Electronic Circular Dichroism of [16]Helicene With Simplified TD-DFT: Beyond the Single Structure Approach.

PubMed

Bannwarth, Christoph; Seibert, Jakob; Grimme, Stefan

2016-05-01

The electronic circular dichroism (ECD) spectrum of the recently synthesized [16]helicene and a derivative comprising two triisopropylsilyloxy protection groups was computed by means of the very efficient simplified time-dependent density functional theory (sTD-DFT) approach. Different from many previous ECD studies of helicenes, nonequilibrium structure effects were accounted for by computing ECD spectra on "snapshots" obtained from a molecular dynamics (MD) simulation including solvent molecules. The trajectories are based on a molecule specific classical potential as obtained from the recently developed quantum chemically derived force field (QMDFF) scheme. The reduced computational cost in the MD simulation due to the use of the QMDFF (compared to ab-initio MD) as well as the sTD-DFT approach make realistic spectral simulations feasible for these compounds that comprise more than 100 atoms. While the ECD spectra of [16]helicene and its derivative computed vertically on the respective gas phase, equilibrium geometries show noticeable differences, these are "washed" out when nonequilibrium structures are taken into account. The computed spectra with two recommended density functionals (ωB97X and BHLYP) and extended basis sets compare very well with the experimental one. In addition we provide an estimate for the missing absolute intensities of the latter. The approach presented here could also be used in future studies to capture nonequilibrium effects, but also to systematically average ECD spectra over different conformations in more flexible molecules. Chirality 28:365-369, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Photoinduced relaxation dynamics of nitrogen-capped silicon nanoclusters: a TD-DFT study

NASA Astrophysics Data System (ADS)

Liu, Xiang-Yang; Xie, Xiao-Ying; Fang, Wei-Hai; Cui, Ganglong

2018-04-01

Herein we have developed and implemented a TD-DFT-based surface-hopping dynamics simulation method with a recently proposed numerical algorithm capable of efficiently computing nonadiabatic couplings, a semiclassical spectrum simulation method, and an excited-state character analysis method based on one-electron transition density matrix. With the use of these developed methods, we have studied the spectroscopic properties, excited-state characters, and photoinduced relaxation dynamics of three silicon nanoclusters capped with different chromophores (Cl@SiQD, Car@SiQD, Azo@SiQD). Spectroscopically, the main absorption peak is visibly red-shifted from Cl@SiQD via Car@SiQD to Azo@SiQD. In contrast to Cl@SiQD and Car@SiQD, there are two peaks observed in Azo@SiQD. Mechanistically, the excited-state relaxation to the lowest S1 excited singlet state is ultrafast in Cl@SiQD, which is less than 190 fs and without involving excited-state trapping. In comparison, there are clear excited-state trappings in Car@SiQD and Azo@SiQD. In the former, the S2 state is trapped more than 300 fs; in the latter, the S3 excited-state trapping is more than 615 fs. These results demonstrate that the interfacial interaction has significant influences on the spectroscopic properties and excited-state relaxation dynamics. The knowledge gained in this work could be helpful for the design of silicon nanoclusters with better photoluminescence performance.

DFT and TD-DFT calculations of metallotetraphenylporphyrin and metallotetraphenylporphyrin fullerene complexes as potential dye sensitizers for solar cells

NASA Astrophysics Data System (ADS)

El Mahdy, A. M.; Halim, Shimaa Abdel; Taha, H. O.

2018-05-01

Density functional theory (DFT) and time-dependent DFT calculations have been employed to model metallotetraphenylporphyrin dyes and metallotetraphenylporphyrin -fullerene complexes in order to investigate the geometries, electronic structures, the density of states, non-linear optical properties (NLO), IR-vis spectra, molecular electrostatic potential contours, and electrophilicity. To calculate the excited states of the tetraphenyl porphyrin analogs, time-dependent density functional theory (TD-DFT) are used. Their UV-vis spectra were also obtained and a comparison with available experimental and theoretical results is included. The results reveal that the metal and the tertiary butyl groups of the dyes are electron donors, and the tetraphenylporphyrin rings are electron acceptors. The HOMOs of the dyes fall within the (TiO2)60 and Ti38O76 band gaps and support the issue of typical interfacial electron transfer reaction. The resulting potential drop of Mn-TPP-C60 increased by ca. 3.50% under the effect of the tertiary butyl groups. The increase in the potential drop indicates that the tertiary butyl complexes could be a better choice for the strong operation of the molecular rectifiers. The introduction of metal atom and tertiary butyl groups to the tetraphenyl porphyrin moiety leads to a stronger response to the external electric field and induces higher photo-to-current conversion efficiency. This also shifts the absorption in the dyes and makes them potential candidates for harvesting light in the entire visible and near IR region for photovoltaic applications.

Is the Bethe–Salpeter Formalism Accurate for Excitation Energies? Comparisons with TD-DFT, CASPT2, and EOM-CCSD

PubMed Central

2017-01-01

Developing ab initio approaches able to provide accurate excited-state energies at a reasonable computational cost is one of the biggest challenges in theoretical chemistry. In that framework, the Bethe–Salpeter equation approach, combined with the GW exchange-correlation self-energy, which maintains the same scaling with system size as TD-DFT, has recently been the focus of a rapidly increasing number of applications in molecular chemistry. Using a recently proposed set encompassing excitation energies of many kinds [J. Phys. Chem. Lett.2016, 7, 586–591], we investigate here the performances of BSE/GW. We compare these results to CASPT2, EOM-CCSD, and TD-DFT data and show that BSE/GW provides an accuracy comparable to the two wave function methods. It is particularly remarkable that the BSE/GW is equally efficient for valence, Rydberg, and charge-transfer excitations. In contrast, it provides a poor description of triplet excited states, for which EOM-CCSD and CASPT2 clearly outperform BSE/GW. This contribution therefore supports the use of the Bethe–Salpeter approach for spin-conserving transitions. PMID:28301726

Novel push-pull fluorescent dyes - 7-(diethylamino)furo- and thieno[3,2-c]coumarins derivatives: structure, electronic spectra and TD-DFT study

NASA Astrophysics Data System (ADS)

Akchurin, Igor O.; Yakhutina, Anna I.; Bochkov, Andrei Y.; Solovjova, Natalya P.; Medvedev, Michael G.; Traven, Valerii F.

2018-05-01

Novel push-pull fluorescent dyes - 7-(diethylamino)furo- and 7-(diethylamino)thieno[3,2-c]coumarins derivatives have been synthesized using formyl derivatives of furo- and thieno[3,2-c]coumarins as starting materials. Electron absorption and fluorescent spectra of the dyes have been recorded in different solvents. Structure and solvent effects on the dyes spectral characteristics were analyzed. The fusion of five-membered heterocycle to coumarin provides a definite increase of Stokes shifts in all solvents and results in higher quantum yields of fluorescence. The absorption and emission bands of thieno[3,2-c] coumarin derivatives are definitely shifted to the red region (3-30 nm) compared to similar derivatives of furo[3,2-c]coumarin. TD-DFT calculations of some of the studied compounds have shown that hybrid DFT functionals and adequate representation of molecular environment are essential for obtaining accurate UV-Vis absorption spectra for the dyes with extended π-system. The longest-wave electron transitions in the studied compounds were computationally shown to be of push-pull nature.

The electronic spectra and the structures of the individual copper(II) chloride and bromide complexes in acetonitrile according to steady-state absorption spectroscopy and DFT/TD-DFT calculations

NASA Astrophysics Data System (ADS)

Olshin, Pavel K.; Myasnikova, Olesya S.; Kashina, Maria V.; Gorbunov, Artem O.; Bogachev, Nikita A.; Kompanets, Viktor O.; Chekalin, Sergey V.; Pulkin, Sergey A.; Kochemirovsky, Vladimir A.; Skripkin, Mikhail Yu.; Mereshchenko, Andrey S.

2018-03-01

The results of spectrophotometric study and quantum chemical calculations for copper(II) chloro- and bromocomplexes in acetonitrile are reported. Electronic spectra of the individual copper(II) halide complexes were obtained in a wide spectral range 200-2200 nm. Stability constants of the individual copper(II) halide complexes in acetonitrile were calculated: log β1 = 8.5, log β2 = 15.6, log β3 = 22.5, log β4 = 25.7 for [CuCln]2-n and log β1 = 17.0, log β2 = 24.6, log β3 = 28.1, log β4 = 30.4 for [CuBrn]2-n. Structures of the studied complexes were optimized and electronic spectra were simulated using DFT and TD-DFT methodologies, respectively. According to the calculations, the more is the number of halide ligands the less is coordination number of copper ion.

TD-CI simulation of the electronic optical response of molecules in intense fields II: comparison of DFT functionals and EOM-CCSD.

PubMed

Sonk, Jason A; Schlegel, H Bernhard

2011-10-27

Time-dependent configuration interaction (TD-CI) simulations can be used to simulate molecules in intense laser fields. TD-CI calculations use the excitation energies and transition dipoles calculated in the absence of a field. The EOM-CCSD method provides a good estimate of the field-free excited states but is rather expensive. Linear-response time-dependent density functional theory (TD-DFT) is an inexpensive alternative for computing the field-free excitation energies and transition dipoles needed for TD-CI simulations. Linear-response TD-DFT calculations were carried out with standard functionals (B3LYP, BH&HLYP, HSE2PBE (HSE03), BLYP, PBE, PW91, and TPSS) and long-range corrected functionals (LC-ωPBE, ωB97XD, CAM-B3LYP, LC-BLYP, LC-PBE, LC-PW91, and LC-TPSS). These calculations used the 6-31G(d,p) basis set augmented with three sets of diffuse sp functions on each heavy atom. Butadiene was employed as a test case, and 500 excited states were calculated with each functional. Standard functionals yield average excitation energies that are significantly lower than the EOM-CC, while long-range corrected functionals tend to produce average excitation energies slightly higher. Long-range corrected functionals also yield transition dipoles that are somewhat larger than EOM-CC on average. The TD-CI simulations were carried out with a three-cycle Gaussian pulse (ω = 0.06 au, 760 nm) with intensities up to 1.26 × 10(14) W cm(-2) directed along the vector connecting the end carbons. The nonlinear response as indicated by the residual populations of the excited states after the pulse is far too large with standard functionals, primarily because the excitation energies are too low. The LC-ωPBE, LC-PBE, LC-PW91, and LC-TPSS long-range corrected functionals produce responses comparable to EOM-CC.

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Charge Transfer Enhancement in the D-π-A Type Porphyrin Dyes: A Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) Study.

PubMed

Kang, Guo-Jun; Song, Chao; Ren, Xue-Feng

2016-11-25

The electronic geometries and optical properties of two D-π-A type zinc porphyrin dyes (NCH₃-YD2 and TPhe-YD) were systematically investigated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) to reveal the origin of significantly altered charge transfer enhancement by changing the electron donor of the famous porphyrin-based sensitizer YD2-o-C8. The molecular geometries and photophysical properties of dyes before and after binding to the TiO₂ cluster were fully investigated. From the analyses of natural bond orbital (NBO), extended charge decomposition analysis (ECDA), and electron density variations (Δρ) between the excited state and ground state, it was found that the introduction of N(CH₃)₂ and 1,1,2-triphenylethene groups enhanced the intramolecular charge-transfer (ICT) character compared to YD2-o-C8. The absorption wavelength and transition possess character were significantly influenced by N(CH₃)₂ and 1,1,2-triphenylethene groups. NCH₃-YD2 with N(CH₃)₂ groups in the donor part is an effective way to improve the interactions between the dyes and TiO₂ surface, light having efficiency (LHE), and free energy change (ΔG inject ), which is expected to be an efficient dye for use in dye-sensitized solar cells (DSSCs).

Long-range correction for tight-binding TD-DFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humeniuk, Alexander; Mitrić, Roland, E-mail: roland.mitric@uni-wuerzburg.de

2015-10-07

We present two improvements to the tight-binding approximation of time-dependent density functional theory (TD-DFTB): First, we add an exact Hartree-Fock exchange term, which is switched on at large distances, to the ground state Hamiltonian and similarly to the coupling matrix that enters the linear response equations for the calculation of excited electronic states. We show that the excitation energies of charge transfer states are improved relative to the standard approach without the long-range correction by testing the method on a set of molecules from the database in Peach et al. [J. Chem. Phys. 128, 044118 (2008)] which are known tomore » exhibit problematic charge transfer states. The degree of spatial overlap between occupied and virtual orbitals indicates where TD-DFTB and long-range corrected TD-DFTB (lc-TD-DFTB) can be expected to produce large errors. Second, we improve the calculation of oscillator strengths. The transition dipoles are obtained from Slater Koster files for the dipole matrix elements between valence orbitals. In particular, excitations localized on a single atom, which appear dark when using Mulliken transition charges, acquire a more realistic oscillator strength in this way. These extensions pave the way for using lc-TD-DFTB to describe the electronic structure of large chromophoric polymers, where uncorrected TD-DFTB fails to describe the high degree of conjugation and produces spurious low-lying charge transfer states.« less

Synthesis, structure characterization, photoluminescence properties and TD-DFT calculations for two new borates.

PubMed

Hadjadj, Nasreddine; Dems, Mohamed AbdEsselem; Merazig, Hocine; Bendjeddou, Lamia

2018-04-01

Due to their rich structural chemistry and wide variety of applications, borate materials have provided a rich area of research. In a continuation of this research, diethylammonium bis(2-oxidobenzoato-κ 2 O 1 ,O 2 )borate, C 4 H 12 N + ·BO 4 (C 7 H 4 O) 2 - , (1), and propylammonium bis(2-oxidobenzoato-κ 2 O 1 ,O 2 )borate, C 3 H 10 N + ·BO 4 (C 7 H 4 O) 2 - , (2), have been synthesized by the reaction of boric acid with salicylic acid under ambient conditions. In both structures, the B atom exhibits a slightly distorted tetrahedral environment formed by the bidentate coordination of two salicylate anions via the O atoms of the central carboxylate and oxide groups. In the crystals of salts (1) and (2), mixed cation-anion layers lying parallel to the (101) plane are formed through N-H...O, C-H...O and C-H...π/N-H...O hydrogen-bonding interactions, resulting, in each case, in a two-dimensional supramolecular architecture in the solid state. The photoluminescence properties of the salts were studied using the as-synthesized samples and reveal that salts (1) and (2) both display a strong blue-light emission, with maxima at 489 and 491 nm, respectively. In DFT/TD-DFT (time-dependent density functional theory) studies, the blue emission appears to be derived from an intramolecular charge transfer (ICT) excited state. In addition, IR and UV-Vis spectroscopies were used to investigate the title salts.

DFT and PCM-TD-DFT investigation of the electronic structures and spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinone derivatives

NASA Astrophysics Data System (ADS)

El-Taher, Sabry; Metwaly, Mohamed

2017-04-01

UV-Visible absorption spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinones (5pR-PPTT, R = H, CH3, CH3O, and N(CH3)2) were measured in different solvents and investigated using the theoretical PCM-TD-DFT scheme. A benchmark evaluation against experimental results on the accuracy of different DFT functionals has been performed. The best agreement with X-ray data is achieved by using the long-range corrected LC-wPBE functional, while the PBE0 functional provided the most accurate λmax for the studied compounds. The thionic forms of the ZE isomers of the studied compounds are found to be the most stable tautomers. The assignation debate of the second absorption band of rhodanine [2-thioxo-4-thiazolidinone (Rd)] has been solved by confirming on its π-π∗ nature. It was found that the expansion of the π-conjugation system at position 5 of Rd ring leads to significant bathochromic shift. The CT lengths (Δr) and dipole moment change (ΔμCT) indices showed that the charge transfer character of the electronic transitions is directly proportional to the electron-releasing strength of substituted phenyl ring. It was concluded that the red shifting of the maximum absorption is mainly regulated by the solvent polarizability and much less by solvent polarity.

DFT/TD-DFT study on the electronic and spectroscopic properties of hollow cubic and hollow spherical (ZnO) m quantum dots interacting with CO, NO2 and SO3 molecules

NASA Astrophysics Data System (ADS)

Gopalakrishnan, Sankarasubramanian; Shankar, Ramasamy; Kolandaivel, Ponmalai

2018-03-01

Hollow spherical (HS) and hollow cubic (HC) (ZnO) m quantum dots (QDs) were constructed and optimized using density functional theory (DFT) method. CO, NO2 and SO3 molecules were used to interact with the HC and HS (ZnO) m QDs at the centre and on the surface of the QDs. The changes in the electronic energy levels of HC and HS (ZnO) m QDs due to the interactions of CO, NO2 and SO3 molecules have been studied. The electronic and spectroscopic properties, such as density of states, HOMO-LUMO energy gap, absorption spectra, IR and Raman spectra of HC and HS (ZnO) m QDs have been studied using DFT and Time dependent-DFT (TD-DFT) methods. The interaction energy values show that the SO3 molecule has strongly interacted with HC and HS (ZnO) m QDs than the CO and NO2 molecules. The results of the density of states show that the HC QDs have peaks that are very close to each other, whereas the same is found to be broad in the HS QDs. The HOMO-LUMO energy gap is more for the HS QDs than the HC QDs, and also it gets decreased, when the NO2 and SO3 molecules interact at the centre of the HC and HS (ZnO) m QDs. The blue and red shifts were observed in the absorption spectra of HS and HC QDs. The natural transition orbital (NTO) plot reveals that the interaction of the molecules on the surface of the QDs reduce the chance of electron-hole recombination; hence the energy gap increases for NO2 and SO3 molecular interactions on the surface of the HC and HS (ZnO) m QDs. The vibrational assignments have been made for HC and HS QDs interacting with CO, NO2 and SO3 molecules.

Study on conformational stability, molecular structure, vibrational spectra, NBO, TD-DFT, HOMO and LUMO analysis of 3,5-dinitrosalicylic acid by DFT techniques

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sylvestre, S.; Jayabharathi, J.; Ayyapan, S.; Amalanathan, M.; Oudayakumar, K.; Herman, Ignatius A.

2015-02-01

In this work we analyzed the vibrational spectra of 3,5-dinitrosalicylic acid (3,5DNSA) molecule. The total energy of eight possible conformers can be calculated by Density Functional Theory with 6-31G(d,p) as basis set to find the most stable conformer. Computational result identify the most stable conformer of 3,5DNSA is C6. The assignments of the vibrational spectra have been carried out by computing Total Energy Distribution (TED). The molecular geometry, second order perturbation energies and Electron Density (ED) transfer from filled lone pairs of Lewis base to unfilled Lewis acid sites for 3,5-DNSA molecular analyzed on the basis of Natural Bond Orbital (NBO) analysis. The formation of inter and intramolecular hydrogen bonding between sbnd OH and sbnd COOH group gave the evidence for the formation of dimer formation for 3,5-DNSA molecule. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra.

Absorption and emission spectroscopic characteristics of dipterex and its molecularly imprinted recognition: A TD-DFT investigation

NASA Astrophysics Data System (ADS)

Cheng, Xueli; Li, Liqing; Zhao, Yanyun; Wang, Chang'an

2016-05-01

By using G09 program package, the absorption and fluorescence/phosphorescence spectra of dipterex were explored, and its spectroscopic characters were altered by methacrylic acid (MAA) as the imprinted molecule. The TD-DFT results revealed that: (1) All absorption and emission excitations of dipterex are assigned to the nσ∗ transition; (2) without MAA as imprinted molecule, one of the dipterex Csbnd Cl bonds is extended significantly and dipterex is almost destroyed in transition states; (3) dipterex is connected to methacrylic acid via two hydrogen bonds; (4) for the dipterex-MAA complex, the electronic excitation (ππ∗ excitation) in absorption spectra is dominated by the configuration HOMO → LUMO.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Conformational, vibrational, NMR and DFT studies of N-methylacetanilide.

PubMed

Arjunan, V; Santhanam, R; Rani, T; Rosi, H; Mohan, S

2013-03-01

A detailed conformational, vibrational, NMR and DFT studies of N-methylacetanilide have been carried out. In DFT, B3LYP method have been used with 6-31G(**), 6-311++G(**) and cc-pVTZ basis sets. The vibrational frequencies were calculated resulting in IR and Raman frequencies together with intensities and Raman depolarisation ratios. The dipole moment derivatives were computed analytically. Owing to the complexity of the molecule, the potential energy distributions of the vibrational modes of the compound are also calculated. Isoelectronic molecular electrostatic potential surface (MEP) and electron density surface were examined. (1)H and (13)C NMR isotropic chemical shifts were calculated and the assignments made are compared with the experimental values. The energies of important MO's of the compound were also determined from TD-DFT method. Copyright © 2012 Elsevier B.V. All rights reserved.

Valence and charge-transfer optical properties for some SinCm (m, n ≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy.

PubMed

Lutz, Jesse J; Duan, Xiaofeng F; Ranasinghe, Duminda S; Jin, Yifan; Margraf, Johannes T; Perera, Ajith; Burggraf, Larry W; Bartlett, Rodney J

2018-05-07

Accurate optical characterization of the closo-Si 12 C 12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si 12 C 12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC 2 , Si 2 C n (n = 1-3), and Si 3 C n (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of Si n C and Si n-1 C 7-n (n = 4-6). TD-DFT approaches are then applied to the Si n C n (n = 4-12) clusters and unique spectroscopic signatures of closo-Si 12 C 12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si 4 C 4 ) 4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations.

Valence and charge-transfer optical properties for some SinCm (m, n ≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy

NASA Astrophysics Data System (ADS)

Lutz, Jesse J.; Duan, Xiaofeng F.; Ranasinghe, Duminda S.; Jin, Yifan; Margraf, Johannes T.; Perera, Ajith; Burggraf, Larry W.; Bartlett, Rodney J.

2018-05-01

Accurate optical characterization of the closo-Si12C12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si12C12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC2, Si2Cn (n = 1-3), and Si3Cn (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of SinC and Sin-1C7-n (n = 4-6). TD-DFT approaches are then applied to the SinCn (n = 4-12) clusters and unique spectroscopic signatures of closo-Si12C12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si4C4)4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations.

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

NASA Astrophysics Data System (ADS)

Shukla, Madhulata; Srivastava, Nitin; Saha, Satyen

2012-08-01

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

Oligothiophene-based colorimetric and ratiometric fluorescence dual-channel cyanide chemosensor: Sensing ability, TD-DFT calculations and its application as an efficient solid state sensor

NASA Astrophysics Data System (ADS)

Lan, Linxin; Li, Tianduo; Wei, Tao; Pang, He; Sun, Tao; Wang, Enhua; Liu, Haixia; Niu, Qingfen

2018-03-01

An oligothiophene-based colorimetric and ratiometric fluorescence dual-channel cyanide chemosensor 3 T-2CN was reported. Sensor 3 T-2CN showed both naked-eye recognition and ratiometric fluorescence response for CN- with an excellent selectivity and high sensitivity. The sensing mechanism based on the nucleophilic attack of CN- on the vinyl Cdbnd C bond has been successfully confirmed by the optical measurements, 1H NMR titration, FT-IR spectra as well as the DFT/TD-DFT calculations. Moreover, the detection limit was calculated to be 0.19 μM, which is much lower than the maximum permission concentration in drinking water (1.9 μM). Importantly, test strips (filter paper and TLC plates) containing 3 T-2CN were fabricated, which could act as a practical and efficient solid state optical sensor for CN- in field measurements.

Synthesis, spectroscopic and TD-DFT quantum mechanical study of azo-azomethine dyes. A laser induced trans-cis-trans photoisomerization cycle

NASA Astrophysics Data System (ADS)

Georgiev, Anton; Kostadinov, Anton; Ivanov, Deyan; Dimov, Deyan; Stoyanov, Simeon; Nedelchev, Lian; Nazarova, Dimana; Yancheva, Denitsa

2018-03-01

This paper describes the synthesis, spectroscopic characterization and quantum mechanical calculations of three azo-azomethine dyes. The dyes were synthesized via condensation reaction between 4-(dimethylamino)benzaldehyde and three different 4-aminobenzene azo dyes. Quantum chemical calculations on the optimized molecular geometry and electron densities of the trans (E) and cis (Z) isomers and their vibrational frequencies have been computed by using DFT/B3LYP density-functional theory with 6-311 ++G(d,p) basis set in vacuo. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis,ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. After molecular geometry optimization the electronic spectra have been obtained by TD-DFT calculations at same basis set and correlated with the spectra of vapour deposited nanosized films of the dyes. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. Solvatochromism was investigated by UV-VIS spectroscopy in five different organic solvents with increasing polarity. The dynamic photoisomerization experiments have been performed in DMF by pump lasers λ = 355 nm (mostly E → Z) and λ = 491 nm (mostly Z → E) in spectral region 300 nm - 800 nm at equal concentrations and times of illumination in order to investigate the photodynamical trans-cis-trans properties of the sbnd CHdbnd Nsbnd and sbnd Ndbnd Nsbnd chromophore groups of the dyes.

Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

2013-01-01

In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

Oligothiophene-based colorimetric and ratiometric fluorescence dual-channel cyanide chemosensor: Sensing ability, TD-DFT calculations and its application as an efficient solid state sensor.

PubMed

Lan, Linxin; Li, Tianduo; Wei, Tao; Pang, He; Sun, Tao; Wang, Enhua; Liu, Haixia; Niu, Qingfen

2018-03-15

An oligothiophene-based colorimetric and ratiometric fluorescence dual-channel cyanide chemosensor 3 T-2CN was reported. Sensor 3 T-2CN showed both naked-eye recognition and ratiometric fluorescence response for CN - with an excellent selectivity and high sensitivity. The sensing mechanism based on the nucleophilic attack of CN - on the vinyl CC bond has been successfully confirmed by the optical measurements, 1 H NMR titration, FT-IR spectra as well as the DFT/TD-DFT calculations. Moreover, the detection limit was calculated to be 0.19μM, which is much lower than the maximum permission concentration in drinking water (1.9μM). Importantly, test strips (filter paper and TLC plates) containing 3 T-2CN were fabricated, which could act as a practical and efficient solid state optical sensor for CN - in field measurements. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Srivastava, Santosh K.; Singh, Vipin B.

2013-11-01

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

Time dependent-density functional theory (TD-DFT) and experimental studies of UV-Visible spectra and cyclic voltammetry for Cu(II) complex with Et2DTC

NASA Astrophysics Data System (ADS)

Valle, Eliana Maira A.; Maltarollo, Vinicius Gonçalves; Almeida, Michell O.; Honorio, Kathia Maria; dos Santos, Mauro Coelho; Cerchiaro, Giselle

2018-04-01

In this work, we studied the complexation mode between copper(II) ion and the specific ligand investigated as carriers of metals though biological membranes, diethyldithiocarbamate (Et2DTC). It is important to understand how this occurs because it is an important intracellular chelator with potential therapeutic applications. Theoretical and experimental UV visible studies were performed to investigate the complexation mode between copper and the ligand. Electrochemical studies were also performed to complement the spectroscopic analyses. According to the theoretical calculations, using TD-DFT (Time dependent density functional theory), with B3LYP functional and DGDVZP basis set, implemented in Gaussian 03 package, it was observed that the formation of the complex [Cu(Et2DTC)2] is favorable with higher electron density over the sulfur atoms of the ligand. UV/Vis spectra have a charge transfer band at 450 nm, with the DMSO-d6 band shift from 800 to 650 nm. The electrochemical experiments showed the formation of a new redox process, referring to the complex, where the reduction peak potential of copper is displaced to less positive region. Therefore, the results obtained from this study give important insights on possible mechanisms involved in several biological processes related to the studied system.

Assessing the density functional theory-based multireference configuration interaction (DFT/MRCI) method for transition metal complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Escudero, Daniel, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de; Thiel, Walter, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de

2014-05-21

We report an assessment of the performance of density functional theory-based multireference configuration interaction (DFT/MRCI) calculations for a set of 3d- and 4d-transition metal (TM) complexes. The DFT/MRCI results are compared to published reference data from reliable high-level multi-configurational ab initio studies. The assessment covers the relative energies of different ground-state minima of the highly correlated CrF{sub 6} complex, the singlet and triplet electronically excited states of seven typical TM complexes (MnO{sub 4}{sup −}, Cr(CO){sub 6}, [Fe(CN){sub 6}]{sup 4−}, four larger Fe and Ru complexes), and the corresponding electronic spectra (vertical excitation energies and oscillator strengths). It includes comparisons withmore » results from different flavors of time-dependent DFT (TD-DFT) calculations using pure, hybrid, and long-range corrected functionals. The DFT/MRCI method is found to be superior to the tested TD-DFT approaches and is thus recommended for exploring the excited-state properties of TM complexes.« less

Application of MCD spectroscopy and TD-DFT to endohedral metallofullerenes for characterization of their electronic transitions.

PubMed

Yamada, Michio; Slanina, Zdenek; Mizorogi, Naomi; Muranaka, Atsuya; Maeda, Yutaka; Nagase, Shigeru; Akasaka, Takeshi; Kobayashi, Nagao

2013-03-14

We describe, for the first time, the application of magnetic circular dichroism (MCD) spectroscopy and time-dependent density functional theory (TD-DFT) calculations using B3LYP and M06-2X functionals to characterize the electronic transitions of endohedral metallofullerenes (EMFs). Results revealed that the electronic transitions of La@C(2v)-C(82), La(2)@I(h)-C(80), and Sc(3)N@I(h)-C(80) can be assigned using these techniques. Particularly, a difference in the electronic transitions between La(2)@I(h)-C(80) and Sc(3)N@I(h)-C(80), which is invisible in absorption spectra, was observed clearly in MCD spectra. The observed MCD bands agree well with the oscillator strengths calculated using the B3LYP functional. In addition, the MCD bands of La(2)@I(h)-C(80) were altered upon [5,6]-addition, demonstrating that the MCD spectroscopy is sensitive to chemical functionalization of EMFs, and that it is therefore powerful to distinguish [5,6]-adducts from pristine La(2)@I(h)-C(80), although no marked difference exists in their absorption spectra.

DFT/TD-semiempirical study on the structural and electronic properties and absorption spectra of supramolecular fullerene-porphyrine-metalloporphyrine triads based dye-sensitized solar cells.

PubMed

Rezvani, M; Darvish Ganji, M; Jameh-Bozorghi, S; Niazi, A

2018-04-05

In the present work density functional theory (DFT) and time-dependent semiempirical ZNIDO/S (TD-ZNIDO/S) methods have been used to investigate the ground state geometries, electronic structures and excited state properties of triad systems. The influences of the type of metal in the porphyrin ring, change in bridge position and porphyrine-ZnP duplicate on the energies of frontier molecular orbital and UV-Vis spectra has been studied. Geometry optimization, the energy levels and electron density of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), chemical hardness (η), electrophilicity index (ω), electron accepting power (ω + ) were calculated using ZINDO/S method to predict which molecule is the most efficient with a great capability to be used as a triad molecule in solar industry. Moreover the light harvesting efficiency (LHE) was calculated by means of the oscillator strengths which are obtained by TD-ZINDO/S calculation. Theoretical studies of the electronic spectra by ZINDO/S method were helpful in interpreting the observed electronic transitions. This aspect was systematically explored in a series of C 60 -Porphyrine-Metalloporphyrine (C 60 -P-Mp) triad system with M being Fe, Co, Ni, Ti, and Zn. Generally, transition metal coordination compounds are used as effective sensitizers, due to their intense charge-transfer absorption over the whole visible range and highly efficient metal-to-ligand charge transfer. We aim to optimize the performance of the title solar cells by altering the frontier orbital energy gaps. The results reveal that cell efficiency can be enhanced by metal functionalization of the free base porphyrin. Ti-porphyrin was found to be the most efficient dye sensitizer for dye sensitized solar cells (DSSCs) based on C 60 -P-Mptriad system due to C 60 -Por-TiP complex has lower chemical hardness, gap energy and chemical potential as well as higher electron accepting power among other complexes

DFT/TD-semiempirical study on the structural and electronic properties and absorption spectra of supramolecular fullerene-porphyrine-metalloporphyrine triads based dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Rezvani, M.; Darvish Ganji, M.; Jameh-Bozorghi, S.; Niazi, A.

2018-04-01

In the present work density functional theory (DFT) and time-dependent semiempirical ZNIDO/S (TD-ZNIDO/S) methods have been used to investigate the ground state geometries, electronic structures and excited state properties of triad systems. The influences of the type of metal in the porphyrin ring, change in bridge position and porphyrine-ZnP duplicate on the energies of frontier molecular orbital and UV-Vis spectra has been studied. Geometry optimization, the energy levels and electron density of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), chemical hardness (η), electrophilicity index (ω), electron accepting power (ω+) were calculated using ZINDO/S method to predict which molecule is the most efficient with a great capability to be used as a triad molecule in solar industry. Moreover the light harvesting efficiency (LHE) was calculated by means of the oscillator strengths which are obtained by TD-ZINDO/S calculation. Theoretical studies of the electronic spectra by ZINDO/S method were helpful in interpreting the observed electronic transitions. This aspect was systematically explored in a series of C60-Porphyrine-Metalloporphyrine (C60-P-Mp) triad system with M being Fe, Co, Ni, Ti, and Zn. Generally, transition metal coordination compounds are used as effective sensitizers, due to their intense charge-transfer absorption over the whole visible range and highly efficient metal-to-ligand charge transfer. We aim to optimize the performance of the title solar cells by altering the frontier orbital energy gaps. The results reveal that cell efficiency can be enhanced by metal functionalization of the free base porphyrin. Ti-porphyrin was found to be the most efficient dye sensitizer for dye sensitized solar cells (DSSCs) based on C60-P-Mptriad system due to C60-Por-TiP complex has lower chemical hardness, gap energy and chemical potential as well as higher electron accepting power among other complexes. In

0–0 Energies Using Hybrid Schemes: Benchmarks of TD-DFT, CIS(D), ADC(2), CC2, and BSE/GW formalisms for 80 Real-Life Compounds

PubMed Central

2015-01-01

The 0–0 energies of 80 medium and large molecules have been computed with a large panel of theoretical formalisms. We have used an approach computationally tractable for large molecules, that is, the structural and vibrational parameters are obtained with TD-DFT, the solvent effects are accounted for with the PCM model, whereas the total and transition energies have been determined with TD-DFT and with five wave function approaches accounting for contributions from double excitations, namely, CIS(D), ADC(2), CC2, SCS-CC2, and SOS-CC2, as well as Green’s function based BSE/GW approach. Atomic basis sets including diffuse functions have been systematically applied, and several variations of the PCM have been evaluated. Using solvent corrections obtained with corrected linear-response approach, we found that three schemes, namely, ADC(2), CC2, and BSE/GW allow one to reach a mean absolute deviation smaller than 0.15 eV compared to the measurements, the two former yielding slightly better correlation with experiments than the latter. CIS(D), SCS-CC2, and SOS-CC2 provide significantly larger deviations, though the latter approach delivers highly consistent transition energies. In addition, we show that (i) ADC(2) and CC2 values are extremely close to each other but for systems absorbing at low energies; (ii) the linear-response PCM scheme tends to overestimate solvation effects; and that (iii) the average impact of nonequilibrium correction on 0–0 energies is negligible. PMID:26574326

Stabilization of diketo tautomer of curcumin by premicellar anionic surfactants: UV-Visible, fluorescence, tensiometric and TD-DFT evidences

NASA Astrophysics Data System (ADS)

Dutta, Anisha; Boruah, Bornali; Manna, Arun K.; Gohain, Biren; Saikia, Palash M.; Dutta, Robin K.

2013-03-01

A newly observed UV band of aqueous curcumin, a biologically important molecule, in presence of anionic surfactants, viz., sodium dodecylsulfate (SDS), sodium dodecylbenzenesulfonate (SDBS), and sodium dodecylsulfonate (SDSN) in buffered aqueous solutions has been studied experimentally and theoretically. The 425 nm absorption band of curcumin disappears and a new UV-band is observed at 355 nm on addition of the surfactants in the submicellar concentration range which is reversed as the surfactant concentration approaches the critical micelle concentration (CMC). The observed spectral absorption, fluorescence intensity and surface tension behavior, under optimal experimental conditions of submicellar concentration ranges of the surfactants in the pH range of 2.00-7.00, indicate that the new band is due to the β-diketo tautomer of curcumin stabilized by interactions between curcumin and the anionic surfactants. The stabilization of the diketo tautomer by submicellar anionic surfactants described here as well as by submicellar cationic surfactant, reported recently, is unique as this is the only such behavior observed in presence of submicellar surfactants of both charge types. The experimental results are in good agreement with the theoretical calculations using ab initio density functional theory combined with time dependent density functional theory (TD-DFT) calculations.

Synthesis, crystal structure and DFT studies of a dual fluorescent ketamine: Structural changes in the ground and excited states

NASA Astrophysics Data System (ADS)

Latha, V.; Balakrishnan, C.; Neelakantan, M. A.

2015-07-01

A fluorescent probe 2Z,2‧Z-3,3‧-(4,4‧-methylenebis(4,1-phenylene) bis(azanediyl))bis (1,3-diphenylprop-2-en-1-one) (L) was synthesized and characterized by IR, 1H NMR, ESI-mass, UV-visible and fluorescence spectral techniques. The single crystal analysis illustrates the existence of L in ketamine form. The crystal structure is stabilized by intramolecular and intermolecular hydrogen bonding. The thermal stability of L was studied by TG analysis. The fluorescence spectrum of L shows dual emission, and is due to excited state intramolecular proton transfer (ESIPT) process. This is supported by the high Stokes shift value. Electronic structure calculations of L in the ground and excited state have been carried out using DFT and TD-DFT at B3LYP/6-31G (d,p) level, respectively. The vibrational spectrum was computed at this level and compared with experimental values. Major orbital contributions for the electronic transitions were assigned with the help of TD-DFT. The changes in the Mulliken charge, bond lengths and bond angles between the ground and excited states of the tautomers demonstrate that twisted intramolecular charge transfer (TICT) process occurs along with ESIPT in the excited state.

Spectroscopic investigation, HOMO-LUMO and NLO studies on L-histidinium maleate based on DFT approach

NASA Astrophysics Data System (ADS)

Dhanavel, S.; Stephen, A.; Asirvatham, P. Samuel

2017-05-01

The molecular structure of the title compound L-Histidinium Maleate (LHM) was constructed and optimized based on Density Functional Theory method (DFT-B3LYP) with the 6-31G (d,p) basis set. The fundamental vibrational spectral assignment was analyzed with the aid of optimized structure of LHM. The study on electronic properties such as, HOMO-LUMO energies and absorption wavelength were performed using Time dependent DFT (TD-DFT) approach which reveals that energy transfer occur within the molecule. 13C NMR chemical shift values were measured using Gauge independent atomic orbital method (GIAO) and the obtained values are in good agreement with the reported experimental values. Hardness, ionization potential and electrophilicity index also calculated. The electric dipole moment (μtot) and hyperpolarizability (βtot) values of the investigated molecules were computed. The calculated value (β) was 3.7 times higher than that of urea, which confirms the LHM molecule is a potential candidate for NLO applications.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

Relative Stability of the La and Lb Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra.

PubMed

Santoro, Fabrizio; Improta, Roberto; Fahleson, Tobias; Kauczor, Joanna; Norman, Patrick; Coriani, Sonia

2014-06-05

The relative position of La and Lb ππ* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution, exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S0→ La transition from the weak S0→ Lb transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, La < Lb, is the correct one.

Application of MCD spectroscopy and TD-DFT to a highly non-planar porphyrinoid ring system. New insights on red-shifted porphyrinoid spectral bands.

PubMed

Mack, John; Asano, Yoshiaki; Kobayashi, Nagao; Stillman, Martin J

2005-12-21

The first magnetic circular dichroism (MCD) spectra are reported for tetraphenyltetraacenaphthoporphyrin (TPTANP). The impact on the electronic structure of steric interactions between the fused acenaphthalene rings and the meso-tetraphenyl substituents is explored based on an analysis of the optical spectra of the Zn(II) complex (ZnTPTANP) and the free base dication species ([H4TPTANP]2+). In the case of ZnTPTANP, significant folding of the porphyrinoid ligand induces a highly unusual MCD-sign reversal providing the first direct spectroscopic evidence of ligand nonplanarity. Density functional theory (DFT) geometry optimizations for a wide range of Zn(II) porphyrinoids based on the B3LYP functional and TD-DFT calculations of the associated UV-visible absorption spectra are reported, allowing a complete assessment of the MCD data. TPTANP complexes are found to fall into a class of cyclic polyenes, termed as soft MCD chromophores by Michl (J. Pure Appl. Chem. 1980, 52, 1549.), since the signs of the Faraday A1 terms observed in the MCD spectrum are highly sensitive to slight structural changes. The origin of an unusually large red shift of the main B (or Soret) band of MTPTANP (the most red shifted ever reported for fused-ring-expanded metal porphines) and of similar red shifts observed in the spectra of other peripherally crowded porphyrinoid complexes is also explored and explained on this basis.

Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis

PubMed Central

de la Lande, A.; Maddaluno, J.; Parisel, O.; Darden, T. A.; Piquemal, J-P

2010-01-01

Following our previous study (Piquemal et al., New J. Chem., 2003, 27, 909), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu2O2 metallic core (Piquemal and Pilmé, J. Mol. Struct.: Theochem, 2006, 77, 764). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems. PMID:20396590

Assessment of TD-DFT methods and of various spin scaled CIS(D) and CC2 versions for the treatment of low-lying valence excitations of large organic dyes

NASA Astrophysics Data System (ADS)

Goerigk, Lars; Grimme, Stefan

2010-05-01

We present an extension of our previously published benchmark set for low-lying valence transitions of large organic dyes [L. Goerigk et al., Phys. Chem. Chem. Phys. 11, 4611 (2009)]. The new set comprises in total 12 molecules, including two charged species and one with a clear charge-transfer transition. Our previous study on TD-DFT methods is repeated for the new test set with a larger basis set. Additionally, we want to shed light on different spin-scaled variants of the configuration interaction singles with perturbative doubles correction [CIS(D)] and the approximate coupled cluster singles and doubles method (CC2). Particularly for CIS(D) we want to clarify, which of the proposed versions can be recommended. Our results indicate that an unpublished SCS-CIS(D) variant, which is implemented into the TURBOMOLE program package, shows worse results than the original CIS(D) method, while other modified versions perform better. An SCS-CIS(D) version with a parameterization, that has already been used in an application by us recently [L. Goerigk and S. Grimme, ChemPhysChem 9, 2467 (2008)], yields the best results. Another SCS-CIS(D) version and the SOS-CIS(D) method [Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007)] perform very similar, though. For the electronic transitions considered herein, there is no improvement observed when going from the original CC2 to the SCS-CC2 method but further adjustment of the latter seems to be beneficial. Double-hybrid density functionals belong to best methods tested here. Particularly B2GP-PLYP provides uniformly good results for the complete set and is considered to be close to chemical accuracy within an ab initio theory of color. For conventional hybrid functionals, a Fock-exchange mixing parameter of about 0.4 seems to be optimum in TD-DFT treatments of large chromophores. A range-separated functional such as, e.g., CAM-B3LYP seems also to be promising.

Spectroscopic, Homo-Lumo and NLO studies of tetra fluoro phthalate doped Coumarin crystals using DFT method

NASA Astrophysics Data System (ADS)

Latha, B.; Kumaresan, P.; Nithiyanantham, S.; Sampathkumar, K.

2017-08-01

In the present examination, a methodical study has been done on the development of unadulterated and Coumarin doped Tetrafluoro Phthalate precious stones. Powder X-beam diffraction studies were done and the cross section parameters were computed by minimum square technique in pure and doped crystals. FT-IR, UV-Vis, Thermal, Micro-hardness and Dielectric studies were additionally done for the pure and doped crystals. The tentatively watched FT-IR and FT-Raman groups were allotted to various ordinary methods of the atom. The steadiness and charge delocalization of the particle were likewise concentrations were done by characteristic security orbital (NBO) examination. The HOMO-LUMO energies depict the charge exchange happens inside the particle. Atomic electrostatic potential has been broken down the electronic properties such as excitation energies, oscillator quality, wavelengths and HOMO-LUMO energies were acquired by time-subordinate DFT (TD-DFT) approach. The SHG of pure and doped TFP stones were examined through Nd:YAG Q-exchanged laser.

Time-dependent i-DFT exchange-correlation potentials with memory: applications to the out-of-equilibrium Anderson model

NASA Astrophysics Data System (ADS)

Kurth, Stefan; Stefanucci, Gianluca

2018-06-01

We have recently put forward a steady-state density functional theory (i-DFT) to calculate the transport coefficients of quantum junctions. Within i-DFT it is possible to obtain the steady density on and the steady current through an interacting junction using a fictitious noninteracting junction subject to an effective gate and bias potential. In this work we extend i-DFT to the time domain for the single-impurity Anderson model. By a reverse engineering procedure we extract the exchange-correlation (xc) potential and xc bias at temperatures above the Kondo temperature T K. The derivation is based on a generalization of a recent paper by Dittmann et al. [N. Dittmann et al., Phys. Rev. Lett. 120, 157701 (2018)]. Interestingly the time-dependent (TD) i-DFT potentials depend on the system's history only through the first time-derivative of the density. We perform numerical simulations of the early transient current and investigate the role of the history dependence. We also empirically extend the history-dependent TD i-DFT potentials to temperatures below T K. For this purpose we use a recently proposed parametrization of the i-DFT potentials which yields highly accurate results in the steady state.

Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study.

PubMed

Chattopadhyaya, M; Murugan, N Arul; Rinkevicius, Zilvinas

2016-09-15

We study the linear and nonlinear optical properties of a well-known acid-base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral ⇒ anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral ⇒ anionic and open neutral ⇒ dianionic, can contribute to the pH-dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe.

DFT and TD-DFT study of the adsorption and detection of sulfur mustard chemical warfare agent by the C24, C12Si12, Al12N12, Al12P12, Be12O12, B12N12 and Mg12O12 nanocages

NASA Astrophysics Data System (ADS)

Jouypazadeh, Hamidreza; Farrokhpour, Hossein

2018-07-01

In the present research, the interaction of sulfur mustard, a chemical warfare agent, with the surface of C24, C12Si12, Al12N12, Al12P12, Be12O12, B12N12 and Mg12O12 nanocages was studied using the dispersion corrected density function theory (DFT-D3) method. The calculated adsorption energies of sulfur mustard on the surface of the nanocages showed that the Al12N12, C12Si12 and Mg12O12 are useful for the adsorption of the sulfur mustard. The quantum theory atom in molecule (QTAIM) analysis was used to study the nature of interactions of sulfur mustard with the surface of the selected nanocages. Based on QTAIM analysis, the majority of interactions of sulfur and chlorine atoms of sulfur mustard with the surface of the considered nanocages are covalent and quasi covalent whereas the interactions of hydrogen atoms of sulfur mustard with the surface of the nanocages are generally non-covalent. The charge transfer between sulfur mustard and the nanocages as well as chemical quantum descriptors of complexes were calculated using natural bond orbital (NBO) method. The most electron charge transfers from the sulfur mustard to B12N12 nanocage where the S atom of sulfur mustard donor a chemical bond to B atom of the nanocage. The ability of the considered nanocages for detecting sulfur mustard was studied using time-dependent density function theory (TD-DFT) and density of state (DOS) diagram. It is found that the C24, Al12P12, Be12O12 and B12N12 nanocages are useful sensors for this chemical agent.

Travellers' diarrhoea: Impact of TD definition and control group design on study results.

PubMed

Lääveri, Tinja; Pakkanen, Sari H; Kirveskari, Juha; Kantele, Anu

2018-02-02

Travellers' diarrhoea (TD) is a common health problem among visitors to the (sub)tropics. Much research deals with aetiology, prevention, and post-infection sequalae, yet the data may not allow comparisons due to incompatible definitions of TD and No TD control groups. The impact of defining TD and No TD control groups was explored by revisiting our recent data. We set up two TD groups: classical TD i.e. ≥3 loose or liquid stools/day and WHO TD (diarrhoea as defined by the WHO) i.e. any diarrhoea, and four No TD groups by TD definition and timing (no classical/WHO TD during travel, no ongoing classical/WHO TD). TD was recorded for 37% versus 65% of subjects when using classical versus WHO definitions, respectively; the proportions of the various pathogens proved similar. The strictest criterion for the No TD control group (no WHO TD during travel) yielded pathogens among 61% and the least strict (no ongoing classical TD) among 73% of the travellers; the differences were greatest for enteroaggregative Escherichia coli and Campylobacter. Definition of TD and control group design substantially impact on TD study results. The WHO definition yields more cases, but the pathogen selection is similar by both definitions. Design of the No TD control group was found critical: only those remaining asymptomatic throughout the journey should be included. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantum mechanical study of the structure and spectroscopic (FT-IR, FT-Raman, 13C, 1H and UV), first order hyperpolarizabilities, NBO and TD-DFT analysis of the 4-methyl-2-cyanobiphenyl

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sundaraganesan, N.; Karthikeiyan, B.; Srinivasan, V.

2011-02-01

The Fourier transform infrared (FT-IR) and FT-Raman of 4-methyl-2-cyanobiphenyl (4M2CBP) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of density functional theory (DFT) method. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. The first order hyperpolarizability ( β0) of this novel molecular system and related properties ( β, α0 and Δ α) of 4M2CBP are calculated using HF/6-311G(d,p) method on the finite-field approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies ( E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra.

Spectroscopic investigations (FT-IR, UV, 1H and 13C NMR) and DFT/TD-DFT calculations of potential analgesic drug 2-[2-(dimethylamino)ethyl]-6-methoxy-4-(pyridin-2-yl)-1(2H)-phthalazinone

NASA Astrophysics Data System (ADS)

Sroczyński, Dariusz; Malinowski, Zbigniew

2017-12-01

The theoretical molecular geometry and the IR, UV, 1H and 13C NMR spectroscopic properties of 2-[2-(dimethylamino)ethyl]-6-methoxy-4-(pyridin-2-yl)-1(2H)-phthalazinone with the previously demonstrated in vivo analgesic activity were characterized. The conformational analysis, performed using the molecular mechanics method with the General AMBER Force Field (GAFF) and the Density Functional Theory (DFT) approach with the B3LYP hybrid functional and the 6-31 + g(d) basis sets, allowed to determine the most stable rotamer. The theoretical molecular geometry of this conformer was then calculated at the B3LYP/6-311++g(d,p) level of theory, and its phthalazinone core was compared with the experimental geometry of 1(2H)-phthalazinone. The calculated vibrational frequencies and the potential energy distribution enabled to assign the theoretical vibrational modes to the experimental FT-IR bands. The UV spectrum calculated with the Time-Dependent Density Functional Theory (TD-DFT) method in methanol identified the main electronic transitions and their character. 1H and 13C NMR chemical shifts simulated by the Gauge-Independent Atomic Orbital (GIAO) method in chloroform confirmed the previous assignment of the experimental resonance signals. The stability of the molecule was considered taking into account the hyperconjugation and electron density delocalization effects evaluated by the Natural Bond Orbital (NBO) method. The calculated spatial distribution of molecular electrostatic potential made possible to estimate the regions with nucleophilic and electrophilic properties. The results of the potentiodynamic polarization measurements were also indicated the corrosion inhibition activity of the title compound on 100Cr6 bearing steel in 1 mol dm-3 HCl solution.

Diaminomaleonitrile-based azo receptors: Synthesis, DFT studies and their antibacterial activities

NASA Astrophysics Data System (ADS)

Khanmohammadi, Hamid; Arab, Vajihe; Rezaeian, Khatereh; Talei, Gholam Reza; Pass, Maryam; Shabani, Nafiseh

2017-02-01

New unsymmetric diaminomaleonitrile-based azo receptors (H3Ln, n = 1-3) have been synthesized via condensation reaction of 5-(4-X-phenyl)-azo-salicyladehyde (X = NO2, OMe and CH3) with 2-amino-3-(5-bromo-2-hydroxybenzylamino)maleonitrile. The solvatochromic behaviors of the molecules were probed by studying their UV-Vis spectra in five pure organic solvents of different polarities. The p-NO2 substituted receptor shows a dramatic color change from yellow to blue upon the addition of fluoride ion in CH3CN. This capability was studied by systematic TD-DFT calculations. These compounds were assayed for their in vitro antibacterial activities against Gram-positive (S. aureus, S. epidermidis and L. monocytogenes) and Gram-negative (E. coli, P. aeruginosa and K. pneumonia.) bacteria by disc diffusion method. The results indicated that the compounds show good inhibition against Gram positive bacteria namely L. monocytogenes as compared to standard drugs.

Experimental, DFT and molecular docking studies on 2-(2-mercaptophenylimino)-4-methyl-2H-chromen-7-ol

NASA Astrophysics Data System (ADS)

Singh, Ashok Kumar; Singh, Ravindra Kumar

2016-10-01

A new coumarin derivative 2-(2-mercaptophenylimino)-4-methyl-2H-chromen-7-ol (COMSB) was synthesized and characterized with the help of 1H,13C NMR, FT-IR, FT-Raman and mass spectrometry. All quantum calculations were performed at DFT level of theory using B3LYP functional and 6-31G (d,p) as basis set. The UV-Vis spectrum studied by TD-DFT theory, with a hybrid exchange-correlation functional using Coulomb-attenuating method (CAM-B3LYP) in solvent phase gives similar pattern of bands, at energies and is consistent with that of experimental findings. The detailed analysis of vibrational (IR and Raman) spectra and their assignments has been done by computing Potential Energy Distribution (PED) using Gar2ped. Intra-molecular interactions were analyzed by 'Atoms in molecule' (AIM) approach. Computed first static hyperpolarizability (β0 = 8.583 × 10-30 esu) indicates non-linear optical (NLO) response of the molecule. Molecular docking studies show that the title molecule may act as potential acetylcholine esterase (AChE) inhibitor.

Molecular design of donor-acceptor dyes for efficient dye-sensitized solar cells I: a DFT study.

PubMed

El-Shishtawy, Reda M; Asiri, Abdullah M; Aziz, Saadullah G; Elroby, Shaaban A K

2014-06-01

Dye-sensitized solar cells (DSSCs) have drawn great attention as low cost and high performance alternatives to conventional photovoltaic devices. The molecular design presented in this work is based on the use of pyran type dyes as donor based on frontier molecular orbitals (FMO) and theoretical UV-visible spectra in combination with squaraine type dyes as an acceptor. Density functional theory has been used to investigate several derivatives of pyran type dyes for a better dye design based on optimization of absorption, regeneration, and recombination processes in gas phase. The frontier molecular orbital (FMO) of the HOMO and LUMO energy levels plays an important role in the efficiency of DSSCs. These energies contribute to the generation of exciton, charge transfer, dissociation and exciton recombination. The computations of the geometries and electronic structures for the predicted dyes were performed using the B3LYP/6-31+G** level of theory. The FMO energies (EHOMO, ELUMO) of the studied dyes are calculated and analyzed in the terms of the UV-visible absorption spectra, which have been examined using time-dependent density functional theory (TD-DFT) techniques. This study examined absorption properties of pyran based on theoretical UV-visible absorption spectra, with comparisons between TD-DFT using B3LYP, PBE, and TPSSH functionals with 6-31+G (d) and 6-311++G** basis sets. The results provide a valuable guide for the design of donor-acceptor (D-A) dyes with high molar absorptivity and current conversion in DSSCs. The theoretical results indicated 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran dye (D2-Me) can be effectively used as a donor dye for DSSCs. This dye has a low energy gap by itself and a high energy gap with squaraine acceptor type dye, the design that reduces the recombination and improves the photocurrent generation in solar cell.

Hydrogen bonding interactions in nicotinamide Ionic Liquids: A comparative spectroscopic and DFT studies

NASA Astrophysics Data System (ADS)

Shukla, Madhulata

2017-03-01

Being biodegradable in nature nicotinamide based Ionic Liquids (ILs) are gaining much attention now a day. Nicotinamide iodide (i.e 1-methyl-3ethoxy carbonyl pyridinium iodide (mNicI)) and 1-methyl-3ethoxy carbonyl pyridinium trifilimide (mNicNTf2) new ILs has been synthesized and has been characterized using different spectroscopic techniques like NMR, UV visible and infrared spectroscopy. Theoretical studies have been performed on several nicotinamide ILs. Geometry and spectral features were further characterized by Density Functional Theory (DFT) calculation. NBO charge distribution and electrostatic potential diagram presents in depth knowledge about interactions between cation and anion. A comparative theoretical study between mNicI and its other analogues i. e 1-methyl-3 ethoxy carbonyl pyridinium chloride and bromide i. e mNicCl and mNicBr has also been performed. Csbnd H⋯X hydrogen bonding along with C⋯X interaction has been reported for the first time for the nicotinamide based ILs. C2sbnd H stretching frequency shifts to higher wavenumber with change to a lesser electronegative anion. mNicCl and mNicBr are expected to be solid in nature with the evidence from the red shift in stretching frequency as compared to mNicI. TD-DFT calculation of mNicI proved that pale yellow color of liquid is due to inherent transition from anion to cation.

Quantum mechanical study of the structure and spectroscopic (FT-IR, FT-Raman, 13C, 1H and UV), first order hyperpolarizabilities, NBO and TD-DFT analysis of the 4-methyl-2-cyanobiphenyl.

PubMed

Sebastian, S; Sundaraganesan, N; Karthikeiyan, B; Srinivasan, V

2011-02-01

The Fourier transform infrared (FT-IR) and FT-Raman of 4-methyl-2-cyanobiphenyl (4M2CBP) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of density functional theory (DFT) method. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of 4M2CBP are calculated using HF/6-311G(d,p) method on the finite-field approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Copyright © 2010 Elsevier B.V. All rights reserved.

Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver

2017-02-01

Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

Adsorption of alanine with heteroatom substituted fullerene for solar cell application: A DFT study.

PubMed

Dheivamalar, S; Sugi, L; Ravichandran, K; Sriram, S

2018-09-05

C 20 is the most important fullerene cage and alanine is the simplest representation of a backbone unit of the protein. The absorption feasibility of alanine molecule in the Si-doped C 20 and B-doped C 20 fullerenes has been studied based on calculated electronic properties of fullerenes using density functional theory (DFT). In this work, we explore the ability of Si-doped C 20 , B-doped C 20 fullerene to interact with alanine at the DFT-B3LYP/6-31G, RHF level of theory. We find that noticeable structural change takes place in C 20 when one of its carbon is substituted with Si or B. The molecular geometry, electronic properties and vibrational analysis have also been performed on the title compounds. The NMR study reveals the aromaticity of the pure and doped fullerene compounds. Stability of the doped fullerene - alanine compound arises from hyper conjugative interactions. It leads to one of the major property of bioactivity, charge transfer and delocalization of charge and this properties has been analyzed using Natural Bond Orbital (NBO) analysis. The energy gap of the doped fullerene reveals that there is a decrease in the size of energy gap significantly, making them more reactive as compared to C 20 fullerene. Theoretical studies of the electronic spectra by using time - dependent density functional theory (TD-DFT) method were helpful to interpret the observed electronic transition state. We aim to optimize the performance of the solar cells by altering the frontier orbital energy gaps. Considering all studied properties, it may be inferred that the applicability of C 20 fullerene as the non-linear optical (NLO) material and its NLO property would increase on doping fullerene with Si and B atom. Specifically C 19 Si would be better among them. Copyright © 2018. Published by Elsevier B.V.

DFT computations on: Crystal structure, vibrational studies and optical investigations of a luminescent self-assembled material

NASA Astrophysics Data System (ADS)

Kessentini, A.; Ben Ahmed, A.; Dammak, T.; Belhouchet, M.

2018-02-01

The current work undertakes the growth and the physicochemical properties of a novel green-yellow luminescence semi-organic material, the 3-picolylammonium bromide abbreviated (Pico-Br). In this paper, we report the X-ray diffraction measurements which show that the crystal lattice consists of distinct 3-picolylammonium cations and free bromide anions connected via Nsbnd H ⋯ Br and Nsbnd H ⋯ N hydrogen bonds leading to form a two dimensional frameworks. Molecular geometry compared with its optimized counterpart shows that the quantum chemical calculations carried out with density functional method (DFT) well produce the perceived structure by X-ray resolution of the studied material. To provide further insight into the spectroscopic properties, additional characterization of this material have been performed with Raman and infrared studies at room temperature. Theoretical computations have been computed using the (DFT) method at B3LYP/LanL2DZ level of theory implemented within Gaussian 03 program to study the vibrational spectra of the investigated molecule in the ground state. Optical absorption spectrum inspected by UV-visible absorption reveals the appearance of sharp optical gap of 280 nm (4.42 eV) as well as a strong green photoluminescence emission at 550 nm (2.25 eV) is detected on the photoluminescence (PL) spectrum at room temperature. Using the TD/DFT method, HOMO-LUMO energy gap and the Mulliken atomic charges were calculated in order to get an insight into the material. Good agreement between the theoretical results and the experimental ones was predicted.

Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT

NASA Astrophysics Data System (ADS)

Bardak, F.; Karaca, C.; Bilgili, S.; Atac, A.; Mavis, T.; Asiri, A. M.; Karabacak, M.; Kose, E.

2016-08-01

Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, 1H and 13C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm- 1 and 3500-50 cm- 1, respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The 13C and 1H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained.

Synthesis, characterization and DFT studies of two new silver(I) complexes with 3,4-lutidine

NASA Astrophysics Data System (ADS)

Soliman, Saied M.; Assem, Rania; Abu-Youssef, Morsy A. M.; Kassem, Taher S.

2015-04-01

The synthesis, characterization and molecular structure of two new Ag(I) complexes with 3,4-lutidine (34lut) have been reported. The [Ag(34lut)3(OAC)]; 1 and [Ag(34lut)2(TFA)]; 2 complexes, where OAC and TFA are acetate and trifluoroacetate respectively, have been characterized using elemental analysis, FTIR, NMR and mass spectra. Their molecular structures were calculated using DFT quantum chemical calculations. Both 1 and 2 were found to have distorted tetrahedral geometry around the Ag(I). The spectroscopic properties of the studied complexes have been calculated using the same level of theory. The Infrared vibrational frequencies of the COO stretches confirmed that the OAC is monodentate in 1 while the TFA is bidentate in 2. The calculated polarizability (α0) and HOMO-LUMO energy gap (ΔE) values indicated that 1 has higher NLO activity than 2. The electronic spectra of these complexes are calculated using the TD-DFT calculations. The calculated 1H NMR chemical shift values using GIAO approach showed good correlations with the experimental data. The interaction energies using the second order perturbation theory have been used to study the different intramolecular charge transfer interactions in the studied complexes. The NBO calculations indicated that both the Agsbnd O bonds are almost identical in 2 but not in 1.

Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.

