Stobiński, Leszek
2012-05-01
Structure and energy calculations of pristine and COOH-modified model single wall carbon nanotubes (SWCNTs) of different length were performed at B3LYP/6-31G* level of theory. From 1 to 9 COOH groups were added at the end of the nanotube. The differences in structure and energetics of partially and fully functionalized SWCNTs at one end of the nanotube are observed. Up to nine COOH groups could be added at one end of (9,0) zigzag SWCNT in case of full functionalization. However, for (5,5) armchair SWCNT, the full functionalization was impossible due to steric crowding and rim deformation. The dependence of substituent attachment energy on the number of substituents at the carbon nanotube rim was observed.
Li, Zongle; He, Chunying; Wang, Zhao; Gao, Yachen; Dong, Yongli; Zhao, Cheng; Chen, Zhimin; Wu, Yiqun; Song, Weina
2016-07-06
Tetracarboxylic Zn(ii) phthalocyanine-amino functionalized graphene oxide (ZnPcC4-NGO) hybrid materials have been prepared by a covalent functionalization method. The characterizations indicate that the amino-functionalization of GO has an important influence on the structure and photophysical properties of the ZnPcC4-NGO hybrid. The ZnPcC4-NGO hybrid exhibits enhanced photo-induced electron transfer or energy transfer (PET/ET), compared to the ZnPcC4 covalent functionalized GO (ZnPcC4-GO), owing to the presence of the extended sp(2) carbon configurations, along with the partial reduction of the NGO nanosheets and the introduction of electron-donating ethylenediamine. The nonlinear optical (NLO) properties of the hybrids were investigated using the Z-scan technique at 532 nm with 4 ns laser pulses. The results show that the efficient covalent functionalization and partial reduction of NGO cause the ZnPcC4-NGO hybrid to possess evidently larger NLO properties than the individual NGO, ZnPcC4 and the ZnPcC4-GO hybrid. The enhanced NLO performance can be attributed to the increased excited state absorption from the extended sp(2) carbon configurations of the NGO moiety, reverse saturable absorption arising from ZnPcC4 moiety, and the contribution of the efficient PET/ET process between the ZnPcC4 and NGO moieties in the hybrid.
Directory of Open Access Journals (Sweden)
Nathan I. Hammer
2010-01-01
Full Text Available Semiconductor nanocrystals hybridized with functional ligands represent an important new class of composite nanomaterials. The development of these new nanoscale building blocks has intensified over the past few years and offer significant advantages in a wide array of applications. Functional ligands allow for incorporation of nanocrystals into areas where their unique photophysics can be exploited. Energy and charge transfer between the ligands and the nanocrystal also result in enhanced physical properties that can be tuned by the choice of ligand architecture. Here, progress in the development and applications involving this new class of composite materials will be discussed.
Computationally efficient double hybrid density functional theory using dual basis methods
Byrd, Jason N
2015-01-01
We examine the application of the recently developed dual basis methods of Head-Gordon and co-workers to double hybrid density functional computations. Using the B2-PLYP, B2GP-PLYP, DSD-BLYP and DSD-PBEP86 density functionals, we assess the performance of dual basis methods for the calculation of conformational energy changes in C$_4$-C$_7$ alkanes and for the S22 set of noncovalent interaction energies. The dual basis methods, combined with resolution-of-the-identity second-order M{\\o}ller-Plesset theory, are shown to give results in excellent agreement with conventional methods at a much reduced computational cost.
Vacancy formation in MoO3: hybrid density functional theory and photoemission experiments
Salawu, Omotayo Akande
2016-09-29
Molybdenum oxide (MoO3) is an important material that is being considered for numerous technological applications, including catalysis and electrochromism. In the present study, we apply hybrid density functional theory to investigate O and Mo vacancies in the orthorhombic phase. We determine the vacancy formation energies of different defect sites as functions of the electron chemical potential, addressing different charge states. In addition, we investigate the consequences of defects for the material properties. Ultraviolet photoemission spectroscopy is employed to study the valence band of stoichiometric and O defective MoO3. We show that O vacancies result in occupied in-gap states.
Excitons in solids with non-empirical hybrid time-dependent density-functional theory
Ullrich, Carsten; Yang, Zeng-Hui; Sottile, Francesco
2015-03-01
The Bethe-Salpeter equation (BSE) accurately describes the optical properties of solids, but is computationally expensive. Time-dependent density-functional theory (TDDFT) is more efficient, but standard functionals do not produce excitons in extended systems. We present a new, non-empirical hybrid TDDFT approach whose computational cost is much less than BSE, while the accuracy for both bound excitons and the continuum spectra is comparable to that of the BSE. Good performance is observed for both small-gap semiconductors and large-gap insulators. Work supported by NSF Grant DMR-1408904.
A-centers in silicon studied with hybrid density functional theory
Wang, Hao
2013-07-29
Density functional theory employing hybrid functional is used to gain fundamental insight into the interaction of vacancies with oxygen interstitials to form defects known as A-centers in silicon. We calculate the formation energy of the defect with respect to the Fermi energy for all possible charge states. It is found that the neutral and doubly negatively charged A-centers dominate. The findings are analyzed in terms of the density of states and discussed in view of previous experimental and theoretical studies.
Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections
Energy Technology Data Exchange (ETDEWEB)
Chai, Jeng-Da; Head-Gordon, Martin
2008-06-14
We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, {omega}B97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, {omega}B97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as {omega}B97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
A hybrid microsystem with separately functioned temperature controlling substrate and sample operating fluidic microchannel was developed to demonstrate a reconfigurable microfluidics scheme.The temperature controlling substrate integrated a micro heater and a temperature sensor by using traditional silicon-based micromechanical system(MEMS)technique,which guaranteed high performance and robust reliability for repeatable usage.The sample operating fluidic microchannel was prepared by poly-(dimethylsiloxane) (PDMS)based soft lithography technique,which made it cheap enough for disposable applications.The PDMS microchannel chip was attached to the temperature controlling substrate for reconfigurable thermal applications.A thin PDMS film was used to seal the microchannel and bridge the functionalized substrate and the sample inside the channel,which facilitated heat transferring and prevented sample contaminating the temperature controlling substrate.Demonstrated by a one dimensional thermal resistance model,the thin PDMS film was important for the present reconfiguration applications.Thermal performance of this hybrid microsystem was examined,and the experimental results demonstrated that the chip system could work stably over hours with temperature variation less than 0.1oC.Multiple PDMS microchannel chips were tested on one heating substrate sequentially with a maximum intra-chip temperature difference of 1.0oC.DNA extracted from serum of a chronic hepatitis B virus(HBV)patient was amplified by this hybrid microsystem and the gel electrophoresis result indicated that the present reconfigurable microfluidic scheme worked successfully.
Kim, Jun Young; Kim, Jeongyong; Joo, Jinsoo
2016-11-28
Two-dimensional (2-D) transition metal dichalcogenides, such as MoSsub>2sub>, WSesub>2sub>, and WSsub>2sub>, are promising materials for application in field effect transistors, optoelectronics, and sensing devices. In this study, 2-D WSesub>2sub> samples with various numbers of layers were hybridized with functionalized gold nanoparticles (Au-NPs) to achieve surface-enhanced Raman scattering (SERS). The nanoscale Raman and photoluminescence spectra of the WSesub>2sub> layers and WSesub>2sub>/Au-NP hybrids were measured using a high-resolution laser confocal microscope. The WSesub>2sub> exhibited distinct optical characteristics depending on the number of WSesub>2sub> layers. The intensities of the Raman characteristic modes of the WSesub>2sub> layers were significantly enhanced after hybridization with functionalized Au-NPs, indicating the SERS effect. The SERS effect weakened with increasing the number of WSesub>2sub> layers. The SERS effect was more pronounced for mono- and bi-layer WSesub>2sub> systems compared with the multi-layer WSesub>2sub> systems.
Cao, Yixiang; Hughes, Thomas; Giesen, Dave; Halls, Mathew D; Goldberg, Alexander; Vadicherla, Tati Reddy; Sastry, Madhavi; Patel, Bhargav; Sherman, Woody; Weisman, Andrew L; Friesner, Richard A
2016-06-15
We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G*(*) show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G(**) basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G
Bi, Sai; Zhou, Hong; Zhang, Shusheng
2009-10-07
A signal amplification strategy based on bio-bar-code functionalized magnetic nanoparticles as labels holds promise to improve the sensitivity and detection limit of the detection of DNA hybridization and single-nucleotide polymorphisms by flow injection chemiluminescence assays.
Hybrid graded element model for transient heat conduction in functionally graded materials
Institute of Scientific and Technical Information of China (English)
Lei-Lei Cao; Qing-Hua Qin; Ning Zhao
2012-01-01
This paper presents a hybrid graded element model for the transient heat conduction problem in functionally graded materials (FGMs).First,a Laplace transform approach is used to handle the time variable.Then,a fundamental solution in Laplace space for FGMs is constructed.Next,a hybrid graded element is formulated based on the obtained fundamental solution and a frame field.As a result,the graded properties of FGMs are naturally reflected by using the fundamental solution to interpolate the intra-element field.Further,Stefest's algorithm is employed to convert the results in Laplace space back into the time-space domain.Finally,the performance of the proposed method is assessed by several benchmark examples.The results demonstrate well the efficiency and accuracy of the proposed method.
Organic-inorganic hybrid foams with diatomite addition: Effect on functional properties
Verdolotti, L.; D'Auria, M.; Lavorgna, M.; Vollaro, P.; Iannace, S.; Capasso, I.; Galzerano, B.; Caputo, D.; Liguori, B.
2016-05-01
Organic-inorganic hybrid foams were prepared by using metakaolin, diatomite as a partial (or total) replacement of metakaolin, as matrix, silicon and whipped protein as pore forming. The foamed systems were hardened at defined temperature and time and then characterized by mechanical point of view through compression tests and by functional point of view through fire reaction and acoustic tests. The experimental findings highlighted that the replacement of diatomite in the formulation affected the morphological structure of the foams and consequently their mechanical properties. In particular, the consolidation mechanism in the diatomite based-hybrid foams changed from geopolymerization to a silicate polycondensation mechanism. Therefore, mechanical performances enhanced with increasing of the diatomite content. Fire reaction tests, such as non-combustibility and cone calorimeter tests, showed positive thermal inertia of samples regardless of the content of diatomite.
Institute of Scientific and Technical Information of China (English)
LI LeLe; SUN LingDong; ZHANG YaWen; YAN ChunHua
2009-01-01
Since the discovery of a surfactant directed self-assembly approach for the fabrication of mesoporous silica in 1992,increasing attention has been focused on the design and synthesis of mesostructured functional materials.Organic functionalization is becoming a major topic in this research field,since highly ordered mesostructured organic-inorganic hybrids offer novel functionalities and enhanced performance over their individual components.We begin with a brief overview of the three fundamental methods (post-synthetic grafting technique,co-condensation method,and preparation of periodic mesoporous organosilicas) for the preparation of organically functionalized mesostructured silica,and focus on one of the most promising approaches,which herein was named as functional-template directed self-assembly (FTDSA) approach,and in the eyes of the authors it has a special position in the preparation of this class of hybrid materials.A comprehensive overview of the state of research in the area of FTDSA and its potential applications will be given.
Verma, Harish Kumar; Jain, Cheshta
2016-09-01
In this article, a hybrid algorithm of particle swarm optimization (PSO) with statistical parameter (HSPSO) is proposed. Basic PSO for shifted multimodal problems have low searching precision due to falling into a number of local minima. The proposed approach uses statistical characteristics to update the velocity of the particle to avoid local minima and help particles to search global optimum with improved convergence. The performance of the newly developed algorithm is verified using various standard multimodal, multivariable, shifted hybrid composition benchmark problems. Further, the comparative analysis of HSPSO with variants of PSO is tested to control frequency of hybrid renewable energy system which comprises solar system, wind system, diesel generator, aqua electrolyzer and ultra capacitor. A significant improvement in convergence characteristic of HSPSO algorithm over other variants of PSO is observed in solving benchmark optimization and renewable hybrid system problems.
Wang, Xinquan; Dvorac, Marc; Wu, Zhigang
2016-11-01
Hybrid functionals mixing the exact exchange with (semi)local functionals to reinstall the missing derivative discontinuity have been successfully employed to predict band gaps (Eg) in bulk semiconductors. Here we show that traditional hybrid functionals with fixed fractions of exact exchange do not perform significantly better than the most popular semilocal PBE-GGA functional for Eg of semiconductor nanostructures, since their band-gap corrections are essentially size independent. This is because they cannot respond properly to the variation in screening when size changes. They merely predict constant band-gap corrections to the PBE gaps in silicon nanowires (Si NWs) when wire diameter reduces, instead of the dramatic increase predicted by many-body G W calculations. Moreover, these hybrid functionals generate almost identical wave functions compared with PBE for both bulk Si and Si NWs, whose overlaps with corresponding quasiparticle wave functions become much smaller than 1 for narrow NWs.
Singh, Gurpreet; Dogra, Sukh Dev; Kaur, Sarvpreet; Tripathi, S K; Prakash, Satya; Rai, Bimal; Saini, G S S
2015-01-01
The vibrational properties of glutathione have been investigated by infrared absorption and Raman spectroscopic techniques, and density functional theory calculations at the B3LYP/6-31+G(d,p) level. Assignments of all the experimentally observed vibrational bands have been done with the help of simulated vibrational spectra and potential energy distribution calculations of glutathione water cluster, which includes the effect of hydrogen bonding. Optimized molecular parameters of energy minimized structure have been compared with the available experimental values. Calculated molecular parameters of glutathione-water cluster match well with the experimental values. Some of the calculated molecular parameters and vibrational frequencies of vapor phase glutathione-water cluster suggest participation of some atoms of glutathione in hydrogen bonding. Experimentally observed UV-Visible absorption spectrum of glutathione has also been reported. Observed band at 203 nm has been assigned to electronic transitions calculated with time dependent density functional theory. Copyright © 2015 Elsevier B.V. All rights reserved.
Indian Academy of Sciences (India)
Vijayanand Kalamse; Sanjay Gaikwad; Ajay Chaudhari
2010-06-01
5-metal mononitrides and monoborides viz. X–N and X–B (X = La, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg) are studied using density functional method based B3LYP functional with LANL2DZ and SDD basis set. The lowest spin state, electron affinities, ionization potentials and binding energies for mononitrides and monoborides are obtained. The electronic state and electronic configuration of mononitrides and monoborides are discussed. Orbitals involved in bond formation are identified. The properties of mononitrides and monoborides are compared. It is found that 5-metal atoms form stronger bond with nitrogen atom than the boron atom. The range of binding energy, electron affinity and ionization potential is wider for mononitrides than that for monoborides. The properties of 5-metal mononitrides and 3-metal mononitrides are also compared. The binding energies for the former are lower than those for the latter.
Energy Technology Data Exchange (ETDEWEB)
Ringholm, Magnus; Ruud, Kenneth [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø – The Arctic University of Norway, 9037 Tromsø (Norway); Bast, Radovan [Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-10691 Stockholm (Sweden); PDC Center for High Performance Computing, Royal Institute of Technology, S-10044 Stockholm (Sweden); Oggioni, Luca [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø – The Arctic University of Norway, 9037 Tromsø (Norway); Department of Physics G. Occhialini, University of Milano Bicocca, Piazza della scienza 3, 20126 Milan (Italy); Ekström, Ulf [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo (Norway)
2014-10-07
We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields, reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.
Ringholm, Magnus; Bast, Radovan; Oggioni, Luca; Ekström, Ulf; Ruud, Kenneth
2014-10-01
We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields, reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.
LuChunHai; Liao Jun Sheng; Sun Ying; WangXiaoLin
2002-01-01
The density functional theory method using B3' exchange and Lee-Yang-Parr's correlation function (B3LYP) with 6-31G** basis set were used to study and optimize equilibrium structure and fundamental vibrational frequencies in the equilibrium for CH4, CH3D, CH2D2, CHD3 and CD4. The relative result error from 1.1% to 6.3% were obtained between the calculation and the observation values of fundamental vibrational frequencies. After scaled, the relative result error is between 0.1% and - 2.9%. This method is used to study period properties of methane that some hydrogen atoms are replaced by tritium atoms. Following deuterium or tritium atom number rising in methane, entropy increases, but zero-point vibrational energy, heat capacity and enthalpy reduces
Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation
Energy Technology Data Exchange (ETDEWEB)
Kühn, Michael [Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe (Germany); Weigend, Florian, E-mail: florian.weigend@kit.edu [Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe (Germany); Institut für Nanotechnologie, Karlsruher Institut für Technologie, Postfach 3640, 76021 Karlsruhe (Germany)
2015-01-21
We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy){sub 3} (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its “spin-forbidden” triplet-singlet transition.
Francesko, Antonio; Blandón, Lucas; Vázquez, Mario; Petkova, Petya; Morató, Jordi; Pfeifer, Annett; Heinze, Thomas; Mendoza, Ernest; Tzanov, Tzanko
2015-05-13
Laccase-assisted assembling of hybrid biopolymer-silver nanoparticles and cork matrices into an antimicrobial material with potential for water remediation is herein described. Amino-functional biopolymers were first used as doping agents to stabilize concentrated colloidal dispersions of silver nanoparticles (AgNP), additionally providing the particles with functionalities for covalent immobilization onto cork to impart a durable antibacterial effect. The solvent-free AgNP synthesis by chemical reduction was carried out in the presence of chitosan (CS) or 6-deoxy-6-(ω-aminoethyl) aminocellulose (AC), leading to simultaneous AgNP biofunctionalization. This approach resulted in concentrated hybrid NP dispersion stable to aggregation and with hydrodynamic radius of particles of about 250 nm. Moreover, laccase enabled coupling between the phenolic groups in cork and amino moieties in the biopolymer-doped AgNP for permanent modification of the material. The antibacterial efficiency of the functionalized cork matrices, aimed as adsorbents for wastewater treatment, was evaluated against Escherichia coli and Staphylococcus aureus during 5 days in conditions mimicking those in constructed wetlands. Both intrinsically antimicrobial CS and AC contributed to the bactericidal effect of the enzymatically grafted on cork AgNP. In contrast, unmodified AgNP were easily washed off from the material, confirming that the biopolymers potentiated a durable antibacterial functionalization of the cork matrices.
DEFF Research Database (Denmark)
Kuhlman, Thomas Scheby; Mikkelsen, Kurt V.; Møller, Klaus Braagaard;
2009-01-01
We present a study on the excited states of an ethylene dimer as to investigate the presence of and perturbation from low-lying charge-resonance states calculated by linear response density functional theory (DFT) using the B3LYP and CAM-B3LYP functionals. The calculations are compared to a refer......We present a study on the excited states of an ethylene dimer as to investigate the presence of and perturbation from low-lying charge-resonance states calculated by linear response density functional theory (DFT) using the B3LYP and CAM-B3LYP functionals. The calculations are compared...
Directory of Open Access Journals (Sweden)
Prashanta Dhoj Adhikari
2014-01-01
Full Text Available We report the surface functionalization of graphene films grown by chemical vapor deposition and fabrication of a hybrid material combining multi-walled carbon nanotubes and graphene (CNT–G. Amine-terminated self-assembled monolayers were prepared on graphene by the UV-modification of oxidized groups introduced onto the film surface. Amine-termination led to effective interaction with functionalized CNTs to assemble a CNT–G hybrid through covalent bonding. Characterization clearly showed no defects of the graphene film after the immobilization reaction with CNT. In addition, the hybrid graphene material revealed a distinctive CNT–G structure and p–n type electrical properties. The introduction of functional groups on the graphene film surface and fabrication of CNT–G hybrids with the present technique could provide an efficient, novel route to device fabrication.
Directory of Open Access Journals (Sweden)
H. S. Mansur
2012-01-01
Full Text Available This study reports the synthesis and characterization of novel tridimensional porous hybrids based on PVA combined with bioactive glass and reinforced by chemically functionalized carbon nanotubes (CNT for potential use in bone tissue engineering. The functionalization of CNT was performed by introducing carboxylic groups in multiwall nanotubes. This process aimed at enhancing the affinity of CNTs with the water-soluble PVA polymer derived by the hydrogen bonds formed among alcohol (PVA and carboxylic groups (CNT–COOH. In the sequence, the CNT–COOH (0.25 wt% were used as the nanostructure modifier for the hybrid system based on PVA associated with the bioactive glass (BaG. The mechanical properties of the nanostructured hybrids reinforced with CNT–COOH were evaluated by axial compression tests, and they were compared to reference hybrid. The averaged yield stresses of macroporous hybrids were (2.3 ± 0.9 and (4.4 ± 1.0 MPa for the reference and the CNT reinforced materials, respectively. Moreover, yield strain and Young's modulus were significantly enhanced by about 30% for the CNT–COOH hybrids. Hence, as far as the mechanical properties are concerned, the results have clearly showed the feasibility of utilizing these new hybrids reinforced with functionalized CNT in repairing cancellous bone tissues.
Zhong, Y D; Sun, X Y; Liu, E Y; Li, Y Q; Gao, Z; Yu, F X
2016-06-24
Liriodendron hybrids (Liriodendron chinense x L. tulipifera) are important landscaping and afforestation hardwood trees. To date, little genomic research on adventitious rooting has been reported in these hybrids, as well as in the genus Liriodendron. In the present study, we used adventitious roots to construct the first cDNA library for Liriodendron hybrids. A total of 5176 expressed sequence tags (ESTs) were generated and clustered into 2921 unigenes. Among these unigenes, 2547 had significant homology to the non-redundant protein database representing a wide variety of putative functions. Homologs of these genes regulated many aspects of adventitious rooting, including those for auxin signal transduction and root hair development. Results of quantitative real-time polymerase chain reaction showed that AUX1, IRE, and FB1 were highly expressed in adventitious roots and the expression of AUX1, ARF1, NAC1, RHD1, and IRE increased during the development of adventitious roots. Additionally, 181 simple sequence repeats were identified from 166 ESTs and more than 91.16% of these were dinucleotide and trinucleotide repeats. To the best of our knowledge, the present study reports the identification of the genes associated with adventitious rooting in the genus Liriodendron for the first time and provides a valuable resource for future genomic studies. Expression analysis of selected genes could allow us to identify regulatory genes that may be essential for adventitious rooting.
The resilient hybrid fiber sensor network with self-healing function.
Xu, Shibo; Liu, Tiegen; Ge, Chunfeng; Chen, Qinnan; Zhang, Hongxia
2015-03-01
This paper presents a novel resilient fiber sensor network (FSN) with multi-ring architecture, which could interconnect various kinds of fiber sensors responsible for more than one measurands. We explain how the intelligent control system provides sensors with self-healing function meanwhile sensors are working properly, besides each fiber in FSN is under real-time monitoring. We explain the software process and emergency mechanism to respond failures or other circumstances. To improve the efficiency in the use of limited spectrum resources in some situations, we have two different structures to distribute the light sources rationally. Then, we propose a hybrid sensor working in FSN which is a combination of a distributed sensor and a FBG (Fiber Bragg Grating) array fused in a common fiber sensing temperature and vibrations simultaneously with neglectable crosstalk to each other. By making a failure to a working fiber in experiment, the feasibility and effectiveness of the network with a hybrid sensor has been demonstrated, hybrid sensors could not only work as designed but also survive from destructive failures with the help of resilient network and smart and quick self-healing actions. The network has improved the viability of the fiber sensors and diversity of measurands.
Kumar Pramanik, Sumit; Losada-Pérez, Patricia; Reekmans, Gunter; Carleer, Robert; D'Olieslaeger, Marc; Vanderzande, Dirk; Adriaensens, Peter; Ethirajan, Anitha
2017-04-01
With recent advances in the field of diagnostics and theranostics, liposomal technology has secured a fortified position as a potential nanocarrier. Specifically, radiation/photo-sensitive liposomes containing photo-polymerizable cross-linking lipids are intriguing as they can impart the vesicles with highly interesting properties such as response to stimulus and improved shell stability. In this work, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphoethanolamine (DTPE) is used as a photo-polymerizable lipid to form functional hybrid-liposomes as it can form intermolecular cross-linking through the diacetylenic groups. Hybrid-liposomes were formulated using mixtures of DTPE and saturated lipids of different chain lengths (dipalmitoylphosphatidylcholine (DPPC) and dimirystoilphosphatidylcholine (DMPC)) at different molar ratios. The physico-chemical characteristics of the liposomes has been studied before and after UV irradiation using a combination of techniques: DSC, QCM-D and solid-state NMR. The results signify the importance of a subtle modification in alkyl chain length on the phase behavior of the hybrid-liposomes and on the degree of crosslinking in the shell.
Energy Technology Data Exchange (ETDEWEB)
Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan; Hobza, Pavel
2008-03-13
A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A)—where F and W are of aromatic character—is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone–aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals—not covering this energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.
Functionalized hybrid nanofibers to mimic native ECM for tissue engineering applications
Energy Technology Data Exchange (ETDEWEB)
Karuppuswamy, Priyadharsini [Center for Nanofibers and Nanotechnology, Nanoscience and Nanotechnology Initiative, Faculty of Engineering, National University of Singapore, Singapore (Singapore); Department Physics and Nanotechnology, SRM University, Kattankulathur, Chennai (India); Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Venugopal, Jayarama Reddy, E-mail: nnijrv@nus.edu.sg [Center for Nanofibers and Nanotechnology, Nanoscience and Nanotechnology Initiative, Faculty of Engineering, National University of Singapore, Singapore (Singapore); Navaneethan, Balchandar [Center for Nanofibers and Nanotechnology, Nanoscience and Nanotechnology Initiative, Faculty of Engineering, National University of Singapore, Singapore (Singapore); Department Physics and Nanotechnology, SRM University, Kattankulathur, Chennai (India); Laiva, Ashang Luwang; Sridhar, Sreepathy; Ramakrishna, Seeram [Center for Nanofibers and Nanotechnology, Nanoscience and Nanotechnology Initiative, Faculty of Engineering, National University of Singapore, Singapore (Singapore)
2014-12-15
Highlights: • Functionalized hybrid polymer mats fabricated for tissue engineering. • Hybrid polymer mats showed high surface area, high porosity and good wettability. • Incorporation of natural polymers modified the properties of nanofiber mats more biologically favorable for biomedical applications. - Abstract: Nanotechnology being one of the most promising technologies today shows an extremely huge potential in the field of tissue engineering to mimic the porous topography of natural extracellular matrix (ECM). Natural polymers are incorporated into the synthetic polymers to fabricate functionalized hybrid nanofibrous scaffolds, which improve cell and tissue compatibility. The present study identified the biopolymers – aloe vera, silk fibroin and curcumin incorporated into polycaprolactone (PCL) as suitable substrates for tissue engineering. Different combinations of PCL with natural polymers – PCL/aloe vera, PCL/silk fibroin, PCL/aloe vera/silk fibroin, PCL/aloe vera/silk fibroin/curcumin were electrospun into nanofibrous scaffolds. The fabricated two dimensional nanofibrous scaffolds showed high surface area, appropriate mechanical properties, hydrophilicity and porosity, required for the regeneration of diseased tissues. The nanofibrous scaffolds were characterized by Scanning electron microscope (SEM), porometry, Instron tensile tester, VCA optima contact angle measurement and FTIR to analyze the fiber diameter and morphology, porosity and pore size distribution, mechanical strength, wettability, chemical bonds and functional groups, respectively. The average fiber diameter of obtained fibers ranged from 250 nm to 350 nm and the tensile strength of PCL scaffolds at 4.49 MPa increased upto 8.3 MPa for PCL/silk fibroin scaffolds. Hydrophobicity of PCL decreased with the incorporation of natural polymers, especially for PCL/aloe vera scaffolds. The properties of as-spun nanofiber scaffolds showed their potential as promising scaffold materials in
G-centers in irradiated silicon revisited: A screened hybrid density functional theory approach
Wang, H.
2014-05-13
Electronic structure calculations employing screened hybrid density functional theory are used to gain fundamental insight into the interaction of carbon interstitial (Ci) and substitutional (Cs) atoms forming the CiCs defect known as G-center in silicon (Si). The G-center is one of the most important radiation related defects in Czochralski grown Si. We systematically investigate the density of states and formation energy for different types of CiCs defects with respect to the Fermi energy for all possible charge states. Prevalence of the neutral state for the C-type defect is established.
Collision avoidance for a mobile robot based on radial basis function hybrid force control technique
Institute of Scientific and Technical Information of China (English)
Wen Shu-Huan
2009-01-01
Collision avoidance is always difficult in the planning path for a mobile robot. In this paper, the virtual force field between a mobile robot and an obstacle is formed and regulated to maintain a desired distance by hybrid force control algorithm. Since uncertainties from robot dynamics and obstacle degrade the performance of a collision avoidance task, intelligent control is used to compensate for the uncertainties. A radial basis function (RBF) neural network is used to regulate the force field of an accurate distance between a robot and an obstacle in this paper and then simulation studies are conducted to confirm that the proposed algorithm is effective.
Wen, Shu-Huan
2009-10-01
Collision avoidance is always difficult in the planning path for a mobile robot. In this paper, the virtual force field between a mobile robot and an obstacle is formed and regulated to maintain a desired distance by hybrid force control algorithm. Since uncertainties from robot dynamics and obstacle degrade the performance of a collision avoidance task, intelligent control is used to compensate for the uncertainties. A radial basis function (RBF) neural network is used to regulate the force field of an accurate distance between a robot and an obstacle in this paper and then simulation studies are conducted to confirm that the proposed algorithm is effective.
Hybrid density functional theory description of N- and C-doping of NiO.
Nolan, Michael; Long, Run; English, Niall J; Mooney, Damian A
2011-06-14
The large intrinsic bandgap of NiO hinders its potential application as a photocatalyst under visible-light irradiation. In this study, we have performed first-principles screened exchange hybrid density functional theory with the HSE06 functional calculations of N- and C-doped NiO to investigate the effect of doping on the electronic structure of NiO. C-doping at an oxygen site induces gap states due to the dopant, the positions of which suggest that the top of the valence band is made up primarily of C 2p-derived states with some Ni 3d contributions, and the lowest-energy empty state is in the middle of the gap. This leads to an effective bandgap of 1.7 eV, which is of potential interest for photocatalytic applications. N-doping induces comparatively little dopant-Ni 3d interactions, but results in similar positions of dopant-induced states, i.e., the top of the valence band is made up of dopant 2p states and the lowest unoccupied state is the empty gap state derived from the dopant, leading to bandgap narrowing. With the hybrid density functional theory (DFT) results available, we discuss issues with the DFT corrected for on-site Coulomb description of these systems.
Cho, Kie Yong; Yeom, Yong Sik; Seo, Heun Young; Park, Young Hun; Jang, Ha Na; Baek, Kyung-Youl; Yoon, Ho Gyu
2015-05-13
The design of amphiphilic polymer compatibilizers for solubility manipulation of CNT composites was systematically generalized in this study. Structurally tailored multiamphiphilic compatibilizer were designed and synthesized by applying simple, high-yield reactions. This multiamphiphilic compatibilizer was applied for noncovalent functionalization of CNTs as well as provided CNTs with outstanding dispersion stability, manipulation of solubility, and hybridization with Ag nanoparticles (NPs). With regard to the dispersion properties, superior records in maximum concentration (2.88-3.10 mg/mL in chloroform), and mass ratio of the compatibilizer for good CNT dispersion (36 wt %) were achieved by MWCNTs functionalized with a multiamphiphilic block copolymer compatibilizer. In particular, the solubility limitations of MWCNT dispersion in solvents ranging from toluene (nonpolar) to aqueous solution (polar) are surprisingly resolved by introducing this multiamphiphilic polymer compatibilizer. Furthermore, this polymer compatibilizer allowed the synthesis of the hybrid CNT nanocomposites with Ag nanoparticles by an in situ nucleation process. As such, the multiamphiphilic compatibilizer candidate as a new concept for the noncovalent functionalization of CNTs can extend their use for a wide range of applications.
Electronic structure modeling of InAs/GaSb superlattices with hybrid density functional theory
Garwood, T.; Modine, N. A.; Krishna, S.
2017-03-01
The application of first-principles calculations holds promise for greatly improving our understanding of semiconductor superlattices. Developing a procedure to accurately predict band gaps using hybrid density functional theory lays the groundwork for future studies investigating more nuanced properties of these structures. Our approach allows a priori prediction of the properties of SLS structures using only the band gaps of the constituent materials. Furthermore, it should enable direct investigation of the effects of interface structure, e.g., intermixing or ordering at the interface, on SLS properties. In this paper, we present band gap data for various InAs/GaSb type-II superlattice structures calculated using the generalized Kohn-Sham formulation of density functional theory. A PBE0-type hybrid functional was used, and the portion of the exact exchange was tuned to fit the band gaps of the binary compounds InAs and GaSb with the best agreement to bulk experimental values obtained with 18% of the exact exchange. The heterostructures considered in this study are 6 monolayer (ML) InAs/6 ML GaSb, 8 ML InAs/8 ML GaSb and 10 ML InAs/10 ML GaSb with deviations from the experimental band gaps ranging from 3% to 11%.
Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude
2011-07-28
in this work, (B3LYP, B3PW91, BhandHLYP, PBE0, CAM-B3LYP, LC-BLYP, LC-BPW91) only B3PW91 and PBE0 out of the seven provided a consistent quantitative performance for both polarizabilities and hyperpolarizabilities with respect to the ab initio methods utilized here. On the other hand, the long range corrected functionals LC-(U)BLYP and LC-(U)BPW91 (μ = 0.47) failed to supply quantitatively accurate hyperpolarizability results in all the studied clusters while the CAM-(U)B3LYP functional performs satisfactory only in the case of the Na and K doped systems. © 2011 American Institute of Physics
Brea, Roberto J.; Hardy, Michael D.; Devaraj, Neal K.
2015-01-01
There has been increasing interest in utilizing bottom-up approaches to develop synthetic cells. A popular methodology is the integration of functionalized synthetic membranes with biological systems, producing “hybrid” artificial cells. This Concept article covers recent advances and the current state-of-the-art of such hybrid systems. Specifically, we describe minimal supramolecular constructs that faithfully mimic the structure and/or function of living cells, often by controlling the assembly of highly ordered membrane architectures with defined functionality. These studies give us a deeper understanding of the nature of living systems, bring new insights into the origin of cellular life, and provide novel synthetic chassis for advancing synthetic biology. PMID:26149747
Energy Technology Data Exchange (ETDEWEB)
Lee, C.C.; Ku, W.; Hsueh, H.C.
2010-08-30
Within the framework of time-dependent density-functional theory (TDDFT), we derive the dynamical linear response of local-density approximation plus U functional and benchmark it on NiO, a prototypical Mott insulator. Formulated using real-space Wannier functions, our computationally inexpensive framework gives detailed insights into the formation of tightly bound Frenkel excitons with reasonable accuracy. Specifically, a strong hybridization of multiple excitons is found to significantly modify the exciton properties. Furthermore, our study exposes a significant generic limitation of adiabatic approximation in TDDFT with hybrid functionals and in existing Bethe-Salpeter-equation approaches, advocating the necessity of strongly energy-dependent kernels in future development.
Kesharwani, Manoj Kumar; Martin, Jan M L
2015-01-01
We have compared the performance of Grimme style DH/DSD and Zhang-Xu-Goddard type xDH/xDSD forms for double hybrids. In the DH and DSD forms, KS orbitals with elevated HF exchange and damped DFT correlation are used, while in the xDH and xDSD forms, the KS orbitals are obtained from a conventional hybrid functional with undamped DFT correlation. Generally, the difference in performance between DSD and xDSD functionals is small, slightly favoring xDSD. Augmentation of the xDH form with either same-spin MP2 correlation or a dispersion correction markedly improves performance. Best xDSD results appear to be obtained for orbitals obtained with `exact exchange' fractions in the 50-70% range. The orbitals for xDSD appear to be fairly transferable between different correlation functionals.
Synthesis and Properties of Cellulose-Functionalized POSS-SiO2/TiO2 Hybrid Composites.
Hong, Gwang-Wook; Ramesh, Sivalingam; Kim, Joo-Hyung; Kim, Hyeon-Ju; Lee, Ho-Saeng
2015-10-01
The mechanical, thermal, optical, electrical and morphological properties of cellulose, an excellent natural biomaterial, can be improved by organic-inorganic hybrid composite methods. Based on the pristine properties of cellulose, the preparation of cellulose-metal oxide hybrid nanocomposites using a dispersion process of nanoparticles into the cellulose host matrix by traditional methods, has limitations. Recently, the functionalized cellulose-polymer-based materials were considered to be an important class of high-performance materials, providing the synthesis of various functional hybrid nanocomposites using a sol-gel method. Transparent cellulose-POSS-amine-silica/titania hybrids were prepared by an in-situ sol-gel process in the presence of γ-aminopropyltrimethoxylsilane (γ-APTES). The methodology involves the formation of covalent bonding between the cellulose-POSS amine and SiO2/TiO2 hybrid nanocomposite material. An analysis of the synthesized hybrid material by Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, differential thermal calorimetry, scanning electron microscopy, and transmission electron microscopy indicated that the silica/titania nanoparticles were bonded covalently and dispersed uniformly into the cellulose-POSS amine matrix. In addition, biological properties of the cellulose-POSS-silica/titania hybrid material were examined using an antimicrobial test against pathogenic bacteria, such as Bacillus cereus (F481072) and E. coli (ATCC35150) for the bacterial effect.
Moshonov, Moshe; Frey, Gitti L
2015-11-24
The simplicity and versatility of block copolymer self-assembly offers their use as templates for nano- and meso-structured materials. However, in most cases, the material processing requires multiple steps, and the block copolymer is a sacrificial building block. Here, we combine a self-assembled block copolymer template and atomic layer deposition (ALD) of a metal oxide to generate functional hybrid films in a simple process with no etching or burning steps. This approach is demonstrated by using the crystallization-induced self-assembly of a rod-coil block copolymer, P3HT-b-PEO, and the ALD of ZnO. The block copolymer self-assembles into fibrils, ∼ 20 nm in diameter and microns long, with crystalline P3HT cores and amorphous PEO corona. The affinity of the ALD precursors to the PEO corona directs the exclusive deposition of crystalline ZnO within the PEO domains. The obtained hybrid structure possesses the properties desired for photovoltaic films: donor-acceptor continuous nanoscale interpenetrated networks. Therefore, we integrated the films into single-layer hybrid photovoltaics devices, thus demonstrating that combining self-assembly of functional block copolymers and ALD is a simple approach to direct desired complex hybrid morphologies.
Chung, Kyung-Hoon; Koo, Bon-Gil; Kim, Howon; Yoon, Jong Keon; Kim, Ji-Hoon; Kwon, Young-Kyun; Kahng, Se-Jong
2012-05-28
The electronic structures of self-assembled hybrid chains comprising Ag atoms and organic molecules were studied using scanning tunneling microscopy (STM) and spectroscopy (STS) in parallel with density functional theory (DFT). Hybrid chains were prepared by catalytic breaking of Br-C bonds in 4,4″-dibromo-p-terphenyl molecules, followed by spontaneous formation of Ag-C bonds on Ag(111). An atomic model was proposed for the observed hybrid chain structures. Four electronic states were resolved using STS measurements, and strong energy dependence was observed in STM images. These results were explained using first-principles calculations based on DFT.
Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO
Institute of Scientific and Technical Information of China (English)
HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)
2002-01-01
The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.
On the binding mode of urease active site inhibitors: A density functional study
Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M.
The way with which boric acid, a rapid reversible competitive inhibitor, binds the urease active site was explored at density functional B3LYP level of theory. The catalytic core of the enzyme was simulated by two models of different size. In both cases, amino acid residues belonging to the inner and to the outer coordination spheres of nickel ions were replaced by smaller molecular species. Contrary to the experimental indication that attributes the inhibitory ability of this acid to the lack of a nucleophilic attack by the enzyme to the boron atom, we instead found that another possibility exists based on the presence of a strong covalent sigma bond between boron and urease that we think can be hardly broken to allow any course of the reaction.
Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: A density functional study
DEFF Research Database (Denmark)
Hemmingsen, Lars Bo Stegeager; Olsen, L.; Antony, J.
2003-01-01
. For most studied systems, the tetrahedral structure is a stable intermediate. Moreover, the C-N bond in the lactam ring is intact in this intermediate, as well as in the following transition state-its cleavage is induced by proton transfer to the nitrogen atom in the lactam ring. However, for the model...... with Asp as a proton shuttle, attack of the zinc-bond hydroxide ion seems to be concerted with the proton transfer. We have also studied the effect of replacing one of the histidine ligands by an asparagine or glutamine residue, giving a zinc site representative of other subclasses of metallo......Two central steps in the hydrolysis of lactam antibiotics catalyzed by mononuclear metallo-beta-lactamases, formation of the tetrahedral intermediate and its breakdown by proton transfer, are studied for model systems using the density functional B3LYP method. Metallo-beta-lactamases have two metal...
Density Functional Theory Study of the Interaction between Thymine and Luteolin
Institute of Scientific and Technical Information of China (English)
王晓岚; 蔡皖飞; 郑妍; 李来才; 田安民
2012-01-01
The density function B3LYP method has been used to optimize the geometries of the luteolin, thymine and lute- olin-thymine complexes at 6-31＋G＊ basis. The vibrational frequencies have been studied at the same level to ana- lyze these seventeen complexes, respectively. Theories of atoms in molecules （AIM） and natural bond orbital （NBO） have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of the complexes corrected by basis set superposition error are between -93.00-76.69 kJ/mol. The calculating results indicate that strong hydrogen bonding interactions have been found in the luteolin-thymine complexes.
Rajavel, A.; Aditya Prasad, A.; Jeyakumar, T.
2017-02-01
The structural features of conformational isomerism in 4-isopropylbenzylidine thiophene-2-carbohydrazide (ITC) polymorphs have been investigated to conquer distinguishable strong Nsbnd H⋯O and weak Csbnd H⋯S hydrogen bond interactions. The single crystals were grown at constant temperature and have characterized by density functional theory computations using B3LYP method by 3-21G basis set. The conformational isomers of ITC were compared and spectroscopically characterized by FT-IR and Raman spectroscopy. The bulk phases were studied by the powder X-ray diffraction patterns. External morphology of ITC was discussed using scanning electron microscopic and transmission electron microscopic studies. Comparisons between various types of intermolecular interactions in the two polymorphic forms have been quantified via Fingerprint and Hirshfeld surface analysis. DFT computations were used to illustrate molecular electrostatic potential, HOMO-LUMO, mulliken atomic charges and electron density of states.
Energy Technology Data Exchange (ETDEWEB)
Wang Xiaowei; Wang Qiang, E-mail: qiangwang@cjlu.edu.cn [Department of Quality and Safety Engineering, China Jiliang University, Hangzhou, 310018 (China)
2011-02-01
In the room temperature and nitrogen conditions, we presented well-resolved absorption spectra and indexes of refraction of bactericide molecules in the far infrared radiation (FIR) spectral region recorded by terahertz time-domain spectroscopy (THz-TDS). As illustrative examples we discussed the absorption spectra of captan and folpet in THz region. The absorption coefficient and index of refraction of them were obtained. Meanwhile, density functional theory (DFT) with software package Gaussian 03 using B3LYP theory was employed for optimization and vibration analysis. With the help of Gaussian View 3.09, the distinct absorption peaks of those molecules were assigned with reliable accuracy. They were caused by intermolecular hydrogen-bonding, molecular torsion or vibration modes, absorption of water molecules, etc. As the absorption spectra are highly sensitive to the overall structure and configuration of the molecules, the THz-TDS procedure can provide a direct fingerprint of the molecular structure or conformational state of a compound.
Functionalization of SBA-15 mesoporous silica by Cu-phosphonate units: Probing of synthesis route
Laskowski, Lukasz; Laskowska, Magdalena
2014-12-01
Mesoporous silica SBA-15 containing propyl-copper phosphonate units was investigated. The structure of mesoporous samples was tested by N2 isothermal sorption (BET and BHJ analysis), TEM microscopy and X-Ray scattering. Quantitative analysis EDX has given information about proportions between component atoms in the sample. Quantitative elemental analysis has been carried out to support EDX. To examine bounding between copper atoms and phosphonic units the Raman spectroscopy was carried out. As a support of Raman scattering, the theoretical calculations were made based on density functional theory, with the B3LYP method. By comparison of the calculated vibrational spectra of the molecule with experimental results, distribution of the active units inside silica matrix has been determined.
Density functional theory study of neutral AlSn(n = 2-9) clusters
Institute of Scientific and Technical Information of China (English)
Li Ting-Xin; Wang Lin; Wang Fei; Chen Jun; Jiang Zhen-Yi; Li Li-Sha
2011-01-01
This paper investigates the geometrical structures and relative stabilities of neutral AlSn(n = 2-9) using the density functional theory. Structural optimisation and frequency analysis are performed at the B3LYP/6-311G(d) level. The ground state structures of the AlSn show that the sulfur atoms prefer not only to evenly distribute on both sides of the aluminum atom but also to form stable structures in AlSn clusters. The structures of pure Sn are fundamentally changed due to the doping of the Al atom. The fragmentation energies and the second-order energy differences are calculated and discussed. Among neutral AlSn(n = 2-9) clusters, AlS4 and AlS6 are the most stable.