PubMed

Arjunan, V; Rani, T; Mythili, C V; Mohan, S

2011-08-01

A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand

NASA Astrophysics Data System (ADS)

Naseem, Saira; Khalid, Muhammad; Tahir, Muhammad Nawaz; Halim, Mohammad A.; Braga, Ataualpa A. C.; Naseer, Muhammad Moazzam; Shafiq, Zahid

2017-09-01

Herein, we present the synthesis of novel xanthene-based hydrazone (1). The chemical structure of 1 was resolved using spectroscopic techniques such as NMR, FT-IR, UV-VIS and X-ray crystallographic approaches. X-ray diffraction analysis shows that the compound (1) crystallizes in triclinic crystal lattice with the Pbar1 space group and diffused to form multi-layered structure due to non-covalent interactions such as intramolecular hydrogen bonding (H.B). In addition to experimental investigation, density functional theory (DFT) calculation with M06-2X/6-31G(d,p) and B3LYP/6-31G(d,p) level of theories was performed on compound (1) to obtain optimized geometry, spectroscopic and electronic properties. DFT optimized geometry shows good agreement with the experimental XRD structure. The hyper conjugative interactions and hydrogen bonding network are responsible for the stability of compound (1) as revealed by natural bond orbital (NBO) calculation. Moreover, hydrogen bonding network in the dimer is confirmed by FT-IR and thermodynamic studies showing excellent agreement with XRD and NBO findings. TD-DFT/UV-VIS analysis provides insight that maximum excitation is found in 1 which shows good agreement with experimental UV-VIS result. The global reactivity parameters are calculated using the energies of frontier molecular orbitals also disclosed that the compound is more stable might be due to hydrogen bonding network. Experimental and molecular docking studies indicated that this compound has anti-bacterial and anti-diabetic properties. The binding affinity of this compound against the multidrug efflux pump subunit AcrB OS=Escherichia coli (strain K12) and Human Pancreatic Alpha-Amylase is -9.2 and -10.00 kcal/mol which are higher than the control drugs. Pi-Pi, Pi-anaion, amide-pi and pi-alkyl bonds play key role in drug-protein complexes.

Synthesis, molecular structure, vibrational spectroscopy, optical investigation and DFT study of a novel hybrid material: 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate

NASA Astrophysics Data System (ADS)

Kessentini, A.; Dammak, T.; Belhouchet, M.

2017-12-01

In his work we investigate a new halogenotin (IV) organic inorganic material. The structure, determined by single-crystal X-ray diffraction at 293 K of 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate abbreviated 3,3‧(DDS)SnCl6, can be viewed as inorganic layers built from (SnCl6)2- octahedra and H2O molecules, between which, the organic entities [C12H14N2O2S]2+ are inserted. Experimental room-temperature X-ray studies were supported by theoretical methods using density functional theory (DFT). The detailed examination of the vibrational spectra of our material was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. The optical properties in the UV-visible region have been explored by the UV-visible absorption. This material shows a single absorption band centred at 325 nm (318 eV). The energy difference between Occupied, HOMO and Lowest Unoccupied, LUMO orbital which is called energy gap can be used to predict the strength and stability of metal complexes, as well as in determining molecular electrical transport properties. For the calculation of excitation energies in the optical studies we used Time-Dependent Density Functional Theory (TD-DFT). In addition, Mulliken population method and molecular electrostatic potential (MEP) of the title material have been theoretically studied by GAUSSIAN 03 package.

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

PubMed

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

2014-08-14

The solvatochromic behavior of trimethoprim (TMP) was analyzed using UV-Vis spectroscopy and DFT methods in neat and binary aqueous solvent mixtures. The effects of solvent dipolarity/polarizability and solvent-solute hydrogen bonding interactions on the absorption maxima were evaluated by means of the linear solvation energy relationship concept of Kamlet and Taft. This analysis indicated that both interactions play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra of TMP and TMP:(solvent)n complexes in ACN and H2O using TD-DFT methods were in agreement with the experimental ones. Binary aqueous mixtures containing as co-solvents DMSO, ACN and EtOH were studied. Preferential solvation was detected as a nonideal behavior of the wavenumber curve respective to the analytical mole fraction of co-solvent in all binary systems. TMP molecules were preferentially solvated by the organic solvent over the whole composition range. Index of preferential solvation, as well as the influence of solvent parameters were calculated as a function of solvent composition. Copyright © 2014 Elsevier B.V. All rights reserved.

Spectroscopic and DFT-based computational studies on the molecular electronic structural characteristics and the third-order nonlinear property of an organic NLO crystal: (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide

NASA Astrophysics Data System (ADS)

Sasikala, V.; Sajan, D.; Joseph, Lynnette; Balaji, J.; Prabu, S.; Srinivasan, P.

2017-04-01

Single crystals of (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide (CBMBSH) have been grown by slow evaporation crystal growth method. The structure stabilizing intramolecular donor-acceptor interactions and the presence of the Nsbnd H⋯O, Csbnd H⋯O and Csbnd H⋯C(π) hydrogen bonds in the crystal were confirmed by vibrational spectroscopic and DFT methods. The linear optical absorption characteristics of the solvent phase of CBMBSH were investigated using UV-Vis-NIR spectroscopic and TD-DFT approaches. The 2PA assisted RSA nonlinear absorption and the optical limiting properties of CBMBSH were studied using the open-aperture Z-scan method. The topological characteristics of the electron density have been determined using the quantum theory of atoms in molecules method.

Crystal growth, spectroscopic, DFT computational and third harmonic generation studies of nicotinic acid

NASA Astrophysics Data System (ADS)

Thaya Kumari, C. Rathika; Nageshwari, M.; Raman, R. Ganapathi; Caroline, M. Lydia

2018-07-01

An organic centrosymmetric nicotinic acid (NA) single crystal has been grown employing slow evaporation method in water. NA crystallizes in monoclinic system with centric space group P21/C. The experimental and theoretical investigation includes vibrational spectra based on Hartree - Fock (HF) and density functional theory (DFT) has been applied using different function at B3LYP level of theory using 6-311G++(d,p) basis set. The optical transparency of the title molecule was examined by TD- DFT analysis and for comparison basis experimental UV-Vis spectrum was recorded. The interaction of charge within the molecule was analyzed and the HOMO - LUMO energy gap was evaluated. The value of dipole moment, Mulliken charge and molecular electrostatic potential were estimated at the same level of theory. Also the first order hyper polarizability for NA was calculated. The dielectric behavior of the grown crystal was determined for few selected temperatures. The third order nonlinear response of NA has been examined using Z-scan technique and nonlinear susceptibility (χ3), nonlinear refraction (n2) and nonlinear absorption coefficient (β) has been calculated. The current results clearly indicate that the title compound is an excellent applicant in the domain of opto - electronic applications.

GW/Bethe-Salpeter calculations for charged and model systems from real-space DFT

NASA Astrophysics Data System (ADS)

Strubbe, David A.

GW and Bethe-Salpeter (GW/BSE) calculations use mean-field input from density-functional theory (DFT) calculations to compute excited states of a condensed-matter system. Many parts of a GW/BSE calculation are efficiently performed in a plane-wave basis, and extensive effort has gone into optimizing and parallelizing plane-wave GW/BSE codes for large-scale computations. Most straightforwardly, plane-wave DFT can be used as a starting point, but real-space DFT is also an attractive starting point: it is systematically convergeable like plane waves, can take advantage of efficient domain parallelization for large systems, and is well suited physically for finite and especially charged systems. The flexibility of a real-space grid also allows convenient calculations on non-atomic model systems. I will discuss the interfacing of a real-space (TD)DFT code (Octopus, www.tddft.org/programs/octopus) with a plane-wave GW/BSE code (BerkeleyGW, www.berkeleygw.org), consider performance issues and accuracy, and present some applications to simple and paradigmatic systems that illuminate fundamental properties of these approximations in many-body perturbation theory.

Interdiffusion in the Ni/TD-NiCr and Cr/TD-NiCr systems

NASA Technical Reports Server (NTRS)

Pawar, A. V.; Tenney, D. R.

1974-01-01

The diffusion of Ni and Cr into TD-NiCr has been studied over the 900 to 1100 C temperature range. The diffusion couples were prepared by electroplating Cr and Ni on polished TD-NiCr wafers. Concentration profiles produced as a result of isothermal diffusion at 905, 1000, and 1100 C were determined by electron microprobe analysis. The Boltzmann-Matano analysis was used to determine concentration-dependent diffusion coefficients which were found to compare favorably with previously reported values. These data suggest that 2 vol % ThO2 distribution has no appreciable effect on the rates of diffusion in TD-NiCr with a large grain size. This supports the view that an inert dispersoid in an alloy matrix will not in itself lead to enhanced diffusion unless a short-circuit diffusion structure is stabilized.

Exploratory study of friction welds in Udimet 700 and TD-Nickel bar

NASA Technical Reports Server (NTRS)

Moore, T. J.

1971-01-01

Friction welded butt joints were made in both Udimet 700 and TD-Nickel bar. Also, dissimilar metal friction welds were made between these materials. Friction welding of Udimet 700 shows great promise because the welds were found to be as strong as the parent metal in stress rupture and tensile tests at 760 and 980 C. The weld line was not detectable metallographically in the heat treated condition. Friction welding for TD-Nickel, however, holds little if any promise. TD-Nickel friction weldments could support only 9 percent as much stress as the base metal for a 10-hour stress-rupture life at 1090 C. Dissimilar Udimet 700/TD-Nickel friction welds could sustain only 15 percent as much stress as the TD-Nickel parent metal for a 10-hour rupture life at 930 C.

Investigating the features in differential absorbance spectra of NOM associated with metal ion binding: A comparison of experimental data and TD-DFT calculations for model compounds.

PubMed

Yan, Mingquan; Han, Xuze; Zhang, Chenyang

2017-11-01

In this study, seven model compounds containing typical functional groups (phenolic and carboxylic groups) present in nature organic matter (NOM) were used to ascertain the nature of the characteristic bands in differential absorbance spectra (DAS) of NOM that are induced by metal ion binding. Some similarities were found between the DAS of the examined model compounds, caffeic acid, ferulic acid, sinapic acid, terephthalic acid, isophthalic acid, esculetin and myricetin and those of NOM. The binding of Cu(II) with carboxylic group might produce two peaks, A1 and A2, while the binding of Cu(II) with phenolic group might produce all four Gaussian peaks, from A1 to A4 displayed in the DAS of NOM. The UV-visible spectra predicted using time-dependent density functional theory (TD-DFT)-based methods met well with the experimental DAS of model compounds at different stages of Cu(II) binding. It demonstrates that the features in absorbance spectra are chiefly caused by HOMO (Highest Occupied Molecular Orbital) - LUMO (Lowest Unoccupied Molecular Orbital) transitions in the molecule and that the appearance of peaks in DAS reflects the changes of the molecular orbitals around reactive functional groups in a molecule before and after metal ion binding. The basis of the DAS features of NOM that are induced by metal ion binding could be identified primarily by the frontier molecular orbital theory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis, characterization, spectroscopic properties and DFT study of a new pyridazinone family

NASA Astrophysics Data System (ADS)

Arrue, Lily; Rey, Marina; Rubilar-Hernandez, Carlos; Correa, Sebastian; Molins, Elies; Norambuena, Lorena; Zarate, Ximena; Schott, Eduardo

2017-11-01

Nitrogen compounds are widely investigated due to their pharmacological properties such as antihypertensive, antinociceptive, antibacterial, antifungal, analgesic, anticancer and inhibition activities and lately even as pesticide. In this context, we present the synthesis of new compounds: (E)-6-(3,4-dimethoxyphenyl)-3-(3-(3,4-dimethoxyphenyl)acryloyl)-1-(4-R-phenyl)- 5,6-dihydropyridazin-4(1H)-one (with R = sbnd H(1), -Cl(2), -Br(3), sbnd I(4) and sbnd COOH(5)) that was carried out by reaction of (1E, 6E)-1,7-bis(3,4-dimethoxyphenyl)hepta-1,6-diene-3,5-dione with a substituted phenylamine with general formula p-R-C6H4sbnd NH2 (R = sbnd H (1), sbnd Cl (2), -Br(3), sbnd I(4) and sbnd COOH(5)). This is the first synthesis report of a pyridazinone using as precursors a curcuminoid derivative and a diazonium salt formed in situ. All compounds were characterized by EA, FT-IR, UV-Vis, Emission,1H- and13C-NMR spectroscopy and the crystalline and molecular structure of 4 was solved by X-rays diffraction method. DFT and TD-DFT quantum chemical calculations were also employed to characterize the compounds and provide a rational explanation to the spectroscopic properties. To assess the biological activity of the systems, we focused on pesticide tests on compound 2, which showed an inhibitory effect in plant growth of Agrostis tenuis Higland.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

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

PubMed

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

2012-08-01

FT-IR and FT-Raman spectra of α,α,α-trichlorotoluene have been recorded and analyzed. The geometry, fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) B3LYP/6-311++G(d,p) method and a comparative study between HF level and various basis sets combination. The fundamental vibrational wavenumbers as well as their intensities were calculated and a good agreement between observed and scaled calculated wavenumbers has been achieved. The complete vibrational assignments of wavenumbers are made on the basis of potential energy distribution (PED). The effects due to the substitutions of methyl group and halogen were investigated. The absorption energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT). The electric dipole moment, polarizability and the first hyperpolarizability values of the α,α,α-trichlorotoluene have been calculated. (1)H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF and B3LYP methods with 6-311++G(d,p) basis set. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken and natural charges of the title molecule were also calculated and interpreted. Copyright © 2012 Elsevier B.V. All rights reserved.

Spectroscopic and molecular structure investigation of 2-furanacrylic acid monomer and dimer using HF and DFT methods

NASA Astrophysics Data System (ADS)

Ghalla, H.; Issaoui, N.; Govindarajan, M.; Flakus, H. T.; Jamroz, M. H.; Oujia, B.

2014-02-01

In the present work, we reported a combined experimental and theoretical study on molecular structure and vibrational spectra of 2-furanacrylic acid (abbreviated as 2FAA). The FT-IR and FT-Raman spectra of 2FAA have been recorded in the regions 4000-400 and 4000-100 cm-1. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The monomer and dimer structures of the title molecule have been obtained from Hartree-Fock (HF) and density functional theory (DFT) B3LYP methods with 6-311++G(d,p) as basis set calculations. The vibrational frequencies were calculated by DFT method and compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. Intermolecular OH⋯O hydrogen bonds are discussed in dimer structure of the molecule. The infrared and Raman spectra were also predicted from the calculated intensities. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. A study on the electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. In addition, Milliken atomic charges, possible charge transfer, natural bond orbital (NBO) and AIM topological analysis were performed. Moreover, molecular electrostatic potential (MEP) and the thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

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

NASA Astrophysics Data System (ADS)

Singh, Ravindra Kumar; Singh, Ashok Kumar

2017-02-01

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

A G protein-coupled receptor (GPCR) in red: live cell imaging of the kappa opioid receptor-tdTomato fusion protein (KOPR-tdT) in neuronal cells

PubMed Central

Huang, Peng; Chiu, Yi-Ting; Chen, Chongguang; Wang, Yujun; Liu-Chen, Lee-Yuan

2013-01-01

Introduction In contrast to green fluorescent protein and variants (GFPs), red fluorescent proteins (RFPs) have rarely been employed for generation of GPCR fusion proteins, likely because of formation of aggregates and cell toxicity of some RFPs. Among all the RFPs available, tdTomato (tdT), one of the non-aggregating RFP, has the highest brightness score (about 3 times that of eGFP) and unsurpassed photostability. Methods We fused tdT to the KOPR C-terminus. The KOPR-tdT cDNA construct was transfected into Neuro2A mouse neuroblastoma cell line (Neuro2A cells) and rat cortical primary neurons for characterization of pharmacological properties and imaging studies on KOPR trafficking. Results KOPR-tdT retained KOPR properties (cell surface expression, ligand binding, agonist-induced signaling and internalization) when expressed in Neuro2A cells and rat primary cortical neurons. Live cell imaging of KOPR-tdT enables visualization of time course of agonist-induced internalization of KOPR in real time for 60 min, without photobleaching and apparent cell toxicity. U50,488H-induced KOPR internalization occurred as early as 4 min and plateaued at about 30 min. A unique pattern of internalized KOPR in processes of primary neurons was induced by U50,488H. Discussion tdT is an alternative to, or even a better tool than, GFPs for fusing to GPCR for trafficking studies, because tdT has higher brightness and thus better resolution and less photobleaching problems due to reduced laser power used. It also has advantages associated with its longer-wavelength emission including spectral separation from autofluorescence and GFPs, reduced cell toxicity the laser may impose, and greater tissue penetration. These advantages of tdT over GPFs may be critical for live cell imaging studies of GPCRs in vitro and for studying GPCRs in vivo because of their low abundance. PMID:23856011

TdT activity in acute myeloid leukemias defined by monoclonal antibodies.

PubMed

San Miguel, J F; González, M; Cañizo, M C; Anta, J P; Portero, J A; López-Borrasca, A

1986-09-01

Blast cells from eight out of 71 patients diagnosed with acute myeloid leukemia (AML) by morphological, cytochemical, and immunological criteria showed TdT activity. Their distribution according to the FAB classification was one M1, one M2, one M4, two M5a, one M5b, one M6, and one undifferentiated case. The TdT+ AML cases did not show major clinical and hematological differences when compared with the classical TdT- AML patients. Other phenotypical aberrations in the expression of membrane antigens, apart from the presence of nuclear TdT, were not observed in these TdT+ cases after study with a large panel of monoclonal antibodies. A higher incidence of TdT+ cases was found among the monocytic variants of AML (M4 and M5)--four cases--than in the granulocytic variants (M1, M2, and M3)--2 cases. These TdT+ cases should be distinguished from mixed leukemias by double labeling techniques, assessing in the TdT+ AML the coexpression of TdT and myeloid markers in individual cells as shown in four of our cases.

Spectroscopic (FT-IR/FT-Raman) and computational (HF/DFT) investigation and HOMO/LUMO/MEP analysis on 1,1-difluoro-2-vinyl-cyclopropane

NASA Astrophysics Data System (ADS)

Senthil Raj, P.; Shoba, D.; Ramalingam, S.; Periandy, S.

2015-08-01

All the computational calculations were made in the ground state using the HF and DFT (B3LYP) methods with 6-31++G (d,p) and 6-311++G (d,p) basis sets. Making use of the recorded data, the complete vibrational assignments were made and analysis of the observed fundamental bands of molecule was carried out. The shifting of the frequencies in the vibrational pattern of the title molecule due to the substitutions; sbnd CHdbnd CH2 and F were deeply investigated by the vibrational analysis. Moreover, 13C NMR and 1H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF/B3LYP methods with 6-311++G (d,p). A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Mulliken charges of the 1DF2VCP were also calculated and interpreted. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

A systematic theoretical study of the electronic structures of porphyrin dimers: DFT and TD-DFT calculations on diporphyrins linked by ethane, ethene, ethyne, imine, and azo bridges.

PubMed

Rintoul, Llew; Harper, Shannon R; Arnold, Dennis P

2013-11-21

Theoretical calculations of the geometries, electronic structures and electronic absorption spectra of a series of covalently-linked porphyrin dimers are reported. The diporphyrins comprise 5,10,15-triphenylporphyrinatozinc(II) (ZnTriPP) units linked through the meso carbons by two-atom bridges, namely 1,2-ethanediyl (1), trans-1,2-ethenediyl (2), ethynediyl (3), 1,2-iminomethenediyl (4), and transdiazenediyl (5). The structures were optimised in toluene solvent by Density Functional Theory (DFT), using the integral equation formalism variant of the polarizable continuum model. The calculations were performed using the B3LYP functional and the 6-31G(d,p) basis set. The complete molecules were modelled, with no substitution of smaller groups on the periphery. In parallel, the compounds 2–5 were prepared by known or novel synthetic routes, to enable comparisons of experimental electronic absorption spectra with those calculated using time dependent-DFT at the same level of theory. As the ethane dimer 1 is not yet synthetically accessible, the model monomer meso-2-phenylethylZnTriPP was used for comparisons with the theoretical predictions. The results form a self-consistent set, enabling for the first time legitimate comparisons of the electronic structures of the series, especially regarding the degree to which the porphyrin p-systems interact by conjugation across the bridges. The theoretical calculations of the electronic transitions match the observed spectra in toluene to a remarkable degree, especially with respect to the peak maximum of the Q band, which represents to a large degree the energy of the HOMO–LUMO transition. The imine 4 is intrinsically polar due to the asymmetric bridge, and the HOMO is located almost exclusively on the ZnTriPP unit attached to the nitrogen of the imine, and the LUMO on the C-attached ring. Thus the Q-band transition is mapped as a comprehensive charge-transfer from the former ring to the latter. This may have consequences

Experimental and theoretical studies of (FT-IR, FT-Raman, UV-Visible and DFT) 4-(6-methoxynaphthalen-2-yl) butan-2-one.

PubMed

Govindasamy, P; Gunasekaran, S

2015-01-01

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000-50 cm(-1) and 4000-450 cm(-1) respectively for 4-(6-methoxynaphthalen-2-yl) butan-2-one (abbreviated as 4MNBO) molecule. Theoretical calculations were performed by density functional theory (DFT/B3LYP) method using 6-311G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and calculated wavenumber value of most of the fundamentals were very small. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The UV-Vis spectrum was recorded in the methanol solution. The energy, wavelength and oscillator's strength were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Thermodynamic properties of 4MNBO at different temperature have been calculated. The molecular electrostatic potential surface (MESP) and Frontier molecular orbital's (FMO's) analysis were investigated using theoretical calculations. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthesis, spectroscopic studies, DFT calculations, electrochemical evaluation, BSA binding and molecular docking of an aroylhydrazone -based cis-dioxido Mo(VI) complex

NASA Astrophysics Data System (ADS)

Mohamadi, Maryam; Faghih-Mirzaei, Ehsan; Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Haase, Wolfgang; Foro, Sabine

2017-07-01

A cis-dioxido Mo(VI) complex, [MoO2(L)(MeOH)], [L2-: (3-methoxy-2-oxidobenzylidene) benzohydrazonate], has been synthesized and characterized using physicochemical and spectroscopic techniques including elemental analysis, FT-IR, 1HNMR, UV-Vis spectroscopy, molar conductivity and single crystal X-ray diffraction. DFT calculations in the ground state of the complex were carried out using hybrid functional B3LYP with DGDZVP as basis set. Non-linear optical properties including electric dipole moment (μ), polarizability (α) and molecular first hyperpolarizability (β) of the compound were also computed. The values of linear polarizability and first hyperpolarizability obtained for the studied molecule indicated that the compound could be a good candidate of nonlinear optical materials. TD-DFT calculation and molecular electrostatic potential (MEP) were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the complex at different temperatures have been calculated. The interaction of a synthesized complex, with bovine serum albumin was also thoroughly investigated using experimental and theoretical studies. UV-Vis absorption and fluorescence quenching techniques were used to determine the binding parameters as well as the mechanism of the interaction. The values of binding constants were in the range of 104-105 M-1 demonstrating a moderate interaction between the synthesized complex and BSA making the protein suitable for transportation and delivery of the compound. Thermodynamic parameters were also indicating a binding through van der Waals force or hydrogen bond of [MoO2(L)(MeOH)] to BSA. The results obtained from docking studies were consistent to those obtained from experimental studies.

Scavenging performance and antioxidant activity of γ-alumina nanoparticles towards DPPH free radical: Spectroscopic and DFT-D studies.

PubMed

Zamani, Mehdi; Moradi Delfani, Ali; Jabbari, Morteza

2018-05-03

The radical scavenging performance and antioxidant activity of γ-alumina nanoparticles towards 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical were investigated by spectroscopic and computational methods. The radical scavenging ability of γ-alumina nanoparticles in the media with different polarity (i.e. i-propanol and n-hexane) was evaluated by measuring the DPPH absorbance in UV-Vis absorption spectra. The structure and morphology of γ-alumina nanoparticles before and after adsorption of DPPH were studied using XRD, FT-IR and UV-Vis spectroscopic techniques. The adsorption of DPPH free radical on the clean and hydrated γ-alumina (1 1 0) surface was examined by dispersion corrected density functional theory (DFT-D) and natural bond orbital (NBO) calculations. Also, time-dependent density functional theory (TD-DFT) was used to predict the absorption spectra. The adsorption was occurred through the interaction of radical nitrogen N and NO 2 groups of DPPH with the acidic and basic sites of γ-alumina surface. The high potential for the adsorption of DPPH radical on γ-alumina nanoparticles was investigated. Interaction of DPPH with Brønsted and Lewis acidic sites of γ-alumina was more favored than Brønsted basic sites. The following order for the adsorption of DPPH over the different active sites of γ-alumina was predicted: Brønsted base < Lewis acid < Brønsted acid. These results are of great significance for the environmental application of γ-alumina nanoparticles in order to remove free radicals. Copyright © 2018. Published by Elsevier B.V.

Using DFT Methods to Study Activators in Optical Materials

DOE PAGES

Du, Mao-Hua

2015-08-17

Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns 2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for newmore » materials. DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn 4+ activated red phosphors, scintillators activated by Ce 3+, Eu 2+, Tl +, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.« less

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

Studying breaking of inverted emulsions with thermolysis purification TD600

NASA Astrophysics Data System (ADS)

Tarasova, G. I.; Shevaga, O. N.; Grachyova, E. O.

2018-03-01

Currently, emulsions are used in many branches of industry and agriculture. It explains significant attention paid to issues in production, stabilization and breaking of emulsion. Besides, producing steady emulsions is of importance in many processes; the reverse problem, that of demulsification, is important as well in oil production and treatment of oil emulsion waste water. This paper studies the breaking (demulsification) of inverted emulsions with the help of thermolysis purification TD600, produced by thermal modification of purification, a large-scale waste of the sugar industry.

Deformation and annealing response of TD-nickel chromium sheet

NASA Technical Reports Server (NTRS)

Kane, R. D.; Ebert, L. J.

1973-01-01

The deformation and annealing response of TD-nickel chromium (TD-NiCr) 0.1 inch thick sheet was examined using various cold-rolling and annealing treatments. Upon annealing (above 816 C (1500 F), the as-received material was converted from an initially ultra-fine grain size (average grain dimension 0.51 micron) to a large grain structure. Increases in grain size by a factor of 100 to 200 were observed for this transformation. However, in those material states where the large grain transformation was absent, a fine grain recrystallized structure formed upon annealing (above 732 C (1350 F)). The deformation and annealing response of TD-NiCr sheet was evaluated with respect to the processing related variables as mode and severity of deformation and annealing temperature. Results indicate that the large grain transformation, classical primary recrystallization occurs. Using selected materials produced during the deformation and annealing study, the elevated temperature tensile properties of TD-NiCr sheet were examined in the temperature range 593 C (1100 F) to 1093 C (2000 F). It was observed that the elevated temperature tensile properties of TD-NiCr sheet could be optimized by the stabilization of a large grain size in this material using the cold working and/or annealing treatments developed during the present investigation.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-01

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms.

PubMed

Mohamed, Gehad G; Hamed, Maher M; Zaki, Nadia G; Abdou, Mohamed M; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-05

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL -1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase. Copyright © 2017 Elsevier B.V. All rights reserved.

Cyclic creep and fatigue of TD-NiCr (thoria-dispersion-strengthened nickel-chromium), TD-Ni, and NiCr sheet at 1200 C

NASA Technical Reports Server (NTRS)

Hirschberg, M. H.; Spera, D. A.; Klima, S. J.

1972-01-01

The resistance of thin TD-NiCr sheet to cyclic deformation was compared with that of TD-Ni and a conventional nickel-chromium alloy. Strains were determined by a calibration technique which combines room-temperature strain gage and deflection measurements with high-temperature deflection measurements. Analyses of the cyclic tests using measured tensile and creep-rupture data indicated that the TD-NiCr and NiCr alloy specimens failed by a cyclic creep mechanism. The TD-Ni specimens, on the other hand, failed by a fatigue mechanism.

Hydrogen bond strengthening between o-nitroaniline and formaldehyde in electronic excited states: A theoretical study

NASA Astrophysics Data System (ADS)

Yang, Juan; Li, An Yong

2018-06-01

To study the hydrogen bonds upon photoexcited, the time dependent density function method (TD DFT) was performed to investigate the excited state hydrogen bond properties of between o-nitroaniline (ONA) and formaldehyde (CH2O). The optimized structures of the complex and the monomers both in the ground state and the electronically excited states are calculated using DFT and TD DFT method respectively. Quantum chemical calculations of the electronic and vibrational absorption spectra are also carried out by TD DFT method at the different level. The complex ONA⋯CH2O forms the intramolecular hydrogen bond and intermolecular hydrogen bonds. Since the strength of hydrogen bonds can be measured by studying the vibrational absorption spectra of the characteristic groups on the hydrogen bonding acceptor and donor, it evidently confirms that the hydrogen bonds is strengthened in the S1/S2/T1 excited states upon photoexcitation. As a result, the hydrogen bonds cause that the CH stretch frequency of the proton donor CH2O has a blue shift, and the electron excitations leads to a frequency red shift of Ndbnd O and Nsbnd H stretch modes in the o-nitroaniline(ONA) and a small frequency blue shift of CH stretch mode in the formaldehyde(CH2O) in the S1 and S2 excited states. The excited states S1, S2 and T1 are locally excited states where only the ONA moiety is excited, but the CH2O moiety remains in its ground state.

Why use DFT methods in the study of carbohydrates?

USDA-ARS?s Scientific Manuscript database

The recent advances in density functional theory (DFT) and computer technology allow us to study systems with more than 100 atoms routinely. This makes it feasible to study large carbohydrate molecules via quantum mechanical methods, whereas in the past, studies of carbohydrates were restricted to ...

A novel thiazolidinedione derivative TD118 showing selective algicidal effects for red tide control.

PubMed

Wu, Ying; Lee, Yew; Jung, Seul-Gi; Kim, Minju; Eom, Chi-Yong; Kim, Si Wouk; Cho, Hoon; Jin, Eonseon

2014-05-01

Thiazolidinedione (TD) derivatives have been found to have an algicidal effect on harmful algal bloom microalgae. In this study, 75 TD derivatives were synthesized and analyzed for algicidal activity. Among these synthetic TDs, 18 TD derivatives showed specific algicidal activity on two strains belonging to the classes Raphidophyceae (Chattonella marina and Heterosigma akashiwo) and Dinophyceae (Cochlodinium polykrikoides). Two strains belonging to Bacillariophyceae (Navicula pelliculosa and Phaeodactylum EPV), one strain belonging to Dinophyceae (Amphidinium sp.), and a Eustigmatophycean microalga (Nannochloropsis oculata) showed less sensitivity to the TD derivatives than the other two phyla. The most reactive TD derivative, compound 2 (TD118), was selected and tested for morphological and physiological changes. TD118 effectively damaged the cell membrane of C. marina, H. akashiwo and C. polykrikoides. The O₂ evolution and photosystem II efficiency (F(v)/F(m)) of C. marina, H. akashiwo and C. polykrikoides were also severely reduced by TD118 treatment. Amphidinium sp., N. pelliculosa, Phaeodactylum EPV and N. oculata showed less reduction of O₂ evolution and the F(v)/F(m) by TD118. These results imply that the species-specific TD structure relationship may be due to structural and/or physiological differences among microalgal species.

Synthesis, spectroscopic investigations (FT-IR, NMR, UV-Vis, and TD-DFT), and molecular docking of (E)-1-(benzo[d][1, 3]dioxol-6-yl)-3-(6-methoxynaphthalen-2-yl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Therasa Alphonsa, A.; Loganathan, C.; Athavan Alias Anand, S.; Kabilan, S.

2017-02-01

The compound (E)-1-(benzo [d] [1, 3] dioxol-6-yl)-3-(6-methoxy naphthalen-2-yl) prop-2-en-1-one (AKN) was synthesized and characterized by FT-IR, NMR, and UV-Vis spectrometer. The optimized molecular geometry, bond lengths, bond angles, atomic charges, harmonic vibrational wave numbers and intensities of vibrational bonds of the title compound have been investigated by Time dependent- Density Functional Theory (TD-DFT) using a standard B3LYP method with 6-31 G (d, p) basis set available in the Gaussian 09W package. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-independent atomic orbital method (GIAO). Experimental excitation energies of the molecules were matched with the theoretically calculated energies. The atomic charge distributions of the various atoms present in the AKN were obtained by Mulliken charge population analysis. The Molecular Electrostatic Potential (MEP) analysis reveals the sites for electrophilic attack and nucleophilic reactions in the molecule. The difference between the observed and scaled frequencies was small. The HOMO to LUMO transition implies an electron density transfer. The intramolecular contacts have been interpreted using Natural Bond Orbital (NBO) analysis. The calculation results were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. To provide information about the interactions between human cytochrome protein and the novel compound theoretically, docking studies were carried out using Schrödinger software.

Structure, IR and Raman spectra of phosphotrihydrazide studied by DFT

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2016-09-01

The FTIR and FT Raman measurements of the phosphotrihydrazide (S)P[N(Me)-NH2]3 have been performed. This compound is a zero generation dendrimer G0 with terminal amine groups. Structural optimization and normal mode analysis were obtained for G0 by the density functional theory (DFT). Optimized geometric bond length and angles obtained by DFT show good agreement with experiment. The amine terminal groups are characterized by the well-defined bands at 3321, 3238, 1614 cm- 1 in the experimental IR spectrum and by bands at 3327, 3241 cm- 1 in the Raman spectrum of G0. The experimental frequencies of asymmetric and symmetric NH2 stretching vibrations of amine group are lower than theoretical values due to intramolecular Nsbnd H ⋯ S hydrogen bond. This hydrogen bond is also responsible for higher experimental infrared intensity of these bands as compared with theoretical values. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimer.

Spectroscopic and DFT study of solvent effects on the electronic absorption spectra of sulfamethoxazole in neat and binary solvent mixtures

NASA Astrophysics Data System (ADS)

Almandoz, M. C.; Sancho, M. I.; Blanco, S. E.

2014-01-01

The solvatochromic behavior of sulfamethoxazole (SMX) was investigated using UV-vis spectroscopy and DFT methods in neat and binary solvent mixtures. The spectral shifts of this solute were correlated with the Kamlet and Taft parameters (α, β and π*). Multiple lineal regression analysis indicates that both specific hydrogen-bond interaction and non specific dipolar interaction play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra using TD-DFT methods were in good agreement with the experimental ones. Binary mixtures consist of cyclohexane (Cy)-ethanol (EtOH), acetonitrile (ACN)-dimethylsulfoxide (DMSO), ACN-dimethylformamide (DMF), and aqueous mixtures containing as co-solvents DMSO, ACN, EtOH and MeOH. Index of preferential solvation was calculated as a function of solvent composition and non-ideal characteristics are observed in all binary mixtures. In ACN-DMSO and ACN-DMF mixtures, the results show that the solvents with higher polarity and hydrogen bond donor ability interact preferentially with the solute. In binary mixtures containing water, the SMX molecules are solvated by the organic co-solvent (DMSO or EtOH) over the whole composition range. Synergistic effect is observed in the case of ACN-H2O and MeOH-H2O, indicating that at certain concentrations solvents interact to form association complexes, which should be more polar than the individual solvents of the mixture.

Synthesis, characterization, crystal structure and DFT study of two new polymorphs of a Schiff base (E)-2-((2,6-dichlorobenzylidene)amino)benzonitrile

NASA Astrophysics Data System (ADS)

Benarous, N.; Cherouana, A.; Aubert, Emmanuel; Durand, Pierrick; Dahaoui, S.

2016-02-01

Two new polymorphs of Schiff base, (E)-2-((2,6-dichlorobenzylidene)amino)benzonitrile, were prepared from the condensation of 4-amino-benzonitrile and 2,6-dichlorobenzaldehyde. The two polymorphs crystallize in two different space groups: P21/c for polymorph (I) with volume 1264.23(2) Å3 and Pbca for polymorph (II) with volume 2469.3(2) Å3. The two polymorphs have been characterized by FT-IR and UV-VIS spectroscopy. The crystal structures of both compounds were determined by single X-ray analysis. The difference between the two polymorphs was observed at the angle between the two phenyl rings which is 4.81° for the first one and 82.27° for the second one. Both crystal structures are built on the basis of moderate and weak hydrogen bonds. Theoretical calculations on isolated molecules at the MP2 cc-pVDZ level show that the two polymorphs correspond to two molecular conformations that are within less than 1 kJ mol-1 and DFT periodic calculations indicate that (II) is more stable than (I) by 4.1 kJ mol-1 of formula unit. Additionally, we performed TD-DFT calculation for free ligands to support the experimental data.

TD-60 links RalA GTPase function to the CPC in mitosis

PubMed Central

Papini, Diana; Langemeyer, Lars; Abad, Maria A.; Kerr, Alastair; Samejima, Itaru; Eyers, Patrick A.; Jeyaprakash, A. Arockia; Higgins, Jonathan M. G.; Barr, Francis A.; Earnshaw, William C.

2015-01-01

TD-60 (also known as RCC2) is a highly conserved protein that structurally resembles the Ran guanine exchange factor (GEF) RCC1, but has not previously been shown to have GEF activity. TD-60 has a typical chromosomal passenger complex (CPC) distribution in mitotic cells, but associates with integrin complexes and is involved in cell motility during interphase. Here we show that TD-60 exhibits GEF activity, in vitro and in cells, for the small GTPase RalA. TD-60 or RalA depletion causes spindle abnormalities in prometaphase associated with abnormal centromeric accumulation of CPC components. TD-60 and RalA apparently work together to contribute to the regulation of kinetochore–microtubule interactions in early mitosis. Importantly, several mitotic phenotypes caused by TD-60 depletion are reverted by the expression of a GTP-locked mutant, RalA (Q72L). The demonstration that a small GTPase participates in the regulation of the CPC reveals a level of mitotic regulation not suspected in previous studies. PMID:26158537

Tetanus, Diphtheria (Td) Vaccine

MedlinePlus

... Headache (about 1 person in 4) Tiredness (about 1 person in 4) Moderate Problems following Td vaccine:(Interfered with activities, but did not require medical attention)Fever over 102°F (rare) Severe Problems following ...

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Synthesis of 4-((1E, 6E)-7-(4-hydroxy-3-methoxyphenyl)-3, 5-dioxohepta-1, 6-dienyl)-2-methoxyphenyl 4-fluorobenzoate, a novel monoester derivative of curcumin, its experimental and theoretical (DFT) studies

NASA Astrophysics Data System (ADS)

Srivastava, Sangeeta; Gupta, Preeti; Amandeep; Singh, Ranvijay Pratap

2016-04-01

Curcumin (1), isolated as a major component from the chloroform extract of Curcuma longa was converted to its ester derivative 4-((1E, 6E)-7-(4-hydroxy-3-methoxyphenyl)-3,5-dioxohepta-1,6-dienyl)-2-methoxyphenyl 4-fluorobenzoate (2). The compound has been characterized with the help of 1H, 13C NMR, UV, IR and mass spectrometry. The molecular geometry of synthesized compound was calculated in ground state by Density functional theory (DFT/B3LYP) using 6-31G (d,p) basis set. 1H and 13C NMR chemical shifts were calculated in ground state by using Gauge-Including Atomic Orbital (GIAO) approach and these values were correlated with experimental observations. The electronic properties such as HOMO and LUMO energies were calculated using time dependent Density Functional Theory (TD-DFT). Stability of the molecule as a result of hyper conjugative interactions and electron delocalization were analysed using Natural bond orbital (NBO) analysis. Intramolecular interactions were analysed by AIM (Atom in molecule) approach. Global reactivity descriptors were calculated to study the reactive site within molecule. The vibrational wavenumbers were calculated using DFT method and assigned with the help of potential energy distribution (PED). First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compounds. Molecular electrostatic potential (MEP) analysis has also been carried out.

TD-1792 versus Vancomycin for Treatment of Complicated Skin and Skin Structure Infections

PubMed Central

Potgieter, Peter D.; Li, Yu-Ping; Barriere, Steven L.; Churukian, Allan; Kingsley, Jeff; Corey, G. Ralph

2012-01-01

TD-1792 is a first-in-class glycopeptide-cephalosporin heterodimer that exhibits bactericidal activity against Gram-positive pathogens. We conducted a randomized, double-blind, active-control, phase II trial in patients with complicated skin and skin structure infections caused by suspected or confirmed Gram-positive organisms. Patients 18 to 65 years old were randomized to receive 7 to 14 days of either TD-1792 (2 mg/kg of body weight intravenously [i.v.] every 24 h [q24h]) or vancomycin (1 g i.v. q12h, with dosage regimens adjusted per site-specific procedures). A total of 197 patients were randomized and received at least one dose of study medication. Rates of clinical success at the test-of-cure evaluation were similar in all analysis populations. Among 170 clinically evaluable patients, cure rates were 91.7% and 90.7% in the TD-1792 and vancomycin groups, respectively (95% confidence interval [CI] of −7.9 to 9.7 for the difference). In microbiologically evaluable patients with methicillin-resistant Staphylococcus aureus at baseline (n = 75), cure rates were 94.7% in the TD-1792 group and 91.9% in the vancomycin group. Microbiological eradication of Gram-positive pathogens (n = 126) was achieved in 93.7% and 92.1% of patients in the TD-1792 and vancomycin groups, respectively. Seven patients were discontinued from study medication due to an adverse event (AE): 2 and 5 in the TD-1792 and vancomycin groups, respectively. AEs were of similar types and severities between the two groups, other than pruritus, which was more common in patients who received vancomycin. No patients in the TD-1792 group experienced a serious AE. This study supports further clinical development of TD-1792 in patients with Gram-positive infection. PMID:22869571

Intentionally Designed Three-Phase Time Diary (TD) as a Multi-Pronged Practice

ERIC Educational Resources Information Center

Chen, Hsin-Yu; Yarnal, Careen

2017-01-01

Adopting qualitative approaches, this study highlights the value of integrating cognitive understanding with students' daily experiences through a time diary (TD) project. Using an innovative three-phase design, the TD effectively heightened self-awareness, promoted self-reflection, inspired the desire to change, and facilitated knowledge…

FT-Raman, FT-IR spectroscopic and DFT studies of hexaphenoxycyclotriphosphazene

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Padie, C.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2016-07-01

The FTIR and FT Raman measurements of zero Gc0‧ -H and first Gc1‧ -H generations of phosphorus dendrimer built from cyclotriphosphazene core with phenoxy and deuterophenoxy terminal groups have been performed. In order to evaluate how much the frequencies, shift when changing the electronics of the system the FTIR and FT Raman spectra of phosphorus‒containing dendron with five terminal oxybenzaldehyde and one ester function Gci‧ have been also studied. Structural optimization and normal mode analysis were obtained for Gc0‧ -H and Gc0‧ -D by the density functional theory (DFT). It is discovered that dendrimer molecule exists in a stable conformation with six phenoxy terminal groups spaced above and below the flat cyclotriphosphazene core. Optimized geometric bond length and angles obtained by DFT show good agreement with a previously-published X-ray study. The phenoxy terminal groups are characterized by the well-defined line at 993 cm-1 in the experimental Raman spectrum of Gc0‧ -H and by line at 960 cm-1 in the Raman spectrum of Gc0‧ -D. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimers. The frequencies and relative intensity of the bands at 1589, 1487 cm-1 in the IR spectra show marked difference in dependence of the substituents on the aromatic ring.

Exact PsTd invariant and PsTd symmetric breaking solutions, symmetry reductions and Bäcklund transformations for an AB-KdV system

NASA Astrophysics Data System (ADS)

Jia, Man; Lou, Sen Yue

2018-05-01

In natural and social science, many events happened at different space-times may be closely correlated. Two events, A (Alice) and B (Bob) are defined as correlated if one event is determined by another, say, B = f ˆ A for suitable f ˆ operators. A nonlocal AB-KdV system with shifted-parity (Ps, parity with a shift), delayed time reversal (Td, time reversal with a delay) symmetry where B =Ps ˆ Td ˆ A is constructed directly from the normal KdV equation to describe two-area physical event. The exact solutions of the AB-KdV system, including PsTd invariant and PsTd symmetric breaking solutions are shown by different methods. The PsTd invariant solution show that the event happened at A will happen also at B. These solutions, such as single soliton solutions, infinitely many singular soliton solutions, soliton-cnoidal wave interaction solutions, and symmetry reduction solutions etc., show the AB-KdV system possesses rich structures. Also, a special Bäcklund transformation related to residual symmetry is presented via the localization of the residual symmetry to find interaction solutions between the solitons and other types of the AB-KdV system.

Tree Data (TD)

Treesearch

Robert E. Keane

2006-01-01

The Tree Data (TD) methods are used to sample individual live and dead trees on a fixed-area plot to estimate tree density, size, and age class distributions before and after fire in order to assess tree survival and mortality rates. This method can also be used to sample individual shrubs if they are over 4.5 ft tall. When trees are larger than the user-specified...

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

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-02-01

In this work, the molecular conformation, vibrational and electronic transition analysis of 2-amino-5-bromobenzoic acid (2A5BrBA) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000 cm(-1) and 50-4000 cm(-1), respectively. There are four conformers, C1, C2, C3 and C4 for this molecule. The geometrical parameters, energies and wavenumbers have been obtained for all four conformers. The computational results diagnose the most stable conformer of 2A5BrBA as the C1 form. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. The UV spectra of investigated compound were recorded in the region of 200-400 nm for ethanol and water solutions. The electronic properties were evaluated with help of time-dependent DFT (TD-DFT) theoretically and results were compared with experimental observations. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. The observed and the calculated geometric parameters, vibrational wavenumbers and electronic transitions were compared with observed data and found to be in good agreement. Copyright © 2011 Elsevier B.V. All rights reserved.

Structural, electronic and optical properties of LiNbO3 using GGA-PBE and TB-mBJ functionals: A DFT study

NASA Astrophysics Data System (ADS)

Arshad Javid, M.; Khan, Zafar Ullah; Mehmood, Zahid; Nabi, Azeem; Hussain, Fayyaz; Imran, M.; Nadeem, Muhammad; Anjum, Naeem

2018-06-01

In the present work, first-principles calculations were performed to obtain the structural, electronic and optical properties of lithium niobate crystal using two exchange-correlation functionals (GGA-PBE and TB-mBJ). The calculated structural parameters were very close to the experimental values. TB-mBJ functional was found to be good when compared to LDA and GGA functionals in case of bandgap energy of 3.715 eV of lithium niobate. It was observed that the upper valence and lower conduction bands consist mainly the O-2p and Nb-4d states, respectively. Furthermore, calculations for real and imaginary parts of frequency-dependent dielectric function 𝜀(ω) of lithium niobate crystal were performed using TD-DFT method. The ordinary refractive index no(ω), extraordinary refractive index ne(ω), its birefringence and absorption peaks in imaginary dielectric function 𝜀2(ω) were also calculated.

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

PubMed

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

2016-07-01

The extensive usage of OTC and Cu(2+) in livestock and poultry industry caused high residues in natural environment. Co-contamination of OTC and Cu(2+) was a considerable environmental problem in surface waters. In this study, Cu(2+) mediated direct photolysis of OTC was studied. Cu(2+) chelating with OTC was found to greatly inhibit OTC photodegradation. To reveal the chelation mechanism of OTC-Cu complexes, multiple methods including UV-Vis absorption spectra, Infrared (IR) spectra, mass spectroscopy, and density functional theoretical (DFT) modeling were performed. Four OTC-Cu complexes were proposed. Cu(2+) preferably bond to O11O12 site with the binding constants logK = 8.19 and 7.86 for CuHL+ and CuL±, respectively. The second chelating site was suggested to be O2O3 with the binding constants of logK = 4.41 and 4.62 for Cu2HL3+ and Cu2L2+, respectively. The suppressed quantum yield of OTC by Cu2+ chelation was accused for their intra-/inter-molecular electron transfer, by which the energy in activated states was distributed. The occurrence of electron transfer between BCD ring and A ring also from BCD ring to Cu was evidenced by the TD-DFT result only for the OTC-Cu complexes. Besides, the cyclic voltammetry measurement also suggested one OTC-Cu(II)/OTC-Cu(I) redox couple. These results suggested that the persistence of OTC in environmental surface waters will probably be underestimated for neglecting the chelating effect of Cu2+. The photolysis quantum yield of OTC-Cu complexes, as well as the specific molar absorption constants, the equilibrium binding constants of Cu2+ with OTC could contribute to more accurate kinetic models of OTC. Copyright © 2016 Elsevier Ltd. All rights reserved.

Experimental and DFT study of thiol-stabilized Pt/CNTs catalysts.

PubMed

Li, L; Chen, S G; Wei, Z D; Qi, X Q; Xia, M R; Wang, Y Q

2012-12-28

Using a combination of experiments and density functional theory (DFT) calculations, we explored the mechanisms of the stabilization effect of the thiolized (-SH) group on the Pt/SH-CNTs catalyst. Pt particles supported on the hydroxyl functionalized CNTs (Pt/OH-CNTs) are synthesized as a baseline for comparison. Experimentally, the platinum on OH-CNTs has a stronger tendency for aggregation than that on SH-CNTs. The differences in the oxidation resistance, migration activation energy, and corrosion resistance between the Pt/SH-CNTs and Pt/OH-CNTs are calculated using DFT. The DFT calculations indicate that the -SH group enhances the oxidation resistance of the Pt cluster and CNTs and restricts Pt migration on the CNTs. DFT calculations also suggest that the enhanced stability of Pt/SH-CNTs originates from the increased interaction between Pt and SH-CNTs and the depressed d-band center of the Pt NPs. Thus, the functional groups on the CNTs used for stabilization of supported Pt NPs should provide a deposit and anchor site for Pt NPs and maintain the perfect structure of CNTs rather than destroying it.

Uplink scheduling and adjacent-channel coupling loss analysis for TD-LTE deployment.

PubMed

Yeo, Woon-Young; Moon, Sung Ho; Kim, Jae-Hoon

2014-01-01

TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI.

Benchmark studies of UV-vis spectra simulation for cinnamates with UV filter profile.

PubMed

Garcia, Ricardo D'A; Maltarollo, Vinícius G; Honório, Káthia M; Trossini, Gustavo H G

2015-06-01

Skin cancer is a serious public health problem worldwide, being incident over all five continents and affecting an increasing number of people. As sunscreens are considered an important preventive measure, studies to develop better and safer sunscreens are crucial. Cinnamates are UVB filters with good efficiency and cost-benefit, therefore, their study could lead to the development of new UV filters. A benchmark to define the most suitable density functional theory (DFT) functional to predict UV-vis spectra for ethylhexyl methoxycinnamate was performed. Time-dependent DFT (TD-DFT) calculations were then carried out [B3LYP/6-311 + G(d,p) and B3P86/6-311 + G(d,p) in methanol environment] for seven cinammete derivatives implemented in the Gaussian 03 package. All DFT/TD-DFT simulations were performed after a conformational search with the Monte-Carlo method and MMFF94 force field. B3LYP and B3P86 functionals were better at reproducing closely the experimental spectra of ethylhexyl methoxycinnamate. Calculations of seven cinnamates showed a λmax of around 310 nm, corroborating literature reports. It was observed that the energy for the main electronic transition was around 3.95 eV and could be explained by electron delocalization on the aromatic ring and ester group, which is important to UV absorption. The methodology employed proved to be suitable for determination of the UV spectra of cinnamates and could be used as a tool for the development of novel UV filters.

One pot synthesis of Curcumin-NSAIDs prodrug, spectroscopic characterization, conformational analysis, chemical reactivity, intramolecular interactions and first order hyperpolarizability by DFT method

NASA Astrophysics Data System (ADS)

Srivastava, Sangeeta; Gupta, Preeti; Sethi, Arun; Singh, Ranvijay Pratap

2016-08-01

A novel Curcumin-NSAIDs prodrug 4-((1E, 3Z, 6E)-3-hydroxy-(4-hydroxy-3-methoxyphenyl)-5-oxohepta-1,3,3-trienyl)-2-methoxyphenyl-2-(4-isobutylphenyl) propanoate (2) derivative was synthesized by Steglich esterification in high yield and characterized with the help of 1H, 13C NMR, 1H-1H COSY, UV, FT-IR spectroscopy and mass spectrometry. The molecular geometry of synthesized compound was calculated in ground state by Density functional theory (DFT/B3LYP) using two different basis set 6-31G (d, p) and 6-311G (d, p). Conformational analysis of 2 was carried out to determine the most stable conformation. Stability of the molecule as a result of hyperconjugative interactions and electron delocalization were analysed using Natural bond orbital (NBO) analysis. Intramolecular interactions were analysed by AIM (Atom in molecule) approach. Global and local reactivity descriptors were calculated to study the reactive site within molecule. The electronic properties such as HOMO and LUMO energies were calculated using time dependent Density Functional Theory (TD-DFT). The vibrational wavenumbers were calculated using DFT method and assigned with the help of potential energy distribution (PED). First hyperpolarizability value has been calculated to describe the nonlinear optical (NLO) property of the synthesized compound. Molecular electrostatic potential (MEP) for synthesized compounds have also been determined to check their electrophilic or nucleophilic reactivity.

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Experimental (X-ray, FT-IR and UV-vis spectra) and theoretical methods (DFT study) of (E)-3-methoxy-2-[(p-tolylimino)methyl]phenol.

PubMed

Demircioğlu, Zeynep; Albayrak, Çiğdem; Büyükgüngör, Orhan

2014-07-15

A suitable single crystal of (E)-3-methoxy-2-[(p-tolylimino)methyl]phenol, formulated as C15H15N1O2, reveals that the structure is adopted to its E configuration about the azomethine C=N double bond. The compound adopts a enol-imine tautomeric form with a strong intramolecular O-H⋯N hydrogen bond. The single crystal X-ray diffraction analysis at 296K crystallizes in the monoclinic space group P21/c with a = 13.4791(11) Å, b = 6.8251(3) Å, c = 18.3561(15) Å, α = 90°, β = 129.296(5)°, γ = 90° and Z = 4. Comprehensive theoretical and experimental structural studies on the molecule have been carried out by FT-IR and UV-vis spectrometry. Optimized molecular structure and harmonic vibrational frequencies have been investigated by DFT/B3LYP method with 6-31G(d,p) basis set. Stability of the molecule, hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed by using natural bond orbital (NBO) analysis. Electronic structures were discussed by TD-DFT method and the relocation of the electron density were determined. The energetic behavior of the title compound has been examined in solvent media using polarizable continuum model (PCM). Molecular electrostatic potential (MEP), Mulliken population method and natural population analysis (NPA) have been studied. Nonlinear optical (NLO) properties were also investigated. In addition, frontier molecular orbitals analysis have been performed from the optimized geometry. An ionization potential (I), electron affinity (A), electrophilicity index (ω), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S), have been investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

Uplink Scheduling and Adjacent-Channel Coupling Loss Analysis for TD-LTE Deployment

PubMed Central

Yeo, Woon-Young; Moon, Sung Ho

2014-01-01

TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI. PMID:24707214

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

PubMed

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

2015-12-05

FT-IR and FT-Raman spectra of 3-pentyl-2,6-di(furan-2-yl) piperidin-4-one (3-PFPO) were recorded in the solid phase. The structural and spectroscopic analyses of 3-PFPO were made by using B3LYP/HF level with 6-311++G(d, p) basis set. The fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Comparison of the observed fundamental vibrational frequencies of 3-PFPO with calculated results by HF and DFT methods indicates that B3LYP is superior to HF method for molecular vibrational problems. The electronic properties such as excitation energies, oscillator strength, wavelengths and HOMO-LUMO energies were obtained by time-dependent DFT (TD-DFT) approach. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The hyperconjugative interaction energy (E((2))) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. In addition, MEP and atomic charges of carbon, nitrogen, oxygen and hydrogen were calculated using B3LYP/6-311++G(d, p) level theory. Moreover, thermodynamic properties (heat capacities, entropy and enthalpy) of the title compound at different temperatures were calculated in gas phase. Copyright © 2015 Elsevier B.V. All rights reserved.

The Efficiency of Delone Coverings of the Canonical Tilings T^*(A4) and T}(*(D_6)) -> T^*(D6)

NASA Astrophysics Data System (ADS)

Papadopolos, Zorka; Kasner, Gerald

This chapter is devoted to the coverings of the two quasiperiodic canonical tilings T^*(A4) and T}(*(D_6)) equiv {cal T}(*(2F)) -> T^*(D6) T^*(2F), obtained by projection from the root lattices A4 and D6, respectively. In the first major part of this chapter, in Sect. 5.2, we shall introduce a Delone covering C^sT^*(A4) of the 2-dimensional decagonal tiling T^*(A4). In the second major part of this chapter, Sect. 5.3, we summarize the results related to the Delone covering of the icosahedral tiling T}(*(D_6)) -> T^*(D6), T}(*(D_6)}) -> CT^*(D6) and determine the zero-, single-, and double- deckings and the resulting thickness of the covering. In the conclusions section, we give some suggestions as to how the definition of the Delone covering might be changed in order to reach some real (full) covering of the icosahedral tiling T}(*(D_6)) -> T^*(D6). In Section 5.2 the definition of the Delone covering is also changed in order to avoid an unnecessary large thickness of the covering.

Microwave-assisted synthesis, structural characterization, DFT studies, antibacterial and antioxidant activity of 2-methyl-4-oxo-1,2,3,4-tetrahydroquinazoline-2-carboxylic acid

NASA Astrophysics Data System (ADS)

Obafemi, Craig A.; Fadare, Olatomide A.; Jasinski, Jerry P.; Millikan, Sean P.; Obuotor, Efere M.; Iwalewa, Ezekiel O.; Famuyiwa, Samson O.; Sanusi, Kayode; Yilmaz, Yusuf; Ceylan, Ümit

2018-03-01

In the present study a new tetrahydroquinazoline-2-carboxylic, C10H10N2O3, 1‧, was synthesized and its structure was characterized by elemental analysis, IR, 1H NMR, 13C NMR data and high-resolution mass spectrometry. The spectral results are in line with the proposed structure. Single crystal X-ray structural analysis of the compound showed that the crystal structure adopts a monoclinic space group P21/c, with the packing of the molecule stabilized by Cdbnd O … …Hsbnd O, Nsbnd H … ….Odbnd Csbnd Osbnd intermolecular hydrogen bonding. The theoretical geometrical parameters of the compound have been calculated using density functional (DFT) and time-dependent density functional (TD-DFT) theory methods and have been used to predict the thermodynamic one-electron redox potential and the electronic absorption property of the compound. The theoretical characterization matched the experimental measurements, showing a good correlation. The calculated HOMO-LUMO gap (4.79 eV) suggests that compound 1‧ could be a potential antioxidant. The synthesized compound was screened for its in vitro antimicrobial activity against selected bacterial strains and antioxidant activity using the TAC, FRAP, NO and ABTS models. In vitro antioxidant activity of 1' showed a moderate activity, but weaker scavenging activity than the standards of ascorbic acid and trolox. Results of the antibacterial activity of the tested compound showed that it possesses a higher activity against Bacillus anthracis, Bacillus cereus, Bacillus polymyxa, Bacillus subtilis and Staphylococcus aureus than the two standard drugs, streptomycin and tetracycline, and better activity than tetracycline against Escherichia coli.

Optical, Fluorescence with quantum analysis of hydrazine (1, 3- Dinitro Phenyl) by DFT and Ab initio approach

NASA Astrophysics Data System (ADS)

Cecily Mary Glory, D.; Sambathkumar, K.; Madivanane, R.; Velmurugan, G.; Gayathri, R.; Nithiyanantham, S.; Venkatachalapathy, M.; Rajkamal, N.

2018-07-01

Experimental and computational study of molecular structure, vibrational and UV-spectral analysis of Hydrazine (1, 3- Dinitrophenyl) (HDP) derivatives. The crystal was grown by slow cooling method and the crystalline perfection of single crystals was evaluated by high resolution X-ray diffractometry (HRXRD) using a multicrystal X-ray diffractometer. Fluorescence, FT-IR and FT-Raman spectra of HDP crystal were recorded. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) followed by scaled quantum force field methodology (SQMFF). NMR studies have confirmed respectively the crystal structure and functional groups of the grown crystal. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) result complements the experimental findings. The calculated MESP, UV, HOMO-LUMO energies show that charge transfer done within the molecule. And various thermodynamic parameters are studied. Fukui determines the local reactive site of electrophilic, nucleophilic, descriptor.

Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, UV-Visible) study, potential energy surface scan, Fukui function analysis and HOMO-LUMO analysis of 3-tert-butyl-4-methoxyphenol by DFT methods.

PubMed

Saravanan, S; Balachandran, V

2014-09-15

This study represents an integral approach towards understanding the electronic and structural aspects of 3-tert-butyl-4-methoxyphenol (TBMP). Fourier-transform Infrared (FT-IR) and Fourier-transform Raman (FT-Raman) spectra of TBMP was recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The molecular structures, vibrational wavenumbers, infrared intensities and Raman activities were calculated using DFT (B3LYP and LSDA) methods using 6-311++G (d,p) basis set. The most stable conformer of TBMP was identified from the computational results. The assignments of vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of TBMP have been discussed. The stability and charge delocalization of the molecule was studied by Natural Bond Orbital (NBO) analysis. UV-Visible spectrum and effects of solvents have been discussed and the electronic properties such as HOMO and LUMO energies were determined by time-dependent TD-DFT approach with B3LYP/6-311++G (d,p) level of theory. The molecule orbital contributions are studied by density of energy states (DOSs). The reactivity sites are identified by mapping the electron density into electrostatic potential surface (MEP). Mulliken analysis of atomic charges is also calculated. The thermodynamic properties at different temperatures were calculated, revealing the correlations between standard heat capacities, standard entropy and standard enthalpy changes with temperatures. Global hardness, global softness, global electrophilicity and ionization potential of the title compound are determined. Copyright © 2014 Elsevier B.V. All rights reserved.

Conformational stability, vibrational spectra, molecular structure, NBO and HOMO-LUMO analysis of 5-nitro-2-furaldehyde oxime based on DFT calculations.

PubMed

Arivazhagan, M; Jeyavijayan, S; Geethapriya, J

2013-03-01

The FTIR and FT-Raman spectra of 5-nitro-2-furaldehyde oxime (NFAO) have been recorded in the regions 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The total energies of different conformations have been obtained from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The computational results identify the most stable conformer of NFAO as the C1 form. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of NFAO is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. Besides, molecular electrostatic potential (MEP), HOMO and LUMO analysis, and several thermodynamic properties were performed by the DFT method. Mulliken's net charges have been calculated and compared with the natural atomic charges. Ultraviolet-visible spectrum of the title molecule has also been calculated using TD-DFT method. Copyright © 2012 Elsevier B.V. All rights reserved.

Functional heterogeneity of memory B lymphocytes: in vivo analysis of TD-primed B cells responsive to secondary stimulation with TD and TI antigens.