Infrared and density functional theory studies of formic acid hydrate clusters in noble gas matrices
Ito, Fumiyuki
2016-08-01
Infrared absorption spectra of formic acid hydrate clusters (HCOOH)m(H2O)n have been measured in noble gas matrices (Ar and Kr). The concentration dependence of the spectra and the comparison with a previous experimental study on HCOOH(H2O) and HCOOH(H2O)2 [Geoge et al., Spectrochim. Acta, Part A 60 (2004) 3225] led to the identification of large clusters. Density functional theory calculations at the B3LYP-DCP/6-31+G(2d,2p) level were carried out to determine the anharmonic vibrational properties of the clusters, enabling a consistent assignment of the observed vibrational peaks to specific clusters.
Institute of Scientific and Technical Information of China (English)
LI; Ming; ZHENG; Wenxu
2006-01-01
The enantioselective reduction of keto oxime ether with borane catalyzed by oxazaborolidine is discussed by the density functional theory (DFT) method. The main intermediates and transition states for this reaction are optimized completely at the B3LYP/6-31g(d) level, and the transition states are verified by vibrational modes. As shown, the chirality-controlled steps for this reaction are the hydride transfer from borane to carbonyl carbon and oxime carbon of keto oxime ether, and the chirality for the reduced products is determined in these two reaction steps. In all examined reaction paths, the first hydride is transferred via a six-membered ring and the second hydride via a five-membered ring or a four-membered ring.
A new hybrid genetic algorithm for optimizing the single and multivariate objective functions
Energy Technology Data Exchange (ETDEWEB)
Tumuluru, Jaya Shankar [Idaho National Laboratory; McCulloch, Richard Chet James [Idaho National Laboratory
2015-07-01
In this work a new hybrid genetic algorithm was developed which combines a rudimentary adaptive steepest ascent hill climbing algorithm with a sophisticated evolutionary algorithm in order to optimize complex multivariate design problems. By combining a highly stochastic algorithm (evolutionary) with a simple deterministic optimization algorithm (adaptive steepest ascent) computational resources are conserved and the solution converges rapidly when compared to either algorithm alone. In genetic algorithms natural selection is mimicked by random events such as breeding and mutation. In the adaptive steepest ascent algorithm each variable is perturbed by a small amount and the variable that caused the most improvement is incremented by a small step. If the direction of most benefit is exactly opposite of the previous direction with the most benefit then the step size is reduced by a factor of 2, thus the step size adapts to the terrain. A graphical user interface was created in MATLAB to provide an interface between the hybrid genetic algorithm and the user. Additional features such as bounding the solution space and weighting the objective functions individually are also built into the interface. The algorithm developed was tested to optimize the functions developed for a wood pelleting process. Using process variables (such as feedstock moisture content, die speed, and preheating temperature) pellet properties were appropriately optimized. Specifically, variables were found which maximized unit density, bulk density, tapped density, and durability while minimizing pellet moisture content and specific energy consumption. The time and computational resources required for the optimization were dramatically decreased using the hybrid genetic algorithm when compared to MATLAB's native evolutionary optimization tool.
Wungu, T. D. K.; Marsha, S. E.; Widayani; Suprijadi
2017-07-01
In order to find an alternative biosensor material which enables to detect the glucose level, therefore in this study, the interaction between Methacrylic Acid (MAA) based Molecularly Imprinted Polymer (MIP) with D-Glucose is investigated using the Density Functional Theory (DFT). The aim of this study is to determine whether a molecule of the MAA can be functioned as a bio-sensing of glucose. In this calculation, the Gaussian 09 with B3LYP and 631+G(d) basis sets is used to calculate all electronic properties. It is found that the interaction between a molecule of MAA and a molecule of D-Glucose was observed through the shortened distance between the two molecules. The binding energy of MAA/D-glucose and the Mulliken population analysis are investigated for checking possible interaction. From analysis, the MAA based MIP can be used as a bio-sensing material.
The Variety of Carbon-Metal Bonds inside Cu-ZSM-5 Zeolites: A Density Functional Theory Study
Directory of Open Access Journals (Sweden)
Takashi Yumura
2010-04-01
Full Text Available Large-scale density functional theory calculations (DFT found various types of binding of an unsaturated hydrocarbon (C2H2 and C2H4 to a ZSM-5 zeolite extraframework copper cation. We employed the DFT calculations based on the B3LYP functional to obtain local minima of an unsaturated hydrocarbon adsorbed on one or two copper cations embedded inside ZSM-5, and then compared their stabilization energies. The DFT results show that the stabilization energies are strongly dependent on the copper coordination environment as well as configurations of two copper cations. Consequently, the inner copper-carbon bonds are influenced substantially by a nanometer-scale cavity of ZSM-5.
Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin
2016-12-01
Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.
Range-separated double-hybrid density-functional theory applied to periodic systems
Sansone, Giuseppe; Usvyat, Denis; Toulouse, Julien; Sharkas, Kamal; Maschio, Lorenzo
2015-01-01
Quantum chemistry methods exploiting density-functional approximations for short-range electron-electron interactions and second-order M{{\\o}}ller-Plesset (MP2) perturbation theory for long-range electron-electron interactions have been implemented for periodic systems using Gaussian-type basis functions and the local correlation framework. The performance of these range-separated double hybrids has been benchmarked on a significant set of systems including rare-gas, molecular, ionic, and covalent crystals. The use of spin-component-scaled MP2 for the long-range part has been tested as well. The results show that the value of $\\mu$ = 0.5 bohr^{--1} for the range-separation parameter usually used for molecular systems is also a reasonable choice for solids. Overall, these range-separated double hybrids provide a good accuracy for binding energies using basis sets of moderate sizes such as cc-pVDZ and aug-cc-pVDZ.
Range-separated double-hybrid density-functional theory applied to periodic systems
Energy Technology Data Exchange (ETDEWEB)
Sansone, Giuseppe; Civalleri, Bartolomeo; Maschio, Lorenzo, E-mail: lorenzo.maschio@unito.it [Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre, Università di Torino, via Giuria 5, I-10125 Torino (Italy); Usvyat, Denis [Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstrasse 31, D-93040 Regensburg (Germany); Toulouse, Julien [Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris (France); CNRS, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris (France); Sharkas, Kamal [Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000 (United States)
2015-09-14
Quantum chemistry methods exploiting density-functional approximations for short-range electron-electron interactions and second-order Møller-Plesset (MP2) perturbation theory for long-range electron-electron interactions have been implemented for periodic systems using Gaussian-type basis functions and the local correlation framework. The performance of these range-separated double hybrids has been benchmarked on a significant set of systems including rare-gas, molecular, ionic, and covalent crystals. The use of spin-component-scaled MP2 for the long-range part has been tested as well. The results show that the value of μ = 0.5 bohr{sup −1} for the range-separation parameter usually used for molecular systems is also a reasonable choice for solids. Overall, these range-separated double hybrids provide a good accuracy for binding energies using basis sets of moderate sizes such as cc-pVDZ and aug-cc-pVDZ.
High performance hybrid functional Petri net simulations of biological pathway models on CUDA.
Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru
2011-01-01
Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.
A Hybrid PSO-BFGS Strategy for Global Optimization of Multimodal Functions.
Shutao Li; Mingkui Tan; Tsang, I W; Kwok, James Tin-Yau
2011-08-01
Particle swarm optimizer (PSO) is a powerful optimization algorithm that has been applied to a variety of problems. It can, however, suffer from premature convergence and slow convergence rate. Motivated by these two problems, a hybrid global optimization strategy combining PSOs with a modified Broyden-Fletcher-Goldfarb-Shanno (BFGS) method is presented in this paper. The modified BFGS method is integrated into the context of the PSOs to improve the particles' local search ability. In addition, in conjunction with the territory technique, a reposition technique to maintain the diversity of particles is proposed to improve the global search ability of PSOs. One advantage of the hybrid strategy is that it can effectively find multiple local solutions or global solutions to the multimodal functions in a box-constrained space. Based on these local solutions, a reconstruction technique can be adopted to further estimate better solutions. The proposed method is compared with several recently developed optimization algorithms on a set of 20 standard benchmark problems. Experimental results demonstrate that the proposed approach can obtain high-quality solutions on multimodal function optimization problems.
Rong, Yang; Bin, Tang; Tao, Gao; BingYun, Ao
2016-06-01
Hybrid density functional theory is employed to systematically investigate the structural, magnetic, vibrational, thermodynamic properties of plutonium monocarbide (PuC and PuC0.75). For comparison, the results obtained by DFT, DFT + U are also given. For PuC and PuC0.75, Fock-0.25 hybrid functional gives the best lattice constants and predicts the correct ground states of antiferromagnetic (AFM) structure. The calculated phonon spectra suggest that PuC and PuC0.75 are dynamically stable. Values of the Helmholtz free energy ΔF, internal energy ΔE, entropy S, and constant-volume specific heat C v of PuC and PuC0.75 are given. The results are in good agreement with available experimental or theoretical data. As for the chemical bonding nature, the difference charge densities, the partial densities of states and the Bader charge analysis suggest that the Pu-C bonds of PuC and PuC0.75 have a mixture of covalent character and ionic character. The effect of carbon vacancy on the chemical bonding is also discussed in detail. We expect that our study can provide some useful reference for further experimental research on the phonon density of states, thermodynamic properties of the plutonium monocarbide. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160 and 21401173).
Feasibility of a Hybrid Brain-Computer Interface for Advanced Functional Electrical Therapy
Directory of Open Access Journals (Sweden)
Andrej M. Savić
2014-01-01
Full Text Available We present a feasibility study of a novel hybrid brain-computer interface (BCI system for advanced functional electrical therapy (FET of grasp. FET procedure is improved with both automated stimulation pattern selection and stimulation triggering. The proposed hybrid BCI comprises the two BCI control signals: steady-state visual evoked potentials (SSVEP and event-related desynchronization (ERD. The sequence of the two stages, SSVEP-BCI and ERD-BCI, runs in a closed-loop architecture. The first stage, SSVEP-BCI, acts as a selector of electrical stimulation pattern that corresponds to one of the three basic types of grasp: palmar, lateral, or precision. In the second stage, ERD-BCI operates as a brain switch which activates the stimulation pattern selected in the previous stage. The system was tested in 6 healthy subjects who were all able to control the device with accuracy in a range of 0.64–0.96. The results provided the reference data needed for the planned clinical study. This novel BCI may promote further restoration of the impaired motor function by closing the loop between the “will to move” and contingent temporally synchronized sensory feedback.
Hybrid ultrasound and dual-wavelength optoacoustic biomicroscopy for functional neuroimaging
Rebling, Johannes; Estrada, Hector; Zwack, Michael; Sela, Gali; Gottschalk, Sven; Razansky, Daniel
2017-03-01
Many neurological disorders are linked to abnormal activation or pathological alterations of the vasculature in the affected brain region. Obtaining simultaneous morphological and physiological information of neurovasculature is very challenging due to the acoustic distortions and intense light scattering by the skull and brain. In addition, the size of cerebral vasculature in murine brains spans an extended range from just a few microns up to about a millimeter, all to be recorded in 3D and over an area of several dozens of mm2. Numerous imaging techniques exist that excel at characterizing certain aspects of this complex network but are only capable of providing information on a limited spatiotemporal scale. We present a hybrid ultrasound and dual-wavelength optoacoustic microscope, capable of rapid imaging of murine neurovasculature in-vivo, with high spatial resolution down to 12 μm over a large field of view exceeding 50mm2. The dual wavelength imaging capability allows for the visualization of functional blood parameters through an intact skull while pulse-echo ultrasound biomicroscopy images are captured simultaneously by the same scan head. The flexible hybrid design in combination with fast high-resolution imaging in 3D holds promise for generating better insights into the architecture and function of the neurovascular system.
Huang, Lulu; Matta, Chérif F; Massa, Lou
2011-11-17
We investigate anew the possible equilibrium geometries of ion induced dipole clusters of hydrogen molecular ions, of molecular formula H(n)(-) (3 ≤ n-odd ≤ 13). Our previous publications [Sapse, A. M.; et al. Nature 1979, 278, 332; Rayez, J. C.; et al., J. Chem. Phys. 1981, 75, 5393] indicated these molecules would have a shallow minimum and adopt symmetrical geometries that accord with the valence shell electron pair repulsion (VSEPR) rules for geometries defined by electron pairs surrounding a central point of attraction. These earlier calculations were all based upon Hartree-Fock (HF) calculations with a fairly small basis of atomic functions, except for the H3(-) ion for which configuration interaction (CI) calculations were carried out. A related paper [Hirao, K.; et al., Chem. Phys. 1983, 80, 237] carried out similar calculations on the same clusters, finding geometries similar to our earlier calculations. However, although that paper argued that the stabilization energy of negative ion clusters H(n)(-) is small, vibration frequencies for the whole set of clusters was not reported, and so a definitive assertion of a true equilibrium was not present. In this paper we recalculate the energetics of the ion induced dipole clusters using density function theory (DFT) B3LYP method calculations in a basis of functions (6-311++G(d,p)). By calculating the vibration frequencies of the VSEPR geometries, we prove that in general they are not true minima because not all the resulting frequencies correspond to real values. By searching the energy surface of the B3LYP calculations, we find the true minimum geometries, which are surprising configurations and are perhaps counterintuitive. We calculate the total energy and binding energy of the new geometries. We also calculate the bond paths associated with the quantum theory of atoms in molecules (QTAIM). The B3LYP/6-311++G(d,p) results, for each molecule, deliver bond paths that radiate between each polarized H2
Stochastic Optimally-Tuned Ranged-Separated Hybrid Density Functional Theory
Neuhauser, Daniel; Cytter, Yael; Baer, Roi
2015-01-01
We develop a stochastic formulation of the optimally-tuned range-separated hybrid density functional theory which enables significant reduction of the computational effort and scaling of the non-local exchange operator at the price of introducing a controllable statistical error. Our method is based on stochastic representations of the Coulomb convolution integral and of the generalized Kohn-Sham density matrix. The computational cost of the approach is similar to that of usual Kohn-Sham density functional theory, yet it provides much more accurate description of the quasiparticle energies for the frontier orbitals. This is illustrated for a series of silicon nanocrystals up to sizes exceeding 3000 electrons. Comparison with the stochastic GW many-body perturbation technique indicates excellent agreement for the fundamental band gap energies, good agreement for the band-edge quasiparticle excitations, and very low statistical errors in the total energy for large systems. The present approach has a major advan...
Li, Li
2016-01-01
© 2016 The Royal Society of Chemistry. The solubility behavior of Hf and Zr based hybrid nanoparticles with different surface ligands in different concentrations of photoacid generator as potential EUV photoresists was investigated in detail. The nanoparticles regardless of core or ligand chemistry have a hydrodynamic diameter of 2-3 nm and a very narrow size distribution in organic solvents. The Hansen solubility parameters for nanoparticles functionalized with IBA and 2MBA have the highest contribution from the dispersion interaction than those with tDMA and MAA, which show more polar character. The nanoparticles functionalized with unsaturated surface ligands showed more apparent solubility changes after exposure to DUV than those with saturated ones. The solubility differences after exposure are more pronounced for films containing a higher amount of photoacid generator. The work reported here provides material selection criteria and processing strategies for the design of high performance EUV photoresists.
Generation of novel functional metalloproteins via hybrids of cytochrome c and peroxidase.
Ying, Tianlei; Zhong, Fangfang; Wang, Zhong-Hua; Xie, Jin; Tan, Xiangshi; Huang, Zhong-Xian
2013-06-01
The continued interest in protein engineering has led to intense efforts in developing novel stable enzymes, which could not only give boost to industrial and biomedical applications, but also enhance our understanding of the structure-function relationships of proteins. We present here the generation of three hybrid proteins of cytochrome c (cyt c) and peroxidase via structure-based rational mutagenesis of cyt c. Several residues (positions 67, 70, 71 and 80) in the distal heme region of cyt c were mutated to the highly conserved amino acids in the heme pocket of peroxidases. The multiple mutants were found to exhibit high peroxidase activity and conserve the impressive stability of cyt c. We expect that this strategy could be extended to other cases of metalloprotein engineering, and lead to the development of stable and active biocatalysts for industrial uses. Besides, this study also provides insight into the structure-function relationships of hemoproteins.
A hybrid Evolutionary Functional Link Artificial Neural Network for Data mining and Classification
Directory of Open Access Journals (Sweden)
Faissal MILI
2012-08-01
Full Text Available This paper presents a specific structure of neural network as the functional link artificial neural network (FLANN. This technique has been employed for classification tasks of data mining. In fact, there are a few studies that used this tool for solving classification problems. In this present research, we propose a hybrid FLANN (HFLANN model, where the optimization process is performed using 3 known population based techniques such as genetic algorithms, particle swarm and differential evolution. This model will be empirically compared to FLANN based back-propagation algorithm and to others classifiers as decision tree, multilayer perceptron based back-propagation algorithm, radical basic function, support vector machine, and K-nearest Neighbor. Our results proved that the proposed model outperforms the other single model. (Abstract
Spin polarized HSE hybrid functional calculations of VO{sub 2}
Energy Technology Data Exchange (ETDEWEB)
Schwingenschloegl, Udo; Wang, Hao [KAUST, PSE Division, Thuwal (Saudi Arabia); Grau-Crespo, Ricardo [University College London, London (United Kingdom)
2013-07-01
We study the rutile (R) and monoclinic (M1) phases of the prototypical compound VO{sub 2} by first principles calculations based on density functional theory, employing the Heyd-Scuseria-Ernzerhof (HSE) screened hybrid functional. Our results show that the HSE lowest-energy solutions for both the low-temperature M1 phase and the high-temperature R phase, which are obtained upon inclusion of spin polarization, are at odds with experimental observations. For the M1 phase the groundstate is (but should not be) magnetic, while the groundstate of the R phase, which is also spin-polarized, is not (but should be) metallic. The energy difference between the low-temperature and high-temperature phases is also in strong discrepancy with the experimental latent heat.
GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking
Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok
2017-07-01
Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.
Li, Li; Chakrabarty, Souvik; Jiang, Jing; Zhang, Ben; Ober, Christopher; Giannelis, Emmanuel P.
2016-01-01
The solubility behavior of Hf and Zr based hybrid nanoparticles with different surface ligands in different concentrations of photoacid generator as potential EUV photoresists was investigated in detail. The nanoparticles regardless of core or ligand chemistry have a hydrodynamic diameter of 2-3 nm and a very narrow size distribution in organic solvents. The Hansen solubility parameters for nanoparticles functionalized with IBA and 2MBA have the highest contribution from the dispersion interaction than those with tDMA and MAA, which show more polar character. The nanoparticles functionalized with unsaturated surface ligands showed more apparent solubility changes after exposure to DUV than those with saturated ones. The solubility differences after exposure are more pronounced for films containing a higher amount of photoacid generator. The work reported here provides material selection criteria and processing strategies for the design of high performance EUV photoresists.The solubility behavior of Hf and Zr based hybrid nanoparticles with different surface ligands in different concentrations of photoacid generator as potential EUV photoresists was investigated in detail. The nanoparticles regardless of core or ligand chemistry have a hydrodynamic diameter of 2-3 nm and a very narrow size distribution in organic solvents. The Hansen solubility parameters for nanoparticles functionalized with IBA and 2MBA have the highest contribution from the dispersion interaction than those with tDMA and MAA, which show more polar character. The nanoparticles functionalized with unsaturated surface ligands showed more apparent solubility changes after exposure to DUV than those with saturated ones. The solubility differences after exposure are more pronounced for films containing a higher amount of photoacid generator. The work reported here provides material selection criteria and processing strategies for the design of high performance EUV photoresists. Electronic supplementary
Oosterhout, Stefan D.; Koster, L. Jan Anton; van Bavel, Svetlana S.; Loos, Joachim; Stenzel, Ole; Thiedmann, Ralf; Schmidt, Volker; Campo, Bert; Cleij, Thomas J.; Lutzen, Laurence; Vanderzande, Dirk; Wienk, Martijn M.; Janssen, Rene A. J.
2011-01-01
The efficiency of polymer - metal oxide hybrid solar cells depends critically on the intimacy of mixing of the two semiconductors. The effect of side chain functionalization on the morphology and performance of conjugated polymer:ZnO solar cells is investigated. Using an ester-functionalized side ch
Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf
2013-03-12
The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.
The Hybrid Aesthetic Functional (HAF) Appliance: A Less Visible Proposal for Functional Orthodontics
2013-01-01
In modern orthodontics, aesthetics appear to have a decisive influence on orthodontic appliance preferences and acceptability. This paper reports the early application of a newly emerged functional device with enhanced aesthetics in a Class II treatment. Patient perspectives and technical considerations are discussed along with recommendations for further design development. It can be assumed that the use of thermoplastic material-based appliances may meet both the therapeutic and aesthetic demands of young age groups. PMID:23956884
Dong, Sheng; Hu, Zhicheng; Zhang, Kai; Yin, Qingwu; Jiang, Xiaofang; Huang, Fei; Cao, Yong
2017-06-20
A cross-linkable dual functional polymer hybrid electron transport layer (ETL) is developed by simply adding an amino-functionalized polymer dopant (PN4N) and a light crosslinker into a commercialized n-type semiconductor (N2200) matrix. It is found that the resulting hybrid ETL not only has a good solvent resistance, facilitating multilayers device fabrication but also exhibits much improved electron transporting/extraction properties due to the doping between PN4N and N2200. As a result, by using PTB7-Th:PC71 BM blend as an active layer, the inverted device based on the hybrid ETL can yield a prominent power conversion efficiency of around 10.07%. More interestingly, photovoltaic property studies of bilayer devices suggest that the absorption of the hybrid ETL contributes to photocurrent and hence the hybrid ETL simultaneously acts as both cathode interlayer material and an electron acceptor. The resulting inverted polymer solar cells function like a novel device architectures with a combination of a bulk heterojunction device and miniature bilayer devices. This work provides new insights on function of ETLs and may be open up a new direction for the design of new ETL materials and novel device architectures to further improve device performance. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Gil, Eun Seok; Park, Sang-Hyug; Tien, Lee W; Trimmer, Barry; Hudson, Samuel M; Kaplan, David L
2010-10-05
A route toward mechanically robust, rapidly actuating, and biologically functionalized polymeric actuators using macroporous soft materials is described. The materials were prepared by combining silk protein and a synthetic polymer (poly(N-isopropylacrylamide) (PNIAPPm)) to form interpenetrating network materials and macroporous structures by freeze-drying, with hundreds of micrometer diameter pores and exploiting the features of both polymers related to dynamic materials and structures. The chemically cross-linked PNIPAAm networks provided stimuli-responsive features, while the silk interpenetrating network formed by inducing protein β-sheet crystallinity in situ for physical cross-links provided material robustness, improved expansion force, and enzymatic degradability. The macroporous hybrid hydrogels showed enhanced thermal-responsive properties in comparison to pure PNIPAAm hydrogels, nonporous silk/PNIPAAm hybrid hydrogels, and previously reported macroporous PNIPAAm hydrogels. These new systems reach near equilibrium sizes in shrunken/swollen states in less than 1 min, with the structural features providing improved actuation rates and stable oscillatory properties due to the macroporous transport and the mechanically robust silk network. Confocal images of the hydrated hydrogels around the lower critical solution temperature (LCST) revealed macropores that could be used to track changes in the real time morphology upon thermal stimulus. The material system transformed from a macroporous to a nonporous structure upon enzymatic degradation. To extend the utility of the system, an affinity platform for a switchable or tunable system was developed by immobilizing biotin and avidin on the macropore surfaces.