PubMed

Rennick, D M; Morrow, P R; Benjamini, E

1983-08-01

The functional heterogeneity of memory B cells induced by a single determinant, consisting of a decapeptide representing amino acid residues 103-112 of tobacco mosaic virus protein (TMVP), was analyzed. Decapeptide specific antibodies were elicited in mice adoptively transferred with TMVP-immune spleen cells when challenged with TMVP, decapeptide conjugated to succinylated human gamma-globulin (SHGG), or decapeptide conjugated to Brucella abortus (BA). Whereas secondary stimulation by either TMVP or decapeptide-SHGG was dependent on appropriately primed T cells, stimulation by decapeptide-BA was independent of conventional T cell help. Furthermore, memory B cells responsive to TMVP (TD), decapeptide-SHGG (TD), or decapeptide-BA (TI. 1 prototype) were shown to consist of overlapping populations because adoptive recipients of TMVP-primed cells challenged simultaneously with TD and TI decapeptide antigens did not result in a higher antibody response than that elicited by one of the TD antigens injected alone. However, decapeptide-BA consistently induced a smaller antidecapeptide response than either TMVP or decapeptide-SHGG. This suggested that only a fraction of the memory B cell population which was activated by the original priming antigen (thymus-dependent) was also responsive to secondary in vivo stimulation by the priming hapten conjugated to Brucella abortus. Detailed analyses of the antibodies induced in the recipients of TMVP-immune spleen cells after secondary challenge with either TMVP, decapeptide-SHGG, or decapeptide-BA failed to distinguish between the responsive memory B cells; the antidecapeptide antibodies induced by all three immunogens shared the same fine specificities and immunoglobulin isotype composition. These data are viewed as further evidence that subsets of TD-primed B cells, which may display differential sensitivity to cross-stimulation with TD and TI forms of the antigen, represent distinct stages of memory B cell maturation within a

An investigation of the magnetic field of Transient Disturbances (TD) at the Earth's orbit, and a determination of solar sources of TD from their characteristics at R = 1 AU

NASA Technical Reports Server (NTRS)

Fainshtein, V. .G.; Kaigorodov, A. P.

1995-01-01

We have investigated and intercompared the typical features of the magnetic field of two types of solar wind transient disturbances with shock waves: the shock wave is accompanied by a magnetic cloud (MC), and the shock wave is followed by a region with bidirectional solar wind electron heat flux (BEHF), with no MC present. In this case, a separate study was made of the field features in two typical TD structures: in the region of impact-compressed solar wind between the shock wave and MC or BEHF, as well as in MC and BEHF. The study has provided new results on the influence of the ambient SW upon the TD magnetic field and the relationship between fields in various TD structures. A new test for the existence of interplanetary magnetic field draping around MC and BEHF is proposed and verified. It is concluded that the magnetic field configuration around MC is more adequately consistent with the concept of magnetic line draping than is the case around BEHF Two methods are proposed to infer the location of solar sources of TD from their characteristics at R = 1 AU.

State-of-technology for joining TD-NiCr sheet.

NASA Technical Reports Server (NTRS)

Holko, K. H.; Moore, T. J.; Gyorgak, C. A.

1972-01-01

At the current state-of-technology there are many joining processes that can be used to make sound welds in TD-NiCr sheet. Some of these that are described in this report are electron beam welding (EBW), gas-tungsten arc welding (GTAW), diffusion welding (DFW), resistance spot welding (RSW), resistance seam welding (RSEW), and brazing. Roll welding (RW) and explosion welding (EXW) have not been developed to the point where they can be used to make sound welds in TD-NiCr. Joining work that has previously been done on TD-NiCr by various organizations, both privately supported and under Air Force and NASA contracts, is described in this summary. Current work is also described that is being done at General Dynamics/Convair (under NASA contract) and at NASA/Lewis to develop and evaluate DFW, RSW, RSEW, and brazing. Preliminary comparisons of joining processes are made for typical applications. A brief description of the manufacture of TD-NiCr sheet by a recently standardized process (under NASA contract) also is given.

Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes.

PubMed

Holland, Jason P; Green, Jennifer C

2010-04-15

The electronic absorption spectra of a range of copper and zinc complexes have been simulated by using time-dependent density functional theory (TD-DFT) calculations implemented in Gaussian03. In total, 41 exchange-correlation (XC) functionals including first-, second-, and third-generation (meta-generalized gradient approximation) DFT methods were compared in their ability to predict the experimental electronic absorption spectra. Both pure and hybrid DFT methods were tested and differences between restricted and unrestricted calculations were also investigated by comparison of analogous neutral zinc(II) and copper(II) complexes. TD-DFT calculated spectra were optimized with respect to the experimental electronic absorption spectra by use of a Matlab script. Direct comparison of the performance of each XC functional was achieved both qualitatively and quantitatively by comparison of optimized half-band widths, root-mean-squared errors (RMSE), energy scaling factors (epsilon(SF)), and overall quality-of-fit (Q(F)) parameters. Hybrid DFT methods were found to outperform all pure DFT functionals with B1LYP, B97-2, B97-1, X3LYP, and B98 functionals providing the highest quantitative and qualitative accuracy in both restricted and unrestricted systems. Of the functionals tested, B1LYP gave the most accurate results with both average RMSE and overall Q(F) < 3.5% and epsilon(SF) values close to unity (>0.990) for the copper complexes. The XC functional performance in spin-restricted TD-DFT calculations on the zinc complexes was found to be slightly worse. PBE1PBE, mPW1PW91 and B1LYP gave the most accurate results with typical RMSE and Q(F) values between 5.3 and 7.3%, and epsilon(SF) around 0.930. These studies illustrate the power of modern TD-DFT calculations for exploring excited state transitions of metal complexes. 2009 Wiley Periodicals, Inc.

Deformation and annealing response of TD-nickel chromium

NASA Technical Reports Server (NTRS)

Kane, R. D.; Ebert, L. J.

1975-01-01

The recrystallization and grain growth processes occurring in TD-NiCr were examined with respect to deformation severity, annealing time, and temperature. Results indicated that two different annealing responses of TD-NiCr are possible, depending on the initial state and processing history prior to annealing. As-received sheet showed a dramatic increase in grain size with decreasing annealing temperature, whereas sheet prior-annealed at 1316 C for 1 hr exhibited very little variation with subsequent annealing temperature.

Shedding light on the Early Pleistocene of TD6 (Gran Dolina, Atapuerca, Spain): The technological sequence and occupational inferences

PubMed Central

2018-01-01

This paper aims to update the information available on the lithic assemblage from the entire sequence of TD6 now that the most recent excavations have been completed, and to explore possible changes in both occupational patterns and technological strategies evidenced in the unit. This is the first study to analyse the entire TD6 sequence, including subunits TD6.3 and TD6.1, which have never been studied, along with the better-known TD6.2 Homo antecessor-bearing subunit. We also present an analysis of several lithic refits found in TD6, as well as certain technical features that may help characterise the hominin occupations. The archaeo-palaeontological record from TD6 consists of 9,452 faunal remains, 443 coprolites, 1,046 lithic pieces, 170 hominin remains and 91 Celtis seeds. The characteristics of this record seem to indicate two main stages of occupation. In the oldest subunit, TD6.3, the lithic assemblage points to the light and limited hominin occupation of the cave, which does, however, grow over the course of the level. In contrast, the lithic assemblages from TD6.2 and TD6.1 are rich and varied, which may reflect Gran Dolina cave’s establishment as a landmark in the region. Despite the occupational differences between the lowermost subunit and the rest of the deposit, technologically the TD6 lithic assemblage is extremely homogeneous throughout. In addition, the composition and spatial distribution of the 12 groups of lithic refits found in unit TD6, as well as the in situ nature of the assemblage demonstrate the high degree of preservation at the site. This may help clarify the nature of the Early Pleistocene hominin occupations of TD6, and raise reasonable doubt about the latest interpretations that support the ex situ character of the assemblage as a whole. PMID:29370188

Shedding light on the Early Pleistocene of TD6 (Gran Dolina, Atapuerca, Spain): The technological sequence and occupational inferences.

PubMed

Mosquera, Marina; Ollé, Andreu; Rodríguez-Álvarez, Xose Pedro; Carbonell, Eudald

2018-01-01

This paper aims to update the information available on the lithic assemblage from the entire sequence of TD6 now that the most recent excavations have been completed, and to explore possible changes in both occupational patterns and technological strategies evidenced in the unit. This is the first study to analyse the entire TD6 sequence, including subunits TD6.3 and TD6.1, which have never been studied, along with the better-known TD6.2 Homo antecessor-bearing subunit. We also present an analysis of several lithic refits found in TD6, as well as certain technical features that may help characterise the hominin occupations. The archaeo-palaeontological record from TD6 consists of 9,452 faunal remains, 443 coprolites, 1,046 lithic pieces, 170 hominin remains and 91 Celtis seeds. The characteristics of this record seem to indicate two main stages of occupation. In the oldest subunit, TD6.3, the lithic assemblage points to the light and limited hominin occupation of the cave, which does, however, grow over the course of the level. In contrast, the lithic assemblages from TD6.2 and TD6.1 are rich and varied, which may reflect Gran Dolina cave's establishment as a landmark in the region. Despite the occupational differences between the lowermost subunit and the rest of the deposit, technologically the TD6 lithic assemblage is extremely homogeneous throughout. In addition, the composition and spatial distribution of the 12 groups of lithic refits found in unit TD6, as well as the in situ nature of the assemblage demonstrate the high degree of preservation at the site. This may help clarify the nature of the Early Pleistocene hominin occupations of TD6, and raise reasonable doubt about the latest interpretations that support the ex situ character of the assemblage as a whole.

Reactive sites influence in PMMA oligomers reactivity: a DFT study

NASA Astrophysics Data System (ADS)

Paz, C. V.; Vásquez, S. R.; Flores, N.; García, L.; Rico, J. L.

2018-01-01

In this work, we present a theoretical study of methyl methacrylate (MMA) living anionic polymerization. The study was addressed to understanding two important experimental observations made for Michael Szwarc in 1956. The unexpected effect of reactive sites concentration in the propagation rate, and the self-killer behavior of MMA (deactivating of living anionic polymerization). The theoretical calculations were performed by density functional theory (DFT) to obtain the frontier molecular orbitals values. These values were used to calculate and analyze the chemical interaction descriptors in DFT-Koopmans’ theorem. As a result, it was observed that the longest chain-length species (related with low concentration of reactive sites) exhibit the highest reactivity (behavior associated with the increase of the propagation rate). The improvement in this reactivity was attributed to the crosslinking produced in the polymethyl methacrylate chains. Meanwhile, the self-killer behavior was associated with the intermolecular forces present in the reactive sites. This behavior was associated to an obstruction in solvation, since the active sites remained active through all propagation species. The theoretical results were in good agreement with the Szwarc experiments.

DFT and ENDOR Study of Bixin Radical Cations and Neutral Radicals on Silica-Alumina.

PubMed

Tay-Agbozo, Sefadzi S; Krzyaniak, Matthew D; Bowman, Michael K; Street, Shane; Kispert, Lowell D

2015-06-18

Bixin, a carotenoid found in annatto (Bixa orellana), is unique among natural carotenoids by being water-soluble. We stabilized free radicals from bixin on the surface of silica-alumina (Si-Al) and characterized them by pulsed electron-nuclear double resonance (ENDOR). DFT calculations of unpaired electron spin distribution for various bixin radicals predict the EPR hyperfine couplings. Least-square fitting of experimental ENDOR spectra by spectra calculated from DFT hyperfine couplings characterized the radicals trapped on Si-Al. DFT predicts that the trans bixin radical cation is more stable than the cis bixin radical cation by 1.26 kcal/mol. This small energy difference is consistent with the 26% trans and 23% cis radical cations in the ENDOR spectrum. The remainder of the ENDOR spectrum is due to several neutral radicals formed by loss of a H(+) ion from the 9, 9', 13, or 13' methyl group, a common occurrence in all water-insoluble carotenoids previously studied. Although carboxyl groups of bixin strongly affect its solubility relative to other natural carotenoids, they do not alter properties of its free radicals based on DFT calculations and EPR measurements which remain similar to typical water-insoluble carotenoids.

Effects of TD-5108 on Gastrointestinal Transit and Bowel Function in Health and Pharmacokinetics in Health and Constipation

PubMed Central

Manini, Mhd Louai; Camilleri, Michael; Goldberg, Michael; Sweetser, Seth; McKinzie, Sanna; Burton, Duane; Wong, Shekman; Kitt, Michael M.; Li, Yu-Ping; Zinsmeister, Alan R.

2010-01-01

Background TD-5108 is a potent, selective high intrinsic activity serotonin 5-HT4 receptor agonist. Aim To assess effects of TD-5108 on gastrointestinal transit and compare its pharmacokinetics (PK) in healthy volunteers (HV) and chronic constipation (CC) patients. Methods 60 HV were randomly assigned, double-blind to placebo, 5, 15, 30 or 50 mg TD-5108 (single and 6-day dosing). Primary endpoints were colonic transit (geometric center at 24 hours, GC24) and ascending colon emptying (ACE) T1/2 after first dose. Secondary endpoints included gastric emptying (GE) T1/2 and colonic filling at 6 h (CF6). Results Single dose TD-5108 significantly accelerated GC24, ACE T1/2, and CF6; 30 and 50°mg TD-5108 accelerated all 3 endpoints. With multiple doses, TD-5108 30 mg accelerated GC24, and overall accelerated GE T1/2 at 15–50 mg. PK studies showed dose proportionality in health, and no significant differences between health and chronic constipation with a 15 mg oral dose of TD-5108. Stimulation of bowel function after15 mg TD-5108 were similar in CC and controls. There were no serious adverse events; notable adverse were the predictable GI effects such as diarrhea or altered bowel movements. Conclusions TD-5108 significantly accelerated intestinal and colonic transit after single dosing and accelerated gastric emptying after multiple dosing. Further studies of its potential as a gastrointestinal and colonic prokinetic are warranted. PMID:19691492

Diffusion of anthracene derivatives on Cu(111) studied by STM and DFT

NASA Astrophysics Data System (ADS)

Wyrick, Jonathan; Bartels, Ludwig; Einstein, Theodore

2014-03-01

Substituted anthracenes have drawn attention due to their ability to diffuse uniaxially on a Cu(111) surface. We compare anthracene to three of its derivatives whose 9,10 hydrogens are replaced by elements of the chalcogen group that act as linkers binding the molecules to a Cu(111) substrate. DFT calculations shed light on STM imaging and diffusion studies on the three substituted species. We present an analysis of the DFT results in which energetic contributions to the diffusion barriers are partitioned among the Kohn-Sham orbitals, allowing us to make assignments as to how each orbital affects diffusion for each species and draw comparisons between them. Present address: Center for Nanoscale Science and Technology, NIST, Gaithersburg, MD.

Solvatochromic benzo[h] coumarins: Synthesis, solvatochromism, NLO and DFT study

NASA Astrophysics Data System (ADS)

Warde, Umesh; Sekar, Nagaiyan

2017-10-01

Three benzo[h] coumarins were synthesized and analyzed for their potential NLOphoric properties. Coumarins were synthesized using Knoevenagel condensation method by reacting hydroxyl-naphthalene aldehyde with cyano-methylelene-benzazoles containing NH, O and S elements respectively as the active methylene compounds. The absorption maxima for the coumarins are not affected by the solvent polarity but emission maxima does. Emission solvatochromism was analyzed using various solvent polarity functions which highlights the polarity dependency of the emission profile. Coumarins showed satisfactory values for first and second hyperpolarizability which are comparable using solvatochromism and DFT. NLO properties are also compared with the limits of hyperpolarizability calculated using sum rule of quantum mechanics. Results show that the NLO properties predicted by DFT are close to the upper limits of hyperpolarizability. The functional CAM-B3LYP is proven to be suitable for predicting NLO properties for these coumarins compared to functional B3LYP. The present study highlights the importance of such molecules for incorporating in advanced NLOphores.

DFT Study of Optical Properties of Pt-based Complexes

NASA Astrophysics Data System (ADS)

Oprea, Corneliu I.; Dumbravǎ, Anca; Moscalu, Florin; Nicolaides, Atnanassios; Gîrţu, Mihai A.

2010-01-01

We report Density Functional Theory (DFT) calculations providing the geometrical and electronic structures, as well as the vibrational and optical properties of the homologous series of Pt-pyramidalized olefin complexes (CH2)n-(C8H10)Pt(PH3)2, where n = 0, 1, and 2, in their neutral and oxidized states. All complexes were geometry optimized for the singlet ground state in vacuum using DFT methods with B3LYP exchange-correlation functional and the Effective Core Potential LANL2DZ basis set, within the frame of Gaussian03 quantum chemistry package. We find the coordination geometry of Pt to be distorted square planar, with dihedral angles ranging from 0°, for n = 0 and 1, which have C2V symmetry to 3.4°, for n = 2 with C2 symmetry. The Mulliken charge analysis allows a discussion of the oxidation state of the Pt ion. Electronic transitions were calculated at the same level of theory by means of Time Dependant-DFT. For n = 2 the electronic absorption bands are located in the UV region of the spectrum, the transitions being assigned to metal to ligand charge transfers. The relevance of these Pt-based compounds as possible pigments for dye-sensitized solar cells is discussed.

Study on the prediction of visible absorption maxima of azobenzene compounds

PubMed Central

Liu, Jun-na; Chen, Zhi-rong; Yuan, Shen-feng

2005-01-01

The geometries of azobenzene compounds are optimized with B3LYP/6-311G* method, and analyzed with nature bond orbital, then their visible absorption maxima are calculated with TD-DFT method and ZINDO/S method respectively. The results agree well with the observed values. It was found that for the calculation of visible absorption using ZINDO/S method could rapidly yield better results by adjusting OWFπ-π (the relationship between π-π overlap weighting factor) value than by the TD-DFT method. The method of regression showing the linear relationship between OWFπ-π and BLN-N (nitrogen-nitrogen bond lengths) as OWF π-π=−8.1537+6.5638BL N-N, can be explained in terms of quantum theory, and also be used for prediction of visible absorption maxima of other azobenzne dyes in the same series. This study on molecules’ orbital geometry indicates that their visible absorption maxima correspond to the electron transition from HOMO (the highest occupied molecular orbital) to LUMO (the lowest unoccupied molecular orbital). PMID:15909349

Theoretical studies on the electronic structure and spectroscopic properties of transition metals bis(dipyrrinate)s

NASA Astrophysics Data System (ADS)

Ksenofontov, Alexander A.; Guseva, Galina B.; Antina, Elena V.

2016-10-01

Density functional theory (DFT) and Time-dependent density functional theory (TD- DFT) computations have been used to reveal structural, molecular, electronic and spectral-luminescent parameters and features of several homoleptic transition metals bis(dipyrrine) complexes. The influence of complexing agent and ligand nature on the regularities in geometric, spectral-luminescent properties, kinetic and thermal stability changes in the [M2L2] complexes series were studied. Special attention is paid to the influence of the solvating media (PCM/TD-B3LYP/Def2-SVP) on changing spectral-luminescent properties of d-metals bis(dipyrrinate)s. The interpretation of the dependence between spectral-luminescent properties of the complexes and HOMO-LUMO (highest occupied molecular orbital and lowest unoccupied molecular orbital) energy gap's width was given. It was shown that the regularities in changing the helicates' quantum yield depending on the nature of complexing agent, ligand and solvent properties, obtained from quantum-chemical calculations, are in the agreement with our previously obtained experimental data. Thus, structural and spectral-luminescent characteristics of new [M2L2] luminophors can be evaluated with high reliability, and good forecast prospects for their use as fluorescent dyes for optical devices can be made in terms of the results of theoretical studies (B3LYP/Def2-SVP and TD-B3LYP/Def2-SVP).

DFT analysis and spectral characteristics of Celecoxib a potent COX-2 inhibitor

NASA Astrophysics Data System (ADS)

Vijayakumar, B.; Kannappan, V.; Sathyanarayanamoorthi, V.

2016-10-01

Extensive quantum mechanical studies are carried out on Celecoxib (CXB), a new generation drug to understand the vibrational and electronic spectral characteristics of the molecule. The vibrational frequencies of CXB are computed by HF and B3LYP methods with 6-311++G (d, p) basis set. The theoretical scaled vibrational frequencies have been assigned and they agreed satisfactorily with experimental FT-IR and Raman frequencies. The theoretical maximum wavelength of absorption of CXB are calculated in water and ethanol by TD-DFT method and these values are compared with experimentally determined λmax values. The spectral and Natural bonds orbital (NBO) analysis in conjunction with spectral data established the presence of intra molecular interactions such as mesomeric, hyperconjugative and steric effects in CXB. The electron density at various positions and reactivity descriptors of CXB indicate that the compound functions as a nucleophile and establish that aromatic ring system present in the molecule is the site of drug action. Electronic distribution and HOMO - LUMO energy values of CXB are discussed in terms of intra-molecular interactions. Computed values of Mulliken charges and thermodynamic properties of CXB are reported.

Transceiver Multiplexers TD-1288( )/GRC and TD-1289( )(V)/GRC.

DTIC Science & Technology

1982-02-01

TRASITCAS TD-1289( )iV)1/GRC C.76 IR BANPAS FLER TERMINATION UNIT CU26()/GRC] G -42 RC MX-10080t )/GRC F’igure l-l. X1liF’ MultipleXer amily Tree. F1- CU-2266...the equations become: Y G o t Q 1Q+/Qu C o s 0 = j2 + Q QU L° l~ Qu I+j L=010 log 4 + j 2 Qt The passband loss expression may be simplified to read: 4...a character istic impedance of 50 oims. The linle len,_tli was 16i.5 inches and was tet oiinated inl a -ohio If load. The tap pointt was nojusted to g

Characterization of Thermophilic Halotolerant Aeribacillus pallidus TD1 from Tao Dam Hot Spring, Thailand

PubMed Central

Yasawong, Montri; Areekit, Supatra; Pakpitchareon, Arda; Santiwatanakul, Somchai; Chansiri, Kosum

2011-01-01

The bacterial strain TD1 was isolated from Tao Dam hot spring in Thailand. Strain TD1 was Gram positive, rod-shaped, aerobic, motile, and endospore forming. The cell was 2.0–40 μm in length and about 0.4 μm in diameter. The optimum growth occurred at 55–60 °C and at pH 7–8. Strain TD1 was able to grow on medium containing up to 10% NaCl. The DNA G+C content was 38.9 mol%. The cellular fatty acid content was mainly C16:0, which comprised 25.04% of the total amount of cellular fatty acid. 16S rDNA showed 99% identity to Aeribacillus pallidus DSM 3670T. Bayesian tree analysis strongly supported the idea that strain TD1 is affiliated with genus Aeribacillus, as Aeribacillus pallidus strain TD1. Although the 16S rDNA of A. pallidus strain TD1 is similar to that of A. pallidus DSM 3670T, some physiological properties and the cellular fatty acid profiles differ significantly. A. pallidus strain TD1 can produce extracellular pectate lyase, which has not been reported elsewhere for other bacterial strains in the genus Aeribacillus. A. pallidus strain TD1 may be a good candidate as a pectate lyase producer, which may have useful industrial applications. PMID:21954359

Enhanced efficacy of TD53, a novel algicidal agent, against the harmful algae via the liposomal delivery system.

PubMed

Han, Hyo-Kyung; Kim, Yeon-Mi; Lim, Soo-Jeong; Hong, Soon-Seok; Jung, Seul-Gi; Cho, Hoon; Lee, Wonjae; Jin, Eonseon

2011-02-28

The present study aimed to design the liposomal delivery system for TD53, a novel algicial drug in order to improve the delivery properties of TD53 and evaluate its algicidal effects as well as selectivity against harmful and non-harmful algae. Liposomes of TD53 were prepared with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) by a lyophilization, resulting in relatively small size vesicles (234±38nm) and narrow size distribution (PI=0.130±0.027). The drug leakage from the liposome was negligible in the F/2 media (<2% during 96h incubation). Subsequently algicidal activity of liposomal TD53 against harmful and nonharmful algae was evaluated at various concentrations. The IC(50) values of TD53 in liposome against harmful algae such as Chattonella marina, Heterosigma akashiwo and Cocholodinium polykrikoides were 2.675, 2.029, and 0.480μM, respectively, and were reduced by approximately 50% compared to those obtained from non-liposomal TD53. In contrast, the algicidal effect of liposomal TD53 was insignificant against non-harmful algae including Navicula pelliculosa, Nannochloropsis oculata and Phaeodactylum EPV. Those results suggested that liposomal delivery systems might be effective to enhance the efficacy of TD53 while maintaining the selectivity to harmful algal species. Copyright © 2010 Elsevier B.V. All rights reserved.

Theoretical study on physicochemical properties of curcumin

NASA Astrophysics Data System (ADS)

Shen, Liang; Ji, Hong-Fang

2007-07-01

Curcumin is a yellow-orange pigment, which has attracted considerable attention due to its wide spectrum of biological and pharmacological activities. In spite of much effort devoted on curcumin, there still exist some open questions concerning its fundamental physicochemical properties. The present study suggests that the DFT and TD-DFT calculations are useful to answer these questions. Firstly, the thermodynamic as well as spectral parameters support that curcumin exists predominantly in enol form in solution. Secondly, the calculated absorption spectra of curcumin anions provides direct evidence that the lowest p Ka of curcumin corresponds to the dissociation of enolic proton, which not only reconciles the controversy on this topic, but also has important implications on the proton-transfer/dissociation-associated radical-scavenging mechanisms of curcumin.

Elevated temperature deformation of TD-nickel base alloys

NASA Technical Reports Server (NTRS)

Petrovic, J. J.; Kane, R. D.; Ebert, L. J.

1972-01-01

Sensitivity of the elevated temperature deformation of TD-nickel to grain size and shape was examined in both tension and creep. Elevated temperature strength increased with increasing grain diameter and increasing L/D ratio. Measured activation enthalpies in tension and creep were not the same. In tension, the internal stress was not proportional to the shear modulus. Creep activation enthalpies increased with increasing L/D ratio and increasing grain diameter, to high values compared with that of the self diffusion enthalpy. It has been postulated that two concurrent processes contribute to the elevated temperature deformation of polycrystalline TD-nickel: (1) diffusion controlled grain boundary sliding, and (2) dislocation motion.

75 FR 49023 - Proposed Collection; Comment Request for Form TD F 90-22.1

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-12

... TD F 90-22.1 AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice and request for... Form TD F 90-22.1, Report of Foreign Bank and Financial Accounts. DATES: Written comments should be.... OMB Number: 1545-2038. Form Number: TD F 90-22.1. Abstract: This information is collected because of...

A conceptual DFT study of the molecular properties of glycating carbonyl compounds.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2017-01-01

Several glycating carbonyl compounds have been studied by resorting to the latest Minnesota family of density functional with the objective of determinating their molecular properties. In particular, the chemical reactivity descriptors that arise from conceptual density functional theory and chemical reactivity theory have been calculated through a [Formula: see text]SCF protocol. The validity of the KID (Koopmans' in DFT) procedure has been checked by comparing the reactivity descriptors obtained from the values of the HOMO and LUMO with those calculated through vertical energy values. The reactivity sites have been determined by means of the calculation of the Fukui function indices, the condensed dual descriptor [Formula: see text] and the electrophilic and nucleophilic Parr functions. The glycating power of the studied compounds have been compared with the same property for simple carbohydrates.Graphical abstractSeveral glycating carbonyl compounds have been studied by resorting to the latest Minnesota family of density functional with the objective of determinating their molecular properties, the chemical reactivity descriptors and the validity of the KID (Koopmans' in DFT) procedure.

Earliest humans in Europe: The age of TD6 Gran Dolina, Atapuerca, Spain

USGS Publications Warehouse

Falgueres, Christophe; Bahain, J.-J.; Yokoyama, Y.; Arsuaga, J.L.; Bermudez de Castro, Jose Maria; Carbonell, E.; Bischoff, J.L.; Dolo, J.-M.

1999-01-01

Hominid remains found in 1994 from the stratified Gran Dolina karst-filling at the Atapuerca site in NE Spain were dated to somewhat greater than 780 ka based on palaeomagnetic measurements, making these the oldest known hominids in Europe (sensu stricto). We report new ESR and U-series results on teeth from four levels of the Gran Dolina deposit which confirm the palaeomagnetic evidence, and indicate that TD6 (from which the human remains have been recovered) dates to the end of the Early Pleistocene. The results for the other levels are consistent with estimates based mainly on microfaunal evidence, and suggest that TD8, TD10 and TD11 date to the Middle Pleistocene. (C) 1999 Academic Press.

Zinc binding in HDAC inhibitors: a DFT study.

PubMed

Wang, Difei; Helquist, Paul; Wiest, Olaf

2007-07-06

Histone deacetylases (HDACs) are attractive targets for the treatment of cancers and a variety of other diseases. Most currently studied HDAC inhibitors contain hydroxamic acids, which are potentially problematic in the development of practical drugs. DFT calculations of the binding modes and free energies of binding for a variety of other functionalities in a model active site of HDAC are described. The protonation state of hydroxamic acids in the active site and the origin of the high affinity are discussed. These results emphasize the importance of a carefully chosen pKa for zinc binding and provide guidance for the design of novel, non-hydroxamic acid HDAC inhibitors.

Development of forming and joining technology for TD-NiCr sheet

NASA Technical Reports Server (NTRS)

Torgerson, R. T.

1973-01-01

Forming joining techniques and properties data were developed for thin-gage TD-NiCr sheet in the recrystallized and unrecrystallized conditions. Theoretical and actual forming limit data are presented for several gages of each type of material for five forming processes: brake forming, corrugation forming, joggling, dimpling and beading. Recrystallized sheet can be best formed at room temperature, but unrecrystallized sheet requires forming at elevated temperature. Formability is satisfactory with most processes for the longitudinal orientation but poor for the transverse orientation. Dimpling techniques require further development for both material conditions. Data on joining techniques and joint properties are presented for four joining processes: resistance seam welding (solid-state), resistance spot welding (solid-state), resistance spot welding (fusion) and brazing. Resistance seam welded (solid-state) joints with 5t overlap were stronger than parent material for both material conditions when tested in tensile-shear and stress-rupture. Brazing studies resulted in development of NASA 18 braze alloy (Ni-16Cr-15Mo-8Al-4Si) with several properties superior to baseline TD-6 braze alloy, including lower brazing temperture, reduced reaction with Td-Ni-Cr, and higher stress-rupture properties.

Electronic structure, hydrogen bonding and spectroscopic profile of a new 1,2,4-triazole-5(4H)-thione derivative: A combined experimental and theoretical (DFT) analysis

NASA Astrophysics Data System (ADS)

Al-Tamimi, Abdul-Malek S.

2016-09-01

Density functional theory has been implemented to study the electronic structure, molecular properties and vibrational spectra of 3-(adamantan-1-yl)-4-(4-chlorophenyl)-1H-1,2,4-triazole-5(4H)-thione, a novel 1,2,4-triazole-5(4H)-thione derivative. Hydrogen bonded dimer of the title molecule has been studied using B3LYP, M06-2X and X3LYP functionals at 6-311++ G(d,p) level of theory. The intermolecular hydrogen bonding has been studied using NBO analysis of the dimer. Bader's AIM theory was also used to evaluate the strength as well as the hydrogen bonding characteristics. Experimental FT-IR and FT-Raman spectra of the title molecule were related with the spectral data obtained with DFT/B3LYP method. The 1H NMR chemical shifts of the title molecule were calculated by the GIAO method and compared with experimental results. Dipole moment, polarizability (α), first order static hyperpolarizability (β) along with molecular electrostatic potential surface have been calculated. Frequency-dependent first hyperpolarizabilities, β(-2ω;ω,ω) and β(-ω;ω,0) have also been evaluated to study the non-linear optical behavior of the title compound. UV-Vis spectrum of the title molecule was recorded and TD-DFT method has been used to calculate six lowest excited states and the corresponding excitation energies.

Safety and immunogenicity of a single intramuscular dose of a tetanus-diphtheria toxoid (Td) vaccine (BR-TD-1001) in healthy Korean adult subjects.

PubMed

Hong, Taegon; Chung, Yong-Ju; Kim, Tae-Yeon; Kim, Ik-Hwan; Choe, Yong-Kyung; Lee, Jongtae; Jeon, Sangil; Han, Seunghoon; Yim, Dong-Seok

2015-01-01

BR-TD-1001 was developed as a booster for the immunity maintenance of diphtheria and tetanus. The aim of this study was to evaluate the safety and immunogenicity of BR-TD-1001 (test vaccine) in comparison with placebo and an active comparator in healthy Korean adults. A randomized, double-blind, placebo-controlled, active comparator, phase I clinical trial was conducted. Fifty subjects were randomly assigned to one of 3 treatment groups in a ratio of 2:2:1, and were administered a single intramuscular dose of test vaccine, active comparator, or placebo, respectively. All subjects were monitored for 4 weeks after injection. The antibody titers of the patients 2 and 4 weeks after vaccination were compared with the baseline. The frequencies of all adverse events including adverse drug reactions in the test group were not statistically different from those of the other treatment groups (P = 0.4974, 0.3061). No serious adverse event occurred, and no subject was withdrawn from the study for safety. The seroprotection rates against both tetanus and diphtheria at 4 weeks after vaccination were over 0.95. For anti-tetanus antibody, the geometric mean titer in the test group was significantly higher than those of the other groups (P = 0.0364, 0.0033). The geometric mean titer of anti-diphtheria antibody in the test group was significantly higher than the value of the placebo (P = 0.0347) while it was not for the value of the active comparator (P = 0.8484). In conclusion, BR-TD-1001 was safe, well-tolerated, and showed sufficient immunogenicity as a booster for diphtheria and tetanus.

Applicability of DFT model in reactive distillation

NASA Astrophysics Data System (ADS)

Staszak, Maciej

2017-11-01

The density functional theory (DFT) applicability to reactive distillation is discussed. Brief modeling techniques description of distillation and rectification with chemical reaction is provided as a background for quantum method usage description. The equilibrium and nonequilibrium distillation models are described for that purpose. The DFT quantum theory is concisely described. The usage of DFT in the modeling of reactive distillation is described in two parts. One of the fundamental and very important component of distillation modeling is vapor-liquid equilibrium description for which the DFT quantum approach can be used. The representative DFT models, namely COSMO-RS (Conductor like Screening Model for Real Solvents), COSMOSPACE (COSMO Surface Pair Activity Coefficient) and COSMO-SAC (SAC - segment activity coefficient) approaches are described. The second part treats the way in which the chemical reaction is described by means of quantum DFT method. The intrinsic reaction coordinate (IRC) method is described which is used to find minimum energy path of substrates to products transition. The DFT is one of the methods which can be used for that purpose. The literature data examples are provided which proves that IRC method is applicable for chemical reaction kinetics description.

Interaction between transition metals and phenylalanine: a combined experimental and computational study.

PubMed

Elius Hossain, Md; Mahmudul Hasan, Md; Halim, M E; Ehsan, M Q; Halim, Mohammad A

2015-03-05

Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic. Copyright © 2014 Elsevier B.V. All rights reserved.

Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valsson, Omar; Filippi, Claudia, E-mail: c.filippi@utwente.nl; Casida, Mark E., E-mail: mark.casida@ujf-grenoble.fr

2015-04-14

The excited-state relaxation of retinal protonated Schiff bases (PSBs) is an important test case for biological applications of time-dependent (TD) density-functional theory (DFT). While well-known shortcomings of approximate TD-DFT might seem discouraging for application to PSB relaxation, progress continues to be made in the development of new functionals and of criteria allowing problematic excitations to be identified within the framework of TD-DFT itself. Furthermore, experimental and theoretical ab initio advances have recently lead to a revised understanding of retinal PSB photochemistry, calling for a reappraisal of the performance of TD-DFT in describing this prototypical photoactive system. Here, we re-investigate themore » performance of functionals in (TD-)DFT calculations in light of these new benchmark results, which we extend to larger PSB models. We focus on the ability of the functionals to describe primarily the early skeletal relaxation of the chromophore and investigate how far along the out-of-plane pathways these functionals are able to describe the subsequent rotation around formal single and double bonds. Conventional global hybrid and range-separated hybrid functionals are investigated as the presence of Hartree-Fock exchange reduces problems with charge-transfer excitations as determined by the Peach-Benfield-Helgaker-Tozer Λ criterion and by comparison with multi-reference perturbation theory results. While we confirm that most functionals cannot render the complex photobehavior of the retinal PSB, do we also observe that LC-BLYP gives the best description of the initial part of the photoreaction.« less

Comparison of discrete Fourier transform (DFT) and principal component analysis/DFT as forecasting tools for absorbance time series received by UV-visible probes installed in urban sewer systems.

PubMed

Plazas-Nossa, Leonardo; Torres, Andrés

2014-01-01

The objective of this work is to introduce a forecasting method for UV-Vis spectrometry time series that combines principal component analysis (PCA) and discrete Fourier transform (DFT), and to compare the results obtained with those obtained by using DFT. Three time series for three different study sites were used: (i) Salitre wastewater treatment plant (WWTP) in Bogotá; (ii) Gibraltar pumping station in Bogotá; and (iii) San Fernando WWTP in Itagüí (in the south part of Medellín). Each of these time series had an equal number of samples (1051). In general terms, the results obtained are hardly generalizable, as they seem to be highly dependent on specific water system dynamics; however, some trends can be outlined: (i) for UV range, DFT and PCA/DFT forecasting accuracy were almost the same; (ii) for visible range, the PCA/DFT forecasting procedure proposed gives systematically lower forecasting errors and variability than those obtained with the DFT procedure; and (iii) for short forecasting times the PCA/DFT procedure proposed is more suitable than the DFT procedure, according to processing times obtained.

DFT Performance Prediction in FFTW

NASA Astrophysics Data System (ADS)

Gu, Liang; Li, Xiaoming

Fastest Fourier Transform in the West (FFTW) is an adaptive FFT library that generates highly efficient Discrete Fourier Transform (DFT) implementations. It is one of the fastest FFT libraries available and it outperforms many adaptive or hand-tuned DFT libraries. Its success largely relies on the huge search space spanned by several FFT algorithms and a set of compiler generated C code (called codelets) for small size DFTs. FFTW empirically finds the best algorithm by measuring the performance of different algorithm combinations. Although the empirical search works very well for FFTW, the search process does not explain why the best plan found performs best, and the search overhead grows polynomially as the DFT size increases. The opposite of empirical search is model-driven optimization. However, it is widely believed that model-driven optimization is inferior to empirical search and is particularly powerless to solve problems as complex as the optimization of DFT.

75 FR 47893 - Proposed Collection; Comment Request for REG-111583-07, (T.D. 9405) (Final)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-09

...-111583-07, (T.D. 9405) (Final) AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice and... comments concerning temporary and final regulations (REG-111583-07) (T.D. 9405), Employment Tax Adjustments... Adjustments. OMB Number: 1545-2097. Form Number: REG-111583-07 (T.D. 9405) (final). Abstract: This document...

Synthesis, structures, nuclease activity, cytotoxicity, DFT and molecular docking studies of two nitrato bridged homodinuclear (Cu-Cu, Zn-Zn) complexes containing 2,2'-bipyridine and a chalcone derivative.

PubMed

Gaur, Ruchi; Choubey, Diksha Kumari; Usman, Mohammad; Ward, Benzamin D; Roy, Jagat Kumar; Mishra, Lallan

2017-08-01

Nitrato briged dinuclear complexes of type [Cu 2 (L) 2 (bpy) 2 (NO 3 )](NO 3 )·4H 2 O, 1 and [Zn 2 (L) 2 (bpy) 2 (NO 3 )](NO 3 )·4H 2 O, 2 (L=deprotonated form of free ligand LH, [1-(2-hydroxyphenyl)-3-(9-anthracenyl) propenone; bpy=2,2'bipyridine] are synthesized and characterized using a battery of physicochemical techniques and X-ray crystallography. A distorted square pyramidal geometry is assigned to them with N 2 O 3 coordination core around the metal ion. The co-ligand L binds the metal ions through its O,O' atoms in anti-syn mode. The metal centers in complexes 1 and 2 are separated via bridging nitrato group at a distance of 6.073Å and 5.635Å respectively. Their structures and absorption spectra are supported by the computational studies using density functional theory (DFT) and TD-DFT. Both complexes exhibit nuclease activity and cleave supercoiled (form I) DNA. The complex 1 preferentially binds major groove of DNA and follows an oxidative pathway whereas complex 2 binds with minor groove of DNA via hydrolytic pathway. Both complexes inhibit topoisomerase I relaxation activity with IC 50 values of 7 and 35μM. Molecular docking studies support the groove binding and topoisomerase I binding of the complexes. The complex 1 showed a significant cytotoxicity against HeLa cell lines (a cervical cancer cell lines) in vitro with IC 50 value calculated as 2.9±0.021μM as compared to 28.2±0. 044μΜ for complex 2. Complex 2 induces the cell apoptosis at a later-stage as compared to complex 1. The cell apoptosis and topoisomerase inhibition by complexes enable them to be potential candidates as future anticancer drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

Tight-binding approximations to time-dependent density functional theory — A fast approach for the calculation of electronically excited states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rüger, Robert, E-mail: rueger@scm.com; Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam; Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig

2016-05-14

We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of twomore » compared to TD-DFTB.« less

Spectroscopic and DFT Study of RhIII Chloro Complex Transformation in Alkaline Solutions.

PubMed

Vasilchenko, Danila B; Berdyugin, Semen N; Korenev, Sergey V; O'Kennedy, Sean; Gerber, Wilhelmus J

2017-09-05

The hydrolysis of [RhCl 6 ] 3- in NaOH-water solutions was studied by spectrophotometric methods. The reaction proceeds via successive substitution of chloride with hydroxide to quantitatively form [Rh(OH) 6 ] 3- . Ligand substitution kinetics was studied in an aqueous 0.434-1.085 M NaOH matrix in the temperature range 5.5-15.3 °C. Transformation of [RhCl 6 ] 3- into [RhCl 5 (OH)] 3- was found to be the rate-determining step with activation parameters of ΔH † = 105 ± 4 kJ mol -1 and ΔS † = 59 ± 10 J K -1 mol -1 . The coordinated hydroxo ligand(s) induces rapid ligand substitution to form [Rh(OH) 6 ] 3- . By simulating ligand substitution as a dissociative mechanism, using density functional theory (DFT), we can now explain the relatively fast and slow kinetics of chloride substitution in basic and acidic matrices, respectively. Moreover, the DFT calculated activation energies corroborated experimental data that the kinetic stereochemical sequence of [RhCl 6 ] 3- hydrolysis in an acidic solution proceeds as [RhCl 6 ] 3- → [RhCl 5 (H 2 O)] 2- → cis-[RhCl 4 (H 2 O) 2 ] - . However, DFT calculations predict in a basic solution the trans route of substitution [RhCl 6 ] 3- → [RhCl 5 (OH)] 3- → trans-[RhCl 4 (OH) 2 ] 3- is kinetically favored.

Review of FD-TD numerical modeling of electromagnetic wave scattering and radar cross section

NASA Technical Reports Server (NTRS)

Taflove, Allen; Umashankar, Korada R.

1989-01-01

Applications of the finite-difference time-domain (FD-TD) method for numerical modeling of electromagnetic wave interactions with structures are reviewed, concentrating on scattering and radar cross section (RCS). A number of two- and three-dimensional examples of FD-TD modeling of scattering and penetration are provided. The objects modeled range in nature from simple geometric shapes to extremely complex aerospace and biological systems. Rigorous analytical or experimental validatons are provided for the canonical shapes, and it is shown that FD-TD predictive data for near fields and RCS are in excellent agreement with the benchmark data. It is concluded that with continuing advances in FD-TD modeling theory for target features relevant to the RCS problems and in vector and concurrent supercomputer technology, it is likely that FD-TD numerical modeling will occupy an important place in RCS technology in the 1990s and beyond.

An improved diffusion welding technique for TD-NiCr

NASA Technical Reports Server (NTRS)

Holko, K. H.

1973-01-01

An improved diffusion welding technique has been developed for TD-NiCr sheet. In the most preferred form, the improved technique consists of diffusion welding 320-grit sanded plus chemically polished surfaces of unrecrystallized TD-NiCr at 760 C under 140 MN/m2 pressure for 1hr followed by postheating at 1180 C for 2hr. Compared to previous work, this improved technique has the advantages of shorter welding time, lower welding temperature, lower welding pressure, and a simpler and more reproducible surface preparation procedure. Weldments were made that had parent-metal creep-rupture shear strength at 1100 C.

Orientation of N-benzoyl glycine on silver nanoparticles: SERS and DFT studies

NASA Astrophysics Data System (ADS)

Parameswari, A.; Asath, R. Mohamed; Premkumar, R.; Benial, A. Milton Franklin

2017-05-01

Surface enhanced Raman scattering (SERS) studies of N-benzoyl glycine (NBG) adsorbed on silver nanoparticles (AgNPs) was studied by experimental and density functional theory (DFT) approach. Single crystals of NBG were prepared using slow evaporation method. The AgNPs were prepared and characterized. The DFT/ B3PW91 method with LanL2DZ basis set was used to optimize the molecular structure of NBG and NBG adsorbed on silver cluster. The calculated and observed vibrational frequencies were assingned on the basis of potential energy distribution calculation. The reduced band gap value was obtained for NBG adsorbed on silver nanoparticles from the frontier molecular orbitals analysis. Natural bond orbital analysis was carried out to inspect the intra-molecular stabilization interactions, which are responsible for the bio activity and nonlinear optical property of the molecule. The spectral analysis was also evidenced that NBG would adsorb tilted orientation on the silver surface over the binding sites such as lone pair electron of N atom in amine group and through phenyl ring π system.

Absorption spectra of PTCDI: A combined UV-Vis and TD-DFT study

NASA Astrophysics Data System (ADS)

Oltean, Mircea; Calborean, Adrian; Mile, George; Vidrighin, Mihai; Iosin, Monica; Leopold, Loredana; Maniu, Dana; Leopold, Nicolae; Chiş, Vasile

2012-11-01

Absorption spectra of PTCDI (3,4,9,10-perylene-tetracarboxylic-diimide) have been investigated in chloroform, N,N'-dimethylformamide (DMF) and dimethylsulfoxide (DMSO). While no signature of assembled PTCDI molecules is observed in chloroform solution, distinct bands assigned to their aggregation have been identified in DMF and DMSO solutions. PTCDI monomers show very similar absorption patterns in chloroform and DMSO solutions. Experimental data, including the vibronic structure of the absorption spectra were explained based on the Franck-Condon approximation and quantum chemical results obtained at PBE0-DCP/6-31+G(d,p) level of theory. Geometry optimization of the first excited state leads to a nice agreement between the calculated adiabatic transition energies and experimental data.

BK/TD models for analyzing in vitro impedance data on cytotoxicity.

PubMed

Teng, S; Barcellini-Couget, S; Beaudouin, R; Brochot, C; Desousa, G; Rahmani, R; Pery, A R R

2015-06-01

The ban of animal testing has enhanced the development of new in vitro technologies for cosmetics safety assessment. Impedance metrics is one such technology which enables monitoring of cell viability in real time. However, analyzing real time data requires moving from static to dynamic toxicity assessment. In the present study, we built mechanistic biokinetic/toxicodynamic (BK/TD) models to analyze the time course of cell viability in cytotoxicity assay using impedance. These models account for the fate of the tested compounds during the assay. BK/TD models were applied to analyze HepaRG cell viability, after single (48 h) and repeated (4 weeks) exposures to three hepatotoxic compounds (coumarin, isoeugenol and benzophenone-2). The BK/TD models properly fit the data used for their calibration that was obtained for single or repeated exposure. Only for one out of the three compounds, the models calibrated with a single exposure were able to predict repeated exposure data. We therefore recommend the use of long-term exposure in vitro data in order to adequately account for chronic hepatotoxic effects. The models we propose here are capable of being coupled with human biokinetic models in order to relate dose exposure and human hepatotoxicity. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Experimental and theoretical investigation on the molecular structure, spectroscopic and electric properties of 2,4-dinitrodiphenylamine, 2-nitro-4-(trifluoromethyl)aniline and 4-bromo-2-nitroaniline

NASA Astrophysics Data System (ADS)

Hernández-Paredes, Javier; Hernández-Negrete, Ofelia; Carrillo-Torres, Roberto C.; Sánchez-Zeferino, Raúl; Duarte-Moller, Alberto; Alvarez-Ramos, Mario E.

2015-10-01

2,4-Dinitrodiphenylamine (I), 2-nitro-4-(trifluoromethyl)aniline (II) and 4-bromo-2-nitroaniline (III) have been investigated by DFT and experimental FTIR, Raman and UV-Vis spectroscopies. The gas-phase molecular geometries were consistent with similar compounds already reported in the literature. From the vibrational analysis, the main functional groups were identified and their absorption bands were assigned. Some differences were found between the calculated and the experimental UV-Vis spectra. These differences were analyzed and explained in terms of the TD-DFT/B3LYP limitations, which were mainly attributed to charge-transfer (CT) effects. These findings were in agreement with previous works, which reported that TD-DFT/B3LYP calculations diverge from experimental results when the electronic transitions involve CT. Despite this, TD-DFT/B3LYP calculations provided satisfactory results and a detailed description of the electronic transitions involved in the absorption bands of the UV-Vis spectra. In terms of the NLO properties, it was found that compound (I) is a good candidate for NLO applications and deserves further study due to its good β values. However, the β values for compounds (II) and (III) were negatively affected compared to those found on o-nitroaniline.

Experimental and theoretical investigation on the molecular structure, spectroscopic and electric properties of 2,4-dinitrodiphenylamine, 2-nitro-4-(trifluoromethyl)aniline and 4-bromo-2-nitroaniline.

PubMed

Hernández-Paredes, Javier; Hernández-Negrete, Ofelia; Carrillo-Torres, Roberto C; Sánchez-Zeferino, Raúl; Duarte-Moller, Alberto; Alvarez-Ramos, Mario E

2015-10-05

2,4-Dinitrodiphenylamine (I), 2-nitro-4-(trifluoromethyl)aniline (II) and 4-bromo-2-nitroaniline (III) have been investigated by DFT and experimental FTIR, Raman and UV-Vis spectroscopies. The gas-phase molecular geometries were consistent with similar compounds already reported in the literature. From the vibrational analysis, the main functional groups were identified and their absorption bands were assigned. Some differences were found between the calculated and the experimental UV-Vis spectra. These differences were analyzed and explained in terms of the TD-DFT/B3LYP limitations, which were mainly attributed to charge-transfer (CT) effects. These findings were in agreement with previous works, which reported that TD-DFT/B3LYP calculations diverge from experimental results when the electronic transitions involve CT. Despite this, TD-DFT/B3LYP calculations provided satisfactory results and a detailed description of the electronic transitions involved in the absorption bands of the UV-Vis spectra. In terms of the NLO properties, it was found that compound (I) is a good candidate for NLO applications and deserves further study due to its good β values. However, the β values for compounds (II) and (III) were negatively affected compared to those found on o-nitroaniline. Copyright © 2015 Elsevier B.V. All rights reserved.

Ab initio DFT+U study of He atom incorporation into UO(2) crystals.

PubMed

Gryaznov, Denis; Heifets, Eugene; Kotomin, Eugene

2009-09-07

We present and discuss results of the density functional theory (DFT) for perfect UO(2) crystals with He atoms in octahedral interstitial positions therein. We have calculated basic bulk crystal properties and He incorporation energies into the low temperature anti-ferromagnetic UO(2) phase using several exchange-correlation functionals within the spin-polarized local density (LDA) and generalized gradient (GGA) approximations. In all DFT calculations we included the on-site correlation corrections using the Hubbard model (DFT+U approach). We analysed a potential crystalline symmetry reduction from tetragonal down to orthorhombic structure and confirmed the presence of the Jahn-Teller effect in a perfect UO(2). We discuss also the problem of a conducting electronic state arising when He is placed into a tetragonal antiferromagnetic phase of UO(2) commonly used in defect modelling. Consequently, we found a specific monoclinic lattice distortion which allowed us to restore the semiconducting state and properly estimate He incorporation energies. Unlike the bulk properties, the He incorporation energy strongly depends on several factors, including the supercell size, the use of spin polarization, the exchange-correlation functionals and on-site correlation corrections. We compare our results for the He incorporation with the previous shell model and ab initio DFT calculations.

Detailed solvent, structural, quantum chemical study and antimicrobial activity of isatin Schiff base

NASA Astrophysics Data System (ADS)

Brkić, Dominik R.; Božić, Aleksandra R.; Marinković, Aleksandar D.; Milčić, Miloš K.; Prlainović, Nevena Ž.; Assaleh, Fathi H.; Cvijetić, Ilija N.; Nikolić, Jasmina B.; Drmanić, Saša Ž.

2018-05-01

The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.

Doped phosphorene for hydrogen capture: A DFT study

NASA Astrophysics Data System (ADS)

Zhang, Hong-ping; Hu, Wei; Du, Aijun; Lu, Xiong; Zhang, Ya-ping; Zhou, Jian; Lin, Xiaoyan; Tang, Youhong

2018-03-01

Hydrogen capture and storage is the core of hydrogen energy application. With its high specific surface area, direct bandgap, and variety of potential applications, phosphorene has attracted much research interest. In this study, density functional theory (DFT) is utilized to study the interactions between doped phosphorenes and hydrogen molecules. The effects of different dopants and metallic or nonmetallic atoms on phosphorene/hydrogen interactions is systematically studied by adsorption energy, electron density difference, partial density of states analysis, and Hirshfeld population. Our results indicate that the metallic dopants Pt, Co, and Ni can help to improve the hydrogen capture ability of phosphorene, whereas the nonmetallic dopants have no effect on it. Among the various metallic dopants, Pt performs very differently, such that it can help to dissociate H2 on phosphorene. Specified doped phosphorene could be a promising candidate for hydrogen storage, with behaviors superior to those of intrinsic graphene sheet.

Development and evaluation of the TD97 measles virus vaccine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuki, K.; Morita, M.; Katoh, M.

1990-11-01

The TD97 strain vaccine virus was prepared from the Tanabe strain measles virus by low-temperature passages in primary cell cultures and ultraviolet (UV) mutagenesis. The TD97 strain exhibited the following characteristics: highly temperature sensitive, neither multiplying nor forming any plaques at 40 degrees C in Vero cells; genetically stable, maintaining high temperature sensitivity after ten successive passages in CE cells at 30 degrees C or 35 degrees C; and M proteins of this virus about 1 KD slower in mobility in SDS-PAGE than that of the Tanabe strain. The TD97 strain was further confirmed to be attenuated by an inoculationmore » test into primate brain. In field trials, 752 healthy children were inoculated with a live virus vaccine prepared with this strain, and the following results were obtained: the seroconversion rate was 97% (517/533), and the average HI antibody titer was 2(5.2). An antibody-increasing effect was also observed in children who were initially seropositive. In children who seroconverted, the rates of fever were 15.7% (55/351) for 37.5 degrees C or higher and 4.0% (14/351) for 39 degrees C or higher. The rash rate was 7.7% (27/351), and the incidence of local reaction was 5.4% (19/351). The TD97 strain is thus considered to be suitable in use for an attenuated measles vaccine.« less

Synthesis and spectroscopical study of rhodanine derivative using DFT approaches

NASA Astrophysics Data System (ADS)

Anbarasan, R.; Dhandapani, A.; Manivarman, S.; Subashchandrabose, S.; Saleem, H.

2015-07-01

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of (E)-5-benzylidene-2-thioxothiazolidine-4-one (E5BTTO) have been investigated experimentally and theoretically based on Density Functional Theory (DFT) approach. The FT-Raman and FT-IR spectra of E5BTTO were recorded in solid phase. Theoretical calculations were performed at the DFT level using the Gaussian 03 program. The experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumber by their Total Energy Distribution (TED). The results of the calculation were applied to simulate infrared and raman spectra of the title compound which showed good agreement with the observed spectra. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Stability arising from hyperconjugative interactions leading to its NLO activity and charge delocalization were analyzed using Natural Bond Orbital (NBO) analysis.

Semiempirical modeling of Ag nanoclusters: New parameters for optical property studies enable determination of double excitation contributions to plasmonic excitation

DOE PAGES

Gieseking, Rebecca L.; Ratner, Mark A.; Schatz, George C.

2016-06-03

Quantum mechanical studies of Ag nanoclusters have shown that plasmonic behavior can be modeled in terms of excited states where collectivity among single excitations leads to strong absorption. However, new computational approaches are needed to provide understanding of plasmonic excitations beyond the single-excitation level. We show that semiempirical INDO/CI approaches with appropriately selected parameters reproduce the TD-DFT optical spectra of various closed-shell Ag clusters. The plasmon-like states with strong optical absorption comprise linear combinations of many singly excited configurations that contribute additively to the transition dipole moment, whereas all other excited states show significant cancellation among the contributions to themore » transition dipole moment. The computational efficiency of this approach allows us to investigate the role of double excitations at the INDO/SDCI level. The Ag cluster ground states are stabilized by slight mixing with doubly excited configurations, but the plasmonic states generally retain largely singly excited character. The consideration of double excitations in all cases improves the agreement of the INDO/CI absorption spectra with TD-DFT, suggesting that the SDCI calculation effectively captures some of the ground-state correlation implicit in DFT. Furthermore, these results provide the first evidence to support the commonly used assumption that single excitations are in many cases sufficient to describe the optical spectra of plasmonic excitations quantum mechanically.« less

Computational study of AuSi{sub n} (n=1-9) nanoalloy clusters invoking DFT based descriptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ranjan, Prabhat; Kumar, Ajay; Chakraborty, Tanmoy, E-mail: tanmoy.chakraborty@jaipur.manipal.edu, E-mail: tanmoychem@gmail.com

2016-04-13

Nanoalloy clusters formed between Au and Si are topics of great interest today from both scientific and technological point of view. Due to its remarkable catalytic, electronic, mechanical and magnetic properties Au-Si nanoalloy clusters have extensive applications in the field of microelectronics, catalysis, biomedicine, and jewelry industry. Density Functional Theory (DFT) is a new paradigm of quantum mechanics, which is very much popular to study the electronic properties of materials. Conceptual DFT based descriptors have been invoked to correlate the experimental properties of nanoalloy clusters. In this venture, we have systematically investigated AuSi{sub n} (n=1-9) nanoalloy clusters in the theoreticalmore » frame of the B3LYP exchange correlation. The experimental properties of AuSi{sub n} (n=1-9) nanoalloy clusters are correlated in terms of DFT based descriptors viz. HOMO-LUMO gap, Electronegativity (χ), Global Hardness (η), Global Softness (S) and Electrophilicity Index (ω). The calculated HOMO-LUMO gap exhibits interesting odd-even alteration behaviour, indicating that even numbered clusters possess higher stability as compare to their neighbour odd numbered clusters. This study also reflects a very well agreement between experimental bond length and computed data.« less

Synthesis, characterization, and DFT studies of a new chiral ionic liquid from (S)-1-phenylethylamine

NASA Astrophysics Data System (ADS)

Cui, Shuya; Wang, Tao; Hu, Xiaoli

2014-12-01

A new chiral ionic liquid was synthesized from (S)-1-phenylethylamine and it was studied by IR, Raman, polarimetry, NMR and X-ray crystal diffraction. Its vibrational spectral bands are precisely ascribed to the studied structure with the aid of DFT theoretical calculations. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from IR and Raman spectra are assigned based on the results of the theoretical calculations by the DFT-B3LYP method at 6-311G(d,p) level. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The vibrational modes assignments were performed by using the animation option of GaussView5.0 graphical interface for Gaussian program.

First-Principles DFT Studies of the Vibrational Properties of Germanene Nanoflakes

NASA Astrophysics Data System (ADS)

Richardson, Steven; Peroparde, Borja; Andrade, Xavier; Aspuru-Guzik, AláN.

The germanium analogue of graphene, germanene, is a potentially new atomically thin quantum material which theory predicts will possess unique transport and optoelectronic properties. Recently, there have been a number of experimental efforts to successfully grow two-dimensional films of germanene on noble metal substrates using molecular beam epitaxy. In addition to this top-down approach of synthesizing large scale films of germanene, we would like to focus on a bottom-up approach where nanoflakes of germanene could be used as molecular seeds or precursors to grow large films of two-dimensional germanene. A knowledge of their infrared and Raman spectra will be critical for characterizing these germanene nanoflakes in future experiments. In this work we used density-functional theory (DFT) to compute the vibrational spectra of a selected number of lower order germanene nanoflakes (e.g. hexagermabenzene, germa-naphthalene, germa-anthracene, germa-phenanthrene, germa-pyrene, germa-tetracene, and germa-pentacene). Our DFT studies also reveal that these germanene nanoflakes are vibrationally stable with buckling of these molecules from their normal two-dimensional planar forms which exist in graphene nanoflakes. This research is supported by NSF Grant No. DMR-1231319.

Metallographic examination of TD-nickel base alloys. [thermal and chemical etching technique evaluation

NASA Technical Reports Server (NTRS)

Kane, R. D.; Petrovic, J. J.; Ebert, L. J.

1975-01-01

Techniques are evaluated for chemical, electrochemical, and thermal etching of thoria dispersed (TD) nickel alloys. An electrochemical etch is described which yielded good results only for large grain sizes of TD-nickel. Two types of thermal etches are assessed for TD-nickel: an oxidation etch and vacuum annealing of a polished specimen to produce an etch. It is shown that the first etch was somewhat dependent on sample orientation with respect to the processing direction, the second technique was not sensitive to specimen orientation or grain size, and neither method appear to alter the innate grain structure when the materials were fully annealed prior to etching. An electrochemical etch is described which was used to observe the microstructures in TD-NiCr, and a thermal-oxidation etch is shown to produce better detail of grain boundaries and to have excellent etching behavior over the entire range of grain sizes of the sample.

Design of donor-acceptor copolymers for organic photovoltaic materials: a computational study.

PubMed

Turan, Haydar Taylan; Kucur, Oğuzhan; Kahraman, Birce; Salman, Seyhan; Aviyente, Viktorya

2018-01-31

80 different push-pull type organic chromophores which possess Donor-Acceptor (D-A) and Donor-Thiophene-Acceptor-Thiophene (D-T-A-T) structures have been systematically investigated by means of density functional theory (DFT) and time-dependent DFT (TD-DFT) at the B3LYP/6-311G* level. The introduction of thiophene (T) in the chain has allowed us to monitor the effect of π-spacers. Benchmark studies on the methodology have been carried out to predict the HOMO and LUMO energies and optical band gaps of the D-A systems accurately. The HOMO and LUMO energies and transition dipoles are seen to converge for tetrameric oligomers, and the latter have been used as optimal chain length to evaluate various geometrical and optoelectronic properties such as bond length alternations, distortion energies, frontier molecular orbital energies, reorganization energies and excited-state vertical transition of the oligomers. Careful analysis of our findings has allowed us to propose potential donor-acceptor couples to be used in organic photovoltaic cells.