Output Tracking Control of Switched Hybrid Systems: A Fliess Functional Expansion Approach
Directory of Open Access Journals (Sweden)
Fenghua He
2013-01-01
Full Text Available The output tracking problem is investigated for a nonlinear affine system with multiple modes of continuous control inputs. We convert the family of nonlinear affine systems under consideration into a switched hybrid system by introducing a multiple-valued logic variable. The Fliess functional expansion is adopted to express the input and output relationship of the switched hybrid system. The optimal switching control is determined for a multiple-step output tracking performance index. The proposed approach is applied to a multitarget tracking problem for a flight vehicle aiming for one real target with several decoys flying around it in the terminal guidance course. These decoys appear as apparent targets and have to be distinguished with the approaching of the flight vehicle. The guidance problem of one flight vehicle versus multiple apparent targets should be considered if no large miss distance might be caused due to the limitation of the flight vehicle maneuverability. The target orientation at each time interval is determined. Simulation results show the effectiveness of the proposed method.
Short- and long-range corrected hybrid density functionals with the D3 dispersion corrections
Wang, Chih-Wei; Chai, Jeng-Da
2016-01-01
We propose a short- and long-range corrected (SLC) hybrid scheme employing 100% Hartree-Fock (HF) exchange at both zero and infinite interelectronic distances, wherein three SLC hybrid density functionals with the D3 dispersion corrections (SLC-LDA-D3, SLC-PBE-D3, and SLC-B97-D3) are developed. SLC-PBE-D3 and SLC-B97-D3 are shown to be accurate for a very diverse range of applications, such as core ionization and excitation energies, thermochemistry, kinetics, noncovalent interactions, dissociation of symmetric radical cations, vertical ionization potentials, vertical electron affinities, fundamental gaps, and valence, Rydberg, and long-range charge-transfer excitation energies. Relative to omegaB97X-D, SLC-B97-D3 provides significant improvement for core ionization and excitation energies and noticeable improvement for the self-interaction, asymptote, energy-gap, and charge-transfer problems, while performing similarly for thermochemistry, kinetics, and noncovalent interactions.
A hybrid density functional view of native vacancies in gallium nitride.
Gillen, Roland; Robertson, John
2013-10-09
We investigated the transition energy levels of the vacancy defects in gallium nitride by means of a hybrid density functional theory approach (DFT). We show that, in contrast to predictions from a recent study on the level of purely local DFT, the inclusion of screened exchange stabilizes the triply positive charge state of the nitrogen vacancy for Fermi energies close to the valence band. On the other hand, the defect levels associated with the negative charge states of the nitrogen vacancy hybridize with the conduction band and turn out to be energetically unfavorable, except for high n-doping. For the gallium vacancy, the increased magnetic splitting between up-spin and down-spin bands due to stronger exchange interactions in sX-LDA pushes the defect levels deeper into the band gap and significantly increases the associated charge transition levels. Based on these results, we propose the ϵ(0| - 1) transition level as an alternative candidate for the yellow luminescence in GaN.
Probing the structure and function of biopolymer-carbon nanotube hybrids with molecular dynamics
Johnson, Robert R.
2009-12-01
active and function as a nanobiosensor with specific recognition of Knob proteins from the adenovirus capsid. Simulation also shows that the rigid CNT damps structural fluctuations in bound proteins, which may have important ramifications for biosensing devices composed of protein-CNT hybrids. These results expand current knowledge of Bio-CNT and demonstrate the effectiveness of MD for investigations of nanobiomolecular systems.
Fermi Surface Topology of Na0.5CoO2 from the Hybrid Density Functional
Institute of Scientific and Technical Information of China (English)
CHEN Zhao-Ying; XIANG Hong-Jun; YANG Jin-Long
2005-01-01
@@ The Fermi surface topology of Na0.5CoO2 is studied using the hybrid density functional theory. We first study a single (CoO2)0.5- layer model with the percentage of the nonlocal Hartree-Fock exchange changing from 0% to 20%. The results show that only when the mixed nonlocal Hartree-Fock exchange is between 1% and 5%, the Fermi surface topology is similar to the experimental one. With 3% HF exchange in the hybrid density functional,considering the effects of Na ions in the Na0.sCoO2 system, we find that the Fermi surface is split to double holes and small gaps open near the intersections between the Brillouin zone and the Fermi surface. Our results show that both the amounts of the nonlocal Hartree-Fock exchange in the hybrid density functional and the Na ions have much influence on the Fermi surface topology.
Directory of Open Access Journals (Sweden)
Loay A. Elalfy
2013-01-01
Full Text Available Density functional theory calculations using B3LYP/3-21G level of theory have been implemented on 6 carbon nanotubes (CNTs structures (3 zigzag and 3 armchair CNTs to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2-3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.
Institute of Scientific and Technical Information of China (English)
Wang Yan-Li; Zhang Jun-Ping; Su Ke-He; Wang Xin; Liu Yan; Sun Xu
2012-01-01
Armchair (n,n) single walled boron nitride nanotubes with n=2-17 are studied by the density functional theory at the B3LYP/3-21G(d) level combined with the periodic boundary conditions for simulating the ultra long model.The results show that the structure parameters and the formation energies bear a strong relationship to n.The fitted analytical equations are developed with correlation coefficients larger than 0.999.The energy gaps of (2,2) and (3,3)tubes are indirect gaps,and the larger tubes (n=4-17) have direct energy gaps.Results show that the armchair boron nitride nanotubes (n=2-17) are insulators with wide energy gaps of between 5.93 eV and 6.23 eV.
Gupta, Mayuri; da Silva, Eirik F; Hartono, Ardi; Svendsen, Hallvard F
2013-08-15
Temperature dependent correlations for enthalpy of deprotonation, carbamate formation, and heat of absorption of the overall reaction between aqueous MEA and MDEA and gaseous CO2 are calculated on the basis of computational chemistry based ln K values input to the Gibbs-Helmholtz equation. Temperature dependency of reaction equilibrium constants for deprotonation and carbamate formation reactions is calculated with the SM8T continuum solvation model coupled with density functional theoretical calculations at the B3LYP/6-311++G(d,p) level of theory. Calculated reaction equilibrium constants and enthalpies of individual reactions and overall heat of absorption are compared against experimental data in the temperature range 273.15-373 K. Temperature dependent correlations for different reaction equilibrium constants and enthalpies of reactions are given. These correlated results can be used in thermodynamic models such as UNIQUAC and NRTL for better understanding of post-combustion CO2 capture solvent chemistry.
Sharma, Ashwani; Ohanessian, Gilles; Clavaguéra, Carine
2014-09-01
The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dipeptide were selected for our study. Geometry and harmonic frequency deviations were investigated, pointing out the contribution of dispersion interactions on diethyl-phosphate, [Gly-pTyr+H](+) and the phosphoric acid dimer. The B3LYP-D functional, followed by CC2 and MP2 methods, revealed significant accuracy for frequency calculations of the majority of the phosphorylated compounds in comparison with available experimental data. These investigations provide a guide to the accurate computation of phosphorylated biological compounds.
Indian Academy of Sciences (India)
G SUBHAPRIYA; S KALYANARAMAN; S GANDHIMATHI; N SURUMBARKUZHALI; V KRISHNAKUMAR
2017-02-01
An extensive theoretical study on the molecular structure and vibrational analysis of 3-amino-4-methoxy benzamide (3A4MBA) was undertaken using density functional theoretical (DFT) method. The possibility of formation of intramolecular hydrogen bonding was identified from structural parameter analysis andconfirmed with the natural bond orbital (NBO), molecular electrostatic potential (MEP) and natural charge analysis. The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bonding in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The lowwavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence of hydrogen bonding. Bands are assigned for vibrational frequencies using DFT/B3LYP/6-311++G** level of theory.
Indian Academy of Sciences (India)
G SUBHAPRIYA; S KALYANARAMAN; S GANDHIMATHI; N SURUMBARKUZHALI; V KRISHNAKUMAR
2017-02-01
An extensive theoretical study on the molecular structure and vibrational analysis of 3-amino-4- methoxy benzamide (3A4MBA) was undertaken using density functional theoretical (DFT) method. The possibility of formation of intramolecular hydrogen bonding was identified from structural parameter analysis and confirmed with the natural bond orbital (NBO), molecular electrostatic potential (MEP) and natural charge analysis. The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bonding in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The lowwavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence of hydrogen bonding. Bands are assigned for vibrational frequencies using DFT/B3LYP/6-311++G** level of theory.
Reda, S M; Soliman, K A
2016-02-01
This work presents an experimental and theoretical study of cyanidin natural dye as a sensitizer for ZnO dye-sensitized solar cells. ZnO nanoparticles were prepared using ammonia and oxalic acid as a capping agent. The calculated average size of the synthesized ZnO with different capping agents was found to be 32.1 nm. Electronic properties of cyanidin and delphinidin dye were studied using density functional theory (DFT) and time-dependent DFT with a B3LYP/6-31G(d,p) level. By comparing the theoretical results with the experimental data, the cyanidin dye can be used as a sensitizer in dye-sensitized solar cells. An efficiency of 0.006% under an AM-1.5 illumination at 100 mW/cm(2) was attained. The influence of dye adsorption time on the solar cell performance is discussed.
Directory of Open Access Journals (Sweden)
Omar Bin Shawkataly
Full Text Available A series of complexes of the type LAuCl where L = tris(p-tolylarsane, tris(m-tolylarsane, bis(diphenylarsanoethane, and tris(naphthylarsane have been synthesized. All of the new complexes, 1-4, have been fully characterized by means of ¹H NMR and ¹³C NMR spectroscopy and single crystal X-ray crystallography. The structures of complexes 1-4 have been determined from X-ray diffraction data. The linear molecules have an average bond distance between gold-arsenic and gold-chlorine of 2.3390Å and 2.2846Å, respectively. Aurophilic interaction was prominent in complex 1 and 3, whereas complex 2 and 4 do not show any such interaction. The intermolecular gold interaction bond length was affected by the electronegativity of the molecule. The computed values calculated at DFT level using B3LYP function are in good agreement with the experimental results.
Padmaja, L.; Amalanathan, M.; Ravikumar, C.; Hubert Joe, I.
2009-10-01
Vibrational analysis of the 2,6-bis(p-methyl benzylidene cyclohexanone) [PMBC] compound was carried out by using NIR FT-Raman and FT-IR spectroscopic techniques. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of PMBC have been investigated with the help of B3LYP/6-31G(d) density functional theory method. The optimized geometry clearly demonstrates cyclohexanone ring chair conformation is changed into half-chair conformation. The shortening of C-H bond length and blue shifting of the CH stretching wavenumber suggest the existence of improper weak C-H⋯O hydrogen bonding, which is confirmed by the natural bond orbital analysis. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy are also calculated.
Institute of Scientific and Technical Information of China (English)
Chen Yuan-Zheng; Li Shuo; Zhou Mi; Li Zuo-Wei; Sun Cheng-Lin
2013-01-01
We report on a temperature-dependent resonance Raman spectral characterization of the polyene chain of canthaxanthin.It is observed that all vibrational intensities of the polyene chain are inversely proportional to temperature,which is analyzed by the resonance Raman effect and the coherent weakly damped electron/lattice vibrations.The increase in intensity of the CC overtone/combination relative to the fundamental with temperature decreasing is detected and discussed in terms of electron/phonon coupling and the activation energy Uop.Moreover,the polyene chain studies using the density functional theory B3LYP/6-31G* level reveal a prominent peak at 1525 cm-1 consisting of two closely spaced modes that are both dominated by C=C stretching coordinates of the polyene chain.
Liaw, Chih-Chuang; Chang, Jia-Lin; Chen, Shou-Fong; Huang, Jhih-Hong; Sie, Jyun-Fu; Cheng, Yung-Yi
2011-11-01
We present the first theoretical study on a pair of diterpene enantiomers of formula C 21H 34O 5, which were newly isolated from plants and identified as 3β,5β-dihydroxy-16 α/ β-methoxyhalima-13(14)-en-15,16-olide. The equilibrium geometries and harmonic vibrational frequencies of their low-lying conformers were obtained by using the AM1 and B3LYP/6-31+G(d) methods. At the optimized geometries, rotatory strengths of six excited states of each conformer were computed by the time-dependent density functional theory. The electronic circular dichroism spectra were simulated by taking Boltzmann averaging and considering the solvent effect, from which the absolute configurations of the enantiomers were determined. Their vibrational circular dichroism spectra were also predicted.
Institute of Scientific and Technical Information of China (English)
LI Xiao-Hong; TANG Zheng-Xin; Abraham F.Jalbout; ZHANG Xian-Zhou; CHENG Xin-Lu
2008-01-01
The N-NO2 bond dissociation energies (BDEs) for 7 energetic materials were computed by means of accurate density functional theory (B3LYP, B3PW91 and B3P86) with 6-31G** and 6-311G** basis sets. By comparing the computed energies and experimental results, we find that the B3P86/6-311G** method can give good results of BDE, which has the mean absolute deviation of 1.30 kcal/mol. In addition, substituent effects were also taken into account. It is noted that the Hammett constants of substituent groups are related to the BDEs of the N-NO2 bond and the bond dissociation energies of the energetic materials studied decrease when increasing the number of NO2 group.
DEFF Research Database (Denmark)
Bohr, Henrik; Jalkanen, Karl J.; Elstner, M.
1999-01-01
Recently we have looked for spectroscopic probes for secondary structural elements in the vibrational spectra of N-acetyl-L-alanine N'-methyl amide (NALANMA), L-alanine (LA), N-acetyl-L-alanyl-L-alanine N'-methyl amide (NALALANMA) and L-alanyl-L-alanine (LALA). Our goal has been to identify...
Bağlayan, Özge; Kaya, Mehmet Fatih; Güneş, Esma; Şenyel, Mustafa
2016-10-01
FT-IR and FT-Raman spectra of 1-butylpiperazine (1bpa) were experimentally recorded in the region of 4000-10 cm-1 and 4000-100 cm-1, respectively. The optimized geometric parameters, conformational equilibria, normal mode frequencies and corresponding vibrational assignments of 1bpa (C8H18N2) are theoretically examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-31++G(d,p) basis set. Also, reliable conformational investigation and vibrational assignments have been performed by the potential energy surface (PES) and potential energy distribution (PED) analysis, respectively. Calculations are made for four possible conformations. According to the experimental and theoretical data, density functional B3LYP method provides reliable results for predicting vibrational wavenumbers and equatorial-equatorial conformer is considered to be the most stable form of 1bpa.
Chen, Feifei; Wang, Yujiao; Xie, Xiaomei; Chen, Meng; Li, Wei
2014-07-15
A comparative study of DFT and DFT-D3 has been carried out on the UV-vis absorption of permethrin, cypermethrin and their β-cyclodextrin inclusion complexes. The TDDFT method with PCM (or COSMO) model was adopted and B3LYP, BLYP and BLYP-D3 functionals were selected. Comparing the simulated spectra with experimental one, we can notice that pure BLYP functional can better reproduce the UV-vis spectra than hybrid B3LYP, but empirical dispersion corrections BLYP-D3 has better performance than BLYP. BLYP-D3 calculations reveal that the main absorption bands of permethrin and cypermethrin arise from the π→π(*) transition, after encapsulated by β-CD to form inclusion complexes, the host-guest intermolecular charge transfer (ICT) makes the main absorption bands to be changed significantly in wavelength and intensity.
Preparation and toxicological assessment of functionalized carbon nanotube-polymer hybrids.
Directory of Open Access Journals (Sweden)
Nikos D Koromilas
Full Text Available Novel Carbon Nanotube-Polymer Hybrids were synthesized as potential materials for the development of membranes for water treatment applications in the field of Membrane Bioreactors (MBRs. Due to the toxicological concerns regarding the use of nanomaterials in water treatment as well as the rising demand for safe drinking water to protect public health, we studied the functionalization of MWCNTs and Thin-MWCNTs as to control their properties and increase their ability of embedment into porous anisotropic polymeric membranes. Following the growth of the hydrophilic monomer on the surface of the properly functionalized CNTs, that act as initiator for the controlled radical polymerization (ATRP of sodium styrene sulfonate (SSNa, the antimicrobial quaternized phosphonium and ammonium salts were attached on CNTs-g-PSSNa through non-covalent bonding. In another approach the covalent attachment of quaternized ammonium polymeric moieties of acrylic acid-vinyl benzyl chloride copolymers with N,N-dimethylhexadecylamine (P(AA12-co-VBCHAM on functionalized CNTs has also been attempted. Finally, the toxicological assessment in terms of cell viability and cell morphological changes revealed that surface characteristics play a major role in the biological response of functionalized CNTs.
Todde, Guido; Hovmöller, Sven; Laaksonen, Aatto
2016-03-01
Four mutated hemoglobin (Hb) variants and wild type hemoglobin as a reference have been investigated using density functional theory methods focusing on oxygen binding. Dispersion-corrected B3LYP functional is used and found to provide reliable oxygen binding energies. It also correctly reproduces the spin distribution of both bound and free heme groups as well as provides correct geometries at their close vicinity. Mutations in hemoglobin are not only an intrigued biological problem and it is also highly important to understand their effects from a clinical point of view. This study clearly shows how even small structural differences close to the heme group can have a significant effect in reducing the oxygen binding of mutated hemoglobins and consequently affecting the health condition of the patient suffering from the mutations. All of the studied mutated Hb variants did exhibit much weaker binding of molecular oxygen compared to the wild type of hemoglobin.
Tsuchimochi, Takashi; Kobayashi, Masato; Nakata, Ayako; Imamura, Yutaka; Nakai, Hiromi
2008-11-15
The Sakurai-Sugiura projection (SS) method was implemented and numerically assessed for diagonalization of the Hamiltonian in time-dependent density functional theory (TDDFT). Since the SS method can be used to specify the range in which the eigenvalues are computed, it may be an efficient tool for use with eigenvalues in a particular range. In this article, the SS method is applied to core excited calculations for which the eigenvalues are located within a particular range, since the eigenvalues are unique to atomic species in molecules. The numerical assessment of formaldehyde molecule by TDDFT with core-valence Becke's three-parameter exchange (B3) plus Lee-Yang-Parr (LYP) correlation (CV-B3LYP) functional demonstrates that the SS method can be used to selectively obtain highly accurate eigenvalues and eigenvectors. Thus, the SS method is a new and powerful alternative for calculating core-excitation energies without high computation costs.
Birke, Ronald L; Znamenskiy, Vasiliy; Lombardi, John R
2010-06-07
Vibrational frequency calculations were made for a Ag(10)-pyridine vertex complex with density functional theory (DFT) for static simulated spectra and with time-dependent DFT (TD-DFT) for preresonance and resonance simulated spectra using both B3LYP/LANL2DZ and BP86/TZP methodologies. In addition, 40 excited states of the complex were calculated and assigned symmetry based on a C(2v) symmetry of the optimized complex found with B3LYP/LANL2DZ. Molecular orbital isosurfaces show that the excited states involve both Ag(10) intercluster excitations and charge-transfer (CT) excitations between the Ag nanocluster and the pyridine molecule. An excitation around 500 nm involving CT from the Ag cluster to pyridine was found in both calculations. For free pyridine, the relative average deviations between unscaled calculated and experimental results were 1.5 cm(-1) for BP86 and 3.1 cm(-1) for the B3LYP calculations. For the complex, simulated spectra at a variety of excitation wavelengths were calculated. In the case of 514 nm excitation, the simulated Raman cross section from the TD-DFT calculations (near the CT resonance) was plotted versus Raman shift frequency and compared with an experimental surface enhanced Raman scattering (SERS) spectrum obtained on an oxidation-reduction cycle, ORC roughened Ag electrode. The BP86 TD-DFT calculation with finite damping term showed a better fit to experimental spectrum with respect to both relative intensities and frequencies. The average deviation of the unscaled BP86 calculations for 16 bands in the experimental spectrum was 13.0 cm(-1). The calculated spectrum in both cases shows many contributions from nontotally symmetric as well as totally symmetric modes, indicating the contribution of Herzberg-Teller (HT) scattering. The simulated intensities of the Raman modes of different symmetry from Ag(10)-pyridine can be correlated with HT intensity borrowing from excited states of given symmetry and decent oscillator strength. These
Diffusion of interstitial oxygen in silicon and germanium: a hybrid functional study
Colleoni, Davide; Pasquarello, Alfredo
2016-12-01
The minimum-energy paths for the diffusion of an interstitial O atom in silicon and germanium are studied through the nudged-elastic-band method and hybrid functional calculations. The reconsideration of the diffusion of O in silicon primarily serves the purpose of validating the procedure for studying the O diffusion in germanium. Our calculations show that the minimum energy path goes through an asymmetric transition state in both silicon and germanium. The stability of these transition states is found to be enhanced by the generation of unpaired electrons in the highest occupied single-particle states. Calculated energy barriers are 2.54 and 2.14 eV for Si and Ge, in very good agreement with corresponding experimental values of 2.53 and 2.08 eV, respectively.
A hybrid density functional study on the electron and hole trap states in anatase titanium dioxide.
Yamamoto, Takenori; Ohno, Takahisa
2012-01-14
We present a theoretical study on electron and hole trap states in the bulk and (001) surface of anatase titanium dioxide using screened hybrid density functional calculations. In both the bulk and surface, calculations suggest that the neutral and ionized oxygen vacancies are possible electron traps. The doubly ionized oxygen vacancy is the most stable in the bulk, and is a candidate for a shallow donor in colorless anatase crystals. The hole trap states are localized at oxygen anions in both the bulk and surface. The self-trapped electron centered at a titanium cation cannot be produced in the bulk, but can be formed at the surface. The electron trap level at the surface oxygen vacancy is consistent with observations by photoelectron spectroscopy. The optical absorptions and luminescence in UV-irradiated anatase nanoparticles are found to come from the surface self-trapped hole and the surface oxygen vacancy.
Oxygen defects in amorphous Al{sub 2}O{sub 3}: A hybrid functional study
Energy Technology Data Exchange (ETDEWEB)
Guo, Zhendong, E-mail: zhendong.guo@epfl.ch; Ambrosio, Francesco; Pasquarello, Alfredo [Chaire de Simulation à l' Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)
2016-08-08
The electronic properties of the oxygen vacancy and interstitial in amorphous Al{sub 2}O{sub 3} are studied via ab initio molecular dynamics simulations and hybrid functional calculations. Our results indicate that these defects do not occur in amorphous Al{sub 2}O{sub 3}, due to structural rearrangements which assimilate the defect structure and cause a delocalization of the associated defect levels. The imbalance of oxygen leads to a nonstoichiometric compound in which the oxygen occurs in the form of O{sup 2–} ions. Intrinsic oxygen defects are found to be unable to trap excess electrons. For low Fermi energies, the formation of peroxy linkages is found to be favored leading to the capture of holes. The relative +2/0 defect levels occur at 2.5 eV from the valence band.
Directory of Open Access Journals (Sweden)
Li Mao
2016-01-01
Full Text Available Artificial bee colony (ABC algorithm has good performance in discovering the optimal solutions to difficult optimization problems, but it has weak local search ability and easily plunges into local optimum. In this paper, we introduce the chemotactic behavior of Bacterial Foraging Optimization into employed bees and adopt the principle of moving the particles toward the best solutions in the particle swarm optimization to improve the global search ability of onlooker bees and gain a hybrid artificial bee colony (HABC algorithm. To obtain a global optimal solution efficiently, we make HABC algorithm converge rapidly in the early stages of the search process, and the search range contracts dynamically during the late stages. Our experimental results on 16 benchmark functions of CEC 2014 show that HABC achieves significant improvement at accuracy and convergence rate, compared with the standard ABC, best-so-far ABC, directed ABC, Gaussian ABC, improved ABC, and memetic ABC algorithms.
Why the Heyd-Scuseria-Ernzerhof hybrid functional description of VO2 phases is not correct
Grau-Crespo, Ricardo
2012-08-06
In contrast with recent claims that the Heyd-Scuseria-Ernzerhof (HSE) screened hybrid functional can provide a good description of the electronic and magnetic structures of VO2 phases, we show here that the HSE lowest-energy solutions for both the low-temperature monoclinic (M1) phase and the high-temperature rutile (R) phase, which are obtained upon inclusion of spin polarization, are at odds with experimental observations. For the M1 phase the ground state is (but should not be) magnetic, while the ground state of the R phase, which is also spin polarized, is not (but should be) metallic. The energy difference between the low-temperature and high-temperature phases has strong discrepancies with the experimental latent heat.
Implementation of Special Function Unit for Vertex Shader Processor Using Hybrid Number System
Directory of Open Access Journals (Sweden)
Avni Agarwal
2014-01-01
Full Text Available The world of 3D graphic computing has undergone a revolution in the recent past, making devices more computationally intensive, providing high-end imaging to the user. The OpenGL ES Standard documents the requirements of graphic processing unit. A prime feature of this standard is a special function unit (SFU, which performs all the required mathematical computations on the vertex information corresponding to the image. This paper presents a low-cost, high-performance SFU architecture with improved speed and reduced area. Hybrid number system is employed here in order to reduce the complexity of operations by suitably switching between logarithmic number system (LNS and binary number system (BNS. In this work, reduction of area and a higher operating frequency are achieved with almost the same power consumption as that of the existing implementations.
Doping strategies to control A-centres in silicon: Insights from hybrid density functional theory
Wang, Hao
2014-01-01
Hybrid density functional theory is used to gain insights into the interaction of intrinsic vacancies (V) and oxygen-vacancy pairs (VO, known as A-centres) with the dopants (D) germanium (Ge), tin (Sn), and lead (Pb) in silicon (Si). We determine the structures as well as binding and formation energies of the DVO and DV complexes. The results are discussed in terms of the density of states and in view of the potential of isovalent doping to control A-centres in Si. We argue that doping with Sn is the most efficient isovalent doping strategy to suppress A-centres by the formation of SnVO complexes, as these are charge neutral and strongly bound. © 2014 the Owner Societies.
G-centers in irradiated silicon revisited: A screened hybrid density functional theory approach
Energy Technology Data Exchange (ETDEWEB)
Wang, H.; Schwingenschlögl, U., E-mail: Udo.Schwingenschlogl@kaust.edu.sa [PSE Division, KAUST, Thuwal 23955-6900 (Saudi Arabia); Chroneos, A., E-mail: Alex.Chroneos@open.ac.uk [Engineering and Innovation, The Open University, Milton Keynes MK7 6AA (United Kingdom); Department of Materials, Imperial College, London SW7 2AZ (United Kingdom); Londos, C. A.; Sgourou, E. N. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece)
2014-05-14
Electronic structure calculations employing screened hybrid density functional theory are used to gain fundamental insight into the interaction of carbon interstitial (C{sub i}) and substitutional (C{sub s}) atoms forming the C{sub i}C{sub s} defect known as G-center in silicon (Si). The G-center is one of the most important radiation related defects in Czochralski grown Si. We systematically investigate the density of states and formation energy for different types of C{sub i}C{sub s} defects with respect to the Fermi energy for all possible charge states. Prevalence of the neutral state for the C-type defect is established.
Zeng, Xiang-Yang; Wang, Shu-Guang; Gao, Li-Ping
2010-09-01
As the basic data for virtual auditory technology, head-related transfer function (HRTF) has many applications in the areas of room acoustic modeling, spatial hearing and multimedia. How to individualize HRTF fast and effectively has become an opening problem at present. Based on the similarity and relativity of anthropometric structures, a hybrid HRTF customization algorithm, which has combined the method of principal component analysis (PCA), multiple linear regression (MLR) and database matching (DM), has been presented in this paper. The HRTFs selected by both the best match and the worst match have been applied into obtaining binaurally auralized sounds, which are then used for subjective listening experiments and the results are compared. For the area in the horizontal plane, the localization results have shown that the selection of HRTFs can enhance the localization accuracy and can also abate the problem of front-back confusion.
He, Jiangang; Franchini, Cesare
2017-08-16
In this paper we assess the predictive power of the self-consistent hybrid functional scPBE0 in calculating the band gap of oxide semiconductors. The computational procedure is based on the self-consistent evaluation of the mixing parameter α by means of an iterative calculation of the static dielectric constant using the perturbation expansion after discretization (PEAD) method and making use of the relation α = 1/ε_{∞}. Our materials dataset is formed by 30 compounds covering a wide range of band gaps and dielectric properties, and includes materials with a wide spectrum of application as thermoelectrics, photocatalysis, photovoltaics, transparent conducting oxides, and refractory materials. Our results show that the scPBE0 functional provides better band gaps than the non self-consistent hybrids PBE0 and HSE06, but scPBE0 does not show significant improvement on the description of the static dielectric constants. Overall, the scPBE0 data exhibit a mean absolute percentage error of 14 % (band gaps) and 10 % (α = 1/ε_{∞}). For materials with weak dielectric screening and large excitonic biding energies scPBE0, unlike PBE0 and HSE06, overestimates the band gaps, but the value of the gap become very close to the experimental value when excitonic effects are included (e.g. for SiO_{2}). However, special caution must be given to the compounds with small band gaps due to the tendency of scPBE0 to overestimate the dielectric constant in proximity of the metallic limit. © 2017 IOP Publishing Ltd.
D., I. Bilc; R., Orlando; R., Shaltaf; G., M. Rignanese; J., Íñiguez; Ph., Ghosez
2008-01-01
Using a linear combination of atomic orbitals approach, we report a systematic comparison of various Density Functional Theory (DFT) and hybrid exchange-correlation functionals for the prediction of the electronic and structural properties of prototypical ferroelectric oxides. It is found that none of the available functionals is able to provide, at the same time, accurate electronic and structural properties of the cubic and tetragonal phases of BaTiO$_3$ and PbTiO$_3$. Some, although not al...
Energy Technology Data Exchange (ETDEWEB)
Luca, V. [Programa Nacional de Gestion de Residuos Radiactivos, Comision Nacional de Energia Atomica, Centro Atomico Constituyentes, Av. General, Paz 1499, 1650 San Martin, Provincia de Buenos Aires (Argentina)
2013-07-01
Functionalized meso-porous materials are a class of hybrid organic-inorganic material in which a meso-porous metal oxide framework is functionalized with multifunctional organic molecules. These molecules may contain one or more anchor groups that form strong bonds to the pore surfaces of the metal oxide framework and free functional groups that can impart and or modify the functionality of the material such as for binding metal ions in solution. Such materials have been extensively studied over the past decade and are of particular interest in absorption applications because of the tremendous versatility in choosing the composition and architecture of the metal oxide framework and the nature of the functional organic molecule as well as the efficient mass transfer that can occur through a well-designed hierarchically porous network. A sorbent for nuclear applications would have to be highly selective for particular radio nuclides, it would need to be hydrolytically and radiolytically stable, and it would have to possess reasonable capacity and fast kinetics. The sorbent would also have to be available in a form suitable for use in a column. Finally, it would also be desirable if once saturated with radio nuclides, the sorbent could be recycled or converted directly into a ceramic or glass waste form suitable for direct repository disposal or even converted directly into a material that could be used as a transmutation target. Such a cradle-to- grave strategy could have many benefits in so far as process efficiency and the generation of secondary wastes are concerned.This paper will provide an overview of work done on all of the above mentioned aspects of the development of functionalized meso-porous adsorbent materials for the selective separation of lanthanides and actinides and discuss the prospects for future implementation of a cradle-to-grave strategy with such materials. (author)
Cao, Li; Kong, Lei; Kong, Lingqian; Zhang, Xingxiang; Shi, Haifeng
2015-12-01
Hybrid membranes (SPI/ZGO) composed of sulfonated polyimide (SPI) and zwitterionic polymer-functionalized graphene oxide (ZGO) are fabricated via a solution-casting method for vanadium redox flow battery (VRB). Successful preparation of ZGO fillers and SPI/ZGO hybrid membranes are demonstrated by FT-IR, XPS and SEM, indicating that ZGO fillers is homogeneously dispersed into SPI matrix. Through controlling the interfacial interaction between SPI matrix and ZGO fillers, the physicochemical properties, e.g., vanadium ion barrier and proton transport pathway, of hybrid membranes are tuned via the zwitterionic acid-base interaction in the hybrid membrane, showing a high ion selectivity and good stability with the incorporated ZGO fillers. SPI/ZGO-4 hybrid membrane proves a higher cell efficiencies (CE: 92-98%, EE: 65-79%) than commercial Nafion 117 membrane (CE: 89-94%, EE: 59-70%) for VRB application at 30-80 mA cm-2. The assembled VRB with SPI/ZGO-4 membrane presents a stable cycling charge-discharge performance over 280 times, which demonstrates its excellent chemical stability under the strong acidic and oxidizing conditions. SPI/ZGO hybrid membranes show a brilliant perspective for VRB application.
Indian Academy of Sciences (India)
M K Subramanian; P M Anbarasan; S Manimegalai
2010-05-01
Quantum mechanical calculations of energies, geometries and vibrational wave numbers of 7-amino-4-trifluoromethyl coumarin (7A4TFMC) were carried out using Hartree–Fock (HF) and density functional theory (DFT) using hybrid functional BLYP and B3LYP with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by HF and DFT calculations are in good agreement with the experimental X-ray data. The best method to reproduce the experimental wave numbers is B3LYP method with the 6-31G(d,p) basis set. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the infrared spectra of 7A4TFMC was also reported. The entropy of the title compound was also performed at HF using the hybrid functional BLYP and B3LYP with 6-31 G(d,p) as basis set levels of theory. Natural bond orbital (NBO) analysis of the title molecule is also carried out. The theoretical spectrogram for FTIR spectra of the title molecule has been constructed.
Assessment of DFT methods for studying acid gas capture by ionic liquids.
García, Gregorio; Atilhan, Mert; Aparicio, Santiago
2015-10-28
For the first time, this work reports an analysis of the performance of Density Functional methods for studying acid gas capture (CO2 and SO2) by ionic liquids (ILs). The considered functionals were selected as representatives of the available families: pure GGA (PBE and BLYP), hybrid (PBE0 and B3LYP), hybrid meta-GGA (M06, M06-2X and M06-HF), long range corrected (LC-PBEPBE, CAM-B3LYP, ωB97X) and dispersion corrected (PBE-D2, B3LYP-D2 and ωB97XD). Likewise, HF and MP2 were also applied. Binding energies of cation-anion interacting pairs as well as IL-CO2 and IL-SO2 systems were calculated for a set of 54 ILs and compared against MP2/aug-cc-pvDZ. Unlike previously reported DFT benchmarks on ILs, which calculated binding energies through single point calculations on fixed geometries, properties in this work were calculated for geometries optimized at each theoretical level. DFT functionals that are suitable for describing ion-ion and ion-gas interactions were identified, considering both Coulombic forces and dispersion interactions. The reported results allowed us to infer relationships to the rational design of ILs for acid gas capture.
Energy Technology Data Exchange (ETDEWEB)
Krukiewicz, Katarzyna, E-mail: katarzyna.krukiewicz@polsl.pl [Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Strzody 9, 44-100 Gliwice (Poland); Herman, Artur P., E-mail: artur.herman@polsl.pl [Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Krzywoustego 4, Gliwice 44-100 (Poland); Turczyn, Roman, E-mail: roman.turczyn@polsl.pl [Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Strzody 9, 44-100 Gliwice (Poland); Szymańska, Katarzyna, E-mail: katarzyna.szymanska@polsl.pl [Department of Chemical and Process Engineering, Silesian University of Technology, Strzody 7, 44-100 Gliwice (Poland); Koziol, Krzysztof K.K., E-mail: kk292@cam.ac.uk [Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom); Boncel, Sławomir, E-mail: slawomir.boncel@polsl.pl [Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Krzywoustego 4, Gliwice 44-100 (Poland); Zak, Jerzy K., E-mail: jerzy.zak@polsl.pl [Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Strzody 9, 44-100 Gliwice (Poland)
2014-10-30
Highlights: • The effect of MWCNT functionalization on properties of PPy composites was explained. • The behavior of pristine, pyrrole-modified and oxidized MWCNT was explained. • Functionalization of MWCNT improved their dispersibility and processability. • Different mechanisms of (f-)MWCNT incorporation into PPy composites were explained. • Orientation of growing PPy chains was tailored through the addition of (f-)MWCNT. - Abstract: The effect of the functionalization of multi-walled carbon nanotubes (MWCNTs) on the process of electrochemical co-deposition of MWCNTs and polypyrrole (PPy), as well as the morphology of obtained composites have been demonstrated. As the nanotube components of the hybrids, three types of MWCNT were used, namely c-CVD derived (pristine) MWCNTs, their oxidized counterparts MWCNT-Ox and pyrrole-modified MWCNT-Py. The stability of pristine and functionalized MWCNTs (f-MWCNT) dispersions in tetrahydrofuran and water was studied together with the description of the process of formation PPy/(f-)MWCNT hybrid materials via electrochemical co-deposition. The structural and morphological properties of the hybrids were characterized by Raman spectroscopy, scanning electron microscopy and atomic force microscopy revealing substantial differences among hybrid materials in their surface morphology and the influence of MWCNT functionalization on the orientation of growing PPy chains.
Hybrid functional study rationalizes the simple cubic phase of calcium at high pressures.
Liu, Hanyu; Cui, Wenwen; Ma, Yanming
2012-11-14
Simple cubic (SC) phase has been long experimentally determined as the high-pressure phase III of elemental calcium (Ca) since 1984. However, recent density functional calculations within semi-local approximation showed that this SC phase is structurally unstable by exhibiting severely imaginary phonons, and is energetically unstable with respect to a theoretical body-centered tetragonal I4(1)/amd structure over the pressure range of phase III. These calculations generated extensive debates on the validity of SC phase. Here we have re-examined the SC structure by performing more precise density functional calculations within hybrid functionals of Heyd-Scuseria-Erhzerhof and PBE0. Our calculations were able to rationalize fundamentally the phase stability of SC structure over all other known phases by evidence of its actual energetic stability above 33 GPa and its intrinsically dynamical stability without showing any imaginary phonons in the entire pressure range studied. We further established that the long-thought theoretical I4(1)/amd structure remains stable in a narrow pressure range before entering SC phase and is actually the structure of experimental Ca-III(') synthesized recently at low temperature 14 K as supported by the excellent agreement between our simulated x-ray diffraction patterns and the experimental data. Our results shed strong light on the crucial role played by the precise electron exchange energy in a proper description of the potential energy of Ca.
Functionalization of hybrid monolithic columns via thiol-ene click reaction for proteomics analysis.
Liu, Zhongshan; Liu, Jing; Liu, Zheyi; Wang, Hongwei; Ou, Junjie; Ye, Mingliang; Zou, Hanfa
2017-05-19
The vinyl-functionalized hybrid monolithic columns (75 and 150μm i.d.) were prepared via sol-gel chemistry of tetramethoxysilane (TMOS) and vinyltrimethoxysilane (VTMS). The content of accessible vinyl groups was further improved after the monolithic column was post-treated with vinyldimethylethoxysilane (VDMES). The surface properties of monolithic columns were tailored via thiol-ene click reaction by using 1-octadecanethiol, sodium 3-mercapto-1-propanesulfonate and 2,2'-(ethylenedioxy)diethanethiol/vinylphosphonic acid, respectively. The preparing octadecyl-functionalized monolithic columns were adopted for proteomics analysis in cLC-MS/MS. A 37-cm-long×75-μm-i.d. monolithic column could identify 3918 unique peptides and 1067 unique proteins in the tryptic digest of proteins from HeLa cells. When a 90-cm-long×75-μm-i.d. monolithic column was used, the numbers of unique peptides and proteins were increased by 82% and 32%, respectively. Furthermore, strong cation exchange (SCX) monolithic columns (4cm in length×150μm i.d.) were also prepared and coupled with the 37-cm-long×75-μm-i.d. octadecyl-functionalized monolithic column for two-dimensional SCX-RPLC-MS/MS analysis, which could identify 17114 unique peptides and 3211 unique proteins. Copyright © 2017 Elsevier B.V. All rights reserved.
Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R
2016-09-13
The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.
Zhong, Chang; Zhao, Min; Goslinski, Tomasz; Stern, Charlotte; Barrett, Anthony G M; Hoffman, Brian M
2006-05-15
We report the synthesis and physical characterization of a new family of peripherally functionalized porphyrazine (pz) compounds, denoted 1[M1, M2], where metal ion M1 is incorporated into the pz core and metal ion M2 is bound to a salicylidene/picolinamide "hybrid" chelate built onto two nitrogen atoms attached to the pz periphery. The complexes 1[MnCl, Cu], 1[VO, Cu], and 1[Cu, Cu] have been prepared, and crystal structures show 1[MnCl, Cu] and 1[VO, Cu] to be isostructural. These complexes have been subjected to electron paramagnetic resonance and temperature-dependent magnetic susceptibility measurements. The variation of the ligand-mediated exchange splittings (delta) in these complexes is striking: delta/k(B) values for 1[MnCl, Cu] and 1[VO, Cu] are 22 and 40 K, respectively, while delta/k(B) for 1[Cu, Cu] is only 1 K. These coupling results are explained in terms of the relative orientation of the M1 and M2 orbitals and reflect the fact that the ligand set of M2 in the periphery is rotated in-plane by 45 degrees relative to the effectively coplanar pz ligand set of M1. The exchange couplings are essentially the same as those we determined for the Schiff base porphyrazines (pzs). Thus, the hybrid ligand has eliminated the dimerization found to occur when Cu(II) is bound to the periphery of bis(picolinamido) pzs and has created a more robust ligand system than the Schiff base pzs while retaining the ability they show to promote spin coupling between M1 and M2.
Chihaoui, Nejla; Hamdi, Besma; Dammak, Thameur; Zouari, Ridha
2016-11-01
This paper gathers the synthesis and study of a novel nonlinear organic-inorganic (1,2-diammoniumcyclohexane tetrabromozincate (II) monohydrate; [C6H10(NH3)2]ZnBr4·H2O) hybrid. The newly developed hybrid was characterized by XRD and spectroscopic (FT-IR, Raman, UV-Visible and CP/MAS-NMR) studies. All theoretical calculations and structural optimization parameters were conducted by using DFT approach with B3LYP/6-31G(d) basis set and the vibrational wavenumbers were evaluated for the affectation of [C6H10(NH3)2]ZnBr4·H2O compound by using transferable scale factor. The inspection of intermolecular links in the studied framework has been executed by the Hirshfeld surface analysis. The nonlinear optical characteristics of this compound were theoretically explored also the molecular orbitals (HOMO) and (LUMO) properties are performed to describe the charge transfer within the crystal.
Rohm, Martin; Schneiders, Matthias; Müller, Constantin; Kreilinger, Alex; Kaiser, Vera; Müller-Putz, Gernot R; Rupp, Rüdiger
2013-10-01
The bilateral loss of the grasp function associated with a lesion of the cervical spinal cord severely limits the affected individuals' ability to live independently and return to gainful employment after sustaining a spinal cord injury (SCI). Any improvement in lost or limited grasp function is highly desirable. With current neuroprostheses, relevant improvements can be achieved in end users with preserved shoulder and elbow, but missing hand function. The aim of this single case study is to show that (1) with the support of hybrid neuroprostheses combining functional electrical stimulation (FES) with orthoses, restoration of hand, finger and elbow function is possible in users with high-level SCI and (2) shared control principles can be effectively used to allow for a brain-computer interface (BCI) control, even if only moderate BCI performance is achieved after extensive training. The individual in this study is a right-handed 41-year-old man who sustained a traumatic SCI in 2009 and has a complete motor and sensory lesion at the level of C4. He is unable to generate functionally relevant movements of the elbow, hand and fingers on either side. He underwent extensive FES training (30-45min, 2-3 times per week for 6 months) and motor imagery (MI) BCI training (415 runs in 43 sessions over 12 months). To meet individual needs, the system was designed in a modular fashion including an intelligent control approach encompassing two input modalities, namely an MI-BCI and shoulder movements. After one year of training, the end user's MI-BCI performance ranged from 50% to 93% (average: 70.5%). The performance of the hybrid system was evaluated with different functional assessments. The user was able to transfer objects of the grasp-and-release-test and he succeeded in eating a pretzel stick, signing a document and eating an ice cream cone, which he was unable to do without the system. This proof-of-concept study has demonstrated that with the support of hybrid FES
Shamsipur, Mojtaba; Allahyari, Leila; Fasihi, Javad; Taherpour, Avat (Arman); Asfari, Zuhair; Valinejad, Azizollah
2016-03-01
Complexation of two 1,3-alternate calix[4]crown ligands with alkali metals (K+, Rb+ and Cs+) has been investigated by electrospray ionization mass spectrometry (ESI-MS) and density functional theory calculations. The binding selectivities of the ligands and the binding constants of their complexes in solution have been determined using the obtained mass spectra. Also the percentage of each formed complex species in the mixture of each ligand and alkali metal has been experimentally evaluated. For both calix[4]crown-5 and calix[4]crown-6 ligands the experimental and theoretical selectivity of their alkali metal complexes found to follow the trend K+ > Rb+ > Cs+. The structures of ligands were optimized by DFT-B3LYP/6-31G method and the structures of complexes were obtained by QM-SCF-MO/PM6 method and discussed in the text.