Ferrocene-isocoumarin conjugated molecules: synthesis, structural characterization, electronic properties, and DFT-TDDFT computational study.

PubMed

Peng, Ye-Dong; Zhou, Lin-Sen; Chen, Li-Li; Ma, Lu; Zhao, Yue; Zhang, Wen-Wei; Zuo, Jing-Lin

2015-08-28

Two ferrocene-isocoumarin conjugated molecules, methyl 3-ferrocenyl-1-oxo-1H-isochromene-6-carboxylate () and 3,8-bisferrocenylpyrano[3,4-g]isochromene-1,6-dione (), have been synthesized through the acid-prompted regioselective oxidative cyclization from dimethyl 2-(ferrocenylethynyl)terephthalate () and dimethyl 2,5-bis(ferrocenylethynyl)terephthalate (), respectively. Single-crystal X-ray diffraction, together with the density functional theory (DFT) calculations, shows that the ferrocene-isocoumarin conjugated compounds display better coplanarity than the corresponding ferrocenylethynyl terephthalates. All the compounds exhibit characteristic MLCT, ICT and π-π* transitions in the UV-visible range in solution, and and show higher oscillator strength of the absorption than and , which are verified by time-dependent DFT (TDDFT) theoretical calculations. The electrochemical properties are studied by cyclic voltammetry (CV), which are also in accord with the theoretical calculations.

SERS and DFT study of p-hydroxybenzoic acid adsorbed on colloidal silver particles.

PubMed

Chen, Y; Chen, S J; Li, S; Wei, J J

2015-10-16

In this study, normal Raman spectra of p—hydroxybenzoic acid (PHBA) powder and its surface—enhanced Raman scattering (SERS) spectra in silver colloidal solutions were measured under near infrared excitation conditions. In theoretical calculation, two models of PHBA adsorbed on the surfaces of silver nanoparticles were established. The Raman frequencies of these two models using density functional theory (DFT) method were calculated, and compared with the experimental results. It was found that the calculated Raman frequencies were in good agreement with experimental values, which indicates that there are two enhanced mechanism physical (electromagnetic, EM) enhancement and chemical (charge—transfer, CT) enhancement, in silver colloidal solutions regarding SERS effect. Furthermore, from high—quality SERS spectrum of PHBA obtained in silver colloids, we inferred that PHBA molecules in silver colloids adsorb onto the metal surfaces through carboxyl at a perpendicular orientation. The combination of SERS spectra and DFT calculation is thus useful for studies of the adsorption—orientation of a molecule on a metal colloid.

Uranyl extraction by N,N-dialkylamide ligands studied using static and dynamic DFT simulations.

PubMed

Sieffert, Nicolas; Wipff, Georges

2015-02-14

We report DFT static and dynamic studies on uranyl complexes [UO(2)(NO(3))x(H(2)O)(y)L(z)](2-x) involved in the uranyl extraction from water to an "oil" phase (hexane) by an amide ligand L (N,N-dimethylacetamide). Static DFT results "in solution" (continuum SMD models for water and hexane) predict that the stepwise formation of [UO(2)(NO(3))(2)L(2)] from the UO(2)(H(2)O)(5)(2+) species is energetically favourable, and allow us to compare cis/trans isomers of penta- and hexa-coordinated complexes and key intermediates in the two solvents. DFT-MD simulations of [UO(2)(NO(3))(2)L(2)], [UO(2)(NO(3))(2)(H(2)O)L(2)], and [UO(2)(NO(3))(H(2)O)L(2)](+) species in explicit solvent environments (water, hexane, or the water/hexane interface) represented at the MM or full-DFT level reveal a versatile solvent dependent binding mode of nitrates, also evidenced by metadynamics simulations. In water and at the interface, the latter exchange from bi- to monodentate, via in plane rotational motions in some cases. Remarkably, structures of complexes at the interface are more "water-like" than gas phase- or hexane-like. Thus, the order of U-O(NO(3))/U-O(L) bond distances observed in the gas phase (U-O(nit) < U-OL) is inverted at the interface and in water. Overall, the results are consistent with the experimental observation of uranyl extraction from nitric acid solutions by amide analogues (bearing "fatty" substituents), and allow us to propose possible extraction mechanisms, involving complexation of L "right at the interface". They also point to the importance of the solvent environment and the dynamics on the structure and stability of the complexes.

Spectroscopic (FT-IR and UV-Vis) and theoretical (HF and DFT) investigation of 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline

NASA Astrophysics Data System (ADS)

Ceylan, Ümit; Tarı, Gonca Özdemir; Gökce, Halil; Ağar, Erbil

2016-04-01

Crystal structure of the title compound, 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline, C13H12N2O2S, has been synthesized and characterized by FT-IR and UV-Vis spectrum. The compound crystallized in the monoclinic space group P 21/c with a = 11.3578 (4) Å, b = 7.4923 (2) Å, c = 14.9676 (6) Å and β = 99.589 (3)° and Z = 4 in the unit cell. The molecular geometry was also calculated using the Gaussian 03 software and structure was optimized using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set in ground state. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311++G(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. It was seen that the optimized structure was in excellent agreement with the X-ray crystal structure. The energetic behaviors of the title compound in solvent media were examined using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set applying the polarizable continuum model (PCM). In addition, the molecular orbitals (FMOs) analysis, molecular electrostatic potential (MEP), nonlinear optical and thermodynamic properties of the title compound were performed using the same methods with the 6-311++G(d,p) basis set.

A combined spectroscopic and TDDFT study of natural dyes extracted from fruit peels of Citrus reticulata and Musa acuminata for dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Prima, Eka Cahya; Hidayat, Novianto Nur; Yuliarto, Brian; Suyatman; Dipojono, Hermawan Kresno

2017-01-01

This study reports the novel spectroscopic investigations and enhanced the electron transfers of Citrus reticulata and Musa acuminata fruit peels as the photosensitizers for the dye-sensitized solar cells. The calculated TD-DFT-UB3LYP/6-31 + G(d,p)-IEFPCM(UAKS), experiment spectra of ultra-violet-visible spectroscopy, and Fourier transform infrared spectroscopy studies indicate the main flavonoid (hesperidin and gallocatechin) structures of the dye extracts. The optimized flavonoid structures are calculated using Density functional theory (DFT) at 6-31 + G(d,p) level. The rutinosyl group of the hesperidin pigment (Citrus reticulata) will be further investigated compared to the gallocatechin (Musa acuminata) pigment. The acidity of the dye extract is treated by adding 2% acetic acid. The energy levels of the HOMO-LUMO dyes are measured by a combined Tauc plot and cyclic voltammetry contrasted with the DFT data. The electrochemical impedance spectroscopy will be performed to model the dye electron transfer. As for the rutinosyl group presence and the acidic treatment, the acidified Citrus reticulata cell under continuous light exposure of 100 mW·cm- 2 yields a short-circuit current density (Jsc) of 3.23 mA/cm2, a photovoltage (Voc) of 0.48 V, and a fill factor of 0.45 corresponding to an energy conversion efficiency (η) of 0.71% because the shifting down HOMO-LUMO edges and the broadening dye's absorbance evaluated by a combined spectroscopic and TD-DFT method. The result also leads to the longest diffusion length of 32.2 μm, the fastest electron transit of 0.22 ms, and the longest electron lifetime of 4.29 ms.

SSCC TD: A Serial and Simultaneous Configural-Cue Compound Stimuli Representation for Temporal Difference Learning

PubMed Central

Mondragón, Esther; Gray, Jonathan; Alonso, Eduardo; Bonardi, Charlotte; Jennings, Dómhnall J.

2014-01-01

This paper presents a novel representational framework for the Temporal Difference (TD) model of learning, which allows the computation of configural stimuli – cumulative compounds of stimuli that generate perceptual emergents known as configural cues. This Simultaneous and Serial Configural-cue Compound Stimuli Temporal Difference model (SSCC TD) can model both simultaneous and serial stimulus compounds, as well as compounds including the experimental context. This modification significantly broadens the range of phenomena which the TD paradigm can explain, and allows it to predict phenomena which traditional TD solutions cannot, particularly effects that depend on compound stimuli functioning as a whole, such as pattern learning and serial structural discriminations, and context-related effects. PMID:25054799

Inertial Navigation System for India's Reusable Launch Vehicle-Technology Demonstrator (RLV-TD HEX) Mission

NASA Astrophysics Data System (ADS)

Umadevi, P.; Navas, A.; Karuturi, Kesavabrahmaji; Shukkoor, A. Abdul; Kumar, J. Krishna; Sreekumar, Sreejith; Basim, A. Mohammed

2017-12-01

This work presents the configuration of Inertial Navigation System (INS) used in India's Reusable Launch Vehicle-Technology Demonstrator (RLV-TD) Program. In view of the specific features and requirements of the RLV-TD, specific improvements and modifications were required in the INS. A new system was designed, realised and qualified meeting the mission requirements of RLV-TD, at the same time taking advantage of the flight heritage attained in INS through various Launch vehicle Missions of the country. The new system has additional redundancy in acceleration channel, in-built inclinometer based bias update scheme for acceleration channels and sign conventions as employed in an aircraft. Data acquisition in micro cycle periodicity (10 ms) was incorporated which was required to provide rate and attitude information at higher sampling rate for ascent phase control. Provision was incorporated for acquisition of rate and acceleration data with high resolution for aerodynamic characterisation and parameter estimation. GPS aided navigation scheme was incorporated to meet the stringent accuracy requirements of the mission. Navigation system configuration for RLV-TD, specific features incorporated to meet the mission requirements, various tests carried out and performance during RLV-TD flight are highlighted.

Synthesis, characterization, and DFT studies of a new chiral ionic liquid from (S)-1-phenylethylamine.

PubMed

Cui, Shuya; Wang, Tao; Hu, Xiaoli

2014-12-10

A new chiral ionic liquid was synthesized from (S)-1-phenylethylamine and it was studied by IR, Raman, polarimetry, NMR and X-ray crystal diffraction. Its vibrational spectral bands are precisely ascribed to the studied structure with the aid of DFT theoretical calculations. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from IR and Raman spectra are assigned based on the results of the theoretical calculations by the DFT-B3LYP method at 6-311G(d,p) level. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies.The vibrational modes assignments were performed by using the animation option of GaussView5.0 graphical interface for Gaussian program. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of a HTS transceiver sub-system for 3G mobile communication TD-SCDMA base station

NASA Astrophysics Data System (ADS)

Zhang, Xueqiang; He, Xiaofeng; Wang, Yuehui; Duan, Tao; Wang, Guizhen; Zhang, Yan; Li, Chunguang; Zhang, Qiang; Li, Hong; He, Yusheng

2010-02-01

A prototype of a high temperature superconducting (HTS) transceiver sub-system for applications in a TD-SCDMA, one of the third generation (3G) communication standards, base station has been developed. Both the HTS sub-system and the conventional counterpart have been implemented into a TD-SCDMA commercial communication network and comparison test studies were carried out. The measured results showed that the HTS sub-system could remarkably improve the RF performance of both transmitting and receiving chains.

Teaching Inorganic Photophysics and Photochemistry with Three Ruthenium(II) Polypyridyl Complexes: A Computer-Based Exercise

ERIC Educational Resources Information Center

Garino, Claudio; Terenzi, Alessio; Barone, Giampaolo; Salassa, Luca

2016-01-01

Among computational methods, DFT (density functional theory) and TD-DFT (time-dependent DFT) are widely used in research to describe, "inter alia," the optical properties of transition metal complexes. Inorganic/physical chemistry courses for undergraduate students treat such methods, but quite often only from the theoretical point of…

Binaphthyl-containing Schiff base complexes with carboxyl groups for dye sensitized solar cell: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Tsaturyan, Arshak; Machida, Yosuke; Akitsu, Takashiro; Gozhikova, Inna; Shcherbakov, Igor

2018-06-01

We report on synthesis and characterization of binaphthyl containing Schiff base Ni(II), Cu(II), and Zn(II) complexes as promising photosensitizers for dye-sensitized solar cells (DSSC). Based on theoretical and experimental data, the possibility of their application in DSSC was confirmed. To our knowledge, we find dye performance of complex is steric and rigid structure widely spread to efficiency. The spatial and electronic structures of the complexes were studied by means of the quantum chemical modeling using DFT and TD-DFT approaches. The adsorption energies of the complexes on TiO2 cluster were calculated and appeared to be very close in value. The Zn(II) complex has the biggest value of molar extinction.

Quantitative DFT modeling of product concentration in organometallic reactions: Cu-mediated pentafluoroethylation of benzoic acid chlorides as a case study.

PubMed

Jover, Jesús

2017-11-08

DFT calculations are widely used for computing properties, reaction mechanisms and energy profiles in organometallic reactions. A qualitative agreement between the experimental and the calculated results seems to usually be enough to validate a computational methodology but recent advances in computation indicate that a nearly quantitative agreement should be possible if an appropriate DFT study is carried out. Final percent product concentrations, often reported as yields, are by far the most commonly reported properties in experimental metal-mediated synthesis studies but reported DFT studies have not focused on predicting absolute product amounts. The recently reported stoichiometric pentafluoroethylation of benzoic acid chlorides (R-C 6 H 4 COCl) with [(phen)Cu(PPh 3 )C 2 F 5 ] (phen = 1,10-phenanthroline, PPh 3 = triphenylphosphine) has been used as a case study to check whether the experimental product concentrations can be reproduced by any of the most popular DFT approaches with high enough accuracy. To this end, the Gibbs energy profile for the pentafluoroethylation of benzoic acid chloride has been computed using 14 different DFT methods. These computed Gibbs energy profiles have been employed to build kinetic models predicting the final product concentration in solution. The best results are obtained with the D3-dispersion corrected B3LYP functional, which has been successfully used afterwards to model the reaction outcomes of other simple (R = o-Me, p-Me, p-Cl, p-F, etc.) benzoic acid chlorides. The product concentrations of more complex reaction networks in which more than one position of the substrate may be activated by the copper catalyst (R = o-Br and p-I) are also predicted appropriately.

Final Phase Flight Performance and Touchdown Time Assessment of TDV in RLV-TD HEX-01 Mission

NASA Astrophysics Data System (ADS)

Yadav, Sandeep; Jayakumar, M.; Nizin, Aziya; Kesavabrahmaji, K.; Shyam Mohan, N.

2017-12-01

RLV-TD HEX-01 mission was configured as a precursor flight to actual two stages to orbit vehicle. In this mission RLV-TD was designed as a two stage vehicle for demonstrating the hypersonic flight of a winged body vehicle at Mach No. 5. One of the main objectives of this mission was to generate data for better understanding of new technologies required to design the future vehicle. In this mission, the RLV-TD vehicle was heavily instrumented to get data related to performance of different subsystems. As per the mission design, RLV-TD will land in sea after flight duration of 700 s and travelling a distance of nearly 500 km in Bay of Bengal from the launch site for a nominal trajectory. The visibility studies for telemetry data of vehicle for the nominal and off nominal trajectories were carried out. Based on that, three ground stations were proposed for the telemetry data reception (including one in sea). Even with this scheme it was seen that during the final phase of the flight there will not be any ground station visible to the flight due to low elevation. To have the mission critical data during final phase of the flight, telemetry through INSAT scheme was introduced. During the end of the mission RLV-TD will be landing in the sea on a hypothetical runway. To know the exact time of touchdown for the flight in sea, there was no direct measurement available. Simultaneously there were all chances of losing ground station visibility just before touchdown, making it difficult to assess flight performance during that phase. In this work, telemetry and instrumentation scheme of RLV-TD HEX-01 mission is discussed with an objective to determine the flight performance during the final phase. Further, using various flight sensor data the touchdown time of TDV is assessed for this mission.

First principle study of a potential bioactive molecule with tetrahydroisoquinoline, carbothiomide and adamantane scaffolds

NASA Astrophysics Data System (ADS)

Al-Shehri, Mona M.; Al-Majed, Abdul-Rahman A.; Aljohar, Haya I.; El-Emam, Ali A.; Pathak, Shilendra K.; Sachan, Alok K.; Prasad, Onkar; Sinha, Leena

2017-09-01

The FT-Raman and FT-IR spectra of N-(adamantan-1-yl)-1,2,3,4-tetrahydroisoquinoline-2-carbothioamide were recorded and investigated. The DFT/M06-2X/6-311++G(d,p) method was used to compute the vibrational wavenumbers. The effect of solvents (water, carbon tetrachloride and chloroform) on the dipole moment and polarizability has been evaluated. UV-Vis spectrum of the title compound was recorded and compared with the theoretical spectrum calculated by TD-DFT approach. To investigate the movement of electrons within the system when excited, the difference of the excited and ground state densities has also been plotted. The molecular docking studies reveals that the investigated compound may exhibit HIV-1 Protease inhibitory activity.

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

PubMed

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). Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

Sulphonamides as corrosion inhibitor: Experimental and DFT studies

NASA Astrophysics Data System (ADS)

Obayes, Hasan R.; Al-Amiery, Ahmed A.; Alwan, Ghadah H.; Abdullah, Thamer Adnan; Kadhum, Abdul Amir H.; Mohamad, Abu Bakar

2017-06-01

Inhibitors are synthetic and natural molecules have various functional groups like double or triple bonds and heteroatoms; N, O or S, which permit adsorption onto the MS (metal surface). These inhibitors have the ability to adsorb onto the MS and block the active site that was reducing the corrosion rate. Inhibition efficiencies of the investigated compounds: Sulfacetamide (SAM), Sulfamerazine (SMR), Sulfapyridine (SPY) and Sulfathiazole (STI), as inhibitors in corrosive solution were evaluated based on weight loss technique. Nitro and Amino groups were chosen for the study of the substituted reaction of four corrosion inhibitor compounds: SAM, SMR, SPY and STI, theoretically utilizing the thickness capacities hypothesis DFT (density functions theory) method with the level [rB3LYP/6-311G(d,p)]. Our research demonstrated that the nitration of studied molecules lead to a diminishing in inhibition efficiencies, group lead to an increase in inhibition efficiency. Compared with corrosion inhibitor molecules these results gave a significant improvement in inhibition efficiency for corrosion inhibitor molecules.

Synthesis, spectral and quantum chemical studies on NO-chelating sulfamonomethoxine-cyclophosph(V)azane and its Er(III) complex.

PubMed

Alaghaz, Abdel-Nasser M A; Ammar, Reda A A; Koehler, Gottfried; Wolschann, Karl Peter; El-Gogary, Tarek M

2014-07-15

Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of novel ethane-1,2-diol-dichlorocyclophosph(V)azane of sulfamonomethoxine (L), and its binuclear Er(III) complex. Different tautomers of the ligand were optimized at the ab initio DFT level. Keto-form structure is about 15.8 kcal/mol more stable than the enol form (taking zpe correction into account). Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which show good agreement with measured electronic spectra. The structures of the novel isolated products are proposed based on elemental analyses, IR, UV-VIS, (1)H NMR, (31)P NMR, SEM, XRD spectra, effective magnetic susceptibility measurements and thermogravimetric analysis (TGA). Copyright © 2014 Elsevier B.V. All rights reserved.

Quantum mechanical and spectroscopic (FT-IR, 13C, 1H NMR and UV) investigations of 2-(5-(4-Chlorophenyl)-3-(pyridin-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole by DFT method

NASA Astrophysics Data System (ADS)

Diwaker

2014-07-01

The electronic, NMR, vibrational, structural properties of a new pyrazoline derivative: 2-(5-(4-Chlorophenyl)-3-(pyridine-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole has been studied using Gaussian 09 software package. Using VEDA 4 program we have reported the PED potential energy distribution of normal mode of vibrations of the title compound. We have also reported the 1H and 13C NMR chemical shifts of the title compound using B3LYP level of theory with 6-311++G(2d,2p) basis set. Using time dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, electronic spectrum of the title compound has been studied and reported. NBO analysis and MEP surface mapping has also been calculated and reported using ab initio methods.

FT-IR and DFT study of lemon peel

NASA Astrophysics Data System (ADS)

Berezin, K. V.; Likhter, A. M.; Shagautdinova, I. T.; Chernavina, M. L.; Novoselova, A. V.

2017-03-01

Experimental FT-IR spectra of lemon peel are registered in the 650 - 3800 cm-1 range. The influence of peel artificial and natural dehydration on its vibrational spectrum is studied. The colored outer surface of lemon peel is proved not to have a significant impact on FT-IR spectrum. It is determined that only dehydration processes affect the FT-IR vibrational spectrum of the peel when a lemon is stored for 28 days under natural laboratory conditions. Polymer molecule models for dietary fibers, such as cellulose, hemicellulose, pectin, lignin, as well as hesperidin - flavonoid glycoside, and free moisture cluster are developed within the framework of DFT/B3LYP/6-31G(d) theoretical method. By implementing supramolecular approach, modeling of the vibrational FT-IR spectrum of lemon peel is carried out and its detailed theoretical interpretation is presented.

Theoretical Study of Effect of Introducing π-Conjugation on Efficiency of Dye-Sensitized Solar Cell.

PubMed

Lee, Geon Hyeong; Kim, Young Sik

2018-09-01

In this study, phenoxazine (PXZ)-based dye sensitizers with triphenylamine (TPA) as a dual-electron donor and thiophen and benzothiadiazole (BTD) or 4,7-diethynylbenzo[c][1,2,5]thiadiazole (DEBT) as an electron acceptor (dye1, dye2, and dye3) were designed and investigated. dye3 can significantly stabilize the lowest unoccupied molecular orbital (LUMO) energy level of an organic dye. We used density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations to better understand the factors responsible for the photovoltaic performance. The absorption spectrum of the dyes showed different forms because of the different energy levels of the molecular orbital (MO) of each dye and the intramolecular energy transfer (EnT). Among the three dyes, dye3 showed greater red-shift, broader absorption spectra, and higher molar extinction coefficient. These results indicate that adding a withdrawing unit and π-conjugation to a dye can result in good photovoltaic properties for dye-sensitized solar cells (DSSCs).

A computational DFT study of structural transitions in textured solid-fluid interfaces

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Parry, Andrew O.; Kalliadasis, Serafim

2015-11-01

Fluids adsorbed at walls, in capillary pores and slits, and in more exotic, sculpted geometries such as grooves and wedges can exhibit many new phase transitions, including wetting, pre-wetting, capillary-condensation and filling, compared to their bulk counterparts. As well as being of fundamental interest to the modern statistical mechanical theory of inhomogeneous fluids, these are also relevant to nanofluidics, chemical- and bioengineering. In this talk we will show using a microscopic Density Functional Theory (DFT) for fluids how novel, continuous, interfacial transitions associated with the first-order prewetting line, can occur on steps, in grooves and in wedges, that are sensitive to both the range of the intermolecular forces and interfacial fluctuation effects. These transitions compete with wetting, filling and condensation producing very rich phase diagrams even for relatively simple geometries. We will also discuss practical aspects of DFT calculations, and demonstrate how this statistical-mechanical framework is capable of yielding complex fluid structure, interfacial tensions, and regions of thermodynamic stability of various fluid configurations. As a side note, this demonstrates that DFT is an excellent tool for the investigations of complex multiphase systems. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031.

TD-LTE Wireless Private Network QoS Transmission Protection

NASA Astrophysics Data System (ADS)

Zhang, Jianming; Cheng, Chao; Wu, Zanhong

With the commencement of construction of the smart grid, the demand power business for reliability and security continues to improve, the reliability transmission of power TD-LTE Wireless Private Network are more and more attention. For TD-LTE power private network, it can provide different QoS services according to the user's business type, to protect the reliable transmission of business. This article describes in detail the AF module of PCC in the EPC network, specifically introduces set up AF module station and QoS mechanisms in the EPS load, fully considers the business characteristics of the special power network, establishing a suitable architecture for mapping QoS parameters, ensuring the implementation of each QoS business. Through using radio bearer management, we can achieve the reliable transmission of each business on physical channel.

An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV-Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure

NASA Astrophysics Data System (ADS)

Uludağ, Nesimi; Serdaroğlu, Goncagül

2018-03-01

This study examines the synthesis of azocino[4,3-b]indole structure, which constitutes the tetracyclic framework of uleine, dasycarpidoneand tubifolidineas well as ABDE substructure of the strychnosalkaloid family. It has been synthesized by Fischer indolization of 2 and through the cylization of 4 by 2,3-dichlor-5-6-dicyanobenzoquinone (DDQ). 1H and 1C NMR chemical shifts have been predicted with GIAO approach and the calculated chemical shifts show very good agreement with observed shifts. FT-IR spectroscopy is important for the analysis of functional groups of synthesized compounds and we also supported FT-IR vibrational analysis with computational IR analysis. The vibrational spectral analysis was performed at B3LYP level of the theory in both the gas and the water phases and it was compared with the observed IR values for the important functional groups. The DFT calculations have been conducted to determine the most stable structure of the 1,2,3,4,5,6,7-Hexahydro-1,5-methanoazocino [4,3-b] indole (5). The Frontier Molecular Orbital Analysis, quantum chemical parameters, physicochemical properties have been predicted by using the same theory of level in both gas phase and the water phase, at 631 + g** and 6311++g** basis sets. TD- DFT calculations have been performed to predict the UV- Vis spectral analysis for this synthesized molecule. The Natural Bond Orbital (NBO) analysis have been performed at B3LYP level of theory to elucidate the intra-molecular interactions such as electron delocalization and conjugative interactions. NLO calculations were conducted to obtain the electric dipole moment and polarizability of the title compound.

Spectroscopic (FT-IR, FT-Raman and UV-Visible) investigations, NMR chemical shielding anisotropy (CSA) parameters of 2,6-Diamino-4-chloropyrimidine for dye sensitized solar cells using density functional theory.

PubMed

Gladis Anitha, E; Joseph Vedhagiri, S; Parimala, K

2015-02-05

The molecular structure, geometry optimization, vibrational frequencies of organic dye sensitizer 2,6-Diamino-4-chloropyrimidine (DACP) were studied based on Hartree-Fock (HF) and density functional theory (DFT) using B3LYP methods with 6-311++G(d,p) basis set. Ultraviolet-Visible (UV-Vis) spectrum was investigated by time dependent DFT (TD-DFT). Features of the electronic absorption spectrum in the UV-Visible regions were assigned based on TD-DFT calculation. The absorption bands are assigned to transitions. The interfacial electron transfer between semiconductor TiO2 electrode and dye sensitizer DACP is due to an electron injection process from excited dye to the semiconductor's conduction band. The observed and the calculated frequencies are found to be in good agreement. The energies of the frontier molecular orbitals (FMOS) have also been determined. The chemical shielding anisotropic (CSA) parameters are calculated from the NMR analysis, Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

DFT Studies of SN2 Dechlorination of Polychlorinated Biphenyls.

PubMed

Krzemińska, Agnieszka; Paneth, Piotr

2016-06-21

Nucleophilic dechlorination of all 209 PCBs congeners by ethylene glycol anion has been studied theoretically at the DFT level. The obtained Gibbs free energies of activation are in the range 7-22 kcal/mol. The reaction Gibbs free energies indicate that all reactions are virtually irreversible. Due to geometric constrains these reactions undergo rather untypical attack with attacking oxygen atom being nearly perpendicular to the attacked C-Cl bond. The most prone to substitution are chlorine atoms that occupy ortho- (2, 2', 6, 6') positions. These results provide extensive information on the PEG/KOH dependent PCBs degradation. They can also be used in further developments of reaction class transition state theory (RC-TST) for description of complex reactive systems encountered for example in combustion processes.

Diffusional creep and creep degradation in the dispersion-strengthened alloy TD-NiCr

NASA Technical Reports Server (NTRS)

Whittenberger, J. D.

1972-01-01

Dispersoid-free regions were observed in TD-NiCr (Ni-20Cr-2ThO2) after slow strain rate testing in air from 1145 to 1590 K. Formation of the dispersoid-free regions appears to be the result of diffusional creep. The net effect of this creep is the degradation of TD-NiCr to a duplex microstructure. Degradation is further enhanced by the formation of voids and integranular oxidation in the thoria-free regions. These regions apparently provided sites for void formation and oxide growth since the strength and oxidation resistance of Ni-20Cr is much less than Ni-20Cr-2ThO2. This localized oxidation does not appear to reduce the static load bearing capacity of TD-NiCr since long stress rupture lives were observed even with heavily oxidized microstructures. But this oxidation does significantly reduce the ductility and impact resistance of the material. Dispersoid-free bands and voids were also observed for two other dispersion strengthened alloys, TD-NiCrAl and IN-853. Thus, it appears that diffusional creep is charactertistic of dispersion-strengthened alloys and can play a major role in the creep degradation of these materials.

A real-time fluorescent sensor specific to Mg2+: crystallographic evidence, DFT calculation and its use for quantitative determination of magnesium in drinking water.

PubMed

Men, Guangwen; Chen, Chunrong; Zhang, Shitong; Liang, Chunshuang; Wang, Ying; Deng, Mengyu; Shang, Hongxing; Yang, Bing; Jiang, Shimei

2015-02-14

An "off-the-shelf" fluorescence "turn-on" Mg(2+) chemosensor 3,5-dichlorosalicylaldehyde (BCSA) was rationally designed and developed. This proposed sensor works based on Mg(2+)-induced formation of the 2 : 1 BCSA-Mg(2+) complex. The coordination of BSCA to Mg(2+) increases its structural rigidity generating a chelation-enhanced fluorescence (CHEF) effect which was confirmed by single crystal XRD studies of the BSCA-Mg(2+) complex and TD/DFT calculations. This sensor exhibits high sensitivity and selectivity for the quantitative monitoring of Mg(2+) with a wide detection range (0-40 μM), a low detection limit (2.89 × 10(-7) mol L(-1)) and a short response time (<0.5 s). It can also resist the interference from the other co-existing metal ions, especially Ca(2+). Consequently, this fluorescent sensor can be utilized to monitor Mg(2+) in real time within actual samples from drinking water.

Robust 3D DFT video watermarking

NASA Astrophysics Data System (ADS)

Deguillaume, Frederic; Csurka, Gabriela; O'Ruanaidh, Joseph J.; Pun, Thierry

1999-04-01

This paper proposes a new approach for digital watermarking and secure copyright protection of videos, the principal aim being to discourage illicit copying and distribution of copyrighted material. The method presented here is based on the discrete Fourier transform (DFT) of three dimensional chunks of video scene, in contrast with previous works on video watermarking where each video frame was marked separately, or where only intra-frame or motion compensation parameters were marked in MPEG compressed videos. Two kinds of information are hidden in the video: a watermark and a template. Both are encoded using an owner key to ensure the system security and are embedded in the 3D DFT magnitude of video chunks. The watermark is a copyright information encoded in the form of a spread spectrum signal. The template is a key based grid and is used to detect and invert the effect of frame-rate changes, aspect-ratio modification and rescaling of frames. The template search and matching is performed in the log-log-log map of the 3D DFT magnitude. The performance of the presented technique is evaluated experimentally and compared with a frame-by-frame 2D DFT watermarking approach.

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile

NASA Astrophysics Data System (ADS)

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K.; Kant, Rajni; Khajuria, Yugal

2015-04-01

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800 nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity.

A combined spectroscopic and TDDFT study of natural dyes extracted from fruit peels of Citrus reticulata and Musa acuminata for dye-sensitized solar cells.

PubMed

Prima, Eka Cahya; Hidayat, Novianto Nur; Yuliarto, Brian; Suyatman; Dipojono, Hermawan Kresno

2017-01-15

This study reports the novel spectroscopic investigations and enhanced the electron transfers of Citrus reticulata and Musa acuminata fruit peels as the photosensitizers for the dye-sensitized solar cells. The calculated TD-DFT-UB3LYP/6-31+G(d,p)-IEFPCM(UAKS), experiment spectra of ultra-violet-visible spectroscopy, and Fourier transform infrared spectroscopy studies indicate the main flavonoid (hesperidin and gallocatechin) structures of the dye extracts. The optimized flavonoid structures are calculated using Density functional theory (DFT) at 6-31+G(d,p) level. The rutinosyl group of the hesperidin pigment (Citrus reticulata) will be further investigated compared to the gallocatechin (Musa acuminata) pigment. The acidity of the dye extract is treated by adding 2% acetic acid. The energy levels of the HOMO-LUMO dyes are measured by a combined Tauc plot and cyclic voltammetry contrasted with the DFT data. The electrochemical impedance spectroscopy will be performed to model the dye electron transfer. As for the rutinosyl group presence and the acidic treatment, the acidified Citrus reticulata cell under continuous light exposure of 100mW·cm -2 yields a short-circuit current density (J sc ) of 3.23mA/cm 2 , a photovoltage (V oc ) of 0.48V, and a fill factor of 0.45 corresponding to an energy conversion efficiency (η) of 0.71% because the shifting down HOMO-LUMO edges and the broadening dye's absorbance evaluated by a combined spectroscopic and TD-DFT method. The result also leads to the longest diffusion length of 32.2μm, the fastest electron transit of 0.22ms, and the longest electron lifetime of 4.29ms. Copyright © 2016 Elsevier B.V. All rights reserved.

Proton-transfer reaction mass spectrometry (PTRMS) in combination with thermal desorption (TD) for sensitive off-line analysis of volatiles.

PubMed

Crespo, Elena; Devasena, Samudrala; Sikkens, Cor; Centeno, Raymund; Cristescu, Simona M; Harren, Frans J M

2012-04-30

When performing trace gas analysis, it is not always possible to bring the source of volatiles and the gas analyzer together. In these cases, volatile storage containers, such as thermal desorption (TD) tubes, can be used for off-line measurement. TD is routinely combined with gas chromatography/mass spectrometry (GC/MS), but so far not with proton-transfer reaction mass spectrometry (PTRMS), which has a faster response. A PTR-quadrupole-MS instrument and a PTR-ion-trap-MS instrument were separately coupled to a TD unit for off-line analysis of trace volatiles in air. Carbograph 1TD/Carbopack X sorbent tubes were filled with different concentrations of a trace gas mixture containing low molecular weight volatiles (32 g/mol up to 136 g/mol) and measured with the above-mentioned combinations. The carrier gas in the TD unit was changed from helium to nitrogen to be able to combine this instrument with the mass spectrometer. Good linearity and reproducibility with the amount of gas stored were obtained. The storage capacity over time (up to 14 days) showed larger variability (<11% for all compounds, except for acetone 27%). Several tubes were filled with breath of different persons, and the breath of a smoker showed increased levels of acetonitrile and benzene. The combination of the PTR ion-trap instrument with the TD unit was also investigated. Due to its higher sampling rate, the ion-trap system showed higher throughput capabilities than the quadrupole system. The combination of TD with PTRMS using both a quadrupole and an ion trap for off-line volatile analysis has been validated. TD tubes can be a robust and compact volatile storage method when the mass spectrometry and the sampling cannot be performed in the same place, for example in large screening studies. In addition, a higher measurement throughput than with GC/MS could be obtained. Copyright © 2012 John Wiley & Sons, Ltd.

Absence of Change in Total Daily Energy Expenditure (EE(sub TD)) in Young and Mature Rats During 14 Days of Hypergravity

NASA Technical Reports Server (NTRS)

Wade, C. E.; Moran, M. M.; Stein, T. P.; Hoban-Higgins, T. M.; Fuller, P.; Fuller, C. A.; Dalton, Bonnie P. (Technical Monitor)

1999-01-01

Effect of age on the response of EE(sub TD) to an increase in gravity was assessed in young (Y; 1.5 month old) and mature (M; 8 month old) Sprague-Dawley rats. Rats were implanted with transmitters to monitor activity, and metabolism was determined by the double labeled water technique. Daily food intake was measured. For each age, rats (n=8 per treatment) were exposed to centrifugation at 2G, or remained at 1G. There was a difference in EE(sub TD) between age groups, 182 plus or minus 11 and 143 plus or minus 5 kcal/kg/day in Y and M, respectively. This difference was attributed in part to a lower activity level in M animals, 48% of Y rats. After day 6 there was no effect on EE(sub TD) of exposure to 2G, or on food intake per 100g BW. Prior studies show a 20% increase in resting EE with hypergravity. In our study the level of activity was reduced to 41% of 1G in both age groups during 2G. For Y at 1G resting EE accounted for 78% of the EE(sub TD) and activity 22%, while at 2G resting EE was 96% of EE(sub TD) and activity 4%. M rats had similar changes. Independent of age, with exposure to hypergravity EE(sub TD) is maintained by behavioral changes.

Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

DTIC Science & Technology

2017-05-05

dependent density functional theory (TD-DFT). The size of the clusters considered is relatively large compared to those considered in previous studies...are characterized by many different geometries, which potentially can be optimized with respect to specific materials design criteria, i.e., molecular...SixOy molecular clusters using density functional theory (DFT). The size of the clusters considered, however, is relatively large compared to those

Phenothiazine-anthraquinone donor-acceptor molecules: synthesis, electronic properties and DFT-TDDFT computational study.

PubMed

Zhang, Wen-Wei; Mao, Wei-Li; Hu, Yun-Xia; Tian, Zi-Qi; Wang, Zhi-Lin; Meng, Qing-Jin

2009-09-17

Two donor-acceptor molecules with different pi-electron conjugative units, 1-((10-methyl-10H-phenothiazin-3-yl)ethynyl)anthracene-9,10-dione (AqMp) and 1,1'-(10-methyl-10H-phenothiazine-3,7-diyl)bis(ethyne-2,1-diyl)dianthracene-9,10-dione (Aq2Mp), have been synthesized and investigated for their photochemical and electrochemical properties. Density functional theory (DFT) calculations provide insights into their molecular geometry, electronic structures, and properties. These studies satisfactorily explain the electrochemistry of the two compounds and indicate that larger conjugative effect leads to smaller HOMO-LUMO gap (Eg) in Aq2Mp. Both compounds show ICT and pi --> pi* transitions in the UV-visible range in solution, and Aq2Mp has a bathochromic shift and shows higher oscillator strength of the absorption, which has been verified by time-dependent DFT (TDDFT) calculations. The differences between AqMp and Aq2Mp indicate that the structural and conjugative effects have great influence on the electronic properties of the molecules.

Design and qualification of the SEU/TD Radiation Monitor chip

NASA Technical Reports Server (NTRS)

Buehler, Martin G.; Blaes, Brent R.; Soli, George A.; Zamani, Nasser; Hicks, Kenneth A.

1992-01-01

This report describes the design, fabrication, and testing of the Single-Event Upset/Total Dose (SEU/TD) Radiation Monitor chip. The Radiation Monitor is scheduled to fly on the Mid-Course Space Experiment Satellite (MSX). The Radiation Monitor chip consists of a custom-designed 4-bit SRAM for heavy ion detection and three MOSFET's for monitoring total dose. In addition the Radiation Monitor chip was tested along with three diagnostic chips: the processor monitor and the reliability and fault chips. These chips revealed the quality of the CMOS fabrication process. The SEU/TD Radiation Monitor chip had an initial functional yield of 94.6 percent. Forty-three (43) SEU SRAM's and 14 Total Dose MOSFET's passed the hermeticity and final electrical tests and were delivered to LL.

An electron microscopy examination of primary recrystallization in TD-nickel.

NASA Technical Reports Server (NTRS)

Petrovic, J. J.; Ebert, L. J.

1972-01-01

Primary recrystallization in TD-nickel 1 in. bar has previously been regarded as the process by which the initial fine grain structure is converted to a coarse grain size (increases in grain size by 500 times) under suitable deformation and annealing conditions. This process is dependent on deformation mode. While it occurs readily after rolling transverse to the bar axis and annealing (800 C), it is completely inhibited by longitudinal rolling and swaging deformations, even for very high (1320 C) annealing temperatures. A transmission electron microscopy examination of deformation and annealing substructures indicates that primary recrystallization in TD-nickel 1 in. bar actually occurs on the sub-light optical level, to produce a grain structure similar in size to the initial fine grained state.

De(side chain) model of epothilone: bioconformer interconversions DFT study.

PubMed

Rusinska-Roszak, Danuta; Lozynski, Marek

2009-07-01

Using ab initio methods, we have studied conformations of the de(sidechain)de(dioxy)difluoroepothilone model to quantify the effect of stability change between the exo and endo conformers of the epoxy ring. The DFT minimization of the macrolactone ring reveals four low energy conformers, although MP2 predicted five stable structures. The model tested with DFT hybride functional (B3LYP/6-31+G(d,p)) exhibits the global minimum for one of the exo forms (C), experimentally observed in the solid state, but unexpectedly with the MP2 electron correlation method for the virtual endo form (W). Using the QST3 technique, several pathways were found for the conversion of the low energy conformers to the other low energy exo representatives, as well as within the endo analog subset. The potential energy relationships obtained for several exo forms suggest a high conformational mobility between three, experimentally observed, conformers. The high rotational barrier, however, excludes direct equilibrium with experimental EC-derived endo form S. The highest calculated transition state for the conversion of the most stable exo M interligand to the endo S form is approximately a 28 kcal/mol above the energy of the former. The two-step interconversion of the exo H conformer to the endo S requires at least 28 kcal/mol. Surprisingly, we found that the transition state energy of the H form to the virtual endo W has the acceptable value of about 9 kcal/mol and the next energy barrier for free interconversion of endo W to endo S is 13 kcal/mol.

Quantum mechanical and spectroscopic (FT-IR, 13C, 1H NMR and UV) investigations of 2-(5-(4-Chlorophenyl)-3-(pyridin-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole by DFT method.

PubMed

Diwaker

2014-07-15

The electronic, NMR, vibrational, structural properties of a new pyrazoline derivative: 2-(5-(4-Chlorophenyl)-3-(pyridine-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole has been studied using Gaussian 09 software package. Using VEDA 4 program we have reported the PED potential energy distribution of normal mode of vibrations of the title compound. We have also reported the (1)H and (13)C NMR chemical shifts of the title compound using B3LYP level of theory with 6-311++G(2d,2p) basis set. Using time dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, electronic spectrum of the title compound has been studied and reported. NBO analysis and MEP surface mapping has also been calculated and reported using ab initio methods. Copyright © 2014 Elsevier B.V. All rights reserved.

OH-initiated transformation and hydrolysis of aspirin in AOPs system: DFT and experimental studies.

PubMed

He, Lin; Sun, Xiaomin; Zhu, Fanping; Ren, Shaojie; Wang, Shuguang

2017-08-15

Advanced oxidation processes (AOPs) are widely used in wastewater treatment of pharmaceutical and personal care products (PPCPs). In this work, the OH-initiated transformation as well as the hydrolysis of a typical PPCPs, aspirin, was investigated using density functional theory (DFT) calculations and laboratory experiments. For DFT calculations, the frontier electron densities and bond dissociation energies were analyzed. Profiles of the potential energy surface were constructed, and all the possible pathways were discussed. Additionally, rate constants for each pathway were calculated with transition state theory (TST) method. UV/H 2 O 2 experiments of aspirin were performed and degradation intermediates were identified by UPLC-MS-MS analysis. Different findings from previous experimental works were reported that the H-abstraction pathways at methyl position were dominated and OH-addition pathways on benzene ring were also favored. Meantime, hydroxyl ASA was confirmed as the main stable intermediate. Moreover, it was the first time to use DFT method to investigate the hydrolysis mechanisms of organic ester compound. Copyright © 2017 Elsevier B.V. All rights reserved.

NTO-Picryl Constitutional Isomers—A DFT Study

NASA Astrophysics Data System (ADS)

Türker, Lemi; Çelik Bayar, Çağlar

2012-01-01

The quantum chemical properties and the detonation performance of some new explosives, 5-nitro-4-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class A) and 5-nitro-2-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class B), and their constitutional isomers have been investigated theoretically using the density functional theory (DFT) 6-31G(d,p) method. All of the constitutional isomers were found to be more sensitive than 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) and TNT but more insensitive than RDX and HMX. Their detonation performance is higher than that of NTO and TNT and all except two had lower detonation performance than RDX and HMX.

Cooperative enhancement of the nonlinear optical response in conjugated energetic materials: A TD-DFT study

DOE PAGES

Sifain, Andrew E.; Tadesse, Loza F.; Bjorgaard, Josiah August; ...

2017-03-21

Conjugated energetic molecules (CEMs) are a class of explosives with high nitrogen content that posses both enhanced safety and energetic performance properties and are ideal for direct optical initiation. As isolated molecules, they absorb within the range of conventional lasers. Crystalline CEMs are used in practice, however, and their properties can differ due to intermolecular interaction. Herein, time-dependent density functional theory was used to investigate one-photon absorption (OPA) and two-photon absorption (TPA) of monomers and dimers obtained from experimentally determined crystal structures of CEMs. OPA scales linearly with the number of chromophore units, while TPA scales nonlinearly, where a moremore » than 3-fold enhancement in peak intensity, per chromophore unit, is calculated. Cooperative enhancement depends on electronic delocalization spanning both chromophore units. An increase in sensitivity to nonlinear laser initiation makes these materials suitable for practical use. This is the first study predicting a cooperative enhancement of the nonlinear optical response in energetic materials composed of relatively small molecules. Finally, the proposed model quantum chemistry is validated by comparison to crystal structure geometries and the optical absorption of these materials dissolved in solution.« less

Theoretical Investigation of the Electronic Structure of Fe(II) Complexes at Spin-State Transitions

PubMed Central

2013-01-01

The electronic structure relevant to low spin (LS)↔high spin (HS) transitions in Fe(II) coordination compounds with a FeN6 core are studied. The selected [Fe(tz)6]2+ (1) (tz = 1H-tetrazole), [Fe(bipy)3]2+ (2) (bipy = 2,2′-bipyridine), and [Fe(terpy)2]2+ (3) (terpy = 2,2′:6′,2″-terpyridine) complexes have been actively studied experimentally, and with their respective mono-, bi-, and tridentate ligands, they constitute a comprehensive set for theoretical case studies. The methods in this work include density functional theory (DFT), time-dependent DFT (TD-DFT), and multiconfigurational second order perturbation theory (CASPT2). We determine the structural parameters as well as the energy splitting of the LS–HS states (ΔEHL) applying the above methods and comparing their performance. We also determine the potential energy curves representing the ground and low-energy excited singlet, triplet, and quintet d6 states along the mode(s) that connect the LS and HS states. The results indicate that while DFT is well suited for the prediction of structural parameters, an accurate multiconfigurational approach is essential for the quantitative determination of ΔEHL. In addition, a good qualitative agreement is found between the TD-DFT and CASPT2 potential energy curves. Although the TD-DFT results might differ in some respect (in our case, we found a discrepancy at the triplet states), our results suggest that this approach, with due care, is very promising as an alternative for the very expensive CASPT2 method. Finally, the two-dimensional (2D) potential energy surfaces above the plane spanned by the two relevant configuration coordinates in [Fe(terpy)2]2+ were computed at both the DFT and CASPT2 levels. These 2D surfaces indicate that the singlet–triplet and triplet–quintet states are separated along different coordinates, i.e., different vibration modes. Our results confirm that in contrast to the case of complexes with mono- and bidentate ligands, the

Activation mechanism of ammonium ions on sulfidation of malachite (-201) surface by DFT study

NASA Astrophysics Data System (ADS)

Wu, Dandan; Mao, Yingbo; Deng, Jiushuai; Wen, Shuming

2017-07-01

The activation mechanism of ammonium ions on the sulfidation of malachite (-201) was determined by density functional theory (DFT) calculations. Results of DFT calculations indicated that interlayer sulfidation occurs during the sulfidation process of malachite (-201). The absorption of both the ammonium ion and sulfide ion on the malachite (-201) surface is stronger than that of sulfur ion. After sulfidation was activated with ammonium ion, the Cu 3d orbital peak is closer to the Fermi level and characterized by a stronger peak value. Therefore, the addition of ammonium ions activated the sulfidation of malachite (-201), thereby improving the flotation performance.

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

PubMed

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

2015-01-01

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings. Copyright © 2015 Elsevier B.V. All rights reserved.

Oxidation behavior of TD-NiCr in a dynamic high temperature environment

NASA Technical Reports Server (NTRS)

Tenney, D. R.; Young, C. T.; Herring, H. W.

1974-01-01

The oxidation behavior of TD-NiCr has been studied in static and high-speed flowing air environments at 1100 and 1200 C. It has been found that the stable oxide morphologies formed on the specimens exposed to the static and dynamic environments were markedly different. The faceted crystal morphology characteristic of static oxidation was found to be unstable under high-temperature, high-speed flow conditions and was quickly replaced by a porous NiO 'mushroom' type structure. Also, it was found that the rate of formation of CrO3 from Cr2O3 was greatly enhanced by high gas velocity conditions. The stability of Cr2-O3 was found to be greatly improved by the presence of an outer NiO layer, even though the NiO layer was very porous. An oxidation model is proposed to explain the observed microstructures and overall oxidation behavior of TD-NiCr alloys.

Antimicrobial activities, DNA interactions, spectroscopic (FT-IR and UV-Vis) characterizations, and DFT calculations for pyridine-2-carboxylic acid and its derivates

NASA Astrophysics Data System (ADS)

Tamer, Ömer; Tamer, Sevil Arabacı; İdil, Önder; Avcı, Davut; Vural, Hatice; Atalay, Yusuf

2018-01-01

In this paper, pyridine- 2- carboxylic acid, also known as picolinic acid (pic), and its two derivate, 4- methoxy-pyridine- 2- carboxylic acid (4-Mpic) and 4- chloro-pyridine- 2- carboxylic acid (4-Clpic) have been characterized by FT-IR and UV-Vis spectroscopy techniques as well as DFT calculations. B3LYP level of Density Functional Theory (DFT) method was used to obtain ground state geometries, vibration wavenumbers, first order hyperpolarizabilities and molecular electrostatic potential (MEP) surfaces for pic, 4Clpic and 4Mpic. The electronic absorption wavelengths and HOMO-LUMO energies were investigated by time dependent B3LYP (TD-B3LYP) level with the conductor-like polarizable continuum model (CPCM). The effects of Cl atom and OCH3 group on HOMO-LUMO energy gaps and first order hyperpolarizability parameters of pic, 4Clpic and 4Mpic molecules were examined. All molecules were screened for their antibacterial activities against Gram-positive and Gram-negative bacteria and for their antifungal activities against yeast strains by using minimal inhibitory concentration method (MIC). All compounds (pic, 4Mpic and 4Clpic) have been found to be very active against to the Gram (+) and Gram (-) bacteria. The DNA interactions of pic, 4Clpic and 4Mpic were analyzed by molecular docking simulations, and the interaction of the 4Mpic molecule with DNA is found to be higher than 4Clpic and pic.

Spin-adapted open-shell random phase approximation and time-dependent density functional theory. I. Theory.

PubMed

Li, Zhendong; Liu, Wenjian

2010-08-14

The spin-adaptation of single-reference quantum chemical methods for excited states of open-shell systems has been nontrivial. The primary reason is that the configuration space, generated by a truncated rank of excitations from only one component of a reference multiplet, is spin-incomplete. Those "missing" configurations are of higher ranks and can, in principle, be recaptured by a particular class of excitation operators. However, the resulting formalisms are then quite involved and there are situations [e.g., time-dependent density functional theory (TD-DFT) under the adiabatic approximation] that prevent one from doing so. To solve this issue, we propose here a tensor-coupling scheme that invokes all the components of a reference multiplet (i.e., a tensor reference) rather than increases the excitation ranks. A minimal spin-adapted n-tuply excited configuration space can readily be constructed by tensor products between the n-tuple tensor excitation operators and the chosen tensor reference. Further combined with the tensor equation-of-motion formalism, very compact expressions for excitation energies can be obtained. As a first application of this general idea, a spin-adapted open-shell random phase approximation is first developed. The so-called "translation rule" is then adopted to formulate a spin-adapted, restricted open-shell Kohn-Sham (ROKS)-based TD-DFT (ROKS-TD-DFT). Here, a particular symmetry structure has to be imposed on the exchange-correlation kernel. While the standard ROKS-TD-DFT can access only excited states due to singlet-coupled single excitations, i.e., only some of the singly excited states of the same spin (S(i)) as the reference, the new scheme can capture all the excited states of spin S(i)-1, S(i), or S(i)+1 due to both singlet- and triplet-coupled single excitations. The actual implementation and computation are very much like the (spin-contaminated) unrestricted Kohn-Sham-based TD-DFT. It is also shown that spin-contaminated spin

Synthesis, spectroscopic characterizations, crystal structures and DFT studies of nalidixic acid carbonyl hydrazones derivatives

NASA Astrophysics Data System (ADS)

Bergamini, F. R. G.; Ribeiro, M. A.; Lancellotti, M.; Machado, D.; Miranda, P. C. M. L.; Cuin, A.; Formiga, A. L. B.; Corbi, P. P.

2016-09-01

This article describes the synthesis and characterization of the 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide (hzd) and six carbonyl hydrazones derivatives of the nalidixic with 1H-pyrrol-2-ylmethylidene (hpyrr), 1H-imidazol-2-ylmethylidene (h2imi), pyridin-2-ylmethylidene (h2py), pyridin-3-ylmethylidene (h3py), pyridin-4-ylmethylidene(h4py) and (2-hydroxyphenyl)methylidene (hsali). The carbonyl hydrazones were characterized by elemental and ESI-QTOF-MS analyses, IR and detailed NMR spectroscopic measurements. The 2D NMR experiments allowed the unambiguous assignment of the hydrogen, carbon and nitrogen atoms, which have not been reported for nalidixic acid carbonyl hydrazone derivatives so far. Crystal structures of hzd and the new carbonyl hydrazones h2imi, hpyrr and h3py were determined by X-ray diffraction studies. Although the synthesis of hzd was reported decades ago, the hzd crystal structure have not been reported yet. Geometric optimizations of all the characterized structures were performed with the aid of DFT studies. Despite the fact that the hydrazones with 2-pyridine carboxylic acid (h2py) and salicyl aldehyde (hsali) were already reported by literature, a detailed spectroscopic study followed by DFT studies are also reported for such compounds in this manuscript. Antimicrobial studies of the compounds are also presented.

Mobility spectrum analytical approach for the type-II Weyl semimetal Td-MoTe2

NASA Astrophysics Data System (ADS)

Pei, Q. L.; Luo, X.; Chen, F. C.; Lv, H. Y.; Sun, Y.; Lu, W. J.; Tong, P.; Sheng, Z. G.; Han, Y. Y.; Song, W. H.; Zhu, X. B.; Sun, Y. P.

2018-02-01

The extreme magnetoresistance (XMR) in orthorhombic W/MoTe2 arises from the combination of the perfect electron-hole (e-h) compensation effect and the unique orbital texture topology, which have comprised an intriguing research field in materials physics. Herein, we apply a special analytical approach as a function of mobility (μ-spectrum) without any hypothesis. Based on the interpretations of longitudinal and transverse electric transport of Td-MoTe2, the types and the numbers of carriers can be obtained. There are three observations: the large residual resistivity ratio can be observed in the MoTe2 single crystal sample, which indicates that the studied crystal is of high quality; we observed three electron-pockets and three hole-ones from the μ-spectrum and that the ratio of h/e is much less than 1, which shows that MoTe2 is more e-like; different from the separated peaks obtained from the hole-like μ-spectrum, those of the electron-like one are continuous, which may indicate the topological feature of electron-pockets in Td-MoTe2. The present results may provide an important clue to understanding the mechanism of the XMR effect in Td-MoTe2.

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

NASA Astrophysics Data System (ADS)

Muthu, S.; Elamurugu Porchelvi, E.

2013-11-01

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

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

PubMed

Muthu, S; Elamurugu Porchelvi, E

2013-11-01

The Fourier Transform Infrared (FT-IR) and FT-Raman of N,N-diethyl-4-methylpiperazine-1-carboxamide (NND4MC) have been recorded and analyzed. The structure of the compound was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d,p) and 6-311G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) antibonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using Density Functional Theory (DFT/B3LYP) with 6-31G(d,p) and 6-311G(d,p) basis sets. The calculated results also show that the NND4MC molecule may have microscopy nonlinear optical (NLO) behavior with non zero values. Mulliken atomic charges of NND4MC were calculated. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. The UV-Vis spectrum of the compound was recorded. The theoretical electronic absorption spectra have been calculated by using CIS, TD-DFT methods. A study on the electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) were also performed. Copyright © 2013 Elsevier B

Signal-on electrochemical assay for label-free detection of TdT and BamHI activity based on grown DNA nanowire-templated copper nanoclusters.

PubMed

Hu, Yufang; Zhang, Qingqing; Xu, Lihua; Wang, Jiao; Rao, Jiajia; Guo, Zhiyong; Wang, Sui

2017-11-01

Electrochemical methods allow fast and inexpensive analysis of enzymatic activity. Here, a simple and yet efficient "signal-on" electrochemical assay for sensitive, label-free detection of DNA-related enzyme activity was established on the basis of terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. TdT, which is a template-independent DNA polymerase, can catalyze the sequential addition of deoxythymidine triphosphate (dTTP) at the 3'-OH terminus of single-stranded DNA (ssDNA); then, the TdT-yield T-rich DNA nanowires can be employed as the synthetic template of copper nanoclusters (CuNCs). Grown DNA nanowires-templated CuNCs (noted as DNA-CuNCs) were attached onto graphene oxide (GO) surface and exhibited unique electrocatalytic activity to H 2 O 2 reduction. Under optimal conditions, the proposed biosensor was utilized for quantitatively monitoring TdT activity, with the observed LOD of 0.1 U/mL. It also displayed high selectivity to TdT with excellent stability, and offered a facile, convenient electrochemical method for TdT-relevant inhibitors screening. Moreover, the proposed sensor was successfully used for BamHI activity detection, in which a new 3'-OH terminal was exposed by the digestion of a phosphate group. Ultimately, it has good prospects in DNA-related enzyme-based biochemical studies, disease diagnosis, and drug discovery. Graphical Abstract Extraordinary TdT-generated DNA-CuNCs are synthesized and act as a novel electrochemical sensing platform for sensitive detection of TdT and BamHI activity in biological environments.

DFT and ab initio study of the unimolecular decomposition of the lowest singlet and triplet states of nitromethane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manaa, M.R.; Fried, L.E.

1998-11-26

The fully optimized potential energy curves for the unimolecular decomposition of the lowest singlet and triplet states of nitromethane through the C-NO{sub 2} bond dissociation pathway are calculated using various DFT and high-level ab initio electronic structure methods. The authors perform gradient corrected density functional theory (DFT) and multiconfiguration self-consistent field (MCSCF) to conclusively demonstrate that the triplet state of nitromethane is bound. The adiabatic curve of this state exhibits a 33 kcal/mol energy barrier as determined at the MCSCF level. DFT methods locate this barrier at a shorter C-N bond distance with 12--16 kcal/mol lower energy than does MCSCF.more » In addition to MCSCF and DFT, quadratic configuration interactions with single and double substitutions (QCISD) calculations are also performed for the singlet curve. The potential energy profiles of this state predicted by FT methods based on Becke`s 1988 exchange functional differ by as much as 17 kcal/mol from the predictions of MCSCF and QCISD in the vicinity of the equilibrium structure. The computational methods predict bond dissociation energies 5--9 kcal/mol lower than the experimental value. DFT techniques based on Becke`s 3-parameter exchange functional show the best overall agreement with the higher level methods.« less

Molecular structure, nonlinear optical studies and spectroscopic analysis of chalcone derivative (2E)-3-[4-(methylsulfanyl) phenyl]-1-(3-bromophenyl) prop-2-en-1-one by DFT calculations

NASA Astrophysics Data System (ADS)

Kumar, Amit; Kumar, Rajesh; Gupta, Archana; Tandon, Poonam; D'silva, E. Deepak

2017-12-01

A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of nonlinear optical chalcone derivative (2E)-3-[4-(methylsulfanyl) phenyl]-1-(3-bromophenyl) prop-2-en-1-one (3Br4MSP). The FT-IR and FT-Raman spectra of the molecule in the solid phase have been recorded. Density functional theory (DFT) calculations at B3LYP level with 6-311++G (d,p) basis set have been carried out to derive useful information about the molecular structure and to assign the relevant electronic and vibrational features. These calculations reveal that the optimized geometry closely resembles the experimental XRD data. The vibrational spectra were analyzed on the basis of the potential energy distribution (PED) of each vibrational mode, which allowed us to obtain a quantitative as well as qualitative interpretation of FT-IR and FT-Raman spectra. The UV-vis spectrum was recorded in methanol solution. The excited state properties have been determined by TD-DFT method and the effect of solvent was analyzed by PCM model. The most prominent transition corresponds to π→π∗. The reactivity parameters as chemical potential, global hardness, and electrophilicity index have also been calculated. To provide an explicit assignment and analysis of 13C and 1H NMR spectra, theoretical calculations on chemical shift of the title compound were done through GIAO method at B3LYP/6-311++G (d,p) level. The Mulliken's population analysis shows one of the simplest pictures of charge distribution. The standard statistical thermodynamic functions like heat capacity at constant pressure (Cop,m), entropy (Som) and enthalpy (Hom) were obtained from the theoretical harmonic frequencies for the optimized molecule. The nonlinear optical properties of title molecule are also addressed theoretically. Two contributions, vibrational and electronic, to the electrical properties polarizability and first order hyperpolarizability of 3Br4MSP have been evaluated using the

HCOOH decomposition on Pt(111): A DFT study

DOE PAGES

Scaranto, Jessica; Mavrikakis, Manos

2015-10-13

Formic acid (HCOOH) decomposition on transition metal surfaces is important for hydrogen production and for its electro-oxidation in direct HCOOH fuel cells. HCOOH can decompose through dehydrogenation leading to formation of CO 2 and H 2 or dehydration leading to CO and H 2O; because CO can poison metal surfaces, dehydrogenation is typically the desirable decomposition path. Here we report a mechanistic analysis of HCOOH decomposition on Pt(111), obtained from a plane wave density functional theory (DFT-PW91) study. We analyzed the dehydrogenation mechanism by considering the two possible pathways involving the formate (HCOO) or the carboxyl (COOH) intermediate. We alsomore » considered several possible dehydration paths leading to CO formation. We studied HCOO and COOH decomposition both on the clean surface and in the presence of other relevant co-adsorbates. The results suggest that COOH formation is energetically more difficult than HCOO formation. In contrast, COOH dehydrogenation is easier than HCOO decomposition. Here, we found that CO 2 is the main product through both pathways and that CO is produced mainly through the dehydroxylation of the COOH intermediate.« less

HCOOH decomposition on Pt(111): A DFT study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scaranto, Jessica; Mavrikakis, Manos

Formic acid (HCOOH) decomposition on transition metal surfaces is important for hydrogen production and for its electro-oxidation in direct HCOOH fuel cells. HCOOH can decompose through dehydrogenation leading to formation of CO 2 and H 2 or dehydration leading to CO and H 2O; because CO can poison metal surfaces, dehydrogenation is typically the desirable decomposition path. Here we report a mechanistic analysis of HCOOH decomposition on Pt(111), obtained from a plane wave density functional theory (DFT-PW91) study. We analyzed the dehydrogenation mechanism by considering the two possible pathways involving the formate (HCOO) or the carboxyl (COOH) intermediate. We alsomore » considered several possible dehydration paths leading to CO formation. We studied HCOO and COOH decomposition both on the clean surface and in the presence of other relevant co-adsorbates. The results suggest that COOH formation is energetically more difficult than HCOO formation. In contrast, COOH dehydrogenation is easier than HCOO decomposition. Here, we found that CO 2 is the main product through both pathways and that CO is produced mainly through the dehydroxylation of the COOH intermediate.« less

Water dissociation and CO oxidation over Au/anatase catalyst. A DFT-D2 study

NASA Astrophysics Data System (ADS)

Saqlain, Muhammad Adnan; Hussain, Akhtar; Siddiq, Muhammad; Leitão, Alexandre A.