Behzadi, Hadi; Hadipour, Nasser L; Mirzaei, Mahmoud
2007-01-01
A density functional theory (DFT) study was carried out to calculate (17)O, (14)N and (2)H electric field gradient (EFG) tensors in accurate neutron diffraction structures of alpha-glycine at 288 and 427 K. B3LYP is the used method and 6-311+G(*) and 6-311++G(**) are the basis sets in the calculations of EFG tensors at the sites of (17)O, (14)N and (2)H nuclei in the monomer and the octameric cluster of alpha-glycine at two temperatures. Quadrupole coupling constants and asymmetry parameters are the converted parameters of calculated EFG tensors to experimentally measurable ones. The calculated results of monomer and the target molecule in octameric cluster reveal that hydrogen-bonding interactions play an important role in the crystalline structure of alpha-glycine where the results of the target molecule in octameric cluster are in good agreement with the experiments.
Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile
2007-06-01
The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.
Öner, Nazmiye; Tamer, Ömer; Başoǧlu, Adil; Avcı, Davut; Atalay, Yusuf
2017-02-01
In this paper, quantum chemical calculations of (2e)-3-(3-Bromo-4-methoxyphenyl) -1-(pyridin-2-yl)prop-2-en-1-one were performed by using B3LYP and CAMB3LYP levels of density functional theory (DFT) with 6-311++G(d, p) basis set. Geometric parameters of the title molecule in the ground state were found to be in good agreement with experimental data. 13C and 1H NMR chemical shifts were calculated within GIAO approach which is one of the most common approaches. The frontier molecular orbitals (HOMO and LUMO) were simulated by the same levels. Nonlinear optical parameters (NLO) were also evaluated by determining of dipole moment, polarizability and first hyperpolarizability. All of calculations were carried out Gaussian 09 package program.
McWilliams, Sean F; Brennan-Wydra, Emma; MacLeod, K Cory; Holland, Patrick L
2017-06-30
The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together.
Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha
2011-11-01
Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.
Villamena, Frederick A; Hadad, Christopher M; Zweier, Jay L
2004-02-18
The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.
Directory of Open Access Journals (Sweden)
Mnaza Noreen
2015-11-01
Full Text Available A variety of novel 5-aryl thiophenes 4a–g containing sulphonylacetamide (sulfacetamide groups were synthesized in appreciable yields via Pd[0] Suzuki cross coupling reactions. The structures of these newly synthesized compounds were determined using spectral data and elemental analysis. Density functional theory (DFT studies were performed using the B3LYP/6-31G (d, p basis set to gain insight into their structural properties. Frontier molecular orbital (FMOs analysis of all compounds 4a–g was computed at the same level of theory to get an idea about their kinetic stability. The molecular electrostatic potential (MEP mapping over the entire stabilized geometries of the molecules indicated the reactive sites. First hyperpolarizability analysis (nonlinear optical response were simulated at the B3LYP/6-31G (d, p level of theory as well. The compounds were further evaluated for their promising antibacterial and anti-urease activities. In this case, the antibacterial activities were estimated by the agar well diffusion method, whereas the anti-urease activities of these compounds were determined using the indophenol method by quantifying the evolved ammonia produced. The results revealed that all the sulfacetamide derivatives displayed antibacterial activity against Bacillus subtiles, Escherichia coli, Staphylococcus aureus, Shigella dysenteriae, Salmonella typhae, Pseudomonas aeruginosa at various concentrations. Furthermore, the compound 4g N-((5-(4-chlorophenylthiophen-2-ylsulfonyl acetamide showed excellent urease inhibition with percentage inhibition activity ~46.23 ± 0.11 at 15 µg/mL with IC50 17.1 µg/mL. Moreover, some other compounds 4a–f also exhibited very good inhibition against urease enzyme.
Noreen, Mnaza; Rasool, Nasir; Gull, Yasmeen; Zubair, Muhammad; Mahmood, Tariq; Ayub, Khurshid; Nasim, Faiz-Ul-Hassan; Yaqoob, Asma; Zia-Ul-Haq, Muhammad; de Feo, Vincenzo
2015-11-05
A variety of novel 5-aryl thiophenes 4a-g containing sulphonylacetamide (sulfacetamide) groups were synthesized in appreciable yields via Pd[0] Suzuki cross coupling reactions. The structures of these newly synthesized compounds were determined using spectral data and elemental analysis. Density functional theory (DFT) studies were performed using the B3LYP/6-31G (d, p) basis set to gain insight into their structural properties. Frontier molecular orbital (FMOs) analysis of all compounds 4a-g was computed at the same level of theory to get an idea about their kinetic stability. The molecular electrostatic potential (MEP) mapping over the entire stabilized geometries of the molecules indicated the reactive sites. First hyperpolarizability analysis (nonlinear optical response) were simulated at the B3LYP/6-31G (d, p) level of theory as well. The compounds were further evaluated for their promising antibacterial and anti-urease activities. In this case, the antibacterial activities were estimated by the agar well diffusion method, whereas the anti-urease activities of these compounds were determined using the indophenol method by quantifying the evolved ammonia produced. The results revealed that all the sulfacetamide derivatives displayed antibacterial activity against Bacillus subtiles, Escherichia coli, Staphylococcus aureus, Shigella dysenteriae, Salmonella typhae, Pseudomonas aeruginosa at various concentrations. Furthermore, the compound 4g N-((5-(4-chlorophenyl)thiophen-2-yl)sulfonyl) acetamide showed excellent urease inhibition with percentage inhibition activity ~46.23 ± 0.11 at 15 µg/mL with IC50 17.1 µg/mL. Moreover, some other compounds 4a-f also exhibited very good inhibition against urease enzyme.
Xu, Ting; Zhao, Xin; Zhang, Junxian; Dong, Jie; Zhang, Qinghua
2016-04-01
Two kinds of ternary hybrids were prepared by anchoring different shapes and loadings of Au nanoparticles (NPs) on poly(dopamine) (PDA) functionalized polystyrene (PS) microspheres with two different strategies, i.e., in situ reduction and self-assembly approach. PDA coatings were firstly introduced to functionalize the hydrophobic PS surface with sufficient amino and hydroxyl groups, which enhanced the interaction between Au NPs and the polymer spheres. Thus, Au NPs could be easily immobilized onto the surface of the PDA/PS microspheres, and the hierarchical composite microspheres exhibited a well-defined core/shell structure without sacrificing the spherical PS morphology. PS/PDA/Au-R and PS/PDA/Au-A microspheres fabricated by in situ reduction and self-assembly approach showed different distinct Au nano-shell morphology with the corresponding optical, catalytic and electrochemical properties. Field emission scanning electron microscopy and transmission electronic microscopy verified these hierarchical structures with the ultrathin PDA film incorporating between the inner PS core and the outer Au NPs shell. X-ray diffraction and X-ray photoelectron spectroscopy confirmed the presence of PDA and Au layer on the surface of the composite particles. These green and facile methods with mild experimental conditions can extend to fabricate other polymer or inorganic substrates coated by various noble metals.
Functionalized hybrid nanofibers to mimic native ECM for tissue engineering applications
Karuppuswamy, Priyadharsini; Venugopal, Jayarama Reddy; Navaneethan, Balchandar; Laiva, Ashang Luwang; Sridhar, Sreepathy; Ramakrishna, Seeram
2014-12-01
Nanotechnology being one of the most promising technologies today shows an extremely huge potential in the field of tissue engineering to mimic the porous topography of natural extracellular matrix (ECM). Natural polymers are incorporated into the synthetic polymers to fabricate functionalized hybrid nanofibrous scaffolds, which improve cell and tissue compatibility. The present study identified the biopolymers - aloe vera, silk fibroin and curcumin incorporated into polycaprolactone (PCL) as suitable substrates for tissue engineering. Different combinations of PCL with natural polymers - PCL/aloe vera, PCL/silk fibroin, PCL/aloe vera/silk fibroin, PCL/aloe vera/silk fibroin/curcumin were electrospun into nanofibrous scaffolds. The fabricated two dimensional nanofibrous scaffolds showed high surface area, appropriate mechanical properties, hydrophilicity and porosity, required for the regeneration of diseased tissues. The nanofibrous scaffolds were characterized by Scanning electron microscope (SEM), porometry, Instron tensile tester, VCA optima contact angle measurement and FTIR to analyze the fiber diameter and morphology, porosity and pore size distribution, mechanical strength, wettability, chemical bonds and functional groups, respectively. The average fiber diameter of obtained fibers ranged from 250 nm to 350 nm and the tensile strength of PCL scaffolds at 4.49 MPa increased upto 8.3 MPa for PCL/silk fibroin scaffolds. Hydrophobicity of PCL decreased with the incorporation of natural polymers, especially for PCL/aloe vera scaffolds. The properties of as-spun nanofiber scaffolds showed their potential as promising scaffold materials in tissue engineering applications.
Properties of carbon impurities in ZnO: A hybrid functional study
Li, Ping; Luo, Weidong
2016-08-01
The mechanism of the room temperature (RT) ferromagnetism in C-doped ZnO and the trend that the higher the C concentration, the smaller the saturation magnetic moment (Ms), have remained controversial and puzzling for a long time. Using density-functional calculations with hybrid functional, we qualitatively understand these experimental phenomena. The substitutional CO defects dominate in Zn-rich conditions and n -type materials. They carry 1 or 2 μB/C , depending on the position of the Fermi level. In low C concentrations and at RT, the CO defects are kept isolated and prefer to couple ferromagnetically, thus the Ms is larger. As the C concentration increases, nonmagnetic C2 dimers form through binding of two CO defects or binding of one CO defect with one interstitial C, thus decreasing the Ms. Our results also suggest that the ferromagnetism from CO defects can be quenched by higher annealing temperatures. Furthermore, the p -type conductivity from carbon dopant is not supported in the present study.
Ab-initio study of germanium di-interstitial using a hybrid functional (HSE)
Igumbor, E.; Ouma, C. N. M.; Webb, G.; Meyer, W. E.
2016-01-01
In this work, we present ab-initio calculation results of Ge di-interstitials (I2(Ge)) in the framework of the density functional theory (DFT) using the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional. The formation energy, transition levels and minimum energy configurations were obtained for I2(Ge) -2, -1, 0, +1 and +2 charge states. The calculated formation energies show that for all charge states of I2(Ge), the double tetrahedral (T) configuration formed the most stable defect with a binding energy of 1.24 eV in the neutral state. We found the (+2/+1) charge state transition level for the T lying below the conduction band minimum and (+2/+1) for the split[110]-tetrahedral configuration lying deep at 0.41 eV above the valence band maximum. The di-interstitials in Ge exhibited the properties of both shallow and deep donor levels at (+2/+1) within the band gap and depending on the configurations. I2(Ge) gave rise to negative-U, with effective-U values of -0.61 and -1.6 eV in different configurations. We have compared our results with calculations of di-interstitials in silicon and available experimental data.
Rare Earth Interstitials in Ge: A Hybrid Density Functional Theory Study
Igumbor, E.; Andrew, R. C.; Meyer, W. E.
2017-02-01
In this work, the results of density functional theory calculations for rare earth (Ce, Pr, Eu, and Er) interstitials in Ge are presented. We employed the hybrid functional of Heyd, Scuseria, and Ernzerhof (HSE06) for all the calculations. We calculated the formation energies and charge state transition levels for the tetrahedral (T) and hexagonal (H) configurations of the Ce, Pr, Eu, and Er interstitials in Ge. While for the T configuration, the charge states of the Ce and Pr did not induce any thermodynamic accessible transition state level within the band gap of Ge, for both the T and H configurations the Eu and Er interstitials in Ge induce deep levels in the band gap. The H configuration of the Ce interstitial in Ge induces a shallow donor level at 0.03 eV below the conduction band. The Eu interstitial exhibits negative-U properties for the (+2/-2) transition level and the Er interstitial displays characteristics of charge state controlled metastability.
Covercrete with hybrid functions - A novel approach to durable reinforced concrete structures
Energy Technology Data Exchange (ETDEWEB)
Tang, L.; Zhang, E.Q. [Chalmers University of Technology, SE-412 96 Gothenburg (Sweden); Fu, Y. [KTH Royal Institute of Technology, SE-106 91 Stockholm (Sweden); Schouenborg, B.; Lindqvist, J.E. [CBI Swedish Cement and Concrete Research Institute, c/o SP, Box 857, SE-501 15 Boraas (Sweden)
2012-12-15
Due to the corrosion of steel in reinforced concrete structures, the concrete with low water-cement ratio (w/c), high cement content, and large cover thickness is conventionally used for prolonging the passivation period of steel. Obviously, this conventional approach to durable concrete structures is at the sacrifice of more CO{sub 2} emission and natural resources through consuming higher amount of cement and more constituent materials, which is against sustainability. By placing an economically affordable conductive mesh made of carbon fiber or conductive polymer fiber in the near surface zone of concrete acting as anode we can build up a cathodic prevention system with intermittent low current density supplied by, e.g., the solar cells. In such a way, the aggressive negative ions such as Cl{sup -}, CO{sub 3}{sup 2-}, and SO{sub 4}{sup 2-} can be stopped near the cathodic (steel) zone. Thus the reinforcement steel is prevented from corrosion even in the concrete with relatively high w/c and small cover thickness. This conductive mesh functions not only as electrode, but also as surface reinforcement to prevent concrete surface from cracking. Therefore, this new type of covercrete has hybrid functions. This paper presents the theoretical analysis of feasibility of this approach and discusses the potential durability problems and possible solutions to the potential problems. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Ab‐initio study of germanium di-interstitial using a hybrid functional (HSE)
Energy Technology Data Exchange (ETDEWEB)
Igumbor, E., E-mail: elgumuk@gmail.com [Department of Physics, University of Pretoria, Pretoria 0002 (South Africa); Department of Mathematics and Physical Sciences, Samuel Adegboyega University, Km 1 Ogwa/Ehor Rd, Ogwa, Edo State (Nigeria); Ouma, C.N.M.; Webb, G. [Department of Physics, University of Pretoria, Pretoria 0002 (South Africa); Meyer, W.E., E-mail: wmeyer@up.ac.za [Department of Physics, University of Pretoria, Pretoria 0002 (South Africa)
2016-01-01
In this work, we present ab‐initio calculation results of Ge di-interstitials (I{sub 2(Ge)}) in the framework of the density functional theory (DFT) using the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional. The formation energy, transition levels and minimum energy configurations were obtained for I{sub 2(Ge)} −2, −1, 0, +1 and +2 charge states. The calculated formation energies show that for all charge states of I{sub 2(Ge)}, the double tetrahedral (T) configuration formed the most stable defect with a binding energy of 1.24 eV in the neutral state. We found the (+2/+1) charge state transition level for the T lying below the conduction band minimum and (+2/+1) for the split[110]-tetrahedral configuration lying deep at 0.41 eV above the valence band maximum. The di-interstitials in Ge exhibited the properties of both shallow and deep donor levels at (+2/+1) within the band gap and depending on the configurations. I{sub 2(Ge)} gave rise to negative-U, with effective-U values of −0.61 and −1.6 eV in different configurations. We have compared our results with calculations of di-interstitials in silicon and available experimental data.
Zanuy, David; Hamley, Ian W; Alemán, Carlos
2011-07-21
The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helical-like arrangements. Furthermore, calculations indicate that backbone···side chain interactions involving the N-H of the amide groups and the π clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand, MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.
Functionalized Self-Assembled InAs/GaAs Quantum-Dot Structures Hybridized with Organic Molecules
DEFF Research Database (Denmark)
Chen, Miaoxiang Max; Kobashi, K.; Chen, B.
2010-01-01
Low-dimensional III-V semiconductors have many advantages over other semiconductors; however, they are not particularly stable under physiological conditions. Hybridizing biocompatible organic molecules with advanced optical and electronic semiconductor devices based on quantum dots (QDs......) and quantum wires could provide an efficient solution to realize stress-free and nontoxic interfaces to attach larger functional biomolecules. Monitoring the modifications of the optical properties of the hybrid molecule-QD systems by grafting various types of air-stable diazonium salts onto the QD structures...
Oliveira, Leonardo B. A.; Fonseca, Tertius L.; Coutinho, Kaline; Canuto, Sylvio
2011-10-01
Solvatochromic shifts of the π-π∗ and n-π∗ transitions for the pyridinium-N-phenoxide [2-(pyridinium-1-yl)phenolate] betaine changing from vacuum to water, have been investigated using Monte Carlo simulations and time-dependent density functional theory schemes using standard and long-range corrected functionals. The classical Boltzmann distribution of the interring twist angle obtained from the calculated free energy agrees with a Car-Parrinello distribution. For the calculated spectral shifts BHandHLYP/6-311+G(2d,p) performs better than the CAM-B3LYP/6-311+G(2d,p) or LC-ωPBE/6-311+G(2d,p) model but the experimental shift is very well reproduced only after the inclusion of solute polarization and proper consideration of the twist geometry relaxation associated with the intramolecular charge transfer.
Energy Technology Data Exchange (ETDEWEB)
Na, Moonkyong, E-mail: nmk@keri.re.kr [HVDC Research Division, Korea Electrotechnology Research Institute, Changwon, 642-120 (Korea, Republic of); System on Chip Chemical Process Research Center, Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 (Korea, Republic of); Kang, Young Taec [Creative and Fundamental Research Division, Korea Electrotechnology Research Institute, Changwon, 642-120 (Korea, Republic of); Department of Polymer Science and Engineering, Pusan National University, Busan, 609-735 (Korea, Republic of); Kim, Sang Cheol [HVDC Research Division, Korea Electrotechnology Research Institute, Changwon, 642-120 (Korea, Republic of); Kim, Eun Dong [Creative and Fundamental Research Division, Korea Electrotechnology Research Institute, Changwon, 642-120 (Korea, Republic of)
2013-07-31
Thermal-cured hybrid materials were synthesized from homogenous hybrid sols of epoxy resins and organoalkoxysilane-functionalized silica. The chemical structures of raw materials and obtained hybrid materials were characterized using Fourier transform infrared spectroscopy. The thermal resistance of the hybrids was enhanced by hybridization. The interaction between epoxy matrix and the silica particles, which caused hydrogen bonding and van der Waals force was strengthened by organoalkoxysilane. The degradation temperature of the hybrids was improved by approximately 30 °C over that of the parent epoxy material. The hybrid materials were formed into uniformly coated thin films of about 50 nm-thick using a spin coater. An optimum mixing ratio was used to form smooth-surfaced hybrid films. The electrical property of the hybrid film was characterized, and the leakage current was found to be well below 10{sup −6} A cm{sup −2}. - Highlights: • Preparation of thermal-curable hybrid materials using epoxy resin and silica. • The thermal stability was enhanced through hybridization. • The insulation property of hybrid film was investigated as gate dielectrics.
Alipour, Mojtaba; Karimi, Niloofar
2017-06-01
Organic light emitting diodes (OLEDs) based on thermally activated delayed fluorescence (TADF) emitters are an attractive category of materials that have witnessed a booming development in recent years. In the present contribution, we scrutinize the accountability of parameterized and parameter-free single-hybrid (SH) and double-hybrid (DH) functionals through the two formalisms, full time-dependent density functional theory (TD-DFT) and Tamm-Dancoff approximation (TDA), for the estimation of photophysical properties like absorption energy, emission energy, zero-zero transition energy, and singlet-triplet energy splitting of TADF molecules. According to our detailed analyses on the performance of SHs based on TD-DFT and TDA, the TDA-based parameter-free SH functionals, PBE0 and TPSS0, with one-third of exact-like exchange turned out to be the best performers in comparison to other functionals from various rungs to reproduce the experimental data of the benchmarked set. Such affordable SH approximations can thus be employed to predict and design the TADF molecules with low singlet-triplet energy gaps for OLED applications. From another perspective, considering this point that both the nonlocal exchange and correlation are essential for a more reliable description of large charge-transfer excited states, applicability of the functionals incorporating these terms, namely, parameterized and parameter-free DHs, has also been evaluated. Perusing the role of exact-like exchange, perturbative-like correlation, solvent effects, and other related factors, we find that the parameterized functionals B2π-PLYP and B2GP-PLYP and the parameter-free models PBE-CIDH and PBE-QIDH have respectable performance with respect to others. Lastly, besides the recommendation of reliable computational protocols for the purpose, hopefully this study can pave the way toward further developments of other SHs and DHs for theoretical explorations in the field of OLEDs technology.
DEFF Research Database (Denmark)
Verma, Ashok K.; Modak, P.; Sharma, Surinder M.;
2013-01-01
First-principles calculations have been performed for americium (Am) metal using the generalized gradient approximation + orbital-dependent onsite Coulomb repulsion via Hubbard interaction (GGA+U) and hybrid density functional theory (HYB-DFT) methods to investigate various ground state properties...... spectrum at ambient pressure relate, for some parameter choices, well to peak positions in the calculated density of states function of Am-I....
SOME QUANTUM CHEMICAL STUDY ON THE STRUCTURAL ...
African Journals Online (AJOL)
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Formula. Formula weight. (gmol-1) ... Quantum chemical calculations (Density Functional Theory, B3LYP/6-31G (d)) were used to purposed the ... correlation functional [B3LYP/6-31G(d)]) calculations were done by using Gaussian 03 program ...
Thompson, Joshua A.