2018-03-01

With the help of DFT-D2 methodology, we have investigated the adsorption of water on clean anatase(001) and Au/anatase(001). In the former case, adsorption energies of H2O differ to small extent computed employing GGA = PW91 and DFT-D2 methods. While the GGA = PW91 predicts that water would desorb close to 650 K on the TiO2 surface, the DFT-D2 predicts that desorption is most likely to occur above 700 K. A comparison of water adsorption on TiO2 and Au/TiO2 surfaces shows that the TiO2 prefers dimer adsorption whereas the Au/TiO2 prefers monomer adsorption. We found that the diffusion of surface hydroxyls on to the Au cluster from the Au/TiO2 periphery is unlikely and it seems that the CO oxidation would occur at the Au/TiO2 boundary. The results show that water dissociation and CO oxidation steps occur easily on Au/TiO2 indicating that this could be good alternative catalyst for water gas shift reaction industry.

Adsorption of CGA on colloidal silver particles: DFT and SERS study

NASA Astrophysics Data System (ADS)

Biswas, Nandita; Kapoor, Sudhir; Mahal, Harbir S.; Mukherjee, Tulsi

2007-08-01

Raman and surface-enhanced Raman scattering (SERS) of chlorogenic acid (CGA) have been investigated. CGA is an important plant metabolite with anti-viral and anti-bacterial properties and thus, it is useful to study its surface adsorption characteristics. The experimental Raman data is supported with DFT calculations using B3LYP functional with 6-31G ∗ and LANL2DZ basis set. This is the first report on the vibrational analysis of CGA and its silver complex. From the SERS spectra as well as theoretical calculations, it has been inferred that the molecule is chemisorbed to the silver surface through the oxygen atoms of the carboxylate group.

Armchair and zigzag nanoribbons of gold and silver: A DFT study

NASA Astrophysics Data System (ADS)

Kapoor, Pooja; Sharma, Munish; Kumar, Ashok; Ahluwalia, P. K.

2018-04-01

This paper presents the results from a DFT-based computational study of structural and electronic properties of zigzag and armchair edge shaped nanoribbons of gold and silver in hexagonal phase. The cohesive energy of the considered nanoribbons are found to be more than the corresponding 2D counterpart, thereby, suggesting Au and Ag nanoribbons to be more stable in 1D as compared to 2D. All nanoribbons are found to be metallic with a modulation in quantum ballistic conductance with length and edge type of the nanoribbon. Au nanoribbons are found to have higher conductance than Ag nanoribbon. There is increase in conductance with increase in length of nanoribbon.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verma, Prakash; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energymore » corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.« less

Increasing the applicability of density functional theory. V. X-ray absorption spectra with ionization potential corrected exchange and correlation potentials.

PubMed

Verma, Prakash; Bartlett, Rodney J

2016-07-21

Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.

Molecular structure, spectroscopic (FT-IR, FT Raman, UV, NMR and THz) investigation and hyperpolarizability studies of 3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl) prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Kumar, Rajesh; Kumar, Amit; Deval, Vipin; Gupta, Archana; Tandon, Poonam; Patil, P. S.; Deshmukh, Prathmesh; Chaturvedi, Deepika; Watve, J. G.

2017-02-01

In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of the chalcone derivative 3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl) prop-2-en-1-one (2C6F2SC) is reported. Initial geometry generated from single crystal X-ray diffraction parameters was minimized at DFT level employing B3LYP/6-311++G (d,p) without any constraint to the potential energy surface. The molecule has been characterized using various experimental techniques FT-IR, FT-Raman, UV-Vis, 1H NMR, TD-THz and the spectroscopic data have been analyzed theoretically by Density Functional Theory (DFT) method. Harmonic vibrational frequencies were calculated theoretically using the optimized ground state geometry and the spectra were interpreted by means of potential energy distribution. Time Dependent Density Functional Theory (TD-DFT) has been used to calculate energies, absorption wavelengths, oscillator strengths of electronic singlet-singlet transitions. The calculated energy and oscillator strength complement with the experimental findings. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. Good correlations between the experimental 1H NMR chemical shifts and calculated GIAO shielding tensors were found. Stability of the molecule, hyperconjugative interactions and charge delocalization has been analyzed by natural bond orbital (NBO) analysis. The first order hyperpolarizability (β) of this molecular system and related properties (μ, <α> and Δα) have been calculated using the finite-field approach.

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

PubMed

Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

2015-08-05

Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.

DFT and TD-DFT insights, photolysis and photocatalysis investigation of three dyes with similar structure under UV irradiation with and without TiO2 as a catalyst: Effect of adsorption, pH and light intensity.

PubMed

Bendjabeur, Seyfeddine; Zouaghi, Razika; Zouchoune, Bachir; Sehili, Tahar

2018-02-05

TiO 2 -mediated photocatalytic degradation of three triphenylmethane dyes (basic fuchsin, acid fuchsin and Gentian violet), was investigated in aqueous suspensions in the presence and the absence of titanium dioxide P25 Degussa as photocatalyst. The photodegradation process was investigated using UV-A (365nm) and UV-C (254nm) light alone and UV-A in the presence of TiO 2 ·The effects of various operational parameters were investigated such as: the effect of adsorption in the dark, the influence of pH, the influence of irradiation wavelength and the effect of light intensity. The study of the effect of various parameters reveals that the photolysis of dyes increases with the increase of light intensity, the degradation rate under UV-C (254nm) was found better than under UV-A 365nm. The photocatalytic degradation was found to follow the same order of adsorption. The decolorization and the degradation kinetics were found to follow the pseudo-first-order kinetics. The mineralization of dye was found to follow the same order of disappearance as the photocatalytic degradation and depended directly to its functional groups and its number of carbons. Additionally, density functional theory (DFT) was applied for calculations of both electronic structure and spectroscopic properties of the studied compounds, where the obtained results of the three dyes show that the theoretical electronic spectra and the experimental UV-visible ones are similar in shapes, positions and intensities. Copyright © 2017. Published by Elsevier B.V.

DFT and TD-DFT insights, photolysis and photocatalysis investigation of three dyes with similar structure under UV irradiation with and without TiO2 as a catalyst: Effect of adsorption, pH and light intensity

NASA Astrophysics Data System (ADS)

Bendjabeur, Seyfeddine; Zouaghi, Razika; Zouchoune, Bachir; Sehili, Tahar

2018-02-01

TiO2-mediated photocatalytic degradation of three triphenylmethane dyes (basic fuchsin, acid fuchsin and Gentian violet), was investigated in aqueous suspensions in the presence and the absence of titanium dioxide P25 Degussa as photocatalyst. The photodegradation process was investigated using UV-A (365 nm) and UV-C (254 nm) light alone and UV-A in the presence of TiO2·The effects of various operational parameters were investigated such as: the effect of adsorption in the dark, the influence of pH, the influence of irradiation wavelength and the effect of light intensity. The study of the effect of various parameters reveals that the photolysis of dyes increases with the increase of light intensity, the degradation rate under UV-C (254 nm) was found better than under UV-A 365 nm. The photocatalytic degradation was found to follow the same order of adsorption. The decolorization and the degradation kinetics were found to follow the pseudo-first-order kinetics. The mineralization of dye was found to follow the same order of disappearance as the photocatalytic degradation and depended directly to its functional groups and its number of carbons. Additionally, density functional theory (DFT) was applied for calculations of both electronic structure and spectroscopic properties of the studied compounds, where the obtained results of the three dyes show that the theoretical electronic spectra and the experimental UV-visible ones are similar in shapes, positions and intensities.

Water adsorption on a copper formate paddlewheel model of CuBTC: A comparative MP2 and DFT study

NASA Astrophysics Data System (ADS)

Toda, Jordi; Fischer, Michael; Jorge, Miguel; Gomes, José R. B.

2013-11-01

Simultaneous adsorption of two water molecules on open metal sites of the HKUST-1 metal-organic framework (MOF), modeled with a Cu2(HCOO)4 cluster, was studied by means of density functional theory (DFT) and second-order Moller-Plesset (MP2) approaches together with correlation consistent basis sets. Experimental geometries and MP2 energetic data extrapolated to the complete basis set limit were used as benchmarks for testing the accuracy of several different exchange-correlation functionals in the correct description of the water-MOF interaction. M06-L and some LC-DFT methods arise as the most appropriate in terms of the quality of geometrical data, energetic data and computational resources needed.

Blue M2: an intermediate melanoidin studied via conceptual DFT.

PubMed

Frau, Juan; Glossman-Mitnik, Daniel

2018-05-31

In this computational study, ten density functionals, viz. CAM-B3LYP, LC-ω PBE, M11, M11L, MN12L, MN12SX, N12, N12SX, ω B97X, and ω B97XD, related to the Def2TZVP basis sets, are assessed together with the SMD solvation model for calculation of the molecular properties and structure of blue-M2 intermediate melanoidin pigment. All the chemical reactivity descriptors for the system are calculated via conceptual density functional theory (DFT). The active sites suitable for nucleophilic, electrophilic, and radical attacks are selected by linking them with the Fukui function indices, electrophilic Parr functions, and condensed dual descriptors Δf(r), respectively. The prediction of the maximum absorption wavelength is considerably accurate relative to its experimental value. The study reveals that the MN12SX and N12SX density functionals are the most appropriate density functionals for predicting the chemical reactivity of the molecule under study.

Study of B to X \\gamma Decays and Determination of |V_{td}/V_{ts}|

DOE Office of Scientific and Technical Information (OSTI.GOV)

del Amo Sanchez, P.; Lees, J.P.; Poireau, V.

2011-08-22

Using a sample of 471 million B{bar B} events collected with the BABAR detector, we study the sum of seven exclusive final states B {yields} X{sub s(d){gamma}}, where X{sub s(d)} is a strange (non-strange) hadronic system with a mass of up to 2.0 GeV/c{sup 2}. After correcting for unobserved decay modes, we obtain a branching fraction for b {yields} d{gamma} of (9.2 {+-} 2.0(stat.) {+-} 2.3(syst.)) x 10{sup -6} in this mass range, and a branching fraction for b {yields} s{gamma} of (23.0 {+-} 0.8(stat.) {+-} 3.0(syst.)) x 10{sup -5} in the same mass range. We find {Beta}(b{yields}d{gamma})/{Beta}(b{yields}s{gamma}) = 0.040more » {+-} 0.009(stat.) {+-} 0.010(syst.), from which we determine |V{sub td}/V{sub ts}| = 0.199 {+-} 0.022(stat.) {+-} 0.024(syst.) {+-} 0.002(th.).« less

RNA-Binding Protein L1TD1 Interacts with LIN28 via RNA and is Required for Human Embryonic Stem Cell Self-Renewal and Cancer Cell Proliferation

PubMed Central

Närvä, Elisa; Rahkonen, Nelly; Emani, Maheswara Reddy; Lund, Riikka; Pursiheimo, Huha-Pekka; Nästi, Juuso; Autio, Reija; Rasool, Omid; Denessiouk, Konstantin; Lähdesmäki, Harri; Rao, Anjana; Lahesmaa, Ritta

2012-01-01

Human embryonic stem cells (hESC) have a unique capacity to self-renew and differentiate into all the cell types found in human body. Although the transcriptional regulators of pluripotency are well studied, the role of cytoplasmic regulators is still poorly characterized. Here, we report a new stem cell-specific RNA-binding protein L1TD1 (ECAT11, FLJ10884) required for hESC self-renewal and cancer cell proliferation. Depletion of L1TD1 results in immediate downregulation of OCT4 and NANOG. Furthermore, we demonstrate that OCT4, SOX2, and NANOG all bind to the promoter of L1TD1. Moreover, L1TD1 is highly expressed in seminomas, and depletion of L1TD1 in these cancer cells influences self-renewal and proliferation. We show that L1TD1 colocalizes and interacts with LIN28 via RNA and directly with RNA helicase A (RHA). LIN28 has been reported to regulate translation of OCT4 in complex with RHA. Thus, we hypothesize that L1TD1 is part of the L1TD1-RHA-LIN28 complex that could influence levels of OCT4. Our results strongly suggest that L1TD1 has an important role in the regulation of stemness. PMID:22162396

Elucidation of the new generation fluorescent protein tdTomato for space related radiobiological research

NASA Astrophysics Data System (ADS)

Chishti, Arif Ali; Baumstark-Khan, Christa; Hellweg, Christine; Reitz, Guenther

Astronauts in space are exposed to a potentially harmful radiation field, which does not exist in its quality and quantity on earth. Radiation exposure in space can lead to delayed or acute health effects. A successful long-term space mission requires better risk estimation and development of appropriate countermeasures, therefore study of the cellular radiation response is necessary. Ionizing radiation can provoke active cellular responses (cell cycle arrest, DNA repair, apoptosis or other forms of cell type). Exposure to ionizing radiation also activates various signaling pathways in human cells. In the cellular radiation-response, two pivotal signal transduction pathways have to be comprehensively studied i.e. the p53-pathway and NF-κB-pathway. Discovery of fluorescent proteins has revolutionized biological research by making it possible to carry out functional studies in living cells and understanding complex signaling pathways. Previously the green fluorescent proteins EGFP and d2EGFP were used for signaling pathway studies. In this work the new red fluorescent protein tdTomato will be used for comprehensive investigation of NF-κB and other transcription factor activation after exposure of human cells to ionizing radiation (X-rays, heavy ions; space conditions). tdTomato has many advantages over EGFP because of its high fluorescence signals and a better signal/noise ratio in human cells. The previously constructed reporter system with d2EGFP was used to evaluate NF-kB activation after exposure to heavy ion particles of different biological effectiveness. The sensitivity threshold of this system was determined to be 2 particle traversals per cell nucleus. In the current study a more sensitive reporter assay will be constructed using a GAL4-VP16 turbo system that comprises a receptor plasmid and a reporter plasmid. This reporter assay will be designed and constructed with tdTomato and evaluation will be done with different molecular techniques.

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile.

PubMed

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K; Kant, Rajni; Khajuria, Yugal

2015-04-05

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity. Copyright © 2014 Elsevier B.V. All rights reserved.

Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency

PubMed Central

Yang, Lei; Neme, Rafik; Wichman, Holly A.; Malik, Harmit S.

2014-01-01

Mammalian genomes comprise many active and fossilized retroelements. The obligate requirement for retroelement integration affords host genomes an opportunity to ‘domesticate’ retroelement genes for their own purpose, leading to important innovations in genome defense and placentation. While many such exaptations involve retroviruses, the L1TD1 gene is the only known domesticated gene whose protein-coding sequence is almost entirely derived from a LINE-1 (L1) retroelement. Human L1TD1 has been shown to play an important role in pluripotency maintenance. To investigate how this role was acquired, we traced the origin and evolution of L1TD1. We find that L1TD1 originated in the common ancestor of eutherian mammals, but was lost or pseudogenized multiple times during mammalian evolution. We also find that L1TD1 has evolved under positive selection during primate and mouse evolution, and that one prosimian L1TD1 has ‘replenished’ itself with a more recent L1 ORF1 from the prosimian genome. These data suggest that L1TD1 has been recurrently selected for functional novelty, perhaps for a role in genome defense. L1TD1 loss is associated with L1 extinction in several megabat lineages, but not in sigmodontine rodents. We hypothesize that L1TD1 could have originally evolved for genome defense against L1 elements. Later, L1TD1 may have become incorporated into pluripotency maintenance in some lineages. Our study highlights the role of retroelement gene domestication in fundamental aspects of mammalian biology, and that such domesticated genes can adopt different functions in different lineages. PMID:25211013

Td Vaccine (Tetanus and Diphtheria): What You Need to Know

MedlinePlus

... protect adolescents and adults from both of these diseases. Both tetanus and diphtheria are infections caused by bacteria. Diphtheria ... cases of diphtheria and hundreds of cases of tetanus were reported in the United ... both diseases have dropped by about 99%. 2 Td vaccine ...

Spectroscopic and time-dependent density functional investigation of the role of structure on the acid-base effects of citrinin detection

USDA-ARS?s Scientific Manuscript database

A time dependent density functional (TD-DFT) study was carried out on tautomers and ionic forms of citrinin to gain insight into the role of chemical structure and micellar environments on detection. Steady state fluorescence studies of citrinin in micellar aqueous solutions produced unusual results...

Plane-Wave DFT Methods for Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.

A detailed description of modern plane-wave DFT methods and software (contained in the NWChem package) are described that allow for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e. hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite+water interface and the hydrolysis of nitroaromatic molecules are described.

Synthesis, characterisation and DFT studies of three Schiff bases derived from histamine

NASA Astrophysics Data System (ADS)

Touafri, Lasnouni; Hellal, Abdelkader; Chafaa, Salah; Khelifa, Abdellah; Kadri, Abdelaziz.

2017-12-01

In this paper, we report first, the synthesis and characterisation of three Schiff bases derived from histamine by condensation of histamine with various aldehydes. Then, we present a detailed DFT study based on B3LYP/6-31G(d,p) of geometrical structures and electronic properties of these compounds. The study was extended to the HOMO-LUMO analysis to calculate the energy gap (Δ), Ionisation potential (I), Electron Affinity (A), Global Hardness (η), Chemical Potential (μ), Electrophilicity (ω), Electronegativity (χ) and Polarisability (α). The calculated HOMO and LUMO energy reveals that the charge transfers occurring within the molecule. On the basis of vibration analyses, the thermodynamic properties of the titles compound were also calculated.

New interpretation of the Gran Dolina-TD6 bearing Homo antecessor deposits through sedimentological analysis

PubMed Central

Campaña, I.; Pérez-González, A.; Benito-Calvo, A.; Rosell, J.; Blasco, R.; de Castro, J. M. Bermúdez; Carbonell, E.; Arsuaga, J. L.

2016-01-01

Gran Dolina is a cavity infilled by at least 25 m of Pleistocene sediments. This sequence contains the TD6 stratigraphic unit, whose records include around 170 hominin bones that have allowed the definition of a new species, Homo antecessor. This fossil accumulation was studied as a single assemblage and interpreted as a succession of several human home bases. We propose a complete stratigraphic context and sedimentological interpretation for TD6, analyzing the relationships between the sedimentary facies, the clasts and archaeo-palaeontological remains. The TD6 unit has been divided into three sub-units and 13 layers. Nine sedimentary facies have been defined. Hominin remains appear related to three different sedimentary facies: debris flow facies, channel facies and floodplain facies. They show three kinds of distribution: first a group of scattered fossils, then a group with layers of fossils in fluvial facies, and third a group with a layer of fossils in mixed fluvial and gravity flow facies. The results of this work suggest that some of these hominin remains accumulated in the cave by geological processes, coming from the adjacent slope above the cave or the cave entry, as the palaeogeography and sedimentary characteristics of these allochthonous facies suggest. PMID:27713562

Emittance of TD-NiCr after simulated reentry

NASA Technical Reports Server (NTRS)

Clark, R. K.; Dicus, D. L.; Lisagor, W. B.

1978-01-01

The effects of simulated reentry heating on the emittance of TD-NiCr were investigated. Groups of specimens with three different preconditioning treatments were exposed to 6, 24, and 30 half-hour simulated reentry exposure cycles in a supersonic arc tunnel at each of three conditions intended to produce surface temperatures of 1255, 1365, and 1475 K. Emittance was determined at 1300 K on specimens which were preconditioned only and specimens after completion of reentry simulation exposure. Oxide morphology and chemistry were studied by scanning electron microscopy and X-ray diffraction analysis. A consistent relationship was established between oxide morphology and total normal emittance. Specimens with coarser textured oxides tended to have lower emittances than specimens with finer textured oxides.

Responses of transgenic Arabidopsis plants and recombinant yeast cells expressing a novel durum wheat manganese superoxide dismutase TdMnSOD to various abiotic stresses.

PubMed

Kaouthar, Feki; Ameny, Farhat-Khemakhem; Yosra, Kamoun; Walid, Saibi; Ali, Gargouri; Faiçal, Brini

2016-07-01

In plant cells, the manganese superoxide dismutase (Mn-SOD) plays an elusive role in the response to oxidative stress. In this study, we describe the isolation and functional characterization of a novel Mn-SOD from durum wheat (Triticum turgidum L. subsp. Durum), named TdMnSOD. Molecular phylogeny analysis showed that the durum TdMnSOD exhibited high amino acids sequence identity with other Mn-SOD plants. The three-dimensional structure showed that TdMnSOD forms a homotetramer and each subunit is composed of a predominantly α-helical N-terminal domain and a mixed α/β C-terminal domain. TdMnSOD gene expression analysis showed that this gene was induced by various abiotic stresses in durum wheat. The expression of TdMnSOD enhances tolerance of the transformed yeast cells to salt, osmotic, cold and H2O2-induced oxidative stresses. Moreover, the analysis of TdMnSOD transgenic Arabidopsis plants subjected to different environmental stresses revealed low H2O2 and high proline levels as compared to the wild-type plants. Compared with the non-transformed plants, an increase in the total SOD and two other antioxidant enzyme activities including catalase (CAT) and peroxidases (POD) was observed in the three transgenic lines subjected to abiotic stress. Taken together, these data provide evidence for the involvement of durum wheat TdMnSOD in tolerance to multiple abiotic stresses in crop plants. Copyright © 2016 Elsevier GmbH. All rights reserved.

A simplified Tamm-Dancoff density functional approach for the electronic excitation spectra of very large molecules

NASA Astrophysics Data System (ADS)

Grimme, Stefan

2013-06-01

Two approximations in the Tamm-Dancoff density functional theory approach (TDA-DFT) to electronically excited states are proposed which allow routine computations for electronic ultraviolet (UV)- or circular dichroism (CD) spectra of molecules with 500-1000 atoms. Speed-ups compared to conventional time-dependent DFT (TD-DFT) treatments of about two to three orders of magnitude in the excited state part at only minor loss of accuracy are obtained. The method termed sTDA ("s" for simplified) employs atom-centered Löwdin-monopole based two-electron repulsion integrals with the asymptotically correct 1/R behavior and perturbative single excitation configuration selection. It is formulated generally for any standard global hybrid density functional with given Fock-exchange mixing parameter ax. The method performs well for two standard benchmark sets of vertical singlet-singlet excitations for values of ax in the range 0.2-0.6. The mean absolute deviations from reference data are only 0.2-0.3 eV and similar to those from standard TD-DFT. In three cases (two dyes and one polypeptide), good mutual agreement between the electronic spectra (up to 10-11 eV excitation energy) from the sTDA method and those from TD(A)-DFT is obtained. The computed UV- and CD-spectra of a few typical systems (e.g., C60, two transition metal complexes, [7]helicene, polyalanine, a supramolecular aggregate with 483 atoms and about 7000 basis functions) compare well with corresponding experimental data. The method is proposed together with medium-sized double- or triple-zeta type atomic-orbital basis sets as a quantum chemical tool to investigate the spectra of huge molecular systems at a reliable DFT level.

A randomized controlled trial [corrected] administration of tetanus toxoid (TT) versus tetanus and reduced diphtheria (Td) in pregnant women.

PubMed

Salama, Maha M; Hady, Osama A W; Ashour, Wael; Mostafa, Amal; El Alkamy, Sahar; El Sayed, Nehad; El Yazeed, Remon Abu

2009-07-01

The present study was designed as a randomized clinical trial to compare the immunogenicity, reactogenicity, and efficacy of tetanus toxoid (TT) and the combined tetanus and reduced diphtheria (Td) in pregnant women in four rural communities in Egypt. The pregnant women in each four villages received either TT or Td randomly. Both TT and Td vaccines are manufactured by the Egyptian Company for Biological Products & Vaccines (VACSERA) in Egypt. A total of 131 pregnant women were enrolled during the time of antenatal care visit (at 20 weeks gestational age of pregnancy) in one of four health units in Abu Homos district, Beheira Governorate, Egypt. Unimmunized women received two random doses of either TT or Td 8 weeks apart during their pregnancy. Outpatient follow-up for adverse reactions occurred at the third day after each vaccine dose as either local effects such as pain, redness, and swelling or systematic effects such as fever, malaise, and headache or body aches which was served as primary safety endpoint. Blood was collected three times from each woman for determination of antibody titer against tetanus and diphtheria by using enzyme-linked immunosorbent assay technique. The first sample was collected immediately before the first dose, the second before the second dose, and the third sample 1 week after delivery. Active surveillance home visits to all study participants were done twice: the first home visit during the first week after delivery and the second 1 month after labor to report the health status of the mother and the baby. A total of 122 pregnant women received two ordinary doses with interdose intervals within the allowable range and three blood samples were collected in each protocol analysis (62 in the TT group and 60 in the Td group). There was no statistically significant difference between groups in the percentage of reporting a primary safety endpoint (fever, malaise, body ache, headache) or local reactions at the site of injection as redness

Atmospheric Pressure-Thermal Desorption (AP-TD)/Electrospray Ionization-Mass Spectrometry for the Rapid Analysis of Bacillus Spores

USDA-ARS?s Scientific Manuscript database

A technique is described where an atmospheric pressure-thermal desorption (AP-TD) device and electrospray ionization (ESI)-mass spectrometry are coupled and used for the rapid analysis of Bacillus spores in complex matrices. The resulting AP-TD/ESI-MS technique combines the generation of volatile co...

Photo-physics study of an hydroxy-quinoline derivative as inhibitor of Pim-1 kinase: ultraviolet-visible linear dichroism spectroscopy and quantum chemical calculations.

PubMed

Lamhasni, T; Ait Lyazidi, S; Hnach, M; Haddad, M; Desmaële, D; Spanget-Larsen, J; Nguyen, D D; Ducasse, L

2013-09-01

The photophysical properties of the antiviral 7-nicotinoyl-styrylquinoline (MB96) were investigated by means of UV-Vis linear dichroism (LD) spectroscopy on molecular samples aligned in stretched polyvinylalcohol (PVA), supported by time dependent density functional theory (TD-DFT) calculations. Experimentally, the directions of the transitions moments with respect to the long axis of the molecule were deduced from the orientation K factors, determined by means of "trial-and-error" procedure. The absorption spectrum presents two parts. The main transition in the lowest energy part, observed around 365 nm and showing the highest K value 0.8, is longitudinally in-plane polarized. The highest energy part which is extended between 230 and 320 nm, large, diffuse, and of weak intensity, shows estimated K values between 0.2 and 0.5. This complex structure is transversally polarized with some contamination by the longitudinal character of the first strong band. The TD-DFT results agree fairly well with the LD measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

Dispersion interactions with linear scaling DFT: a study of planar molecules on charged polar surfaces

NASA Astrophysics Data System (ADS)

Andrinopoulos, Lampros; Hine, Nicholas; Haynes, Peter; Mostofi, Arash

2010-03-01

The placement of organic molecules such as CuPc (copper phthalocyanine) on wurtzite ZnO (zinc oxide) charged surfaces has been proposed as a way of creating photovoltaic solar cellsfootnotetextG.D. Sharma et al., Solar Energy Materials & Solar Cells 90, 933 (2006) ; optimising their performance may be aided by computational simulation. Electronic structure calculations provide high accuracy at modest computational cost but two challenges are encountered for such layered systems. First, the system size is at or beyond the limit of traditional cubic-scaling Density Functional Theory (DFT). Second, traditional exchange-correlation functionals do not account for van der Waals (vdW) interactions, crucial for determining the structure of weakly bonded systems. We present an implementation of recently developed approachesfootnotetextP.L. Silvestrelli, P.R.L. 100, 102 (2008) to include vdW in DFT within ONETEPfootnotetextC.-K. Skylaris, P.D. Haynes, A.A. Mostofi and M.C. Payne, J.C.P. 122, 084119 (2005) , a linear-scaling package for performing DFT calculations using a basis of localised functions. We have applied this methodology to simple planar organic molecules, such as benzene and pentacene, on ZnO surfaces.

Replication of transformation-defective mutants of the Prague strain of Rous sarcoma virus and isolation of a td mutant from duck-adapted PR-RSV-C.

PubMed

Geryk, J; Mazo, A; Svoboda, J; Hlozánek, I

1980-01-01

The replication of transformation-defective mutants of the Prague strain of Rous sarcoma virus subgroup C was studied using roller cultures. Under such conditions, 10(5)--10(6) infectous units of virus per 0.2 ml were produced, as revealed in both the reverse transcriptase and 16Q complementation tests. A new td daPR-RSV-C mutant was isolated from duck-adapted PR-RSV-C. This mutant replicated in roller cultures with equal efficiency as the original td PR-RSV-C. It was verified that td daPR-RSV-C does not transform chicken fibroblasts, is not oncogenic for 3-week-old chickens and has subgroup C host-range specificity. Both td mutants replicate in duck cells and reach the same titres.

Structures, mechanical properties, equations of state, and electronic properties of β-HMX under hydrostatic pressures: a DFT-D2 study.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; De, Suvranu

2014-10-07

We report the hydrostatic compression studies of the β-polymorph of a cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using DFT-D2, a first-principles calculation based on density functional theory (DFT) with van der Waals (vdW) corrections. The molecular structure, mechanical properties, electronic properties, and equations of state of β-HMX are investigated. For the first time, we predict the elastic constants of β-HMX using DFT-D2 studies. The equations of state under hydrostatic compression are studied for pressures up to 100 GPa. We found that the N-N bonds along the minor axis are responsible for the sensitivity of β-HMX. The analysis of the charge distribution shows that the electronic charge is transferred from hydrogen atoms to nitro groups with the amount of 0.131 and 0.064e for the nitro groups along the minor axis and major axis, respectively, when pressure changes from 0 GPa to 100 GPa. The electronic energy band gap changes from direct at a pressure of 0 GPa to indirect at a pressure of 50 GPa and higher. The band gap decreases with respect to an increase in pressure, implying that the impact sensitivity increases with compression. Our study suggests that the van der Waals interactions are critically important in modeling the mechanical properties of this molecular crystal.

Synthesis, spectra and X-ray crystallography of dipyridin-2-ylmethanone oxime and its CuX2(oxime)2 complexes: Thermal, Hirshfeld surface and DFT analysis

NASA Astrophysics Data System (ADS)

Warad, Ismail; Abdoh, Muneer; Al Ali, Anas; Shivalingegowda, Naveen; Kumara, Karthik; Zarrouk, Abdelkader; Lokanath, Neartur Krishnappagowda

2018-02-01

Dipyridin-2-ylmethanone oxime (C11H9N3O), was prepared using di-2-pyridyl ketone. The oxime ligand and its neutral CuX2 (oxime)2 (X = Cl or Br) complexes have been identified with the aid of several spectroscopic techniques such as: IR, EI-MS, EA, UV-visible, TG, 1H-NMR and finally the structure of the free oxime ligand was confirmed by X-ray diffraction studies. The oxime crystallizes in the monoclinic space group P21/c, with cell parameters a = 8.8811 (8) Å, b = 10.6362 (8) Å, c = 11.2050 (8) Å, β = 109.085 (4) º, V = 1000.26 (14) Å3 and Z = 4. The molecular conformation is stabilized by a strong intramolecular Osbnd H⋯N hydrogen bonding between the hydroxyl group of the oxime moiety and the nitrogen of the pyridine ring. Since the oxime structure was solved by XRD, the ligand structure parameters like bond length and angles were compared to the DFT computed one, the UV-visible to TD-SCF and Hirshfeld surface to MEP analysis.

TdKT, a new killer toxin produced by Torulaspora delbrueckii effective against wine spoilage yeasts.

PubMed

Villalba, María Leticia; Susana Sáez, Julieta; Del Monaco, Silvana; Lopes, Christian Ariel; Sangorrín, Marcela Paula

2016-01-18

Microbiological spoilage is a major concern throughout the wine industry, and control tools are limited. This paper addresses the identification and partial characterization of a new killer toxin from Torulaspora delbrueckii with potential biocontrol activity of Brettanomyces bruxellensis, Pichia guilliermondii, Pichia manshurica and Pichia membranifaciens wine spoilage. A panel of 18 different wine strains of T. delbrueckii killer yeasts was analysed, and the strain T. delbrueckii NPCC 1033 (TdKT producer) showed a significant inhibitory effect on the growth of all different spoilage yeasts evaluated. The TdKT toxin was then subjected to a partial biochemical characterization. Its estimated molecular weight was N30 kDa and it showed glucanase and chitinase enzymatic activities. The killer activity was stable between pH 4.2 and 4.8 and inactivated at temperature above 40 °C. Pustulan and chitin — but not other cell wall polysaccharides — prevented sensitive yeast cells from being killed by TdKT, suggesting that those may be the first toxin targets in the cell wall. TdKT provoked an increase in necrosis cell death after 3 h treatment and apoptotic cell death after 24 h showing time dependence in its mechanisms of action. Killer toxin extracts were active at oenological conditions, confirming their potential use as a biocontrol tool in winemaking.

Isolation and molecular characterization of a novel WIN1/SHN1 ethylene-responsive transcription factor TdSHN1 from durum wheat (Triticum turgidum. L. subsp. durum).

PubMed

Djemal, Rania; Khoudi, Habib

2015-11-01

Over the last decade, APETALA2/Ethylene Responsive Factor (AP2/ERF) proteins have become the subject of intensive research activity due to their involvement in a variety of biological processes. This research led to the identification of AP2/ERF genes in many species; however, little is known about these genes in durum wheat, one of the most important cereal crops in the world. In this study, a new member of the AP2/ERF transcription factor family, designated TdSHN1, was isolated from durum wheat using thermal asymetric interlaced PCR (TAIL-PCR) method. Protein sequence analysis showed that TdSHN1 contained an AP2/ERF domain of 63 amino acids and a putative nuclear localization signal (NLS). Phylogenetic analysis showed that TdSHN1 belongs to a group Va protein in the ERF subfamily which contains the Arabidopsis ERF proteins (SHN1, SHN2, and SHN3). Expression of TdSHN1 was strongly induced by salt, drought, abscisic acid (ABA), and cold. In planta, TdSHN1 protein was able to activate the transcription of GUS reporter gene driven by the GCC box and DRE element sequences. In addition, TdSHN1 was targeted to the nucleus when transiently expressed in tobacco epidermal cells. In transgenic yeast, overexpression of TdSHN1 increased tolerance to multiple abiotic stresses. Taken together, the results showed that TdSHN1 encodes an abiotic stress-inducible, transcription factor which confers abiotic stress tolerance in yeast. TdSHN1 is therefore a promising candidate for improvement of biotic and abiotic stress tolerance in wheat as well as other crops.

The structural and spectroscopic investigation of 2-chloro-3-methylquinoline by DFT method and UV-Vis, NMR and vibrational spectral techniques combined with molecular docking analysis

NASA Astrophysics Data System (ADS)

Kose, Etem; Atac, Ahmet; Bardak, Fehmi

2018-07-01

This study comprises the structural and spectroscopic evaluation of a quinoline derivative, 2-chloro-3-methylquinoline (2Cl3MQ), via UV-Vis, 1H and 13C NMR, FT-IR and FT-Raman techniques experimentally, theoretically with DFT and TD-DFT quantum chemical calculations at B3LYP/6-311++G (d, p) level of theory, and investigation of the in silico pharmaceutical potent of 2Cl3MQ in comparison to 2ClnMQ (n = 3,4,7,8,9,10) substituted quinolines. The experimental measurements were recorded as follows; UV-vis spectra were obtained in the range of 200-400 nm in the water and ethanol solvents. 1H and 13C NMR spectra were recorded in CDCl3. Vibrational spectra were obtained in the region of 4000-400 cm-1 and 3500-10 cm-1 for FT-IR and FT-Raman spectra, respectively. Structural and spectroscopic features obtained through theoretical evaluations include: electrostatic features, atomic charges and molecular electrostatic potential surface, the frontier molecular orbital characteristics, the density of states and their overlapping nature, the electronic transition properties, thermodynamical and nonlinear optical characteristics, and predicted UV-Vis, 1H and 13C NMR, FT-IR and FT-Raman spectra. Ligand-enzyme interactions of 2ClnMQ (n = 3,4,7,8,9,10) substituted quinolines with Malate Synthase from Mycobacterium Tuberculosis (MtbMS) were investigated via molecular docking. The role of position of methyl substitution on the inhibitor character of the ligands was discussed on the basis of noncovalent interaction profiles.

Comparative study of DFT+U functionals for non-collinear magnetism

NASA Astrophysics Data System (ADS)

Ryee, Siheon; Han, Myung Joon

2018-07-01

We performed comparative analysis for DFT+U functionals to better understand their applicability to non-collinear magnetism. Taking LiNiPO4 and Sr2IrO4 as examples, we investigated the results out of two formalisms based on charge-only density and spin density functional plus U calculations. Our results show that the ground state spin order in terms of tilting angle is strongly dependent on Hund J. In particular, the opposite behavior of canting angles as a function of J is found for LiNiPO4. The dependence on the other physical parameters such as Hubbard U and Slater parameterization is investigated. We also discuss the formal aspects of these functional dependences as well as parameter dependences. The current study provides useful information and important intuition for the first-principles calculation of non-collinear magnetic materials.

Melamine derivatives as effective corrosion inhibitors for mild steel in acidic solution: Chemical, electrochemical, surface and DFT studies

NASA Astrophysics Data System (ADS)

Verma, Chandrabhan; Haque, J.; Ebenso, Eno E.; Quraishi, M. A.

2018-06-01

In present study two condensation products of melamine (triazine) and glyoxal namely, 2,2-bis(4,6-diamino-1,3,5-triazin-2-ylamino)acetaldehyde (ME-1) and (N2,N2‧E,N2,N2‧E)-N2,N2‧-(ethane-1,2-diylidene)-bis-(1,3,5-triazine-2,4,6-triamine) (ME-2) are tested as mild steel corrosion inhibitors in acidic solution (1M HCl). The inhibition efficiency of ME-1 and ME-2 increases with increase in their concentrations and maximum values of 91.47% and 94.88% were derived, respectively at 100 mgL-1 (34.20 × 10-5 M) concentration. Adsorption of ME-1 and ME-2 on the surface of metal obeyed the Langmuir adsorption isotherm. Polarization investigation revealed that ME-1 and ME-2 act as mixed type inhibitors with minor cathodic prevalence. The chemical and electrochemical analyses also supported by surface characterization methods where significant smoothness in the surface morphologies was observed in the images of SEM and AFM spectra. Several DFT indices such as EHOMO and ELUMO, ΔE, η, σ, χ, μ and ΔN were derived for both ME-1 and ME-2 molecules and correlated with experimental results. The DFT studies have also been carried out for protonated or cationic form of the inhibitor molecules by considering that in acidic medium the heteroatoms of organic inhibitors easily undergo protonation. The experimental and density functional theory (DFT) studies (neutral and protonated) were in good agreement.

Multiconfigurational and DFT analyses of the electromeric formulation and UV-vis absorption spectra of the superoxide adduct of ferrous superoxide reductase.

PubMed

Attia, Amr A A; Cioloboc, Daniela; Lupan, Alexandru; Silaghi-Dumitrescu, Radu

2016-12-01

The putative initial adduct of ferrous superoxide reductase (SOR) with superoxide has been alternatively formulated as ferric-peroxo or ferrous-superoxo. The ~600-nm UV-vis absorption band proposed to be assigned to this adduct (either as sole intermediate in the SOR catalytic cycle, or as one of the two intermediates) has recently been interpreted as due to a ligand-to-metal charge transfer, involving thiolate and superoxide in a ferrous complex, contrary to an alternative assignment as a predominantly cysteine thiolate-to-ferric charge transfer in a ferric-peroxo electromer. In an attempt to clarify the electromeric formulation of this adduct, we report a computational study using a multiconfigurational complete active space self-consistent field (MC-CASSCF) wave function approach as well as modelling the UV-vis absorption spectra with time-dependent density functional theory (TD-DFT). The MC-CASSCF calculations disclose a weak interaction between iron and the dioxygenic ligand and a dominant configuration with an essentially ferrous-superoxo character. The computed UV-vis absorption spectra reveal a marked dependence on the choice of density functional - both in terms of location of bands and in terms of orbital contributors. For the main band in the visible region, besides the recently reported thiolate-to-superoxide charge transfer, a more salient, and less functional-dependent, feature is a thiolate-to-ferric iron charge transfer, consistent with a ferric-peroxo electromer. By contrast, the computed UV-vis spectra of a ferric-hydroperoxo SOR model match distinctly better (and with no qualitative dependence on the DFT methodology) the 600-nm band as due to a mainly thiolate-to-ferric character - supporting the assignment of the SOR "600-nm intermediate" as a S=5/2 ferric-hydroperoxo species. Copyright © 2016 Elsevier Inc. All rights reserved.

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs.

PubMed

Raeber, Alexandra E; Wong, Bryan M

2015-05-12

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

A theoretical study of a series of water-soluble triphenylamine photosensitizers for two-photon photodynamic therapy.

PubMed

Wang, Xin; Yin, Xue; Lai, Xiao-Yong; Liu, Ying-Tao

2018-10-05

In this study, the therapeutic activity of a series of water-soluble triphenylamine (TP) photosensitizers (Ps) was explored by using theoretical simulations. The key photophysical parameters which determined the efficiency of Ps, such as absorption electronic spectra, singlet-triplet energy gaps and spin-orbit matrix elements were calculated at density functional theory and its time-dependent extension (DFT, TD-DFT). The calculated results showed that these TP photosensitizers possessed large two-photon absorption cross-section in the near-infrared region (NIR), efficient intersystem crossing (ISC) transition from the first singlet excited state to the low lying triplet excited states and sufficient energy for generating reactive oxygen species (ROS). These suitable features made these TP series holding great promise for applications in two-photon photodynamic therapy (PDT). These TP photosensitizers studied here in principle extended the application range of two-photon PDT in water solution. Copyright © 2018 Elsevier B.V. All rights reserved.

Identification of rat Rosa26 locus enables generation of knock-in rat lines ubiquitously expressing tdTomato.

PubMed

Kobayashi, Toshihiro; Kato-Itoh, Megumi; Yamaguchi, Tomoyuki; Tamura, Chihiro; Sanbo, Makoto; Hirabayashi, Masumi; Nakauchi, Hiromitsu

2012-11-01

Recent discovery of a method for derivation and culture of germline-competent rat pluripotent stem cells (PSCs) enables generation of transgenic rats or knock-out rats via genetic modification of such PSCs. This opens the way to use rats, as is routine in mice, for analyses of gene functions or physiological features. In mouse or human, one widely used technique to express a gene of interest stably and ubiquitously is to insert that gene into the Rosa26 locus via gene targeting of PSCs. Rosa26 knock-in mice conditionally expressing a reporter or a toxin gene have contributed to tracing or ablation of specific cell lineages. We successfully identified a rat orthologue of the mouse Rosa26 locus. Insertion of tdTomato, a variant of red fluorescent protein, into the Rosa26 locus of PSCs of various rat strains allows ubiquitous expression of tdTomato. Through germline transmission of one Rosa26-tdTomato knock-in embryonic stem cell line, we also obtained tdTomato knock-in rats. These expressed tdTomato ubiquitously throughout their bodies, which indicates that the rat Rosa26 locus conserves functions of its orthologues in mouse and human. The new tools described here (targeting vectors, knock-in PSCs, and rats) should be useful for a variety of research using rats.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

Torras, Juan; Zanuy, David; Aradilla, David; Alemán, Carlos

2016-09-21

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

BH-DFTB/DFT calculations for iron clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aktürk, Abdurrahman; Sebetci, Ali, E-mail: asebetci@mevlana.edu.tr

2016-05-15

We present a study on the structural, electronic, and magnetic properties of Fe{sub n}(n  =  2  −  20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima havemore » been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe{sub 9−13}), centered hexagonal antiprism (Fe{sub 14−17}, Fe{sub 20}), and truncated decahedral (Fe{sub 17(2)}, Fe{sub 18−19}). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fe{sub n}(n = 2 − 20) clusters is between 2.4 and 3.6 μ{sub B} for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe{sub 13} icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.« less

Electron affinity of perhalogenated benzenes: A theoretical DFT study

NASA Astrophysics Data System (ADS)

Volatron, François; Roche, Cécile

2007-10-01

The potential energy surfaces (PES) of unsubstituted and perhalogenated benzene anions ( CX6-, X = F, Cl, Br, and I) were explored by means of DFT-B3LYP calculations. In the F and Cl cases seven extrema were located and characterized. In the Br and I cases only one minimum and two extrema were found. In each case the minimum was recomputed at the CCSD(T) level. The electron affinities of C 6X 6 were calculated (ZPE included). The results obtained agree well with the experimental determinations when available. The values obtained in the X = Br and the X = I cases are expected to be valuable predictions.

On the calculation of charge transfer transitions with standard density functionals using constrained variational density functional theory.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo

2010-08-21

It is well known that time-dependent density functional theory (TD-DFT) based on standard gradient corrected functionals affords both a quantitative and qualitative incorrect picture of charge transfer transitions between two spatially separated regions. It is shown here that the well known failure can be traced back to the use of linear response theory. Further, it is demonstrated that the inclusion of higher order terms readily affords a qualitatively correct picture even for simple functionals based on the local density approximation. The inclusion of these terms is done within the framework of a newly developed variational approach to excitation energies called constrained variational density functional theory (CV-DFT). To second order [CV(2)-DFT] this theory is identical to adiabatic TD-DFT within the Tamm-Dancoff approximation. With inclusion of fourth order corrections [CV(4)-DFT] it affords a qualitative correct description of charge transfer transitions. It is finally demonstrated that the relaxation of the ground state Kohn-Sham orbitals to first order in response to the change in density on excitation together with CV(4)-DFT affords charge transfer excitations in good agreement with experiment. The new relaxed theory is termed R-CV(4)-DFT. The relaxed scheme represents an effective way in which to introduce double replacements into the description of single electron excitations, something that would otherwise require a frequency dependent kernel.

Study of gas-phase O-H bond dissociation enthalpies and ionization potentials of substituted phenols - Applicability of ab initio and DFT/B3LYP methods

NASA Astrophysics Data System (ADS)

Klein, Erik; Lukeš, Vladimír

2006-11-01

In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O-H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O-H BDEs of meta- and para-substituted phenols from calculated IPs.

AV-block and conduction slowing prevail over TdP arrhythmias in the methoxamine-sensitized pro-arrhythmic rabbit model.

PubMed

Varkevisser, Rosanne; Vos, Marc A; Beekman, Jet D; Tieland, Ralph G; Van Der Heyden, Marcel A

2015-01-01

The methoxamine-sensitized rabbit model is widely used to screen drugs for proarrhythmic properties, especially repolarization-dependent TdP arrhythmias. With the change of anesthesia and/or sensitizing agent, conduction disturbances have been reported as well. Therefore, we compared currently available in-house anesthetics in order to preserve arrhythmia sensitivity and preclude conduction disturbances. Rabbits were randomly assigned to 3 groups: (1) 35 mg/kg ketamine + 5 mg/kg xylazine; (2) 0.5 mL/kg hypnorm + 3 mg/kg midazolam; (3) 35 mg/kg ketamine + 20 mg/kg propofol. Anesthesia was maintained by 1.5% isoflurane. Concomitant infusion of methoxamine (17 μg/kg/min for 40 minutes) and dofetilide (10 μg/kg/min for 30 minutes) was used to induce arrhythmias. Sole methoxamine infusion exclusively decreased HR in groups 1 and 3. Dofetilide lengthened repolarization, followed in time by PQ/QRS prolongation, second-degree AV block, and subsequently TdP arrhythmias. TdP was seen in 80%, 0%, and 33% of the rabbits in groups 1, 2, and 3, respectively. Decreasing the dose of dofetilide to 5 μg/kg/min in ketamine/xylazine anesthetized rabbits resulted in a drop in TdP incidence (25%) while conduction disturbances persisted. Flunarizine (n = 6) suppressed all TdP arrhythmias while conduction disturbances remained present. TdP incidence in the methoxamine-sensitized rabbit could be dramatically influenced by anesthesia, drug dose, and flunarizine, while conduction slowing remained present. Thus, conduction slowing seems to be the integral outcome in this model. © 2014 Wiley Periodicals, Inc.

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

PubMed

Levy, Ronald M; Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki

2017-04-20

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bagayoko, Diola

2014-12-15

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

Oxidation of TD nickel at 1050 C and 1200 C as compared with three grades of nickel of different purity

NASA Technical Reports Server (NTRS)

Lowell, C. E.; Grisaffe, S. J.; Deadmore, D. L.

1972-01-01

The isothermal oxidation of three nickels of different purity, Ni-200, Ni-270, and JM-Ni, was compared with that of TD-Ni in air at 1050 and 1200 C. The samples were oxidized as ground, as polished, or as annealed and polished. Weight change, metal loss, scale thickness, oxide morphology, and scale texture were determined. In degree of oxidation, TD-Ni was nearly the same as the higher purity materials, Ni-270 and JM-Ni; and less pure Ni-200 oxidized more than the others. However, in microstructure and scale texture the TD-Ni more closely resembled Ni-200. Grinding only charged the texture of the oxides of Ni_200 and TD-Ni.

Mission Management Computer and Sequencing Hardware for RLV-TD HEX-01 Mission

NASA Astrophysics Data System (ADS)

Gupta, Sukrat; Raj, Remya; Mathew, Asha Mary; Koshy, Anna Priya; Paramasivam, R.; Mookiah, T.

2017-12-01

Reusable Launch Vehicle-Technology Demonstrator Hypersonic Experiment (RLV-TD HEX-01) mission posed some unique challenges in the design and development of avionics hardware. This work presents the details of mission critical avionics hardware mainly Mission Management Computer (MMC) and sequencing hardware. The Navigation, Guidance and Control (NGC) chain for RLV-TD is dual redundant with cross-strapped Remote Terminals (RTs) interfaced through MIL-STD-1553B bus. MMC is Bus Controller on the 1553 bus, which does the function of GPS aided navigation, guidance, digital autopilot and sequencing for the RLV-TD launch vehicle in different periodicities (10, 20, 500 ms). Digital autopilot execution in MMC with a periodicity of 10 ms (in ascent phase) is introduced for the first time and successfully demonstrated in the flight. MMC is built around Intel i960 processor and has inbuilt fault tolerance features like ECC for memories. Fault Detection and Isolation schemes are implemented to isolate the failed MMC. The sequencing hardware comprises Stage Processing System (SPS) and Command Execution Module (CEM). SPS is `RT' on the 1553 bus which receives the sequencing and control related commands from MMCs and posts to downstream modules after proper error handling for final execution. SPS is designed as a high reliability system by incorporating various fault tolerance and fault detection features. CEM is a relay based module for sequence command execution.

Early Pleistocene hominin deciduous teeth from the Homo antecessor Gran Dolina-TD6 bearing level (Sierra de Atapuerca, Spain).

PubMed

Bermúdez de Castro, José María; Martinón-Torres, María; Martín-Francés, Laura; Martínez de Pinillos, Marina; Modesto-Mata, Mario; García-Campos, Cecilia; Wu, Xiujie; Xing, Song; Liu, Wu

2017-07-01

During the last 13 years, the late Early Pleistocene Gran Dolina-TD6-2 level (Sierra de Atapuerca, northern Spain) has yielded an additional sample of 26 dental specimens attributed to Homo antecessor. In this report, we present a descriptive and comparative study of the six deciduous teeth. We provide external and internal morphological descriptions following classical terminology, as well as the mesiodistal and buccolingual measurements of the teeth. The internal morphology was described by means of micro-CT technique. The TD6 deciduous teeth preserve primitive features regarding the Homo clade, such as the presence of styles in lower and upper canines and developed anterior and posterior foveae in the dm 2 . However, other features related to the complexity of the crown morphology (e.g., cingulum) are not present in this sample. Furthermore, the great reduction of the talonid of the dm 1 s is also noteworthy. Despite the limited comparative evidence, the presence of a remarkably well-developed tuberculum molare in the dm 1 and dm 1 s from TD6 can be also considered a derived feature in the genus Homo. The TD6 hominins exhibit dental dimensions similar to those of other Pleistocene hominins. The dm 1 s are buccolingually elongated and the buccolingual diameter of ATD6-93 is the largest recorded so far in the Homo fossil record. This study expands the list of plesiomorphic features of H. antecessor, and provides some information on the evolutionary status of this species. However, the identification of some advanced traits evinces a step towards the derived morphology of European Pleistocene teeth. The study of the deciduous dentition confirms the mosaic pattern of H. antecessor morphology revealed in previous studies of this hominin sample. © 2017 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

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

2014-08-01

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

DFT study of IR and Raman spectra of phosphotrihydrazone dendrimer with terminal phenolic groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2017-09-01

FT Raman and infrared spectra of phosphotrihydrazone (S)P[N(CH3)Ndbnd CHsbnd C6H4sbnd OH]3 (G0) were recorded. This compound is a zero generation phosphorus dendrimer with terminal phenolic groups. Optimal geometry and vibrational frequencies were calculated for G0 using the density functional theory (DFT). The molecule studied has C3 symmetry. In the molecule G0, each sbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P arm is flat. Optimized geometric parameters correspond to experimental data. The core of the dendrimer manifests itself as a band at 647 cm-1 in the Raman spectrum of G0 related to Pdbnd S stretching. Phenolic end functions exhibit a well-defined band at 3374 cm-1 in the experimental IR spectrum of G0. The observed frequency of the OH stretching vibrations of the phenolic groups is lower than the theoretical value due to the intermolecular Osbnd H⋯O hydrogen bond. This hydrogen bond is also responsible for the higher intensity of this band in the experimental IR spectrum compared with the theoretical value. DFT calculations suggest full assignment of normal modes. Global and local descriptors characterize the reactivity of the core and end groups.

Spectral and quantum chemical studies on 1,3-bis(N(1)-4-amino-6-methoxypyrimidinebenzenesulfonamide-2,2,4,4-ethane-1,2-dithiol)-2,4-dichlorocyclodiphosph(V)azane and its erbium complex.

PubMed

Al-Mogren, Muneerah M; Alaghaz, Abdel-Nasser M A; El-Gogary, Tarek M

2014-01-24

Novel 1,3-bis(N(1)-4-amino-6-methoxypyrimidine-benzenesulfonamide-2,2,4,4-ethane-1,2-dithiol)-2,4-dichlorocyclodiphosph(V)azane (L), was prepared and their coordinating behavior towards the lanthanide ion Er(III) was studied. The structures of the isolated products are proposed based on elemental analyses, IR, UV-VIS., (1)H NMR, (13)C NMR, (31)P NMR, SEM, XRD, mass spectra, effective magnetic susceptibility measurements and thermogravimetric analysis (TGA). Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of L and its binuclear Er(III) complex. Different tautomers of the ligand were optimized at the ab initio DFT level. Keto-form structure is about 17.7 kcal/mol more stable than the enol form (taking zpe correction into account). Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which compared by the measured electronic spectra. Copyright © 2013 Elsevier B.V. All rights reserved.

Spectral analysis and DFT computations of the hydrogen bonded complex between 2,6-diaminopyridine with 2,6-dichloro-4-nitrophenol in different solvents

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Soliman, Saied M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2017-09-01

New hydrogen bonded complex between 2,6-dichloro-4-nitrophenol (DCNP), proton donor with the proton acceptor 2,6-diaminopyridine (DAP) has been synthesized and characterized in solution and solid state by different spectroscopic techniques. Electronic spectra were used to identify the novel proton transfer complex through appearance of new absorption bands in acetonitrile (CH3CN), methanol (CH3OH) and mixture composed from 1:1 methanol and acetonitrile (AN-Me). The complex stoichiometry was determined to be 1:1 by job's method and photometric titrations. The formation constant was determined by applying minimum-maximum absorbances method where it reached high values confirming the complex high stability. A spectroscopic method for determining DAP was presented and validated statistically. The solid complex was characterized by elemental analysis, infrared and 1H NMR studies where the hydrogen bonded reaction occurs between the phenolic OH with the pyridine ring nitrogen as well as one amino group of DNP. The density functional theory DFT (B3LYP) method has been used to energy optimization of the reactants and complex in the ground state using two basis sets 6-31G(d) and 6-31 G+(d,p). The first one led to energy optimized structure through bifurcated hydrogen bond between OH of DCNP with the ring nitrogen and one amino group of DAP with optimization energy -1998.7 Hartree. The second one gave an optimized structure thought hydrogen bonding between OH and one amino group with lowered optimization energy -2018.1 Hartree. Hence, the experimental results will be simulated with the most stable one at DFT/B3LYB 6-31G+ (d,p). The most reactive electrophilic and nucleophilic sites of DCNP and DAP were predicted using the molecular electrostatic potential. The theoretical electronic spectra in the gas phase and the investigated solvents were calculated at TD-DFT/B3LYP 6-31G+ (d,p) and compared with measured electronic spectra where a satisfactory results have been obtained

Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of manganese (II) complex of picolinate: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Tamer, Ömer; Avcı, Davut; Atalay, Yusuf; Çoşut, Bünyemin; Zorlu, Yunus; Erkovan, Mustafa; Yerli, Yusuf

2016-02-01

A novel manganese (II) complex with picolinic acid (pyridine 2-carboxylic acid, Hpic), namely, [Mn(pic)2(H2O)2] was prepared and its crystal structure was fully characterized by using single crystal X-ray diffraction. Picolinate (pic) ligands were coordinated to the central manganese(II) ion as bidentate N,O-donors through the nitrogen atoms of pyridine rings and the oxygen atoms of carboxylate groups forming five-membered chelate rings. The spectroscopic characterization of Mn(II) complex was performed by the applications of FT-IR, Raman, UV-vis and EPR techniques. In order to support these studies, density functional theory (DFT) calculations were carried out by using B3LYP level. IR and Raman spectra were simulated at B3LYP level, and obtained results indicated that DFT calculations generally give compatible results to the experimental ones. The electronic structure of the Mn(II) complex was predicted using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength were investigated by applying natural bond orbital (NBO) analysis. Nonlinear optical properties of Mn(II) complex were investigated by the determining of molecular polarizability (α) and hyperpolarizability (β) parameters.

A comparative study of DFT calculated and experimental UV/Visible spectra for thirty carboline and carbazole based compounds

NASA Astrophysics Data System (ADS)

Zara, Zeenat; Iqbal, Javed; Ayub, Khurshid; Irfan, Muhammad; Mahmood, Athar; Khera, Rasheed Ahmad; Eliasson, Bertil

2017-12-01

A comparative study of UV/Visible spectra of carboline and carbazole derivatives was conducted by employing the Density Functional Theory (DFT) approach. In this study, the geometries of ground and excited states, excitation energy and absorption spectra were estimated by using seven different DFT functional; CAM-B3LYP, B3LYP, MPW1PW91, PBE, B3PW91, WB97XD and HSE06 with 6-31G basis set. Moreover, five different basis sets 3-21G, 6-31G, DGDZVP, DGTZVP and SDD were also investigated with the CAM-B3LYP and WB97XD functional to take out the best combination of functional and basis set. CAM-B3LYP/6-31G and WB97XD/DGDZVP combination were found to have closest agreement with the experimental values of β-carboline derivatives and carbazole derivatives, respectively. This study provided an insight about the electronic characteristics of the selected compounds and provided an effective tool for developing and designing the better UV absorber compounds.

Proposed Project Selection Method for Human Support Research and Technology Development (HSR&TD)

NASA Technical Reports Server (NTRS)

Jones, Harry

2005-01-01

The purpose of HSR&TD is to deliver human support technologies to the Exploration Systems Mission Directorate (ESMD) that will be selected for future missions. This requires identifying promising candidate technologies and advancing them in technology readiness until they are acceptable. HSR&TD must select an may of technology development projects, guide them, and either terminate or continue them, so as to maximize the resulting number of usable advanced human support technologies. This paper proposes an effective project scoring methodology to support managing the HSR&TD project portfolio. Researchers strongly disagree as to what are the best technology project selection methods, or even if there are any proven ones. Technology development is risky and outstanding achievements are rare and unpredictable. There is no simple formula for success. Organizations that are satisfied with their project selection approach typically use a mix of financial, strategic, and scoring methods in an open, established, explicit, formal process. This approach helps to build consensus and develop management insight. It encourages better project proposals by clarifying the desired project attributes. We propose a project scoring technique based on a method previously used in a federal laboratory and supported by recent research. Projects are ranked by their perceived relevance, risk, and return - a new 3 R's. Relevance is the degree to which the project objective supports the HSR&TD goal of developing usable advanced human support technologies. Risk is the estimated probability that the project will achieve its specific objective. Return is the reduction in mission life cycle cost obtained if the project is successful. If the project objective technology performs a new function with no current cost, its return is the estimated cash value of performing the new function. The proposed project selection scoring method includes definitions of the criteria, a project evaluation

Electronic Structure of Fullerene Acceptors in Organic Bulk-Heterojunctions. A Combined EPR and DFT Study

DOE PAGES

Mardis, Kristy L.; Webb, J.; Holloway, Tarita; ...

2015-12-03

Organic photovoltaic (OPV) devices are a promising alternative energy source. Attempts to improve their performance have focused on the optimization of electron-donating polymers, while electron-accepting fullerenes have received less attention. Here, we report an electronic structure study of the widely used soluble fullerene derivatives PC61BM and PC71BM in their singly reduced state, that are generated in the polymer:fullerene blends upon light-induced charge separation. Density functional theory (DFT) calculations characterize the electronic structures of the fullerene radical anions through spin density distributions and magnetic resonance parameters. The good agreement of the calculated magnetic resonance parameters with those determined experimentally by advancedmore » electron paramagnetic resonance (EPR) allows the validation of the DFT calculations. Thus, for the first time, the complete set of magnetic resonance parameters including directions of the principal g-tensor axes were determined. For both molecules, no spin density is present on the PCBM side chain, and the axis of the largest g-value lies along the PCBM molecular axis. While the spin density distribution is largely uniform for PC61BM, it is not evenly distributed for PC71BM.« less

Adaptation of the TdT assay for semi-quantitative flow cytometric detection of DNA strand breaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bromidge, T.J.; Howe, D.J.; Johnson, S.A.

The enzyme Terminal Deoxynucleotidyl Transferase (TdT) is a DNA polymerase which can be used to label DNA strand breaks by the incorporation of a labelled nucleotide followed by a fluorescent detection step. The amount of label incorporated can then be assessed by flow cytometry. The mechanism of action of TdT, however, will allow the addition of varying numbers of nucleotides to the free 3{prime} termini produced by DNA strand breaks. The substitution of Digoxigenin (DIG){trademark} labelled dideoxynucleotides for labelled deoxy-nucleotides in the TdT assay will limit the addition of label to a DNA break to a single nucleotide, thus ensuringmore » a direct relationship between an increase in DNA strand breaks and an increase in fluorescence. We have used this adaptation of the TdT assay to evaluate DNA damage incurred in lymphocytes, from patients with Chronic Lymphocytic Leukemia (CLL), on exposure to UV irradiation and apoptosis-inducing drugs, fludarabine and 2-Chloro-2{prime}-deoxyadenosine (2-CdA). This technique may give a good indication of the susceptibility of CLL patients to apoptosis inducing drugs, and hence an indication of the likely response to these therapies. 7 refs., 2 figs., 2 tabs.« less

Using SpaceClaim/TD Direct for Modeling Components with Complex Geometries for the Thermal Desktop-Based Advanced Stirling Radioisotope Generator Model

NASA Technical Reports Server (NTRS)

Fabanich, William

2014-01-01

SpaceClaim/TD Direct has been used extensively in the development of the Advanced Stirling Radioisotope Generator (ASRG) thermal model. This paper outlines the workflow for that aspect of the task and includes proposed best practices and lessons learned. The ASRG thermal model was developed to predict component temperatures and power output and to provide insight into the prime contractors thermal modeling efforts. The insulation blocks, heat collectors, and cold side adapter flanges (CSAFs) were modeled with this approach. The model was constructed using mostly TD finite difference (FD) surfaces solids. However, some complex geometry could not be reproduced with TD primitives while maintaining the desired degree of geometric fidelity. Using SpaceClaim permitted the import of original CAD files and enabled the defeaturing repair of those geometries. TD Direct (a SpaceClaim add-on from CRTech) adds features that allowed the mark-up of that geometry. These so-called mark-ups control how finite element (FE) meshes were generated and allowed the tagging of features (e.g. edges, solids, surfaces). These tags represent parameters that include: submodels, material properties, material orienters, optical properties, and radiation analysis groups. TD aliases were used for most tags to allow analysis to be performed with a variety of parameter values. Domain-tags were also attached to individual and groups of surfaces and solids to allow them to be used later within TD to populate objects like, for example, heaters and contactors. These tools allow the user to make changes to the geometry in SpaceClaim and then easily synchronize the mesh in TD without having to redefine these objects each time as one would if using TD Mesher.The use of SpaceClaim/TD Direct has helped simplify the process for importing existing geometries and in the creation of high fidelity FE meshes to represent complex parts. It has also saved time and effort in the subsequent analysis.

Muon contact hyperfine field in metals: A DFT calculation

NASA Astrophysics Data System (ADS)

Onuorah, Ifeanyi John; Bonfà, Pietro; De Renzi, Roberto

2018-05-01

In positive muon spin rotation and relaxation spectroscopy it is becoming customary to take advantage of density functional theory (DFT) based computational methods to aid the experimental data analysis. DFT-aided muon site determination is especially useful for measurements performed in magnetic materials, where large contact hyperfine interactions may arise. Here we present a systematic analysis of the accuracy of the ab initio estimation of muon's hyperfine contact field on elemental transition metals, performing state-of-the-art spin-polarized plane-wave DFT and using the projector-augmented pseudopotential approach, which allows one to include the core state effects due to the spin ordering. We further validate this method in not-so-simple, noncentrosymmetric metallic compounds, presently of topical interest for their spiral magnetic structure giving rise to skyrmion phases, such as MnSi and MnGe. The calculated hyperfine fields agree with experimental values in all cases, provided the spontaneous spin magnetization of the metal is well reproduced within the approach. To overcome the known limits of the conventional mean-field approximation of DFT on itinerant magnets, we adopt the so-called reduced Stoner theory [L. Ortenzi et al., Phys. Rev. B 86, 064437 (2012), 10.1103/PhysRevB.86.064437]. We establish the accuracy of the estimated muon contact field in metallic compounds with DFT and our results show improved agreement with experiments compared to those of earlier publications.

Users manual and modeling improvements for axial turbine design and performance computer code TD2-2

NASA Technical Reports Server (NTRS)

Glassman, Arthur J.

1992-01-01

Computer code TD2 computes design point velocity diagrams and performance for multistage, multishaft, cooled or uncooled, axial flow turbines. This streamline analysis code was recently modified to upgrade modeling related to turbine cooling and to the internal loss correlation. These modifications are presented in this report along with descriptions of the code's expanded input and output. This report serves as the users manual for the upgraded code, which is named TD2-2.

Optical Gaps in Pristine and Heavily Doped Silicon Nanocrystals: DFT versus Quantum Monte Carlo Benchmarks.

PubMed

Derian, R; Tokár, K; Somogyi, B; Gali, Á; Štich, I

2017-12-12

We present a time-dependent density functional theory (TDDFT) study of the optical gaps of light-emitting nanomaterials, namely, pristine and heavily B- and P-codoped silicon crystalline nanoparticles. Twenty DFT exchange-correlation functionals sampled from the best currently available inventory such as hybrids and range-separated hybrids are benchmarked against ultra-accurate quantum Monte Carlo results on small model Si nanocrystals. Overall, the range-separated hybrids are found to perform best. The quality of the DFT gaps is correlated with the deviation from Koopmans' theorem as a possible quality guide. In addition to providing a generic test of the ability of TDDFT to describe optical properties of silicon crystalline nanoparticles, the results also open up a route to benchmark-quality DFT studies of nanoparticle sizes approaching those studied experimentally.

DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials.

PubMed

Georgieva, Ivelina; Danchova, Nina; Gutzov, Stoyan; Trendafilova, Natasha

2012-06-01

Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as IR and UV-Vis transmittance and diffuse reflectance spectroscopies. Based on DFT model calculations and simulated and experimental UV-Vis and IR spectra of all the studied structures, the most probable building units of the Zr(IV)-AcAc gel were predicted: the dimeric double hydroxo-bridged complex Zr(2)(AcAc)(2)(OH)(4)(OH)(2br) 9 and the monooxo-bridged complex Zr(2)(AcAc)(2)(OH)(4)O(br)·2H(2)O 12. In both structures, the two AcAc ligands are coordinated to one Zr atom. It was shown that building units 9 and 12 determine the photophysical and vibrational properties of the gel material. The observed UV-Vis and IR spectra of Zr(IV)-AcAc gel were interpreted and a relation between the spectroscopic and structural data was derived. The observed UV-Vis bands at 315 nm and 298/288 nm were assigned to partial ligand-metal transitions and to intra-/inter-AcAc ligand transitions, respectively.

Density functional theory studies on the structures and electronic communication of meso-ferrocenylporphyrins: long range orbital coupling via porphyrin core.

PubMed

Zhang, Lijuan; Qi, Dongdong; Zhang, Yuexing; Bian, Yongzhong; Jiang, Jianzhuang

2011-02-01

The molecular and electronic structures together with the electronic absorption spectra of a series of metal free meso-ferrocenylporphyrins, namely 5-ferrocenylporphyrin (1), 5,10-diferrocenylporphyrin (2), 5,15-diferrocenylporphyrin (3), 5,10,15-triferrocenylporphyrin (4), and 5,10,15,20-tetraferrocenylporphyrin (5) have been studied with the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. For the purpose of comparative studies, metal free porphyrin without any ferrocenyl group (0) and isolated ferrocene (6) were also calculated. The effects of the number and position of meso-attached ferrocenyl substituents on their molecular and electronic structures, atomic charges, molecular orbitals, and electronic absorption spectra of 1-5 were systematically investigated. The orbital coupling is investigated in detail, explaining well the long range coupling of ferrocenyl substituents connected via porphyrin core and the systematic change in the electronic absorption spectra of porphyrin compounds. Copyright © 2010 Elsevier Inc. All rights reserved.

Synthesis, spectroscopic investigation and theoretical studies of 2-((E)-(2-(2-cyanoacetyl)hydrazono)methyl)-4-((E)-phenyldiazenyl)phenyl methyl carbonate

NASA Astrophysics Data System (ADS)

Arokiasamy, A.; Manikandan, G.; Thanikachalam, V.; Gokula Krishnan, K.

2017-04-01

Synthesis and computational optimization studies have been carried out by Hartree-Fock (HF) and Density Functional Theory (DFT-B3LYP) methods with 6-31+G(d, p) basis set for 2-((E)-(2-(2-cyanoacetyl)hydrazono)methyl)-4-((E)-phenyldiazenyl)phenyl methyl carbonate (CHPMC). The stable configuration of CHPMC was confirmed theoretically by potential energy surface scan analysis. The complete vibrational assignments were performed on the basis of total energy distribution (TED) analysis. The vibrational properties studied by IR and Raman spectroscopic data complemented by quantum chemical calculations support the formation of intramolecular hydrogen bond. Furthermore, the UV-Vis spectra are interpreted in terms of TD-DFT quantum chemical calculations. The shapes of the simulated absorption spectra are in good agreement with the experimental data. The comparison between the experimental and theoretical values of FT-IR, FT-Raman vibrational spectra, NMR (1H and 13C) and UV-Vis spectra have also been discussed.

Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

PubMed

Barakat, Assem; Al-Najjar, Hany J; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-05

The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

In search for an optimal methodology to calculate the valence electron affinities of temporary anions.

PubMed

Puiatti, Marcelo; Vera, D Mariano A; Pierini, Adriana B

2009-10-28

Recently, we have proposed an approach for finding the valence anion ground state, based on the stabilization exerted by a polar solvent; the methodology used standard DFT methods and relatively inexpensive basis sets and yielded correct electron affinity (EA) values by gradually decreasing the dielectric constant of the medium. In order to address the overall performance of the new methodology, to find the best conditions for stabilizing the valence state and to evaluate its scope and limitations, we gathered a pool of 60 molecules, 25 of them bearing the conventional valence state as the ground anion and 35 for which the lowest anion state found holds the extra electron in a diffuse orbital around the molecule (non valence state). The results obtained by testing this representative set suggest a very good performance for most species having an experimental EA less negative than -3.0 eV; the correlation at the B3LYP/6-311+G(2df,p) level being y = 1.01x + 0.06, with a correlation index of 0.985. As an alternative, the time dependent DFT (TD-DFT) approach was also tested with both B3LYP and PBE0 functionals. The methodology we proposed shows a comparable or better accuracy with respect to TD-DFT, although the TD-DFT approach with the PBE0 functional is suggested as a suitable estimate for species with the most negative EAs (ca.-2.5 to -3.5 eV), for which stabilization strategies can hardly reach the valence state. As an application, a pool of 8 compounds of key biological interest with EAs which remain unknown or unclear were predicted using the new methodology.

DFT studies of hydrocarbon combustion on metal surfaces.

PubMed

Arya, Mina; Mirzaei, Ali Akbar; Davarpanah, Abdol Mahmood; Barakati, Seyed Masoud; Atashi, Hossein; Mohsenzadeh, Abas; Bolton, Kim

2018-02-02

Catalytic combustion of hydrocarbons is an important technology to produce energy. Compared to conventional flame combustion, the catalyst enables this process to operate at lower temperatures; hence, reducing the energy required for efficient combustion. The reaction and activation energies of direct combustion of hydrocarbons (CH → C + H) on a series of metal surfaces were investigated using density functional theory (DFT). The data obtained for the Ag, Au, Al, Cu, Rh, Pt, and Pd surfaces were used to investigate the validity of the Brønsted-Evans-Polanyi (BEP) and transition state scaling (TSS) relations for this reaction on these surfaces. These relations were found to be valid (R 2  = 0.94 for the BEP correlation and R 2  = 1.0 for the TSS correlation) and were therefore used to estimate the energetics of the combustion reaction on Ni, Co, and Fe surfaces. It was found that the estimated transition state and activation energies (E TS  = -69.70 eV and E a  = 1.20 eV for Ni, E TS  = -87.93 eV and E a  = 1.08 eV for Co and E TS  = -92.45 eV and E a  = 0.83 eV for Fe) are in agreement with those obtained by DFT calculations (E TS  = -69.98 eV and E a  = 1.23 eV for Ni, E TS  = -87.88 eV and E a  = 1.08 eV for Co and E TS  = -92.57 eV and E a  = 0.79 eV for Fe). Therefore, these relations can be used to predict energetics of this reaction on these surfaces without doing the time consuming transition state calculations. Also, the calculations show that the activation barrier for CH dissociation decreases in the order Ag ˃ Au ˃ Al ˃ Cu ˃ Pt ˃ Pd ˃ Ni > Co > Rh > Fe.

An EQT-cDFT approach to determine thermodynamic properties of confined fluids.

PubMed

Mashayak, S Y; Motevaselian, M H; Aluru, N R

2015-06-28

We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.

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

PubMed

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

2014-08-14

The molecular structure of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) was optimized by the DFT/B3LYP method with 6-311G (d,p), 6-311++G (d,p) and cc-pVTZ basis sets using the Gaussian 09 program. The most stable optimized structure of the molecule was predicted by the DFT/B3LYP method with cc-pVTZ basis set. The vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals and thermodynamical parameters were calculated. These calculations were done at the ground state energy level of BABP without applying any constraint on the potential energy surface. The vibrational spectra were experimentally recorded using Fourier Transform-Infrared (FT-IR) and micro-Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of Potential Energy Distribution (PED) calculation using the VEDA 4.0 program. The vibrational modes assignments were performed by using the animation option of GaussView 05 graphical interface for Gaussian program. The Mulliken atomic charge distribution was calculated for BABP molecule. The molecular reactivity and stability of BABP were also studied by frontier molecular orbitals (FMOs) analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, spectroscopic characterization, theoretical study and anti-hepatic cancer activity study of 4-(1E,3Z,6E)-3-hydroxy-7-(4-hydroxy-3-methoxyphenyl)-5-oxohepta-1,3,6-trien-1-yl)-2-methoxyphenyl 4-nitrobenzoate, a novel curcumin congener

NASA Astrophysics Data System (ADS)

Srivastava, Sangeeta; Gupta, Preeti; Singh, Ranvijay Pratap; Jafri, Asif; Arshad, M.; Banerjee, Monisha

2017-08-01

In the present work 4-(1E,3Z,6E)-3-hydroxy-7-(4-hydroxy-3-methoxyphenyl)-5-oxohepta-1,3,6-trien-1-yl)-2-methoxyphenyl 4-nitrobenzoate (2), a novel curcumin ester was synthesized. The molecular structure and spectroscopic analysis were performed using experimental techniques like FT-IR, 1H,13C NMR, mass and UV-visible as well as theoretical calculations. The theoretical calculations were done by DFT level of theory using B3LYP/6-31G (d,p) basis set. The vibrational wavenumbers were calculated using DFT method and assigned with the help of potential energy distribution (PED). The electronic properties such as frontier orbitals and band gap energies have been calculated using time dependent density functional theory (TD-DFT). The strength and nature of weak intramolecular interactions have been studied by AIM approach. Global and local reactivity descriptors have been computed to predict reactivity and reactive sites in the molecule. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compounds. Molecular electrostatic potential (MEP) analysis has also been carried out. The anti-hepatic cancer activity of compound 2 was also carried out.

Two-Photon Absorption Properties of Gold Fluorescent Protein: A Combined Molecular Dynamics and Quantum Chemistry Study.

PubMed

Şimşek, Yusuf; Brown, Alex

2018-06-07

Molecular dynamics (MD) simulations were carried out to obtain the conformational changes of the chromophore in the gold fluorescent protein (PDB ID: 1OXF ). To obtain two-photon absorption (TPA) cross-sections, time dependent density functional theory (TD-DFT) computations were performed for chromophore geometries sampled along the trajectory. The TD-DFT computations used the CAM-B3LYP functional and 6-31+G(d) basis set. Results showed that two dihedral angles change remarkably over the simulation time. TPA cross-sections were found to average 13.82 GM for the excitation to S 1 computed from the equilibrium geometries; however, extending the structures with a water molecule and GLU residue, which make H bonds with the chromophore molecule, increased excitation energies and TPA cross-sections significantly. Besides the effects of the surrounding residues and the dihedrals on the spectroscopic properties, some bond lengths affected the excitation energies and the TPA cross-sections significantly (up to ±25-30%), while the effects of the bond angles were smaller (±5%). Overall the present results provide insight into the effects of the conformational flexibility on TPA (with gold fluorescent protein as a specific example) and suggest that further experimental measurements of TPA for the gold fluorescent protein should be undertaken.

Ethylene dissociation on flat and stepped Ni(1 1 1): A combined STM and DFT study

NASA Astrophysics Data System (ADS)

Vang, Ronnie T.; Honkala, Karoliina; Dahl, Søren; Vestergaard, Ebbe K.; Schnadt, Joachim; Lægsgaard, Erik; Clausen, Bjerne S.; Nørskov, Jens K.; Besenbacher, Flemming

2006-01-01

The dissociative adsorption of ethylene (C 2H 4) on Ni(1 1 1) was studied by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The STM studies reveal that ethylene decomposes exclusively at the step edges at room temperature. However, the step edge sites are poisoned by the reaction products and thus only a small brim of decomposed ethylene is formed. At 500 K decomposition on the (1 1 1) facets leads to a continuous growth of carbidic islands, which nucleate along the step edges. DFT calculations were performed for several intermediate steps in the decomposition of ethylene on both Ni(1 1 1) and the stepped Ni(2 1 1) surface. In general the Ni(2 1 1) surface is found to have a higher reactivity than the Ni(1 1 1) surface. Furthermore, the calculations show that the influence of step edge atoms is very different for the different reaction pathways. In particular the barrier for dissociation is lowered significantly more than the barrier for dehydrogenation, and this is of great importance for the bond-breaking selectivity of Ni surfaces. The influence of step edges was also probed by evaporating Ag onto the Ni(1 1 1) surface. STM shows that the room temperature evaporation leads to a step flow growth of Ag islands, and a subsequent annealing at 800 K causes the Ag atoms to completely wet the step edges of Ni(1 1 1). The blocking of the step edges is shown to prevent all decomposition of ethylene at room temperature, whereas the terrace site decomposition at 500 K is confirmed to be unaffected by the Ag atoms. Finally a high surface area NiAg alloy catalyst supported on MgAl 2O 4 was synthesized and tested in flow reactor measurements. The NiAg catalyst has a much lower activity for ethane hydrogenolysis than a similar Ni catalyst, which can be rationalized by the STM and DFT results.

Symmetry properties of the electron density and following from it limits on the KS-DFT applications

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.

2018-03-01

At present, the Density Functional Theory (DFT) approach elaborated by Kohn with co-authors more than 50 years ago became the most widely used method for study molecules and solids. Using modern computation facilities, it can be applied to systems with million atoms. In the atmosphere of such great popularity, it is particularly important to know the limits of the applicability of DFT methods. In this report, I will discuss two cases when the conventional DFT approaches, using only electron density ρ and its gradients, cannot be applied (I will not consider the Ψ-versions of DFT). The first case is quite evident. In the degenerated states, the electron density may not be defined, since electronic and nuclear motions cannot be separated, the vibronic interaction mixed them. The second case is related to the spin of the state. As it was rigorously proved by group theoretical methods at the theorem level, the electron density does not depend on the total spin S of the arbitrary N-electron state. It means that the Kohn-Sham equations have the same form for states with different S. The critical survey of elaborated DFT procedures, taking into account spin, shows that they modified only exchange functionals, the correlation functionals do not correspond to the spin of the state. The point is that the conception of spin cannot be defined in the framework of the electron density formalism, which corresponds to the one-particle reduced density matrix. This is the main reason of the problems arising in the study by DFT of magnetic properties of the transition metals. The possible way of resolving these problems can be found in the two-particle reduced density matrix formulation of DFT.

DFT-Assisted Polymorph Identification from Lattice Raman Fingerprinting

PubMed Central

2017-01-01

A combined experimental and theoretical approach, consisting of lattice phonon Raman spectroscopy and density functional theory (DFT) calculations, is proposed as a tool for lattice dynamics characterization and polymorph phase identification. To illustrate the reliability of the method, the lattice phonon Raman spectra of two polymorphs of the molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]benzothiophene are investigated. We show that DFT calculations of the lattice vibrations based on the known crystal structures, including many-body dispersion van der Waals (MBD-vdW) corrections, predict experimental data within an accuracy of ≪5 cm–1 (≪0.6 meV). Due to the high accuracy of the simulations, they can be used to unambiguously identify different polymorphs and to characterize the nature of the lattice vibrations and their relationship to the structural properties. More generally, this work implies that DFT-MBD-vdW is a promising method to describe also other physical properties that depend on lattice dynamics like charge transport. PMID:28731723

Computational tests of quantum chemical models for excited and ionized states of molecules with phosphorus and sulfur atoms.

PubMed

Hahn, David K; RaghuVeer, Krishans; Ortiz, J V

2014-05-15

Time-dependent density functional theory (TD-DFT) and electron propagator theory (EPT) are used to calculate the electronic transition energies and ionization energies, respectively, of species containing phosphorus or sulfur. The accuracy of TD-DFT and EPT, in conjunction with various basis sets, is assessed with data from gas-phase spectroscopy. TD-DFT is tested using 11 prominent exchange-correlation functionals on a set of 37 vertical and 19 adiabatic transitions. For vertical transitions, TD-CAM-B3LYP calculations performed with the MG3S basis set are lowest in overall error, having a mean absolute deviation from experiment of 0.22 eV, or 0.23 eV over valence transitions and 0.21 eV over Rydberg transitions. Using a larger basis set, aug-pc3, improves accuracy over the valence transitions via hybrid functionals, but improved accuracy over the Rydberg transitions is only obtained via the BMK functional. For adiabatic transitions, all hybrid functionals paired with the MG3S basis set perform well, and B98 is best, with a mean absolute deviation from experiment of 0.09 eV. The testing of EPT used the Outer Valence Green's Function (OVGF) approximation and the Partial Third Order (P3) approximation on 37 vertical first ionization energies. It is found that OVGF outperforms P3 when basis sets of at least triple-ζ quality in the polarization functions are used. The largest basis set used in this study, aug-pc3, obtained the best mean absolute error from both methods -0.08 eV for OVGF and 0.18 eV for P3. The OVGF/6-31+G(2df,p) level of theory is particularly cost-effective, yielding a mean absolute error of 0.11 eV.

Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost

NASA Astrophysics Data System (ADS)

Bajaj, Akash; Janet, Jon Paul; Kulik, Heather J.

2017-11-01

The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and molecules. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such physically intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT.

Design Techniques for Uniform-DFT, Linear Phase Filter Banks

NASA Technical Reports Server (NTRS)

Sun, Honglin; DeLeon, Phillip

1999-01-01

Uniform-DFT filter banks are an important class of filter banks and their theory is well known. One notable characteristic is their very efficient implementation when using polyphase filters and the FFT. Separately, linear phase filter banks, i.e. filter banks in which the analysis filters have a linear phase are also an important class of filter banks and desired in many applications. Unfortunately, it has been proved that one cannot design critically-sampled, uniform-DFT, linear phase filter banks and achieve perfect reconstruction. In this paper, we present a least-squares solution to this problem and in addition prove that oversampled, uniform-DFT, linear phase filter banks (which are also useful in many applications) can be constructed for perfect reconstruction. Design examples are included illustrate the methods.

Study of B{yields}X{gamma} decays and determination of |V{sub td}/V{sub ts}|

DOE Office of Scientific and Technical Information (OSTI.GOV)

del Amo Sanchez, P.; Lees, J. P.; Poireau, V.

2010-09-01

Using a sample of 471x10{sup 6} BB events collected with the BABAR detector, we study the sum of seven exclusive final states B{yields}X{sub s(d){gamma}}, where X{sub s(d)} is a strange (nonstrange) hadronic system with a mass of up to 2.0 GeV/c{sup 2}. After correcting for unobserved decay modes, we obtain a branching fraction for b{yields}d{gamma} of (9.2{+-}2.0(stat){+-}2.3(syst))x10{sup -6} in this mass range, and a branching fraction for b{yields}s{gamma} of (23.0{+-}0.8(stat){+-}3.0(syst))x10{sup -5} in the same mass range. We find (B(b{yields}d{gamma})/B(b{yields}s{gamma}))=0.040{+-}0.009(stat){+-}0.010(syst), from which we determine |V{sub td}/V{sub ts}|=0.199{+-}0.022(stat){+-}0.024(syst){+-}0.002(th).

ERBB3: A potential serum biomarker for early detection and therapeutic target for devil facial tumour 1 (DFT1)

PubMed Central

Kunde, Dale A.; Taylor, Robyn L.; Pyecroft, Stephen B.; Sohal, Sukhwinder Singh; Snow, Elizabeth T.

2017-01-01

Devil Facial Tumour 1 (DFT1) is one of two transmissible neoplasms of Tasmanian devils (Sarcophilus harrisii) predominantly affecting their facial regions. DFT1’s cellular origin is that of Schwann cell lineage where lesions are evident macroscopically late in the disease. Conversely, the pre-clinical timeframe from cellular transmission to appearance of DFT1 remains uncertain demonstrating the importance of an effective pre-clinical biomarker. We show that ERBB3, a marker expressed normally by the developing neural crest and Schwann cells, is immunohistohemically expressed by DFT1, therefore the potential of ERBB3 as a biomarker was explored. Under the hypothesis that serum ERBB3 levels may increase as DFT1 invades local and distant tissues our pilot study determined serum ERBB3 levels in normal Tasmanian devils and Tasmanian devils with DFT1. Compared to the baseline serum ERBB3 levels in unaffected Tasmanian devils, Tasmanian devils with DFT1 showed significant elevation of serum ERBB3 levels. Interestingly Tasmanian devils with cutaneous lymphoma (CL) also showed elevation of serum ERBB3 levels when compared to the baseline serum levels of Tasmanian devils without DFT1. Thus, elevated serum ERBB3 levels in otherwise healthy looking devils could predict possible DFT1 or CL in captive or wild devil populations and would have implications on the management, welfare and survival of Tasmanian devils. ERBB3 is also a therapeutic target and therefore the potential exists to consider modes of administration that may eradicate DFT1 from the wild. PMID:28591206

3-Iodobenzaldehyde: XRD, FT-IR, Raman and DFT studies.

PubMed

Kumar, Chandraju Sadolalu Chidan; Parlak, Cemal; Tursun, Mahir; Fun, Hoong-Kun; Rhyman, Lydia; Ramasami, Ponnadurai; Alswaidan, Ibrahim A; Keşan, Gürkan; Chandraju, Siddegowda; Quah, Ching Kheng

2015-06-15

The structure of 3-iodobenzaldehyde (3IB) was characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 3IB were examined using density functional theory (DFT) method, with the Becke-3-Lee-Yang-Parr (B3LYP) functional and the 6-311+G(3df,p) basis set for all atoms except for iodine. The LANL2DZ effective core basis set was used for iodine. Potential energy distribution (PED) analysis of normal modes was performed to identify characteristic frequencies. 3IB crystallizes in monoclinic space group P21/c with the O-trans form. There is a good agreement between the theoretically predicted structural parameters, and vibrational frequencies and those obtained experimentally. In order to understand halogen effect, 3-halogenobenzaldehyde [XC6H4CHO; X=F, Cl and Br] was also studied theoretically. The free energy difference between the isomers is small but the rotational barrier is about 8kcal/mol. An atypical behavior of fluorine affecting conformational preference is observed. Copyright © 2015 Elsevier B.V. All rights reserved.

A DFT study of the mechanism and the regioselectivity of [3 + 2] cycloaddition reactions of nitrile oxides with α,β-acetylenic aldehyde

NASA Astrophysics Data System (ADS)

Sobhi, Chafia; Nacereddine, Abdelmalek Khorief; Nasri, Lilia; Lechtar, Zohra; Djerourou, Abdelhafid

2016-11-01

A DFT study of the (32CA) reaction of a series of some nitrile oxides with electron-deficient alkyne (3-phenylpropionlaldehyde) in gas phase and in toluene has been carried out using B3LYP functional with 6-31G(d) basis set. Two reactive channels 4- and 5-associated with the two regioisomeric modes have been located and characterised. These 32CA reactions are characterised by a low asynchronous one-step mechanism with a low-polar character. Analysis of the DFT reactivity indices indicates that the nucleophilic centre of the different nitrile oxides accounts for the 4-regioselectivity. Our calculations are in a good agreement with the experimental findings.

Quantum Chemical Design Guidelines for Absorption and Emission Color Tuning of fac-Ir(ppy)₃ Complexes.

PubMed

Natori, Yoshiki; Kitagawa, Yasutaka; Aoki, Shogo; Teramoto, Rena; Tada, Hayato; Era, Iori; Nakano, Masayoshi

2018-03-05

The fac -Ir(ppy)₃ complex, where ppy denotes 2-phenylpyridine, is one of the well-known luminescent metal complexes having a high quantum yield. However, there have been no specific molecular design guidelines for color tuning. For example, it is still unclear how its optical properties are changed when changing substitution groups of ligands. Therefore, in this study, differences in the electronic structures and optical properties among several substituted fac -Ir(ppy)₃ derivatives are examined in detail by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. On the basis of those results, we present rational design guidelines for absorption and emission color tuning by modifying the species of substituents and their substitution positions.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Vibrational spectroscopic study, charge transfer interaction and nonlinear optical properties of L-asparaginium picrate: a density functional theoretical approach.

PubMed

Elleuch, Nabil; Amamou, Walid; Ben Ahmed, Ali; Abid, Younes; Feki, Habib

2014-07-15

Single crystals of L-asparaginium picrate (LASP) were grown by slow evaporation technique at room temperature and were the subject of an X-ray powder diffraction study to confirm the crystalline nature of the synthesized compound. FT-IR and Raman spectra were recorded and analyzed with the aid of the density functional theory (DFT) calculations in order to make a suitable assignment of the observed bands. The optimum molecular geometry, normal mode wavenumbers, infrared and Raman intensities and the first hyperpolarizability were investigated with the help of B3LYP method using 6-31G(d) basis set. The theoretical FT-IR and Raman spectra of LASP were simulated and compared with the experimental data. A good agreement was shown and a reliable vibrational assignment was made. Natural bond orbital (NBO) analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of the title compound leading to high NLO activity. A study on the electronic properties was performed by time-dependent DFT (TD-DFT) approach. The lowering in the HOMO and LUMO energy gap explains the eventual charge transfer interactions that take place within the molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Nonlinear modeling of crystal system transition of black phosphorus using continuum-DFT model.

PubMed

Setoodeh, A R; Farahmand, H

2018-01-24

In this paper, the nonlinear behavior of black phosphorus crystals is investigated in tandem with dispersion-corrected density functional theory (DFT-D) analysis under uniaxial loadings. From the identified anisotropic behavior of black phosphorus due to its morphological anisotropy, a hyperelastic anisotropic (HA) model named continuum-DFT is established to predict the nonlinear behavior of the material. In this respect, uniaxial Cauchy stresses are employed on both the DFT-D and HA models along the zig-zag and armchair directions. Simultaneously, the transition of the crystal system is recognized at about 4.5 GPa of the applied uniaxial tensile stress along the zig-zag direction on the DFT-D simulation in the nonlinear region. In order to develop the nonlinear continuum model, unknown constants are surveyed with the optimized least square technique. In this regard, the continuum model is obtained to reproduce the Cauchy stress-stretch and density of strain-stretch results of the DFT-D simulation. Consequently, the modified HA model is introduced to characterize the nonlinear behavior of black phosphorus along the zig-zag direction. More importantly, the specific transition of the crystal system is successfully predicted in the new modified continuum-DFT model. The results reveal that the multiscale continuum-DFT model is well defined to replicate the nonlinear behavior of black phosphorus along the zig-zag and armchair directions.

The photophysics of fac-[Re(CO)3(NN)(bpa)](+) complexes: a theoretical/experimental study.

PubMed

Sousa, S F; Sampaio, R N; Barbosa Neto, N M; Machado, A E H; Patrocinio, A O T

2014-08-01

The influence of the polypyridyl ligand on the photophysics of fac-[Re(CO)3(NN)(bpa)](+), bpa = 1,2-bis-(4-pyridyl)ethane and NN = 1,10-phenanthroline (phen), pyrazino[2,3-f][1,10]-phenanthroline (dpq), and dipyrido[3,2-a:2'3'-c]phenazine (dppz) has been investigated by steady state and time-resolved emission spectroscopy combined with theoretical calculations using time-dependent density functional theory (TD-DFT). The fac-[Re(CO)3(phen)(bpa)](+) is a typical MLCT emitter in acetonitrile with ϕ = 0.11 and τ = 970 ns. The emission lifetime and quantum yield decrease significantly in fac-[Re(CO)3(dpq)(bpa)](+) (ϕ = 0.05; τ = 375 ns) due to the presence of a close lying dark charge transfer state located at the pyrazine ring of dpq, as indicated by TD-DFT data. The luminescence of these complexes is quenched by hydroquinone with kq = (2.9 ± 0.1) × 10(9) and (2.6 ± 0.1) × 10(9) L mol(-1) s(-1), respectively, for NN = phen or dpq. These values are increased respectively to (4.6 ± 0.1) × 10(9) and (4.2 ± 0.1) × 10(9) L mol(-1) s(-1) in the 1 : 1 H2O-CH3CN mixture. In this medium Stern-Volmer constants determined by steady-state and time-resolved measurements differ from each other, which is indicative of static quenching, i.e. the pre-association of hydroquinone and the complexes through hydrogen bonding between the remote N-atom in the bpa ligand (KA ≅ 1-2 × 10(1) L mol(-1)), followed by a concerted proton-electron transfer. In contrast to other investigated complexes, fac-[Re(CO)3(dppz)(bpa)](+) is weakly emissive in acetonitrile at room temperature (ϕ ≅ 10(-4)) and does not exhibit a rigidochromic effect. This photophysical behaviour as well as TD-DFT data indicate that the lowest lying triplet excited state can be described as (3)ILdppz. The results provide additional insight into the influence of the polypyridyl ligand on the photophysical properties of Re(I) complexes.

Using SpaceClaimTD Direct for Modeling Components with Complex Geometries for the Thermal Desktop-Based Advanced Stirling Radioisotope Generator Model

NASA Technical Reports Server (NTRS)

Fabanich, William A., Jr.

2014-01-01

SpaceClaim/TD Direct has been used extensively in the development of the Advanced Stirling Radioisotope Generator (ASRG) thermal model. This paper outlines the workflow for that aspect of the task and includes proposed best practices and lessons learned. The ASRG thermal model was developed to predict component temperatures and power output and to provide insight into the prime contractor's thermal modeling efforts. The insulation blocks, heat collectors, and cold side adapter flanges (CSAFs) were modeled with this approach. The model was constructed using mostly TD finite difference (FD) surfaces/solids. However, some complex geometry could not be reproduced with TD primitives while maintaining the desired degree of geometric fidelity. Using SpaceClaim permitted the import of original CAD files and enabled the defeaturing/repair of those geometries. TD Direct (a SpaceClaim add-on from CRTech) adds features that allowed the "mark-up" of that geometry. These so-called "mark-ups" control how finite element (FE) meshes are to be generated through the "tagging" of features (e.g. edges, solids, surfaces). These tags represent parameters that include: submodels, material properties, material orienters, optical properties, and radiation analysis groups. TD aliases were used for most tags to allow analysis to be performed with a variety of parameter values. "Domain-tags" were also attached to individual and groups of surfaces and solids to allow them to be used later within TD to populate objects like, for example, heaters and contactors. These tools allow the user to make changes to the geometry in SpaceClaim and then easily synchronize the mesh in TD without having to redefine the objects each time as one would if using TDMesher. The use of SpaceClaim/TD Direct helps simplify the process for importing existing geometries and in the creation of high fidelity FE meshes to represent complex parts. It also saves time and effort in the subsequent analysis.

Single-particle energies and density of states in density functional theory

NASA Astrophysics Data System (ADS)

van Aggelen, H.; Chan, G. K.-L.

2015-07-01

Time-dependent density functional theory (TD-DFT) is commonly used as the foundation to obtain neutral excited states and transition weights in DFT, but does not allow direct access to density of states and single-particle energies, i.e. ionisation energies and electron affinities. Here we show that by extending TD-DFT to a superfluid formulation, which involves operators that break particle-number symmetry, we can obtain the density of states and single-particle energies from the poles of an appropriate superfluid response function. The standard Kohn- Sham eigenvalues emerge as the adiabatic limit of the superfluid response under the assumption that the exchange- correlation functional has no dependence on the superfluid density. The Kohn- Sham eigenvalues can thus be interpreted as approximations to the ionisation energies and electron affinities. Beyond this approximation, the formalism provides an incentive for creating a new class of density functionals specifically targeted at accurate single-particle eigenvalues and bandgaps.

Insufficient Hartree–Fock Exchange in Hybrid DFT Functionals Produces Bent Alkynyl Radical Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oyeyemi, Victor B.; Keith, John A.; Pavone, Michele

2012-01-11

Density functional theory (DFT) is often used to determine the electronic and geometric structures of molecules. While studying alkynyl radicals, we discovered that DFT exchange-correlation (XC) functionals containing less than ~22% Hartree–Fock (HF) exchange led to qualitatively different structures than those predicted from ab initio HF and post-HF calculations or DFT XCs containing 25% or more HF exchange. We attribute this discrepancy to rehybridization at the radical center due to electron delocalization across the triple bonds of the alkynyl groups, which itself is an artifact of self-interaction and delocalization errors. Inclusion of sufficient exact exchange reduces these errors and suppressesmore » this erroneous delocalization; we find that a threshold amount is needed for accurate structure determinations. Finally, below this threshold, significant errors in predicted alkyne thermochemistry emerge as a consequence.« less

FAST TRACK COMMUNICATION A DFT + DMFT approach for nanosystems

NASA Astrophysics Data System (ADS)

Turkowski, Volodymyr; Kabir, Alamgir; Nayyar, Neha; Rahman, Talat S.

2010-11-01

We propose a combined density-functional-theory-dynamical-mean-field-theory (DFT + DMFT) approach for reliable inclusion of electron-electron correlation effects in nanosystems. Compared with the widely used DFT + U approach, this method has several advantages, the most important of which is that it takes into account dynamical correlation effects. The formalism is illustrated through different calculations of the magnetic properties of a set of small iron clusters (number of atoms 2 <= N <= 5). It is shown that the inclusion of dynamical effects leads to a reduction in the cluster magnetization (as compared to results from DFT + U) and that, even for such small clusters, the magnetization values agree well with experimental estimations. These results justify confidence in the ability of the method to accurately describe the magnetic properties of clusters of interest to nanoscience.

Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT

NASA Astrophysics Data System (ADS)

Selli, Daniele; Fazio, Gianluca; Di Valentin, Cristiana

2017-10-01

TiO2 nanoparticles (NPs) are nowadays considered fundamental building blocks for many technological applications. Morphology is found to play a key role with spherical NPs presenting higher binding properties and chemical activity. From the experimental point of view, the characterization of these nano-objects is extremely complex, opening a large room for computational investigations. In this work, TiO2 spherical NPs of different sizes (from 300 to 4000 atoms) have been studied with a two-scale computational approach. Global optimization to obtain stable and equilibrated nanospheres was performed with a self-consistent charge density functional tight-binding (SCC-DFTB) simulated annealing process, causing a considerable atomic rearrangement within the nanospheres. Those SCC-DFTB relaxed structures have been then optimized at the DFT(B3LYP) level of theory. We present a systematic and comparative SCC-DFTB vs DFT(B3LYP) study of the structural properties, with particular emphasis on the surface-to-bulk sites ratio, coordination distribution of surface sites, and surface energy. From the electronic point of view, we compare HOMO-LUMO and Kohn-Sham gaps, total and projected density of states. Overall, the comparisons between DFTB and hybrid density functional theory show that DFTB provides a rather accurate geometrical and electronic description of these nanospheres of realistic size (up to a diameter of 4.4 nm) at an extremely reduced computational cost. This opens for new challenges in simulations of very large systems and more extended molecular dynamics.

In Vitro Activity of TD-1792, a Multivalent Glycopeptide-Cephalosporin Antibiotic, against 377 Strains of Anaerobic Bacteria and 34 Strains of Corynebacterium Species

PubMed Central

Citron, Diane M.; Warren, Yumi A.; Goldstein, Ellie J. C.

2012-01-01

TD-1792 is a multivalent glycopeptide-cephalosporin heterodimer antibiotic with potent activity against Gram-positive bacteria. We tested TD-1792 against 377 anaerobes and 34 strains of Corynebacterium species. Against nearly all Gram-positive strains, TD-1792 had an MIC90 of 0.25 μg/ml and was typically 3 to 7 dilutions more active than vancomycin and daptomycin. PMID:22290981

RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo

PubMed Central

Waldsich, Christina; Grossberger, Rupert; Schroeder, Renée

2002-01-01

Efficient splicing of the td group I intron in vivo is dependent on the ribosome. In the absence of translation, the pre-mRNA is trapped in nonnative-splicing-incompetent conformations. Alternatively, folding of the pre-mRNA can be promoted by the RNA chaperone StpA or by the group I intron-specific splicing factor Cyt-18. To understand the mechanism of action of RNA chaperones, we probed the impact of StpA on the structure of the td intron in vivo. Our data suggest that StpA loosens tertiary interactions. The most prominent structural change was the opening of the base triples, which are involved in the correct orientation of the two major intron core domains. In line with the destabilizing activity of StpA, splicing of mutant introns with a reduced structural stability is sensitive to StpA. In contrast, Cyt-18 strengthens tertiary contacts, thereby rescuing splicing of structurally compromised td mutants in vivo. Our data provide direct evidence for protein-induced conformational changes within catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the overall compactness of the td intron in vivo. PMID:12208852

NLO properties of ester containing fluorescent carbazole based styryl dyes - Consolidated spectroscopic and DFT approach

NASA Astrophysics Data System (ADS)

Rajeshirke, Manali; Sekar, Nagaiyan

2018-02-01

The linear and nonlinear optical (NLO) properties of new fluorescent styryl dyes based on anchoring ester containing carbazole as donor appended to different acceptor groups to have a conjugated π-system with push-pull geometry are studied. The NLO properties have been determined using solvatochromic and computational methods. Three different TD-DFT functional are used namely, B3LYP, BHandHLYP, and CAM-B3LYP, with aim of elucidating better functional for NLOphores. Further, the two photon properties (σ2PA) have been described theoretically by two level model considering the dipole moment difference between the ground and the final electronic states and bypassing the intermediated resonance state. The compounds with a high charge transfer from the acceptor group to the carbazole ring have relatively high two-photon absorption cross-sections (60-317 GM). The linear polarizability (αCT), first order hyperpolarizability (β) and second order hyperpolarizability (ɣ) for 4c dye was the highest among the studied dyes which is attributed to the lesser energy gap evident by both the methods. But in contrary, the σ2PA cross-section value was low for dye 4c which is due to the presence of freely rotatable twisted phenyl ring in the conjugation path, pulling the electron density towards itself and thus lead to decrease in σ2PA cross-section. Structure-property relationship is better understood by the correlation of bond length alternation/bond order alternation (BLA/BOA) with NLO properties of dyes. Thus by simple solvatochromic method and computational method, we have screened the carbazole styryls as NLO candidates with good first order hyperpolarizability and good two photon cross-section.

DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule.

PubMed

Pandey, Urmila; Srivastava, Mayuri; Singh, R P; Yadav, R A

2014-08-14

The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G(**) level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G(**) method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of ferulic acid by density functional study

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sundaraganesan, N.; Manoharan, S.

2009-10-01

Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of ferulic acid (FA) (4-hydroxy-3-methoxycinnamic acid) were carried out by using density functional (DFT/B3LYP/BLYP) method with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment ( μ) and the first hyperpolarizability ( β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the FA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of FA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title molecule have been constructed.

The spectroscopic (FTIR, FT-Raman and UV-Vis spectra), DFT and normal coordinate computations of m-nitromethylbenzoate

NASA Astrophysics Data System (ADS)

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

2013-08-01

A combined experimental and theoretical study on molecular structure, vibrational spectra, NBO and UV-spectral analysis of m-nitromethylbenzoate (MNMB) has been reported in the present work. The FT-IR solid phase (4000-400 cm-1) and FT-Raman spectra (3500-100 cm-1) of MNMB was recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of MNMB in the ground-state have been calculated by using the density functional method B3LYP with 6-31G (d,p) and 6-31+G(d,p) basis sets. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). Stability of the molecule arising from hyperconjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ∗ antibonding orbitals and E(2) energies confirms the occurrence of ICT (Intra-molecular Charge Transfer) within the molecule. The UV spectrum was measured in ethyl acetate solution. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) result complements the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Finally the calculation results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra.

Structural, theoretical and corrosion inhibition studies on some transition metal complexes derived from heterocyclic system

NASA Astrophysics Data System (ADS)

Gupta, Shraddha Rani; Mourya, Punita; Singh, M. M.; Singh, Vinod P.

2017-06-01

A Schiff base, (E)-N‧-((1H-indol-3-yl)methylene)-2-aminobenzohydrazide (Iabh) and its Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes have been synthesized. These compounds have been characterized by different physico-chemical and spectroscopic tools (UV-Vis, IR, NMR and ESI-Mass). The molecular structure of Iabh is determined by single crystal X-ray diffraction technique. The ligand Iabh displays E-configuration about the >Cdbnd N- bond. The structure of ligand is stabilized by intra-molecular H-bonding. In all the metal complexes the ligand coordinates through azomethine-N and carbonyl-O resulting a distorted octahedral geometry for Mn(II), Co(II) and Cu(II) complexes in which chloride ions occupy axial positions. Ni(II) and Zn(II) complexes, however, form 4-coordinate distorted square planer and tetrahedral geometry around metal ion, respectively. The structures of the complexes have been satisfactorily modeled by calculations based on density functional theory (DFT) and time dependent-DFT (TD-DFT). The corrosion inhibition study of the compounds have been performed against mild steel in 0.5 M H2SO4 solution at 298 K by using weight loss, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). They show appreciable corrosion inhibition property.

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide-M(2+) (M = Ca, Sr).

PubMed

Martín-Sómer, Ana; Gaigeot, Marie-Pierre; Yáñez, Manuel; Spezia, Riccardo

2014-07-28

A kinetic study of the unimolecular reactivity of formamide-M(2+) (M = Ca, Sr) systems was carried out by means of RRKM statistical theory using high-level DFT. The results predict M(2+), [M(NH2)](+) and [HCO](+) as the main products, together with an intermediate that could eventually evolve to produce [M(NH3)](2+) and CO, for high values of internal energy. In this framework, we also evaluated the influence of the external rotational energy on the reaction rate constants. In order to find a method to perform reliable electronic structure calculations for formamide-M(2+) (M = Ca, Sr) at a relatively low computational cost, an assessment of different methods was performed. In the first assessment twenty-one functionals, belonging to different DFT categories, and an MP2 wave function method using a small basis set were evaluated. CCSD(T)/cc-pWCVTZ single point calculations were used as reference. A second assessment has been performed on geometries and energies. We found BLYP/6-31G(d) and G96LYP/6-31+G(d,p) as the best performing methods, for formamide-Ca(2+) and formamide-Sr(2+), respectively. Furthermore, a detailed assessment was done on RRKM reactivity and G96LYP/6-31G(d) provided results in agreement with higher level calculations. The combination of geometrical, energetics and kinetics (RRKM) criteria to evaluate DFT functionals is rather unusual and provides an original assessment procedure. Overall, we suggest using G96LYP as the best performing functional with a small basis set for both systems.

Synthesis, DFT band structure calculations, optical and photoelectrical characterizations of the novel 5-hydroxy-4-methoxy-7-oxo-7H-furo[3,2-g]chromene-6-carbonitrile (HMOFCC)

NASA Astrophysics Data System (ADS)

Ibrahim, Magdy A.; Halim, Shimaa Abdel; Roushdy, N.; Farag, A. A. M.; El-Gohary, Nasser M.

2017-11-01

Reaction of 4-methoxy-5-oxo-5H-furo[3,2-g]chromene-6-carboxaldehyde (1) with hydroxylamine hydrochloride resulted in ring transformation producing the novel 5-hydroxy-4-methoxy-7-oxo-7H-furo[3,2-g]chromene-6-carbonitrile (HMOFCC). The structure was deduced based on its correct elemental analysis and spectral data (IR, 1H NMR, 13C NMR and mass spectra). The geometries of the HMOFCC were completely optimized by means of DFT-B3LYP/6-311++G (d,p) theoretical level. The ground state properties such as; total energy, the energy of HOMO and LUMO and Mulliken atomic charges were also determined. In addition, the two solvents; polar (methanol) and nonpolar (dioxane) were utilized to extract the electronic absorption spectra. The assignment of the detected bands was discussed by TD-DFT calculations. A cauliflower-like, as well as, needle-like leaves morphologies were observed using scanning electron microscope images. Two direct optical band gaps were extracted from the photon energy dependence of absorption coefficient at the band edges and found to be 1.16 and 2.56 eV. A characteristic emission peak of photoluminescence spectrum was observed and shifted depending on the solvent type. A remarkable rectification characteristic of HMOFCC/p-Si heterojunction confirms the diode-like behavior. The main important parameters like series resistance, shunt resistance and reverse saturation current show illumination dependence under influence of the illumination intensity range 20-100 mW/cm2. The heterojunction based HMOFCC showed phototransient properties under various illumination intensities which give the recommendation for the studied heterojunction in the field of optoelectronic device application.

27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

USDA-ARS?s Scientific Manuscript database

DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

Conformations of n-butyl imidazole: matrix isolation infrared and DFT studies.

PubMed

Ramanathan, N; Sundararajan, K; Sankaran, K

2015-03-15

Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(∓)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(∓), tg(±)g(∓)g(∓), tg(±)g(±)g(±), tg(±)g(∓)g(±) and tg(±)g(±)g(∓) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ∼2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID. Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed

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

2015-01-01

Violacein is a bisindole pigment occurring as a biosynthetic product of Chromobacterium violaceum and Janthinobacterium lividum. It has some structural similarities to the cyanobacterial UV-protective pigment scytonemin, which has been the subject of comprehensive spectroscopic and structural studies. A detailed experimental Raman spectroscopic study with visible and near-infrared excitation of violacein produced by C. violaceum has been undertaken and supported using theoretical DFT calculations. Raman spectra with 514 and 785 nm excitation of cultivated cells as well as extracts and Gaussian (B3LYP/6-311++G(d,p)) calculations with proposed molecular vibrational assignments are reported here. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulating Excitons in MoS2 with Time-Dependent Density Functional Theory

NASA Astrophysics Data System (ADS)

Flamant, Cedric; Kolesov, Grigory; Kaxiras, Efthimios

Monolayer molybdenum disulfide, owing to its graphene-like two-dimensional geometry whilst still having a finite bandgap, is a material of great interest in condensed matter physics and for potential application in electronic devices. In particular, MoS2 exhibits significant excitonic effects, a desirable quality for fundamental many-body research. Time-dependent density functional theory (TD-DFT) allows us to simulate dynamical effects as well as temperature-based effects in a natural way given the direct treatment of the time evolution of the system. We present a TD-DFT study of monolayer MoS2 exciton dynamics, examining various qualitative and quantitative predictions in pure samples and in the presence of defects. In particular, we generate an absorption spectrum through simulated pulse excitation for comparison to experiment and also analyze the response of the exciton in an external electric field.In this work we also discuss the electronic structure of the exciton in MoS2 with and without vacancies.

Implementation of DFT application on ternary optical computer

NASA Astrophysics Data System (ADS)

Junjie, Peng; Youyi, Fu; Xiaofeng, Zhang; Shuai, Kong; Xinyu, Wei

2018-03-01

As its characteristics of huge number of data bits and low energy consumption, optical computing may be used in the applications such as DFT etc. which needs a lot of computation and can be implemented in parallel. According to this, DFT implementation methods in full parallel as well as in partial parallel are presented. Based on resources ternary optical computer (TOC), extensive experiments were carried out. Experimental results show that the proposed schemes are correct and feasible. They provide a foundation for further exploration of the applications on TOC that needs a large amount calculation and can be processed in parallel.

First principles DFT study of dye-sensitized CdS quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jain, Kalpna; Singh, Kh. S.; Kishor, Shyam, E-mail: shyam387@gmail.com

2014-04-24

Dye-sensitized quantum dots (QDs) are considered promising candidates for dye-sensitized solar cells. In order to maximize their efficiency, detailed theoretical studies are important. Here, we report a first principles density functional theory (DFT) investigation of experimentally realized dye - sensitized QD / ligand systems, viz., Cd{sub 16}S{sub 16}, capped with acetate molecules and a coumarin dye. The hybrid B3LYP functional and a 6−311+G(d,p)/LANL2dz basis set are used to study the geometric, energetic and electronic properties of these clusters. There is significant structural rearrangement in all the clusters studied - on the surface for the bare QD, and in the positionsmore » of the acetate / dye ligands for the ligated QDs. The density of states (DOS) of the bare QD shows states in the band gap, which disappear on surface passivation with the acetate molecules. Interestingly, in the dye-sensitised QD, the HOMO is found to be localized mainly on the dye molecule, while the LUMO is on the QD, as required for photo-induced electron injection from the dye to the QD.« less

Facile synthesis, single crystal analysis, and computational studies of sulfanilamide derivatives

NASA Astrophysics Data System (ADS)

Tahir, Muhammad Nawaz; Khalid, Muhammad; Islam, Ayesha; Ali Mashhadi, Syed Muddassir; Braga, Ataualpa A. C.

2017-01-01

Antibacterial resistance is a worldwide problem. Sulfanilamide is widely used antibacterial. For the first time, we report here a simple method for the derivative synthesis of the title drugs, single crystal XRD and density functional theory (DFT) studies. The optimized molecular structure, natural bond orbital (NBO), frontier molecular orbitals (FMOs) molecular electrostatic potential studies (MEP) and Mulliken population analysis (MPA) have been performed using M06-2X/6-31G(d, p). The FT-IR spectra and thermodynamic parameters were calculated at M06-2X/6-311 + G(2d,p) and B3LYP/6-31G(d, p) levels respectively, while, the UV-Vis analysis was performed using TD-DFT/B3LYP/6-31G(d, p) method. The experimental FT-IR spectra of both compounds were also carried out to reconfirm sbnd H⋯Osbnd hydrogen bonds. The DFT optimized parameters exhibiting good agreement with the experimental data. NBO analysis explored the hyper conjugative interaction and stability of title crystals, especially, reconfirmed the existence of sbnd H⋯Osbnd hydrogen bonds between the dimers. The FT-IR, thermodynamic parameters, MEP and MPA also revealed the hydrogen bonding detail is harmonious to XRD data. As a matter of the fact, the hydrogen bonding is a significant parameter for the understanding and design of molecular crystals, subsequently; it can also play a vital role in the supramolecular chemistry. Moreover, the global reactivity descriptors suggest that title compounds might be bioactive.

Vibrational spectroscopic studies and DFT calculations of 4-aminoantipyrine

NASA Astrophysics Data System (ADS)

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

2009-08-01

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

SERS and DFT study of copper surfaces coated with corrosion inhibitor

PubMed Central

Muniz-Miranda, Francesco; Caporali, Stefano

2014-01-01

Summary Azole derivatives are common inhibitors of copper corrosion due to the chemical adsorption occurring on the metal surface that gives rise to a protective film. In particular, 1,2,4-triazole performs comparable to benzotriazole, which is much more widely used, but is by no means an environmentally friendly agent. In this study, we have analyzed the adsorption of 1,2,4-triazole on copper by taking advantage of the surface-enhanced Raman scattering (SERS) effect, which highlights the vibrational features of organic ligand monolayers adhering to rough surfaces of some metals such as gold, silver and copper. To ensure the necessary SERS activation, a roughening procedure was implemented on the copper substrates, resulting in nanoscale surface structures, as evidenced by microscopic investigation. To obtain sufficient information on the molecule–metal interaction and the formation of an anticorrosive thin film, the SERS spectra were interpreted with the aid of theoretical calculations based on the density functional theory (DFT) approach. PMID:25671144

Water at silica/liquid water interfaces investigated by DFT-MD simulations

NASA Astrophysics Data System (ADS)

Gaigeot, Marie-Pierre

This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.

Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willow, Soohaeng Y.; Zeng, Xiao Cheng; Xantheas, Sotiris S.

To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trendsmore » derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.« less

Ag nanoparticle decorated molybdenum oxide structures: growth, characterization, DFT studies and their application to enhanced field emission

NASA Astrophysics Data System (ADS)

Guha, Puspendu; Ghosh, Arnab; Thapa, Ranjit; Mathan Kumar, E.; Kirishwaran, Sabari; Singh, Ranveer; Satyam, Parlapalli V.

2017-10-01

We report a simple single step growth of α-MoO3 structures and energetically suitable site specific Ag nanoparticle (NP) decorated α-MoO3 structures on varied substrates, having almost similar morphologies and oxygen vacancies. We elucidate possible growth mechanisms in light of experimental findings and density functional theory (DFT) calculations. We experimentally establish and verified by DFT calculations that the MoO3(010) surface is a weakly interacting and stable surface compared to other orientations. From DFT study, the binding energy is found to be higher for (100) and (001) surfaces (˜-0.98 eV), compared to the (010) surface (˜-0.15 eV) and thus it is likely that Ag NP formation is not favorable on the MoO3(010) surface. The Ag decorated MoO3 (Ag-MoO3) nanostructured sample shows enhanced field emission properties with an approimately 2.1 times lower turn-on voltage of 1.67 V μm-1 and one order higher field enhancement factor (β) of 8.6 × 104 compared to the MoO3 sample without Ag incorporation. From Kelvin probe force microscopy measurements, the average local work function (Φ) is found to be approximately 0.47 eV smaller for the Ag-MoO3 sample (˜5.70 ± 0.05 eV) compared to the MoO3 sample (˜6.17 ± 0.05 eV) and the reduction in Φ can be attributed to the shifting Fermi level of MoO3 toward vacuum via electron injection from Ag NPs to MoO3. The presence of oxygen vacancies together with Ag NPs lead to the highest β and lowest turn-on field among the reported values under the MoO3 emitter category.

Experimental and DFT simulation study of a novel felodipine cocrystal: Characterization, dissolving properties and thermal decomposition kinetics.

PubMed

Yang, Caiqin; Guo, Wei; Lin, Yulong; Lin, Qianqian; Wang, Jiaojiao; Wang, Jing; Zeng, Yanli

2018-05-30

In this study, a new cocrystal of felodipine (Fel) and glutaric acid (Glu) with a high dissolution rate was developed using the solvent ultrasonic method. The prepared cocrystal was characterized using X-ray powder diffraction, differential scanning calorimetry, thermogravimetric (TG) analysis, and infrared (IR) spectroscopy. To provide basic information about the optimization of pharmaceutical preparations of Fel-based cocrystals, this work investigated the thermal decomposition kinetics of the Fel-Glu cocrystal through non-isothermal thermogravimetry. Density functional theory (DFT) simulations were also performed on the Fel monomer and the trimolecular cocrystal compound for exploring the mechanisms underlying hydrogen bonding formation and thermal decomposition. Combined results of IR spectroscopy and DFT simulation verified that the Fel-Glu cocrystal formed via the NH⋯OC and CO⋯HO hydrogen bonds between Fel and Glu at the ratio of 1:2. The TG/derivative TG curves indicated that the thermal decomposition of the Fel-Glu cocrystal underwent a two-step process. The apparent activation energy (E a ) and pre-exponential factor (A) of the thermal decomposition for the first stage were 84.90 kJ mol -1 and 7.03 × 10 7  min -1 , respectively. The mechanism underlying thermal decomposition possibly involved nucleation and growth, with the integral mechanism function G(α) of α 3/2 . DFT calculation revealed that the hydrogen bonding between Fel and Glu weakened the terminal methoxyl, methyl, and ethyl groups in the Fel molecule. As a result, these groups were lost along with the Glu molecule in the first thermal decomposition. In conclusion, the formed cocrystal exhibited different thermal decomposition kinetics and showed different E a , A, and shelf life from the intact active pharmaceutical ingredient. Copyright © 2018 Elsevier B.V. All rights reserved.

Modelling Catalyst Surfaces Using DFT Cluster Calculations

PubMed Central

Czekaj, Izabela; Wambach, Jörg; Kröcher, Oliver

2009-01-01

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

A DFT Study of Pyrrole-Isoxazole Derivatives as Chemosensors for Fluoride Anion

PubMed Central

Jin, Ruifa; Sun, Weidong; Tang, Shanshan

2012-01-01

The interactions between chemosensors, 3-amino-5-(4,5,6,7-tetrahydro-1H-indol-2-yl)isoxazole-4-carboxamide (AIC) derivatives, and different anions (F− Cl−, Br−, AcO−, and H2PO4−) have been theoretically investigated using DFT approaches. It turned out that the unique selectivity of AIC derivatives for F− is ascribed to their ability of deprotonating the host sensors. Frontier molecular orbital (FMO) analyses have shown that the vertical electronic transitions of absorption and emission for the sensing signals are characterized as intramolecular charge transfer (ICT). The study of substituent effects suggests that all the substituted derivatives are expected to be promising candidates for fluoride chemosensors both in UV-vis and fluorescence spectra except for derivative with benzo[d]thieno[3,2-b]thiophene fragment that can serve as ratiometric fluorescent fluoride chemosensor only. PMID:23109833

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide

NASA Astrophysics Data System (ADS)

Saravanan, R. R.; Seshadri, S.; Gunasekaran, S.; Mendoza-Meroño, R.; Garcia-Granda, S.

2015-03-01

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.

Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

NASA Astrophysics Data System (ADS)

Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

2017-10-01

The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

On the number of multiplications necessary to compute a length-2 exp n DFT

NASA Technical Reports Server (NTRS)

Heideman, M. T.; Burrus, C. S.

1986-01-01

The number of multiplications necessary and sufficient to compute a length-2 exp n DFT is determined. The method of derivation is shown to apply to the multiplicative complexity results of Winograd (1980, 1981) for a length-p exp n DFT, for p an odd prime number. The multiplicative complexity of the one-dimensional DFT is summarized for many possible lengths.

Adaptive DFT-based Interferometer Fringe Tracking

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Embedding multiple watermarks in the DFT domain using low- and high-frequency bands

NASA Astrophysics Data System (ADS)

Ganic, Emir; Dexter, Scott D.; Eskicioglu, Ahmet M.