2012-05-22
Zeolitic imidazolate frameworks (ZIFs) are a subclass of nanoporous metal-organic frameworks (MOFs) that exhibit zeolite-like structural topologies and have interesting molecular recognition properties, such as molecular sieving and gate-opening effects associated with their pore apertures. The synthesis and characterization of hybrid ZIFs with mixed linkers in the framework are described in this work, producing materials with properties distinctly different from the parent frameworks (ZIF-8, ZIF-90, and ZIF-7). NMR spectroscopy is used to assess the relative amounts of the different linkers included in the frameworks, whereas nitrogen physisorption shows the evolution of the effective pore size distribution in materials resulting from the framework hybridization. X-ray diffraction shows these hybrid materials to be crystalline. In the case of ZIF-8-90 hybrids, the cubic space group of the parent frameworks is continuously maintained, whereas in the case of the ZIF-7-8 hybrids there is a transition from a cubic to a rhombohedral space group. Nitrogen physisorption data reveal that the hybrid materials exhibit substantial changes in gate-opening phenomena, either occurring at continuously tunable partial pressures of nitrogen (ZIF-8-90 hybrids) or loss of gate-opening effects to yield more rigid frameworks (ZIF-7-8 hybrids). With this synthetic approach, significant alterations in MOF properties may be realized to suit a desired separation or catalytic process. © 2012 American Chemical Society.
A New Hybrid Model of Amino Acid Substitution for Protein Functional Classification
Institute of Scientific and Technical Information of China (English)
Ke Long WANG; Zhi Ning WEN; Fu Sheng NIE; Meng Long LI
2005-01-01
In this paper, a new hybrid model of amino acid substitution is developed and compared with the others in previous works. The results show that the new hybrid model can characterize the protein sequences very well by calculating Fisher weights, which can denote how much the variants contribute to the classification.
Directory of Open Access Journals (Sweden)
Tarek El-Bialy
2010-03-01
Full Text Available Tarek El-Bialy1, Ali Hasan2, Ahmad Janadas3, Tarik Albaghdadi41Division of Orthodontics, Department of Dentistry, University of Alberta, Edmonton, Alberta, Canada; 2Division of Orthodontics, Department of Preventive Dental Sciences, Faculty of Dentistry; 3Division of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Surgery, Faculty of Dentistry; 4Division of Radiology, Faculty of Medicine, King Abdul Aziz University, Jeddah, Saudi ArabiaAim: Conventional treatment of patients with hemifacial microsomia involves orthognathic surgery and/or distraction osteogenesis of the mandible. Previous reports showed that low-intensity pulsed ultrasound (LIPUS enhances mandibular growth in growing rabbits and monkeys. In monkeys, LIPUS enhanced mandibular growth when combined with functional jaw orthopedic appliances. The purpose of this pilot study was to investigate if LIPUS could enhance mandibular growth in children with hemifacial microsomia.Methods: Five children (age range 3–11 years with hemifacial microsomia were treated with hybrid jaw orthopedic functional appliances and treatment of the affected mandibular condyle by LIPUS for 20 minutes per day.Results: The results showed that after one year of treatment, significant improvement of the underdeveloped side of patients’ faces and mandibles was recognized both clinically and radiographically.Discussion: Although improvement took a longer time than did a surgical approach, optimizing this technique may achieve better results in a shorter treatment time. A randomized controlled clinical trial to investigate the effect of optimized LIPUS application or functional appliances in the treatment of hemifacial microsomia is warranted.Keywords: hemifacial microsomia, LIPUS, non-surgical treatment, children
Engineering of a bio-functionalized hybrid off-the-shelf heart valve.
Hinderer, Svenja; Seifert, Jan; Votteler, Miriam; Shen, Nian; Rheinlaender, Johannes; Schäffer, Tilman E; Schenke-Layland, Katja
2014-02-01
Currently available heart valve replacements are limited in long-term performance or fail due to leaflet thickening, lack of growth or remodeling potential. In order to address these issues, it is necessary to mimic multiple factors of the native valvular extracellular matrix (ECM) such as architecture, mechanical behavior and biochemical signals. Here, we successfully generated an electrospun PEGdma-PLA scaffold adapted to the structure and mechanical properties of native valve leaflets. Valvular interstitial cells (VICs) and valvular endothelial cells (VECs) were seeded on the scaffold and when cultured under physiological conditions in a bioreactor, the construct performed like a native leaflet. Atomic force microscopy (AFM) was employed to obtain detailed mechanical information from the leaflets, which enabled the first layer-specific measurement of the Young's modulus. Interestingly, spongiosa stiffness was much lower compared to the fibrosa and ventricularis. Moreover, investigations into human fetal heart valve development identified collagen type I and versican as important structural proteins. As a proof of principle, these proteins were introduced to the scaffold, demonstrating the ability to bio-functionalize the hybrid valve based on natures' blueprint.
Uncertain Quality Function Deployment Using a Hybrid Group Decision Making Model
Directory of Open Access Journals (Sweden)
Ze-Ling Wang
2016-11-01
Full Text Available Quality function deployment (QFD is a widely used quality system tool for translating customer requirements (CRs into the engineering design requirements (DRs of products or services. The conventional QFD analysis, however, has been criticized as having some limitations such as in the assessment of relationships between CRs and DRs, the determination of CR weights and the prioritization of DRs. This paper aims to develop a new hybrid group decision-making model based on hesitant 2-tuple linguistic term sets and an extended QUALIFLEX (qualitative flexible multiple criteria method approach for handling QFD problems with incomplete weight information. First, hesitant linguistic term sets are combined with interval 2-tuple linguistic variables to express various uncertainties in the assessment information of QFD team members. Borrowing the idea of grey relational analysis (GRA, a multiple objective optimization model is constructed to determine the relative weights of CRs. Then, an extended QUALIFLEX approach with an inclusion comparison method is suggested to determine the ranking of the DRs identified in QFD. Finally, an analysis of a market segment selection problem is conducted to demonstrate and validate the proposed QFD approach.
Predictive functional control of temperature in a pharmaceutical hybrid nonlinear batch reactor
Directory of Open Access Journals (Sweden)
Štampar Simon
2013-01-01
Full Text Available These days, in times of recession, we are forced by competitiveness and the optimization of production to lower the costs of the temperature control in pharmaceutical batch reactors and increase the quantity and quality of the produced pharmaceutical product (active pharmaceutical substances. Therefore, a control algorithm is needed which provides us rapid and precise temperature control. This paper deals with the development of a control algorithm, where two predictive functional controllers are connected in a cascade for heating and cooling the content of the hybrid batch reactor. The algorithm has to be designed to cope with the constraints and the mixed discrete and continuous nature of the process of heating and cooling. The main goal of the control law is to achieve rapid and exact tracking of the reference temperature, good disturbance rejection and, in particular, a small number of heating and cooling medium switchings. The simulation results of the proposed algorithm give us much better performance compared to a conventional cascade PI algorithm.
Marangos, P J; Zis, A P; Clark, R L; Goodwin, F K
1978-07-07
Three forms of the glycolytic enzyme, enolase [2-phospho-D-glycerate hydrolase (E.C. No. 4.2.1.11)] have been prepared from rat whole brain extract. The most acidic enolase form is neuron specific enolase (NSE) which had previously been designated neuron specific protein (NSP). The least acidic form designated non-neuronal enolase (NNE) has been purified and compared structurally, immunologically and functionally to NSE. NNE is a dimer of 86,500 M.W. consistint of two very similar subunits. The data establish that NNE is larger than NSE which has been shown to be composed of two apparently identical 39,000 molecular weight subunits (78,000). NNE is less acidic than NSE having a pI of 5.9 compared to the value of 4.7 for NSE. Structural and immunological analysis establishes that the NNE subunit is distinct from the NSE subunit, and are therfore products of two separate genes. The structural designation of NSE is (gammagamma) and that of NNE (alpha' alpha'). NSE is strictly localized in neurons indicating that the gene coding for the gamma subunit is only expressed in neuronal cells. The intermediate brain enolase form has been partially purified; structural and immunological evidence indicate that it is a hybrid molecule consisting of one NNE subunit and one NSE subunit (alpha'gamma).
Preparation and characterization of functional material based on hybrid polymer composites
Agusu, La; Amiruddin; Taswito, Chen Chen; Herdianto; Zamrun, Muh.
2016-08-01
The microstructures and properties of hybrid polymer composites based on polyaniline (PANi)/γ-Fe2O3 nanoparticles/TiO2/carbon have been investigated for multifunctional applications such as heavy metal removal and initial study for radar absorbing material application. γ-Fe2O3 nanoparticles with spherical shape were synthetized by a coprecipitation method from iron sand. By activating the polyethylene glycol (PEG-400) coated carbon of coconut shell, the homogenous shape and size of carbon was achieved. Then, γ- Fe2O3, TiO2, and carbon were mixed with PANi by an in situ polymerization method at low temperature 0-5 oC. Characterization process involved XRD, SEM, FTIR, VSM, and DC conductivity measurements. For radar absorber application, the functionalized polymer composites showed good electrical conductivity 0.45 S/cm to absorb the incoming electromagnetic energy. An efficient and effective reduction of Pb2+ ion from the water has been achieved by using this material.
Huang, Huisheng; Zhang, Tonglai; Zhang, Jianguo; Wang, Liqiong
2010-07-15
The molecular geometry, electronic structure, infrared spectra and thermochemical properties of cobalt and nickel tris(carbohydrazide) perchlorates (CoCP and NiCP) as well as copper bis(carbohydrazide) perchlorate (CuCP) were investigated using the Heyd-Scuseria-Ernzerhof (HSE) screened hybrid density functional. The results show that both perchlorate ions coordinate with the copper atom, and the interactions between copper and perchlorate are ionic, whereas all the metal-carbohydrazide interactions are covalent. Due to the delocalization from the sigma(N-H) bond orbital to the n*(M) antibond orbital, the amino stretching vibrations of these complexes show considerable red-shift compared with those of free carbohydrazide ligand. The calculated heats of reaction and formation indicate that the formations of these complexes are exothermic, and the order of their thermal stability is NiCP>CoCP>CuCP. These agree well with the experimental results. Finally, we find that there is a relationship between the energy gap and impact sensitivity.
Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics
Falk von Rudorff, Guido; Jakobsen, Rasmus; Rosso, Kevin M.; Blumberger, Jochen
2016-10-01
The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O-) and doubly protonated oxygens (-OH2+ ) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.
Calculation of point defects in rutile TiO2 by the Screened Exchange Hybrid Functional
Lee, Hsin-Yi; Robertson, John
2012-01-01
The formation energies of the oxygen vacancy and titanium interstitial in rutile TiO2 were calculated by the screened exchange (sX) hybrid density functional method, which gives a band gap of 3.1 eV, close to the experimental value. The O vacancy gives rise to a gap state lying 0.7 eV below the conduction band edge, whose charge density is localised around the two of three Ti atoms next to the vacancy. The Ti interstitial generates four defect states in the gap, whose unpaired electrons lie on the interstitial and the adjacent Ti 3d orbitals. The formation energy for the neutral O vacancy is 1.9 eV for the O-poor chemical potential, and similar to that of the neutral Ti interstitial, and has a lower formation energy for Ti interstitial under O-rich conditions. This indicates that both the O vacancy and Ti interstitial are relevant for oxygen deficiency in rutile TiO2 but the O vacancy will dominate under O-rich conditions. This resolves the questions about defect localisation and defect predominance in the li...
Heats of Formation of Medium-Size Organic Compounds from Contemporary Electronic Structure Methods
Minenkov, Yury
2017-06-21
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the “gold standard” coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach. As for comparison, 8 density functional theory (B3LYP, B3LYP-D3, PBE0, PBE0-D3, M06, M06-2X, ωB97X-D3, and ωB97M-V) and MP2-based (B2PLYP-D3, PWPB95-D3, B2T-PLYP, B2T-PLYP-D, B2GP-PLYP, DSD-PBEP86-D3, SCS-MP2, and OO-SCS-MP2) methods have been tested. The worst performance has been obtained for the standard hybrid DFT functionals, PBE0 (Mean unsigned error (MUE)/ Mean Signed Error (MSE)=9.1/6.0 kcal/mol) and B3LYP (MUE/MSE=13.5/-13.3 kcal/mol). An influence of an empirical dispersion correction term on these functionals performance is not homogenous: B3LYP performance is improved (B3LYP-D3 (MUE/MSE=6.0/0.8 kcal/mol)) meanwhile PBE0 performance is worse (PBE0-D3 (MUE/MSE=14.1/13.6 kcal/mol)). The Minnesota functionals, M06 (MUE/MSE=3.8/-2.0 kcal/mol) and M06-2X (MUE/MSE=3.5/3.0 kcal/mol), and recently developed ωB97X-D3 (MUE/MSE=3.2/0.2 kcal/mol) and ωB97M-V (MUE/MSE=2.2/1.3 kcal/mol) methods provided significantly better formation enthalpies. Enthalpies of similar quality can also be obtained from some double hybrid methods (B2PLYP-D3 (MUE/MSE=4.7/2.0 kcal/mol), PWPB95-D3 (MUE/MSE=4.3/3.2 kcal/mol), B2T-PLYP (MUE/MSE=4.1/-3.0 kcal/mol) and B2T-PLYP-D (MUE/MSE=3.3/1.7 kcal/mol)). The two spin component scaled (SCS) MP2 methods resulted in
Energy Technology Data Exchange (ETDEWEB)
Xu, Jun [Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China); Jia, Lei [Department of Physics and Chemistry, Henan Polytechnic University, Jiaozuo 454000 (China); Ma, Yufei; Liu, Xiao; Tian, Hao; Liu, Weisheng [Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China); Tang, Yu, E-mail: tangyu@lzu.edu.cn [Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China)
2012-09-14
Functional luminescent hybrid materials have emerged as fascinating and promising materials for their versatile applications. In this report, novel efficient luminescent lanthanide (Tb{sup 3+}, Eu{sup 3+}) hybrid materials with a new kind of amide-type {beta}-diketone ligands covalently bonded to the silica gels have been assembled through the sol-gel progresses. The hybrid materials have been characterized by the Fourier transform infrared (FTIR) spectra, UV-vis absorption spectra, powder X-ray diffraction (PXRD), scanning electron microscope (SEM), and thermal analyses. The relationship between structures and photophysical behaviors of these materials was discussed in detail. The materials assembled by the precursors containing aromatic end group (Si-L{sup 1}-Ln) exhibited longer luminescence lifetimes and higher quantum efficiencies, suggesting that the existence of a suitable conjugated system should allow a more efficient energy transfer. Under UV irradiation, the materials emitted either bright green light or red light with different intensity which may lead to potential functional applications in optical devices and electronic devices. Highlights: Black-Right-Pointing-Pointer A new kind of efficient luminescent lanthanide hybrid materials has been assembled. Black-Right-Pointing-Pointer The materials can efficiently emit green or red light under UVA irradiation. Black-Right-Pointing-Pointer The relationship between photophysical behaviors and structures was discussed. Black-Right-Pointing-Pointer A suitable conjugated system should allow a more efficient energy transfer.
Mahmood, Ayyaz; Longo, Ricardo L
2016-06-22
The performances of 26 combinations of density-functional theory (DFT) functionals or second-order Møller-Plesset (MP2) methods and basis sets were evaluated for the calculation of the activation energy (Δ(‡)E), the energy available (ΔRCE) to the reactant complex, the energy of reaction (ΔrE), and rotational constants of the main structures involved in the methylation reactions of nitronates, [R(1)R(2)CNO2](-) + CH3I, in the gas phase, where R(1) = R(2) = H, R(1) = H and R(2) = CH3, R(1) = R(2) = CH3, and R(1) + R(2) = c-(CH2)2. The separated reactants and products, the reactant and product complexes, and the transition states were considered, leading to 43 data points for the statistical analysis for each method under assessment. Five statistical quantifiers: the mean signed error (MSE), the mean unsigned error (MUE), the percent mean relative error (% MRE), best and worse (BW), and the confidence interval (CI) were used to assess the performance of methods relative to the CCSD(T)/CBS//MP2/aug-cc-pVTZ reference method. The DFT functionals included the widely applied B3LYP and M06-2X global-hybrids and the recently available DSD-PBEP86, DSD-PBEP86-D3BJ and PWPB95 double-hybrids. The basis sets involved an effective core potential (ECP) for describing the inner electrons of iodine such as LANL2DZdp and aug-cc-pVXZ-PP (X = D, T, and Q), and all-electron basis sets for the remaining atoms. The energy available to the reactant complex is described quite well by all methods, however, only the MP2/aug-cc-pVTZ-PP method provided values within 2 kcal mol(-1) (8.4 kJ mol(-1)) from the reference method for Δ(‡)E and ΔrE. Amongst the DFT methods, the global-hybrid M06-2X functional produced the best overall results including BW and CI. Notice that all methods yielded the smallest Δ(‡)E for the C-methylation pathway. The rotational constants of the reactant complexes and the transition state structures were compared, for which the MP2 method and the M06-2X
Experimental and computational thermochemical study of oxindole
Energy Technology Data Exchange (ETDEWEB)
Miranda, Margarida S., E-mail: msmirand@fc.up.p [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Centro de Geologia da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Matos, M. Agostinha R., E-mail: marmatos@fc.up.p [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Morais, Victor M.F., E-mail: vmmorais@icbas.up.p [Centro de Investigacao em Quimica, Departamento de Quimica e Bioquimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Instituto de Ciencias Biomedicas Abel Salazar, ICBAS, Universidade do Porto, P-4099-003 Porto (Portugal); Liebman, Joel F., E-mail: jliebman@umbc.ed [Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250 (United States)
2010-09-15
An experimental and computational thermochemical study was performed for oxindole. The standard (p{sup 0}=0.1MPa) molar enthalpy of formation of solid oxindole was derived from the standard molar energy of combustion, in oxygen, at T = 298.15 K, measured by static bomb combustion calorimetry. The respective standard molar enthalpy of sublimation, at T = 298.15 K, was measured by Calvet microcalorimetry. The standard molar enthalpy of formation in the gas phase was derived as -(66.8 {+-} 3.2) kJ . mol{sup -1}. Density functional theory calculations with the B3LYP hybrid functional and the 6-31G* and 6-311G** sets have also been performed in order to obtain the most stable conformation of oxindole. A comparison has been made between the structure of oxindole and that of the related two-ring molecules: indoline and 2-indanone and the one-ring molecules: pyrrolidine and 2,3-dihydropyrrole. The G3(MP2)//B3LYP method and appropriate reactions were used to obtain estimates of the standard molar enthalpy of formation of oxindole in the gas phase, at T = 298.15 K. Computationally obtained estimates of the enthalpy of formation of oxindole are in very good agreement with the experimental gas phase value. The aromaticity of oxindole was evaluated through the analysis of the nucleus independent chemical shifts (NICS) obtained from the B3LYP/6-311G** wave functions.
Experimental and DFT studies on the vibrational spectra of 1H-indene-2-boronic acid
Alver, Özgur; Kaya, Mehmet Fatih
2014-11-01
Stable conformers and geometrical molecular structures of 1H-indene-2-boronic acid (I-2B(OH)2) were studied experimentally and theoretically using FT-IR and FT-Raman spectroscopic methods. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm-1, and 3700-400 cm-1, respectively. The optimized geometric structures were searched by Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-31++G(d,p) basis set. Vibrational wavenumbers of I-2B(OH)2 were calculated using B3LYP density functional methods including 6-31++G(d,p) basis set. Experimental and theoretical results show that density functional B3LYP method gives satisfactory results for predicting vibrational wavenumbers except OH stretching modes which is probably due to increasing unharmonicity in the high wave number region and possible intra and inter molecular interaction at OH edges. To support the assigned vibrational wavenumbers, the potential energy distribution (PED) values were also calculated using VEDA 4 (Vibrational Energy Distribution Analysis) program.
Energy Technology Data Exchange (ETDEWEB)
Xu, Ting; Zhao, Xin; Zhang, Junxian; Dong, Jie; Zhang, Qinghua, E-mail: qhzhang@dhu.edu.cn
2016-04-30
Highlights: • PS/PDA with well-defined core/shell structures was prepared in aqueous solution. • Au NPs were coated on PS/PDA by in-situ reduction and self-assembly approach. • PS/PDA/Au had homogeneous and dense Au coatings with different shape. • Hierarchical spheres exhibited a well-defined core/shell structure maintaining the spherical morphology. - Abstract: Two kinds of ternary hybrids were prepared by anchoring different shapes and loadings of Au nanoparticles (NPs) on poly(dopamine) (PDA) functionalized polystyrene (PS) microspheres with two different strategies, i.e., in situ reduction and self-assembly approach. PDA coatings were firstly introduced to functionalize the hydrophobic PS surface with sufficient amino and hydroxyl groups, which enhanced the interaction between Au NPs and the polymer spheres. Thus, Au NPs could be easily immobilized onto the surface of the PDA/PS microspheres, and the hierarchical composite microspheres exhibited a well-defined core/shell structure without sacrificing the spherical PS morphology. PS/PDA/Au-R and PS/PDA/Au-A microspheres fabricated by in situ reduction and self-assembly approach showed different distinct Au nano-shell morphology with the corresponding optical, catalytic and electrochemical properties. Field emission scanning electron microscopy and transmission electronic microscopy verified these hierarchical structures with the ultrathin PDA film incorporating between the inner PS core and the outer Au NPs shell. X-ray diffraction and X-ray photoelectron spectroscopy confirmed the presence of PDA and Au layer on the surface of the composite particles. These green and facile methods with mild experimental conditions can extend to fabricate other polymer or inorganic substrates coated by various noble metals.
Energy Technology Data Exchange (ETDEWEB)
Nishimura, Yoshifumi [Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); Lee, Yuan-Pern [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan (China); Irle, Stephan [Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Witek, Henryk A., E-mail: hwitek@mail.nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China)
2014-09-07
Vibrational infrared (IR) spectra of gas-phase O–H⋅⋅⋅O methanol clusters up to pentamer are simulated using self-consistent-charge density functional tight-binding method using two distinct methodologies: standard normal mode analysis and Fourier transform of the dipole time-correlation function. The twofold simulations aim at the direct critical assignment of the C–H stretching region of the recently recorded experimental spectra [H.-L. Han, C. Camacho, H. A. Witek, and Y.-P. Lee, J. Chem. Phys. 134, 144309 (2011)]. Both approaches confirm the previous assignment (ibid.) of the C–H stretching bands based on the B3LYP/ANO1 harmonic frequencies, showing that ν{sub 3}, ν{sub 9}, and ν{sub 2} C–H stretching modes of the proton-accepting (PA) and proton-donating (PD) methanol monomers experience only small splittings upon the cluster formation. This finding is in sharp discord with the assignment based on anharmonic B3LYP/VPT2/ANO1 vibrational frequencies (ibid.), suggesting that some procedural faults, likely related to the breakdown of the perturbational vibrational treatment, led the anharmonic calculations astray. The IR spectra based on the Fourier transform of the dipole time-correlation function include new, previously unaccounted for physical factors such as non-zero temperature of the system and large amplitude motions of the clusters. The elevation of temperature results in a considerable non-homogeneous broadening of the observed IR signals, while the presence of large-amplitude motions (methyl group rotations and PA-PD flipping), somewhat surprisingly, does not introduce any new features in the spectrum.