2005-03-01

Although semi-blind and blind watermarking schemes based on Discrete Cosine Transform (DCT) or Discrete Wavelet Transform (DWT) are robust to a number of attacks, they fail in the presence of geometric attacks such as rotation, scaling, and translation. The Discrete Fourier Transform (DFT) of a real image is conjugate symmetric, resulting in a symmetric DFT spectrum. Because of this property, the popularity of DFT-based watermarking has increased in the last few years. In a recent paper, we generalized a circular watermarking idea to embed multiple watermarks in lower and higher frequencies. Nevertheless, a circular watermark is visible in the DFT domain, providing a potential hacker with valuable information about the location of the watermark. In this paper, our focus is on embedding multiple watermarks that are not visible in the DFT domain. Using several frequency bands increases the overall robustness of the proposed watermarking scheme. Specifically, our experiments show that the watermark embedded in lower frequencies is robust to one set of attacks, and the watermark embedded in higher frequencies is robust to a different set of attacks.

Synthesis and antibacterial activity of sulfonamides. SAR and DFT studies

NASA Astrophysics Data System (ADS)

Boufas, Wahida; Dupont, Nathalie; Berredjem, Malika; Berrezag, Kamel; Becheker, Imène; Berredjem, Hajira; Aouf, Nour-Eddine

2014-09-01

A series of substituted sulfonamide derivatives were synthesized from chlorosulfonyl isocyanate (CSI) in tree steps (carbamoylation, sulfamoylation and deprotection). Antibacterial activity in vitro of some newly formed compounds investigated against clinical strains Gram-positive and Gram-negative: Escherichia coli and Staphylococcus aureus applying the method of dilution and minimal inhibition concentration (MIC) methods. These compounds have significant bacteriostatic activity with totalities of bacterial strains used. DFT calculations with B3LYP/6-31G(d) level have been used to analyze the electronic and geometric characteristics deduced for the stable structure of three compounds presenting conjugation between a nitrogen atom N through its lone pair and an aromatic ring next to it. The principal quantum chemical descriptors have been correlated with the antibacterial activity.

Unexpected formation of chiral pincer CNN nickel complexes with β-diketiminato type ligands via C-H activation: synthesis, properties, structures, and computational studies.

PubMed

Lu, Zhengliang; Abbina, Srinivas; Sabin, Jared R; Nemykin, Victor N; Du, Guodong

2013-02-04

Reaction of lithiated chiral, unsymmetric β-diketimine type ligands HL(2a-e) containing oxazoline moiety (HL(2a-e) = 2-(2'-R(1)NH)-phenyl-4-R(2)-oxazoline) with trans-NiCl(Ph)(PPh(3))(2) afforded a series of new chiral CNN pincer type nickel complexes (3a-3e) via an unexpected cyclometalation at benzylic or aryl C-H positions. Single crystal X-ray diffraction analysis established the pincer coordination mode and the strained conformation. Chirality, and in one case, racemization of the target nickel complexes were confirmed by circular dichroism (CD) spectroscopy. Electronic structure and band assignments in experimental UV-vis and CD spectra were discussed on the basis of Density Functional Theory (DFT) and time-dependent (TD) DFT calculations.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

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

PubMed

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

2015-02-25

In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

A fast D.F.T. algorithm using complex integer transforms

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.

1978-01-01

Winograd (1976) has developed a new class of algorithms which depend heavily on the computation of a cyclic convolution for computing the conventional DFT (discrete Fourier transform); this new algorithm, for a few hundred transform points, requires substantially fewer multiplications than the conventional FFT algorithm. Reed and Truong have defined a special class of finite Fourier-like transforms over GF(q squared), where q = 2 to the p power minus 1 is a Mersenne prime for p = 2, 3, 5, 7, 13, 17, 19, 31, 61. In the present paper it is shown that Winograd's algorithm can be combined with the aforementioned Fourier-like transform to yield a new algorithm for computing the DFT. A fast method for accurately computing the DFT of a sequence of complex numbers of very long transform-lengths is thus obtained.

Acridine-1, 8-diones - A new class of thermally stable NLOphores: Photophysical, (hyper)polarizability and TD-DFT studies

NASA Astrophysics Data System (ADS)

Thorat, Kishor G.; Tayade, Rajratna P.; Sekar, Nagaiyan

2016-12-01

Linear and non-linear optical properties of a series of new acridine-1, 8-dione derivatives are investigated in different solvents by using solvatochromic and computational methods. Values of first-order hyperpolarizabilities (βCT or β0) obtained using solvatochromic and computational methods are compared with the reported values for urea and 3-aminoxanthone. The new materials under study show first hyperpolarizability values 2.3 to 5.6 times larger than that of urea and 2 to 15.6 times more than that of 3-aminoxanthone. The dyes possess very high thermal stabilities. The dyes are prepared using one pot multicomponent reaction between dimedone, various aromatic aldehydes and amino acids, and characterized by spectroscopic techniques.

Thermal properties of black phosphorene and doped phosphorene (C, N & O): A DFT study

NASA Astrophysics Data System (ADS)

Devi, Anjna; Singh, Amarjeet

2018-04-01

In this work, we present the results from a DFT based computational study of pristine phosphorene and doped (C, N & O) phosphorene. We systematically investigated the lattice thermal properties of black phosphorene and the effect of doping on its thermal properties. We first determined the vibrational properties of pristine and doped phosphorene and from these results we calculated their thermal properties. We doped the phosphorene with C, N and O and observed that the structural stability of doped phosphorene decreases, while the thermal stability is increased as compared to pristine phosphorene. The presence of finite temperature effects in the doped system can contribute to acceleration of progress in future nano-scale technology.

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

NASA Astrophysics Data System (ADS)

Halim, Shimaa Abdel; Ibrahim, Magdy A.

2017-02-01

New derivative of heteroannulated chromone identified as 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6]naphthyridine-6(5H),8-dione (5, MBCND) was easily and efficiently synthesized from DBU catalyzed condensation reaction of 2-aminochromone-3-carboxaldehyde (1) with 4-hydroxy-1-methylquinolin-2(1H)-one (2). The same product 5 was isolated from condensation reaction of aldeyde 1 with 3-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-3-oxopropanoic acid (3) or ethyl 4-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-2,4-dioxobutanoate (4). Structure of compound (5, MBCND) was deduced based on their elemental analyses and spectral data (IR, 1H NMR and mass spectra). Density Functional Theory (DFT) calculations at the B3LYP/6-311G (d,p) level of theory have been carried out to investigate the equilibrium geometry of the novel compound (5, MBCND). Moreover, total energy, energy of HOMO and LUMO and Mullikan atomic charges were calculated. In addition, the dipole moment, theoretical study of the electronic structure, nonlinear optical properties (NLO), and natural bonding orbital (NBO) analysis and orientation have been performed and discussed. Also the electronic absorption spectra were measured in polar (methanol) as well as non polar (dioxane) solvents and the assignment of the observed bands has been discussed by TD-DFT calculations. The correspondences between calculated and experimental transitions energies are satisfactory.

Secure Image Transmission over DFT-precoded OFDM-VLC systems based on Chebyshev Chaos scrambling

NASA Astrophysics Data System (ADS)

Wang, Zhongpeng; Qiu, Weiwei

2017-08-01

This paper proposes a physical layer image secure transmission scheme for discrete Fourier transform (DFT) precoded OFDM-based visible light communication systems by using Chebyshev chaos maps. In the proposed scheme, 256 subcarriers and QPSK modulation are employed. The transmitted digital signal of the image is encrypted with a Chebyshev chaos sequence. The encrypted signal is then transformed by a DFT precoding matrix to reduce the PAPR of the OFDM signal. After that, the encrypted and DFT-precoded OFDM are transmitted over a VLC channel. The simulation results show that the proposed image security transmission scheme can not only protect the DFT-precoded OFDM-based VLC from eavesdroppers but also improve BER performance.

Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.

Molecular structure, spectral studies, NBO, HOMO-LUMO profile, MEP and Mulliken analysis of 3β,6β-dichloro-5α-hydroxy-5α-cholestane

NASA Astrophysics Data System (ADS)

Alam, Mahboob; Park, Soonheum

2018-05-01

The synthesis of 3β,6β-dichloro-5α-hydroxy-5α-cholestane (in general, steroidal chlorohydrin or steroidal halohydrin) and theoretical study of the structure are reported in this paper. The individuality of chlorohydrin was confirmed by FT-IR, NMR, MS, CHN microanalysis and X-ray crystallography. DFT calculations on the titled molecule have been performed. The molecular structure and spectra explained by Gaussian hybrid computational analysis theory (B3LYP) are found to be in correlation with the experimental data obtained from the various spectrophotometric techniques. The theoretical geometry optimization data were compared with the X-ray data. The vibrational bands appearing in the FT-IR are assigned with accuracy using harmonic frequencies along with intensities and animated modes. Molecular properties like NBO, HOMO-LUMO analysis, chemical reactivity descriptors, MEP mapping and dipole moment have been dealt at same level of theory. The calculated electronic spectrum of chlorohydrin is interpreted on the basis of TD-DFT calculations.

Comparative DFT study of structure, reactivity and IR spectra of phosphorus-containing dendrons with Pdbnd Nsbnd Pdbnd S linkages, vinyl and azide functional groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Gottis, S.; Laurent, R.; Kovalenko, V. I.

2015-07-01

Fourier transform IR spectra of the first generation dendrons built from thiophosphoryl core with terminal Psbnd Cl groups, vinyl (G1) and azide (G2) functional group at the level of the core have been recorded. The optimized geometries of low energy isomers of G1 and G2 have been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. DFT is used for analyzing the properties of each structural part (core, branches, surface). It was found that the repeated branching units of G1 and G2 contain planar sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd Prbond2 fragments. DFT results for the structure of G1 and G2 are in good agreement with X-ray diffraction measurements. A complete vibrational assignment is proposed for different parts of G1 and G2. The global and local reactivity descriptors have been used to characterize the reactivity pattern of the core functional and terminal groups. Natural bond orbital (NBO) analysis has been applied to comparative study of charge delocalization. Our study reveals why azide group linked to phosphorus has a different reactivity when compared to organic azides.

One-dimensional mercury(II) halide coordination polymers of 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine ligand: Synthesis, crystal structure, spectroscopic and DFT studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saghatforoush, Lotfali, E-mail: saghatforoush@gmail.com; Khoshtarkib, Zeinab; Amani, Vahid

2016-01-15

Three new coordination polymers, [Hg(μ-bptz)X{sub 2}]{sub n} (X=Cl (1), Br (2)) and [Hg{sub 2}(μ-bptz)(μ-I){sub 2}I{sub 2}]{sub n} (3) (bptz=3,6-bis(2-pyridyl)-1,2,4,5-tetrazine) were synthesized. X-ray structural analysis indicated that compounds 1 and 2 are composed of one-dimensional (1D) linear chains while the compound 3 has 1D stair-stepped structure. The electronic band structure along with density of states (DOS) calculated by the DFT method indicates that compound 1 and 2 are direct band gap semiconductors; however, compound 3 is an indirect semiconductor. The linear optical properties of the compounds are also calculated by DFT method. According to the DFT calculations, the observed emission bandmore » of the compounds in solid state is due to electron transfer from an excited bptz-π* state (CBs) to the top of VBs. {sup 1}H NMR spectra of the compounds indicate that, in solution phase, the compounds don’t decompose completely. Thermal stability of the compounds is studied using TG, DTA methods. - Graphical abstract: Synthesis, crystal structure and emission spectra of [Hg(μ-bptz)X{sub 2}]{sub n} (X=Cl and Br) and [Hg{sub 2}(μ-bptz)(μ-I){sub 2}I{sub 2}]{sub n} are presented. The electronic band structure and linear optical properties of the compounds are calculated by the DFT method. - Highlights: • Three 1D Hg(II) halide coordination polymers with bptz ligand have been prepared. • The structures of the compounds are determined by single crystal XRD. • DFT calculations show that [Hg(μ-bptz)X{sub 2}]{sub n} (X=Cl and Br) have a direct band gap. • DFT calculations show that [Hg{sub 2}(μ-bptz)(μ-I){sub 2}I{sub 2}]{sub n} has an indirect band gap. • The compounds show an intraligand electron transfer emission band in solid state.« less

TdERF1, an ethylene response factor associated with dehydration responses in durum wheat (Triticum turgidum L. subsp. durum).

PubMed

Makhloufi, Emna; Yousfi, Fatma-Ezzahra; Pirrello, Julien; Bernadac, Anne; Ghorbel, Abdelwahed; Bouzayen, Mondher

2015-01-01

Water deficit and increasing salinization reduce productivity of wheat, the leading crop for human diet. While the complete genome sequence of this crop has not been deciphered, a BAC library screening allowed the isolation of TdERF1, the first ethylene response factor gene from durum wheat. This gene is putatively involved in mediating salt stress tolerance and its characterization provides clues toward understanding the mechanisms underlying the adaptation/tolerance of durum wheat to suboptimal growth conditions. TdERF1 expression is differentially induced by high salt treatment in 2 durum wheat varieties, the salt-tolerant Grecale (GR) and the salt-sensitive Om Rabiaa (OR). To further extend these findings, we show here that the expression of this ERF is correlated with physiological parameters, such as the accumulation of osmo-regulators and membrane integrity, that discriminate between the 2 contrasted wheat genotypes. The data confirm that GR and OR are 2 contrasted wheat genotypes with regard to salt-stress and show that TdERF1 is also induced by water stress with an expression pattern clearly discriminating between the 2 genotypes. These findings suggest that TdERF1 might be involved in responses to salt and water stress providing a potential genetic marker discriminating between tolerant and sensitive wheat varieties.

DFT Studies on Interaction between Lanthanum and Hydroxyamide

NASA Astrophysics Data System (ADS)

Pati, Anindita; Kundu, T. K.; Pal, Snehanshu

2018-03-01

Extraction and separation of individual rare earth elements has been a challenge as they are chemically very similar. Solvent extraction is the most suitable way for extraction of rare earth elements. Acidic, basic, neutral, chelating are the major classes of extractants for solvent extraction of rare earth elements. The coordination complex of chelating extractants is very selective with positively charged metal ion. Hence they are widely used. Hydroxyamide is capable of forming chelates with metal cations. In this present study interactions of hydroxyamide ligand with lanthanum have been investigated using density functional theory (DFT). Two different functional such as raB97XD and B3LYP are applied along with 6-31+G(d,p) basis set for carbon, nitrogen, hydrogen and SDD basis set for lanthanum. Stability of formed complexes has been evaluated based on calculated interaction energies and solvation energies. Frontier orbital (highest occupied molecular orbital or HOMO and lowest unoccupied molecular orbital or LUMO) energies of the molecule have also been calculated. Electronegativity, chemical hardness, chemical softness and chemical potential are also determined for these complexes to get an idea about the reactivity. From the partial charge distribution it is seen that oxygen atoms in hydroxyamide have higher negative charge. The double bonded oxygen atom present in the hydroxyamide structure has higher electron density and so it forms bond with lanthanum but the singly bonded oxygen atom in the hydroxyamide structure is weaker donor atom and so it is less available for interaction with lanthanum.

Synthesis, molecular, electronic structure, linear and non-linear optical and phototransient properties of 8-methyl-1,2-dihydro-4H-chromeno[2,3-b]quinoline-4,6(3H)-dione (MDCQD): Experimental and DFT investigations

NASA Astrophysics Data System (ADS)

Farag, A. A. M.; Roushdy, N.; Halim, Shimaa Abdel; El-Gohary, Nasser M.; Ibrahim, Magdy A.; Said, Sara

2018-02-01

Base catalysed ring opening ring closure (RORC) reaction of 6-methylchromone-3-carbonitrile (1) with 1,3-cyclohexanedione afforded 8-methyl-1,2-dihydro-4H-chromeno[2,3-b]quinoline-4,6(3H)-dione (MDCQD). Theoretical calculations by Density Functional Theory (DFT) at the B3LYP/6-311G (d,p) level of theory was utilized to illustrate the equilibrium geometries of MDCQD. Also, the nonlinear optical properties, simple harmonic vibrational frequencies, thermo-chemical parameters and Mullikan atomic charges were calculated. In addition, the electronic absorption spectra in polar and non polar solvents were discussed on the basis of TD-DFT calculations. A nanofiber-like structure with high aggregation was resolved by using scanning electron microscopy images and its particle sizes were measured by particle size analyzer. The spectroscopic characteristics of the prepared thin film of MDCQD were studied in a wide spectral range of 200-2500 nm. The analysis of the absorption edges affords two direct optical band gaps with energies of 1.00 and 2.76 eV. A characteristic emission peak of photoluminescence spectrum in the visible region was detected and has a red-shift as a result of solvent polarity. The MDCQD film based heterojunction showed rectification behavior and diode-like characteristics. The photovoltaic characteristics under illumination of 100 mW/cm2 were studied. The open-circuit voltage and short-circuit current were found to be 0.22 V and 4.25 × 10- 7 A/cm2, respectively. Moreover, the prepared heterojunction showed remarkable phototransient characteristics which afford the probability for the operation as a photodiode.

Synthesis, molecular, electronic structure, linear and non-linear optical and phototransient properties of 8-methyl-1,2-dihydro-4H-chromeno[2,3-b]quinoline-4,6(3H)-dione (MDCQD): Experimental and DFT investigations.

PubMed

Farag, A A M; Roushdy, N; Halim, Shimaa Abdel; El-Gohary, Nasser M; Ibrahim, Magdy A; Said, Sara

2018-02-15

Base catalysed ring opening ring closure (RORC) reaction of 6-methylchromone-3‑carbonitrile (1) with 1,3-cyclohexanedione afforded 8-methyl-1,2-dihydro-4H-chromeno[2,3-b]quinoline-4,6(3H)-dione (MDCQD). Theoretical calculations by Density Functional Theory (DFT) at the B3LYP/6-311G (d,p) level of theory was utilized to illustrate the equilibrium geometries of MDCQD. Also, the nonlinear optical properties, simple harmonic vibrational frequencies, thermo-chemical parameters and Mullikan atomic charges were calculated. In addition, the electronic absorption spectra in polar and non polar solvents were discussed on the basis of TD-DFT calculations. A nanofiber-like structure with high aggregation was resolved by using scanning electron microscopy images and its particle sizes were measured by particle size analyzer. The spectroscopic characteristics of the prepared thin film of MDCQD were studied in a wide spectral range of 200-2500nm. The analysis of the absorption edges affords two direct optical band gaps with energies of 1.00 and 2.76eV. A characteristic emission peak of photoluminescence spectrum in the visible region was detected and has a red-shift as a result of solvent polarity. The MDCQD film based heterojunction showed rectification behavior and diode-like characteristics. The photovoltaic characteristics under illumination of 100mW/cm 2 were studied. The open-circuit voltage and short-circuit current were found to be 0.22V and 4.25×10 -7 A/cm 2 , respectively. Moreover, the prepared heterojunction showed remarkable phototransient characteristics which afford the probability for the operation as a photodiode. Copyright © 2017. Published by Elsevier B.V.

Quantum Mechanical Calculations of Vibrational Sum-Frequency-Generation (SFG) Spectra of Cellulose: Dependence of the CH and OH Peak Intensity on the Polarity of Cellulose Chains within the SFG Coherence Domain.

PubMed

Lee, Christopher M; Chen, Xing; Weiss, Philip A; Jensen, Lasse; Kim, Seong H

2017-01-05

Vibrational sum-frequency-generation (SFG) spectroscopy is capable of selectively detecting crystalline biopolymers interspersed in amorphous polymer matrices. However, the spectral interpretation is difficult due to the lack of knowledge on how spatial arrangements of crystalline segments influence SFG spectra features. Here we report time-dependent density functional theory (TD-DFT) calculations of cellulose crystallites in intimate contact with two different polarities: parallel versus antiparallel. TD-DFT calculations reveal that the CH/OH intensity ratio is very sensitive to the polarity of the crystallite packing. Theoretical calculations of hyperpolarizability tensors (β abc ) clearly show the dependence of SFG intensities on the polarity of crystallite packing within the SFG coherence length, which provides the basis for interpretation of the empirically observed SFG features of native cellulose in biological systems.

Charge transfer properties of pentacene adsorbed on silver: DFT study

NASA Astrophysics Data System (ADS)

N, Rekha T.; Rajkumar, Beulah J. M.

2015-06-01

Charge transfer properties of pentacene adsorbed on silver is investigated using DFT methods. Optimized geometry of pentacene after adsorption on silver indicates distortion in hexagonal structure of the ring close to the silver cluster and deviations in co-planarity of carbon atoms due to the variations in bond angles and dihedral angles. Theoretically simulated absorption spectrum has a symmetric surface plasmon resonance peak around 486nm corresponding to the transfer of charge from HOMO-2 to LUMO. Theoretical SERS confirms the process of adsorption, tilted orientation of pentacene on silver surface and the charge transfers reported. Localization of electron density arising from redistribution of electrostatic potential together with a reduced bandgap of pentacene after adsorption on silver suggests its utility in the design of electro active organic semiconducting devices.

Stages of Se adsorption on Au(111): A combined XPS, LEED, TOF-DRS, and DFT study

NASA Astrophysics Data System (ADS)

Ruano, G.; Tosi, E.; Sanchez, E.; Abufager, P.; Martiarena, M. L.; Grizzi, O.; Zampieri, G.

2017-08-01

We have studied the adsorption of Se on the surface Au(111) using XPS, TOF-DRS, LEED and DFT calculations. The use of a doser that operates in vacuum allowed us to investigate all the stages of the adsorption from the clean surface up to the formation of multilayers. In the monolayer regime we have found two ordered phases with distinctive LEED patterns. The LEED pattern of the first phase presents three fractional spots arranged symmetrically around the positions of the spots in a √3x√3 pattern. The analysis of this pattern suggests the formation of either a nxn superstructure of √3x√3 domains with n=19 or n=22, or that the adsorption occurs without removing the 22x√3 herringbone reconstruction of the gold surface. This last possibility is in accordance with DFT calculations which show that the charge transfer to a Se adsorbate might not be enough to destabilize the surface reconstruction. Increasing the coverage, beyond 0.3 ML a new LEED pattern appears with broad spots which upon annealing at 150 °C become well defined indicating a 1×8 periodicity. At the highest doses we have observed the formation of multilayers with no discernible LEED pattern. The comparison with adsorption experiments carried out in liquid solutions show similarities and also some important differences.

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

NASA Astrophysics Data System (ADS)

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

2011-05-01

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

Structure Determination of Au on Pt(111) Surface: LEED, STM and DFT Study

PubMed Central

Krupski, Katarzyna; Moors, Marco; Jóźwik, Paweł; Kobiela, Tomasz; Krupski, Aleksander

2015-01-01

Low-energy electron diffraction (LEED), scanning tunneling microscopy (STM) and density functional theory (DFT) calculations have been used to investigate the atomic and electronic structure of gold deposited (between 0.8 and 1.0 monolayer) on the Pt(111) face in ultrahigh vacuum at room temperature. The analysis of LEED and STM measurements indicates two-dimensional growth of the first Au monolayer. Change of the measured surface lattice constant equal to 2.80 Å after Au adsorption was not observed. Based on DFT, the distance between the nearest atoms in the case of bare Pt(111) and Au/Pt(111) surface is equal to 2.83 Å, which gives 1% difference in comparison with STM values. The first and second interlayer spacing of the clean Pt(111) surface are expanded by +0.87% and contracted by −0.43%, respectively. The adsorption energy of the Au atom on the Pt(111) surface is dependent on the adsorption position, and there is a preference for a hollow fcc site. For the Au/Pt(111) surface, the top interlayer spacing is expanded by +2.16% with respect to the ideal bulk value. Changes in the electronic properties of the Au/Pt(111) system below the Fermi level connected to the interaction of Au atoms with Pt(111) surface are observed.

Time-Domain Nuclear Magnetic Resonance (TD-NMR) and Chemometrics for Determination of Fat Content in Commercial Products of Milk Powder.

PubMed

Nascimento, Paloma Andrade Martins; Barsanelli, Paulo Lopes; Rebellato, Ana Paula; Pallone, Juliana Azevedo Lima; Colnago, Luiz Alberto; Pereira, Fabíola Manhas Verbi

2017-03-01

This study shows the use of time-domain (TD)-NMR transverse relaxation (T2) data and chemometrics in the nondestructive determination of fat content for powdered food samples such as commercial dried milk products. Most proposed NMR spectroscopy methods for measuring fat content correlate free induction decay or echo intensities with the sample's mass. The need for the sample's mass limits the analytical frequency of NMR determination, because weighing the samples is an additional step in this procedure. Therefore, the method proposed here is based on a multivariate model of T2 decay, measured with Carr-Purcell-Meiboom-Gill pulse sequence and reference values of fat content. The TD-NMR spectroscopy method shows high correlation (r = 0.95) with the lipid content, determined by the standard extraction method of Bligh and Dyer. For comparison, fat content determination was also performed using a multivariate model with near-IR (NIR) spectroscopy, which is also a nondestructive method. The advantages of the proposed TD-NMR method are that it (1) minimizes toxic residue generation, (2) performs measurements with high analytical frequency (a few seconds per analysis), and (3) does not require sample preparation (such as pelleting, needed for NIR spectroscopy analyses) or weighing the samples.

A DFT+U study of A-site and B-site substitution in BaFeO3-δ.

PubMed

Baiyee, Zarah Medina; Chen, Chi; Ciucci, Francesco

2015-09-28

BaFeO3-δ (BFO)-based perovskites have emerged as cheap and effective oxygen electrocatalysts for oxygen reduction reaction at high temperatures. The BFO cubic phase facilitates a high oxygen deficiency and is commonly stabilised by partial substitution. Understanding the electronic mechanisms of substitution and oxygen deficiency is key to rational material design, and can be realised through DFT analysis. In this work an in-depth first principle DFT+U study is undertaken to determine site distinctive characteristics for 12.5%, Y, La and Ce substitutions in BFO. In particular, it is shown that B-site doped structures exhibit a lower energy cost for oxygen vacancy formation relative to A site doping and pristine BFO. This is attributed to the stabilisation of holes in the oxygen sub-lattice and increased covalency of the Fe-O bonds of the FeO6 octahedra in B-site-substituted BFO. Charge analysis shows that A-site substitution amounts to donor doping and consequently impedes the accommodation of other donors (i.e. oxygen vacancies). However, A-site substitution may also exhibit a higher electronic conductivity due to less lattice distortion for oxygen deficiency compared to B-site doped structures. Furthermore, analysis of the local structural effects provides physical insight into stoichiometric expansions observed for this material.

Combined MCD/DFT/TDDFT Study of the Electronic Structure of Axially Pyridine Coordinated Metallocorroles.

PubMed

Rhoda, Hannah M; Crandall, Laura A; Geier, G Richard; Ziegler, Christopher J; Nemykin, Victor N

2015-05-18

A series of metallocorroles were investigated by UV-vis and magnetic circular dichroism spectroscopies. The diamagnetic distorted square-pyramidal main-group corrole Ga(tpfc)py (2), the diamagnetic distorted octahedral transition-metal adduct Co(tpfc)(py)2 (3), and paramagnetic distorted octahedral transition-metal complex Fe(tpfc)(py)2 (4) [H3tpfc = tris(perfluorophenyl)corrole] were studied to investigate similarities and differences in the electronic structure and spectroscopy of the closed- and open-shell metallocorroles. Similar to the free-base H3tpfc (1), inspection of the MCD Faraday B-terms for all of the macrocycles presented in this report revealed that a ΔHOMO < ΔLUMO [ΔHOMO is the energy difference between two highest energy corrole-centered π-orbitals and ΔLUMO is the energy difference between two lowest energy corrole-centered π*-orbitals originating from ML ± 4 and ML ± 5 pairs of perimeter] condition is present for each complex, which results in an unusual sign-reversed sequence for π-π* transitions in their MCD spectra. In addition, the MCD spectra of the cobalt and the iron complexes were also complicated by a number of charge-transfer states in the visible region. Iron complex 4 also exhibits a low-energy absorption in the NIR region (1023 nm). DFT and TDDFT calculations were used to elaborate the electronic structures and provide band assignments in UV-vis and MCD spectra of the metallocorroles. DFT and TDDFT calculations predict that the orientation of the axial pyridine ligand(s) has a very minor influence on the calculated electronic structures and absorption spectra in the target systems.

Introducing asymmetry in tetradentate azadipyrromethene chromophores: a systematic study of the impact on electronic and photophysical properties.

PubMed

Bessette, André; Cibian, Mihaela; Bélanger, Francis; Désilets, Denis; Hanan, Garry S

2014-10-28

As analogues of the porphyrinoid and dipyrromethene families of dye, azadipyrromethene (ADPM) derivatives exhibit exciting photophysical properties. Their high absorbance (ε up to 100,000 M(-1) cm(-1)) in the yellow-to-red region and the strong NIR luminescence encountered in boron-chelated aza-BODIPY analogues are especially interesting in the context of light-harvesting and life science applications. In the present study, we endeavoured to compare symmetric and asymmetric tetradentate ADPM derivatives 1-6 versus two related bidentate ADPM references in order to gain insights into their structure-property relationship. This is of interest since the tetradentate motif opens the way for extended π-conjugation through metal-mediated planarization, in a bio-mimicry fashion of metalloporphyrinoids, and is known to induce a bathochromic shift toward the NIR. A new straightforward synthetic approach is used to access asymmetric derivatives 4-6 that avoids the tedious heterocycle formation of nitroso-pyrrole intermediates. In addition, photophysics, electrochemistry, computational modelization (DFT and TD-DFT) and X-ray structural characterization of ADPMs are used to better understand the potential of these new chromophores.

Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Roonasi, Payman; Assle taghipour, Khatoon; van der Spoel, David; Manzetti, Sergio

2015-07-01

The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including EHOMO, ELUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.

DFT and experimental studies of the structure and vibrational spectra of curcumin

NASA Astrophysics Data System (ADS)

Kolev, Tsonko M.; Velcheva, Evelina A.; Stamboliyska, Bistra A.; Spiteller, Michael

The potential energy surface of curcumin [1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione] was explored with the DFT correlation functional B3LYP method using 6-311G* basis. The single-point calculations were performed at levels up to B3LYP/6-311++G**//B3LYP/6-311G*. All isomers were located and relative energies determined. According to the calculation the planar enol form is more stable than the nonplanar diketo form. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. In addition, harmonic vibrational frequencies of the molecule were evaluated theoretically using B3LYP density functional methods. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. Our vibrational data show that in both the solid state and in all studied solutions curcumin exists in the enol form.

Cooperative Metal+Ligand Oxidative Addition and Sigma-Bond Metathesis: A DFT Study

DOE PAGES

Lopez, Kent G.; Cundari, Thomas R.; Gary, J. Brannon

2018-01-17

A computational study of the experimentally proposed mechanism of alkyne diboration by a PDICo complex yielded two fundamental catalytic steps that undergo remarkable electronic changes, PDI = bis(imino)-pyridine. The reactions are envisaged via DFT (density functional theory) and MCSCF (multi-configuration self-consistent field) simulations as (i) a cooperative metal+ligand oxidative addition, and (ii) a sigma-bond metathesis induced ligand-to-metal charge transfer. Analysis of the bonding of pertinent intermediates/TSs also yielded important insight that may be illuminating with regards to the larger field of green catalysis that seeks to ennoble base metals through synergy with potentially redox non-innocent (RNI) ligands. For the presentmore » case, massive changes in electronic structure do not incur massive energetic penalties. Finally, in conjunction with previous research, one may postulate that structural and energetic “fluidity” among several electronic states of RNI-M 3d along the reaction coordinate is an essential signature of redox cooperativity and thus ennoblement.« less

Functionalization of ( n, 0) CNTs ( n = 3-16) by uracil: DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Mahmoud; Harismah, Kun; Jafari, Elham; Gülseren, Oğuz; Rad, Ali Shokuhi

2018-01-01

Density functional theory (DFT) calculations were performed to investigate stabilities and properties for uracil (U)-functionalized carbon nanotubes (CNTs). To this aim, the optimized molecular properties were evaluated for ( n, 0) models of CNTs ( n = 3-16) in the original and U-functionalized forms. The results indicated that the dipole moments and energy gaps were independent of tubular diameters whereas the binding energies showed that the U-functionalization could be better achieved for n = 8-11 curvatures of ( n, 0) CNTs. Further studies based on the evaluated atomic-scale properties, including quadrupole coupling constants ( C Q ), indicated that the electronic properties of atoms could detect the effects of diameters variations of ( n, 0) CNTs, in which the effects were very much significant for the atoms around the U-functionalization regions. Finally, the achieved results of singular U, original CNTs, and CNT-U hybrids were compared to each other to demonstrate the stabilities and properties for the U-functionalized ( n, 0) CNTs.

Cooperative Metal+Ligand Oxidative Addition and Sigma-Bond Metathesis: A DFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopez, Kent G.; Cundari, Thomas R.; Gary, J. Brannon

A computational study of the experimentally proposed mechanism of alkyne diboration by a PDICo complex yielded two fundamental catalytic steps that undergo remarkable electronic changes, PDI = bis(imino)-pyridine. The reactions are envisaged via DFT (density functional theory) and MCSCF (multi-configuration self-consistent field) simulations as (i) a cooperative metal+ligand oxidative addition, and (ii) a sigma-bond metathesis induced ligand-to-metal charge transfer. Analysis of the bonding of pertinent intermediates/TSs also yielded important insight that may be illuminating with regards to the larger field of green catalysis that seeks to ennoble base metals through synergy with potentially redox non-innocent (RNI) ligands. For the presentmore » case, massive changes in electronic structure do not incur massive energetic penalties. Finally, in conjunction with previous research, one may postulate that structural and energetic “fluidity” among several electronic states of RNI-M 3d along the reaction coordinate is an essential signature of redox cooperativity and thus ennoblement.« less

Relative stability of radicals derived from artemisinin: A semiempirical and DFT study

NASA Astrophysics Data System (ADS)

Arantes, C.; de Araujo, M. T.; Taranto, A. G.; de M. Carneiro, J. W.

The semiempirical AM1 and PM3 methods, as well as the density functional (DFT/B3LYP) approach using the 6-31g(d) basis set, were employed to calculate the relative stability of intermediate radicals derived from artemisinin, a sesquiterpene lactone having an endoperoxide bridge that is essential for its antimalarial activity. The compounds studied have their nonperoxidic oxygen atom of the trioxane ring and/or the carbonyl group replaced by a CH2 unit. Relative stabilities were calculated by means of isodesmic equations using artemisinin as reference. It was found that replacement of oxygen atoms decreases the relative stability of the anionic radical intermediates. In contrast, for compounds with inverted stereochemistry the intermediate radicals were found to be more stable than those with the artemisinin-like stereochemistry. These relative stabilities may modulate the antimalarial potency. Radicals centered on carbon are always more stable than the corresponding radicals centered on oxygen.

Quantum chemical study, spectroscopic investigations, NBO and HOMO-LUMO analyses of 3-aminoquinoline (3AQ) and [Ag(3AQ)2(TCA)] complex (TCA = Trichloroacetate)

NASA Astrophysics Data System (ADS)

Soliman, Saied M.; Kassem, Taher S.; Badr, Ahmed M. A.; Abu Youssef, Morsy A.; Assem, Rania

2014-09-01

The new [Ag(3AQ)2(TCA)]; (3AQ = 3-aminoquinoline and TCA = Trichloroacetate) complex is synthesized and characterized using elemental analysis, FTIR, NMR and mass spectroscopy. The molecular geometry, vibrational frequencies, gauge-including atomic orbital (GIAO) 1H chemical shift values of the free and coordinated 3AQ in the ground state have been calculated by using DFT/B3LYP method. The TD-DFT results of the [Ag(3AQ)2(TCA)] complex showed a π-π* transition band at 240.3-242.6 nm (f = 0.1334-0.1348) which has longer wavelength and lower absorption intensity than that for the free 3AQ (233.2 nm, f = 0.3958). Dipole moment, polarizability and HOMO-LUMO gap values predicted better nonlinear optical properties (NLO) for the [Ag(3AQ)2(TCA)] than the 3AQ ligand. NBO analysis has been used to predict the most accurate Lewis structure of the studied molecules. The energies of the different intramolecular charge transfer (ICT) interactions within the studied molecules were estimated using second order perturbation theory.

Design of Servo Scheme and Drive Electronics for the Integrated Electrohydraulic Actuation System of RLV-TD

NASA Astrophysics Data System (ADS)

Kurian, Priya C.; Gopinath, Anish; Shinoy, K. S.; Santhi, P.; Sundaramoorthy, K.; Sebastian, Baby; Jaya, B.; Namboodiripad, M. N.; Mookiah, T.

2017-12-01

Reusable Launch Vehicle-Technology Demonstrator (RLV-TD) is a system which has the ability to carry a payload from the earth's surface to the outer space more than once. The control actuation forms the major component of the control system and it actuates the control surfaces of the RLV-TD based on the control commands. Eight electro hydraulic actuators were used in RLV-TD for vectoring the control surfaces about their axes. A centralised Hydraulic Power Generating Unit (HPU) was used for powering the eight actuators located in two stages. The actuation system had to work for the longest ever duration of about 850 s for an Indian launch vehicle. High bandwidth requirement from autopilot was met by the servo design using the nonlinear mathematical model. Single Control Electronics which drive four electrohydraulic actuators was developed for each stage. High power electronics with soft start scheme was realized for driving the BLDC motor which is the prime mover for hydraulic pump. Many challenges arose due to single HPU for two stages, uncertainty of aero load, higher bandwidth requirements etc. and provisions were incorporated in the design to successfully overcome them. This paper describes the servo design and control electronics architecture of control actuation system.

The relationship between anisotropic magnetoresistance and topology of Fermi surface in Td-MoTe2 crystal

NASA Astrophysics Data System (ADS)

Lv, Yang-Yang; Li, Xiao; Pang, Bin; Cao, Lin; Lin, Dajun; Zhang, Bin-Bin; Yao, Shu-Hua; Chen, Y. B.; Zhou, Jian; Dong, Song-Tao; Zhang, Shan-Tao; Lu, Ming-Hui; Chen, Yan-Feng

2017-07-01

Layered transition-metal dichalcogenides have been recently attracted a lot of attention because of their unique physical properties, such as extremely large and anisotropic magnetoresistance (MR) in WTe2. In this work, we observed the abnormally anisotropic MR on Td-MoTe2 crystal that is strongly dependent on the temperature, as well as the orientations of both magnetic field B and electric field E with respect to crystallographic axes of Td-MoTe2. When E//a-axis and B//c-axis, MR is parabolically dependent on B and is as high as 520% under 9 T and 2 K conditions; the MR is quasi-linearly dependent on B when E//a-axis and B//b-axis (E//b-axis and B//c-axis), and the corresponding MR is only 130% (220%); MR is initially parabolically dependent on B, then linearly on B, and finally shows a saturate trend under E//B//a-axis (or E//B//b-axis) conditions, and the MR is about 16% (30%). These anisotropic MR behaviors can be qualitatively explained by the features of the Fermi surface of Td-MoTe2. This work may demonstrate the rich anisotropic physical behavior in layered transition-metal dichalcognides.

The structure of N2 adsorbed on the rumpled NaCl(100) surface—A combined LEED and DFT-D study

NASA Astrophysics Data System (ADS)

Vogt, Jochen

2012-11-01

The structure of N2 physisorbed on the NaCl(100) single crystal surface is investigated by means of quantitative low-energy electron diffraction (LEED) in combination with dispersion corrected density functional theory (DFT-D). In the temperature range between 20 K and 45 K, a p(1 × 1) structure is observed in the LEED experiment. According to the structure analysis based on the measured diffraction spot intensity profiles, the N2 molecules are adsorbed over the topmost Na+ ions. The experimental distance of the lower nitrogen to the Na+ ion underneath is (2.55 ± 0.07) Å; the corresponding DFT-D value is 2.65 Å. The axes of the molecules are tilted (26 ± 3)° with respect to the surface normal, while in the zero Kelvin optimum structure from DFT-D, the molecules have a perpendicular orientation. The experimental monolayer heat of adsorption, deduced from a Fowler-Guggenheim kinetic model of adsorption is -(13.6 ± 1.6) kJ mol-1, including a lateral molecule-molecule interaction energy of -(2.0 ± 0.4) kJ mol-1. The zero Kelvin adsorption energy from DFT-D, including zero point energy correction, is -15.6 kJ mol-1; the molecule-molecule interaction is -2.4 kJ mol-1. While the rumpling of the NaCl(100) surface is unchanged upon adsorption of nitrogen, the best-fit root mean square thermal displacements of the ions in the topmost substrate layer are significantly reduced.

Structural influence in the interaction of cysteine with five coordinated copper complexes: Theoretical and experimental studies

NASA Astrophysics Data System (ADS)

Huerta-Aguilar, Carlos Alberto; Thangarasu, Pandiyan; Mora, Jesús Gracia

2018-04-01

Copper complexes of N,N,N‧,N‧-tetrakis(pyridyl-2-ylmethyl)-1,2-diaminoethane (L1) and N,N,N‧,N‧-tetrakis(pyridyl-2-ylmethyl)-1,3-diaminopropane (L2) prepared were characterized completely by different analytical methods. The X-structure of the complexes shows that Cu(II) presents in trigonal bi-pyramidal (TBP) geometry, consisting with the electronic spectra where two visible bands corresponding to five coordinated structure were observed. Thus TD-DFT was used to analyze the orbital contribution to the electronic transitions for the visible bands. Furthermore, the interaction of cysteine with the complexes was spectrally studied, and the results were explained through DFT analysis, observing that the geometrical parameters and oxidation state of metal ions play a vital role in the binding of cysteine with copper ion. It appears that the TBP structure is being changed into octahedral geometry during the addition of cysteine to the complexes as two bands (from complex) is turned to a broad band in visible region, signifying the occupation of cysteine molecule at sixth position of octahedral geometry. In the molecular orbital analysis, the existence of a strong overlapping of HOMOs (from cysteine) with LUMOs of Cu ion was observed. The total energy of the systems calculated by DFT shows that cysteine binds favorably with copper (I) than that with Cu(II).

Experimental and theoretical spectroscopic studies of anticancer drug rosmarinic acid using HF and density functional theory.

PubMed

Mariappan, G; Sundaraganesan, N; Manoharan, S

2012-11-01

In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of anticancer drug of rosmarinic acid. The optimized molecular structure, atomic charges, vibrational frequencies, natural bond orbital analysis and ultraviolet-visible spectral interpretation of rosmarinic acid have been studied by performing HF and DFT/B3LYP/6-31G(d,p) level of theory. The FT-IR (solid and solution phase), FT-Raman (solid phase) spectra were recorded in the region 4000-400 and 3500-50 cm(-1), respectively. The UV-Visible absorption spectra of the compound that dissolved in ethanol were recorded in the range of 200-800 nm. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The formation of hydrogen bond was investigated in terms of the charge density by the NBO calculations. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations. Copyright © 2012 Elsevier B.V. All rights reserved.

Accurate Energies and Orbital Description in Semi-Local Kohn-Sham DFT

NASA Astrophysics Data System (ADS)

Lindmaa, Alexander; Kuemmel, Stephan; Armiento, Rickard

2015-03-01

We present our progress on a scheme in semi-local Kohn-Sham density-functional theory (KS-DFT) for improving the orbital description while still retaining the level of accuracy of the usual semi-local exchange-correlation (xc) functionals. DFT is a widely used tool for first-principles calculations of properties of materials. A given task normally requires a balance of accuracy and computational cost, which is well achieved with semi-local DFT. However, commonly used semi-local xc functionals have important shortcomings which often can be attributed to features of the corresponding xc potential. One shortcoming is an overly delocalized representation of localized orbitals. Recently a semi-local GGA-type xc functional was constructed to address these issues, however, it has the trade-off of lower accuracy of the total energy. We discuss the source of this error in terms of a surplus energy contribution in the functional that needs to be accounted for, and offer a remedy for this issue which formally stays within KS-DFT, and, which does not harshly increase the computational effort. The end result is a scheme that combines accurate total energies (e.g., relaxed geometries) with an improved orbital description (e.g., improved band structure).

Adaptive DFT-Based Interferometer Fringe Tracking

NASA Astrophysics Data System (ADS)

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

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

New foot remains from the Gran Dolina-TD6 Early Pleistocene site (Sierra de Atapuerca, Burgos, Spain).

PubMed

Pablos, Adrián; Lorenzo, Carlos; Martínez, Ignacio; Bermúdez de Castro, José María; Martinón-Torres, María; Carbonell, Eudald; Arsuaga, Juan Luis

2012-10-01

This paper presents and describes new foot fossils from the species Homo antecessor, found in level TD6 of the site of Gran Dolina (Sierra de Atapuerca, Burgos, Spain). These new fossils consist of an almost complete left talus (ATD6-95) and the proximal three-quarters of a right fourth metatarsal (ATD6-124). The talus ATD6-95 is tentatively assigned to Hominin 10 of the TD6 sample, an adult male specimen with which the second metatarsal ATD6-70+107 (already published) is also tentatively associated. Analysis of these fossils and other postcranial remains has made possible to estimate a stature similar to those of the specimens from the Middle Pleistocene site of Sima de los Huesos (Sierra de Atapuerca, Burgos, Spain). The morphology of the TD6 metatarsals does not differ significantly from that of modern humans, Neanderthals and the specimens from Sima de los Huesos. Talus ATD6-95, however, differs from the rest of the comparative samples in being long and high, having a long and wide trochlea, and displaying a proportionally short neck. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evaluation of DFT methods for computing the interaction energies of homomolecular and heteromolecular dimers of monosubstituted benzene

NASA Astrophysics Data System (ADS)

Godfrey-Kittle, Andrew; Cafiero, Mauricio

We present density functional theory (DFT) interaction energies for the sandwich and T-shaped conformers of substituted benzene dimers. The DFT functionals studied include TPSS, HCTH407, B3LYP, and X3LYP. We also include Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory calculations (MP2), as well as calculations using a new functional, P3LYP, which includes PBE and HF exchange and LYP correlation. Although DFT methods do not explicitly account for the dispersion interactions important in the benzene-dimer interactions, we find that our new method, P3LYP, as well as HCTH407 and TPSS, match MP2 and CCSD(T) calculations much better than the hybrid methods B3LYP and X3LYP methods do.

Constitutive expression of tdTomato protein as a cytotoxicity and proliferation marker for space radiation biology

NASA Astrophysics Data System (ADS)

Chishti, Arif A.; Hellweg, Christine E.; Berger, Thomas; Baumstark-Khan, Christa; Feles, Sebastian; Kätzel, Thorben; Reitz, Günther

2015-01-01

The radiation risk assessment for long-term space missions requires knowledge on the biological effectiveness of different space radiation components, e.g. heavy ions, on the interaction of radiation and other space environmental factors such as microgravity, and on the physical and biological dose distribution in the human body. Space experiments and ground-based experiments at heavy ion accelerators require fast and reliable test systems with an easy readout for different endpoints. In order to determine the effect of different radiation qualities on cellular proliferation and the biological depth dose distribution after heavy ion exposure, a stable human cell line expressing a novel fluorescent protein was established and characterized. tdTomato, a red fluorescent protein of the new generation with fast maturation and high fluorescence intensity, was selected as reporter of cell proliferation. Human embryonic kidney (HEK/293) cells were stably transfected with a plasmid encoding tdTomato under the control of the constitutively active cytomegalovirus (CMV) promoter (ptdTomato-N1). The stably transfected cell line was named HEK-ptdTomato-N1 8. This cytotoxicity biosensor was tested by ionizing radiation (X-rays and accelerated heavy ions) exposure. As biological endpoints, the proliferation kinetics and the cell density reached 100 h after irradiation reflected by constitutive expression of the tdTomato were investigated. Both were reduced dose-dependently after radiation exposure. Finally, the cell line was used for biological weighting of heavy ions of different linear energy transfer (LET) as space-relevant radiation quality. The relative biological effectiveness of accelerated heavy ions in reducing cellular proliferation peaked at an LET of 91 keV/μm. The results of this study demonstrate that the HEK-ptdTomato-N1 reporter cell line can be used as a fast and reliable biosensor system for detection of cytotoxic damage caused by ionizing radiation.

Theoretical Studies of Possible Synthetic Routes for the High Energy Density Material Td N4: Excited Electronic States

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

2001-01-01

Vertical electronic excitation energies for single states have been computed for the high energy density material (HEDM) Td N4 in order to assess possible synthetic routes that originate from excited electronic states of N2 molecules. Several ab initio theoretical approaches have been used, including complete active space self-consistent field (CASSCF), state averaged CASSCF (SA-CASSCF), singles configuration interaction (CIS), CIS with second-order and third-order correlation corrections [CIS(D)) and CIS(3)], and linear response singles and doubles coupled-cluster (LRCCSD), which is the highest level of theory employed. Standard double zeta polarized (DZP) and triple zeta double polarized (TZ2P) one-particle basis sets were used. The CASSCF calculations are found to overestimate the excitation energies, while the SA-CASSCF approach rectifies this error to some extent, but not completely. The accuracy of the CIS calculations varied depending on the particular state, while the CIS(D), CIS(3), and LRCCSD results are in generally good agreement. Based on the LRCCSD calculations, the lowest six excited singlet states are 9.35(l(sup)T1), 10.01(l(sup)T2), 10.04(1(sup)A2), 10.07(1(sup)E), 10.12(2(sup)T1), and 10.42(2(sup)T2) eV above the ground state, respectively. Comparison of these excited state energies with the energies of possible excited states of N2+N2 fragments, leads us to propose that the most likely synthetic route for Td N4 involving this mechanism arises from combination of two bound quintet states of N2.

Structural investigation, spectroscopic and energy level studies of Schiff base: 2-[(3‧-N-salicylidenephenyl)benzimidazole] using experimental and DFT methods

NASA Astrophysics Data System (ADS)

Suman, G. R.; Bubbly, S. G.; Gudennavar, S. B.; Muthu, S.; Roopashree, B.; Gayatri, V.; Nanje Gowda, N. M.

2017-07-01

The Schiff base 2-[(3‧-N-salicylidenephenyl)benzimidazole] (Spbzl) was characterized by FT-Raman, 1H NMR, 13C NMR and single crystal X-ray diffraction technique. Crystallographic studies reveal the presence of two water molecules in the asymmetry unit which aid the intermolecular hydrogen bonding with imidazole ring, and the trans-conformation of the azomethine bond. Theoretical computations conducted using density functional theory (DFT) analysis support the experimental facts. Energy levels estimated by DFT studies are in good agreement with the values obtained from cyclic voltammetry technique. Frontier molecular orbital analysis shows that charge transfer has taken place from donor to acceptor moiety, which is also supported by the high hyperpolarizability values in both gaseous and solution phases, indicating high charge transfer capability of the molecule. A comparative theoretical study of Spbzl with derivative 4-((3-(1H-benzimidazol-2-yl)phenylimino)methyl)-3-hydroxybenzoic acid (Pbzlb) having an added anchor group COOH substituted at para position in the acceptor ring has been made. The result shows the feasibility of charge transfer to the semiconductor surface in dye sensitized solar cell (DSSC) applications for Pbzlb.

Adsorption of various types of amino acids on the graphene and boron-nitride nano-sheet, a DFT-D3 study

NASA Astrophysics Data System (ADS)

Zhiani, Rahele

2017-07-01

The binding properties of the adsorption of five different classes of amino acids, namely, alanine (Ala), arginine (Arg), asparagine (Asn), histidine (His) and cysteine (Cys) on the surface of the graphene (Gra) and the born-nitride (BN) nano-sheet structures were studied from molecular viewpoint using quantum mechanics methods. Density functional theory (DFT) and DFT-D3 calculations were carried out to investigate the electronic properties and the dispersion interaction of the amino acid/adsorbent complexes. Several parameters affecting the interactions between the amino acids and the adsorbent surfaces such as solvent effect, adsorption energy and separation distance were investigated. Findings show that Arg forms the most stable complexes with the graphene and the BN nano-sheet compare to the other amino acids used in this study. The observed frequency results which were related to the band gap energies were consistent with the above statement. Results exhibit that adsorption of the amino acids on the surface of the BN nano-sheet and the graphene accompanied with the release of the energy. Calculations show that there are no bonded interactions between the amino acids and adsorbent surfaces. The polarity of the BN nano-sheet provides the more affinity towards the amino acids. These results were proved by the quantum chemistry studies.

A detailed study of intermolecular interactions, electronic and vibrational properties of the metal complex bis(uracilato)diammine copper(ii) dihydrate

NASA Astrophysics Data System (ADS)

Gramajo Feijoo, M.; Fernández-Liencres, M. P.; Gil, D. M.; Gómez, M. I.; Ben Altabef, A.; Navarro, A.; Tuttolomondo, M. E.

2018-03-01

Density Functional Theory (DFT) calculations were performed with the aim of investigating the vibrational, electronic and structural properties of [Cu(uracilato-N1)2 (NH3)2]ṡ2H2O complex. The IR and Raman spectra were recorded leading to a complete analysis of the normal modes of vibration of the metal complex. A careful study of the intermolecular interactions observed in solid state was performed by using the Hirshfeld surface analysis and their associated 2D fingerprint plots. The results indicated that the crystal packing is stabilized by Nsbnd H⋯O hydrogen bonds and π-stacking interactions. In addition, Csbnd H···π interactions were also observed. Time-dependent density functional theory (TD-DFT) calculations revealed that all the low-lying electronic states correspond to a mixture of intraligand charge transfer (ILCT) and ligand-to-metal charge transfer (LMCT) transitions. Finally, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) analysis were performed to shed light on the intermolecular interactions in the coordination sphere.

A competing, dual mechanism for catalytic direct benzene hydroxylation from combined experimental-DFT studies.

PubMed

Vilella, Laia; Conde, Ana; Balcells, David; Díaz-Requejo, M Mar; Lledós, Agustí; Pérez, Pedro J

2017-12-01

A dual mechanism for direct benzene catalytic hydroxylation is described. Experimental studies and DFT calculations have provided a mechanistic explanation for the acid-free, Tp x Cu-catalyzed hydroxylation of benzene with hydrogen peroxide (Tp x = hydrotrispyrazolylborate ligand). In contrast with other catalytic systems that promote this transformation through Fenton-like pathways, this system operates through a copper-oxyl intermediate that may interact with the arene ring following two different, competitive routes: (a) electrophilic aromatic substitution, with the copper-oxyl species acting as the formal electrophile, and (b) the so-called rebound mechanism, in which the hydrogen is abstracted by the Cu-O moiety prior to the C-O bond formation. Both pathways contribute to the global transformation albeit to different extents, the electrophilic substitution route seeming to be largely favoured.

Vibrational frequency analysis, FT-IR, DFT and M06-2X studies on tert-Butyl N-(thiophen-2yl)carbamate

NASA Astrophysics Data System (ADS)

Sert, Yusuf; Singer, L. M.; Findlater, M.; Doğan, Hatice; Çırak, Ç.

2014-07-01

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized tert-Butyl N-(thiophen-2yl)carbamate have been investigated. The experimental FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with the 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The vibrational frequencies have been assigned using potential energy distribution (PED) analysis by using VEDA 4 software. The computational optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with related literature results. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and are depicted.

Polar Diels-Alder reactions using electrophilic nitrobenzothiophenes. A combined experimental and DFT study

NASA Astrophysics Data System (ADS)

Della Rosa, Claudia D.; Mancini, Pedro M. E.; Kneeteman, Maria N.; Lopez Baena, Anna F.; Suligoy, Melisa A.; Domingo, Luis R.

2015-01-01

The reactions between 2- and 3-nitrobenzothiophenes with three dienes of different nucleophilicity, 1-methoxy-3-trimethylsilyloxy-1,3-butadiene, 1-trimethylsilyloxy-1,3-butadiene and isoprene developed in anhydrous benzene and alternative under microwave irradiation with molecular solvents or in free solvent conditions, respectively, for produce dibenzothiophenes permit to conclude that both nitroheterocycles act as electrophile with the cited dienes. In the cases of the dienes 1-methoxy-3-trimethylsilyloxy-1,3-butadiene and 1-trimethylsilyloxy-1,3-butadiene which posses major nucleophilicity the observed product is the normal cycloaddition one. However when the diene is isoprene the product with both electrophiles follow the hetero Diels-Alder way. These reactions are considered polar cycloaddition reactions and the yields are reasonables. Moreover the polar Diels-Alder reactions of nitrobenzothiophenes with electron rich dienes 1-trimethylsilyloxy-1,3-butadiene have been theoretically studied using DFT methods.

Combined multifrequency EPR and DFT study of dangling bonds in a-Si:H

NASA Astrophysics Data System (ADS)

Fehr, M.; Schnegg, A.; Rech, B.; Lips, K.; Astakhov, O.; Finger, F.; Pfanner, G.; Freysoldt, C.; Neugebauer, J.; Bittl, R.; Teutloff, C.

2011-12-01

Multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy using S-, X-, Q-, and W-band frequencies (3.6, 9.7, 34, and 94 GHz, respectively) was employed to study paramagnetic coordination defects in undoped hydrogenated amorphous silicon (a-Si:H). The improved spectral resolution at high magnetic field reveals a rhombic splitting of the g tensor with the following principal values: gx=2.0079, gy=2.0061, and gz=2.0034, and shows pronounced g strain, i.e., the principal values are widely distributed. The multifrequency approach furthermore yields precise 29Si hyperfine data. Density functional theory (DFT) calculations on 26 computer-generated a-Si:H dangling-bond models yielded g values close to the experimental data but deviating hyperfine interaction values. We show that paramagnetic coordination defects in a-Si:H are more delocalized than computer-generated dangling-bond defects and discuss models to explain this discrepancy.

Dual emission behavior of phenyleneethynylene gold(I) complexes dictated by intersystem crossing: a theoretical perspective.

PubMed

Wang, Li; Li, Yuanyuan; Zhang, Yanxin; He, Hongqing; Zhang, Jinglai

2015-02-25

In commonly studied gold(I) complexes with oligo (o-, p-, or m-phenyleneethynylene) (PE) ligands, an intriguing photophysical behavior is dual emission composed of fluorescence from S1 and phosphorescence from T1 which is dictated by effective intersystem crossing (ISC) process. In order to explore the salient photodynamics of such oligo-PE gold(I) complexes effectively, we have deliberately chosen three model complexes, namely, Ph-C≡C-Au(PMe3) (1a') and Ph-C≡C-(1,m)C6H4-C≡C-Au(PMe3) (m=4, 2a'; m=3, 3a') in place of the real system. Firstly, electronic structure methods based on DFT and TD-DFT are utilized to perform optimization calculations for the ground- and lowest-lying excited states, respectively. Next, basic photophysical properties including absorption and emission spectra are investigated by TD-DFT under the optimized geometries. Besides, on the basis of the electronic spectra herein, we succeed in searching for surface intersections as the minima on the seam of singlet-triplet surface crossings (SCs) at the CASSCF level of theory. By integration of the results available, the process of delayed fluorescence of triplet-triplet annihilation (TTA) and phosphorescence was displayed in detail with SCs playing the lead in monitoring the ISC. Copyright © 2014 Elsevier B.V. All rights reserved.

LIF excitation spectra for S 0 → S 1 transition of deuterated anthranilic acid COOD, ND 2 in supersonic-jet expansion

NASA Astrophysics Data System (ADS)

Kolek, Przemysław; Leśniewski, Sebastian; Andrzejak, Marcin; Góra, Maciej; Cias, Pawel; Weģrzynowicz, Adam; Najbar, Jan

2010-12-01

Laser induced fluorescence (LIF) excitation spectrum for the S 0 → S 1 transition of anthranilic acid molecules deuterated in the substituent groups (COOD, ND 2) was investigated. Analysis of the LIF spectrum allowed for the assignment of the six most prominent fundamental in-plane modes of frequencies up to ca. 850 cm. The experimental results show good correlation with the frequency changes upon deuteration computed with CIS (CI-Singles) and TD-DFT for the S 1 state. Deuteration induced red-shifts of the identified fundamental bands are used for examination of the alternative assignments proposed in earlier studies. Potential energy distributions (PED) and overlaps of the in-plane normal modes with frequencies below 850 cm indicate that the correspondence of the respective vibrations of the deuterated and non-deuterated molecule is very good. A blue-shift of the 00 transition due to the isotopic substitution, is equal to 47 cm. This relatively large value is caused primarily by a significant decrease of the N-H stretching frequency associated with the increase of strength of the intramolecular hydrogen bond upon the electronic excitation. The deuteration shift of the 00 band was interpreted in terms of the differences of the zero point energy (ZPE) between the S 0 and S 1 electronic states, computed with DFT and TD-DFT methods, respectively.

Study of transmission function and electronic transport in one dimensional silver nanowire: Ab-initio method using density functional theory (DFT)

NASA Astrophysics Data System (ADS)

Thakur, Anil; Kashyap, Rajinder

2018-05-01

Single nanowire electrode devices have their application in variety of fields which vary from information technology to solar energy. Silver nanowires, made in an aqueous chemical reduction process, can be reacted with gold salt to create bimetallic nanowires. Silver nanowire can be used as electrodes in batteries and have many other applications. In this paper we investigated structural and electronic transport properties of Ag nanowire using density functional theory (DFT) with SIESTA code. Electronic transport properties of Ag nanowire have been studied theoretically. First of all an optimized geometry for Ag nanowire is obtained using DFT calculations, and then the transport relations are obtained using NEGF approach. SIESTA and TranSIESTA simulation codes are used in the calculations respectively. The electrodes are chosen to be the same as the central region where transport is studied, eliminating current quantization effects due to contacts and focusing the electronic transport study to the intrinsic structure of the material. By varying chemical potential in the electrode regions, an I-V curve is traced which is in agreement with the predicted behavior. Bulk properties of Ag are in agreement with experimental values which make the study of electronic and transport properties in silver nanowires interesting because they are promising materials as bridging pieces in nanoelectronics. Transmission coefficient and V-I characteristic of Ag nano wire reveals that silver nanowire can be used as an electrode device.

DFT study of ethyl xanthate interaction with sphalerite (1 1 0) surface in the absence and presence of copper

NASA Astrophysics Data System (ADS)

Liu, Jian; Wen, Shuming; Deng, Jiushuai; Chen, Xiumin; Feng, Qicheng

2014-08-01

The interaction among sphalerite (1 1 0) surface, copper and ethyl xanthate (EX) was simulated using the density functional theory (DFT). The results of DFT indicate that four types of stable interaction models exist among sphalerite surface, copper and EX, i.e., EX interacts with the Cu substituted for Zn, Cu adsorbed on the top site of S, Cu adsorbed on the bridge site of S and Cu(OH)2 adsorbed on the sphalerite surface. The four interaction models can result in the activation flotation of sphalerite. Density of states (DOS) analysis shows that the energy level discrepancy of the Zn 3d orbital in ZnS and the bonding S 3p orbital in EX results in the weak adsorption of EX on un-activated sphalerite surface. However, after copper activation, the Cu 3d orbital peak and bonding S 3p orbital peak are just maximally overlapped nearby the Fermi level. This study provides an insight into the nature that sphalerite responds not well to EX and also a comprehensive understanding on the possible interaction cases existing among sphalerite surface, copper and EX.

Behaviour of DFT-based approaches to the spin-orbit term of zero-field splitting tensors: a case study of metallocomplexes, MIII(acac)3 (M = V, Cr, Mn, Fe and Mo).

PubMed

Sugisaki, Kenji; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

2017-11-15

Spin-orbit contributions to the zero-field splitting (ZFS) tensor (D SO tensor) of M III (acac) 3 complexes (M = V, Cr, Mn, Fe and Mo; acac = acetylacetonate anion) are evaluated by means of ab initio (a hybrid CASSCF/MRMP2) and DFT (Pederson-Khanna (PK) and natural orbital-based Pederson-Khanna (NOB-PK)) methods, focusing on the behaviour of DFT-based approaches to the D SO tensors against the valence d-electron configurations of the transition metal ions in octahedral coordination. Both the DFT-based approaches reproduce trends in the D tensors. Significantly, the differences between the theoretical and experimental D (D = D ZZ - (D XX + D YY )/2) values are smaller in NOB-PK than in PK, emphasising the usefulness of the natural orbital-based approach to the D tensor calculations of transition metal ion complexes. In the case of d 2 and d 4 electronic configurations, the D SO (NOB-PK) values are considerably underestimated in the absolute magnitude, compared with the experimental ones. The D SO tensor analysis based on the orbital region partitioning technique (ORPT) revealed that the D SO contributions attributed to excitations from the singly occupied region (SOR) to the unoccupied region (UOR) are significantly underestimated in the DFT-based approaches to all the complexes under study. In the case of d 3 and d 5 configurations, the (SOR → UOR) excitations contribute in a nearly isotropic manner, which causes fortuitous error cancellations in the DFT-based D SO values. These results indicate that more efforts to develop DFT frameworks should be directed towards the reproduction of quantitative D SO tensors of transition metal complexes with various electronic configurations and local symmetries around metal ions.

A VLSI pipeline design of a fast prime factor DFT on a finite field

NASA Technical Reports Server (NTRS)

Truong, T. K.; Hsu, I. S.; Shao, H. M.; Reed, I. S.; Shyu, H. C.

1986-01-01

A conventional prime factor discrete Fourier transform (DFT) algorithm is used to realize a discrete Fourier-like transform on the finite field, GF(q sub n). A pipeline structure is used to implement this prime factor DFT over GF(q sub n). This algorithm is developed to compute cyclic convolutions of complex numbers and to decode Reed-Solomon codes. Such a pipeline fast prime factor DFT algorithm over GF(q sub n) is regular, simple, expandable, and naturally suitable for VLSI implementation. An example illustrating the pipeline aspect of a 30-point transform over GF(q sub n) is presented.

Cyclopentadienyl ruthenium-nickel catalysts for biomimetic hydrogen evolution: electrocatalytic properties and mechanistic DFT studies.

PubMed

Canaguier, Sigolène; Vaccaro, Loredana; Artero, Vincent; Ostermann, Rainer; Pécaut, Jacques; Field, Martin J; Fontecave, Marc

2009-09-21

The new dinuclear nickel-ruthenium complexes [Ni(xbsms)RuCp(L)][PF(6)] (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene; Cp(-) = cyclopentadienyl; L = DMSO, CO, PPh(3), and PCy(3)) are reported and are bioinspired mimics of NiFe hydrogenases. These compounds were characterized by X-ray diffraction techniques and display novel structural motifs. Interestingly, [Ni(xbsms)RuCpCO][PF(6)] is stereochemically nonrigid in solution and an isomerization mechanism was derived with the help of density functional theory (DFT) calculations. Because of an increased electron density on the metal centers [Eur. J. Inorg. Chem. 2007, 18, 2613-2626] with respect to the previously described [Ni(xbsms)Ru(CO)(2)Cl(2)] and [Ni(xbsms)Ru(p-cymene)Cl](+) complexes, [Ni(xbsms)RuCp(dmso)][PF(6)] catalyzes hydrogen evolution from Et(3)NH(+) in DMF with an overpotential reduced by 180 mV and thus represents the most efficient NiFe hydrogenase functional mimic. DFT calculations were carried out with several methods to investigate the catalytic cycle and, coupled with electrochemical measurements, allowed a mechanism to be proposed. A terminal or bridging hydride derivative was identified as the active intermediate, with the structure of the bridging form similar to that of the Ni-C active state of NiFe hydrogenases.

Methanol Synthesis from CO2 Hydrogenation over a Pd4/In2O3 Model Catalyst: A Combined DFT and Kinetic Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Jingyun; Liu, Changjun; Mei, Donghai

2014-08-01

Methanol synthesis from CO2 hydrogenation on Pd4/In2O3 has been investigated using density functional theory (DFT) and microkinetic modeling. In this study, three possible routes in the reaction network of CO2 + H2 → CH3OH + H2O have been examined. Our DFT results show that the HCOO route competes with the RWGS route whereas a high activation barrier kinetically blocks the HCOOH route. DFT results also suggest that H2COO* + H* ↔ H2CO* +OH* and cis-COOH* + H* ↔CO* + H2O* are the rate limiting steps in the HCOO route and the RWGS route, respectively. Microkinetic modeling results demonstrate that themore » HCOO route is the dominant reaction route for methanol synthesis from CO2 hydrogenation. We found that the activation of H adatom on the small Pd cluster and the presence of H2O on the In2O3 substrate play important roles in promoting the methanol synthesis. The hydroxyl adsorbed at the interface of Pd4/In2O3 induces the transformation of the supported Pd4 cluster from a butterfly structure into a tetrahedron structure. This important structure change not only indicates the dynamical nature of the supported nanoparticle catalyst structure during the reaction but also shifts the final hydrogenation step from H2COH to CH3O.« less

Adaptive DFT-Based Interferometer Fringe Tracking

NASA Astrophysics Data System (ADS)

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

2005-12-01

An automatic interferometer fringe tracking system has been developed, implemented, and tested at the Infrared Optical Telescope Array (IOTA) Observatory at Mount Hopkins, Arizona. The system can minimize the optical path differences (OPDs) for all three baselines of the Michelson stellar interferometer at IOTA. Based on sliding window discrete Fourier-transform (DFT) calculations that were optimized for computational efficiency and robustness to atmospheric disturbances, the algorithm has also been tested extensively on offline data. Implemented in ANSI C on the 266 MHz PowerPC processor running the VxWorks real-time operating system, the algorithm runs in approximately [InlineEquation not available: see fulltext.] milliseconds per scan (including all three interferograms), using the science camera and piezo scanners to measure and correct the OPDs. The adaptive DFT-based tracking algorithm should be applicable to other systems where there is a need to detect or track a signal with an approximately constant-frequency carrier pulse. One example of such an application might be to the field of thin-film measurement by ellipsometry, using a broadband light source and a Fourier-transform spectrometer to detect the resulting fringe patterns.

DFT Study on the Complexation of Bambus[6]uril with the Perchlorate and Tetrafluoroborate Anions.

PubMed

Toman, Petr; Makrlík, Emanuel; Vaňura, Petr

2011-12-01

By using quantum mechanical DFT calculations, the most probable structures of the bambus[6]uril.ClO4- and bambus[6]uril.BF4- anionic complex species were derived. In these two complexes having C3 symmetry, each of the considered anions, included in the macrocyclic cavity, is bound by 12 weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units and the respective anion.

Crystal structure, vibrational and DFT simulation studies of melaminium dihydrogen phosphite monohydrate

NASA Astrophysics Data System (ADS)

Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

2013-08-01

The crystal structure investigations of melamine with phosphorous acid, namely melaminium dihydrogenphosphite monohydrate (C3N6H7·H2PO3·H2O) have been investigated by means of single crystal X-ray diffraction method. The title compound crystallizes in monoclinic crystal system, and the space group is P21/c with a = 10.069 Å, b = 21.592 Å, c = 12.409 Å and Z = 12. The vibrational assignments and analysis of melaminium dihydrogen phosphite monohydrate have also been performed by FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical simulations were performed with DFT (B3LYP) method using 6-31G**, cc-pVTZ, and 6-311++G** basis sets to determine the energy, structural, thermodynamic parameters and vibrational frequencies of melaminium dihydrogen phosphite monohydrate. The hydrogen atom from phosphorous acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H···O and Nsbnd H···O hydrogen bonds shows notable vibrational effects.

Benchmarking the Bethe–Salpeter Formalism on a Standard Organic Molecular Set

PubMed Central

2015-01-01

We perform benchmark calculations of the Bethe–Salpeter vertical excitation energies for the set of 28 molecules constituting the well-known Thiel’s set, complemented by a series of small molecules representative of the dye chemistry field. We show that Bethe–Salpeter calculations based on a molecular orbital energy spectrum obtained with non-self-consistent G0W0 calculations starting from semilocal DFT functionals dramatically underestimate the transition energies. Starting from the popular PBE0 hybrid functional significantly improves the results even though this leads to an average −0.59 eV redshift compared to reference calculations for Thiel’s set. It is shown, however, that a simple self-consistent scheme at the GW level, with an update of the quasiparticle energies, not only leads to a much better agreement with reference values, but also significantly reduces the impact of the starting DFT functional. On average, the Bethe–Salpeter scheme based on self-consistent GW calculations comes close to the best time-dependent DFT calculations with the PBE0 functional with a 0.98 correlation coefficient and a 0.18 (0.25) eV mean absolute deviation compared to TD-PBE0 (theoretical best estimates) with a tendency to be red-shifted. We also observe that TD-DFT and the standard adiabatic Bethe–Salpeter implementation may differ significantly for states implying a large multiple excitation character. PMID:26207104

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

PubMed

Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Triphenylamine based organic dyes for dye sensitized solar cells: A theoretical approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohankumar, V.; Pandian, Muthu Senthil; Ramasamy, P., E-mail: ramasamyp@ssn.edu.in

2016-05-23

The geometry, electronic structure and absorption spectra for newly designed triphenylamine based organic dyes were investigated by density functional theory (DFT) and time dependent density functional theory (TD-DFT) with the Becke 3-Parameter-Lee-Yang-parr(B3LYP) functional, where the 6-31G(d,p) basis set was employed. All calculations were performed using the Gaussian 09 software package. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Ultraviolet–visible (UV–vis) spectrum was simulated by TD-DFT in gas phase. The calculation shows that all of the dyes can potentially be good sensitizers for DSSC. The LUMOs are just above the conduction band of TiO{sub 2}more » and their HOMOs are under the reduction potential energy of the electrolytes (I{sup −}/I{sub 3}{sup −}) which can facilitate electron transfer from the excited dye to TiO{sub 2} and charge regeneration process after photo oxidation respectively. The simulated absorption spectrum of dyes match with solar spectrum. Frontier molecular orbital results show that among all the three dyes, the “dye 3” can be used as potential sensitizer for DSSC.« less

Synthesis, structural and biochemical activity studies of a new hexadentate Schiff base ligand and its Cu(II), Ni(II), and Co(II) complexes

NASA Astrophysics Data System (ADS)

Ekmekcioglu, Pinar; Karabocek, Nevin; Karabocek, Serdar; Emirik, Mustafa

2015-11-01

A new Schiff base ligand (H2L) and its metal complexes have been prepared and characterized by elemental analysis, magnetic moment and spectral studies. The comparative in-vitro antimicrobial activities against various pathogens with reference to known antibiotics activity under the standard control of different concentrations revealed that the metal complexes (6-8) showed enhanced antimicrobial activities in general as compared to free ligand. As an exception, the free ligand showed better activity against Trichoderma. The antifungal activity experiments were performed in triplicate. The order of biochemical activity for metal complexes were observed as in the following. CuL > CoL > NiL, which is exactly same as the order of stability constants of these complexes. Additionally, we performed DFT and TD-DFT calculation for free ligand and Cu(II) complex to support the experimental data. The geometries of the Cu(II) complex have been optimized using the B3LYP level of theory. The theoretical calculations confirm that the copper (II) center exhibits a distorted square pyramidal geometry which is favored by experimental results.

Vibrational and UV spectroscopic studies of 2-coumaranone by experimental and density functional theory calculations

NASA Astrophysics Data System (ADS)

Priya, Y. Sushma; Rao, K. Ramachandra; Chalapathi, P. V.; Satyavani, M.; Veeraiah, A.

2017-09-01

The vibrational and electronic properties of 2-coumaranone have been reported in the ground state using experimental techniques (FT-IR, FT-Raman, UV spectra and fluorescence microscopic imaging) and density functional theory (DFT) employing B3LYP correlation with the 6-31G(d, p) basis set. The theoretically reported optimized parameters, vibrational frequencies etc., were compared with the experimental values, which yielded good concurrence between the experimental and calculated values. The assignments of the vibrational spectra were done with the help of normal co-ordinate analysis (NCA) following the Scaled Quantum Mechanical Force Field(SQMFF) methodology. The whole assignments of fundamental modes were based on the potential energy distribution (PED) matrix. The electric dipole moment and the first order hyperpolarizability of the 2-coumaranone have been computed using quantum mechanical calculations. NBO and HOMO, LUMO analyses have been carried out. UV spectrum of 2-coumaranone was recorded in the region 100-300 nm and compared with the theoretical UV spectrum using TD-DFT and SAC-CI methods by which a good agreement is observed. Fluorescence microscopic imaging study reflects that the compound fluoresces in the green-yellow region.

Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

NASA Astrophysics Data System (ADS)

Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

2014-01-01

The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

Removal of heavy metal ions from wastewaters using dendrimer-functionalized multi-walled carbon nanotubes.

PubMed

Iannazzo, Daniela; Pistone, Alessandro; Ziccarelli, Ida; Espro, Claudia; Galvagno, Signorino; Giofré, Salvatore V; Romeo, Roberto; Cicero, Nicola; Bua, Giuseppe D; Lanza, Giuseppe; Legnani, Laura; Chiacchio, Maria A

2017-06-01

Dendrimer-functionalized multi-walled carbon nanotubes (MWCNT) for heavy metal ion removal from wastewaters were developed. Triazole dendrimers (TD) were built directly onto the carbon nanotube surface by successive click chemistry reactions affording the zero- and first-generation dendrimer-functionalized MWCNT (MWCNT-TD1 and MWCNT-TD2). The Moedritzer-Irani reaction carried out on the amino groups present on the MWCNT-TD2 sample gave the corresponding α-aminophosphonate nanosystem MWCNT-TD2P. Both MWCNT-TD2 and MWCNT-TD2P nanosystems have been characterized by physical, chemical, and morphological analyses. Their chelating abilities towards the toxic metal ions Pb 2+ , Hg 2+ , and Ni 2+ and the harmless Ca 2+ ion have been experimentally evaluated in the two different sets of experiments and at the salt concentrations of 1 mg/mL or 1 μg/mL by inductively coupled plasma mass spectrometry (ICP-MS). The results of these studies pointed out the interesting chelating behavior for the phosphonated nanosystem towards the Hg 2+ ion. The complexation mode of the best chelating system MWCNT-TD2P with mercury was investigated through density functional theory (DFT) calculations, suggesting a chelation mechanism involving the two oxygen atoms of the phosphate group. The synthesized dendrimers, supported on the multi-walled carbon nanotubes, have shown the potential to be used for the selective toxic metal ion removal and recovery.

Synthesis, characterization and relativistic DFT studies of fac-Re(CO)3(isonicotinic acid)2Cl complex

NASA Astrophysics Data System (ADS)

Zúñiga, César; Oyarzún, Diego P.; Martin-Transaco, Rudy; Yáñez-S, Mauricio; Tello, Alejandra; Fuentealba, Mauricio; Cantero-López, Plinio; Arratia-Pérez, Ramiro

2017-11-01

In this work, new fac-Re(CO)3(PyCOOH)2Cl from isonicotinic acid ligand has been prepared. The complex was characterized by structural (single-crystal X-ray diffraction), elemental analysis and spectroscopic (FTIR, NMR, UV-vis spectroscopy) methods. DFT and TDDFT calculations were performed to obtain the electronic transitions involved in their UV-Vis spectrum. The excitation energies agree with the experimental results. The TDDFT calculations suggest that experimental mixed absorption bands at 270 and 314 nm could be assigned to (MLCT-LLCT)/MLCT transitions. Natural Bond Orbitals (NBO) approach has enabled studying the effects of bonding interactions. E(2) energies confirm the occurrence of ICT (Intra-molecular Charge Transfer) within the molecule.

Improved in silico prediction of carcinogenic potency (TD50) and the risk specific dose (RSD) adjusted Threshold of Toxicological Concern (TTC) for genotoxic chemicals and pharmaceutical impurities.

PubMed

Contrera, Joseph F

2011-02-01

The Threshold of Toxicological Concern (TTC) is a level of exposure to a genotoxic impurity that is considered to represent a negligible risk to humans. The TTC was derived from the results of rodent carcinogenicity TD50 values that are a measure of carcinogenic potency. The TTC currently sets a default limit of 1.5 μg/day in food contact substances and pharmaceuticals for all genotoxic impurities without carcinogenicity data. Bercu et al. (2010) used the QSAR predicted TD50 to calculate a risk specific dose (RSD) which is a carcinogenic potency adjusted TTC for genotoxic impurities. This promising approach is currently limited by the software used, a combination of MC4PC (www.multicase.com) and a Lilly Inc. in-house software (VISDOM) that is not available to the public. In this report the TD50 and RSD were predicted using a commercially available software, SciQSAR (formally MDL-QSAR, www.scimatics.com) employing the same TD50 training data set and external validation test set that was used by Bercu et al. (2010). The results demonstrate the general applicability of QSAR predicted TD50 values to determine the RSDs for genotoxic impurities and the improved performance of SciQSAR for predicting TD50 values. Copyright © 2010 Elsevier Inc. All rights reserved.

Synthesis, spectroscopic and DFT studies of novel 4-(morpholinomethyl)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid

NASA Astrophysics Data System (ADS)

Devi, Poornima; Fatma, Shaheen; Bishnoi, Abha; Srivastava, Krishna; Shukla, Shraddha; Kumar, Roop

2018-04-01

A novel 4-(morpholinomethyl)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid has been synthesized and its structural elucidation has been done by UV, FT-IR, 1H and 13C NMR spectroscopy. All quantum chemical calculations were carried out at level of density functional theory (DFT) with B3LYP function using 6-31G (d, p) basis atomic set. AIM approach has been incorporated for the analysis of various intermolecular interactions. Polarizability and hyperpolarizabilities values have been calculated along with the exploration of nonlinear optical properties of the title compound. DFT computed total first static hyperpolarizability (β0 = 0.2747 × 10-30 esu) indicates that title molecule could be an area of interest as an attractive future NLO material. For the analysis of thermal behaviour of title molecule, thermodynamic properties such as heat capacity, entropy and enthalpy change at various temperatures have been calculated. The NBO computations were done for the correlation of possible transitions with the electronic transitions. Electrophilic and nucleophilic regions were identified with the help of MESP plot. Determination of energy gap has been done by using HOMO and LUMO energy values, along with the computation of electronegativity and electrophilicity indices.

Conformational, vibrational spectroscopic and quantum chemical studies on 5-methoxyindole-3-carboxaldehyde: A DFT approach

NASA Astrophysics Data System (ADS)

Jeyaseelan, S. Christopher; Hussain, Shamima; Premkumar, R.; Rekha, T. N.; Benial, A. Milton Franklin

2018-04-01

Indole and its derivatives are considered as good ligands for various disease causing proteins in human because of presence of the single nitrogen atom. In the present study, the potential energy surface scan was performed for the most stable molecular structure of the 5-Methoxyindole-3-carboxaldehyde (MICA) molecule. The most stable molecular structure was optimized by DFT/B3LYP method with 6-311G++ (d, p) basis set using Gaussian 09 program package. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculations using VEDA 4.0 program. The Frontier molecular orbitals analysis was performed and related molecular propertieswere calculated. The possible electrophilic and nucleophilic reactive sites of the molecule were studied using molecular electrostatic potential analysis, which confirms the bioactivity of the molecule. The natural bond orbital analysis was also performed to confirm the bioactivity of the title molecule.

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

PubMed

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

2014-07-15

Zinc (II) complexes with non-steroidal anti-inflammatory drugs (NSAIDs) naproxen (nap) and ibuprofen (ibu) were synthesized in the presence of nitrogen donor ligands (thiocyanate or azide). The complexes were characterized by elemental analysis, FT-IR, (1)H NMR and UV-Vis spectroscopes. The binding modes of the ligands in complexes were established by means of molecular modeling of the complexes, and calculation of their IR, NMR and absorption spectra at DFT (TDDFT)/B3LYP level were studied. The experimental and calculated data verified monodentate binding through the carboxylic oxygen atoms of anti-inflammatory drugs in the zinc complexes. The calculated (1)H, FT-IR and UV-Vis data are in better agreement with the experimental results, and confirm the predicted tetrahedral structures for the Zn (II) complexes. In addition to DFT calculations of complexes, natural bond orbital (NBO) was performed at B3LYP/6-31+G(d,p) level of theory. Biological studies showed the antibacterial activity of zinc complexes against Gram-positive and Gram-negative bacterial strains. Copyright © 2014 Elsevier B.V. All rights reserved.

DFT, NBO and molecular docking studies of the adsorption of fluoxetine into and on the surface of simple and sulfur-doped carbon nanotubes

NASA Astrophysics Data System (ADS)

Shahabi, Dana; Tavakol, Hossein

2017-10-01

In this study, noncovalent interactions between Fluoxetine (FX) and different carbon nanotubes (CNTs) or sulfur doped carbon nanotubes (SCNTs) were fully considered using DFT, natural bond orbital (NBO) and molecular docking calculations. Two different CNTs (and SCNTs) with 7,7 and 8,8 chiralities were considered as the adsorbents and the adsorption of FX by these adsorbents were studied in two cases: into the nanotubes and on their surfaces. The results of DFT and NBO calculations proposed that the 8,8 nanotubes are more suitable adsorbents for FX because the energies of their adsorptions are minimum. Population: analyses were also proposed that the adsorption of FX by SCNTs lead to more changes in electronic and sensing properties than the adsorption by CNTs. Moreover, the adsorption energies, obtained from molecular docking calculations (using 94 different models), proposed that the adsorption of FX into (versus out of) the nanotubes, adsorption processes by double-walled or triple-walled (versus single-walled) nanotubes and the adsorption by nanotubes with 8,8 chiralities are the most favorable adsorption processes.

Anatase-rutile phase transformation of titanium dioxide bulk material: a DFT + U approach

NASA Astrophysics Data System (ADS)

Vu, Nam H.; Le, Hieu V.; Cao, Thi M.; Pham, Viet V.; Le, Hung M.; Nguyen-Manh, Duc

2012-10-01

The anatase-rutile phase transformation of TiO2 bulk material is investigated using a density functional theory (DFT) approach in this study. According to the calculations employing the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Vanderbilt ultrasoft pseudopotential, it is suggested that the anatase phase is more energetically stable than rutile, which is in variance with the experimental observations. Consequently, the DFT + U method is employed in order to predict the correct structural stability in titania from electronic-structure-based total energy calculations. The Hubbard U term is determined by examining the band structure of rutile with various values of U from 3 to 10 eV. At U = 5 eV, a theoretical bandgap for rutile is obtained as 3.12 eV, which is in very good agreement with the reported experimental bandgap. Hence, we choose the DFT + U method (with U = 5 eV) to investigate the transformation pathway using the newly-developed solid-state nudged elastic band (ss-NEB) method, and consequently obtain an intermediate transition structure that is 9.794 eV per four-TiO2 above the anatase phase. When the Ti-O bonds in the transition state are examined using charge density analysis, seven Ti-O bonds (out of 24 bonds in the anatase unit cell) are broken, and this result is in excellent agreement with a previous experimental study (Penn and Banfield 1999 Am. Miner. 84 871-6).

Vibrational frequency analysis, FT-IR, DFT and M06-2X studies on tert-Butyl N-(thiophen-2yl)carbamate.

PubMed

Sert, Yusuf; Singer, L M; Findlater, M; Doğan, Hatice; Çırak, Ç

2014-07-15

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized tert-Butyl N-(thiophen-2yl)carbamate have been investigated. The experimental FT-IR (4000-400 cm(-1)) spectrum of the molecule in the solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with the 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The vibrational frequencies have been assigned using potential energy distribution (PED) analysis by using VEDA 4 software. The computational optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with related literature results. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and are depicted. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiresolution quantum chemistry in multiwavelet bases: excited states from time-dependent Hartree–Fock and density functional theory via linear response

DOE PAGES

Yanai, Takeshi; Fann, George I.; Beylkin, Gregory; ...

2015-02-25

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using amore » numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2, Be, N 2, H 2O, and C 2H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yanai, Takeshi; Fann, George I.; Beylkin, Gregory

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using amore » numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2, Be, N 2, H 2O, and C 2H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.« less

Error compensation of IQ modulator using two-dimensional DFT

NASA Astrophysics Data System (ADS)

Ohshima, Takashi; Maesaka, Hirokazu; Matsubara, Shinichi; Otake, Yuji

2016-06-01

It is important to precisely set and keep the phase and amplitude of an rf signal in the accelerating cavity of modern accelerators, such as an X-ray Free Electron Laser (XFEL) linac. In these accelerators an acceleration rf signal is generated or detected by an In-phase and Quadrature (IQ) modulator, or a demodulator. If there are any deviations of the phase and the amplitude from the ideal values, crosstalk between the phase and the amplitude of the output signal of the IQ modulator or the demodulator arises. This causes instability of the feedback controls that simultaneously stabilize both the rf phase and the amplitude. To compensate for such deviations, we developed a novel compensation method using a two-dimensional Discrete Fourier Transform (DFT). Because the observed deviations of the phase and amplitude of an IQ modulator involve sinusoidal and polynomial behaviors on the phase angle and the amplitude of the rf vector, respectively, the DFT calculation with these basis functions makes a good approximation with a small number of compensation coefficients. Also, we can suppress high-frequency noise components arising when we measure the deviation data. These characteristics have advantages compared to a Look Up Table (LUT) compensation method. The LUT method usually demands many compensation elements, such as about 300, that are not easy to treat. We applied the DFT compensation method to the output rf signal of a C-band IQ modulator at SACLA, which is an XFEL facility in Japan. The amplitude deviation of the IQ modulator after the DFT compensation was reduced from 15.0% at the peak to less than 0.2% at the peak for an amplitude control range of from 0.1 V to 0.9 V (1.0 V full scale) and for a phase control range from 0 degree to 360 degrees. The number of compensation coefficients is 60, which is smaller than that of the LUT method, and is easy to treat and maintain.

Molecular docking, vibrational, structural, electronic and optical studies of {4 - (2, 6) dichlorophenyl amino 2 - methylidene 4 - oxobutanoic acid and 4- (2, 5)} dichlorophenyl amino 2 - methylidene 4 - oxobutanoic acid - A comparative study

NASA Astrophysics Data System (ADS)

Vanasundari, K.; Balachandran, V.; Kavimani, M.; Narayana, B.

2018-03-01

Spectroscopic and structural investigations of 4 - [(2, 6 - dichlorophenyl) amino] 2 -methylidene 4 - oxobutanoic acid (6DAMB) and 4-[(2, 5- dichlorophenyl) amino] 2 - methylidene 4 - oxobutanoic acid (5DAMB) are presented by using experimental (FT-IR and FT-Raman) spectra and theoretical (DFT approach) calculations. Seventy-two characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization was analyzed using natural bond orbital (NBO) analysis. Several descriptors determined from the energies of frontier molecular orbital (HOMO and LUMO) were applied to describe the reactivity of the title compound. The dipole moment and first hyperpolarizabilities of the studied compounds indicate that the compound is a good candidate of nonlinear optical materials. Theoretical Ultraviolet-Visible spectra of title compounds have been analyzed using the TD-DFT method. The noncovalent interactions like hydrogen bonding and Van der Waals interaction were identified from the molecular geometry and electron localization function. These interactions in molecules have been studied by using reduced density gradient (RDG) and graphed by Multiwfn. Auto-dock studies reveal that butanoic acid derivatives play a vital role in bonding and results draw us to the concluded that both compounds inhibit Placenta growth factor (PIGF-1) and that have good biological activities. This study may also provide further investigation on butanoic acid derivatives for pharmacological importance.

Ortho and para hydrogen dimers on G/SiC(0001): combined STM and DFT study.

PubMed

Merino, P; Švec, M; Martínez, J I; Mutombo, P; Gonzalez, C; Martín-Gago, J A; de Andres, P L; Jelinek, P

2015-01-01

The hydrogen (H) dimer structures formed upon room-temperature H adsorption on single layer graphene (SLG) grown on SiC(0001) are addressed using a combined theoretical-experimental approach. Our study includes density functional theory (DFT) calculations for the full (6√3 × 6√3)R30° unit cell of the SLG/SiC(0001) substrate and atomically resolved scanning tunneling microscopy images determining simultaneously the graphene lattice and the internal structure of the H adsorbates. We show that H atoms normally group in chemisorbed coupled structures of different sizes and orientations. We make an atomic scale determination of the most stable experimental geometries, the small dimers and ellipsoid-shaped features, and we assign them to hydrogen adsorbed in para dimers and ortho dimers configuration, respectively, through comparison with the theory.

Characterization of a Unique Cell Population Marked by Transgene Expression in the Adult Cochlea of Nestin-CreERT2/tdTomato-Reporter Mice

PubMed Central

Chow, Cynthia L.; Guo, Weixiang; Trivedi, Parul; Zhao, Xinyu; Gubbels, Samuel P.

2015-01-01

Hair cells in the adult mammalian cochlea cannot spontaneously regenerate after damage resulting in the permanency of hearing loss. Stem cells have been found to be present in the cochlea of young rodents; however, there has been little evidence for their existence into adulthood. We used nestin-CreERT2/tdTomato-reporter mice to trace the lineage of putative nestin-expressing cells and their progeny in the cochleae of adult mice. Nestin, an intermediate filament found in neural progenitor cells during early development and adulthood, is regarded as a multi-potent and neural stem cell marker. Other investigators have reported its presence in postnatal and young adult rodents; however, there are discrepancies amongst these reports. Using lineage tracing, we documented a robust population of tdTomato-expressing cells and evaluated these cells at a series of adult time points. Upon activation of the nestin promoter, tdTomato was observed just below and medial to the inner hair cell layer. All cells co-localized with the stem cell and cochlear-supporting-cell marker Sox2 as well as the supporting cell and Schwann cell marker Sox10; however, they did not co-localize with the Schwann cell marker Krox20, spiral ganglion marker NF200, or GFAP-expressing supporting cell marker. The cellular identity of this unique population of tdTomato-expressing cells in the adult cochlea of nestin-CreERT2/tdTomato mice remains unclear however these cells may represent a type of supporting cell on the neural aspect of the inner hair cell layer. PMID:25611038

MP2, DFT-D, and PCM study of the HMB-TCNE complex: Thermodynamics, electric properties, and solvent effects

NASA Astrophysics Data System (ADS)

Kysel, Ondrej; Budzák, Scaronimon; Medveď, Miroslav; Mach, Pavel

Geometry, thermodynamic, and electric properties of the pi-EDA complex between hexamethylbenzene (HMB) and tetracyanoethylene (TCNE) are investigated at the MP2/6-31G* and, partly, DFT-D/6-31G* levels. Solvent effects on the properties are evaluated using the PCM model. Fully optimized HMB-TCNE geometry in gas phase is a stacking complex with an interplanar distance 2.87 × 10-10 m and the corresponding BSSE corrected interaction energy is -51.3 kJ mol-1. As expected, the interplanar distance is much shorter in comparison with HF and DFT results. However the crystal structures of both (HMB)2-TCNE and HMB-TCNE complexes have interplanar distances somewhat larger (3.18 and 3.28 × 10-10 m, respectively) than our MP2 gas phase value. Our estimate of the distance in CCl4 on the basis of PCM solvent effect study is also larger (3.06-3.16 × 10-10 m). The calculated enthalpy, entropy, Gibbs energy, and equilibrium constant of HMB-TCNE complex formation in gas phase are: DeltaH0 = -61.59 kJ mol-1, DeltaSc0 = -143 J mol-1 K-1, DeltaG0 = -18.97 kJ mol-1, and K = 2,100 dm3 mol-1. Experimental data, however, measured in CCl4 are significantly lower: DeltaH0 = -34 kJ mol-1, DeltaSc0 = -70.4 J mol-1 K-1, DeltaG0 = -13.01 kJ mol-1, and K = 190 dm3 mol-1. The differences are caused by solvation effects which stabilize more the isolated components than the complex. The total solvent destabilization of Gibbs energy of the complex relatively to that of components is equal to 5.9 kJ mol-1 which is very close to our PCM value 6.5 kJ mol-1. MP2/6-31G* dipole moment and polarizabilities are in reasonable agreement with experiment (3.56 D versus 2.8 D for dipole moment). The difference here is due to solvent effect which enlarges interplanar distance and thus decreases dipole moment value. The MP2/6-31G* study supplemented by DFT-D parameterization for enthalpy calculation, and by the PCM approach to include solvent effect seems to be proper tools to elucidate the properties of pi

Levels of diphtheria and tetanus specific IgG of Portuguese adult women, before and after vaccination with adult type Td. Duration of immunity following vaccination

PubMed Central

Gonçalves, Guilherme; Santos, Maria Augusta; Frade, João Graça; Cunha, José Saraiva

2007-01-01

Background The need for tetanus toxoid decennial booster doses has been questioned by some experts. Several counter arguments have been presented, supporting the maintenance of decennial adult booster doses with tetanus and diphtheria toxoids (adult formulation of the vaccine: Td). This study aimed to evaluate the use of Td in Portuguese adult women under routine conditions. For that purpose we selected a group of women 30+ years of age to which vaccination was recommended. We intended to know if pre-vaccination antibody concentrations were associated with factors as age at first and last vaccination, number of doses and time since last revaccination. We also intended to assess the serological efficacy of Td booster. Methods Following the Portuguese guidelines 100 women were vaccinated with Td. Antitetanus toxin IgG (ATT IgG) and antidiphtheria toxin IgG (ADT IgG) levels were measured (mIU/ml) in 100 pre-vaccination and 91 post-vaccination sera. Detailed vaccination records were available from 88 participants. Results Twenty-two women (Group A) began vaccination with DPT/DT in their early childhood and their pre-vaccination ATT IgG levels increased with the number of doses received (p = 0.022) and decreased with time since last vaccination (p = 0.016). Among the 66 women who began vaccination in adolescence and adulthood (Group B), with monovalent TT, ATT IgG levels decreased with age at first dose (p < 0.001) and with time since last vaccination (p = 0.041). In Group A, antidiphtheria toxin IgG kinetics was very similar to that observed for ATT IgG. Among women not vaccinated with diphtheria toxoid, ADT IgG levels decreased with age. Serological response to both components of Td was good but more pronounced for ATT IgG. Conclusion Our study suggests that, to protect against tetanus, there is no need to administer decennial boosters to the Portuguese adults who have complied with the childhood/adolescent schedule (6 doses of tetanus toxoid). The adult booster

Application of DFT Filter Banks and Cosine Modulated Filter Banks in Filtering

NASA Technical Reports Server (NTRS)

Lin, Yuan-Pei; Vaidyanathan, P. P.

1994-01-01

None given. This is a proposal for a paper to be presented at APCCAS '94 in Taipei, Taiwan. (From outline): This work is organized as follows: Sec. II is devoted to the construction of the new 2m channel under-decimated DFT filter bank. Implementation and complexity of this DFT filter bank are discussed therein. IN a similar manner, the new 2m channel cosine modulated filter bank is discussed in Sec. III. Design examples are given in Sec. IV.

Benchmarks and Reliable DFT Results for Spin Gaps of Small Ligand Fe(II) Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Suhwan; Kim, Min-Cheol; Sim, Eunji

2017-05-01

All-electron fixed-node diffusion Monte Carlo provides benchmark spin gaps for four Fe(II) octahedral complexes. Standard quantum chemical methods (semilocal DFT and CCSD(T)) fail badly for the energy difference between their high- and low-spin states. Density-corrected DFT is both significantly more accurate and reliable and yields a consistent prediction for the Fe-Porphyrin complex

Revisiting the diffusion mechanism of helium in UO2: A DFT+U study

NASA Astrophysics Data System (ADS)

Liu, X.-Y.; Andersson, D. A.

2018-01-01

The understanding of migration properties of helium atoms after their generation through α-decay of actinides in spent nuclear fuels is important for the safety of nuclear fuel storage and disposal. The diffusion of helium in UO2 is revisited by using the DFT+U simulation methodology employing the "U-ramping" method to address the issue of metastable energy states. A novel diffusion mechanism by helium interstitials, the "asymmetric hop" mechanism, is reported and compared to other diffusion mechanisms including an oxygen vacancy mediated mechanism and available experimental diffusion data. The new mechanism is shown to be the dominant one over a wide temperature range.

Complete Genome Sequences of Lactobacillus johnsonii Strain N6.2 and Lactobacillus reuteri Strain TD1.

PubMed

Leonard, Michael T; Valladares, Ricardo B; Ardissone, Alexandria; Gonzalez, Claudio F; Lorca, Graciela L; Triplett, Eric W

2014-05-08

We report here the complete genome sequences of Lactobacillus johnsonii strain N6.2, a homofermentative lactic acid intestinal bacterium, and Lactobacillus reuteri strain TD1, a heterofermentative lactic acid intestinal bacterium, both isolated from a type 1 diabetes-resistant rat model.

Hot corrosion of four superalloys - HA-188, S-57, IN-617, and TD-NiCrAl

NASA Technical Reports Server (NTRS)

Santoro, G. J.

1979-01-01

Cyclic oxidation and hot corrosion tests of two cobalt-base and two nickel-base alloys are reported. The alloys were exposed to maximum temperatures of 900 and 1000 C in a Mach 0.3 burner rig whose flame was doped with various concentrations of sea salt and sodium sulfate for hot corrosion tests. The test data were subjected to a regression analysis for the development of model equations relating corrosion to temperature and for the effects of salt concentration and composition on corrosion. The corrosion resistance varied with temperature, sea salt concentration, and salt composition, concluding that the S-57 cobalt-base alloy was the most hot corrosion-resistant alloy, and the TD-NiCrAl nickel-base alloy was the least resistant. However, under straight oxidation conditions, the TD-NiCrAl was most resistant, while S-57 was the least resistant alloy.

Study on structure, vibrational analysis and molecular characteristics of some halogen substituted azido-phenylethanones using FTIR spectra and DFT

NASA Astrophysics Data System (ADS)

Prashanth, J.; Reddy, Byru Venkatram

2018-03-01

The Fourier transform infrared (FTIR) spectra of organic compounds 4-fluoro-2-azido-1-phenylethanone (FAP), 4-chloro-2-azido-1-phenylethanone (CAP) and 4-bromo-2-azido-1-phenylethanone (BAP) have been recorded in the region 4000-400 cm-1. The optimized molecular structure for global minimum energy of the titled molecules is determined by evaluating torsional potentials as a function of rotation angle about free rotation bonds among the substituent groups subjecting them to DFT employing B3LYP functional with 6-311++G (d,p) basis set. The vibrational frequencies along with infrared intensities are computed by SQM procedure. The rms error between observed and calculated frequencies is found to be 9.27, 8.17 and 7.95 cm-1 for FAP, CAP and BAP, respectively which shows good agreement between experimental and scaled values of calculated frequencies obtained by DFT. The vibrational assignments of all the fundamental bands of each molecule are made unambiguously using PED and eigen vectors obtained in the computations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the titled molecules exhibit NLO behaviour and hence may be considered for potential applicants for the development of NLO materials. HOMO and LUMO energies evaluated in the study demonstrate chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyper conjugative interactions and charge delocalization. The molecular electrostatic surface potential (MESP) and thermodynamic parameters are also evaluated.

Optical characterization of shock-induced chemistry in the explosive nitromethane using DFT and time-dependent DFT

NASA Astrophysics Data System (ADS)

Pellouchoud, Lenson; Reed, Evan

2014-03-01

With continual improvements in ultrafast optical spectroscopy and new multi-scale methods for simulating chemistry for hundreds of picoseconds, the opportunity is beginning to exist to connect experiments with simulations on the same timescale. We compute the optical properties of the liquid phase energetic material nitromethane (CH3NO2) for the first 100 picoseconds behind the front of a simulated shock at 6.5km/s, close to the experimentally observed detonation shock speed. We utilize molecular dynamics trajectories computed using the multi-scale shock technique (MSST) for time-resolved optical spectrum calculations based on both linear response time-dependent DFT (TDDFT) and the Kubo-Greenwood (KG) formula within Kohn-Sham DFT. We find that TDDFT predicts optical conductivities 25-35% lower than KG-based values and provides better agreement with the experimentally measured index of refraction of unreacted nitromethane. We investigate the influence of electronic temperature on the KG spectra and find no significant effect at optical wavelengths. With all methods, the spectra evolve non-monotonically in time as shock-induced chemistry takes place. We attribute the time-resolved absorption at optical wavelengths to time-dependent populations of molecular decomposition products, including NO, CNO, CNOH, H2O, and larger molecules. Supported by NASA Space Technology Research Fellowship (NSTRF) #NNX12AM48H.

Combined DFT and BS study on the exchange coupling of dinuclear sandwich-type POM: comparison of different functionals and reliability of structure modeling.

PubMed

Yin, Bing; Xue, GangLin; Li, JianLi; Bai, Lu; Huang, YuanHe; Wen, ZhenYi; Jiang, ZhenYi

2012-05-01

The exchange coupling of a group of three dinuclear sandwich-type polyoxomolybdates [MM'(AsMo7O27)2](12-) with MM' = CrCr, FeFe, FeCr are theoretically predicted from combined DFT and broken-symmetry (BS) approach. Eight different XC functionals are utilized to calculate the exchange-coupling constant J from both the full crystalline structures and model structures of smaller size. The comparison between theoretical values and accurate experimental results supports the applicability of DFT-BS method in this new type of sandwich-type dinuclear polyoxomolybdates. However, a careful choice of functionals is necessary to achieve the desired accuracy. The encouraging results obtained from calculations on model structures highlight the great potential of application of structure modeling in theoretical study of POM. Structural modeling may not only reduce the computational cost of large POM species but also be able to take into account the external field effect arising from solvent molecules in solution or counterions in crystal.

Advantages of GPU technology in DFT calculations of intercalated graphene

NASA Astrophysics Data System (ADS)

Pešić, J.; Gajić, R.

2014-09-01

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

Analyzing the errors of DFT approximations for compressed water systems

NASA Astrophysics Data System (ADS)

Alfè, D.; Bartók, A. P.; Csányi, G.; Gillan, M. J.

2014-07-01

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm3 where the experimental pressure is 15 kilobars; second, thermal samples of compressed water clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mEh ≃ 15 meV/monomer for the liquid and the

Analyzing the errors of DFT approximations for compressed water systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alfè, D.; London Centre for Nanotechnology, UCL, London WC1H 0AH; Thomas Young Centre, UCL, London WC1H 0AH

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm{sup 3} where the experimental pressure is 15 kilobars; second, thermal samples of compressed watermore » clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mE{sub h} ≃ 15 meV/monomer for the

Theoretical investigation of structures and energetics of sodium adatom and its dimer on graphene: DFT study

NASA Astrophysics Data System (ADS)

Kaur, Gagandeep; Gupta, Shuchi; Rani, Pooja; Dharamvir, Keya

2015-11-01

Extensive ab initio calculations have been performed to study the energetics of a sodium (Na) atom and its dimer adsorbed on graphene using the SIESTA package Soler et al. (2002) [1] which works within a DFT(density functional theory)-GGA (generalized gradient approximation) pseudopotential framework. The adsorption energy, geometry, charge transfer, ionization potential and density of states (DOS), partial density states (PDOS) of adatom/dimer-graphene system have been calculated. After considering various sites for adsorption of Na on graphene, the center of a hexagonal ring of carbon atoms is found to be the preferred site of adsorption while the Na2 dimer prefers to rest parallel to the graphene sheet. We find insignificant energy differences among adsorption configurations involving different possible sites in parallel orientation, which implies high mobility of the dimer on the graphene sheet. We also notice only a slight distortion of the graphene sheet perpendicular to its plane upon adatom adsorption. However, some lateral displacements seen are more perceptible. Summary The adsorption energy, geometry, charge transfer, ionization potential and density of states (DOS) and PDOS of adatom/dimer-graphene system have been calculated using SIESTA package Soler et al. (2002) [1] which works within a DFT(density functional theory)-GGA (generalized gradient approximation) pseudopotential framework. Preferred site for adsorption of a sodium atom on graphene is the hollow site. For the Na dimer adsorption, we found that horizontal orientation is favored over the vertical one. From DOS plots, it is clear that graphene's states are nearly unaffected by the adsorption of Na adatom and Interaction between sodium and graphene is predominantly ionic

Synthesis and photophysical studies of blue phosphorescent Ir(III) complexes with dimethylphenylphospine.

PubMed

Ham, Ho-Wan; Jung, Kyung-Yoon; Kim, Young-Sik

2012-02-01

New blue emitting mixed ligand iridium(III) complexes comprising one cyclometalating, two phosphines trans to each other such as Ir{(CF3)2Meppy}(PPhMe3)2(H)(L) [L = CI, NCMe, CN] [(CF3)2Meppy = 2-(3', 5'-bis-trifluoromethylphenyl)-4-methylpyridine] were synthesized and studied to tune the phosphorescence wavelength to the deep blue region and to enhance the luminescence efficiencies. To achieve deep blue emission, the trifluoromethyl group substituted on the phenyl ring and the methyl group substituted on the pyridyl ring increased HOMO-LUMO gap and achieved the hypsochromic shift. To gain insight into the factors responsible for the emission color change and the different luminescence efficiency, we investigate the electron-withdrawing capabilities of ancillary ligands using the DFT and TD-DFT calculations on the ground and excited states of the complexes. From these results, we discuss how the ancillary ligand influences the emission peak as well as the metal to ligand charge transfer (MLCT) transition efficiency. The maximum emission spectra of Ir{(CF3)2Meppy}(PPhMe3)2(H)(Cl), [Ir{(CF3),Meppy)(PPhMe3),(H)(NCMe)]+ and Ir{(CF3)2Meppy}(PPhMe3)2(H)(CN) were in the ranges of 441, 435, 434 nm, respectively.

Understanding Density Functional Theory (DFT) and Completing it in Practice

NASA Astrophysics Data System (ADS)

Bagayoko, Diola

2015-03-01

A brief review of the seminal article by Hohenberg and Kohn leads to two conditions that have to be met by electronic structure calculations in order for their results to represent the physics content of DFT. One of these conditions is often the verifiable attainment of the absolute minima of the occupied energies. Using the second Hohenberg Kohn theorem, we show that results of calculations that do not meet this condition, when it applies, do not necessarily represent DFT findings. We illustrate this fact with over 100 calculated band gaps that are much smaller than corresponding, measured ones; in contrast, we list calculations that strictly adhered to the aforementioned conditions and whose results are in excellent agreement with experiment. We describe two crucial steps in the latter calculations that add to or complete DFT in practice. Some implications of our findings for academia, industry, and program package developers will be discussed. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

DFT Study of PH3 Physisorption and Chemisorptions on Boron Nitride Nanotubes

NASA Astrophysics Data System (ADS)

Rakhshi, Mahdi; Mohsennia, Mohsen; Rasa, Hossein

2018-03-01

The adsorption of PH3 molecules on the NiB,N-doped(4,4) and (5,5) BNNTS surfaces has been investigated using density functional theory (DFT). The adsorption energies, geometric and electronic structures of the adsorbed systems were studied to judge the possible application of NiB,N-doped BNNTS in PH3 monitoring systems. Our calculated results showed that NiB,N-doped BNNTS had much higher adsorption energy and shorter binding distances than pure BNNTS owning to chemisorptions of the PH3 molecule. The obtained density of states (DOS) and frontier orbitals demonstrated that the orbital hybridization was obvious between the PH3 molecule and NiB,N-doped BNNTS. However, due to weak physisorption according to the total electron density maps, there was no evidence for hybridization between PH3 molecule and pure BNNTS. It was shown that after doping of Ni atom, the primary symmetry of BNNTS decreased which enhanced the chemical activity of BNNTS towards PH3 molecules. According to the obtained results, we highlight the high potential application of NiB,N-doped BNNTS in the design and fabrication of PH3 sensing devices.

The study of intermolecular interactions in NLO crystal melaminium chloride hemihydrate using DFT simulation and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Sangeetha, K.; Kumar, V. R. Suresh; Marchewka, M. K.; Binoy, J.

2018-05-01

Since, the intermolecular interactions play a crucial role in the formation of crystalline network, its analysis throws light on structure dependent crystalline properties. In the present study, DFT based vibrational spectral investigation has been performed in the stretching region (3500 cm-1 - 2800 cm-1) of IR and Raman spectra of melaminium chloride hemihydrates. The intermolecular interaction has been investigated by analyzing the half width of the OH and NH stretching profile of the deconvoluted spectra. Correlation of vibrational spectra with Hirshfeld surface analysis and finger print plot has been contemplated and molecular docking studies has been performed on melaminium chloride hemihydrate to assess its role in the drug transport mechanism and toxicity to human body.

Molecular docking, TG/DTA, molecular structure, harmonic vibrational frequencies, natural bond orbital and TD-DFT analysis of diphenyl carbonate by DFT approach

NASA Astrophysics Data System (ADS)

Xavier, S.; Periandy, S.; Carthigayan, K.; Sebastian, S.

2016-12-01

Vibrational spectral analysis of Diphenyl Carbonate (DPC) is carried out by using FT-IR and FT-Raman spectroscopic techniques. It is found that all vibrational modes are in the expected region. Gaussian computational calculations were performed using B3LYP method with 6-311++G (d, p) basis set. The computed geometric parameters are in good agreement with XRD data. The observation shows that the structure of the carbonate group is unsymmetrical by ∼5° due to the attachment of the two phenyl rings. The stability of the molecule arising from hyperconjugative interaction and charge delocalization are analyzed by Natural Bond Orbital (NBO) study and the results show the lone pair transition has higher stabilization energy compared to all other. The 1H and 13C NMR chemical shifts are calculated using the Gauge-Including Atomic Orbital (GIAO) method with B3LYP/6-311++G (d, p) method. The chemical shifts computed theoretically go very closer to the experimental results. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies and Molecular electrostatic potential (MEP) exhibit the high reactivity nature of the molecule. The non-linear optical property of the DPC molecule predicted theoretically found to be good candidate for NLO material. TG/DTA analysis was made and decomposition of the molecule with respect to the temperature was studied. DPC having the anthelmintic activity is docked in the Hemoglobin of Fasciola hepatica protein. The DPC has been screened to antimicrobial activity and found to exhibit antibacterial effects.

Vibrational spectroscopic, structural and nonlinear optical activity studies on 6-aminonicotinamide: A DFT approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asath, R. Mohamed; Premkumar, S.; Mathavan, T.

2016-05-23

The conformational analysis was carried out for 6-aminonicotinamide (ANA) using potential energy surface scan method and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the related molecular properties were calculated. The ultraviolet-visible spectrum was simulated for both in the gas phase andmore » liquid phase (ethanol) and the π to π* electronic transition was predicted. The nonlinear optical (NLO) activity was studied by means of the first order hyperpolarizability value, which was 8.61 times greater than the urea and the natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the ANA molecule is a promising candidate for the NLO materials.« less

Vibrational spectroscopic, structural and nonlinear optical activity studies on 6-aminonicotinamide: A DFT approach

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Premkumar, S.; Rekha, T. N.; Jawahar, A.; Mathavan, T.; Benial, A. Milton Franklin

2016-05-01

The conformational analysis was carried out for 6-aminonicotinamide (ANA) using potential energy surface scan method and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the related molecular properties were calculated. The ultraviolet-visible spectrum was simulated for both in the gas phase and liquid phase (ethanol) and the л to л* electronic transition was predicted. The nonlinear optical (NLO) activity was studied by means of the first order hyperpolarizability value, which was 8.61 times greater than the urea and the natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the ANA molecule is a promising candidate for the NLO materials.

DFT, Its Impact on Condensed Matter and on ``Materials-Genome'' Research

NASA Astrophysics Data System (ADS)

Scheffler, Matthias

About 40 years ago, two seminal works demonstrated the power of density-functional theory (DFT) for real materials. These studies by Moruzzi, Janak, and Williams on metals and Yin and Cohen on semiconductors visualized the spatial distribution of electrons, predicted the equation of state of solids, crystal stability, pressure-induced phase transitions, and more. They also stressed the importance of identifying trends by looking at many systems (e.g. the whole transition-metal series). Since then, the field has seen numerous applications of DFT to solids, liquids, defects, surfaces, and interfaces providing important descriptions and explanations as well as predictions of experimentally not yet identified systems. - ∖ ∖ About 10 years ago, G. Ceder and his group [Ref. 3 and references therein] started with high-throughput screening calculations in the spirit of what in 2011 became the ``Materials Genome Initiative''. The idea of high-throughput screening is old (a key example is the ammonia catalyst found by A. Mittasch at BASF more than 100 years ago), but it is now increasingly becoming clear that big data of materials does not only provide direct information but that the data is structured. This enables interpolation, (modest) extrapolation, and new routes towards understanding [Ref. 5 and references therein]. - ∖ ∖ The amount of data created by ``computational materials science'' is significant. For instance, the NoMaD Repository (which includes also data from other repositories, e.g. AFLOWLIB and OQMD) now holds more than 18 million total-energy calculations. In fact, the amount of data of computational materials science is steadily increasing, and about hundred million CPU core hours are nowadays used every day, worldwide, for DFT calculations for materials. - ∖ ∖ The talk will summarize this enormous impact of DFT on materials science, and it will address the next steps, e.g. the issue how to exploit big data of materials for doing forefront

A DFT study on surface-enhanced Raman spectroscopy of aromatic dithiol derivatives adsorbed on gold nanojunctions

NASA Astrophysics Data System (ADS)

You, Tingting; Lang, Xiufeng; Huang, Anping; Yin, Penggang

2018-01-01

A computational study on aromatic dithiol derivatives (HS-Ar-X-Ar-SH, X = O, S, Se, NH, CH2, Ndbnd N, CHdbnd CH, Ctbnd C) interacting with gold cluster(s) was presented to investigate the chemical enhancement mechanism related to surface-enhanced Raman spectroscopy (SERS) for molecular junctions. Density functional theory (DFT) were performed on derivatives molecules as well as their single-end-linked (SEL) or double-end-linked (DEL) complexes for geometric, spectra, electronic and excitation properties, leading to discussions on dominant factor during SERS process. The resulted enhancement factors of SEL and DEL complexes exhibited specific dependency on linking atom or functional group between two phenyls, which was in accordance with the variation of polarizabilities and molecule-cluster transition energy.

DFT investigations of hydrogen storage materials

NASA Astrophysics Data System (ADS)

Wang, Gang

Hydrogen serves as a promising new energy source having no pollution and abundant on earth. However the most difficult problem of applying hydrogen is to store it effectively and safely, which is smartly resolved by attempting to keep hydrogen in some metal hydrides to reach a high hydrogen density in a safe way. There are several promising metal hydrides, the thermodynamic and chemical properties of which are to be investigated in this dissertation. Sodium alanate (NaAlH4) is one of the promising metal hydrides with high hydrogen storage capacity around 7.4 wt. % and relatively low decomposition temperature of around 100 °C with proper catalyst. Sodium hydride is a product of the decomposition of NaAlH4 that may affect the dynamics of NaAlH4. The two materials with oxygen contamination such as OH- may influence the kinetics of the dehydriding/rehydriding processes. Thus the solid solubility of OH - groups (NaOH) in NaAlH4 and NaH is studied theoretically by DFT calculations. Magnesium boride [Mg(BH4)2] is has higher hydrogen capacity about 14.9 wt. % and the decomposition temparture of around 250 °C. However one flaw restraining its application is that some polyboron compounds like MgB12H12 preventing from further release of hydrogen. Adding some transition metals that form magnesium transition metal ternary borohydride [MgaTMb(BH4)c] may simply the decomposition process to release hydrogen with ternary borides (MgaTMbBc). The search for the probable ternary borides and the corresponding pseudo phase diagrams as well as the decomposition thermodynamics are performed using DFT calculations and GCLP method to present some possible candidates.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2017-06-01

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

DFT modeling of chemistry on the Z machine

NASA Astrophysics Data System (ADS)

Mattsson, Thomas

2013-06-01

Density Functional Theory (DFT) has proven remarkably accurate in predicting properties of matter under shock compression for a wide-range of elements and compounds: from hydrogen to xenon via water. Materials where chemistry plays a role are of particular interest for many applications. For example the deep interiors of Neptune, Uranus, and hundreds of similar exoplanets are composed of molecular ices of carbon, hydrogen, oxygen, and nitrogen at pressures of several hundred GPa and temperatures of many thousand Kelvin. High-quality thermophysical experimental data and high-fidelity simulations including chemical reaction are necessary to constrain planetary models over a large range of conditions. As examples of where chemical reactions are important, and demonstration of the high fidelity possible for these both structurally and chemically complex systems, we will discuss shock- and re-shock of liquid carbon dioxide (CO2) in the range 100 to 800 GPa, shock compression of the hydrocarbon polymers polyethylene (PE) and poly(4-methyl-1-pentene) (PMP), and finally simulations of shock compression of glow discharge polymer (GDP) including the effects of doping with germanium. Experimental results from Sandia's Z machine have time and again validated the DFT simulations at extreme conditions and the combination of experiment and DFT provide reliable data for evaluating existing and constructing future wide-range equations of state models for molecular compounds like CO2 and polymers like PE, PMP, and GDP. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT.

PubMed

Latosińska, Jolanta N; Seliger, Janez; Zagar, Veselko; Burchardt, Dorota V

2012-01-01

A potential antileukemic and anticancer agent, 2-thiocytosine (2-TC), has been studied experimentally in the solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT). Eighteen resonance frequencies on (14)N were detected at 180 K and assigned to particular nitrogen sites (-NH(2), -N=, and -NH-) in 2-thiocytosine. Factors such as the nonequivalence of molecules (connected to the duplication of sites) and possible prototropic tautomerism (capable of modifying the type of site due to proton transfer) were taken into account during frequency assignment. The result of replacing oxygen with sulfur, which leads to changes in the intermolecular interaction pattern and molecular aggregation, is discussed. This study demonstrates the advantages of combining NQDR and DFT to extract detailed information on the H-bonding properties of crystals with complex H-bonding networks. Solid-state properties were found to have a profound impact on the stabilities and reactivities of both compounds.

Synthesis, crystal structure, vibrational spectroscopy, optical properties and theoretical studies of a new organic-inorganic hybrid material: [((CH3)2NH2)(+)]6·[(BiBr6)(3-)]2.

PubMed

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.

Photodissolution of ferrihydrite in the presence of oxalic acid: an in situ ATR-FTIR/DFT study.

PubMed

Bhandari, Narayan; Hausner, Douglas B; Kubicki, James D; Strongin, Daniel R

2010-11-02

The photodissolution of the iron oxyhydroxide, ferrihydrite, in the presence of oxalic acid was investigated with vibrational spectroscopy, density functional theory (DFT) calculations, and batch geochemical techniques that determined the composition of the solution phase during the dissolution process. Specifically, in situ attenuated total reflection Fourier transform infrared spectroscopy (ATR- FTIR) was used to determine the structure of the adsorbed layer during the dissolution process at a solution pH of 4.5. DFT based computations were used to interpret the vibrational data associated with the surface monolayer in order to help determine the structure of the adsorbed complexes. Results showed that at pH 4.5, oxalate adsorbed on ferrihydrite adopted a mononuclear bidentate (MNBD) binding geometry. Photodissolution at pH 4.5 exhibited an induction period where the rate of Fe(II) release was limited by a low concentration of adsorbed oxalate due to the site-blocking of carbonate that was intrinsic to the surface of the ferrihydrite starting material. Oxalate displaced this initial carbonate over time, and the dissolution rate showed a corresponding increase. Irradiation of oxalate/ferrihydrite at pH 4.5 also ultimately led to the appearance of carbonate reaction product (distinct from carbonate intrinsic to the starting material) on the surface.

Single-layer ZnS supported on Au(111): A combined XPS, LEED, STM and DFT study

DOE PAGES

Deng, Xingyi; Sorescu, Dan C.; Lee, Junseok

2016-12-31

Single-layer of ZnS, consisting of one atomic layer of ZnS(111) plane, has been grown on Au(111) and characterized using X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and scanning tunneling microscopy (STM). While the LEED measurement indicates a coincidence structure of ZnS-(3×3)/Au(111)-(4×4), high resolution STM images reveal hexagonal unit cells of 6.7×6.7 Å 2 and 11.6×11.6 Å 2, corresponding to √3 and 3 times the unit cell of the ideal zincblende ZnS-(1×1), respectively, depending on the tunneling conditions. Calculations based on density functional theory (DFT) indicate a significantly reconstructed non-planar structure of ZnS single-layer on Au(111) with 2/3 ofmore » the S anions being located nearly in the plane of the Zn cations and the rest 1/3 of the S anions protruding above the Zn plane. In conclusion, the calculated STM image shows similar characteristics to those of the experimental STM image. Additionally, the DFT calculations reveal the different bonding nature of the S anions in ZnS single-layer supported on Au(111).« less

DFT treatment of transport through Anderson junction: exact results and approximations

NASA Astrophysics Data System (ADS)

Burke, Kieron

2012-02-01

Since the pioneering break-junction experiments of Reed and Tour measuring the conductance of dithiolated benzene between gold leads, many researchers in physics and chemistry have been calculating conductance for such systems using density functional theory (DFT). Off resonance, the predicted current is often 10-100 times larger than that measured. This error is often ascribed to the application of ground-state DFT to a non-equilibrium problem. I will argue that, in fact, this is largely due to errors in the density functional approximations in popular use, rather than necessarily errors in the methodology. A stark illustration of this principle is the ability of DFT to reproduce the exact transmission through an Anderson junction at zero-temperature and weak bias, including the Kondo plateau, but only if the exact ground-state density functional is used. In fact, this case can be used to reverse-engineer the exact functional for this problem. Popular approximations can also be tested, including both smooth and discontinuous functionals of the density, as well as symmetry-broken approaches. [4pt] [1] Kondo effect given exactly by density functional theory, J. P. Bergfield, Z. Liu, K. Burke, and C. A. Stafford, arXiv:1106.3104; [0pt] [2] Broadening of the Derivative Discontinuity in Density Functional Theory, F. Evers, and P. Schmitteckert, arXiv:1106.3658; [0pt] [3] DFT-based transport calculations, Friedel's sum rule and the Kondo effect, P. Tr"oster, P. Schmitteckert, and F. Evers, arXiv:1106.3669; [0pt] [4] Towards a description of the Kondo effect using time-dependent density functional theory, G. Stefanucci, and S. Kurth, arXiv:1106.3728.