Dutton, Andrew S; Suhrada, Christopher P; Miranda, Katrina M; Wink, David A; Fukuto, Jon M; Houk, K N
2006-03-20
Isopropylamine diazeniumdiolate, IPA/NO, the product of the reaction of isopropylamine and nitric oxide, NO, decomposes in a pH-dependent manner to afford nitroxyl, HNO, in the pH range of 13 to above 5, and NO below pH 7. Theoretical studies using B3LYP/6-311+G(d) density functional theory, the polarizable continuum and conductor-like polarizable continuum solvation models, and the high-accuracy CBS-QB3 method on the simplified model compound methylamine diazeniumdiolate predict a mechanism involving HNO production via decomposition of the unstable tautomer MeNN+(O-)NHO-. The production of NO at lower pH is predicted to result from fragmentation of the amide/NO adduct upon protonation of the amine nitrogen.
Dutton, Andrew S.; Suhrada, Christopher P.; Miranda, Katrina M.; Wink, David A.; Fukuto, Jon M.; Houk, K. N.
2011-01-01
Isopropylamine diazeniumdiolate, IPA/NO, the product of the reaction of isopropylamine and nitric oxide, NO, decomposes in a pH dependent manner to afford nitroxyl, HNO, in the pH range of 13 to above 5 and NO below pH 7. Theoretical studies using B3LYP/6-311+G(d) density functional theory, the PCM and CPCM solvation models and the high accuracy CBS-QB3 method on the simplified model compound, methylamine diazeniumdiolate, predict a mechanism involving HNO production via decomposition of the unstable tautomer MeNN+(O−)NHO−. The production of NO at lower pH is predicted to result from fragmentation of the amide/NO adduct upon protonation of the amine nitrogen. PMID:16529464
Rahman, Taj Ur; Arfan, Mohammad; Mahmood, Tariq; Liaqat, Wajiha; Gilani, Mazhar Amjad; Uddin, Ghias; Ludwig, Ralf; Zaman, Khair; Choudhary, M. Iqbal; Khattak, Khanzadi Fatima; Ayub, Khurshid
2015-07-01
The phytochemical examination of chloroform soluble fraction (FX2) of methanolic extract of bark of Millettia ovalifolia yielded a new flavonoid; 7-(4-methoxyphenyl)-9H-furo [2,3-f]chromen-9-one (1). Compound 1 is characterized by spectroscopic analytical techniques such as UV, IR, 1D, 2D NMR spectroscopy, and mass spectrometry. A theoretical model is also developed for obtaining geometric, electronic and spectroscopic properties of 1. The geometry optimization and harmonic vibration simulations have been carried out at B3LYP/6-31G(d,p). The vibrational spectrum of compound 1 shows nice correlation with the experimental IR spectrum, through a scaling factor of 0.9613. 1H and 13C NMR chemical shifts are simulated using Cramer's re-parameterized function WP04 at 6-31G(d,p) basis set, and correlate nicely with the experimental chemical shifts.
帕拉米韦分子的密度泛函理论研究%Density Functional Theory Study on Peramivir
Institute of Scientific and Technical Information of China (English)
焉炳飞; 肖翠平; 李文佐; 程建波
2015-01-01
The peramivir molecule is investigated using density functional theory (DFT) method at B3LYP/6-311+G( d, p) level. The stable geometric configuration of peramivir molecule is obtained. The geometric parameters, such as molecular bond lengths, bond angles, and dihedral angles, are calculated. NBO charge analysis and fron-tier molecular orbital analysis are also performed. The solvent effect of the steric structure of peramivir molecule is investigated using H2 O as solvent. In addition, the infrared spectroscopy of peramivir molecule both in gas and in water is simulated. The present results provide theoretical information for further experimental studies.%采用密度泛函理论(DFT)方法,在B3LYP/6-311+G(d, p)水平上对抗流感药物帕拉米韦进行了计算研究。优化得到了帕拉米韦分子的稳定几何构型,计算了分子的键长、键角、二面角等参数,并对其进行了自然电荷分析和前线轨道分析。以H2 O为溶剂研究了溶剂效应对帕拉米韦分子空间结构的影响。理论模拟了帕拉米韦分子在气相和水溶液中的红外光谱,为进一步实验工作提供了理论信息。
Excitation Gaps of Finite-Sized Systems from Optimally Tuned Range-Separated Hybrid Functionals.
Kronik, Leeor; Stein, Tamar; Refaely-Abramson, Sivan; Baer, Roi
2012-05-08
Excitation gaps are of considerable significance in electronic structure theory. Two different gaps are of particular interest. The fundamental gap is defined by charged excitations, as the difference between the first ionization potential and the first electron affinity. The optical gap is defined by a neutral excitation, as the difference between the energies of the lowest dipole-allowed excited state and the ground state. Within many-body perturbation theory, the fundamental gap is the difference between the corresponding lowest quasi-hole and quasi-electron excitation energies, and the optical gap is addressed by including the interaction between a quasi-electron and a quasi-hole. A long-standing challenge has been the attainment of a similar description within density functional theory (DFT), with much debate on whether this is an achievable goal even in principle. Recently, we have constructed and applied a new approach to this problem. Anchored in the rigorous theoretical framework of the generalized Kohn-Sham equation, our method is based on a range-split hybrid functional that uses exact long-range exchange. Its main novel feature is that the range-splitting parameter is not a universal constant but rather is determined from first principles, per system, based on satisfaction of the ionization potential theorem. For finite-sized objects, this DFT approach mimics successfully, to the best of our knowledge for the first time, the quasi-particle picture of many-body theory. Specifically, it allows for the extraction of both the fundamental and the optical gap from one underlying functional, based on the HOMO-LUMO gap of a ground-state DFT calculation and the lowest excitation energy of a linear-response time-dependent DFT calculation, respectively. In particular, it produces the correct optical gap for the difficult case of charge-transfer and charge-transfer-like scenarios, where conventional functionals are known to fail. In this perspective, we overview
Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals
Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo
2015-12-01
We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H+/H2 level defining the standard hydrogen electrode, the OH-/OH∗ level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH∗ level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall
Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals
Energy Technology Data Exchange (ETDEWEB)
Ambrosio, Francesco, E-mail: Francesco.Ambrosio@epfl.ch; Miceli, Giacomo; Pasquarello, Alfredo [Chaire de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)
2015-12-28
We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H{sup +}/H{sub 2} level defining the standard hydrogen electrode, the OH{sup −}/OH{sup ∗} level corresponding to the oxidation of the hydroxyl ion, and the H{sub 2}O/OH{sup ∗} level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band
Muthu, S; Ramachandran, G
2014-01-01
The Fourier transform infrared (FT-IR) and FT-Raman of (1R)-N-(Prop-2-yn-1-yl)-2,3-dihydro-1H-inden-1-amine (1RNPDA) were recorded in the regions 4000-400 cm(-1) and 4000-100 cm(-1) respectively. A complete assignment and analysis of the fundamental vibrational modes of the molecule were carried out. The observed fundamental modes have been compared with the harmonic vibrational frequencies computed using HF method by employing 6-31G(d,p) basis set and DFT(B3LYP) method by employing 6-31G(d,p) basis set. The vibrational studies were interpreted in terms of Potential Energy Distribution (PED). The complete vibrational frequency assignments were made by Normal Co-ordinate Analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The first order hyper polarizability (β0) of this molecular system and related properties (α, μ, and Δα) are calculated using B3LYP/6-31G(d,p) method based on the finite-field approach. The thermodynamic functions of the title compound were also performed at the above methods and basis set. A detailed interpretation of the infrared and Raman spectra of 1RNPDA is reported. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated using the GIAO method confirms with the experimental values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using Natural Bond Orbital (NBO) analysis. UV-vis spectrum of the compound was recorded and electronic properties such as excitation energies, oscillator strength and wavelength were performed by TD-DFT/B3LYP using 6-31G(d,p) basis set. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The observed and calculated wave numbers are formed to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra. Copyright © 2013 Elsevier B.V. All rights reserved.
Tunable functionalization of graphene nanosheets for graphene-organic hybrid photodetectors
Kim, Seong Jun; Song, Wooseok; Kim, Sungho; Kang, Min-A.; Myung, Sung; Lee, Sun Sook; Lim, Jongsun; An, Ki-Seok
2016-02-01
Graphene-organic hybrid thin films are promising candidates for use as advanced transparent electrodes and high-performance photodetectors. In this work, we fabricated hybrid thin film structures consisting of graphene and either tetraphenyl-porphyrin (H2TPP) or metalloporphyrins such as aluminum (III) tetraphenyl-porphyrin (Al(III)TPP) and zinc tetraphenyl-porphyrin (ZnTPP). The optical and electrical characteristics of ultrathin photodetectors based on the graphene-organic hybrid layers were subsequently evaluated. A hybrid deposition system capable of both thermal evaporation and vapor phase metalation was employed to synthesize the tunable metalloporphyrin-based thin films. As a proof of concept, we successfully fabricated various graphene-based photodetectors via the simple and efficient vapor-phase metalation of porphyrin. This work may facilitate the development of new architectures for flexible graphene-organic devices.
Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)
Kupka, Teobald; Wieczorek, Piotr P.
2016-01-01
In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.
Magnetism in Sc-doped ZnO with zinc vacancies: A hybrid density functional and GGA + U approaches
Kanoun, Mohammed
2012-04-01
We investigate the zinc vacancy effects on the electronic structures and magnetic properties of Sc-doped ZnO, by performing first-principles calculations within both GGA + U and Heyd-Scuseria-Ernzerhof hybrid functional methods. We find that Sc impurities stabilize considerably Zn vacancies. The electronic and magnetic analysis shows a half metallic ferromagnetic character with a total magnetic moment of 2.01 μ B. The magnetism mainly stems from the O 2p states around the Zn vacancies. Calculations with the hybrid density functional agree with the GGA + U results but give an accurate description of the electronic structure for pure ZnO and Sc-doped ZnO with Zn vacancies. © 2012 Elsevier B.V. All rights reserved.
Berland, Kristian; Jiao, Yang; Lee, Jung-Hoon; Rangel, Tonatiuh; Neaton, Jeffrey B.; Hyldgaard, Per
2017-06-01
Two hybrid van der Waals density functionals (vdW-DFs) are developed using 25% Fock exchange with (i) the consistent-exchange vdW-DF-cx functional [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)] and (ii) with the vdW-DF2 functional [K. Lee et al., Phys. Rev. B 82, 081101 (2010)]. The ability to describe covalent and non-covalent binding properties of molecules is assessed. For properties related to covalent binding, atomization energies (G2-1 set), molecular reaction energies (G2RC set), and ionization energies (G21IP set) are benchmarked against experimental reference values. We find that hybrid-vdW-DF-cx yields results that are rather similar to those of the standard non-empirical hybrid PBE0 [C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999)], with mean average deviations (MADs) of 4.9 and 5.0 kcal/mol for the G2-1 set, respectively. In this comparison, experimental reference values are used, back corrected by wavefunction-based quantum-chemistry calculations of zero-point energies. Hybrid vdW-DF2 follows somewhat different trends, showing on average significantly larger deviations from the reference energies, with a MAD of 14.5 kcal/mol for the G2-1 set. Non-covalent binding properties of molecules are assessed using the S22 benchmark set of non-covalently bonded dimers and the X40 set of dimers of small halogenated molecules, using wavefunction-based quantum chemistry results as references. For the S22 set, hybrid-vdW-DF-cx performs better than standard vdW-DF-cx for the mostly hydrogen-bonded systems, with MAD dropping from 0.6 to 0.3 kcal/mol, but worse for purely dispersion-bonded systems, with MAD increasing from 0.2 to 0.6 kcal/mol. Hybrid-vdW-DF2 offers a slight improvement over standard vdW-DF2. Similar trends are found for the X40 set, with hybrid-vdW-DF-cx performing particularly well for binding energies involving the strongly polar hydrogen halides, but poorly for systems with tiny binding energies. Our study of the X40 set
A Hybrid Approach to Structure and Function Modeling of G Protein-Coupled Receptors.
Latek, Dorota; Bajda, Marek; Filipek, Sławomir
2016-04-25
The recent GPCR Dock 2013 assessment of serotonin receptor 5-HT1B and 5-HT2B, and smoothened receptor SMO targets, exposed the strengths and weaknesses of the currently used computational approaches. The test cases of 5-HT1B and 5-HT2B demonstrated that both the receptor structure and the ligand binding mode can be predicted with the atomic-detail accuracy, as long as the target-template sequence similarity is relatively high. On the other hand, the observation of a low target-template sequence similarity, e.g., between SMO from the frizzled GPCR family and members of the rhodopsin family, hampers the GPCR structure prediction and ligand docking. Indeed, in GPCR Dock 2013, accurate prediction of the SMO target was still beyond the capabilities of most research groups. Another bottleneck in the current GPCR research, as demonstrated by the 5-HT2B target, is the reliable prediction of global conformational changes induced by activation of GPCRs. In this work, we report details of our protocol used during GPCR Dock 2013. Our structure prediction and ligand docking protocol was especially successful in the case of 5-HT1B and 5-HT2B-ergotamine complexes for which we provide one of the most accurate predictions. In addition to a description of the GPCR Dock 2013 results, we propose a novel hybrid computational methodology to improve GPCR structure and function prediction. This computational methodology employs two separate rankings for filtering GPCR models. The first ranking is ligand-based while the second is based on the scoring scheme of the recently published BCL method. In this work, we prove that the use of knowledge-based potentials implemented in BCL is an efficient way to cope with major bottlenecks in the GPCR structure prediction. Thereby, we also demonstrate that the knowledge-based potentials for membrane proteins were significantly improved, because of the recent surge in available experimental structures.
Miglia, K.J.; McArthur, E.D.; Redman, R.S.; Rodriguez, R.J.; Zak, J.C.; Freeman, D.C.
2007-01-01
When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F1 hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F1 hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden-by-soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F1 hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.
Calculations of Molar Fractions of the IPR C78 Fullerenes
Uhlík, Filip; Slanina, Zdeněk
2002-10-01
There are five isolated-pentagon-rule (IPR) satisfying isomers of C78. In contradiction to theoretical predictions, only three isomers were observed in experiments and the fourth one was not identified until very recently. In this work we calculate structural and energetic data of the five IPR C78 fullerenes, namely we optimized their geometries with the B3LYP density-functional method using the standard 4-31G basis set (B3LYP/4-31G), calculated separation energies at the B3LYP/6-311G* level (B3LYP/6-311G*//B3LYP/4-31G), estimated energies of low lying electronic states with the ZINDO semiempirical method and calculated harmonic vibrational frequencies with the semiempirical SAM1 method. From the obtained data we constructed chirality respecting isomeric partition functions and evaluated molar fractions in the equilibrium isomeric mixture for a wide temperature interval.
Abosadiya, Hamza M; Anouar, El Hassane; Hasbullah, Siti Aishah; Yamin, Bohari M
2015-06-05
A new isomers of thiourea derivatives, namely N-(4-chlorobutanoyl)-N'-(2-methylphenyl)-thiourea (1a), N-(4-chlorobutanoyl)-N'-(3-methylphenyl)thiourea (1b) and N-(4-chlorobutanoyl)-N'-(4-methylphenyl)thiourea (1c) have been synthesized by refluxing mixture of equimolar amounts of 4-chlorobutanoylisothiocyanate with 2, 3 or 4-toluidine, respectively. The three isomers were characterized by spectroscopic (UV/vis, FT-IR and NMR) and X-ray crystallography techniques. To investigate the isomerization effect on spectroscopic data, DFT and TD-DFT calculations have been carried out using five hybrid functionals (B3LYP, B3P86, CAM-B3LYP, M06-2X and PBE0) to predict UV/vis absorption bands (n→π∗ and π→π∗), (1)H and (13)C NMR chemical shifts, FT-IR vibration modes and X-ray parameters (bonds, bond angles and torsion angles) for 1a, 1b and 1c isomers. The results showed that the isomerization effect is significant on λ(MAX) absorption bands, while for IR and NMR the effect is negligible. In accordance with previous studies, B3LYP, B3P86 and PBE0 gave the most reliable to predict the excitation energies of thiourea derivatives.
Kutateladze, Andrei G; Mukhina, Olga A
2015-05-15
We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz.
Ihrig, Arvid Conrad; Wieferink, Jürgen; Zhang, Igor Ying; Ropo, Matti; Ren, Xinguo; Rinke, Patrick; Scheffler, Matthias; Blum, Volker
2015-09-01
A key component in calculations of exchange and correlation energies is the Coulomb operator, which requires the evaluation of two-electron integrals. For localized basis sets, these four-center integrals are most efficiently evaluated with the resolution of identity (RI) technique, which expands basis-function products in an auxiliary basis. In this work we show the practical applicability of a localized RI-variant (‘RI-LVL’), which expands products of basis functions only in the subset of those auxiliary basis functions which are located at the same atoms as the basis functions. We demonstrate the accuracy of RI-LVL for Hartree-Fock calculations, for the PBE0 hybrid density functional, as well as for RPA and MP2 perturbation theory. Molecular test sets used include the S22 set of weakly interacting molecules, the G3 test set, as well as the G2-1 and BH76 test sets, and heavy elements including titanium dioxide, copper and gold clusters. Our RI-LVL implementation paves the way for linear-scaling RI-based hybrid functional calculations for large systems and for all-electron many-body perturbation theory with significantly reduced computational and memory cost.
Erisken, Cevat
Tissue engineering is the application of the principles of engineering and life sciences for the development of biological alternatives for improvement or regeneration of native tissues. Native tissues are complex structures with functions and properties changing spatially and temporally, and engineering of such structures requires functionally graded scaffolds with composition and properties changing systematically along various directions. Utilization of a new hybrid technology integrating the controlled feeding, compounding, dispersion, deaeration, and pressurization capabilities of extrusion process with electrospinning allows incorporation of liquids and solid particles/nanoparticles into polymeric fibers/nanofibers for fabrication of functionally graded non-woven meshes to be used as scaffolds in engineering of tissues. The capabilities of the hybrid technology were demonstrated with a series of scaffold fabrication and cell culturing studies along with characterization of biomechanical properties. In the first study, the hybrid technology was employed to generate concentration gradations of beta-tricalcium phosphate (beta-TCP) nanoparticles in a polycaprolactone (PCL) binder, between two surfaces of nanofibrous scaffolds. These scaffolds were seeded with pre-osteoblastic cell line (MC3T3-E1) to attempt to engineer cartilage-bone interface, and after four weeks, the tissue constructs revealed formation of continuous gradations in extracellular matrix akin to cartilage-bone interface in terms of distributions of mineral concentrations and biomechanical properties. In a second demonstration of the hybrid technology, graded differentiation of stem cells was attempted by using insulin, a known stimulator of chondrogenic differentiation, and beta-glycerol phosphate (beta-GP), for mineralization. Concentrations of insulin and beta-GP in PCL were controlled to monotonically increase and decrease, respectively, along the length of scaffolds, which were then seeded
Directory of Open Access Journals (Sweden)
Jacky Even
2014-01-01
Full Text Available Potentialities of density functional theory (DFT based methodologies are explored for photovoltaic materials through the modeling of the structural and optoelectronic properties of semiconductor hybrid organic-inorganic perovskites and GaAs/GaP heterostructures. They show how the properties of these bulk materials, as well as atomistic relaxations, interfaces, and electronic band-lineups in small heterostructures, can be thoroughly investigated. Some limitations of available standard DFT codes are discussed. Recent improvements able to treat many-body effects or based on density-functional perturbation theory are also reviewed in the context of issues relevant to photovoltaic technologies.
Huyal, Ilkem Ozge; Ozel, Tuncay; Koldemir, Unsal; Nizamoglu, Sedat; Tuncel, Donus; Demir, Hilmi Volkan
2008-01-21
We develop and demonstrate high-quality white light generation that relies on the use of a single-type simple conjugated polymer of polyfluorene functionalized with azide groups (PFA) integrated on a near-UV LED platform. The high-quality white emission from the polyfluorene is achieved by using the azide functionalization to facilitate cross-linking intentionally when cast into solid-state form. Hybridized on n-UV InGaN/GaN LED at 378 nm, the PFA emitters collectively generate a very broad down-converting photoluminescence at longer wavelengths across the entirety of the visible spectrum, yielding high color rendering indices up to 91.
Functional stability of endothelial cells on a novel hybrid scaffold for vascular tissue engineering
Energy Technology Data Exchange (ETDEWEB)
Pankajakshan, Divya; Krishnan, Lissy K [Thrombosis Research Unit, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojapura, Trivandrum 695 012 (India); Krishnan V, Kalliyana, E-mail: lissykk@sctimst.ac.i [Division of Polymer Technology, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojapura, Trivandrum 695 012 (India)
2010-12-15
Porous and pliable conduits made of biodegradable polymeric scaffolds offer great potential for the development of blood vessel substitutes but they generally lack signals for cell proliferation, survival and maintenance of a normal phenotype. In this study we have prepared and evaluated porous poly({epsilon}-caprolactone) (PCL) integrated with fibrin composite (FC) to get a biomimetic hybrid scaffold (FC PCL) with the biological properties of fibrin, fibronectin (FN), gelatin, growth factors and glycosaminoglycans. Reduced platelet adhesion on a human umbilical vein endothelial cell-seeded hybrid scaffold as compared to bare PCL or FC PCL was observed, which suggests the non-thrombogenic nature of the tissue-engineered scaffold. Analysis of real-time polymerase chain reaction (RT-PCR) after 5 days of endothelial cell (EC) culture on a hybrid scaffold indicated that the prothrombotic von Willebrand factor and plasminogen activator inhibitor (PAI) were quiescent and stable. Meanwhile, dynamic expressions of tissue plasminogen activator (tPA) and endothelial nitric oxide synthase indicated the desired cell phenotype on the scaffold. On the hybrid scaffold, shear stress could induce enhanced nitric oxide release, which implicates vaso-responsiveness of EC grown on the tissue-engineered construct. Significant upregulation of mRNA for extracellular matrix (ECM) proteins, collagen IV and elastin, in EC was detected by RT-PCR after growing them on the hybrid scaffold and FC-coated tissue culture polystyrene (FC TCPS) but not on FN-coated TCPS. The results indicate that the FC PCL hybrid scaffold can accomplish a remodeled ECM and non-thrombogenic EC phenotype, and can be further investigated as a scaffold for cardiovascular tissue engineering. (communication)